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revision 1.1561 by jmc, Sat Dec 24 01:22:09 2011 UTC revision 1.1743 by mlosch, Mon Sep 24 15:07:38 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice:
8      - add "multicategory" parameterization for snow in analogy to ice,
9        default is off for now.
10    o pkg/obcs:
11      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
12        see verification/seaice_obcs/input.seaiceSponge for example application.
13      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
14        index setting by master-thread. This fix multi-threads Pb in previous modifs.
15    o pkg/layers :
16      - add diagnostics to pkg/layers
17      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
18        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
19    o pkg/generic_advdiff/gad_implicit_r.F :
20      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
21    o pkg/seaice/seaice_growth.F:
22      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
23    o pkg/obcs:
24      - change default setting of OBCS_UVICE_OLD from defined to undef;
25      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
26        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
27      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
28      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
29        with Southern & Western OB at a tile edge (at least in a simple set-up).
30    o pkg/obcs:
31      - change settings of OB index in case OB coincides with tile edge (shared by
32        2 tiles), so that common OB location is registered by both tiles (instead of
33        only 1). However, for Southern and Western OB, index value = 0 is not
34        recognized as valid OB index (=default null value) and needs to be fixed.
35      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
36      - new parameter "OB_indexNone" for null index value (for now, still zero)
37        to replace hard-coded null index value of zero.
38    o pkg/exch2:
39      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
40        always check buffer-size (but outside the loop); move checking for valid
41        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
42        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
43    o pkg/ctrl (pack & unpack):
44      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
45        (locally defined) for different variables (+ remove the variable-specific
46        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
47        (to be extended to other local file names in ctrl.h).
48    o pkg/flt:
49      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
50    o pkg/mdsio:
51      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
52    o tools/genmake2:
53      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
54        (added by Alistair in version 1.51 for building without make depend);
55      - remove Header files list (H_SRC_FILES) from the dependence of targets
56         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
57        place in version 1.23): this save going through staf when unrelated header
58        file has been modified.
59       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
60        "make depend" step, still need to do "make links" before "make adtaf".
61    o eesupp/src (+ few pkg src files) & genmake2:
62      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
63      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
64      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
65         upper/lower case ; account for space between "#" and undef/define)
66    o pkg/flt (with exch2):
67      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
68      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
69    
70    checkpoint63s (2012/09/05)
71    o pkg/ecco:
72      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
73      - add more relevant #ifdef ALLOW_SMOOTH ones.
74      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
75    o pkg/ctrl:
76      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
77        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
78      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
79        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
80        ctrlSmoothCorrel3D (new).
81        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
82      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
83      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
84        controls when useAtmWind, and vice versa.
85      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
86      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
87          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
88      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
89          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
90      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
91        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
92    o pkg/smooth:
93      - remove un-necessary includes.
94      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
95        Those CPP options were never defined, and not necessary.
96    o model/src:
97      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
98      - standard treatment of useSMOOTH.
99    o pkg/autodiff:
100      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
101        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
102    o pkg/exch2:
103      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
104        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
105      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
106        and tiles to process mapping.
107      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
108        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
109        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
110        from w2_eeboot.F to w2_readparms.F.
111    o eesupp/src:
112      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
113        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
114        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
115      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
116        is defined (remove condition on usingMPI) to match cases where MPI_INIT
117        has been called.
118      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
119      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
120        (so that on 1 proc, get same myPid independently of usingMPI)
121      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
122        useCubedSphereExchange with EXCH-1 (safer).
123      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
124    o pkg/ggl90:
125      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
126        used in ALLOW_GGL90_SMOOTH code.
127    o pkg/flt:
128      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
129        floats at the Southern end of the domain).
130    o eesupp/inc:
131      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
132        but not used (and not to be used) anywhere, just for documentation.
133    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
134      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
135        a) can damage previously written records in any other multi-record files.
136        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
137    o tools/genmake2:
138      - define variable MAKE within Makefile and use it in place of 'make';
139      - update AD_CONFIG.h (if needed) before building any of the executable
140        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
141        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
142      - always print usual warning comment 'this file is automatically generated'
143        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
144    o pkg/cheapaml:
145      - updated to correspond to the code used in accepted paper (Nico Wienders).
