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revision 1.1546 by jmc, Fri Dec 9 01:01:11 2011 UTC revision 1.1744 by dimitri, Tue Sep 25 16:39:20 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/obcs:
8      - fixed some indexing bugs in obcs_seaice_sponge.F
9      - added obcs relaxation subroutines for HSALT and HSNOW
10      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
11    o pkg/seaice:
12      - add "multicategory" parameterization for snow in analogy to ice,
13        default is off for now.
14    o pkg/obcs:
15      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
16        see verification/seaice_obcs/input.seaiceSponge for example application.
17      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
18        index setting by master-thread. This fix multi-threads Pb in previous modifs.
19    o pkg/layers :
20      - add diagnostics to pkg/layers
21      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
22        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
23    o pkg/generic_advdiff/gad_implicit_r.F :
24      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
25    o pkg/seaice/seaice_growth.F:
26      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
27    o pkg/obcs:
28      - change default setting of OBCS_UVICE_OLD from defined to undef;
29      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
30        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
31      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
32      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
33        with Southern & Western OB at a tile edge (at least in a simple set-up).
34    o pkg/obcs:
35      - change settings of OB index in case OB coincides with tile edge (shared by
36        2 tiles), so that common OB location is registered by both tiles (instead of
37        only 1). However, for Southern and Western OB, index value = 0 is not
38        recognized as valid OB index (=default null value) and needs to be fixed.
39      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
40      - new parameter "OB_indexNone" for null index value (for now, still zero)
41        to replace hard-coded null index value of zero.
42    o pkg/exch2:
43      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
44        always check buffer-size (but outside the loop); move checking for valid
45        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
46        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
47    o pkg/ctrl (pack & unpack):
48      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
49        (locally defined) for different variables (+ remove the variable-specific
50        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
51        (to be extended to other local file names in ctrl.h).
52    o pkg/flt:
53      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
54    o pkg/mdsio:
55      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
56    o tools/genmake2:
57      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
58        (added by Alistair in version 1.51 for building without make depend);
59      - remove Header files list (H_SRC_FILES) from the dependence of targets
60         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
61        place in version 1.23): this save going through staf when unrelated header
62        file has been modified.
63       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
64        "make depend" step, still need to do "make links" before "make adtaf".
65    o eesupp/src (+ few pkg src files) & genmake2:
66      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
67      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
68      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
69         upper/lower case ; account for space between "#" and undef/define)
70    o pkg/flt (with exch2):
71      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
72      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
73    
74    checkpoint63s (2012/09/05)
75    o pkg/ecco:
76      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
77      - add more relevant #ifdef ALLOW_SMOOTH ones.
78      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
79    o pkg/ctrl:
80      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
81        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
82      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
83        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
84        ctrlSmoothCorrel3D (new).
85        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
86      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
87      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
88        controls when useAtmWind, and vice versa.
89      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
90      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
91          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
92      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
93          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
94      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
95        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
96    o pkg/smooth:
97      - remove un-necessary includes.
98      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
99        Those CPP options were never defined, and not necessary.
100    o model/src:
101      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
102      - standard treatment of useSMOOTH.
103    o pkg/autodiff:
104      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
105        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
106    o pkg/exch2:
107      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
108        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
109      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
110        and tiles to process mapping.
111      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
112        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
113        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
114        from w2_eeboot.F to w2_readparms.F.
115    o eesupp/src:
116      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
117        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
118        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
119      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
120        is defined (remove condition on usingMPI) to match cases where MPI_INIT
121        has been called.
122      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
123      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
124        (so that on 1 proc, get same myPid independently of usingMPI)
125      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
126        useCubedSphereExchange with EXCH-1 (safer).
127      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
128    o pkg/ggl90:
129      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
130        used in ALLOW_GGL90_SMOOTH code.
131    o pkg/flt:
132      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
133        floats at the Southern end of the domain).
134    o eesupp/inc:
135      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
136        but not used (and not to be used) anywhere, just for documentation.
137    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
138      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
139        a) can damage previously written records in any other multi-record files.
140        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
141    o tools/genmake2:
142      - define variable MAKE within Makefile and use it in place of 'make';
143      - update AD_CONFIG.h (if needed) before building any of the executable
144        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
145        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
146      - always print usual warning comment 'this file is automatically generated'
147        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
148    o pkg/cheapaml:
149      - updated to correspond to the code used in accepted paper (Nico Wienders).
