/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1573 by jmc, Sat Jan 14 16:41:36 2012 UTC revision 1.1811 by jmc, Sun Jan 20 15:16:08 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/thsice:
8      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
9        where just seaice diffusion is used without seaice-dynamics.
10    
11    checkpoint64c (2013/01/18)
12    o pkg/seaice:
13      - add a parameter JFNKres_tFac that can replace JFNKres_t
14        (= JFNKres_tFac*JFNKresidual before JFNK solver)
15      - add a line search option to the JFNK solver
16      - move update of u/vIce and computation of initial residual into a separate
17        routine (same file); makes the code a little easier to read (?)
18      - the line search requires computation of the residual and for some reason
19        I cannot do the update of u/vIce at the beginning of the Newton loop
20        without changing the results, so we move computation of the new residual
21        also to the end of the Newton loop, even without the line search
22    o pkg/mdsio:
23      - write missing value (corresponding to undefined array value) to meta files;
24        skip this if missing value is one (UNSET_RL would be a better value for the
25        case of undefined missing value but it's current the default missing-value);
26        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
27    o pkg/exf & thsice:
28      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
29        diagnostics) even when SHORTWAVE_HEATING is #undef;
30    o verification/cfc_example:
31      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
32        illustrate how to use it).
33    o verification/offline_exf_seaice:
34      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
35        files to only one time-record.
36      in input.thermo: narrow the 2 bands of low initial ice-concentration near
37        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
38        snapshot output; same mcPheePiston value as in thsice with
39        surf-current=0.2m/s.
40      in input.thsice: similar set-up as in input.thermo (channel with same seaice
41        initial conditions).
42    o verification/cfc_example:
43      - update file "data" with more standard choice (default rotationPeriod,
44        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
45        set deltaTFreeSurf to deltaTtracer) and update the output.
46    o pkg/layers:
47      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
48      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
49    o verification/offline_exf_seaice:
50      - set all {field}period to zero for constant-in-time forcing (not tested
51        anywhere else).
52    o verification/offline_exf_seaice:
53      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
54      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
55    o model/src:
56      - implement Finite-Volume method for (hydrostatic) presure gradient
57        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
58    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
59      - In order to be compatible with the default EVP code, this requires changing
60        the EVP code around a little; and because any small change immediately
61        breaks the lab_sea.hb87 verification experiment, the reference output is
62        updated two times (each time the remaining aggrement was only 2 digits):
63        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
64        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
65        The adjoint test lab_sea.evp also needed to be updated.
66      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
67        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
68        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
69        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
70        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
71        kept obscure, because I need to test it a little more.
72    o pkg/cheapaml:
73      - fix few incorrect type (_RL/_RS) in subroutine calls.
74    o pkg/seaice:
75      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
76        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
77    o model/src:
78      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
79        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
80        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
81    o pkg/cheapaml:
82      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
83        update output of experiment cheapAML_box.
84      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
85        and set them only in one place (cheapaml_readparms.F).
86      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
87      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
88        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
89    o model/src/the_main_loop.F:
90      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
91    o pkg/seaice:
92      - remove legacy branch code.
93      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
94    o verification/*/code*/SEAICE_OPTIONS.h:
95      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
96        SEAICE_CAP_HEFF).
97    o pkg/cheapaml:
98      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
99        to load new forcing fields.
100      - add missing "_d 0" where it's needed; + some editing (improve indentation).
101      - remove switch to "-r8" compiler option (no longer needed) in verification
102        cheapAML_box, keep same output (small trucation error differences).
103    o verification/offline_exf_seaice:
104      - add thermodynamics only test.
105    o verification/cheapAML_box:
106      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
107        keep same output (same 14 digits for cg2d).
108      - switch on "-r8" compiler option (some numerical values are missing
109        the "_d 0") and update output (only 6 digits for cg2d were preserved).
110    
111    checkpoint64b (2012/12/24)
112    o pkg/cheapaml:
113      - remove un-used variables (Qnet,EmPmR) from pickup files.
114      - store tendency of advected variables into cheapaml pickup file
115        and fix the AB-2 restart.
116    o verification/offline_exf_seaice and lab_sea adjoint:
117      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
118      - switch to 4 time steps in offline, consistent with lab_sea.
119      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
120      - update results after change of experiment seaice.
121    o pkg/seaice:
122      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
123        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
124        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
125        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
126    o model/src:
127      - add run-time parameter to select CG2D solver minimum-residual solution
128        (in case of a poor convergence).
129    o pkg/seaice/seaice_lsr.F
130      - move calculation of matrix coefficients into new
131        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
132        file; the main purpose of this change is to be able to reuse the code
133        in S/R SEAICE_PRECONDITIONER
134      - modify the computation of the residual so that the mass of sea-ice
135        is not used twice; this simplifies the calculations, but since
136        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
137        not tested in testreport---this does not affect the testreport results.
138    o verification/seaice_obcs:
139      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
140        verification/lab_sea/input.salt_plume; changes results/output.txt*
141    o model/src:
142      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
143    o pkg/seaice:
144      - improve description of parameters in seaice_fgmres.F and start
145        cleaning up the code
146      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
147        second argument
148      - add a metric based on grid cell area to SEAICE_SCALPROD; update
149        results of offline_exf_seaice.dyn_jfnk
150      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
151    o pkg/aim_v23:
152      - fix an other bug in dissipation heating (grid-cell area was missing).
153    o model/src + pkg/seaice:
154      - add global (multi-tile) linear solver for pair of tri-diagonal system
155        along X and Y lines, respectively for U and V component.