146    o pkg/exf:
147        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
148        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
149        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
150    o pkg/exf, autodiff, ctrl, ecco and seaice:
151        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
152    o pkg/ctrl, ecco:
153        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
154        Depending on useAtmWind, one is inactive, and the other is active (see
155        exf_getffields.F/exf_getsurfacefluxes.F).
156    o tools/genmake2:
157      - improve error msg when failing in 2nd test of check_for_broken_Ff
158      - fix option '-makefile' short-name (-mf according to genmake2 -help)
159      - source local config file "genmake_local" just after processing the genmake2
160        command arguments (previously done before processing arg).
161    o pkg/grdchk:
162      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
163        to this routine from cost_final has been dropped in g_cost_final)
164      - improve printed information (more explicit msg, no longer using "print *,"
165         fix fcpertminus printed value).
166    o model/src:
167      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
168        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
169        this prevents getting cost-funct reset in adinitialise_varia recomputations.
170    o pkg/dic:
171      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
172        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
173    o pkg/grdchk:
174      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
175      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
176    o pkg/autodiff/ctrl/grdchk :
177      - attempt to sort out what works and what does not,
178        with regard to I/O, and to warn/stop accordingly.
179    o pkg/grdchk:
180      - attempt to fix grdchk in the case of useSingleCpuIO.
181      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
182       statements were moved from grdchk_main.F and into
183       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
184      - a global sum is applied to record numbers icvrec/layer
185       out of grdchk_loc so that they be passed to I/O routines.
186    o pkg/smooth:
187      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
188        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
189    o verification/testreport:
190      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
191      - can also use compressed (gzip) reference output file;
192      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
193        to be easier to collect by testreport.
194      - update existing TLM output (half out-of-date by more than 3 yrs).
195      - report NETCDF & LAPACK settings (from genmake2) in output dir.
196      - report run-time in each individual summary (previously only for AD test);
197        for TLM test, add also TAF version.
198      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
199    
200    checkpoint63r (2012/08/15)
201    o tools/genmake2:
202      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
203    o pkg/ecco/ecco_cost_final.F :
204      - fix fc print statements (to stdout and costfunction0000) so
205        that the printed value is always after the global sum.
206    o pkg/seaice/seaice_dynsolver.F :
207      - fix ice strength assymptote at SEAICE_area_max<1
208        (no change for the standard case of SEAICE_area_max=1)
209    o some cleaning:
210      - pkg source files: ensure that all *.F files from each pkg included the
211        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
212        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
213        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
214        includes;
215      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
216      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
217        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
218        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
219      - update option-file CPP_OPTIONS.h of all AD experiments:
220        * no longer include PACKAGES_CONFIG.h ;
221        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
222        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
223          including ECCO_CPPOPTIONS.h).
224    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
225      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
226        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
227        not necessary accurate).
228      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
229        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
230        deliberately break compilation (a remainder that it needs to be customized)
231      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
232      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
233      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
234    o tools/genamke2:
235      - check for lapack.
236    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
237      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
238        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
239        from both packages.
240      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
241      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
242      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
243        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
244    o pkg/cost : add comments to explain special and/or untested setups.
245    o pkg/exf:
246      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
247        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
248    o verification/*/code_ad:
249      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
250      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
251      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
252        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
253    o pkg/seaice :
254      - added possibility to change ice strength/PRESS0 relationship to
255        HEFF, according to the following run time parameters
256        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
257        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
258        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
259    o pkg/ggl90 :
260      - added run time flag mxlSurfFlag to include the code that ensure
261        mixing between first and second level (previously included as a comment)
262    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
263      - add test of newly added dumpAdByRec=T option where
264        we write all records to one file per variable.
265    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
266      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
267        to check that this code is ok with taf and compiles in adjoint.
268    o pkg/autodiff :
269      - added run time param dumpAdByRec : ad dump format switch.
270        If true then write all records to one file per variable.
271        Else write one file per record (remains the default).
272      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
273    o pkg/seaice:
274     - Added SEAICEuseTILT run time switch : if set to
275       false then omit the tilt term in seaice dynamics.
276     - Fix free drift calculation.
277    o pkg/shelfice:
278      When initializing SHELFICEDragQuadratic, set default to be
279      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
280      but retain option to set it independently
281      (inconsistenty spotted by Veronique Dansereau)
282    o eesupp/inc:
283      - in EEPARAMS.h, add real-type constant for some frequently used simple number
284         (0,1,2,1/2), with name explicitly referring to RS/RL type.
