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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1825 by mlosch, Fri Feb 15 15:20:03 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice: replace a hard coded parameter by a runtime parameter
8       SEAICE_JFNK_tolIter
9    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
10        preconditioner for JFNK (run LSR into the overlaps as far as possible,
11        i.e OLx/y-2, but overwrite the solution in the overlaps)
12      - extend loop range in seaice_calc_viscosity
13      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
14      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
15      - slightly modify loops in tridiagonal solver lsr-preconditioner
16      - by default remove the extra exchange in seaice_preconditioner with a
17        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
18      - modify offline_exf_seaice so that old results without RAS are reproduced
19        for output.dyn_jfnk.txt
20      in seaice_fgmres.F (unrelated to RAS)
21      - add a cpp-flag option for a re-ordered mapping (potentially more
22        efficient), but because this changes the results, turn it off by
23        default
24      - replace the save statement by local common blocks
25    o utils/matlab:
26      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
27      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
28        instead of local script "load_cs.m".
29    o pkg/seaice:
30      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
31        to the scalarProductMetric and the unrolling. By chance this does not
32        change the verification experiment, because of the particular domain
33        decomposition
34    o pkg/diagnostics:
35      - change default missing_value from UNSET_RL to -999.
36    o pkg/layers: improve vectorization of layers_fluxcalc.F
37      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
38        time spent in this routine by more than a factor of 3 on an NEC-SX8
39      - step 2: replace search algorithm by a bisection algorithm found in
40        Press et al. Numerical Recipes in Fortran. This algorithm can be
41        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
42        For now, use this algorithm only for TARGET_NEC_SX defined.
43      - moved the search algorithm into a separate subroutine, that is kept
44        within the same file for automatic inlining.
45      - modified catching potential errors
46    o pkg/ecco:
47      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
48    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
49      - modifications for ALLOW_GENTIM2D_CONTROL
50      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
51      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
52      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
53      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
54    o model/src:
55      - account for moist thermodynamics in (dry) potential temperature equation;
56        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
57        and cpl_aim+ocn.
58      - also switch to standard compiler (gfortran, was using ifort previously)
59        for fizhi-cs experiments reference output.
60    o pkg/ctrl:
61      - 1st step toward generic time-varying control variable (2D) via CPP option
62        ALLOW_GENTIM2D_CONTROL
63      - note new namelist ctrl_nml_genarr in data.ctrl
64    o verification/global_ocean.cs32x15:
65      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
66        thsice calling sequence and update "output.icedyn.txt" output file.
67    o pkg/ptracers:
68      - from Ryan A.: code to allow to restart a tracer at regular time interval
69        specifying a reset frequency and a reset-phase (for each tracers).
70    o pkg/thsice:
71      - implement new sequence of calls for thsice+seaice:
72          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
73          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
74      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
75        in CPP_OPTIONS.h) to recover old sequence;
76      - update diagnostics for Intermediate State thsice diagnostics: now filled
77        just before advection (instead of just after advection in old sequence);
78      - update output of experiment offline_exf_seaice (standard test);
79      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
80        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
81    o pkg/aim_v23:
82      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
83      - use standard pkg/mdsio routines to read & write CO2 pickup file;
84      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
85      - Implement new sequence of calls for seaice advection (with thsice and
86        seaice diffusion): do ice advection after ice-Thermodynamic (previously
87        was done before); change aim_do_physics.F (split the bi,bj loops block);
88      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
89    o pkg/thsice:
90      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
91        where just seaice diffusion is used without seaice-dynamics.
92    
93    checkpoint64c (2013/01/18)
94    o pkg/seaice:
95      - add a parameter JFNKres_tFac that can replace JFNKres_t
96        (= JFNKres_tFac*JFNKresidual before JFNK solver)
97      - add a line search option to the JFNK solver
98      - move update of u/vIce and computation of initial residual into a separate
99        routine (same file); makes the code a little easier to read (?)
100      - the line search requires computation of the residual and for some reason
101        I cannot do the update of u/vIce at the beginning of the Newton loop
102        without changing the results, so we move computation of the new residual
103        also to the end of the Newton loop, even without the line search
104    o pkg/mdsio:
105      - write missing value (corresponding to undefined array value) to meta files;
106        skip this if missing value is one (UNSET_RL would be a better value for the
107        case of undefined missing value but it's current the default missing-value);
108        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
109    o pkg/exf & thsice:
110      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
111        diagnostics) even when SHORTWAVE_HEATING is #undef;
112    o verification/cfc_example:
113      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
114        illustrate how to use it).
115    o verification/offline_exf_seaice:
116      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
117        files to only one time-record.
118      in input.thermo: narrow the 2 bands of low initial ice-concentration near
119        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
120        snapshot output; same mcPheePiston value as in thsice with
121        surf-current=0.2m/s.
122      in input.thsice: similar set-up as in input.thermo (channel with same seaice
123        initial conditions).
124    o verification/cfc_example:
125      - update file "data" with more standard choice (default rotationPeriod,
126        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
127        set deltaTFreeSurf to deltaTtracer) and update the output.
128    o pkg/layers:
129      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
130      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
131    o verification/offline_exf_seaice:
132      - set all {field}period to zero for constant-in-time forcing (not tested
133        anywhere else).
134    o verification/offline_exf_seaice:
135      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
136      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
137    o model/src:
138      - implement Finite-Volume method for (hydrostatic) presure gradient
139        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
140    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
141      - In order to be compatible with the default EVP code, this requires changing
142        the EVP code around a little; and because any small change immediately
143        breaks the lab_sea.hb87 verification experiment, the reference output is
144        updated two times (each time the remaining aggrement was only 2 digits):
145        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
146        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
147        The adjoint test lab_sea.evp also needed to be updated.
148      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
149        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
150        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
151        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
152        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
153        kept obscure, because I need to test it a little more.
154    o pkg/cheapaml:
155      - fix few incorrect type (_RL/_RS) in subroutine calls.
156    o pkg/seaice:
157      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
158        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
159    o model/src:
160      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
161        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
162        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
163    o pkg/cheapaml:
164      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
165        update output of experiment cheapAML_box.
166      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
167        and set them only in one place (cheapaml_readparms.F).
168      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
169      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
170        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
171    o model/src/the_main_loop.F:
172      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
173    o pkg/seaice:
174      - remove legacy branch code.
175      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
176    o verification/*/code*/SEAICE_OPTIONS.h:
177      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
178        SEAICE_CAP_HEFF).
179    o pkg/cheapaml:
180      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
181        to load new forcing fields.
182      - add missing "_d 0" where it's needed; + some editing (improve indentation).
183      - remove switch to "-r8" compiler option (no longer needed) in verification
184        cheapAML_box, keep same output (small trucation error differences).
185    o verification/offline_exf_seaice:
186      - add thermodynamics only test.
187    o verification/cheapAML_box:
188      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
189        keep same output (same 14 digits for cg2d).
190      - switch on "-r8" compiler option (some numerical values are missing
191        the "_d 0") and update output (only 6 digits for cg2d were preserved).
192    
193    checkpoint64b (2012/12/24)
194    o pkg/cheapaml:
195      - remove un-used variables (Qnet,EmPmR) from pickup files.
196      - store tendency of advected variables into cheapaml pickup file
197        and fix the AB-2 restart.
198    o verification/offline_exf_seaice and lab_sea adjoint:
199      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
200      - switch to 4 time steps in offline, consistent with lab_sea.
201      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
202      - update results after change of experiment seaice.
203    o pkg/seaice:
204      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
205        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
206        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
207        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
208    o model/src:
209      - add run-time parameter to select CG2D solver minimum-residual solution
210        (in case of a poor convergence).
211    o pkg/seaice/seaice_lsr.F
212      - move calculation of matrix coefficients into new
213        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
214        file; the main purpose of this change is to be able to reuse the code
215        in S/R SEAICE_PRECONDITIONER
216      - modify the computation of the residual so that the mass of sea-ice
217        is not used twice; this simplifies the calculations, but since
218        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
219        not tested in testreport---this does not affect the testreport results.
220    o verification/seaice_obcs:
221      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
222        verification/lab_sea/input.salt_plume; changes results/output.txt*
223    o model/src:
224      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
225    o pkg/seaice:
226      - improve description of parameters in seaice_fgmres.F and start
227        cleaning up the code
228      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
229        second argument
230      - add a metric based on grid cell area to SEAICE_SCALPROD; update
231        results of offline_exf_seaice.dyn_jfnk
232      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
233    o pkg/aim_v23:
234      - fix an other bug in dissipation heating (grid-cell area was missing).
235    o model/src + pkg/seaice:
236      - add global (multi-tile) linear solver for pair of tri-diagonal system
237        along X and Y lines, respectively for U and V component.
238        Note: 1) MPI and cube-exchange not yet coded.
239            2) probably not accurate for poorly conditioned / large size problem.
240      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
241        default: not compiled and not used.
242    o pkg/seaice:
243      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
244        introduce bi/bj loops and use global_sum_tile_rl instead of
245        mpi_allreduce in seaice_fgmres.F
246      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
247      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
248      - add a verification experiment for JFNK in offline_exf_seaice
249    o verification:
250      - change (for now, only fwd test) offline_exf_seaice experiment:
251        use a re-entrant channel with idealized coastline (trapezoidal shape)
252        at southern boundary to explore seaice dynamics and thermodynamics
253        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
254        secondary test (input.thsice) use thermodynamics only with SST relaxation.
255      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
256    o pkg/exf:
257      - disable "sstExtrapol" when Nr=1
258    o verification:
259      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
260        to test pkg/cheapaml.
261    o pkg/aim_v23 & pkg/shap_filt:
262      - fix dissipation heating (erroneous gravity multiplication factor).
263    o pkg/seaice:
264      - remove unused field pressPre from jfnk solver
265      - rename two subroutines in seaice_preconditioner.F
266    o eesupp/src:
267       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
268    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
269       - remove wrong parts of the rhs and the lhs (were in there
270         because I did not understand the concept of this preconditioner)
271       - add an exchange between u- and v-sweep. This increases communication
272         by a factor of two but improves the convergence of jfnk. Ideally,
273         one would like the u- and v-sweep to be independent. So far within
274         undocumented ifdefs
275       - reorganize the extra computations for printing the residuals
276    o tools/genmake2:
277      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
278        since it's not necessary (and was preventing to use MNC in some cases).
279    
280    checkpoint64a (2012/11/16)
281    o pkg/autodiff:
282      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
283        autodiff_readparms.F no longer depends on calling order (within
284        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
285        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
286        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
287    o pkg/obcs:
288      - adding tidal velocity forcing capability to obcs
289        for usage example, see verification/seaice_obcs/input.tides
290    o pkg/seaice:
291      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
292        SEAICE_LSRrelaxU/V
293      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
294    o pkg/aim_v23:
295      - implement heating from friction (bottom friction and stratospheric drag).
296    o pkg/shap_filt:
297      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
298        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
299    o model/src:
300      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
301        time-constant addMass field from file (addMassFile);
302      - support for heating due to friction (and Kinetic Energy dissipation):
303        add option, run-time switch and 3-D field array + support code ; each pkg
304        or S/R can add heating contribution (if there is a sink of KE); the sum is
305        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
306    o pkg/seaice:
307      - complete merge of ITD code into seaice_growth.F
308        from MITgcm_contrib/torge/itd/code/
309        no verification so far, but Torge Martin tested
310        "1-D test case and Beaufort set up;
311        deliver okay results after 1 model year."
312      - complete merge of SEAICE_SIZE.h into all relevant routines
313      - move computation of eta at Z-points into calc_viscosities
314        + introduce global field etaZ
315        + add different methods for computing etaZ, for now the old
316          method (simple averages of eta to Z-points) is hardwired
317        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
318          seaice_preconditioner
319      - simplify computations for SEAICE_ZETA_SMOOTHREG
320      - seaice_preconditioner:
321        + replace one remaining press by pressLoc (mistake)
322        + adjust printing of residuals
323      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
324        + add (SEAICE.h) and rename some counters (initiliased in
325          seaice_init_fixed.F)
326        + add _BEGIN/END_MASTER (myThid)  around print statements
327        + print total number of iterations and failures over SEAICE_monFreq
328          interval to STDOUT
329      - move control over output-messages by fgmres to seaice_jfnk to save
330        some operations
331      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
332        in order to make restarts with sol .ne. zero (fgmres with restarts)
333        (seaice_jfnk.F, seaice_fgmres.F)
334      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
335        a serious convergence problem when open boundaries are involved
336    o pkg/ggl90: fix computation of control volumes for the case of
337      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
338      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
339    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
340    o pkg/autodiff
341      - Add inAdMode switch for SEAICEuseDYNAMICS:
342        SEAICEuseDYNAMICSinAdMode
343        (extend logic in ADAUTODIFF_INADMODE_SET)
344    o pkg/seaice
345      - Step 1 of merging ice-thickness distribution (ITD) code from
346        MITgcm_contrib/torge/itd/ (author: Torge Martin)
347        The code implements concept laid out in Thorndike et al. (1975);
348        code is enabled via CPP flag SEAICE_ITD
349        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
350        code is not complete yet!!
