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revision 1.1335 by jmc, Tue Nov 16 17:53:33 2010 UTC revision 1.1542 by jmc, Tue Dec 6 00:42:26 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o verification/advect_xz
8      - scale down the depth by 1/100 (from 200 km to just 2.km)
9      - add secondary test using divergent flow, r-star and implicit vertical advection.
10    o pkg/rbcs:
11      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
12    o pkg/obcs (Stevens BCs):
13      - fix various problems in the phase speed computations of the Stevens
14        boundary conditions:
15        - sign error for western and southern boundaries,
16        - time tendencies were underestimated by factor of dTracerLev and some just
17          zero (for multidim advection schemes) -> now estimate time tendencies
18          from difference between previous (n) time level and the one before (n-1);
19          this requires storing a field per tracer per boundary, also in the pickup
20          files.
21        - replace deltaTmom in cflMer/Zon computation with dTracerLev
22        - set default phase velocity to cflMer/Zon
23      - update verification experiment exp4.stevens
24    o pkg/generic_advdiff (implicit_r):
25      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
26        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
27      - fix implicit vertical diffusion or advection with NonLin FreeSurf
28        (was using current recip_hFacC instead of future recip_hFacC): set future
29        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
30        solver S/R ;
31      - fill diagnostics of vertical advective fluxes (computed from tendency)
32        when using implicit vert. advection;
33      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
34         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
35         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
36         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
37    o pkg/diagnostics:
38      - add diags for T & S tendency which goes through Adams-Bashforth.
39    
40    checkpoint63f (2011/11/30)
41    o pkg/obcs/obcs_calc_stevens.F:
42      - join some loops to reduce number of if-statements
43      - fix a bug in code for northern and southern boundaries.
44    o pkg/seaice/seaice_init_varia.F
45      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
46        caused zero ice-velocities for the B-grid code
47    o pkg/seaice/seaice_init_fixed.F
48      - fix a bug in the initialisation of the second metric terms
49        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
50      - this affects all seaice configurations with useCurviLinearGrid = .true.
51        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
52        = .true. (default)
53      - the only verification experiment affected is global_ocean.cs32x15:
54        icedyn, seaice, and seaice_dynmix (AD)
55    o pkg/thsice/thsice_diagnostics_state.F
56      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
57        not contain garbage that can lead to surprises in diagstats_calc.F
58    o model/src:
59      - move bi,bj loops inside INTEGR_CONTINUITY ;
60      - call INTEGR_CONTINUITY directly from forward_step.F
61        (previously called from momentum_correction_step.F)
62      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
63        forward_step.F and pkg/ecco/the_main_loop.F
64    o model/src/do_oceanic_phys.F:
65      - reset addMass to zero only if useICEFRONT ;
66      - separated k-loop for rhoInSitu calculation ;
67      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
68        and at constant T,S (= WdRHOdP);
69      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
70        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
71        transport of locally-referenced potential density);
72        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
73    o gluemnc:
74      - replace ncrcat with ncks when adding variables to *.glob.nc
75      - change the way variables without record dimensions are handled so that
76        files that have variables with and without record variables can be glued:
77        add a record dimension with a new unique name to be able to differentiate
78        between variable with and without a-prior record dimensions. Remove
79        this record dimension before adding the variable to the *.glob.nc file.
80        This procedure automatically works also for grid.*.nc files that do not
81        have any record dimension.
82    o verification/cpl_aim+ocn:
83      - generate new reference output on baudelaire (gfortran, mpich2) (previously
84        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
85    o pkg/obcs/obcs_calc_stevens.F:
86      - add code for northern and southern boundaries.
87      - reorder some loops to save some operations and so that drFBar can be scalar
88    o model/src:
89      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
90        truncation) and add diagnostics for Adams-Bashforth tendency increment.
91      - update test-exp. AD output:
92        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
93      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
94        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
95        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
96        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
97        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
98        tutorial_plume_on_slope.
99    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
100      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
101      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
102      does not even come with an F77 compiler anymore, this should not be
103      a limitation
104    
105    checkpoint63e (2011/11/06)
106    o pkg/seaice adjoint of LSR:
107      - substantially rework STORE dirs.
108      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
109        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
110        and only perform SOLV_MAX_FIXED adjoint iters.
111        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
112        always goes to same record, meaning that the last forward field will be
113        the one used in the adjoint - an approximation.
114      - now produces non-zero LSR-related gradients, and acceptable gradients for
115        An's zonal (x-z) test case (to be checked in)
116      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
117        (but these are screwed up by the thermodynamics in the first place);
118        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
119        output_adm.txt also reflects changes to seaice_lsr
120      - global_ocean.cs32x15:
121        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
122          (output_adm.seaice.txt was updated)
123        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
124          (output_adm.seaice_dynmix.txt)
125    o test-exp. exp4+stevens:
126      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
127    o pkg/seaice (lsr solver):
128      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
129        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
130      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
131      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
132        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
133      - compute (with new S/R) and print initial (+ free-driff sol. if available)
134        and final residual of linearised system.