285    o model/src:
286      - move balancing of relaxation terms to new S/R balance_relax.F.
287    o pkg/autodiff:
288      re-write active I/O high-level (control) S/R:
289      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
290      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
291      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
292        MDS_READ/WRITE_FIELD); change loops to multi-threads.
293      - update and merge active_file_control_slice.flow into active_file_control.flow
294      - update the calls in lower level S/R (active_file.F, active_file_g.F and
295        active_file_ad.F) keeping the argument list and function unchanged.
296      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
297        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
298      - new low-level active I/O routines, one for each type (RL/RS), for active var
299        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
300        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
301        right type.
302    o autodiff and RS=real*4:
303      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
304        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
305      - change argument type of 3-D mask argument to _RS to match type in the call
306        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
307    o pkg/thsice:
308      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
309      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
310        fresh-water flux: uniform correction or proportional to local precip.
311    o pkg/ctrl:
312      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
313      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
314                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
315      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
316    
317    checkpoint63q (2012/07/30)
318    o pkg/autodiff:
319      note about monitor and snap-shot of ad-variables:
320      a) need to apply ADEXCH before monitor or output of ad-vars to include
321       overlap contributions (was done for adjDump but missing for monitor).
322      b) since ADEXCH implies adding overlap values to interior array, machine
323       truncation error is expected when adding an ADEXCH call in the middle of
324       the time-stepping (although mathematically identical).
325      modifs:
326      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
327        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
328      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
329        apply ADEXCH before monitor or snap-shot of ad-variables:
330           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
331      - implement new method (copy+adexch) for snap-shot and monitor of main model
332        ad-vars (initially not used by default -> output unchanged).
333      - change default (set to 2) to use new method and update few output_adm.txt
334        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
335        and both tutorial_tracer_adjsens tests).
336      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
337        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
338    o pkg/ctrl:
339      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
340      generic control variables via
341      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
342      Only required customization should be S/R ctrl_map_ini_genarr.F
343      (routine in repository contains example)
344    o pkg/exf:
345      - fix and refine checking of surface-relaxation setting when using EXF
346    o verification (adjoint exp):
347      - reduce length of simulation by half for experiment global_ocean.cs32x15
348        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
349    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
350      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
351        of KE that can occur with aggressive optimization
352      + put quadratic bottom drag calculation in separated loops (only done if
353        using bottomDragQuadratic)
354    o model/src: CG2D_NSA
355      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
356         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
357      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
358         change cg2d residual target to be expressed in Wunits (=> do not normalise
359         RHS ; this fix global_max Pb with TAF); update output.
360    o verification/tutorial_tracer_adjsens:
361       improve parameter consistency (and get rid of warnings):
362       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
363       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
364       - use staggerTimeStep (for stability) in som81; use default rotation period.
365    o pkg/exch2:
366      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
367        reset to 0 = 1 long line in X)
368    o pkg/mdsio:
369      - fix reading of dimensions from meta file for large-size domain
370    o model/src:
371      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
372      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
373        Cubed-Sphere Exch with CS-corners inside the domain;
374        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
375        globalArea and to set hasWetCSCorners.
376      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
377        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
378      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
379        useCDscheme and useCubedSphereExchange).
380    o pkg/seaice/seaice_growth.F :
381      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
382        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
383        when the previous code was not correct.
384      - in all cases diagnoze the boundary condition mismatch to SIaaflux
385      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
386        that term to QNET (essentially to set the melt/freeze water to 0degC).
387        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
388    o verification/global_ocean.cs32x15/input.seaice :
389      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
390      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
391      - update results (output.seaice.txt) accordingly.
392    o verification/lab_sea/input/data.seaice :
393      - remove SEAICEheatConsFix, which is now be tested
394        in global_ocean.cs32x15. The presently coded fix
395        is only consistent with real fresh water + nlfs.
396      - update results (output.txt) accordingly.
397    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
398    o AD_CONFIG.h file:
399      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
400      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
401        add it explicitly in each fortran src file where it is needed.
402        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
403        thus introducing potentially wrong dependency; therefore, better to include
404        it only where it's really needed, and after any other included OPTIONS file
405        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
406        or ALLOW_TANGENTLINEAR_RUN).