351      - SEAICE_SIZE.h now included in almost all seaice routines
352    o verification (using seaice):
353      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
354        global_ocean.cs32x15.seaice ; update results.
355      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
356      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
357        offline_exf_seaice (previously compiling B-grid).
358    o pkg/exf:
359      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
360        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
361        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
362    o pkg/layers (adjust changes from Sept 19):
363      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
364        this allows to remove "layers_maxNum" dimension from all layers arrays.
365    o pkg/layers (adjust changes from Sept 19):
366      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
367      - snap-shot extended to all type of layers (not just the 1rst type);
368      - remove layers variables when corresponding CPP option is undef.
369    o pkg/layers:
370      - rename pkg/layers variable and add new output (layer exist & un-weighted
371        velocity in layer)
372    o pkg/seaice:
373      - simplify (?) ocean-drag coefficent computations by using
374        the same routine in all three solvers (saves some code lines)
375      - remove global fields DRAGA and DRAGS from C-grid code and
376        declare them locally in lsr.F (the only place where they are
377        still used)
378      - update AD output of lab_sea.evp (very sensitive anyway).
379    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
380      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
381      and SEAICEuseJFNK=.true. A few things to note:
382      - involves a FGMRES, that is parallel but very inefficient,
383        because of many scalar products (global sums) in the Gram-Schmidt
384        orthogonalization method. Needs to be replaced. Original code
385        from J.-F. Lemieux
386      - preconditioner for FGMRES is a stripped down version of LSOR
387      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
388        preconditioner. For the preconditioner, the default is set to 10.
389      - Jacobian times vector is computed with finite differences
390      - marginally related to JFNK-solver: add a smooth regularization for
391        zeta with tanh that will improve convergence (Lemieux and Tremblay,
392        2009) for any implicit solver (not implemented for EVP because EVP
393        does not need this regularization in the first place). Define
394        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
395    o eesupp/src:
396      - check in genmake2 that intrinsic S/R flush is available.
397      - add S/R to flush IO unit (if intrinsic S/R flush is available)
398      - flush standard & error msg unit before MPI termination
399      - if debugMode, flush IO unit after printing msg
400    o pkg/ctrl:
401      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
402        to ctrl_set_unpack_xyz.
403    
404    checkpoint64 (2012/10/09)
405    o pkg/shelfice
406      - in mom_fluxform.F, mom_vecinv.F:
407        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
408        Bug fix KappaRU -> KappaRV
409        does not change verification/isomip but may change other setups
410        (presumably constant KappaRU=KappaRV)
411      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
412    o pkg/obcs:
413      - fixed some indexing bugs in obcs_seaice_sponge.F
414      - added obcs relaxation subroutines for HSALT and HSNOW
415      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
416    o pkg/seaice:
417      - add "multicategory" parameterization for snow in analogy to ice,
418        default is off for now.
419    o pkg/obcs:
420      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
421        see verification/seaice_obcs/input.seaiceSponge for example application.
422      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
423        index setting by master-thread. This fix multi-threads Pb in previous modifs.
424    o pkg/layers :
425      - add diagnostics to pkg/layers
426      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
427        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
428    o pkg/generic_advdiff/gad_implicit_r.F :
429      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
430    o pkg/seaice/seaice_growth.F:
431      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
432    o pkg/obcs:
433      - change default setting of OBCS_UVICE_OLD from defined to undef;
434      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
435        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
436      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
437      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
438        with Southern & Western OB at a tile edge (at least in a simple set-up).
439    o pkg/obcs:
440      - change settings of OB index in case OB coincides with tile edge (shared by
441        2 tiles), so that common OB location is registered by both tiles (instead of
442        only 1). However, for Southern and Western OB, index value = 0 is not
443        recognized as valid OB index (=default null value) and needs to be fixed.
444      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
445      - new parameter "OB_indexNone" for null index value (for now, still zero)
446        to replace hard-coded null index value of zero.
447    o pkg/exch2:
448      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
449        always check buffer-size (but outside the loop); move checking for valid
450        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
451        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
452    o pkg/ctrl (pack & unpack):
453      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
454        (locally defined) for different variables (+ remove the variable-specific
455        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
456        (to be extended to other local file names in ctrl.h).
457    o pkg/flt:
458      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
459    o pkg/mdsio:
460      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
461    o tools/genmake2:
462      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
463        (added by Alistair in version 1.51 for building without make depend);
464      - remove Header files list (H_SRC_FILES) from the dependence of targets
465         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
466        place in version 1.23): this save going through staf when unrelated header
467        file has been modified.
468       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
469        "make depend" step, still need to do "make links" before "make adtaf".
470    o eesupp/src (+ few pkg src files) & genmake2:
471      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
472      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
473      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
474         upper/lower case ; account for space between "#" and undef/define)
475    o pkg/flt (with exch2):
476      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
477      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
478    
479    checkpoint63s (2012/09/05)
480    o pkg/ecco:
481      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
482      - add more relevant #ifdef ALLOW_SMOOTH ones.
483      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
484    o pkg/ctrl:
485      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
486        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
487      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
488        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
489        ctrlSmoothCorrel3D (new).
490        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
491      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
492      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
493        controls when useAtmWind, and vice versa.
494      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
495      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
496          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
497      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
498          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
499      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
500        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
501    o pkg/smooth:
502      - remove un-necessary includes.
503      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
504        Those CPP options were never defined, and not necessary.
505    o model/src:
506      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
507      - standard treatment of useSMOOTH.
508    o pkg/autodiff:
509      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
510        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
511    o pkg/exch2:
512      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
513        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
514      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
515        and tiles to process mapping.
516      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
517        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
518        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
519        from w2_eeboot.F to w2_readparms.F.
520    o eesupp/src:
521      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
522        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
523        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
524      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
525        is defined (remove condition on usingMPI) to match cases where MPI_INIT
526        has been called.
527      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
528      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
529        (so that on 1 proc, get same myPid independently of usingMPI)
530      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
531        useCubedSphereExchange with EXCH-1 (safer).
532      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
533    o pkg/ggl90:
534      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
535        used in ALLOW_GGL90_SMOOTH code.
536    o pkg/flt:
537      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
538        floats at the Southern end of the domain).
539    o eesupp/inc:
540      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
541        but not used (and not to be used) anywhere, just for documentation.
542    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
543      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
544        a) can damage previously written records in any other multi-record files.
545        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
546    o tools/genmake2:
547      - define variable MAKE within Makefile and use it in place of 'make';
548      - update AD_CONFIG.h (if needed) before building any of the executable
549        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
550        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
551      - always print usual warning comment 'this file is automatically generated'
552        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
553    o pkg/cheapaml:
554      - updated to correspond to the code used in accepted paper (Nico Wienders).
555    o pkg/exf:
556        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
557        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
558        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
559    o pkg/exf, autodiff, ctrl, ecco and seaice:
560        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
561    o pkg/ctrl, ecco:
562        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
563        Depending on useAtmWind, one is inactive, and the other is active (see
564        exf_getffields.F/exf_getsurfacefluxes.F).
565    o tools/genmake2:
566      - improve error msg when failing in 2nd test of check_for_broken_Ff
567      - fix option '-makefile' short-name (-mf according to genmake2 -help)
568      - source local config file "genmake_local" just after processing the genmake2
569        command arguments (previously done before processing arg).
570    o pkg/grdchk:
571      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
572        to this routine from cost_final has been dropped in g_cost_final)
573      - improve printed information (more explicit msg, no longer using "print *,"
574         fix fcpertminus printed value).
575    o model/src:
576      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
577        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
578        this prevents getting cost-funct reset in adinitialise_varia recomputations.
579    o pkg/dic:
580      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
581        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
582    o pkg/grdchk:
583      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
584      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
585    o pkg/autodiff/ctrl/grdchk :
586      - attempt to sort out what works and what does not,
587        with regard to I/O, and to warn/stop accordingly.
588    o pkg/grdchk:
589      - attempt to fix grdchk in the case of useSingleCpuIO.
590      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
591       statements were moved from grdchk_main.F and into
592       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
593      - a global sum is applied to record numbers icvrec/layer
594       out of grdchk_loc so that they be passed to I/O routines.
595    o pkg/smooth:
596      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
597        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
598    o verification/testreport:
599      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
600      - can also use compressed (gzip) reference output file;
601      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
602        to be easier to collect by testreport.
603      - update existing TLM output (half out-of-date by more than 3 yrs).
604      - report NETCDF & LAPACK settings (from genmake2) in output dir.
605      - report run-time in each individual summary (previously only for AD test);
606        for TLM test, add also TAF version.
607      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
608    
609    checkpoint63r (2012/08/15)
610    o tools/genmake2:
611      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
612    o pkg/ecco/ecco_cost_final.F :
613      - fix fc print statements (to stdout and costfunction0000) so
614        that the printed value is always after the global sum.
615    o pkg/seaice/seaice_dynsolver.F :
616      - fix ice strength assymptote at SEAICE_area_max<1
617        (no change for the standard case of SEAICE_area_max=1)
618    o some cleaning:
619      - pkg source files: ensure that all *.F files from each pkg included the
620        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
621        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
622        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
623        includes;
624      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
625      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
626        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
627        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
628      - update option-file CPP_OPTIONS.h of all AD experiments:
629        * no longer include PACKAGES_CONFIG.h ;
630        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
631        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
632          including ECCO_CPPOPTIONS.h).
633    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
634      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
635        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
636        not necessary accurate).
637      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
638        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
639        deliberately break compilation (a remainder that it needs to be customized)
640      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
641      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
642      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
643    o tools/genamke2:
644      - check for lapack.
645    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
646      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
647        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
648        from both packages.
649      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
650      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
651      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
652        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
653    o pkg/cost : add comments to explain special and/or untested setups.
654    o pkg/exf:
655      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
656        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
657    o verification/*/code_ad:
658      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
659      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
660      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
661        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
662    o pkg/seaice :
663      - added possibility to change ice strength/PRESS0 relationship to
664        HEFF, according to the following run time parameters
665        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
666        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
667        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
668    o pkg/ggl90 :
669      - added run time flag mxlSurfFlag to include the code that ensure
670        mixing between first and second level (previously included as a comment)
671    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
672      - add test of newly added dumpAdByRec=T option where
673        we write all records to one file per variable.
674    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
675      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
676        to check that this code is ok with taf and compiles in adjoint.
677    o pkg/autodiff :
678      - added run time param dumpAdByRec : ad dump format switch.
679        If true then write all records to one file per variable.
680        Else write one file per record (remains the default).
681      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
682    o pkg/seaice:
683     - Added SEAICEuseTILT run time switch : if set to
684       false then omit the tilt term in seaice dynamics.
685     - Fix free drift calculation.
686    o pkg/shelfice:
687      When initializing SHELFICEDragQuadratic, set default to be
688      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
689      but retain option to set it independently
690      (inconsistenty spotted by Veronique Dansereau)
691    o eesupp/inc:
692      - in EEPARAMS.h, add real-type constant for some frequently used simple number
693         (0,1,2,1/2), with name explicitly referring to RS/RL type.
694    o model/src:
695      - move balancing of relaxation terms to new S/R balance_relax.F.
696    o pkg/autodiff:
697      re-write active I/O high-level (control) S/R:
698      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
699      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
700      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
701        MDS_READ/WRITE_FIELD); change loops to multi-threads.
702      - update and merge active_file_control_slice.flow into active_file_control.flow
703      - update the calls in lower level S/R (active_file.F, active_file_g.F and
704        active_file_ad.F) keeping the argument list and function unchanged.
705      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
706        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
707      - new low-level active I/O routines, one for each type (RL/RS), for active var
708        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
709        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
710        right type.
711    o autodiff and RS=real*4:
712      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
713        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
714      - change argument type of 3-D mask argument to _RS to match type in the call
715        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
716    o pkg/thsice:
717      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
718      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
719        fresh-water flux: uniform correction or proportional to local precip.
720    o pkg/ctrl:
721      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
722      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
723                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
724      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
725    
726    checkpoint63q (2012/07/30)
727    o pkg/autodiff:
728      note about monitor and snap-shot of ad-variables:
729      a) need to apply ADEXCH before monitor or output of ad-vars to include
730       overlap contributions (was done for adjDump but missing for monitor).
731      b) since ADEXCH implies adding overlap values to interior array, machine
732       truncation error is expected when adding an ADEXCH call in the middle of
733       the time-stepping (although mathematically identical).
734      modifs:
735      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
736        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
737      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
738        apply ADEXCH before monitor or snap-shot of ad-variables:
739           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
740      - implement new method (copy+adexch) for snap-shot and monitor of main model
741        ad-vars (initially not used by default -> output unchanged).
742      - change default (set to 2) to use new method and update few output_adm.txt
743        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
744        and both tutorial_tracer_adjsens tests).