156        Note: 1) MPI and cube-exchange not yet coded.
157            2) probably not accurate for poorly conditioned / large size problem.
158      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
159        default: not compiled and not used.
160    o pkg/seaice:
161      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
162        introduce bi/bj loops and use global_sum_tile_rl instead of
163        mpi_allreduce in seaice_fgmres.F
164      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
165      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
166      - add a verification experiment for JFNK in offline_exf_seaice
167    o verification:
168      - change (for now, only fwd test) offline_exf_seaice experiment:
169        use a re-entrant channel with idealized coastline (trapezoidal shape)
170        at southern boundary to explore seaice dynamics and thermodynamics
171        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
172        secondary test (input.thsice) use thermodynamics only with SST relaxation.
173      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
174    o pkg/exf:
175      - disable "sstExtrapol" when Nr=1
176    o verification:
177      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
178        to test pkg/cheapaml.
179    o pkg/aim_v23 & pkg/shap_filt:
180      - fix dissipation heating (erroneous gravity multiplication factor).
181    o pkg/seaice:
182      - remove unused field pressPre from jfnk solver
183      - rename two subroutines in seaice_preconditioner.F
184    o eesupp/src:
185       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
186    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
187       - remove wrong parts of the rhs and the lhs (were in there
188         because I did not understand the concept of this preconditioner)
189       - add an exchange between u- and v-sweep. This increases communication
190         by a factor of two but improves the convergence of jfnk. Ideally,
191         one would like the u- and v-sweep to be independent. So far within
192         undocumented ifdefs
193       - reorganize the extra computations for printing the residuals
194    o tools/genmake2:
195      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
196        since it's not necessary (and was preventing to use MNC in some cases).
197    
198    checkpoint64a (2012/11/16)
199    o pkg/autodiff:
200      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
201        autodiff_readparms.F no longer depends on calling order (within
202        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
203        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
204        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
205    o pkg/obcs:
206      - adding tidal velocity forcing capability to obcs
207        for usage example, see verification/seaice_obcs/input.tides
208    o pkg/seaice:
209      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
210        SEAICE_LSRrelaxU/V
211      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
212    o pkg/aim_v23:
213      - implement heating from friction (bottom friction and stratospheric drag).
214    o pkg/shap_filt:
215      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
216        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
217    o model/src:
218      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
219        time-constant addMass field from file (addMassFile);
220      - support for heating due to friction (and Kinetic Energy dissipation):
221        add option, run-time switch and 3-D field array + support code ; each pkg
222        or S/R can add heating contribution (if there is a sink of KE); the sum is
223        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
224    o pkg/seaice:
225      - complete merge of ITD code into seaice_growth.F
226        from MITgcm_contrib/torge/itd/code/
227        no verification so far, but Torge Martin tested
228        "1-D test case and Beaufort set up;
229        deliver okay results after 1 model year."
230      - complete merge of SEAICE_SIZE.h into all relevant routines
231      - move computation of eta at Z-points into calc_viscosities
232        + introduce global field etaZ
233        + add different methods for computing etaZ, for now the old
234          method (simple averages of eta to Z-points) is hardwired
235        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
236          seaice_preconditioner
237      - simplify computations for SEAICE_ZETA_SMOOTHREG
238      - seaice_preconditioner:
239        + replace one remaining press by pressLoc (mistake)
240        + adjust printing of residuals
241      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
242        + add (SEAICE.h) and rename some counters (initiliased in
243          seaice_init_fixed.F)
244        + add _BEGIN/END_MASTER (myThid)  around print statements
245        + print total number of iterations and failures over SEAICE_monFreq
246          interval to STDOUT
247      - move control over output-messages by fgmres to seaice_jfnk to save
248        some operations
249      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
250        in order to make restarts with sol .ne. zero (fgmres with restarts)
251        (seaice_jfnk.F, seaice_fgmres.F)
252      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
253        a serious convergence problem when open boundaries are involved
254    o pkg/ggl90: fix computation of control volumes for the case of
255      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
256      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
257    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
258    o pkg/autodiff
259      - Add inAdMode switch for SEAICEuseDYNAMICS:
260        SEAICEuseDYNAMICSinAdMode
261        (extend logic in ADAUTODIFF_INADMODE_SET)
262    o pkg/seaice
263      - Step 1 of merging ice-thickness distribution (ITD) code from
264        MITgcm_contrib/torge/itd/ (author: Torge Martin)
265        The code implements concept laid out in Thorndike et al. (1975);
266        code is enabled via CPP flag SEAICE_ITD
267        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
268        code is not complete yet!!
269      - SEAICE_SIZE.h now included in almost all seaice routines
270    o verification (using seaice):
271      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
272        global_ocean.cs32x15.seaice ; update results.
273      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
274      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
275        offline_exf_seaice (previously compiling B-grid).
276    o pkg/exf:
277      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
278        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
279        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
280    o pkg/layers (adjust changes from Sept 19):
281      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
282        this allows to remove "layers_maxNum" dimension from all layers arrays.
283    o pkg/layers (adjust changes from Sept 19):
284      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
285      - snap-shot extended to all type of layers (not just the 1rst type);
286      - remove layers variables when corresponding CPP option is undef.
287    o pkg/layers:
288      - rename pkg/layers variable and add new output (layer exist & un-weighted
289        velocity in layer)
290    o pkg/seaice:
291      - simplify (?) ocean-drag coefficent computations by using
292        the same routine in all three solvers (saves some code lines)
293      - remove global fields DRAGA and DRAGS from C-grid code and
294        declare them locally in lsr.F (the only place where they are
295        still used)
296      - update AD output of lab_sea.evp (very sensitive anyway).