407    
408    checkpoint63p (2012/07/06)
409    o pkg/autodiff:
410      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
411      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
412        which are now read from new parameter file "data.autodiff" (inAdExact
413        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
414      - add file "data.autodiff" in all verification/*/input_ad/ directories.
415      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
416        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
417    o verification/tutorial_tracer_adjsens/
418      - add extra sub-verification which uses "SOM" advection scheme
419        (2nd Order-Moment Advection Scheme, Prather Limiter) with
420          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
421        and in data:
422          multiDimAdvection=.TRUE.,
423          tempAdvScheme=81,
424          saltAdvScheme=81,
425    o model/src:
426      - introduce ALLOW_BALANCE_RELAX which allow the removal
427       of the global mean of relaxation terms by setting
428       balanceThetaClimRelax and balanceSaltClimRelax
429      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
430       This case is now treated appropriately in seaice_growth.F
431    o pkg/seaice:
432      - do balanceEmPmR and balanceQnet based on the net fluxes
433        (SItflux) that enter the ocean+ice system rather than QNET
434        and EMPMR. Works best in real fresh water.
435      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
436        out of the diagnotics bloc, and stored in global arrays.
437    
438    checkpoint63o (2012/06/29)
439    o vertical mixing schemes:
440      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
441      - replace computation of density (in Function STATE1, opps_calc.F) by a call
442        to S/R FIND_RHO_SCALAR
443      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
444        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
445        affects output (vermix.ggl90) at truncation level.
446    o testreport:
447      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
448        (nSx,nSy) for the number of threads (from eedata.mth)
449    o model/src:
450      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
451        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
452    o verification/tutorial_tracer_adjsens/
453      - compile with ALLOW_CG2D_NSA
454      - run with nonlinFreeSurf=3
455      - update reference output_adm.txt
456    o tools/genmake2:
457      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
458        refine usePROFILES switching off (only when NetCDF is not available).
459    o verification (atmospheric set-up):
460      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
461    o pkg/profiles : refine profiles and files handling.
462    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
463    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
464      - changes to use model/src/the_main_loop.F rather than the ecco version
465        in ecco type adjoint runs.
466    o model/src:
467      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
468      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
469      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
470    o model/src:
471      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
472        update output of test experiment bottom_ctrl_5x5.
473    o pkg/generic_advdiff:
474      - implement vertical bi-harmonic diffusion (for now, only for T & S and
475        only explicitly).
476    o verification/bottom_ctrl_5x5/
477      update reference output (results changed quite some time ago,
478      not sure when; but new reference results look ok in terms of grdchk)
479    o verification/1D_ocean_ice_column/
480      For verification purposes, the exact adjoint rather than an approx.
481      should be used (e.g., to comare against F.D. or TLM).
482      removed autodiff_inadmode*_ad.F routines in code_ad/
483      Update results/ accordingly.
484    o pkg/cal:
485      - change cal_getdate.F so that output date is function of input time only
486        (less ambiguous, not mixed up with input iteration number).
487      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
488    o pkg/diagnostics:
489      - implement calendarDumps also for stats-diags
490      - implement calendarDumps also for snap-shot output (negative freq)
491      - for now, ignores calendarDumps if non-zero phase-lag.
492    
493    checkpoint63n (2012/06/04)
494    o model/src:
495      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
496        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
497      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
498        similar to calc_r_star.F); update results of experiment internal_wave and
499        tutorial_global_oce_in_p (affected @ truncation level).
500    o pkg/shelfice:
501      - add parameterisation of advective-diffusive flux into the ice shelf
502        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
503      - simply eps3/3a computation
504    o eesupp:
505     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
506       between tiles, just fill-in edges assuming locally periodic subdomain) and
507       add corresponding exchange subroutines (EXCH0);
508     - new CG-solver version (_EX0) for disconnected-tiles special case.
509    o model/src (CG-solvers):
510     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
511       (similar final residual output and max-Iter number as with standard version);
512     - allows to store and use lowest-residual solution (standard & _SR versions);
513     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
514     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
515    o eesup/src:
516     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
517       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
518    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
519    
520    checkpoint63m (2012/04/27)
521    o pkg/shelfice:
522     - account for partical cells in surface level below ice-shelf for hydrostatic
523       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
524    o ad test experiments:
525     - update and rename to "ad_optfile.local" local AD-optfile specific to a
526       particular adjoint verification experiment (in verification/*/code_ad/)
527    o pkg/seaice & pkg/exf:
528     - Part two of ECCO-CLIVAR code merges.