745      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
746        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
747    o pkg/ctrl:
748      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
749      generic control variables via
750      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
751      Only required customization should be S/R ctrl_map_ini_genarr.F
752      (routine in repository contains example)
753    o pkg/exf:
754      - fix and refine checking of surface-relaxation setting when using EXF
755    o verification (adjoint exp):
756      - reduce length of simulation by half for experiment global_ocean.cs32x15
757        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
758    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
759      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
760        of KE that can occur with aggressive optimization
761      + put quadratic bottom drag calculation in separated loops (only done if
762        using bottomDragQuadratic)
763    o model/src: CG2D_NSA
764      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
765         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
766      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
767         change cg2d residual target to be expressed in Wunits (=> do not normalise
768         RHS ; this fix global_max Pb with TAF); update output.
769    o verification/tutorial_tracer_adjsens:
770       improve parameter consistency (and get rid of warnings):
771       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
772       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
773       - use staggerTimeStep (for stability) in som81; use default rotation period.
774    o pkg/exch2:
775      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
776        reset to 0 = 1 long line in X)
777    o pkg/mdsio:
778      - fix reading of dimensions from meta file for large-size domain
779    o model/src:
780      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
781      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
782        Cubed-Sphere Exch with CS-corners inside the domain;
783        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
784        globalArea and to set hasWetCSCorners.
785      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
786        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
787      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
788        useCDscheme and useCubedSphereExchange).
789    o pkg/seaice/seaice_growth.F :
790      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
791        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
792        when the previous code was not correct.
793      - in all cases diagnoze the boundary condition mismatch to SIaaflux
794      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
795        that term to QNET (essentially to set the melt/freeze water to 0degC).
796        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
797    o verification/global_ocean.cs32x15/input.seaice :
798      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
799      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
800      - update results (output.seaice.txt) accordingly.
801    o verification/lab_sea/input/data.seaice :
802      - remove SEAICEheatConsFix, which is now be tested
803        in global_ocean.cs32x15. The presently coded fix
804        is only consistent with real fresh water + nlfs.
805      - update results (output.txt) accordingly.
806    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
807    o AD_CONFIG.h file:
808      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
809      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
810        add it explicitly in each fortran src file where it is needed.
811        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
812        thus introducing potentially wrong dependency; therefore, better to include
813        it only where it's really needed, and after any other included OPTIONS file
814        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
815        or ALLOW_TANGENTLINEAR_RUN).
816    
817    checkpoint63p (2012/07/06)
818    o pkg/autodiff:
819      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
820      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
821        which are now read from new parameter file "data.autodiff" (inAdExact
822        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
823      - add file "data.autodiff" in all verification/*/input_ad/ directories.
824      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
825        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
826    o verification/tutorial_tracer_adjsens/
827      - add extra sub-verification which uses "SOM" advection scheme
828        (2nd Order-Moment Advection Scheme, Prather Limiter) with
829          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
830        and in data:
831          multiDimAdvection=.TRUE.,
832          tempAdvScheme=81,
833          saltAdvScheme=81,
834    o model/src:
835      - introduce ALLOW_BALANCE_RELAX which allow the removal
836       of the global mean of relaxation terms by setting
837       balanceThetaClimRelax and balanceSaltClimRelax
838      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
839       This case is now treated appropriately in seaice_growth.F
840    o pkg/seaice:
841      - do balanceEmPmR and balanceQnet based on the net fluxes
842        (SItflux) that enter the ocean+ice system rather than QNET
843        and EMPMR. Works best in real fresh water.
844      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
845        out of the diagnotics bloc, and stored in global arrays.
846    
847    checkpoint63o (2012/06/29)
848    o vertical mixing schemes:
849      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
850      - replace computation of density (in Function STATE1, opps_calc.F) by a call
851        to S/R FIND_RHO_SCALAR
852      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
853        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
854        affects output (vermix.ggl90) at truncation level.
855    o testreport:
856      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
857        (nSx,nSy) for the number of threads (from eedata.mth)
858    o model/src:
859      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
860        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
861    o verification/tutorial_tracer_adjsens/
862      - compile with ALLOW_CG2D_NSA
863      - run with nonlinFreeSurf=3
864      - update reference output_adm.txt
865    o tools/genmake2:
866      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
867        refine usePROFILES switching off (only when NetCDF is not available).
868    o verification (atmospheric set-up):
869      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
870    o pkg/profiles : refine profiles and files handling.
871    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
872    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
873      - changes to use model/src/the_main_loop.F rather than the ecco version
874        in ecco type adjoint runs.
875    o model/src:
876      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
877      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
878      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
879    o model/src:
880      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
881        update output of test experiment bottom_ctrl_5x5.
882    o pkg/generic_advdiff:
883      - implement vertical bi-harmonic diffusion (for now, only for T & S and
884        only explicitly).
885    o verification/bottom_ctrl_5x5/
886      update reference output (results changed quite some time ago,
887      not sure when; but new reference results look ok in terms of grdchk)
888    o verification/1D_ocean_ice_column/
889      For verification purposes, the exact adjoint rather than an approx.
890      should be used (e.g., to comare against F.D. or TLM).
891      removed autodiff_inadmode*_ad.F routines in code_ad/
892      Update results/ accordingly.
893    o pkg/cal:
894      - change cal_getdate.F so that output date is function of input time only
895        (less ambiguous, not mixed up with input iteration number).
896      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
897    o pkg/diagnostics:
898      - implement calendarDumps also for stats-diags
899      - implement calendarDumps also for snap-shot output (negative freq)
900      - for now, ignores calendarDumps if non-zero phase-lag.
901    
902    checkpoint63n (2012/06/04)
903    o model/src:
904      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
905        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
906      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
907        similar to calc_r_star.F); update results of experiment internal_wave and
908        tutorial_global_oce_in_p (affected @ truncation level).
909    o pkg/shelfice:
910      - add parameterisation of advective-diffusive flux into the ice shelf
911        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
912      - simply eps3/3a computation
913    o eesupp:
914     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
915       between tiles, just fill-in edges assuming locally periodic subdomain) and
916       add corresponding exchange subroutines (EXCH0);
917     - new CG-solver version (_EX0) for disconnected-tiles special case.
918    o model/src (CG-solvers):
919     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
920       (similar final residual output and max-Iter number as with standard version);
921     - allows to store and use lowest-residual solution (standard & _SR versions);
922     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
923     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
924    o eesup/src:
925     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
926       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
927    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
928    
929    checkpoint63m (2012/04/27)
930    o pkg/shelfice:
931     - account for partical cells in surface level below ice-shelf for hydrostatic
932       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
933    o ad test experiments:
934     - update and rename to "ad_optfile.local" local AD-optfile specific to a
935       particular adjoint verification experiment (in verification/*/code_ad/)
936    o pkg/seaice & pkg/exf:
937     - Part two of ECCO-CLIVAR code merges.
938       Completes merge of seaice area relax. code.
939       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
940       to be set in EXF_OPTIONS.h since this pkg controls its I/O
941       (and avoids second CPP option in SEAICE_OPTIONS.h)
942     - change default value of costIceStart & costIceEnd to a valid date.
943     - add snowPrecip to HSNOW in seaice_growth
944    o pkg/ptracers:
945     - move ptracers summary and setup check into separated S/R ; add a check for
946       valid PTRACERS_Iter0 value (error+stop or just warning).
947    o pkg/cal (+ pkg/ecco):
948     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
949       as input; and for AD, unless both are not differentiable (e.g., k index)).
950    o model/src:
951     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
952       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
953       temporary set to usingZCoords value (to be changed to F when using shelfice).
954     - hydrostatic pressure: implement partial cell near the surface also for
955       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
956       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
957    o pkg/ctrl/ctrl_init.F:
958     - add a formal parameter to s/r ctrl_init_rec to print
959       xx_$(ctrl_valiable)_file for easier debugging
960     - move call of cal_* routines into the if-block where they are really
961       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
962       to specify a startdate
963    o pkg/seaice:
964     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
965       global_ocean.cs32x15/code versions).
966     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
967       verification experiment global_ocean.cs32x15.seaice and update results.
968    o pkg/exf:
969     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
970       (according to useExfYearlyFields).
971    o pkg/cal:
972     - move calendar setting & summary (previously in cal_readparams.F) into new
973       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
974       length of the simulation is set (after SET_PARMS call); This is an attempt
975       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
976     - For safety: keep a record of pkg/cal parameter settings status
977               to allow to STOP if one pkg/cal S/R is called too early.
978     - add a stop in all basic pkg/cal subroutines if called before setting is done.
979     - modify cal_getdate.F: stop when nothing was returned;
980       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
981       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
982    
983    checkpoint63l (2012/04/04)
984    o pkg/bbl:
985      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
986        update global_with_exf output.yearly.txt file.
987    o pkg/cal:
988      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
989      - remove 2 unsused and very short (1 line only) functions ;
990      - remove unsused subroutines from AD-Diff list.
991    o model/src:
992      - start to implement clean wait to stop in initialization S/R (config_check.F,
993         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
994    o folowing PRINT_MESSAGE changes:
995      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
996    o pkg/bbl:
997      - modification so it can work with z*
998      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
999      - global_with_exf/input.yearly verification; changes output.yearly.txt
1000    o eesupp/src:
1001      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1002        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1003      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1004        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1005      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1006      - when using MPI, always set usingMPI=T ; set default accordingly and stop
1007        if not consistent.
1008      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1009        argument is zero (in case called within single-thread section).
1010    o pkg/fizhi:
1011        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1012        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1013    o pkg/exch2:
1014      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1015        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1016      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1017        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1018        with bad ones coming from a not-yet-updated halo.
1019        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1020    o pkg/frazil:
1021        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1022        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1023    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1024    o verification/lab_sea
1025      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1026      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1027      * nTimeSteps 3 -> 4
1028      * changed reference output accordingly
1029    o pkg/ctrl:
1030      * fix ctrl_get_gen for xx_sst, xx_sss
1031    o pkg/fizhi:
1032      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1033        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1034      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1035        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1036        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1037    o pkg/gmredi:
1038      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1039    o pkg/fizhi:
1040      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1041        (old)aces open64 tuv test.
1042    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1043    o pkg/mom_vecinv:
1044      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1045        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1046        with non-lin free-surf).
1047    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1048      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1049      some compilers (gfortran 4.6.0 on MacOS)
1050    o momentum:
1051      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1052        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1053        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1054    
1055    checkpoint63k (2012/03/17)
1056    o model/src:
1057       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1058         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1059       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1060         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1061    o model/src: solve_*diagonal.F
1062       - replace division with multiplication by inverse (similar to original version)
1063         update output of AD exp. global_ocean.90x40x15.
1064       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1065         to enable the use of the vectorized & differentiable solve_tridiagonal.F
1066       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1067         vertical advection (to get solve_tridiagonal tested in AD mode).
1068    o pkg/seaice: ECCO-CLIVAR merge:
1069      1. seaice AREA relaxation
1070         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1071         * runtime flag: SEAICE_tauAreaObsRelax
1072      2. modified global mean cost imbalance code: CPP option
1073          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1074    o another iteration on solve_*diagonal.F
1075       Make choices independent of AUTODIFF
1076       Default will be the adjoinable vectorized version.
1077       Alternative choices are:
1078       * non-adjoinable original version with low memory footprint:
1079         #define SOLVE_DIAGONAL_LOWMEMORY
1080       * still adjoinable but does not vectorize (k as inner-most loop):
1081         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1082    o testreport
1083     - add option to use a home made wrapper around "make"
1084     - remove MITGCM_IEEE env. variable (no longer active)
1085    o pkg/shelfice
1086     - improve computation of friction velocity for velocity dependent
1087       exchange coefficients: include velocities into SHELFICEBoundaryLayer
1088       block to average velocities vertically
1089     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1090    o Modify diagonal solvers, now three versions (upon request):
1091      #ifndef SOLVE_DIAGONAL_AUTODIFF
1092        1. default version (dating back a while ago)
1093      #else /* def SOLVE_DIAGONAL_AUTODIFF */
1094      # ifdef SOLVE_DIAGONAL_KINNER
1095        2. adjoinable version with k-innermost loop (G. Forget)
1096      # else
1097        3. adjoinable vectorized version of 2.
1098      # endif
1099      #endif /* SOLVE_DIAGONAL_AUTODIFF */
1100      All flags are currently set within routines, but could/should be moved to CPP-options.
1101      Array bounds for 1. are as before, for 2.,3. cover the entire domain
1102      (could be changed for 1. too).
1103    o verification/lab_sea (fwd):
1104      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1105        use 7 categories (except hb87), new solve4temp params (except salt_plume),
1106        constant salinity (=4) or variable salinity (salt_plume) done through
1107        SItracer.
1108    o pkg/seaice:
1109      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1110      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1111         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1112        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1113        SEAICE_freeze got retired) but already better than previously with
1114        SEAICE_freeze=123456.7 deg.C;
1115      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1116        (safer multi-threaded setting); always set SEAICEuseEVP;
1117      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1118        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1119        stop if multiple specifications for the same coeff; make sure default
1120        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1121    o pkg/obcs:
1122      - allow to switch to upwind 1rst order advection scheme for the advective
1123        flux computation at the open-boundary; disabled for adjoint built.
1124    o pkg/ptracers:
1125      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1126      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1127      - add parameter to decide when to start a tracer; use internal flag to
1128        know which tracer to step-forward; switch this internal flag at the top
1129        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1130        for adjoint built.