297    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
298      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
299      and SEAICEuseJFNK=.true. A few things to note:
300      - involves a FGMRES, that is parallel but very inefficient,
301        because of many scalar products (global sums) in the Gram-Schmidt
302        orthogonalization method. Needs to be replaced. Original code
303        from J.-F. Lemieux
304      - preconditioner for FGMRES is a stripped down version of LSOR
305      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
306        preconditioner. For the preconditioner, the default is set to 10.
307      - Jacobian times vector is computed with finite differences
308      - marginally related to JFNK-solver: add a smooth regularization for
309        zeta with tanh that will improve convergence (Lemieux and Tremblay,
310        2009) for any implicit solver (not implemented for EVP because EVP
311        does not need this regularization in the first place). Define
312        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
313    o eesupp/src:
314      - check in genmake2 that intrinsic S/R flush is available.
315      - add S/R to flush IO unit (if intrinsic S/R flush is available)
316      - flush standard & error msg unit before MPI termination
317      - if debugMode, flush IO unit after printing msg
318    o pkg/ctrl:
319      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
320        to ctrl_set_unpack_xyz.
321    
322    checkpoint64 (2012/10/09)
323    o pkg/shelfice
324      - in mom_fluxform.F, mom_vecinv.F:
325        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
326        Bug fix KappaRU -> KappaRV
327        does not change verification/isomip but may change other setups
328        (presumably constant KappaRU=KappaRV)
329      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
330    o pkg/obcs:
331      - fixed some indexing bugs in obcs_seaice_sponge.F
332      - added obcs relaxation subroutines for HSALT and HSNOW
333      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
334    o pkg/seaice:
335      - add "multicategory" parameterization for snow in analogy to ice,
336        default is off for now.
337    o pkg/obcs:
338      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
339        see verification/seaice_obcs/input.seaiceSponge for example application.
340      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
341        index setting by master-thread. This fix multi-threads Pb in previous modifs.
342    o pkg/layers :
343      - add diagnostics to pkg/layers
344      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
345        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
346    o pkg/generic_advdiff/gad_implicit_r.F :
347      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
348    o pkg/seaice/seaice_growth.F:
349      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
350    o pkg/obcs:
351      - change default setting of OBCS_UVICE_OLD from defined to undef;
352      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
353        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
354      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
355      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
356        with Southern & Western OB at a tile edge (at least in a simple set-up).
357    o pkg/obcs:
358      - change settings of OB index in case OB coincides with tile edge (shared by
359        2 tiles), so that common OB location is registered by both tiles (instead of
360        only 1). However, for Southern and Western OB, index value = 0 is not
361        recognized as valid OB index (=default null value) and needs to be fixed.
362      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
363      - new parameter "OB_indexNone" for null index value (for now, still zero)
364        to replace hard-coded null index value of zero.
365    o pkg/exch2:
366      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
367        always check buffer-size (but outside the loop); move checking for valid
368        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
369        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
370    o pkg/ctrl (pack & unpack):
371      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
372        (locally defined) for different variables (+ remove the variable-specific
373        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
374        (to be extended to other local file names in ctrl.h).
375    o pkg/flt:
376      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
377    o pkg/mdsio:
378      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
379    o tools/genmake2:
380      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
381        (added by Alistair in version 1.51 for building without make depend);
382      - remove Header files list (H_SRC_FILES) from the dependence of targets
383         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
384        place in version 1.23): this save going through staf when unrelated header
385        file has been modified.
386       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
387        "make depend" step, still need to do "make links" before "make adtaf".
388    o eesupp/src (+ few pkg src files) & genmake2:
389      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
390      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
391      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
392         upper/lower case ; account for space between "#" and undef/define)
393    o pkg/flt (with exch2):
394      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
395      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
396    
397    checkpoint63s (2012/09/05)
398    o pkg/ecco:
399      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
400      - add more relevant #ifdef ALLOW_SMOOTH ones.
401      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
402    o pkg/ctrl:
403      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
404        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
405      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
406        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
407        ctrlSmoothCorrel3D (new).
408        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
409      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
410      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
411        controls when useAtmWind, and vice versa.
412      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
413      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
414          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
415      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
416          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
417      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
418        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
419    o pkg/smooth:
420      - remove un-necessary includes.
421      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
422        Those CPP options were never defined, and not necessary.
423    o model/src:
424      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
425      - standard treatment of useSMOOTH.
426    o pkg/autodiff:
427      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
428        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
429    o pkg/exch2:
430      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
431        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
432      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
433        and tiles to process mapping.
434      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
435        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
436        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
437        from w2_eeboot.F to w2_readparms.F.
438    o eesupp/src:
439      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
440        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
441        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
442      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
443        is defined (remove condition on usingMPI) to match cases where MPI_INIT
444        has been called.
445      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
446      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
447        (so that on 1 proc, get same myPid independently of usingMPI)
448      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
449        useCubedSphereExchange with EXCH-1 (safer).
450      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
451    o pkg/ggl90:
452      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
453        used in ALLOW_GGL90_SMOOTH code.
454    o pkg/flt:
455      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
456        floats at the Southern end of the domain).
457    o eesupp/inc:
458      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
459        but not used (and not to be used) anywhere, just for documentation.
460    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
461      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
462        a) can damage previously written records in any other multi-record files.