529       Completes merge of seaice area relax. code.
530       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
531       to be set in EXF_OPTIONS.h since this pkg controls its I/O
532       (and avoids second CPP option in SEAICE_OPTIONS.h)
533     - change default value of costIceStart & costIceEnd to a valid date.
534     - add snowPrecip to HSNOW in seaice_growth
535    o pkg/ptracers:
536     - move ptracers summary and setup check into separated S/R ; add a check for
537       valid PTRACERS_Iter0 value (error+stop or just warning).
538    o pkg/cal (+ pkg/ecco):
539     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
540       as input; and for AD, unless both are not differentiable (e.g., k index)).
541    o model/src:
542     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
543       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
544       temporary set to usingZCoords value (to be changed to F when using shelfice).
545     - hydrostatic pressure: implement partial cell near the surface also for
546       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
547       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
548    o pkg/ctrl/ctrl_init.F:
549     - add a formal parameter to s/r ctrl_init_rec to print
550       xx_$(ctrl_valiable)_file for easier debugging
551     - move call of cal_* routines into the if-block where they are really
552       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
553       to specify a startdate
554    o pkg/seaice:
555     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
556       global_ocean.cs32x15/code versions).
557     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
558       verification experiment global_ocean.cs32x15.seaice and update results.
559    o pkg/exf:
560     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
561       (according to useExfYearlyFields).
562    o pkg/cal:
563     - move calendar setting & summary (previously in cal_readparams.F) into new
564       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
565       length of the simulation is set (after SET_PARMS call); This is an attempt
566       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
567     - For safety: keep a record of pkg/cal parameter settings status
568               to allow to STOP if one pkg/cal S/R is called too early.
569     - add a stop in all basic pkg/cal subroutines if called before setting is done.
570     - modify cal_getdate.F: stop when nothing was returned;
571       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
572       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
573    
574    checkpoint63l (2012/04/04)
575    o pkg/bbl:
576      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
577        update global_with_exf output.yearly.txt file.
578    o pkg/cal:
579      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
580      - remove 2 unsused and very short (1 line only) functions ;
581      - remove unsused subroutines from AD-Diff list.
582    o model/src:
583      - start to implement clean wait to stop in initialization S/R (config_check.F,
584         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
585    o folowing PRINT_MESSAGE changes:
586      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
587    o pkg/bbl:
588      - modification so it can work with z*
589      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
590      - global_with_exf/input.yearly verification; changes output.yearly.txt
591    o eesupp/src:
592      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
593        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
594      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
595        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
596      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
597      - when using MPI, always set usingMPI=T ; set default accordingly and stop
598        if not consistent.
599      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
600        argument is zero (in case called within single-thread section).
601    o pkg/fizhi:
602        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
603        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
604    o pkg/exch2:
605      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
606        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
607      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
608        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
609        with bad ones coming from a not-yet-updated halo.
610        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
611    o pkg/frazil:
612        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
613        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
614    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
615    o verification/lab_sea
616      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
617      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
618      * nTimeSteps 3 -> 4
619      * changed reference output accordingly
620    o pkg/ctrl:
621      * fix ctrl_get_gen for xx_sst, xx_sss
622    o pkg/fizhi:
623      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
624        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
625      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
626        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
627        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
628    o pkg/gmredi:
629      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
630    o pkg/fizhi:
631      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
632        (old)aces open64 tuv test.
633    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
634    o pkg/mom_vecinv:
635      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
636        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
637        with non-lin free-surf).
638    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
639      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
640      some compilers (gfortran 4.6.0 on MacOS)
641    o momentum:
642      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
643        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
644        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
645    
646    checkpoint63k (2012/03/17)
647    o model/src:
648       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
649         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
650       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
651         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
652    o model/src: solve_*diagonal.F
653       - replace division with multiplication by inverse (similar to original version)
654         update output of AD exp. global_ocean.90x40x15.
655       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
656         to enable the use of the vectorized & differentiable solve_tridiagonal.F
657       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
658         vertical advection (to get solve_tridiagonal tested in AD mode).