1131    o pkg/seaice:
1132      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1133      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1134      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1135    o pkg/ecco:
1136      - fix writing of output file DiagnosCost_ClimSalt/Theta
1137        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1138    o pkg/seaice:
1139      - add missing initialisation of COR_ICE array in dynsolver.F
1140      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1141        compiled either way, and is tested in all exps (multidim was only tested
1142        in lab_sea ad before).
1143      - cosmetic change to prepare for future addition of ITD. no change to results.
1144        no defaults change.
1145      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1146      - by lack of adequate verification experiments, I further used custom versions
1147        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1148        should be correct.
1149      - avoid recomputations in ad.
1150    o array initialisation in adjoint mode:
1151      1) pkg/mom_common/mom_calc_ke.F:
1152        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1153        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1154        part this initialisation is gone, resulting in Floating Point Exception
1155        (caught by open64 compiler with debug option).
1156      2) model/src/convective_weights.F
1157        set output convectCount over the full array range (instead of doing
1158        an update): this fix a similar issue when called within recomputation (adjoint)
1159        which could by-pass the initialisation (normally done in the caller S/R).
1160    o pkg/seaice:
1161      - final version of turbulent flux params, as agreed at MIT ice meet:
1162           SEAICE_mcPheePiston (default is ~ 0.000875)
1163           SEAICE_mcPheeTaper (default is 0.)
1164           SEAICE_frazilFrac (defualt is 1.)
1165           SEAICE_mcPheeStepFunc (default is false)
1166      - changes results at trunction error level
1167      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1168    o added pkg/frazil:
1169      - see frazil_description.tex for details
1170      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1171    o pkg/shelfice/shelfice_thermodynamics.F
1172      - fix exponents for velocity dependent exchange coefficients: change
1173        from 2/3(=0) to 0.66666666666666667
1174      - move computation of velocity dependent exchange coefficients into
1175        separate loop, so that it applies to both thermodynamics
1176      - move some divisions by constants out of loops
1177    
1178    checkpoint63j (2012/02/16)
1179    o pkg/seaice:
1180      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1181      - SItracer:  added run time params, and allow coupling to ocn salinity.
1182    o pkg/seaice: remove (almost) all divisions by constants within loops
1183      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1184      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1185      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1186      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1187    o pkg/seaice :
1188      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1189        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1190      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1191      - add permanent SItflux diag that corresponds to TFLUX but includes
1192        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1193      - allow activation/testing of a fix for suspected missing term in
1194        ocn-ice heat budget (to be confirmed). To test this, you want to
1195        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1196        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1197      - no change in results, fwd or ad.
1198    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1199      - switch to variable freezing point.
1200           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1201      - bug fix : the sublimation term that was missing is now activated.
1202           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1203      - bug fix : flooding sign term for SIsal0.NE.0.
1204           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1205    o pkg/seaice:
1206      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1207        is now the default, and the old default constant freezing point is recovered
1208        with SEAICE_tempFrz0    = -1.96,
1209             SEAICE_dTempFrz_dS = 0.,
1210      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1211      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1212      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1213        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1214      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1215        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1216      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
1217        seaice_growth r149 for legacy branch (no results change).
1218      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1219        from I. Fenty).
1220      - results did not change except for global_ocean.cs32x15, mostly due to the
1221        switch to variable freezing point (see above item for detail).
1222    o pkg/thsice:
1223      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1224        seawater freezing in thsice_calc_thickn (not used).
1225    o pkg/seaice: turbulent flux term specification via run time params.
1226      - replace CPP switches with run time switches to facilitate testing
1227      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1228                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1229      - added runtime parameter : SEAICEturbFluxFormula
1230      - move Mcphee constants to SEAICE_PARAMS.h
1231      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1232                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1233                 remove seaice_summary call (moved to seaice_init_fixed)
1234      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1235        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1236      - seaice_summary.F : add missing report of read turbulent flux term set up
1237                           and SITRACER.
1238      - seaice_check.F : check range; inform and stop if retired CPPs are used
1239                         (incl. SEAICE_AGE).
1240      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1241             CPP switch, same computation as before for the different options.
1242      - change results at the truncation level.
1243    o pkg/seaice:
1244      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1245        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1246        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1247      - update verification/*/input*/data.seaice:
1248        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1249        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1250        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1251        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1252    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1253      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1254        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1255        difference in results only due to machine truncation.
1256      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1257        MaykutPolySatVap; keep MIN_LWDOWN.
1258      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1259      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1260        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1261    o pkg/salt_plume:
1262      - isolate saltPlumeFlux array exch into a specific S/R called from
1263        do_oceanic_phys.F
1264      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1265    o verification:
1266      - move untested set-up to MITgcm_contrib/verification_other.
1267    o pkg/seaice:
1268      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1269    o pkg/seaice:
1270      - seaice_solve4temp.F (keeping results unchanged):
1271        * add 2 future run-time params to select which saturation vapor pressure
1272          formula is used and how post-iteration fluxes are set.
1273          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1274        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1275          the linearized expression to stay consistent with tsurf finding.
1276      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1277        can be < 0.
1278    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1279      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1280        conductive heat flux F_c , and add it explicitly when updating tsurf as
1281        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1282        so that now F_ia has a consistent meaning through the entire routine.
1283        This causes differences at truncation level: update output of fwd exp.
1284        global_ocean.cs32x15.seaice.
1285    o pkg/seaice:
1286      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1287        of arrays, sign/direction of fluxes; no effect on results.
1288      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1289        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1290        note: this should have been done before changing celsius2K default.
1291      - to keep results unchanged, add back old value of celsius2K in verification
1292        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1293      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1294        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1295        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1296        freezing temp is consistent with value in seaice_growth.F ; this causes
1297        differences at machine truncation level: update lab_sea AD output (3/4).
1298    o pkg/seaice:
1299      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1300        and climsst/sss even when using seaice (to prevent calculation that might
1301        use SST on land); does not affect any verification exp.
1302      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1303        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1304    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1305      over land (non-legacy code)
1306    o vectorize salt_plume package:
1307      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1308      - this code computes plumebk everywhere (also over land), thus requires
1309        code to avoid divisions by zero and catch the case of kLev=Nr.
1310      - efficiency of salt_plume_frac is still sub-optimal
1311    o tools (genmake2):
1312      - fix makefile NAME specification (option: -makefile NAME) by adding
1313        "-f $MAKEFILE" in few places where it was missing including makedepend
1314        command (contribution from Paul).
1315    
1316    checkpoint63i (2012/01/24)
1317    o model/src:
1318      - add factorized versions of some EOS code to find_rho.F,
1319        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1320    o model/src:
1321      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1322      - change default celsius2K from 273.16 to 273.15
1323      - to keep results unchanged, add back old value of celsius2K in verification
1324        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1325         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1326    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1327      to make TAF generate vectorizable code
1328    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1329       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1330       have flags that do this more efficiently.
1331    o pkg/diagnostics/diagstats_calc.F
1332      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1333    o pkg/obcs (with exch2):
1334      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1335        and remove code (in obcs_readparms.F) which was based on EXCH of indices
1336        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1337    o pkg/exf and seaice exp:
1338      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1339        so that switching off area & heff advection flags does not affect results.
1340      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1341      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1342        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1343        results of verification experiments: 1D_ocean_ice_column(fwd),
1344        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1345        and offline_exf_seaice (all 4).
1346    o pkg/seaice:
1347      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1348        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
1349      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
1350        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
1351        not multi-dim advection;
1352      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
1353        SHORTWAVE_HEATING #undef.
1354    o optim: make Makefile more robust (?)
1355    o pkg/obcs:
1356      * fix treatment of obcs_read_pickup for TAF
1357    o pkg/shelfice:
1358      * add missing initialisation of num_shifwflx
1359      * new adjoint verification exp. for isomip
1360      * change Prandtl and Schmidt numbers from generic formulations
1361        (in terms of model diffus. and visc.) to separate runtime
1362        parameters, with Holland and Jenkins (1999) default values.
1363    o pkg/exf (interpolation):
1364      - extended input field (2 rows) near the N & S poles:
1365        * fill in with the symetric value (when even Nb of data in longitude)
1366        * add average value at the poles only for scalar quantities ; for vector
1367          component interpolation, skip the averaging and keep duplicated values,
1368          unless the 2 components have same location (uvInterp=T) in which case
1369          interpolate the 2 components together using S/R EXF_INTERP_UV.
1370      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1371        together: this allows to account properly for local orientation when
1372        averaging at N & S pole.
1373      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1374        exf-interpolation near N & S poles. Undef by default.
1375      - add debug check/print on 1rst iter if debugLevel >=2.
1376    o pkg/exf:
1377      - change masking flags definition (no longer "parameter"), put them in
1378        common block and set them in S/R EXF_INIT_FIXED.
1379      - change recognized masking flag from s,u,v to c,w,s since the mask
1380        to use (maskC,W,S) depends on position on model grid and has little to
1381        do with scalar/vector difference; fix masking if using P-coordinates.
1382      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1383        and update results of exp. global_with_exf (x2).
1384      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1385    o pkg/obcs
1386      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1387    o pkg/exf (interpolation):
1388      - assume periodicity in X only if input field cover full longitude range.
1389      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1390        and should vectorise).
1391      - fix input lat of the 2 added row (in case we provide N.pole data).
1392    
1393    checkpoint63h (2011/12/30)
1394    o pkg/seaice:
1395      - change declaration of UVM from _RL to _RS in order to get B-grid
1396        uIce,vIce monitor when _RS = real*4
1397    o pkg/offline:
1398      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1399      - compute vertical velocity if not read from file (switch on exactConserv
1400        & staggerTimeStep);
1401      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1402    o verification:
1403      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1404        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1405        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1406      - update output of exp. global_ocean.cs32x15.viscA4 after changing
1407        grid-file angles (used here for coriolis-3d);
1408      - remove (or gzip) few files not needed to run fizhi-cs experiments.
1409    o pkg/exf (vector interpolation):
1410      - rotate vector component toward local grid-axis orientation using grid-angles
1411        (stored in GRID.h) instead of locally computed rotation angle; keep old code
1412        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1413    o pkg/seaice:
1414      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1415        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1416    o pkg/PKG_OPTIONS.h files:
1417      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1418        outside of the #ifdef ALLOW_THISPKG / #endif block.
1419      - update verification/*/code/PKG_OPTIONS.h files.
1420    o add a verification experiment (offline_exf_seaice/input.seaice) that test
1421      the B-grid LSOR solver
1422    o pkg/seaice: sort out emissivity and long wave radiation step 2:
1423      - add emissivity for snow and ice as new run-time parameters
1424        (unfortunately) that default to the corresponding exf values; this
1425        changes results in most verification experiments so that for backward
1426        compatibility these parameter have to be set explicitly to inconsistent
1427        values (ugly);
1428      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1429        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1430        until we agree how to handle this bug properly
1431    o pkg/exf (interpolation):
1432      - add a set of run-time param ({inputfield}_interpMethod), one for
1433        each interpolated input field, to select the interpolation method
1434        with a value of zero switching off the interpolation;
1435      - print interpolation parameters to standard output;
1436      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1437        (to use instead runoff_interpMethod=0 in data.exf).
1438      - simplify default setting of interpolation parameters (for all fields,
1439        set position to match model grid cell-center position, leading to trivial
1440        interpolation in case of regular Lat-Lon grid) and fix for the case of
1441        non-uniform delY.
1442    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1443       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1444       this factor is absolutely required, because the lw exitance (= out-going
1445       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1446       where the reflectivity rho = 1-emissivity for conservation reasons. Once
1447       this is established, we can remove the CPP-Flag (if we want to).
1448    o pkg/seaice:
1449      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1450        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1451      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1452        what the name implies (and not emissivity*BoltzmannConstant), this means
1453        the old default value of 5.5e-8 now means
1454        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1455        S/R exf_readparms
1456      - FV-discretization of the B-grid LSOR solver, turn on with
1457        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1458        of the calling routine dynsolver, so that B and C-grid code look a
1459        little more alike.
1460      - fix index bugs in ostres.F (B-grid code)
1461    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1462    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1463      default for SEAICE_emissivity, if useEXF; requires setting a wrong
1464      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1465      backward compatiblity
1466    o model/src: use sigmaR in calc_ivdc
1467    
1468    checkpoint63g (2011/12/16)
1469    o pkg/seaice/seaice_growth.F:
1470      fix heat conservation of the coupled ocean-seaice system.
1471      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1472      solid vs liquid water treatment is resolved via QNET.
1473    o pkg/seaice/seaice_growth.F:
1474      add missing term for sublimation in saltFlux, which was breaking conservation.
1475    o pkg/seaice/seaice_model.F:
1476      Remove this patholigical case treatment in evolution branch,
1477      where it is un-necessary and breaks conservation.
1478      Update global_ocean.cs32x15/results accordingly for
1479      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1480    o model/src:
1481      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1482      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1483    o pkg/obcs:
1484      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1485      tendency for temperature and salinity that is then applied to update
1486      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1487      horizontal advection and diffusion contributions on the boundary (in
1488      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1489      removing the mask in S/R timestep_tracer. The advantage of this approach is
1490      that the updated tracer values include contributions from the surface
1491      forcing and vertical diffusion.
1492      This modification changes exp4.stevens because of vertical diffusion.
1493    o model/src:
1494      change non-curvilinear grid setting to also work with exch2 + blank tiles:
1495      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1496        face dimensions.