463        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
464    o tools/genmake2:
465      - define variable MAKE within Makefile and use it in place of 'make';
466      - update AD_CONFIG.h (if needed) before building any of the executable
467        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
468        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
469      - always print usual warning comment 'this file is automatically generated'
470        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
471    o pkg/cheapaml:
472      - updated to correspond to the code used in accepted paper (Nico Wienders).
473    o pkg/exf:
474        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
475        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
476        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
477    o pkg/exf, autodiff, ctrl, ecco and seaice:
478        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
479    o pkg/ctrl, ecco:
480        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
481        Depending on useAtmWind, one is inactive, and the other is active (see
482        exf_getffields.F/exf_getsurfacefluxes.F).
483    o tools/genmake2:
484      - improve error msg when failing in 2nd test of check_for_broken_Ff
485      - fix option '-makefile' short-name (-mf according to genmake2 -help)
486      - source local config file "genmake_local" just after processing the genmake2
487        command arguments (previously done before processing arg).
488    o pkg/grdchk:
489      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
490        to this routine from cost_final has been dropped in g_cost_final)
491      - improve printed information (more explicit msg, no longer using "print *,"
492         fix fcpertminus printed value).
493    o model/src:
494      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
495        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
496        this prevents getting cost-funct reset in adinitialise_varia recomputations.
497    o pkg/dic:
498      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
499        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
500    o pkg/grdchk:
501      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
502      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
503    o pkg/autodiff/ctrl/grdchk :
504      - attempt to sort out what works and what does not,
505        with regard to I/O, and to warn/stop accordingly.
506    o pkg/grdchk:
507      - attempt to fix grdchk in the case of useSingleCpuIO.
508      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
509       statements were moved from grdchk_main.F and into
510       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
511      - a global sum is applied to record numbers icvrec/layer
512       out of grdchk_loc so that they be passed to I/O routines.
513    o pkg/smooth:
514      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
515        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
516    o verification/testreport:
517      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
518      - can also use compressed (gzip) reference output file;
519      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
520        to be easier to collect by testreport.
521      - update existing TLM output (half out-of-date by more than 3 yrs).
522      - report NETCDF & LAPACK settings (from genmake2) in output dir.
523      - report run-time in each individual summary (previously only for AD test);
524        for TLM test, add also TAF version.
525      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
526    
527    checkpoint63r (2012/08/15)
528    o tools/genmake2:
529      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
530    o pkg/ecco/ecco_cost_final.F :
531      - fix fc print statements (to stdout and costfunction0000) so
532        that the printed value is always after the global sum.
533    o pkg/seaice/seaice_dynsolver.F :
534      - fix ice strength assymptote at SEAICE_area_max<1
535        (no change for the standard case of SEAICE_area_max=1)
536    o some cleaning:
537      - pkg source files: ensure that all *.F files from each pkg included the
538        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
539        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
540        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
541        includes;
542      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
543      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
544        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
545        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
546      - update option-file CPP_OPTIONS.h of all AD experiments:
547        * no longer include PACKAGES_CONFIG.h ;
548        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
549        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
550          including ECCO_CPPOPTIONS.h).
551    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
552      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
553        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
554        not necessary accurate).
555      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
556        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
557        deliberately break compilation (a remainder that it needs to be customized)
558      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
559      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
560      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
561    o tools/genamke2:
562      - check for lapack.
563    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
564      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
565        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
566        from both packages.
567      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
568      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
569      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
570        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
571    o pkg/cost : add comments to explain special and/or untested setups.
572    o pkg/exf:
573      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
574        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
575    o verification/*/code_ad:
576      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
577      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
578      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
579        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
580    o pkg/seaice :
581      - added possibility to change ice strength/PRESS0 relationship to
582        HEFF, according to the following run time parameters
583        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
584        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
585        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
586    o pkg/ggl90 :
587      - added run time flag mxlSurfFlag to include the code that ensure
588        mixing between first and second level (previously included as a comment)
589    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
590      - add test of newly added dumpAdByRec=T option where
591        we write all records to one file per variable.
592    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
593      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
594        to check that this code is ok with taf and compiles in adjoint.
595    o pkg/autodiff :
596      - added run time param dumpAdByRec : ad dump format switch.
597        If true then write all records to one file per variable.
598        Else write one file per record (remains the default).
599      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
600    o pkg/seaice:
601     - Added SEAICEuseTILT run time switch : if set to
602       false then omit the tilt term in seaice dynamics.
603     - Fix free drift calculation.
604    o pkg/shelfice:
605      When initializing SHELFICEDragQuadratic, set default to be
606      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
607      but retain option to set it independently
608      (inconsistenty spotted by Veronique Dansereau)
609    o eesupp/inc:
610      - in EEPARAMS.h, add real-type constant for some frequently used simple number
611         (0,1,2,1/2), with name explicitly referring to RS/RL type.
612    o model/src:
613      - move balancing of relaxation terms to new S/R balance_relax.F.
614    o pkg/autodiff:
615      re-write active I/O high-level (control) S/R:
616      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
617      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
618      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
619        MDS_READ/WRITE_FIELD); change loops to multi-threads.
620      - update and merge active_file_control_slice.flow into active_file_control.flow
621      - update the calls in lower level S/R (active_file.F, active_file_g.F and
622        active_file_ad.F) keeping the argument list and function unchanged.
623      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
624        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
625      - new low-level active I/O routines, one for each type (RL/RS), for active var
626        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
627        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
628        right type.
629    o autodiff and RS=real*4:
630      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
631        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
632      - change argument type of 3-D mask argument to _RS to match type in the call
633        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
634    o pkg/thsice:
635      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
636      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
637        fresh-water flux: uniform correction or proportional to local precip.