659    o pkg/seaice: ECCO-CLIVAR merge:
660      1. seaice AREA relaxation
661         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
662         * runtime flag: SEAICE_tauAreaObsRelax
663      2. modified global mean cost imbalance code: CPP option
664          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
665    o another iteration on solve_*diagonal.F
666       Make choices independent of AUTODIFF
667       Default will be the adjoinable vectorized version.
668       Alternative choices are:
669       * non-adjoinable original version with low memory footprint:
670         #define SOLVE_DIAGONAL_LOWMEMORY
671       * still adjoinable but does not vectorize (k as inner-most loop):
672         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
673    o testreport
674     - add option to use a home made wrapper around "make"
675     - remove MITGCM_IEEE env. variable (no longer active)
676    o pkg/shelfice
677     - improve computation of friction velocity for velocity dependent
678       exchange coefficients: include velocities into SHELFICEBoundaryLayer
679       block to average velocities vertically
680     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
681    o Modify diagonal solvers, now three versions (upon request):
682      #ifndef SOLVE_DIAGONAL_AUTODIFF
683        1. default version (dating back a while ago)
684      #else /* def SOLVE_DIAGONAL_AUTODIFF */
685      # ifdef SOLVE_DIAGONAL_KINNER
686        2. adjoinable version with k-innermost loop (G. Forget)
687      # else
688        3. adjoinable vectorized version of 2.
689      # endif
690      #endif /* SOLVE_DIAGONAL_AUTODIFF */
691      All flags are currently set within routines, but could/should be moved to CPP-options.
692      Array bounds for 1. are as before, for 2.,3. cover the entire domain
693      (could be changed for 1. too).
694    o verification/lab_sea (fwd):
695      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
696        use 7 categories (except hb87), new solve4temp params (except salt_plume),
697        constant salinity (=4) or variable salinity (salt_plume) done through
698        SItracer.
699    o pkg/seaice:
700      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
701      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
702         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
703        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
704        SEAICE_freeze got retired) but already better than previously with
705        SEAICE_freeze=123456.7 deg.C;
706      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
707        (safer multi-threaded setting); always set SEAICEuseEVP;
708      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
709        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
710        stop if multiple specifications for the same coeff; make sure default
711        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
712    o pkg/obcs:
713      - allow to switch to upwind 1rst order advection scheme for the advective
714        flux computation at the open-boundary; disabled for adjoint built.
715    o pkg/ptracers:
716      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
717      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
718      - add parameter to decide when to start a tracer; use internal flag to
719        know which tracer to step-forward; switch this internal flag at the top
720        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
721        for adjoint built.
722    o pkg/seaice:
723      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
724      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
725      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
726    o pkg/ecco:
727      - fix writing of output file DiagnosCost_ClimSalt/Theta
728        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
729    o pkg/seaice:
730      - add missing initialisation of COR_ICE array in dynsolver.F
731      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
732        compiled either way, and is tested in all exps (multidim was only tested
733        in lab_sea ad before).
734      - cosmetic change to prepare for future addition of ITD. no change to results.
735        no defaults change.
736      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
737      - by lack of adequate verification experiments, I further used custom versions
738        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
739        should be correct.
740      - avoid recomputations in ad.
741    o array initialisation in adjoint mode:
742      1) pkg/mom_common/mom_calc_ke.F:
743        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
744        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
745        part this initialisation is gone, resulting in Floating Point Exception
746        (caught by open64 compiler with debug option).
747      2) model/src/convective_weights.F
748        set output convectCount over the full array range (instead of doing
749        an update): this fix a similar issue when called within recomputation (adjoint)
750        which could by-pass the initialisation (normally done in the caller S/R).
751    o pkg/seaice:
752      - final version of turbulent flux params, as agreed at MIT ice meet:
753           SEAICE_mcPheePiston (default is ~ 0.000875)
754           SEAICE_mcPheeTaper (default is 0.)
755           SEAICE_frazilFrac (defualt is 1.)
756           SEAICE_mcPheeStepFunc (default is false)
757      - changes results at trunction error level
758      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
759    o added pkg/frazil:
760      - see frazil_description.tex for details
761      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
762    o pkg/shelfice/shelfice_thermodynamics.F
763      - fix exponents for velocity dependent exchange coefficients: change
764        from 2/3(=0) to 0.66666666666666667
765      - move computation of velocity dependent exchange coefficients into
766        separate loop, so that it applies to both thermodynamics
767      - move some divisions by constants out of loops
768    
769    checkpoint63j (2012/02/16)
770    o pkg/seaice:
771      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
772      - SItracer:  added run time params, and allow coupling to ocn salinity.