1497      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1498        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1499        and INI_SPHERICAL_POLAR_GRID.
1500      change test-experiment global_ocean.90x40x15:
1501      - split the domain in many more tiles (9x4 tiles of 10x10 each);
1502      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1503      - update results of both test (std & dwnslp).
1504    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1505       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1506    o model/src:
1507      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1508        and fix initialisation when using sigma-coords.
1509    o model/src:
1510     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1511       to their current value at the beginning of forward_step.F": add a new run-time
1512       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1513     - set doResetHFactors=T in the following test exp:
1514        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1515        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1516        and tutorial_global_oce_in_p (nonLinFS in p)
1517    o pkg/ecco
1518      - added IES cost term
1519    o verification/advect_xz
1520      - scale down the depth by 1/100 (from 200 km to just 2.km)
1521      - add secondary test using divergent flow, r-star and implicit vertical advection.
1522      - add note (check_conserve_TS.txt) and matlab script to check global
1523        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1524    o pkg/rbcs:
1525      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1526    o pkg/obcs (Stevens BCs):
1527      - fix various problems in the phase speed computations of the Stevens
1528        boundary conditions:
1529        - sign error for western and southern boundaries,
1530        - time tendencies were underestimated by factor of dTracerLev and some just
1531          zero (for multidim advection schemes) -> now estimate time tendencies
1532          from difference between previous (n) time level and the one before (n-1);
1533          this requires storing a field per tracer per boundary, also in the pickup
1534          files.
1535        - replace deltaTmom in cflMer/Zon computation with dTracerLev
1536        - set default phase velocity to cflMer/Zon
1537      - update verification experiment exp4.stevens
1538    o pkg/generic_advdiff (implicit_r):
1539      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1540        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1541      - fix implicit vertical diffusion or advection with NonLin FreeSurf
1542        (was using current recip_hFacC instead of future recip_hFacC): set future
1543        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1544        solver S/R ;
1545      - fill diagnostics of vertical advective fluxes (computed from tendency)
1546        when using implicit vert. advection;
1547      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1548         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1549         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1550         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1551    o pkg/diagnostics:
1552      - add diags for T & S tendency which goes through Adams-Bashforth.
1553    
1554    checkpoint63f (2011/11/30)
1555    o pkg/obcs/obcs_calc_stevens.F:
1556      - join some loops to reduce number of if-statements
1557      - fix a bug in code for northern and southern boundaries.
1558    o pkg/seaice/seaice_init_varia.F
1559      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1560        caused zero ice-velocities for the B-grid code
1561    o pkg/seaice/seaice_init_fixed.F
1562      - fix a bug in the initialisation of the second metric terms
1563        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
1564      - this affects all seaice configurations with useCurviLinearGrid = .true.
1565        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
1566        = .true. (default)
1567      - the only verification experiment affected is global_ocean.cs32x15:
1568        icedyn, seaice, and seaice_dynmix (AD)
1569    o pkg/thsice/thsice_diagnostics_state.F
1570      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
1571        not contain garbage that can lead to surprises in diagstats_calc.F
1572    o model/src:
1573      - move bi,bj loops inside INTEGR_CONTINUITY ;
1574      - call INTEGR_CONTINUITY directly from forward_step.F
1575        (previously called from momentum_correction_step.F)
1576      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
1577        forward_step.F and pkg/ecco/the_main_loop.F
1578    o model/src/do_oceanic_phys.F:
1579      - reset addMass to zero only if useICEFRONT ;
1580      - separated k-loop for rhoInSitu calculation ;
1581      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
1582        and at constant T,S (= WdRHOdP);
1583      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
1584        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
1585        transport of locally-referenced potential density);
1586        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
1587    o gluemnc:
1588      - replace ncrcat with ncks when adding variables to *.glob.nc
1589      - change the way variables without record dimensions are handled so that
1590        files that have variables with and without record variables can be glued:
1591        add a record dimension with a new unique name to be able to differentiate
1592        between variable with and without a-prior record dimensions. Remove
1593        this record dimension before adding the variable to the *.glob.nc file.
1594        This procedure automatically works also for grid.*.nc files that do not
1595        have any record dimension.
1596    o verification/cpl_aim+ocn:
1597      - generate new reference output on baudelaire (gfortran, mpich2) (previously
1598        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
1599    o pkg/obcs/obcs_calc_stevens.F:
1600      - add code for northern and southern boundaries.
1601      - reorder some loops to save some operations and so that drFBar can be scalar
1602    o model/src:
1603      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
1604        truncation) and add diagnostics for Adams-Bashforth tendency increment.
1605      - update test-exp. AD output:
1606        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
1607      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
1608        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
1609        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
1610        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
1611        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
1612        tutorial_plume_on_slope.
1613    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
1614      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
1615      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
1616      does not even come with an F77 compiler anymore, this should not be
1617      a limitation
1618    
1619    checkpoint63e (2011/11/06)
1620    o pkg/seaice adjoint of LSR:
1621      - substantially rework STORE dirs.
1622      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
1623        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
1624        and only perform SOLV_MAX_FIXED adjoint iters.
1625        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
1626        always goes to same record, meaning that the last forward field will be
1627        the one used in the adjoint - an approximation.
1628      - now produces non-zero LSR-related gradients, and acceptable gradients for
1629        An's zonal (x-z) test case (to be checked in)
1630      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
1631        (but these are screwed up by the thermodynamics in the first place);
1632        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
1633        output_adm.txt also reflects changes to seaice_lsr
1634      - global_ocean.cs32x15:
1635        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
1636          (output_adm.seaice.txt was updated)
1637        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
1638          (output_adm.seaice_dynmix.txt)
1639    o test-exp. exp4+stevens:
1640      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1641    o pkg/seaice (lsr solver):
1642      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1643        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1644      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1645      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1646        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1647      - compute (with new S/R) and print initial (+ free-driff sol. if available)
1648        and final residual of linearised system.
1649    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1650      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1651    o pkg/obcs: Stevens BCs (still only for east and west)
1652      - fix Stevens BCs by using intermediate velocities of previous
1653        time step as "baroclinic" contribution rather velocity of one grid cell
1654        inside the boundaries; more consistent but makes the entire treatment
1655        more complicated, requires new pickup files and two new S/Rs:
1656        obcs_copy_uv_n and obcs_save_uv_n
1657        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1658        (undefined by default)
1659      - silently move computation of some grid factors into separate loops to
1660        save some recomputations
1661      - add a hack for non-linear free surface
1662      - add a verification experiment to exp4 that tests this code
1663    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1664    
1665    checkpoint63d (2011/10/25)
1666    o pkg/obcs + seaice-dynamics:
1667      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1668        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1669        values (consistent with an implicit method).
1670      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1671        return to older implementation (same results as before); note that none of
1672        the "experimental" OBCS_SEAICE options are implemented in the new version.
1673      - switch test exp. seaice_obcs to use new version (update output).
1674    o pkg/seaice:
1675      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1676      - add parenthesis in Water-Ice drag calculations (evp & lsr);
1677      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1678        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1679      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1680        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1681    o pkg/layers:
1682      - Include potential density as new coordinate (Thanks to David Munday)
1683    o pkg/dic:
1684      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1685        carbonate computation/output to CALC_PCO2_APPROX
1686    o pkg/generic_advdiff
1687      - make TAF generate code that vectorizes:
1688        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1689    o model/src:
1690      - improve vectorization also for adjoint code of
1691        solve_tridiagonal and solve_pentadiagonal. As this requires up to
1692        5 new 3D-fields, this code is only turned on for the combination of
1693        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1694        for singular matrix check (only for TARGET_NEC_SX).
1695      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1696        ALLOW_AUTODIFF. This flag now needs to be set outside of
1697        solve_tri/pentadiagonal.F
1698    o pkg/exf:
1699      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1700        optional namelist EXF_NML_OBCS).
1701      - add many debug-print (to trace down where pkg/cal error msg comes from)
1702    o pkg/mom_vecinv/mom_vi_hdissip.F
1703      - rearrange loops so that vectorization is improved and in particular
1704        the adjoint routine vectorizes. The code is a little longer now, but I
1705        think easier to read.
1706        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1707    o pkg/seaice:
1708      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1709    o pkg/exch2:
1710      - alternative code (without tile x tile matrix) for cumulated (global) sum;
1711        used as default; keep using matrix version in adjustment.cs-32x32x1.
1712    o tools/build_options:
1713      - after merging some MPI and/or multi-threads specific optfiles so that
1714        the modified default optfile support both built (using genmake2 -mpi
1715        for the MPI built, using genmake2 -omp for OpenMP built),
1716        move now obsolete optfiles to tools/build_options/unsupported/
1717       (add copy of email sent to support list in doc/optfiles_changes.txt)
1718    
1719    checkpoint63c (2011/09/28)
1720    o pkg/ebm:
1721      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1722        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1723    o pkg/seaice (SItracer pickup)
1724    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1725      To be done:
1726      - thorough testing of missing fields in S/R seaice_read_pickup
1727      - thorough matching between generic tracers and specific fields used
1728        (e.g. volume-weighted age, area-weighted age, salinity, ...)
1729    o pkg/grdchk:
1730      - all procs calculate and print finite-difference gradient (for testreport)
1731      - change description output used by testreport;
1732      - AD testing: also compare and report Finite-difference gradient;
1733        => update all output_adm*.txt
1734    o test exp. global_ocean_ebm:
1735      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1736        and turn on exactConserve; update (fwd) output.
1737    o pkg/seaice (LSR):
1738      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1739      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1740        * identical results with non-CS topology (but save up to half of EXCH calls)
1741        * no much changes in cs-32 verification tests since no ice at face edges
1742         (differences due to convergence criteria, since nb of iterations changed)
1743        * expect some differences on lat-lon-cap grid.
1744        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1745    o pkg/exch2:
1746      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1747        many tiles); until alternative coding is added, just add a stop.
1748    o pkg/kpp:
1749      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1750        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1751    o optfiles:
1752      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1753        into corresponding standard one, which now support different build:
1754        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1755      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1756    o pkg/obcs (seaice):
1757      - add missing EXCH for uIce,vIce after applying OBCS;
1758      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1759        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1760        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1761      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1762      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1763        and eedata.mth for MPI and mutlti-threaded testing.
1764    o pkg/flt:
1765      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1766      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1767      - fix pickup and trajectories + profiles output with multi-threads;
1768      - add parameter to select group of fields to write along trajectory and
1769        profile (default unchanged);
1770      - only call PORT_RAND* function when flt_noise <> 0;
1771      - add multi-threaded test for verification exp. flt_example.
1772    o eesupp/src:
1773      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1774      - USE_OMP_THREADING: check that number of threads (from eedata) matches
1775        actual number (from env.var. setting).
1776    o pkg/ebm:
1777      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1778      - add multi-threaded test for verification exp. global_ocean_ebm
1779    
1780    checkpoint63b (2011/08/29)
1781    o pkg/ebm:
1782      - fix sign of runoff;
1783      - update directly forcing fields (Qnet,EmPmR) to use standard
1784        external_forcing_surf.F (remove ebm_forcing_surf.F);
1785      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1786      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1787        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1788      - update global_ocean_ebm parameters file data and update output (fwd+ad).
1789    o verification/matrix_example:
1790      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1791        MPI and mutlti-threaded testing.
1792    o pkg/matrix:
1793      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1794      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1795      - fix for multi-threaded (remove DATA statement);
1796      - use standard DIFFERENT_MULTIPLE function;
1797      - add MATRIX_OPTIONS.h
1798    o verification/matrix_example:
1799       To allow to split the domain in several tiles, change the domain size
1800        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1801        Western side) of land points.
1802    o (*_)write_pickup:
1803      - fix few bugs in mypackage_read/write_pickup.F
1804      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1805        array of length 1 (was caught by compiler syntax-check).
1806    o pkg/diagnostics (velocity potential solver):
1807      - fix initialisation of main diagonal matrix (for overlap values)
1808    o tools/build_options:
1809      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1810        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1811      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1812        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1813        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1814        and use "-devel" testreport option for standard testing on baudelaire.
1815    o pkg/grdchk:
1816      - Assume that all gradient-check position are within the same tile
1817        corresponding to global indices (iGloTile,jGloTile) and that
1818        positions (i,j indices or nbeg) are local to this tile;
1819      - set tile local-indices and proc. number according to tile global-indices;
1820      - remove grdchkwhichproc from namelist (retired param);
1821      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1822      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1823    o adding package bbl (Bottom Boundary Layer)
1824      description in MITgcm/pkg/bbl/bbl_description.tex
1825      example/test experiment in MITgcm_contrib/bbl
1826    o adjoint verifications
1827      - changed 5 experiments to multi-tiles
1828        * global_ocean.90x40x15
1829        * obcs_ctrl
1830        * offline_exf_seaice
1831        * tutorial_dic_adjoffline
1832        * tutorial_tracer_adjsens
1833        changed reference output for those that crossed tile boundaries
1834        (changed choices of gradient check positions)
1835      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1836      - temporary bug fix in grdchk_loc.F for obcs
1837    o genmake2 & testreport
1838      - add target "obj" (just for OBJFILES files) to Makefile;
1839      - add option to specify FEXTRAFLAGS on command line.