638    o pkg/ctrl:
639      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
640      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
641                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
642      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
643    
644    checkpoint63q (2012/07/30)
645    o pkg/autodiff:
646      note about monitor and snap-shot of ad-variables:
647      a) need to apply ADEXCH before monitor or output of ad-vars to include
648       overlap contributions (was done for adjDump but missing for monitor).
649      b) since ADEXCH implies adding overlap values to interior array, machine
650       truncation error is expected when adding an ADEXCH call in the middle of
651       the time-stepping (although mathematically identical).
652      modifs:
653      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
654        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
655      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
656        apply ADEXCH before monitor or snap-shot of ad-variables:
657           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
658      - implement new method (copy+adexch) for snap-shot and monitor of main model
659        ad-vars (initially not used by default -> output unchanged).
660      - change default (set to 2) to use new method and update few output_adm.txt
661        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
662        and both tutorial_tracer_adjsens tests).
663      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
664        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
665    o pkg/ctrl:
666      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
667      generic control variables via
668      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
669      Only required customization should be S/R ctrl_map_ini_genarr.F
670      (routine in repository contains example)
671    o pkg/exf:
672      - fix and refine checking of surface-relaxation setting when using EXF
673    o verification (adjoint exp):
674      - reduce length of simulation by half for experiment global_ocean.cs32x15
675        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
676    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
677      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
678        of KE that can occur with aggressive optimization
679      + put quadratic bottom drag calculation in separated loops (only done if
680        using bottomDragQuadratic)
681    o model/src: CG2D_NSA
682      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
683         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
684      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
685         change cg2d residual target to be expressed in Wunits (=> do not normalise
686         RHS ; this fix global_max Pb with TAF); update output.
687    o verification/tutorial_tracer_adjsens:
688       improve parameter consistency (and get rid of warnings):
689       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
690       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
691       - use staggerTimeStep (for stability) in som81; use default rotation period.
692    o pkg/exch2:
693      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
694        reset to 0 = 1 long line in X)
695    o pkg/mdsio:
696      - fix reading of dimensions from meta file for large-size domain
697    o model/src:
698      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
699      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
700        Cubed-Sphere Exch with CS-corners inside the domain;
701        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
702        globalArea and to set hasWetCSCorners.
703      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
704        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
705      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
706        useCDscheme and useCubedSphereExchange).
707    o pkg/seaice/seaice_growth.F :
708      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
709        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
710        when the previous code was not correct.
711      - in all cases diagnoze the boundary condition mismatch to SIaaflux
712      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
713        that term to QNET (essentially to set the melt/freeze water to 0degC).
714        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
715    o verification/global_ocean.cs32x15/input.seaice :
716      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
717      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
718      - update results (output.seaice.txt) accordingly.
719    o verification/lab_sea/input/data.seaice :
720      - remove SEAICEheatConsFix, which is now be tested
721        in global_ocean.cs32x15. The presently coded fix
722        is only consistent with real fresh water + nlfs.
723      - update results (output.txt) accordingly.
724    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
725    o AD_CONFIG.h file:
726      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
727      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
728        add it explicitly in each fortran src file where it is needed.
729        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
730        thus introducing potentially wrong dependency; therefore, better to include
731        it only where it's really needed, and after any other included OPTIONS file
732        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
733        or ALLOW_TANGENTLINEAR_RUN).
734    
735    checkpoint63p (2012/07/06)
736    o pkg/autodiff:
737      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
738      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
739        which are now read from new parameter file "data.autodiff" (inAdExact
740        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
741      - add file "data.autodiff" in all verification/*/input_ad/ directories.
742      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
743        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
744    o verification/tutorial_tracer_adjsens/
745      - add extra sub-verification which uses "SOM" advection scheme
746        (2nd Order-Moment Advection Scheme, Prather Limiter) with
747          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
748        and in data:
749          multiDimAdvection=.TRUE.,
750          tempAdvScheme=81,
751          saltAdvScheme=81,
752    o model/src:
753      - introduce ALLOW_BALANCE_RELAX which allow the removal
754       of the global mean of relaxation terms by setting
755       balanceThetaClimRelax and balanceSaltClimRelax
756      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
757       This case is now treated appropriately in seaice_growth.F
758    o pkg/seaice:
759      - do balanceEmPmR and balanceQnet based on the net fluxes
760        (SItflux) that enter the ocean+ice system rather than QNET
761        and EMPMR. Works best in real fresh water.
762      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
763        out of the diagnotics bloc, and stored in global arrays.
764    
765    checkpoint63o (2012/06/29)
766    o vertical mixing schemes:
767      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
768      - replace computation of density (in Function STATE1, opps_calc.F) by a call
769        to S/R FIND_RHO_SCALAR
770      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
771        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
772        affects output (vermix.ggl90) at truncation level.
773    o testreport:
774      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
775        (nSx,nSy) for the number of threads (from eedata.mth)
776    o model/src:
777      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
778        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
779    o verification/tutorial_tracer_adjsens/
780      - compile with ALLOW_CG2D_NSA
781      - run with nonlinFreeSurf=3
782      - update reference output_adm.txt
783    o tools/genmake2:
784      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
785        refine usePROFILES switching off (only when NetCDF is not available).
786    o verification (atmospheric set-up):
787      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
788    o pkg/profiles : refine profiles and files handling.
789    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
790    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
791      - changes to use model/src/the_main_loop.F rather than the ecco version
792        in ecco type adjoint runs.
793    o model/src:
794      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
795      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
796      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
797    o model/src:
798      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
799        update output of test experiment bottom_ctrl_5x5.