773    o pkg/seaice: remove (almost) all divisions by constants within loops
774      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
775      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
776      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
777      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
778    o pkg/seaice :
779      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
780        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
781      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
782      - add permanent SItflux diag that corresponds to TFLUX but includes
783        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
784      - allow activation/testing of a fix for suspected missing term in
785        ocn-ice heat budget (to be confirmed). To test this, you want to
786        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
787        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
788      - no change in results, fwd or ad.
789    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
790      - switch to variable freezing point.
791           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
792      - bug fix : the sublimation term that was missing is now activated.
793           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
794      - bug fix : flooding sign term for SIsal0.NE.0.
795           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
796    o pkg/seaice:
797      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
798        is now the default, and the old default constant freezing point is recovered
799        with SEAICE_tempFrz0    = -1.96,
800             SEAICE_dTempFrz_dS = 0.,
801      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
802      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
803      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
804        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
805      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
806        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
807      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
808        seaice_growth r149 for legacy branch (no results change).
809      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
810        from I. Fenty).
811      - results did not change except for global_ocean.cs32x15, mostly due to the
812        switch to variable freezing point (see above item for detail).
813    o pkg/thsice:
814      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
815        seawater freezing in thsice_calc_thickn (not used).
816    o pkg/seaice: turbulent flux term specification via run time params.
817      - replace CPP switches with run time switches to facilitate testing
818      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
819                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
820      - added runtime parameter : SEAICEturbFluxFormula
821      - move Mcphee constants to SEAICE_PARAMS.h
822      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
823                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
824                 remove seaice_summary call (moved to seaice_init_fixed)
825      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
826        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
827      - seaice_summary.F : add missing report of read turbulent flux term set up
828                           and SITRACER.
829      - seaice_check.F : check range; inform and stop if retired CPPs are used
830                         (incl. SEAICE_AGE).
831      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
832             CPP switch, same computation as before for the different options.
833      - change results at the truncation level.
834    o pkg/seaice:
835      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
836        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
837        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
838      - update verification/*/input*/data.seaice:
839        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
840        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
841        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
842        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
843    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
844      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
845        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
846        difference in results only due to machine truncation.
847      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
848        MaykutPolySatVap; keep MIN_LWDOWN.
849      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
850      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
851        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
852    o pkg/salt_plume:
853      - isolate saltPlumeFlux array exch into a specific S/R called from
854        do_oceanic_phys.F
855      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
856    o verification:
857      - move untested set-up to MITgcm_contrib/verification_other.
858    o pkg/seaice:
859      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
860    o pkg/seaice:
861      - seaice_solve4temp.F (keeping results unchanged):
862        * add 2 future run-time params to select which saturation vapor pressure
863          formula is used and how post-iteration fluxes are set.
864          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
865        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
866          the linearized expression to stay consistent with tsurf finding.
867      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
868        can be < 0.
869    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
870      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
871        conductive heat flux F_c , and add it explicitly when updating tsurf as
872        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
873        so that now F_ia has a consistent meaning through the entire routine.
874        This causes differences at truncation level: update output of fwd exp.
875        global_ocean.cs32x15.seaice.
876    o pkg/seaice:
877      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
878        of arrays, sign/direction of fluxes; no effect on results.
879      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
880        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
881        note: this should have been done before changing celsius2K default.
882      - to keep results unchanged, add back old value of celsius2K in verification
883        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
884      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
885        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
886        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
887        freezing temp is consistent with value in seaice_growth.F ; this causes
888        differences at machine truncation level: update lab_sea AD output (3/4).
889    o pkg/seaice:
890      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
891        and climsst/sss even when using seaice (to prevent calculation that might
892        use SST on land); does not affect any verification exp.
893      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
894        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
895    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
896      over land (non-legacy code)
897    o vectorize salt_plume package:
898      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
899      - this code computes plumebk everywhere (also over land), thus requires
900        code to avoid divisions by zero and catch the case of kLev=Nr.