135    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
136      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
137    o pkg/obcs: Stevens BCs (still only for east and west)
138      - fix Stevens BCs by using intermediate velocities of previous
139        time step as "baroclinic" contribution rather velocity of one grid cell
140        inside the boundaries; more consistent but makes the entire treatment
141        more complicated, requires new pickup files and two new S/Rs:
142        obcs_copy_uv_n and obcs_save_uv_n
143        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
144        (undefined by default)
145      - silently move computation of some grid factors into separate loops to
146        save some recomputations
147      - add a hack for non-linear free surface
148      - add a verification experiment to exp4 that tests this code
149    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
150    
151    checkpoint63d (2011/10/25)
152    o pkg/obcs + seaice-dynamics:
153      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
154        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
155        values (consistent with an implicit method).
156      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
157        return to older implementation (same results as before); note that none of
158        the "experimental" OBCS_SEAICE options are implemented in the new version.
159      - switch test exp. seaice_obcs to use new version (update output).
160    o pkg/seaice:
161      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
162      - add parenthesis in Water-Ice drag calculations (evp & lsr);
163      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
164        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
165      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
166        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
167    o pkg/layers:
168      - Include potential density as new coordinate (Thanks to David Munday)
169    o pkg/dic:
170      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
171        carbonate computation/output to CALC_PCO2_APPROX
172    o pkg/generic_advdiff
173      - make TAF generate code that vectorizes:
174        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
175    o model/src:
176      - improve vectorization also for adjoint code of
177        solve_tridiagonal and solve_pentadiagonal. As this requires up to
178        5 new 3D-fields, this code is only turned on for the combination of
179        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
180        for singular matrix check (only for TARGET_NEC_SX).
181      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
182        ALLOW_AUTODIFF. This flag now needs to be set outside of
183        solve_tri/pentadiagonal.F
184    o pkg/exf:
185      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
186        optional namelist EXF_NML_OBCS).
187      - add many debug-print (to trace down where pkg/cal error msg comes from)
188    o pkg/mom_vecinv/mom_vi_hdissip.F
189      - rearrange loops so that vectorization is improved and in particular
190        the adjoint routine vectorizes. The code is a little longer now, but I
191        think easier to read.
192        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
193    o pkg/seaice:
194      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
195    o pkg/exch2:
196      - alternative code (without tile x tile matrix) for cumulated (global) sum;
197        used as default; keep using matrix version in adjustment.cs-32x32x1.
198    o tools/build_options:
199      - after merging some MPI and/or multi-threads specific optfiles so that
200        the modified default optfile support both built (using genmake2 -mpi
201        for the MPI built, using genmake2 -omp for OpenMP built),
202        move now obsolete optfiles to tools/build_options/unsupported/
203       (add copy of email sent to support list in doc/optfiles_changes.txt)
204    
205    checkpoint63c (2011/09/28)
206    o pkg/ebm:
207      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
208        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
209    o pkg/seaice (SItracer pickup)
210    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
211      To be done:
212      - thorough testing of missing fields in S/R seaice_read_pickup
213      - thorough matching between generic tracers and specific fields used
214        (e.g. volume-weighted age, area-weighted age, salinity, ...)
215    o pkg/grdchk:
216      - all procs calculate and print finite-difference gradient (for testreport)
217      - change description output used by testreport;
218      - AD testing: also compare and report Finite-difference gradient;
219        => update all output_adm*.txt
220    o test exp. global_ocean_ebm:
221      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
222        and turn on exactConserve; update (fwd) output.
223    o pkg/seaice (LSR):
224      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
225      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
226        * identical results with non-CS topology (but save up to half of EXCH calls)
227        * no much changes in cs-32 verification tests since no ice at face edges
228         (differences due to convergence criteria, since nb of iterations changed)
229        * expect some differences on lat-lon-cap grid.
230        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
231    o pkg/exch2:
232      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
233        many tiles); until alternative coding is added, just add a stop.
234    o pkg/kpp:
235      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
236        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
237    o optfiles:
238      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
239        into corresponding standard one, which now support different build:
240        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
241      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
242    o pkg/obcs (seaice):
243      - add missing EXCH for uIce,vIce after applying OBCS;
244      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
245        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
246        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
247      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
248      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
249        and eedata.mth for MPI and mutlti-threaded testing.
250    o pkg/flt:
251      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
252      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
253      - fix pickup and trajectories + profiles output with multi-threads;
254      - add parameter to select group of fields to write along trajectory and
255        profile (default unchanged);
256      - only call PORT_RAND* function when flt_noise <> 0;
257      - add multi-threaded test for verification exp. flt_example.
258    o eesupp/src:
259      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
260      - USE_OMP_THREADING: check that number of threads (from eedata) matches
261        actual number (from env.var. setting).
262    o pkg/ebm:
263      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
264      - add multi-threaded test for verification exp. global_ocean_ebm
265    
266    checkpoint63b (2011/08/29)
267    o pkg/ebm:
268      - fix sign of runoff;
269      - update directly forcing fields (Qnet,EmPmR) to use standard
270        external_forcing_surf.F (remove ebm_forcing_surf.F);
271      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
272      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
273        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
274      - update global_ocean_ebm parameters file data and update output (fwd+ad).