800    o pkg/generic_advdiff:
801      - implement vertical bi-harmonic diffusion (for now, only for T & S and
802        only explicitly).
803    o verification/bottom_ctrl_5x5/
804      update reference output (results changed quite some time ago,
805      not sure when; but new reference results look ok in terms of grdchk)
806    o verification/1D_ocean_ice_column/
807      For verification purposes, the exact adjoint rather than an approx.
808      should be used (e.g., to comare against F.D. or TLM).
809      removed autodiff_inadmode*_ad.F routines in code_ad/
810      Update results/ accordingly.
811    o pkg/cal:
812      - change cal_getdate.F so that output date is function of input time only
813        (less ambiguous, not mixed up with input iteration number).
814      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
815    o pkg/diagnostics:
816      - implement calendarDumps also for stats-diags
817      - implement calendarDumps also for snap-shot output (negative freq)
818      - for now, ignores calendarDumps if non-zero phase-lag.
819    
820    checkpoint63n (2012/06/04)
821    o model/src:
822      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
823        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
824      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
825        similar to calc_r_star.F); update results of experiment internal_wave and
826        tutorial_global_oce_in_p (affected @ truncation level).
827    o pkg/shelfice:
828      - add parameterisation of advective-diffusive flux into the ice shelf
829        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
830      - simply eps3/3a computation
831    o eesupp:
832     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
833       between tiles, just fill-in edges assuming locally periodic subdomain) and
834       add corresponding exchange subroutines (EXCH0);
835     - new CG-solver version (_EX0) for disconnected-tiles special case.
836    o model/src (CG-solvers):
837     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
838       (similar final residual output and max-Iter number as with standard version);
839     - allows to store and use lowest-residual solution (standard & _SR versions);
840     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
841     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
842    o eesup/src:
843     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
844       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
845    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
846    
847    checkpoint63m (2012/04/27)
848    o pkg/shelfice:
849     - account for partical cells in surface level below ice-shelf for hydrostatic
850       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
851    o ad test experiments:
852     - update and rename to "ad_optfile.local" local AD-optfile specific to a
853       particular adjoint verification experiment (in verification/*/code_ad/)
854    o pkg/seaice & pkg/exf:
855     - Part two of ECCO-CLIVAR code merges.
856       Completes merge of seaice area relax. code.
857       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
858       to be set in EXF_OPTIONS.h since this pkg controls its I/O
859       (and avoids second CPP option in SEAICE_OPTIONS.h)
860     - change default value of costIceStart & costIceEnd to a valid date.
861     - add snowPrecip to HSNOW in seaice_growth
862    o pkg/ptracers:
863     - move ptracers summary and setup check into separated S/R ; add a check for
864       valid PTRACERS_Iter0 value (error+stop or just warning).
865    o pkg/cal (+ pkg/ecco):
866     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
867       as input; and for AD, unless both are not differentiable (e.g., k index)).
868    o model/src:
869     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
870       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
871       temporary set to usingZCoords value (to be changed to F when using shelfice).
872     - hydrostatic pressure: implement partial cell near the surface also for
873       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
874       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
875    o pkg/ctrl/ctrl_init.F:
876     - add a formal parameter to s/r ctrl_init_rec to print
877       xx_$(ctrl_valiable)_file for easier debugging
878     - move call of cal_* routines into the if-block where they are really
879       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
880       to specify a startdate
881    o pkg/seaice:
882     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
883       global_ocean.cs32x15/code versions).
884     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
885       verification experiment global_ocean.cs32x15.seaice and update results.
886    o pkg/exf:
887     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
888       (according to useExfYearlyFields).
889    o pkg/cal:
890     - move calendar setting & summary (previously in cal_readparams.F) into new
891       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
892       length of the simulation is set (after SET_PARMS call); This is an attempt
893       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
894     - For safety: keep a record of pkg/cal parameter settings status
895               to allow to STOP if one pkg/cal S/R is called too early.
896     - add a stop in all basic pkg/cal subroutines if called before setting is done.
897     - modify cal_getdate.F: stop when nothing was returned;
898       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
899       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
900    
901    checkpoint63l (2012/04/04)
902    o pkg/bbl:
903      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
904        update global_with_exf output.yearly.txt file.
905    o pkg/cal:
906      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
907      - remove 2 unsused and very short (1 line only) functions ;
908      - remove unsused subroutines from AD-Diff list.
909    o model/src:
910      - start to implement clean wait to stop in initialization S/R (config_check.F,
911         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
912    o folowing PRINT_MESSAGE changes:
913      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
914    o pkg/bbl:
915      - modification so it can work with z*
916      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
917      - global_with_exf/input.yearly verification; changes output.yearly.txt
918    o eesupp/src:
919      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
920        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
921      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
922        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
923      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
924      - when using MPI, always set usingMPI=T ; set default accordingly and stop
925        if not consistent.
926      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
927        argument is zero (in case called within single-thread section).
928    o pkg/fizhi:
929        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
930        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
931    o pkg/exch2:
932      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
933        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
934      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
935        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
936        with bad ones coming from a not-yet-updated halo.
937        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
938    o pkg/frazil:
939        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
940        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
941    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
942    o verification/lab_sea
943      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
944      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
945      * nTimeSteps 3 -> 4
946      * changed reference output accordingly
947    o pkg/ctrl:
948      * fix ctrl_get_gen for xx_sst, xx_sss
949    o pkg/fizhi:
950      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
951        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
952      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
953        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
954        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
955    o pkg/gmredi:
956      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
957    o pkg/fizhi:
958      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
959        (old)aces open64 tuv test.