1840    o pkg/mypackage:
1841      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1842    
1843    checkpoint63a (2011/08/02)
1844    o pkg/diagnostics (velocity potential):
1845      - fix velocity-potential calculation when using OBCS: balance net inflow
1846        at each level (new S/R OBCS_DIAG_BALANCE).
1847      - fix some of the problems with OBCS in stream-function calculation.
1848    o pkg/exf/exf_readparms.F
1849      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1850        EXF_NML_OBCS) more consistent, so that you need not have these lists
1851        in data.exf when they are not used.
1852    o optim/optim_readdata.F:
1853      - add some output about obcs variables that might help debugging
1854      - add a check about nvarlength
1855    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1856    o pkg/diagnostics (velocity potential):
1857      - fix mask for OBCS (still problems in stream-function with OBCS);
1858      - add specific parameter (default = main code CG2D params) for solver;
1859      - in case of poor convergence, use solution corresponding to lowest residual.
1860    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1861      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1862      and should be avoided where possible.
1863    o model/src (rStar):
1864      - include r* effect on reference-state (PhiRef) in totPhiHyd
1865        (so that it's really the potential anomaly at the cell center);
1866        affect solution only if z* with full pressure in EOS.
1867      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1868        update output (because of z* in totPhiHyd and viscA4 changes);
1869      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1870        @ constant r) until interpolation at constant r is implemented.
1871    o pkg/diagnostics
1872      - fix RCENTER diagnostics in case cell center is not at interface middle
1873    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1874      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1875      that THETA and SALT are "conservative temperature" and "absolute
1876      salinity"
1877    o pkg/ctrl
1878      - fix computation of endrec in s/r ctrl_init_rec
1879      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1880    o pkg/seaice/seaice_growth.F
1881      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1882        remove then obsolete STORE directives
1883      - fix STORE directives for tice and tices, so that only the
1884        appropriate part of the fields are stored (and not the entire
1885        field); update global_ocean.cs32x15.seaice AD output.
1886      - cosmetic changes: adjust CPP flags and indentation for better
1887        legibilty
1888    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1889      Chris Wilson)
1890    o pkg/gmredi:
1891       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1892       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1893    
1894    checkpoint63  (2011/07/11)
1895    o pkg/exch2:
1896     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1897     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1898       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1899       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1900    o pkg/diagnostics:
1901     - deal with pairs of post-processed diags which are computed together; in
1902       particular, re-order list of diags within 1 file to save 2nd computation.
1903     - add S/R to compute velocity stream-function (called after velocity-potential
1904       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1905     - add parameter to select grid-point location where PsiVEL == 0.
1906    o eesupp/src:
1907       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1908       (specific S/R needed with exch2 topology - for now, just print an error msg)
1909    o pkg/shelfice
1910     - Implement friction velocity-dependent transfer coefficients following
1911       Holland and Jenkins, JPO, 1999
1912       Original code by M. Losch with small modifs.
1913       Enable with CPP option SHI_ALLOW_GAMMAFRICT
1914       and runtime flag SHELFICEuseGammaFrict
1915    o verification lab_sea & global_ocean.cs32x15:
1916     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1917       does not miss some dependencies (but is slower) and also works with many files
1918       (default makedepend limitation for AD built).
1919     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1920    o pkg/diagnostics:
1921     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1922        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1923       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1924     - Extend the use of "missing_value" setting from data.diagnostics for the case
1925       of counter-diagnostics (where fraction-weight is zero). This applies both to
1926       MNC and MDS output files.
1927    o pkg/seaice/seaice_growth.F:
1928      - add 'a priori' cap of latent heat flux based on actual mass considerations
1929        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1930        non-legacy seaice_solve4temp.
1931      - add diagnostic of the residual sublimation freshwater flux (the freshwater
1932        flux taken from the ocean if the total actual latent heat fluxes exceed
1933        the maximum)
1934      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1935       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1936      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1937       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1938      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1939      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1940    o verification 1D_ocean_ice_column:
1941       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1942       update results
1943    o pkg/diagnostics:
1944     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1945       which are not filled-up but computed from other diags ; In this case, the mate
1946       diag points to the primary (filled-up) diag to used for post processing.
1947     - Update Velocity-potential computation using post-processed diag framework.
1948     ==> Change the ordering of fields and time-periods in MDS output file
1949       when using periodic averaging: now writes one time record with the full set
1950       of fields for this time period, then the next time reccord (it used to be
1951       one field with the full set of time records then the next field).
1952         Note: this is now similar to NetCDF (MNC) output file. <==
1953    
1954    checkpoint62z (2011/06/21)
1955    o adjoint monitor:
1956     - Add adjoint monitor output for packages exf, seaice
1957       and update relevant testreport output
1958    o pkg/seaice:
1959     - re-order diags inits so that they appear in order in available_diagnostics.log
1960     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1961       area/heff/hsnow preceeding thermodynamic growth/melt.
1962     - modified diag: SIdA; output actual effect, as the description states.
1963     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1964     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1965       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1966        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1967     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1968     - added diagnostics for seaice generic tracers (SItr*).
1969     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1970     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1971     I. Fenty: 18-Jun-2011:
1972     Minor changes to seaice package:
1973     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1974        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1975       - Differentiated "regularization variables" from "floor variables"
1976        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1977        * hiceMin became SEAICE_hice_reg (old hiceMin)
1978          (with _reg meaning regularization variable)
1979       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1980        so as to ensure energy conservation when going between phases
1981      - A22 was not used anywhere
1982     2) Changed regularization procedure for heffActual and hsnowActual to ensure
1983        well-boundedness and smooth adjoint in seaice_growth.F
1984     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1985        because the old regularization always set heffActual >= 0.05 cm
1986     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1987        on AREA when HEFF > 0.
1988      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1989        requiring that DISABLE_AREA_FLOOR *not* be defined
1990     Affected verifications:
1991      - 1D_ocean_ice_column (output.txt output_adm.txt)
1992      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1993    o pkg/diagnostics:
1994      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1995      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
1996        (was _RL, now integer) with option = 0 to retrieve all levels.
1997      - add pieces of code to compute velocity potential at each level (new diagnostics
1998        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1999        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
2000      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
2001        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
2002        and in diagnostics_fract_fill.F (do not need a valid pointer for the
2003        diagnostics counter-mate); check that definition of counter-diagnostic
2004        includes a valid counter-mate (in diagnostics_set_levels.F).
2005    o model/src (rStar):
2006      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
2007        affect solution only if z* with full pressure in EOS;
2008        update output of test-exp global_ocean.90x40x15.
2009    o pkg/seaice:
2010      - introduce siEps=1e-5 parameter
2011      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
2012      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
2013      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
2014        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
2015        as well as ice cover age and ridging index (attached to AREA).
2016        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
2017        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
2018        Up to SItrMaxNum=3 tracers can be used simultaneously.
2019    o pkg/salt_plume:
2020      -introduce SPsalFRAC run time parameter that sets the fraction of the
2021       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
2022       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
2023    o model debug options:
2024      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
2025        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
2026      - Refine debug-msg printing selection (3 new levels):
2027        debugMode  : controls printing of debug messages (sequence of S/R calls).
2028        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
2029         debLevZero =  0 ; /* level of disabled aux. msg printing */
2030         debLevA =  1 ; /* level of minimum  aux. msg printing */
2031         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
2032         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
2033         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
2034         debLevE =  5 ; /* level of extensive debug printing */
2035        New debugLevel default: with default debugMode value (=F),
2036          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
2037          and if debugMode=T, default debugLevel = 4 (debLevD).
2038        Relation with previous settings:
2039         debLevB (=2) corresponds to former debLevA (=1)
2040         debLevD (=4) corresponds to former debLevB (=2)
2041        Note:
2042         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
2043         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
2044            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
2045      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
2046        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
2047    o pkg/obcs:
2048      - change OBCSfixTopo default from True to False (should not change the results);
2049        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
2050    o pkg/thsice:
2051      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
2052        2nd layer seaice sublimation (unlikely to happen)
2053      - use Interior mask for OBCS in thsice_advection.F (similar to what is
2054        done in gad_advection & seaice_advection).
2055    o adjoint:
2056      bug fix spotted by Gael Forget:
2057      seaice_advection and thsice_advection still had
2058      legacy CPP options to avoid CS corner updates for adjoint
2059    o pkg/seaice:
2060      => Change some of the defaults (2011/05/29):
2061         - change SEAICEuseFluxForm default (from False to True)
2062         - change DIFF1 default (from 0.004 m/s to 0. m/s)
2063         And print warnings if DIFF1 is not set in data.seaice and centered
2064          avection scheme is used without any diffusion.
2065      also:
2066      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
2067      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
2068      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
2069        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
2070        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
2071      update results of test exp.:
2072         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
2073             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
2074             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
2075         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
2076         seaice_obcs: output (SEAICEuseFluxForm=T)
2077      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
2078          for standard fwd & AD lab_sea tests (to keep the same output).
2079    o pkg/seaice/seaice_growth.F:
2080      - use Ian Fenty's capping formulas for actual ice
2081      thickness thoughout EVOLUTION branch.
2082      - put treatment pathological case #2) in CPP brackets
2083      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
2084      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
2085    o pkg/seaice:
2086      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
2087      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
2088      also pass fac as a param, which can be 1. (to update the tendency
2089      field) or the time step (to update the field itself).
2090      - seaice_advdiff.F: for multidim, call seaice_diffusion with
2091      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
2092      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
2093      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
2094      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
2095    o pkg/seaice:
2096      diffusion with centered advection scheme (diffus.F & advect.F):
2097      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
2098        to just compute the laplacian of input-field.
2099      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
2100      - fix flux-form version in diffus.F to conserve tracer.
2101      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
2102       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
2103    
2104    checkpoint62y (2011/05/26)
2105    o pkg/seaice:
2106     - seaice_growth.F : in EVOLUTION branch, always include
2107       a_QSWbyATM_cover in qnet (as it should be).
2108     - verification/global_ocean.cs32x15 : update results accordingly
2109       (output.seaice.txt output_adm.seaice.txt).
2110    o pkg/seaice + obcs:
2111     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
2112       equivalent of assuming no tracer gradient outside the OB region.
2113       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
2114     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
2115       after changes above);
2116     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
2117       only at OB location (instead of over a band of OLx width).
2118    o pkg/seaice:
2119     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
2120       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
2121    o pkg/obcs:
2122      - split header file "OBCS.h" into 4 separated files:
2123        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
2124       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
2125         (contain no conditional statement which depends on OBCS options).
2126      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
2127        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
2128    o ctrl, cost, grdchk & autodiff pkgs:
2129      - make options file more standard (like other {PKG}_OPTIONS.h file but
2130        with AD_CONFIG.h); clean-up some of the included header files.
2131    o pkg/obcs:
2132      - do not mask tracer when applying OB (tracer == 0 could generate problems)
2133      - apply tracer OB values to tracer field only at OB location (instead of
2134        over a band of OLx width)
2135      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
2136      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
2137        obcs_apply_tloc.F & obcs_apply_sloc.F
2138    o obcs in model/src:
2139      - call OBCS_APPLY_W only if NonHydrostatic.
2140      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
2141      - reset dEtaHdt and wVel to zero outside OB interior region ;
2142      - leave tracer unchanged outside OB interior region: This has no effect
2143        on the solution but just to prevent unrealistic tracer value outside OB.
2144      - zero out velocity outside OB interior region: This has no effect on
2145        the solution but just to prevent unrealistic velocity outside OB.
2146    o obcs and non-lin free-surf:
2147       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
2148       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
2149       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
2150       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
2151       update results of test-exp. exp4(nlfs).
2152    o exp4 (nlfs) test-exp:
2153       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
2154       with NonLin-FreeSurf); update output.nlfs.txt
2155    o obcs and 2d/3d solver norm:
2156       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
2157       and outside OB interior region (will allow to place OB further inside the
2158       domain). Depending on the domain, can affects cg2d-Norm (previous
2159       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
2160       and cg3d-Norm (previous Norm was computed before canceling OB terms),
2161       e.g. in tutorial_plume_on_slope.
2162      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
2163    o pkg rbcs:
2164      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
2165      - add capability to apply relaxation to horizontal velocity uVel & vVel.
2166    o pkg/grdchk: add gradient check for control variable xx_shifwflx
2167    o pkg/shelfice/shelfice_init_fixed.F
2168      fix CPP-flag combinations
2169    o pkg/seaice: Merge iceage code of Pierre Rampal
2170      * update/change/correct ice age calculations
2171      * add age updates for pathological cases
2172      Probably needs more testing...
2173    
2174    checkpoint62x (2011/05/13)
2175    o pkg/mom_vecinv:
2176       high-order vorticity scheme: use interior masks (maskInW & S)
2177       to zero-out (outside OB) gradient of vorticity.
2178    o verification exp.:
2179       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
2180       hs94.128x64x5 and seaice_obcs ; update results.
2181    o pkg/obcs:
2182      fix bug in OBeta for YZ sections in obcs_exf_load.F
2183    o pkg/ctrl, pkg/shelfice, and optim:
2184      - add new control variable xx_shifwflx (fresh water flux underneath ice
2185        shelves). This is almost as tedious as obcs-ctrl, because the
2186        variables needs its own mask.