275    o verification/matrix_example:
276      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
277        MPI and mutlti-threaded testing.
278    o pkg/matrix:
279      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
280      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
281      - fix for multi-threaded (remove DATA statement);
282      - use standard DIFFERENT_MULTIPLE function;
283      - add MATRIX_OPTIONS.h
284    o verification/matrix_example:
285       To allow to split the domain in several tiles, change the domain size
286        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
287        Western side) of land points.
288    o (*_)write_pickup:
289      - fix few bugs in mypackage_read/write_pickup.F
290      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
291        array of length 1 (was caught by compiler syntax-check).
292    o pkg/diagnostics (velocity potential solver):
293      - fix initialisation of main diagonal matrix (for overlap values)
294    o tools/build_options:
295      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
296        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
297      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
298        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
299        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
300        and use "-devel" testreport option for standard testing on baudelaire.
301    o pkg/grdchk:
302      - Assume that all gradient-check position are within the same tile
303        corresponding to global indices (iGloTile,jGloTile) and that
304        positions (i,j indices or nbeg) are local to this tile;
305      - set tile local-indices and proc. number according to tile global-indices;
306      - remove grdchkwhichproc from namelist (retired param);
307      - send adjoint gradient to all procs so that all procs print it to STDOUT;
308      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
309    o adding package bbl (Bottom Boundary Layer)
310      description in MITgcm/pkg/bbl/bbl_description.tex
311      example/test experiment in MITgcm_contrib/bbl
312    o adjoint verifications
313      - changed 5 experiments to multi-tiles
314        * global_ocean.90x40x15
315        * obcs_ctrl
316        * offline_exf_seaice
317        * tutorial_dic_adjoffline
318        * tutorial_tracer_adjsens
319        changed reference output for those that crossed tile boundaries
320        (changed choices of gradient check positions)
321      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
322      - temporary bug fix in grdchk_loc.F for obcs
323    o genmake2 & testreport
324      - add target "obj" (just for OBJFILES files) to Makefile;
325      - add option to specify FEXTRAFLAGS on command line.
326    o pkg/mypackage:
327      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
328    
329    checkpoint63a (2011/08/02)
330    o pkg/diagnostics (velocity potential):
331      - fix velocity-potential calculation when using OBCS: balance net inflow
332        at each level (new S/R OBCS_DIAG_BALANCE).
333      - fix some of the problems with OBCS in stream-function calculation.
334    o pkg/exf/exf_readparms.F
335      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
336        EXF_NML_OBCS) more consistent, so that you need not have these lists
337        in data.exf when they are not used.
338    o optim/optim_readdata.F:
339      - add some output about obcs variables that might help debugging
340      - add a check about nvarlength
341    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
342    o pkg/diagnostics (velocity potential):
343      - fix mask for OBCS (still problems in stream-function with OBCS);
344      - add specific parameter (default = main code CG2D params) for solver;
345      - in case of poor convergence, use solution corresponding to lowest residual.
346    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
347      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
348      and should be avoided where possible.
349    o model/src (rStar):
350      - include r* effect on reference-state (PhiRef) in totPhiHyd
351        (so that it's really the potential anomaly at the cell center);
352        affect solution only if z* with full pressure in EOS.
353      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
354        update output (because of z* in totPhiHyd and viscA4 changes);
355      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
356        @ constant r) until interpolation at constant r is implemented.
357    o pkg/diagnostics
358      - fix RCENTER diagnostics in case cell center is not at interface middle
359    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
360      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
361      that THETA and SALT are "conservative temperature" and "absolute
362      salinity"
363    o pkg/ctrl
364      - fix computation of endrec in s/r ctrl_init_rec
365      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
366    o pkg/seaice/seaice_growth.F
367      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
368        remove then obsolete STORE directives
369      - fix STORE directives for tice and tices, so that only the
370        appropriate part of the fields are stored (and not the entire
371        field); update global_ocean.cs32x15.seaice AD output.
372      - cosmetic changes: adjust CPP flags and indentation for better
373        legibilty
374    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
375      Chris Wilson)
376    o pkg/gmredi:
377       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
378       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
379    
380    checkpoint63  (2011/07/11)
381    o pkg/exch2:
382     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
383     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
384       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
385       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
386    o pkg/diagnostics:
387     - deal with pairs of post-processed diags which are computed together; in
388       particular, re-order list of diags within 1 file to save 2nd computation.
389     - add S/R to compute velocity stream-function (called after velocity-potential
390       calculation) from divergence free transport -> new diagnostics "PsiVEL".
391     - add parameter to select grid-point location where PsiVEL == 0.
392    o eesupp/src:
393       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
394       (specific S/R needed with exch2 topology - for now, just print an error msg)
395    o pkg/shelfice
396     - Implement friction velocity-dependent transfer coefficients following
397       Holland and Jenkins, JPO, 1999
398       Original code by M. Losch with small modifs.
399       Enable with CPP option SHI_ALLOW_GAMMAFRICT
400       and runtime flag SHELFICEuseGammaFrict
401    o verification lab_sea & global_ocean.cs32x15:
402     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
403       does not miss some dependencies (but is slower) and also works with many files
404       (default makedepend limitation for AD built).