960    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
961    o pkg/mom_vecinv:
962      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
963        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
964        with non-lin free-surf).
965    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
966      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
967      some compilers (gfortran 4.6.0 on MacOS)
968    o momentum:
969      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
970        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
971        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
972    
973    checkpoint63k (2012/03/17)
974    o model/src:
975       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
976         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
977       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
978         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
979    o model/src: solve_*diagonal.F
980       - replace division with multiplication by inverse (similar to original version)
981         update output of AD exp. global_ocean.90x40x15.
982       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
983         to enable the use of the vectorized & differentiable solve_tridiagonal.F
984       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
985         vertical advection (to get solve_tridiagonal tested in AD mode).
986    o pkg/seaice: ECCO-CLIVAR merge:
987      1. seaice AREA relaxation
988         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
989         * runtime flag: SEAICE_tauAreaObsRelax
990      2. modified global mean cost imbalance code: CPP option
991          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
992    o another iteration on solve_*diagonal.F
993       Make choices independent of AUTODIFF
994       Default will be the adjoinable vectorized version.
995       Alternative choices are:
996       * non-adjoinable original version with low memory footprint:
997         #define SOLVE_DIAGONAL_LOWMEMORY
998       * still adjoinable but does not vectorize (k as inner-most loop):
999         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1000    o testreport
1001     - add option to use a home made wrapper around "make"
1002     - remove MITGCM_IEEE env. variable (no longer active)
1003    o pkg/shelfice
1004     - improve computation of friction velocity for velocity dependent
1005       exchange coefficients: include velocities into SHELFICEBoundaryLayer
1006       block to average velocities vertically
1007     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1008    o Modify diagonal solvers, now three versions (upon request):
1009      #ifndef SOLVE_DIAGONAL_AUTODIFF
1010        1. default version (dating back a while ago)
1011      #else /* def SOLVE_DIAGONAL_AUTODIFF */
1012      # ifdef SOLVE_DIAGONAL_KINNER
1013        2. adjoinable version with k-innermost loop (G. Forget)
1014      # else
1015        3. adjoinable vectorized version of 2.
1016      # endif
1017      #endif /* SOLVE_DIAGONAL_AUTODIFF */
1018      All flags are currently set within routines, but could/should be moved to CPP-options.
1019      Array bounds for 1. are as before, for 2.,3. cover the entire domain
1020      (could be changed for 1. too).
1021    o verification/lab_sea (fwd):
1022      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1023        use 7 categories (except hb87), new solve4temp params (except salt_plume),
1024        constant salinity (=4) or variable salinity (salt_plume) done through
1025        SItracer.
1026    o pkg/seaice:
1027      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1028      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1029         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1030        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1031        SEAICE_freeze got retired) but already better than previously with
1032        SEAICE_freeze=123456.7 deg.C;
1033      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1034        (safer multi-threaded setting); always set SEAICEuseEVP;
1035      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1036        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1037        stop if multiple specifications for the same coeff; make sure default
1038        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1039    o pkg/obcs:
1040      - allow to switch to upwind 1rst order advection scheme for the advective
1041        flux computation at the open-boundary; disabled for adjoint built.
1042    o pkg/ptracers:
1043      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1044      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1045      - add parameter to decide when to start a tracer; use internal flag to
1046        know which tracer to step-forward; switch this internal flag at the top
1047        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1048        for adjoint built.
1049    o pkg/seaice:
1050      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1051      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1052      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1053    o pkg/ecco:
1054      - fix writing of output file DiagnosCost_ClimSalt/Theta
1055        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1056    o pkg/seaice:
1057      - add missing initialisation of COR_ICE array in dynsolver.F
1058      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1059        compiled either way, and is tested in all exps (multidim was only tested
1060        in lab_sea ad before).
1061      - cosmetic change to prepare for future addition of ITD. no change to results.
1062        no defaults change.
1063      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1064      - by lack of adequate verification experiments, I further used custom versions
1065        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1066        should be correct.
1067      - avoid recomputations in ad.
1068    o array initialisation in adjoint mode:
1069      1) pkg/mom_common/mom_calc_ke.F:
1070        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1071        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1072        part this initialisation is gone, resulting in Floating Point Exception
1073        (caught by open64 compiler with debug option).
1074      2) model/src/convective_weights.F
1075        set output convectCount over the full array range (instead of doing
1076        an update): this fix a similar issue when called within recomputation (adjoint)
1077        which could by-pass the initialisation (normally done in the caller S/R).
1078    o pkg/seaice:
1079      - final version of turbulent flux params, as agreed at MIT ice meet:
1080           SEAICE_mcPheePiston (default is ~ 0.000875)
1081           SEAICE_mcPheeTaper (default is 0.)
1082           SEAICE_frazilFrac (defualt is 1.)
1083           SEAICE_mcPheeStepFunc (default is false)
1084      - changes results at trunction error level
1085      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1086    o added pkg/frazil:
1087      - see frazil_description.tex for details
1088      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1089    o pkg/shelfice/shelfice_thermodynamics.F
1090      - fix exponents for velocity dependent exchange coefficients: change
1091        from 2/3(=0) to 0.66666666666666667
1092      - move computation of velocity dependent exchange coefficients into
1093        separate loop, so that it applies to both thermodynamics
1094      - move some divisions by constants out of loops
1095    
1096    checkpoint63j (2012/02/16)
1097    o pkg/seaice:
1098      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1099      - SItracer:  added run time params, and allow coupling to ocn salinity.