2187      - add a cost function term that penalizes the deviation of xx_shifwflx
2188        from the first guess (zero) in analogy to other control variables
2189    o pkg/shelfice:
2190      - start basic adjoint
2191    o pkg/ctrl:
2192      - remove extra 2D field "for good measure" when initializing in
2193        ctrl_set_globfld_[xy/xz/yz].F
2194      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
2195      - improve error messages in ctrl_set_unpack_*
2196    o OBC implementation in momentum:
2197       use interior masks (maskInC,W & S) in momentum S/R:
2198       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
2199       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
2200       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
2201       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
2202       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
2203        (and also with Leith/Smagorinsky harmonic-viscosity).
2204       Update output of experiment dome and exp4 (+nlfs).
2205    o exp4 test-exp:
2206      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
2207        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
2208        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
2209        time-varying OB at Western-side for wVel (NonHyd); update output.
2210      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
2211        and biharmonic-viscosity ; also use prescribed time varying OB.
2212    o pkg/obcs:
2213      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
2214    o model/src:
2215      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
2216      - initialise startTime & nIter0 with unlikely values: allows to set one
2217        from the other without ambiguity.
2218    o seaice_obcs test-exp.:
2219      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
2220    o pkg/obcs:
2221      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
2222        no longer needed with maskInC,W,S in pkg/generic_advdiff.
2223    o pkg/seaice:
2224      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
2225        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
2226      - fixed bug in the initialization of sea ice salinity variable HSALT
2227        in seaice_init_varia.F  (removed dependence on ICE2WATR)
2228    o fizhi-cs test exp.:
2229       switch reference output convention for these 2 non-standard test-exp,
2230        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
2231          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
2232       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
2233    o model/inc:
2234      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
2235        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
2236    o pkg/seaice:
2237      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
2238    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
2239      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
2240        and initial HSALT
2241    
2242    checkpoint62w (2011/04/26)
2243    o pkg/mom_fluxform:
2244      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
2245      - use parameter "sideDragFactor" in no-slip BC side-drag part.
2246      - update output of exp. global_ocean.90x40x15
2247    o pkg/mom_vecinv:
2248      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
2249    o update seaice exp.:
2250      use more consistent parameter values (remove "backward compatability only":
2251       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
2252      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
2253       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
2254    o update test-exp global_ocean.90x40x15:
2255      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
2256      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
2257      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
2258      o turn on zStar & viscA4 in standard set-up (dir input/)
2259        and update output files: output.txt & output.dwnslp.txt
2260    o new AD-test experiment: obcs_ctrl
2261      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
2262    o pkg/dic:
2263      fix two bugs in handling water vapour pressure in carbonate chemistry
2264      and air-sea fluxes. Found by Val Bennington and Galen McKinley
2265      (add DIC Option = WATERVAP_BUG to recover old results)
2266      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
2267    o adding allowInteriorFreezing option to check for water below freezing point
2268      at depth and bring the negative heat anomaly to the surface level
2269    o pkgs _fields_load:
2270      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
2271      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
2272        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
2273        rbcs to get interpolation weights and time reccord number.
2274      - fix multi-threading in aim_fields_load.F
2275      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
2276    o external_fields_load:
2277      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
2278       interpolation weights) to use in a periodic time-series ; do not divide by
2279       time-step to convert to integer:
2280       - this fixes case where externForcingPeriod is not multiple of time-step
2281          (Thanks to Christopher L. Wolfe)
2282       - this fixes case where externForcingPeriod is an odd multiple of time-step
2283         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
2284      store index of time-record which is currently loaded:
2285       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
2286       - needed for the adjoint but not yet used because of extensive recomputations;
2287         (to be fixed soon)
2288    
2289    checkpoint62v (2011/04/02)
2290    o verification/1D_ocean_ice_column added to test Ian Fenty's
2291      pkg/seaice_growth.F modifications for improving sea ice code differentiability
2292    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
2293      (new velocity statistics after changing maskInW & maskInS definition)
2294    o pkg/generic_advdiff with OBCS:
2295      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
2296      equivalent to assumption of no tracer gradient outside the OB region.
2297      This will affect the results if using obcs+biharmonic diffusion.
2298      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
2299    o pkg/obcs:
2300      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
2301      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
2302      in Interior region. No impact on solution but affects Velocity monitor stats.
2303    o pkg/ptracers (adjoint)
2304      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
2305      tape file for each tracer
2306    o model/inc/src and pkg/autodiff: add parameters that allow to turn
2307      of parts of the adjoint code at run time. For now, there are only
2308      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
2309      parameters are set in data.pkg.
2310      This is the lazy coward's version of doing this, but still useful for
2311      debugging. In order to do it right, everything needs to be moved to
2312      pkg/autodiff.
2313    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
2314      the end; this fixes the adjoint balancing code for open boundaries.
2315    o pkg/ctrl:
2316      - change behavior of xx_${varname}period to be analogous to exf-conventions:
2317        xx_${varname}period =   0.,  means time-independent control part
2318        xx_${varname}period = -12., means one-year-periodic monthly control part
2319      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
2320        clean up ctrl_init a little, remove unused variables
2321      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
2322      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
2323    
2324    checkpoint62u (2011/03/15)
2325    o model/src:
2326      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
2327        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
2328      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
2329        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
2330    o pkg/ctrl/obcs/ecco:
2331      - remove obsolete, unused, and partially broken code:
2332        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
2333        ALLOW_CTRL_OBCS_BALANCE
2334      - put a stop statement into ecco/cost_obcsvol.F, but also add
2335        cost_obcsvol to ecco_ad_diff.list
2336    o pkg/ecco: fix counting cost function contributions for obcs (code
2337      by Matt M.) and diffkr for diagnostics
2338    o pkg/ecco, pkg/ctrl, pkg/grdchk:
2339      add cost penalty terms for initial uvel, vvel, eta controls
2340      and I/O for prior error files
2341    o pkg/mdsio:
2342       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
2343       (new argument) to check for tiled file in mdsioLocalDir : this fix the
2344       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
2345    o pkg/ctrl:
2346     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
2347       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
2348       unused and superfluous variables
2349     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
2350    o pkg/ecco
2351     - enable adjoint of Stevens OB
2352    o pkg/ctrl/ecco/grdchk:
2353      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
2354        Fortunately, we do not have any tests for the numerous cpp-flagged
2355        option of "obcs as control parameters" so we will never know
2356        if this is an improvement (but at least now things compile).
2357      - remove an obsolete initialization from ecco_cost_init_barfiles.F
2358      - fix some problems within never used ifdefs to make the code compile
2359    o pkg/obcs:
2360     - Refine Interior mask definition to work with more complex OB (e.g.
2361       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2362       read in Interior mask from file. Check if Interior mask is consistent
2363       with OB list of indices.
2364    o pkg/seaice
2365     - beginning code for a seaice tracer package,
2366       but currently only used for seaice age: SEAICE_AGE
2367       SEAICE_num = 4
2368       iTracer = 1: area-weighted ice age
2369               = 2: volume-weighted ice age
2370               = 3, 4: template for one-year vs. multi-year ice
2371       data.seaice has new namelist SEAICE_PARM03 for arrays related to
2372       SEAICE_num
2373    
2374    checkpoint62t (2011/03/05)
2375    o pkg/obcs:
2376     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2377       then normal component. This ensures that the normal component is set
2378       correctly even when it conficts with tangential setting from an other OB.
2379       Affects results of test-experiment seaice_obcs: update the output.txt
2380    o pkg/obcs:
2381     - add code to monitor statistics of dynamical fields at OB.
2382     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2383       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2384       - change default: balance the Net inflow through all OB (instead of balancing
2385         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2386     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2387       to match Nortern OB inflow (OBCS_balanceFacN=0).
2388    o pkg/seaice:
2389     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2390    o pkg/seaice (seaice_growth v 1.113):
2391     - reverting seaice_growth to v 1.111 in order to have code with exact bit
2392       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2393       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2394       runtime flag SEAICEareaFormula is kept but is inactive
2395    o model/src:
2396     - add new param to scale curvilinear grid distance and area when using
2397       a different sphere radius from the grid-files.
2398     - test/check multi-threads EXCH applied to local variable (cg2d_x)
2399    o adjoint:
2400     - enable adjoint of Stevens OB
2401     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2402       (a bit delicate because of potentially modified adj. common block structure;
2403       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2404    
2405    checkpoint62s (2011/02/15)
2406    o pkg/seaice (seaice_growth v 1.112):
2407     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2408       computing the ice cover tendency from effective thickness tendencies. Include
2409       Ian Fenty's formula.
2410     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2411       SEAICEareaFormula.
2412     - simplify notations for the various d_HEFF/d_AREA terms.
2413    o pkg/gmredi:
2414     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
2415       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
2416       add a verification test-run (front_relax.bvp) to test GM_useBVP.
2417    o pkg/seaice (seaice_growth v 1.111):
2418     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
2419     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
2420       also melt ice.
2421    o pkg/seaice:
2422     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
2423     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
2424    o pkg/cheapaml:
2425     - from Nico Wienders: New version of this package.
2426    o pkg/flt:
2427     - add CPP options to prevent floats to re-enter the opposite side of
2428       a periodic domain (default: keep periodicity)
2429    o pkg/gmredi:
2430     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
2431       (needed for multi-dim advection).
2432     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2433    o model/src:
2434     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2435    o tutorial_tracer_adjsens
2436     - extend to NLFS and replace maskC by hFacC
2437       (change reference output accordingly)
2438    
2439    checkpoint62r (2011/01/24)
2440    o testreport:
2441     - add option -deloutp (-do) to remove output file after successful run
2442     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2443       extract exact list of procs from this file ; adjust COMMAND by
2444       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2445    o pkg/ecco: replace old ineffective way of penalizing deviations from
2446      first guess (of obcs) with code by Matt Mazloff
2447    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2448      exf/cal
2449      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2450        and handle case of obcs?period == 0
2451        Not affected by these changes: There is still an inconsistency in
2452        the computation of start/endrec for the obcs variables for ALLOW_CAL
2453        defined (see comment by Menemenlis, 7-Mar-2003)
2454      - make S/R ctrl_get_gen_rec return something meaningful even if
2455        ALLOW_CAL is not defined
2456      - ctrl_getobcs?: simplify code so that it does not need to use
2457                       S/R exf_swapfields
2458    o testreport:
2459       allow to test MPI with different number of processors for each experiment:
2460       create file "SIZE.h.mpi" in each build dir.
2461       Note: update of "-command" argument not yet implemented.
2462    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2463      alleviate the need for additional 3D tapes when using
2464      the non-inear free surface in the adjoint. This is done
2465      by adding an 'update' of hfacc etc. to their current
2466      value at the beginning of forward_step.F.
2467    o pkg/seaice
2468      seaice_lsr: move stress-divergence computations out of outer pseudo-
2469      timestepping loop
2470    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2471      up, so that the calls of the ctrl_* subroutines are really at the end
2472      of the routine.
2473    o pkg/gmredi:
2474      allow to specify a 2-D horizontal map and a 1-D vertical profil
2475      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2476    o pkg/seaice:
2477      move lsr iterations from seaice_dynsolver to seaice_lsr.
2478    o pkg/seaice:
2479      reduce memory footprint of seaice mutldim advection tapes,
2480      by using a 2D tape independent of the generic_advdiff ones,
2481      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2482    
2483    checkpoint62q (2010/12/29)
2484    o model/src:
2485      - check horizontal grid-spacing for unset or zero/negative values.
2486      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2487    o pkg/flt:
2488      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
2489      - precision of input and output files set according to readBinaryPrec
2490        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
2491      - initial float position from tiled file was not converted to index space
2492        (looks like a bug): fixed to make it similar to initial pos. global file.
2493    o global_ocean.cs32x15:
2494       change SIZE.h of AD set-up to get same tiling as with MPI.
2495       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
2496    o model/src:
2497       add flag to control printing of domain fields (bathymetry, hFac ...) in
2498       ini_mask_etc (call to plot_fieds_xy*).
2499    o pkg/thsice:
2500       if useEXF, some forcing fields are not valid in overlap: fixed by computing
2501       over the interior only + apply EXCH at the end (like with SEAICE advection).
2502    o pkg/mdsio:
2503      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
2504        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
2505      - change barrier call for safe multi-threads access to 3-D shared buffer.
2506      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
2507      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
2508        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
2509    o pkg/flt:
2510      - add fourth-order Runge-Kutta integration
2511      - add basic exch2 support (only 1 facet supported so far!)
2512    o pkg/mdsio+rw:
2513      new S/R to read local (or tile independent) vector (read counterpart of
2514       mds_writevec_loc, and front-end write_glvec_rl/rs).
2515    o global_ocean.cs32x15: additional input_ad.seaice experiment
2516        that uses pkg/seaice rather than pkg/thsice.
2517        (using multidim advection for seaice)
2518    o towards more F95 syntax for array specification in namelist:
2519      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
2520        of all verification experiments.
2521           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
2522          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
2523      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
2524    o global_ocean.cs32x15: additional input.seaice experiment
2525        that uses pkg/seaice rather than pkg/thsice.