405     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
406    o pkg/diagnostics:
407     - add run-time parameter "useMissingValue" (def=False) to fill land-point
408        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
409       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
410     - Extend the use of "missing_value" setting from data.diagnostics for the case
411       of counter-diagnostics (where fraction-weight is zero). This applies both to
412       MNC and MDS output files.
413    o pkg/seaice/seaice_growth.F:
414      - add 'a priori' cap of latent heat flux based on actual mass considerations
415        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
416        non-legacy seaice_solve4temp.
417      - add diagnostic of the residual sublimation freshwater flux (the freshwater
418        flux taken from the ocean if the total actual latent heat fluxes exceed
419        the maximum)
420      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
421       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
422      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
423       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
424      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
425      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
426    o verification 1D_ocean_ice_column:
427       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
428       update results
429    o pkg/diagnostics:
430     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
431       which are not filled-up but computed from other diags ; In this case, the mate
432       diag points to the primary (filled-up) diag to used for post processing.
433     - Update Velocity-potential computation using post-processed diag framework.
434     ==> Change the ordering of fields and time-periods in MDS output file
435       when using periodic averaging: now writes one time record with the full set
436       of fields for this time period, then the next time reccord (it used to be
437       one field with the full set of time records then the next field).
438         Note: this is now similar to NetCDF (MNC) output file. <==
439    
440    checkpoint62z (2011/06/21)
441    o adjoint monitor:
442     - Add adjoint monitor output for packages exf, seaice
443       and update relevant testreport output
444    o pkg/seaice:
445     - re-order diags inits so that they appear in order in available_diagnostics.log
446     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
447       area/heff/hsnow preceeding thermodynamic growth/melt.
448     - modified diag: SIdA; output actual effect, as the description states.
449     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
450     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
451       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
452        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
453     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
454     - added diagnostics for seaice generic tracers (SItr*).
455     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
456     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
457     I. Fenty: 18-Jun-2011:
458     Minor changes to seaice package:
459     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
460        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
461       - Differentiated "regularization variables" from "floor variables"
462        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
463        * hiceMin became SEAICE_hice_reg (old hiceMin)
464          (with _reg meaning regularization variable)
465       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
466        so as to ensure energy conservation when going between phases
467      - A22 was not used anywhere
468     2) Changed regularization procedure for heffActual and hsnowActual to ensure
469        well-boundedness and smooth adjoint in seaice_growth.F
470     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
471        because the old regularization always set heffActual >= 0.05 cm
472     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
473        on AREA when HEFF > 0.
474      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
475        requiring that DISABLE_AREA_FLOOR *not* be defined
476     Affected verifications:
477      - 1D_ocean_ice_column (output.txt output_adm.txt)
478      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
479    o pkg/diagnostics:
480      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
481      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
482        (was _RL, now integer) with option = 0 to retrieve all levels.
483      - add pieces of code to compute velocity potential at each level (new diagnostics
484        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
485        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
486      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
487        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
488        and in diagnostics_fract_fill.F (do not need a valid pointer for the
489        diagnostics counter-mate); check that definition of counter-diagnostic
490        includes a valid counter-mate (in diagnostics_set_levels.F).
491    o model/src (rStar):
492      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
493        affect solution only if z* with full pressure in EOS;
494        update output of test-exp global_ocean.90x40x15.
495    o pkg/seaice:
496      - introduce siEps=1e-5 parameter
497      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
498      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
499      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
500        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
501        as well as ice cover age and ridging index (attached to AREA).
502        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
503        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
504        Up to SItrMaxNum=3 tracers can be used simultaneously.
505    o pkg/salt_plume:
506      -introduce SPsalFRAC run time parameter that sets the fraction of the
507       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
508       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
509    o model debug options:
510      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
511        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
512      - Refine debug-msg printing selection (3 new levels):
513        debugMode  : controls printing of debug messages (sequence of S/R calls).
514        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
515         debLevZero =  0 ; /* level of disabled aux. msg printing */
516         debLevA =  1 ; /* level of minimum  aux. msg printing */
517         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
518         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
519         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
520         debLevE =  5 ; /* level of extensive debug printing */
521        New debugLevel default: with default debugMode value (=F),
522          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
523          and if debugMode=T, default debugLevel = 4 (debLevD).
524        Relation with previous settings:
525         debLevB (=2) corresponds to former debLevA (=1)
526         debLevD (=4) corresponds to former debLevB (=2)
527        Note:
528         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
529         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
530            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
531      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
532        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
533    o pkg/obcs:
534      - change OBCSfixTopo default from True to False (should not change the results);
535        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
536    o pkg/thsice:
537      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
538        2nd layer seaice sublimation (unlikely to happen)
539      - use Interior mask for OBCS in thsice_advection.F (similar to what is
540        done in gad_advection & seaice_advection).