901      - efficiency of salt_plume_frac is still sub-optimal
902    o tools (genmake2):
903      - fix makefile NAME specification (option: -makefile NAME) by adding
904        "-f $MAKEFILE" in few places where it was missing including makedepend
905        command (contribution from Paul).
906    
907    checkpoint63i (2012/01/24)
908    o model/src:
909      - add factorized versions of some EOS code to find_rho.F,
910        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
911    o model/src:
912      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
913      - change default celsius2K from 273.16 to 273.15
914      - to keep results unchanged, add back old value of celsius2K in verification
915        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
916         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
917    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
918      to make TAF generate vectorizable code
919    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
920       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
921       have flags that do this more efficiently.
922    o pkg/diagnostics/diagstats_calc.F
923      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
924    o pkg/obcs (with exch2):
925      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
926        and remove code (in obcs_readparms.F) which was based on EXCH of indices
927        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
928    o pkg/exf and seaice exp:
929      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
930        so that switching off area & heff advection flags does not affect results.
931      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
932      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
933        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
934        results of verification experiments: 1D_ocean_ice_column(fwd),
935        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
936        and offline_exf_seaice (all 4).
937    o pkg/seaice:
938      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
939        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
940      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
941        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
942        not multi-dim advection;
943      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
944        SHORTWAVE_HEATING #undef.
945    o optim: make Makefile more robust (?)
946    o pkg/obcs:
947      * fix treatment of obcs_read_pickup for TAF
948    o pkg/shelfice:
949      * add missing initialisation of num_shifwflx
950      * new adjoint verification exp. for isomip
951      * change Prandtl and Schmidt numbers from generic formulations
952        (in terms of model diffus. and visc.) to separate runtime
953        parameters, with Holland and Jenkins (1999) default values.
954    o pkg/exf (interpolation):
955      - extended input field (2 rows) near the N & S poles:
956        * fill in with the symetric value (when even Nb of data in longitude)
957        * add average value at the poles only for scalar quantities ; for vector
958          component interpolation, skip the averaging and keep duplicated values,
959          unless the 2 components have same location (uvInterp=T) in which case
960          interpolate the 2 components together using S/R EXF_INTERP_UV.
961      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
962        together: this allows to account properly for local orientation when
963        averaging at N & S pole.
964      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
965        exf-interpolation near N & S poles. Undef by default.
966      - add debug check/print on 1rst iter if debugLevel >=2.
967    o pkg/exf:
968      - change masking flags definition (no longer "parameter"), put them in
969        common block and set them in S/R EXF_INIT_FIXED.
970      - change recognized masking flag from s,u,v to c,w,s since the mask
971        to use (maskC,W,S) depends on position on model grid and has little to
972        do with scalar/vector difference; fix masking if using P-coordinates.
973      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
974        and update results of exp. global_with_exf (x2).
975      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
976    o pkg/obcs
977      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
978    o pkg/exf (interpolation):
979      - assume periodicity in X only if input field cover full longitude range.
980      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
981        and should vectorise).
982      - fix input lat of the 2 added row (in case we provide N.pole data).
983    
984    checkpoint63h (2011/12/30)
985    o pkg/seaice:
986      - change declaration of UVM from _RL to _RS in order to get B-grid
987        uIce,vIce monitor when _RS = real*4
988    o pkg/offline:
989      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
990      - compute vertical velocity if not read from file (switch on exactConserv
991        & staggerTimeStep);
992      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
993    o verification:
994      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
995        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
996        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
997      - update output of exp. global_ocean.cs32x15.viscA4 after changing
998        grid-file angles (used here for coriolis-3d);
999      - remove (or gzip) few files not needed to run fizhi-cs experiments.
1000    o pkg/exf (vector interpolation):
1001      - rotate vector component toward local grid-axis orientation using grid-angles
1002        (stored in GRID.h) instead of locally computed rotation angle; keep old code
1003        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1004    o pkg/seaice:
1005      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1006        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1007  o pkg/PKG_OPTIONS.h files:  o pkg/PKG_OPTIONS.h files:
1008    - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",    - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1009      outside of the #ifdef ALLOW_THISPKG / #endif block.      outside of the #ifdef ALLOW_THISPKG / #endif block.
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