1100    o pkg/seaice: remove (almost) all divisions by constants within loops
1101      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1102      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1103      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1104      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1105    o pkg/seaice :
1106      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1107        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1108      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1109      - add permanent SItflux diag that corresponds to TFLUX but includes
1110        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1111      - allow activation/testing of a fix for suspected missing term in
1112        ocn-ice heat budget (to be confirmed). To test this, you want to
1113        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1114        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1115      - no change in results, fwd or ad.
1116    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1117      - switch to variable freezing point.
1118           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1119      - bug fix : the sublimation term that was missing is now activated.
1120           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1121      - bug fix : flooding sign term for SIsal0.NE.0.
1122           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1123    o pkg/seaice:
1124      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1125        is now the default, and the old default constant freezing point is recovered
1126        with SEAICE_tempFrz0    = -1.96,
1127             SEAICE_dTempFrz_dS = 0.,
1128      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1129      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1130      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1131        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1132      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1133        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1134      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
1135        seaice_growth r149 for legacy branch (no results change).
1136      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1137        from I. Fenty).
1138      - results did not change except for global_ocean.cs32x15, mostly due to the
1139        switch to variable freezing point (see above item for detail).
1140    o pkg/thsice:
1141      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1142        seawater freezing in thsice_calc_thickn (not used).
1143    o pkg/seaice: turbulent flux term specification via run time params.
1144      - replace CPP switches with run time switches to facilitate testing
1145      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1146                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1147      - added runtime parameter : SEAICEturbFluxFormula
1148      - move Mcphee constants to SEAICE_PARAMS.h
1149      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1150                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1151                 remove seaice_summary call (moved to seaice_init_fixed)
1152      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1153        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1154      - seaice_summary.F : add missing report of read turbulent flux term set up
1155                           and SITRACER.
1156      - seaice_check.F : check range; inform and stop if retired CPPs are used
1157                         (incl. SEAICE_AGE).
1158      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1159             CPP switch, same computation as before for the different options.
1160      - change results at the truncation level.
1161    o pkg/seaice:
1162      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1163        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1164        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1165      - update verification/*/input*/data.seaice:
1166        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1167        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1168        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1169        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1170    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1171      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1172        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1173        difference in results only due to machine truncation.
1174      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1175        MaykutPolySatVap; keep MIN_LWDOWN.
1176      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1177      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1178        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1179    o pkg/salt_plume:
1180      - isolate saltPlumeFlux array exch into a specific S/R called from
1181        do_oceanic_phys.F
1182      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1183    o verification:
1184      - move untested set-up to MITgcm_contrib/verification_other.
1185    o pkg/seaice:
1186      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1187    o pkg/seaice:
1188      - seaice_solve4temp.F (keeping results unchanged):
1189        * add 2 future run-time params to select which saturation vapor pressure
1190          formula is used and how post-iteration fluxes are set.
1191          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1192        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1193          the linearized expression to stay consistent with tsurf finding.
1194      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1195        can be < 0.
1196    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1197      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1198        conductive heat flux F_c , and add it explicitly when updating tsurf as
1199        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1200        so that now F_ia has a consistent meaning through the entire routine.
1201        This causes differences at truncation level: update output of fwd exp.
1202        global_ocean.cs32x15.seaice.
1203    o pkg/seaice:
1204      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1205        of arrays, sign/direction of fluxes; no effect on results.
1206      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1207        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1208        note: this should have been done before changing celsius2K default.
1209      - to keep results unchanged, add back old value of celsius2K in verification
1210        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1211      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1212        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1213        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1214        freezing temp is consistent with value in seaice_growth.F ; this causes
1215        differences at machine truncation level: update lab_sea AD output (3/4).
1216    o pkg/seaice:
1217      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1218        and climsst/sss even when using seaice (to prevent calculation that might
1219        use SST on land); does not affect any verification exp.
1220      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1221        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1222    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1223      over land (non-legacy code)
1224    o vectorize salt_plume package:
1225      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1226      - this code computes plumebk everywhere (also over land), thus requires
1227        code to avoid divisions by zero and catch the case of kLev=Nr.
1228      - efficiency of salt_plume_frac is still sub-optimal
1229    o tools (genmake2):
1230      - fix makefile NAME specification (option: -makefile NAME) by adding
1231        "-f $MAKEFILE" in few places where it was missing including makedepend
1232        command (contribution from Paul).
1233    
1234    checkpoint63i (2012/01/24)
1235    o model/src:
1236      - add factorized versions of some EOS code to find_rho.F,
1237        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1238    o model/src:
1239      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1240      - change default celsius2K from 273.16 to 273.15
1241      - to keep results unchanged, add back old value of celsius2K in verification
1242        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1243         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1244    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1245      to make TAF generate vectorizable code
1246    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1247       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1248       have flags that do this more efficiently.
1249    o pkg/diagnostics/diagstats_calc.F
1250      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1251    o pkg/obcs (with exch2):
1252      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1253        and remove code (in obcs_readparms.F) which was based on EXCH of indices
1254        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1255    o pkg/exf and seaice exp:
1256      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1257        so that switching off area & heff advection flags does not affect results.
1258      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1259      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1260        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1261        results of verification experiments: 1D_ocean_ice_column(fwd),
1262        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1263        and offline_exf_seaice (all 4).
1264  o pkg/seaice:  o pkg/seaice:
1265    - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;    - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1266      remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.      remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
Legend:
Removed from v.1.1573  
changed lines
  Added in v.1.1811
  ViewVC Help
Powered by ViewVC 1.1.22