541    o adjoint:
542      bug fix spotted by Gael Forget:
543      seaice_advection and thsice_advection still had
544      legacy CPP options to avoid CS corner updates for adjoint
545    o pkg/seaice:
546      => Change some of the defaults (2011/05/29):
547         - change SEAICEuseFluxForm default (from False to True)
548         - change DIFF1 default (from 0.004 m/s to 0. m/s)
549         And print warnings if DIFF1 is not set in data.seaice and centered
550          avection scheme is used without any diffusion.
551      also:
552      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
553      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
554      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
555        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
556        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
557      update results of test exp.:
558         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
559             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
560             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
561         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
562         seaice_obcs: output (SEAICEuseFluxForm=T)
563      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
564          for standard fwd & AD lab_sea tests (to keep the same output).
565    o pkg/seaice/seaice_growth.F:
566      - use Ian Fenty's capping formulas for actual ice
567      thickness thoughout EVOLUTION branch.
568      - put treatment pathological case #2) in CPP brackets
569      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
570      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
571    o pkg/seaice:
572      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
573      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
574      also pass fac as a param, which can be 1. (to update the tendency
575      field) or the time step (to update the field itself).
576      - seaice_advdiff.F: for multidim, call seaice_diffusion with
577      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
578      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
579      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
580      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
581    o pkg/seaice:
582      diffusion with centered advection scheme (diffus.F & advect.F):
583      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
584        to just compute the laplacian of input-field.
585      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
586      - fix flux-form version in diffus.F to conserve tracer.
587      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
588       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
589    
590    checkpoint62y (2011/05/26)
591    o pkg/seaice:
592     - seaice_growth.F : in EVOLUTION branch, always include
593       a_QSWbyATM_cover in qnet (as it should be).
594     - verification/global_ocean.cs32x15 : update results accordingly
595       (output.seaice.txt output_adm.seaice.txt).
596    o pkg/seaice + obcs:
597     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
598       equivalent of assuming no tracer gradient outside the OB region.
599       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
600     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
601       after changes above);
602     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
603       only at OB location (instead of over a band of OLx width).
604    o pkg/seaice:
605     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
606       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
607    o pkg/obcs:
608      - split header file "OBCS.h" into 4 separated files:
609        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
610       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
611         (contain no conditional statement which depends on OBCS options).
612      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
613        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
614    o ctrl, cost, grdchk & autodiff pkgs:
615      - make options file more standard (like other {PKG}_OPTIONS.h file but
616        with AD_CONFIG.h); clean-up some of the included header files.
617    o pkg/obcs:
618      - do not mask tracer when applying OB (tracer == 0 could generate problems)
619      - apply tracer OB values to tracer field only at OB location (instead of
620        over a band of OLx width)
621      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
622      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
623        obcs_apply_tloc.F & obcs_apply_sloc.F
624    o obcs in model/src:
625      - call OBCS_APPLY_W only if NonHydrostatic.
626      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
627      - reset dEtaHdt and wVel to zero outside OB interior region ;
628      - leave tracer unchanged outside OB interior region: This has no effect
629        on the solution but just to prevent unrealistic tracer value outside OB.
630      - zero out velocity outside OB interior region: This has no effect on
631        the solution but just to prevent unrealistic velocity outside OB.
632    o obcs and non-lin free-surf:
633       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
634       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
635       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
636       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
637       update results of test-exp. exp4(nlfs).
638    o exp4 (nlfs) test-exp:
639       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
640       with NonLin-FreeSurf); update output.nlfs.txt
641    o obcs and 2d/3d solver norm:
642       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
643       and outside OB interior region (will allow to place OB further inside the
644       domain). Depending on the domain, can affects cg2d-Norm (previous
645       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
646       and cg3d-Norm (previous Norm was computed before canceling OB terms),
647       e.g. in tutorial_plume_on_slope.
648      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
649    o pkg rbcs:
650      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
651      - add capability to apply relaxation to horizontal velocity uVel & vVel.
652    o pkg/grdchk: add gradient check for control variable xx_shifwflx
653    o pkg/shelfice/shelfice_init_fixed.F
654      fix CPP-flag combinations
655    o pkg/seaice: Merge iceage code of Pierre Rampal
656      * update/change/correct ice age calculations
657      * add age updates for pathological cases
658      Probably needs more testing...
659    
660    checkpoint62x (2011/05/13)
661    o pkg/mom_vecinv:
662       high-order vorticity scheme: use interior masks (maskInW & S)
663       to zero-out (outside OB) gradient of vorticity.
664    o verification exp.:
665       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
666       hs94.128x64x5 and seaice_obcs ; update results.
667    o pkg/obcs:
668      fix bug in OBeta for YZ sections in obcs_exf_load.F
669    o pkg/ctrl, pkg/shelfice, and optim:
670      - add new control variable xx_shifwflx (fresh water flux underneath ice
671        shelves). This is almost as tedious as obcs-ctrl, because the
672        variables needs its own mask.