2526    
2527    checkpoint62p (2010/12/17)
2528    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
2529        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
2530    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
2531        allow for use of multim. advection in seaice adjoint.
2532    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
2533      - first attempt to close budgets by taking into account the freshwater
2534        flux implied by the sublimation of snow and ice. So far only the
2535        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
2536        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
2537    o eesupp/src:
2538      new S/R with new option (NML_EXTENDED_F77) to change array specification
2539      from F95 standard to commonly accepted extended F77 form.
2540      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
2541      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
2542      for less tolerant f77 compiler (e.g., pgf77, g77).
2543    o globalFiles:
2544      commented out in parameter file "data" since it's not safe with MPI
2545      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
2546      in this case); no longer commented out in restart test (tst_2+2).
2547    o add adTapeDir to specify a special directory where adjoint tapes are
2548      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
2549      and cannot be used together with mdsioLocalDir.
2550    o nesting pkgs:
2551      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
2552      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2553      - add parameter files + utils dir + output from short run on beagle.
2554    o pkg/seaice:
2555        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
2556    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
2557      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
2558    
2559    checkpoint62o (2010/11/25)
2560    o pkg/exf:
2561      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
2562    o pkg/seaice:
2563      - seaice_ocean_stress: split a loop for better vectorization of the
2564        adjoint code
2565      - seaice_growth.F: fix bug in conservation of freshwater connected to
2566        capping of heff, put contribution into d_HEFFbyNEG
2567      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
2568        by something more sensible (parameters that are what their name implies)
2569      - change some defaults, so that by default exf-parameters are used for
2570        things like rhoAir, cpAir,latent/sensible heat parameters, in order
2571        to reproduce the old results, many data.seaice now contain funny values
2572        for cpAir and latent heat of sublimation
2573    o packages_readparms.F: move exf_readparms up in line so that
2574        exf-parameters are visible for other packages (e.g. seaice)
2575    o debugMode & debugLevel=2:
2576      - differentiate between debugMode & debugLevel=2:
2577        debugMode: controls printing of debug messages (sequence of S/R calls).
2578        debugLevel: controls printing of algorithm intermediate results and stats.
2579      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
2580        => allows to print debug-stats without all sequence of call messages.
2581      - switch control of debug print from debugLevel to debugMode in many S/R.
2582    o pkg/obcs (obcs-sponge):
2583        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
2584        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
2585    o pkg/generic_advdiff:
2586      - record overlap minimum size for each advection scheme;
2587      - refine criteria on overlap minimum size;
2588      - check and stop (in gad_check) if overlap size is too small.
2589    o pkg/obcs:
2590      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
2591        once, in ptracers_implicit.F)
2592      - with seaice: remove test on empty file name in obcs_apply_seaice (always
2593        apply OB values when tile has OB)
2594    o model/src, coriolis setting:
2595      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
2596        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
2597        files (selectCoriMap=3) with any grid.
2598      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
2599    o pkg/seaice/seaice_growth.F:
2600        a few cosmetic changes that reduce the number of lines of code
2601    o pkg/obcs: add boundary conditions following Stevens (1990)
2602      - the code follows old MOM/NAOSIM code
2603      - so far it is only implemented for the eastern and western boundaries
2604        and NOT for pTracers
2605    o pkg/rbcs:
2606      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
2607        beginning of the first rbcs forcing period.
2608      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
2609        offline package, i.e., one file per time, labeled by iteration number;
2610        deltaTrbcs sets the timestep with which the data was generated;
2611        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
2612      - rbcsForcingCycle=0 makes forcing non-cyclic.
2613      - make arithmetic safe for negative times and odd forcing periods.
2614    
2615    checkpoint62n (2010/11/09)
2616    o pkg/seaice:
2617        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
2618    o pkg/obcs:
2619       New S/R to copy tracer value from the OB location to narrow band region
2620        (width = same as overlap) beyond the OB: preserve OB value (needed for
2621        high-order scheme) which were overwritten by EXCH call if in overlap
2622        region. Applied to theta, salt, ptracer and advected seaice variables.
2623       With seaice: use maskInC in similar way as in gad_advection.F,
2624        in seaice_advection.F and advect.F.
2625       Update output of experiment seaice_obcs and change exp4 to test OBCS with
2626        4th order Adv.Scheme. for pasive salt and ptracer.
2627    o tools/genmake2:
2628      - when looking for an optfile (not specified), only search for Fortran compiler
2629        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
2630      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
2631        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
2632      - set default for CPP to "cpp -traditional -P" (was the case without specifying
2633        an optfile, but otherwise default was just "cpp".
2634      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
2635      - when "CC" is not set in the optfile, look for possible C compiler
2636        (instead of just setting CC=cc)
2637      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
2638        => add a ".F" to ".o" rule for source files with no "#include" (such as
2639           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
2640      - move gfortran before g77 in list of possible Fortran compiler (consistent
2641        with reference compiler switch from g77 to gfortran)
2642    o pkg/seaice:
2643      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
2644        seaice_check that stops the model, when the CPP flag is used.
2645      o seaice_growth.F: make capping of ice volume conserving by returning the
2646        capped ice as freshwater to EmPmR. This does not change the verification
2647        experiments but will change runs where the capping is acutally active
2648    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
2649      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
2650         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
2651         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
2652    o tools/genmake2:
2653      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
2654      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
2655      - clean previous genmake log files before anything else.
2656      - change Makefile to remove testreport log files (*.tr_log) and genmake log
2657        files only with "CLEAN" target (instead of "Clean");
2658    o pkg/generic_advdiff:
2659      Change OBCS in multiDim advection (gad_advection.F):
2660       Use maskInC to prevent intermediate update of tracer-field in OB regions,
2661       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
2662       which were applying future time-step OB values.
2663      This way, all explicit calculations use current-time-step OB values
2664       (simpler and more consistent).
2665      Affects results when set-up uses time-varying OBC and multi-dim advection;
2666       update output of experiment seaice_obcs.
2667    o pkg/seaice:
2668      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
2669       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
2670         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
2671      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
2672       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
2673       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
2674    o pkg aim (2010/10/26):
2675      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
2676        formulation with obliquity, eccentricity, ... as run-time parameters,
2677      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
2678        upward shortwave radition at the surface (all-sky and clear-sky).
2679    o pkg/obcs:
2680      - writing sections with globalFiles=T does not work: switch to tiled-files
2681        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
2682      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
2683      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
2684    
2685    checkpoint62m (2010/10/21)
2686    o pkg/seaice: vectorize seaice_solve4temp.F
2687      - move iterations loops outside of i/j-loops
2688      - requires 2D arrays for TB and effConduct
2689      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
2690        modified in this routine
2691      - a little bit of clean up, adjusting indentation, etc.
2692      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
2693        performance and '**TWO' by '**2' (because TWO is a float),
2694        replaced ONE, ZERO
2695    o eesupp/src:
2696       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
2697    o pkg/seaice/seaice_growth.F
2698      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
2699      merging process. The merged routine has two branches, and one activates the 'evolution'
2700      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
2701      In summary, here is what the '10/10 revision' did consist of
2702        part 1: seaice_growth.F revisions 1.71 to 1.75
2703          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2704            The emphasis here was on improving readability (e.g. by trying to use meaningful
2705            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2706        part 1.5:
2707          - revising the lab_sea experiment to make it a more useful (i.e. stable
2708            and representative of an actual model run). This was done by generating a
2709            (winter) pickup to start from, switching back the main experiment dynamic
2710            solver from evp to lsr, having one of the experiments use the free drift solution.
2711        part 2: seaice_growth.F revisions 1.76 to 1.85
2712          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2713          - Sorting out the various fields units and sign (set early on and reset at the end)
2714            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
2715            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
2716          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
2717            and simplifying logical expressions to further improve readibility.
2718        part 3: seaice_growth.F revisions 1.86 to 1.89
2719          - Re-organize the blocks of code more logically.
2720          - Merging the '_if.F' pieces that add something new.
2721    o pkg/thsice:
2722      - vectorize thsice_solve4temp and thsice_get_exf.
2723        Problem: thsice_solve4temp has an unvectorizable statement that
2724        might also be problematic for TAF
2725      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
2726        does not change the verifcation experiment, but will change all
2727        experiments that have this flag undefined (not tested in verification);
2728        a little reorganization to save a few 2D fields and recomputations
2729      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
2730      - 2nd step:  fix some store dirs
2731        o seems to work somewhat, i.e. using ifort but not g77
2732        o likely cause are incomplete init. or recomputation
2733        o start verification/global_ocean.cs32x15/input_ad.thsice
2734    o pkg/obcs: add support for exch2
2735      - the position of the boundary and prescribed values are specified using
2736        a global domain with exch2 facets stacked
2737        - in x for N,S boundaries (like W2_mapIO=-1)
2738        - in y for E,W boundaries (so E,W boundaries do not overlap)
2739    o pkg/mdsio: add support for writing global sections with exch2
2740        file layout is as for obcs described above:
2741        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
2742        - for y-z sections, facets are stacked in y
2743    o pkg/thsice:
2744       - change a few routines for better vectorization: thsice_albedo.F,
2745         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
2746         not affected, but in particular the latter routine has changed
2747         dramatically (not necessarily easier to read now).
2748       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
2749       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
2750    o verification/lab_sea:
2751      - overhaul of the forward model experiments. The main motivation
2752        for this revision is that lab_sea has proven quite fragile (when
2753        changing the sea-ice code, and switching platforms) to a point
2754        when failures were very hard to attribute to specific code problems.
2755      - the suspected reason for this fragility is noise amplification by evp so,
2756        to start with, we decided to replace evp with lsr in the main experiment.
2757      - the input.lsr experiment thus became obsolete and was removed.
2758      - it was replaced with the input.fd experiment that uses an
2759        analytical "free drift" solution as the ice velocity field.
2760      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
2761        will hopefully allow us to discriminate problems due to dynamic solvers
2762        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
2763        us to test additional options, along with the salt plume package.
2764      - Finally a pickup was generated (at the end of a one year run) to
2765        make the tests more representative of an actual model run. Previously
2766        the tests starting point was a 1m thickness of ice everywhere.
2767    o pkg/seaice:
2768      - introducing S\R seaice_freedrift.F that compute the
2769        analytical solution to an approximate ice momentum
2770        equation (i.e. the simple stress/coriolis balance).
2771      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2772        of the free drift velocity field, and enable its use.
2773        To actually use the free drift solution as the model ice
2774        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
2775    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
2776    
2777    checkpoint62l (2010/10/04)
2778    o pkg/seaice:
2779      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
2780      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
2781       version (with USE_ORIGINAL_SBI undef);
2782    o add hooks for new packages OASIS, the package will follow
2783      (hooks exclude the seaice pkg for now)
2784    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
2785      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
2786      rather than mdsio_readvector.F/mdsio_writevector.F, within
2787      adread_adwrite.F to read/write adjoint-related tapes to disk.
2788    o eesupp and pkg/mdsio: ALLOW_WHIO
2789      Option to write/read 2D fields to files including tiles halos.
2790      The main purpose is for adjoint related "tape I/O".
2791      The secondary purpose is for debugging phases.
2792      A word on those rather specifically intended purposes.
2793      The code was meant to be stripped down to the bare minimum.
2794      Typically, there is a unique and basic mapping to the global
2795      buffer (tile by tile, then proc by proc, then level by level), and
2796      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
2797      meant to generate user friendly outputs of various shapes and forms.
2798      Rather it is intended, for the knowledgeabale developers,
2799      to be largely independent of the many mdsio options, to allow
2800      outputs of tiles+halos in debugging phases and in adjoint runs,
2801      and to allow some flexibility in tuning (adoint) I/O depending on each
2802      file system behavior. With regard to tuning, most of the potential knobs
2803      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
2804      to specify directories, to specify the typical size of I/O calls, etc.)
2805      are not yet included, and will be added if they prove useful.
2806    o pkg/seaice:
2807       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
2808    o pkg/seaice:
2809       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
2810       code (seaice_budget_ice_if.F) which enable to recover old standard
2811       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
2812       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
2813    o model/src (rStar):
2814       use simple average (not area weighted) of rStarFac at U,V point when using
2815       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
2816       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
2817    
2818    checkpoint62k (2010/09/17)
2819    o adjoint
2820       * changed verification/global_ocean.cs32x15 ; adjoint now tests
2821         Adams-Bashforth 3 + NLFS + RSTAR
2822       * some more modifs required for ECCO-GODAE v4
2823    o pkg/seaice
2824       add SEAICE_AGE_VOL option to use volume instead of area for
2825       integrating SEAICE_AGE
2826  o model/src:  o model/src:
2827     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
2828     non-linear free-surface parts ; but pressure-gradient not yet coded.     non-linear free-surface parts ; but pressure-gradient not yet coded.
# Line 273  o tools/build_options: Line 3092  o tools/build_options:
3092      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
3093  o pkg/ecco  o pkg/ecco
3094    - allow user defined cost function contributions    - allow user defined cost function contributions
3095          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
3096          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
3097    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
3098        the two options are complementary.        the two options are complementary.
3099  o pkg/smooth  o pkg/smooth

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