673      - add a cost function term that penalizes the deviation of xx_shifwflx
674        from the first guess (zero) in analogy to other control variables
675    o pkg/shelfice:
676      - start basic adjoint
677    o pkg/ctrl:
678      - remove extra 2D field "for good measure" when initializing in
679        ctrl_set_globfld_[xy/xz/yz].F
680      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
681      - improve error messages in ctrl_set_unpack_*
682    o OBC implementation in momentum:
683       use interior masks (maskInC,W & S) in momentum S/R:
684       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
685       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
686       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
687       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
688       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
689        (and also with Leith/Smagorinsky harmonic-viscosity).
690       Update output of experiment dome and exp4 (+nlfs).
691    o exp4 test-exp:
692      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
693        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
694        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
695        time-varying OB at Western-side for wVel (NonHyd); update output.
696      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
697        and biharmonic-viscosity ; also use prescribed time varying OB.
698    o pkg/obcs:
699      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
700    o model/src:
701      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
702      - initialise startTime & nIter0 with unlikely values: allows to set one
703        from the other without ambiguity.
704    o seaice_obcs test-exp.:
705      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
706    o pkg/obcs:
707      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
708        no longer needed with maskInC,W,S in pkg/generic_advdiff.
709    o pkg/seaice:
710      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
711        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
712      - fixed bug in the initialization of sea ice salinity variable HSALT
713        in seaice_init_varia.F  (removed dependence on ICE2WATR)
714    o fizhi-cs test exp.:
715       switch reference output convention for these 2 non-standard test-exp,
716        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
717          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
718       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
719    o model/inc:
720      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
721        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
722    o pkg/seaice:
723      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
724    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
725      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
726        and initial HSALT
727    
728    checkpoint62w (2011/04/26)
729    o pkg/mom_fluxform:
730      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
731      - use parameter "sideDragFactor" in no-slip BC side-drag part.
732      - update output of exp. global_ocean.90x40x15
733    o pkg/mom_vecinv:
734      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
735    o update seaice exp.:
736      use more consistent parameter values (remove "backward compatability only":
737       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
738      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
739       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
740    o update test-exp global_ocean.90x40x15:
741      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
742      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
743      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
744      o turn on zStar & viscA4 in standard set-up (dir input/)
745        and update output files: output.txt & output.dwnslp.txt
746    o new AD-test experiment: obcs_ctrl
747      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
748    o pkg/dic:
749      fix two bugs in handling water vapour pressure in carbonate chemistry
750      and air-sea fluxes. Found by Val Bennington and Galen McKinley
751      (add DIC Option = WATERVAP_BUG to recover old results)
752      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
753    o adding allowInteriorFreezing option to check for water below freezing point
754      at depth and bring the negative heat anomaly to the surface level
755    o pkgs _fields_load:
756      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
757      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
758        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
759        rbcs to get interpolation weights and time reccord number.
760      - fix multi-threading in aim_fields_load.F
761      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
762    o external_fields_load:
763      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
764       interpolation weights) to use in a periodic time-series ; do not divide by
765       time-step to convert to integer:
766       - this fixes case where externForcingPeriod is not multiple of time-step
767          (Thanks to Christopher L. Wolfe)
768       - this fixes case where externForcingPeriod is an odd multiple of time-step
769         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
770      store index of time-record which is currently loaded:
771       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
772       - needed for the adjoint but not yet used because of extensive recomputations;
773         (to be fixed soon)
774    
775    checkpoint62v (2011/04/02)
776    o verification/1D_ocean_ice_column added to test Ian Fenty's
777      pkg/seaice_growth.F modifications for improving sea ice code differentiability
778    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
779      (new velocity statistics after changing maskInW & maskInS definition)
780    o pkg/generic_advdiff with OBCS:
781      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
782      equivalent to assumption of no tracer gradient outside the OB region.
783      This will affect the results if using obcs+biharmonic diffusion.
784      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
785    o pkg/obcs:
786      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
787      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
788      in Interior region. No impact on solution but affects Velocity monitor stats.
789    o pkg/ptracers (adjoint)
790      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
791      tape file for each tracer
792    o model/inc/src and pkg/autodiff: add parameters that allow to turn
793      of parts of the adjoint code at run time. For now, there are only
794      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
795      parameters are set in data.pkg.
796      This is the lazy coward's version of doing this, but still useful for
797      debugging. In order to do it right, everything needs to be moved to
798      pkg/autodiff.
799    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
800      the end; this fixes the adjoint balancing code for open boundaries.
801    o pkg/ctrl:
802      - change behavior of xx_${varname}period to be analogous to exf-conventions:
803        xx_${varname}period =   0.,  means time-independent control part
804        xx_${varname}period = -12., means one-year-periodic monthly control part
805      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
806        clean up ctrl_init a little, remove unused variables
807      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
808      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
809    
810    checkpoint62u (2011/03/15)
811    o model/src:
812      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
813        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
814      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
815        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
816    o pkg/ctrl/obcs/ecco:
817      - remove obsolete, unused, and partially broken code:
818        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
819        ALLOW_CTRL_OBCS_BALANCE
820      - put a stop statement into ecco/cost_obcsvol.F, but also add
821        cost_obcsvol to ecco_ad_diff.list
822    o pkg/ecco: fix counting cost function contributions for obcs (code
823      by Matt M.) and diffkr for diagnostics
824    o pkg/ecco, pkg/ctrl, pkg/grdchk:
825      add cost penalty terms for initial uvel, vvel, eta controls
826      and I/O for prior error files
827    o pkg/mdsio:
828       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
829       (new argument) to check for tiled file in mdsioLocalDir : this fix the
830       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
831    o pkg/ctrl:
832     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
833       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
834       unused and superfluous variables
835     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
836    o pkg/ecco
837     - enable adjoint of Stevens OB
838    o pkg/ctrl/ecco/grdchk:
839      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
840        Fortunately, we do not have any tests for the numerous cpp-flagged
841        option of "obcs as control parameters" so we will never know
842        if this is an improvement (but at least now things compile).
843      - remove an obsolete initialization from ecco_cost_init_barfiles.F
844      - fix some problems within never used ifdefs to make the code compile
845    o pkg/obcs:
846     - Refine Interior mask definition to work with more complex OB (e.g.
847       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
848       read in Interior mask from file. Check if Interior mask is consistent
849       with OB list of indices.
850    o pkg/seaice
851     - beginning code for a seaice tracer package,
852       but currently only used for seaice age: SEAICE_AGE
853       SEAICE_num = 4
854       iTracer = 1: area-weighted ice age
855               = 2: volume-weighted ice age
856               = 3, 4: template for one-year vs. multi-year ice
857       data.seaice has new namelist SEAICE_PARM03 for arrays related to
858       SEAICE_num
859    
860    checkpoint62t (2011/03/05)
861    o pkg/obcs:
862     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
863       then normal component. This ensures that the normal component is set
864       correctly even when it conficts with tangential setting from an other OB.
865       Affects results of test-experiment seaice_obcs: update the output.txt
866    o pkg/obcs:
867     - add code to monitor statistics of dynamical fields at OB.
868     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
869       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
870       - change default: balance the Net inflow through all OB (instead of balancing
871         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
872     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
873       to match Nortern OB inflow (OBCS_balanceFacN=0).
874    o pkg/seaice:
875     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
876    o pkg/seaice (seaice_growth v 1.113):
877     - reverting seaice_growth to v 1.111 in order to have code with exact bit
878       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
879       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
880       runtime flag SEAICEareaFormula is kept but is inactive
881    o model/src:
882     - add new param to scale curvilinear grid distance and area when using
883       a different sphere radius from the grid-files.
884     - test/check multi-threads EXCH applied to local variable (cg2d_x)
885    o adjoint:
886     - enable adjoint of Stevens OB
887     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
888       (a bit delicate because of potentially modified adj. common block structure;
889       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
890    
891    checkpoint62s (2011/02/15)
892    o pkg/seaice (seaice_growth v 1.112):
893     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
894       computing the ice cover tendency from effective thickness tendencies. Include
895       Ian Fenty's formula.
896     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
897       SEAICEareaFormula.
898     - simplify notations for the various d_HEFF/d_AREA terms.
899    o pkg/gmredi:
900     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
901       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
902       add a verification test-run (front_relax.bvp) to test GM_useBVP.
903    o pkg/seaice (seaice_growth v 1.111):
904     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
905     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
906       also melt ice.
907    o pkg/seaice:
908     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
909     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
910    o pkg/cheapaml:
911     - from Nico Wienders: New version of this package.
912    o pkg/flt:
913     - add CPP options to prevent floats to re-enter the opposite side of
914       a periodic domain (default: keep periodicity)
915    o pkg/gmredi:
916     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
917       (needed for multi-dim advection).
918     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
919    o model/src:
920     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
921    o tutorial_tracer_adjsens
922     - extend to NLFS and replace maskC by hFacC
923       (change reference output accordingly)
924    
925    checkpoint62r (2011/01/24)
926    o testreport:
927     - add option -deloutp (-do) to remove output file after successful run
928     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
929       extract exact list of procs from this file ; adjust COMMAND by
930       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
931    o pkg/ecco: replace old ineffective way of penalizing deviations from
932      first guess (of obcs) with code by Matt Mazloff
933    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
934      exf/cal
935      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
936        and handle case of obcs?period == 0
937        Not affected by these changes: There is still an inconsistency in
938        the computation of start/endrec for the obcs variables for ALLOW_CAL
939        defined (see comment by Menemenlis, 7-Mar-2003)
940      - make S/R ctrl_get_gen_rec return something meaningful even if
941        ALLOW_CAL is not defined
942      - ctrl_getobcs?: simplify code so that it does not need to use
943                       S/R exf_swapfields
944    o testreport:
945       allow to test MPI with different number of processors for each experiment:
946       create file "SIZE.h.mpi" in each build dir.
947       Note: update of "-command" argument not yet implemented.
948    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
949      alleviate the need for additional 3D tapes when using
950      the non-inear free surface in the adjoint. This is done
951      by adding an 'update' of hfacc etc. to their current
952      value at the beginning of forward_step.F.
953    o pkg/seaice
954      seaice_lsr: move stress-divergence computations out of outer pseudo-
955      timestepping loop
956    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
957      up, so that the calls of the ctrl_* subroutines are really at the end
958      of the routine.
959    o pkg/gmredi:
960      allow to specify a 2-D horizontal map and a 1-D vertical profil
961      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
962    o pkg/seaice:
963      move lsr iterations from seaice_dynsolver to seaice_lsr.
964    o pkg/seaice:
965      reduce memory footprint of seaice mutldim advection tapes,
966      by using a 2D tape independent of the generic_advdiff ones,
967      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
968    
969    checkpoint62q (2010/12/29)
970    o model/src:
971      - check horizontal grid-spacing for unset or zero/negative values.
972      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
973    o pkg/flt:
974      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
975      - precision of input and output files set according to readBinaryPrec
976        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
977      - initial float position from tiled file was not converted to index space
978        (looks like a bug): fixed to make it similar to initial pos. global file.
979    o global_ocean.cs32x15:
980       change SIZE.h of AD set-up to get same tiling as with MPI.
981       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
982    o model/src:
983       add flag to control printing of domain fields (bathymetry, hFac ...) in
984       ini_mask_etc (call to plot_fieds_xy*).
985    o pkg/thsice:
986       if useEXF, some forcing fields are not valid in overlap: fixed by computing
987       over the interior only + apply EXCH at the end (like with SEAICE advection).
988    o pkg/mdsio:
989      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
990        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
991      - change barrier call for safe multi-threads access to 3-D shared buffer.
992      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
993      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
994        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
995    o pkg/flt:
996      - add fourth-order Runge-Kutta integration
997      - add basic exch2 support (only 1 facet supported so far!)
998    o pkg/mdsio+rw:
999      new S/R to read local (or tile independent) vector (read counterpart of
1000       mds_writevec_loc, and front-end write_glvec_rl/rs).
1001    o global_ocean.cs32x15: additional input_ad.seaice experiment
1002        that uses pkg/seaice rather than pkg/thsice.
1003        (using multidim advection for seaice)
1004    o towards more F95 syntax for array specification in namelist:
1005      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
1006        of all verification experiments.
1007           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
1008          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
1009      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
1010    o global_ocean.cs32x15: additional input.seaice experiment
1011        that uses pkg/seaice rather than pkg/thsice.
1012    
1013    checkpoint62p (2010/12/17)
1014    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
1015        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
1016    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
1017        allow for use of multim. advection in seaice adjoint.
1018    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
1019      - first attempt to close budgets by taking into account the freshwater
1020        flux implied by the sublimation of snow and ice. So far only the
1021        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
1022        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
1023    o eesupp/src:
1024      new S/R with new option (NML_EXTENDED_F77) to change array specification
1025      from F95 standard to commonly accepted extended F77 form.
1026      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
1027      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
1028      for less tolerant f77 compiler (e.g., pgf77, g77).
1029    o globalFiles:
1030      commented out in parameter file "data" since it's not safe with MPI
1031      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
1032      in this case); no longer commented out in restart test (tst_2+2).
1033    o add adTapeDir to specify a special directory where adjoint tapes are
1034      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
1035      and cannot be used together with mdsioLocalDir.
1036    o nesting pkgs:
1037      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
1038      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1039      - add parameter files + utils dir + output from short run on beagle.
1040    o pkg/seaice:
1041        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
1042    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
1043      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
1044    
1045    checkpoint62o (2010/11/25)
1046    o pkg/exf:
1047      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
1048    o pkg/seaice:
1049      - seaice_ocean_stress: split a loop for better vectorization of the
1050        adjoint code
1051      - seaice_growth.F: fix bug in conservation of freshwater connected to
1052        capping of heff, put contribution into d_HEFFbyNEG
1053      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
1054        by something more sensible (parameters that are what their name implies)
1055      - change some defaults, so that by default exf-parameters are used for
1056        things like rhoAir, cpAir,latent/sensible heat parameters, in order
1057        to reproduce the old results, many data.seaice now contain funny values
1058        for cpAir and latent heat of sublimation
1059    o packages_readparms.F: move exf_readparms up in line so that
1060        exf-parameters are visible for other packages (e.g. seaice)
1061    o debugMode & debugLevel=2:
1062      - differentiate between debugMode & debugLevel=2:
1063        debugMode: controls printing of debug messages (sequence of S/R calls).
1064        debugLevel: controls printing of algorithm intermediate results and stats.
1065      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
1066        => allows to print debug-stats without all sequence of call messages.
1067      - switch control of debug print from debugLevel to debugMode in many S/R.
1068    o pkg/obcs (obcs-sponge):
1069        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
1070        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
1071  o pkg/generic_advdiff:  o pkg/generic_advdiff:
1072    - record overlap minimum size for each advection scheme;    - record overlap minimum size for each advection scheme;
1073    - refine criteria on overlap minimum size;    - refine criteria on overlap minimum size;
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