150    o pkg/exf:
151        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
152        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
153        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
154    o pkg/exf, autodiff, ctrl, ecco and seaice:
155        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
156    o pkg/ctrl, ecco:
157        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
158        Depending on useAtmWind, one is inactive, and the other is active (see
159        exf_getffields.F/exf_getsurfacefluxes.F).
160    o tools/genmake2:
161      - improve error msg when failing in 2nd test of check_for_broken_Ff
162      - fix option '-makefile' short-name (-mf according to genmake2 -help)
163      - source local config file "genmake_local" just after processing the genmake2
164        command arguments (previously done before processing arg).
165    o pkg/grdchk:
166      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
167        to this routine from cost_final has been dropped in g_cost_final)
168      - improve printed information (more explicit msg, no longer using "print *,"
169         fix fcpertminus printed value).
170    o model/src:
171      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
172        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
173        this prevents getting cost-funct reset in adinitialise_varia recomputations.
174    o pkg/dic:
175      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
176        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
177    o pkg/grdchk:
178      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
179      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
180    o pkg/autodiff/ctrl/grdchk :
181      - attempt to sort out what works and what does not,
182        with regard to I/O, and to warn/stop accordingly.
183    o pkg/grdchk:
184      - attempt to fix grdchk in the case of useSingleCpuIO.
185      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
186       statements were moved from grdchk_main.F and into
187       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
188      - a global sum is applied to record numbers icvrec/layer
189       out of grdchk_loc so that they be passed to I/O routines.
190    o pkg/smooth:
191      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
192        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
193    o verification/testreport:
194      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
195      - can also use compressed (gzip) reference output file;
196      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
197        to be easier to collect by testreport.
198      - update existing TLM output (half out-of-date by more than 3 yrs).
199      - report NETCDF & LAPACK settings (from genmake2) in output dir.
200      - report run-time in each individual summary (previously only for AD test);
201        for TLM test, add also TAF version.
202      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
203    
204    checkpoint63r (2012/08/15)
205    o tools/genmake2:
206      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
207    o pkg/ecco/ecco_cost_final.F :
208      - fix fc print statements (to stdout and costfunction0000) so
209        that the printed value is always after the global sum.
210    o pkg/seaice/seaice_dynsolver.F :
211      - fix ice strength assymptote at SEAICE_area_max<1
212        (no change for the standard case of SEAICE_area_max=1)
213    o some cleaning:
214      - pkg source files: ensure that all *.F files from each pkg included the
215        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
216        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
217        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
218        includes;
219      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
220      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
221        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
222        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
223      - update option-file CPP_OPTIONS.h of all AD experiments:
224        * no longer include PACKAGES_CONFIG.h ;
225        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
226        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
227          including ECCO_CPPOPTIONS.h).
228    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
229      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
230        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
231        not necessary accurate).
232      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
233        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
234        deliberately break compilation (a remainder that it needs to be customized)
235      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
236      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
237      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
238    o tools/genamke2:
239      - check for lapack.
240    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
241      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
242        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
243        from both packages.
244      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
245      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
246      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
247        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
248    o pkg/cost : add comments to explain special and/or untested setups.
249    o pkg/exf:
250      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
251        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
252    o verification/*/code_ad:
253      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
254      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
255      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
256        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
257    o pkg/seaice :
258      - added possibility to change ice strength/PRESS0 relationship to
259        HEFF, according to the following run time parameters
260        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
261        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
262        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
263    o pkg/ggl90 :
264      - added run time flag mxlSurfFlag to include the code that ensure
265        mixing between first and second level (previously included as a comment)
266    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
267      - add test of newly added dumpAdByRec=T option where
268        we write all records to one file per variable.
269    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
270      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
271        to check that this code is ok with taf and compiles in adjoint.
272    o pkg/autodiff :
273      - added run time param dumpAdByRec : ad dump format switch.
274        If true then write all records to one file per variable.
275        Else write one file per record (remains the default).
276      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
277    o pkg/seaice:
278     - Added SEAICEuseTILT run time switch : if set to
279       false then omit the tilt term in seaice dynamics.
280     - Fix free drift calculation.
281    o pkg/shelfice:
282      When initializing SHELFICEDragQuadratic, set default to be
283      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
284      but retain option to set it independently
285      (inconsistenty spotted by Veronique Dansereau)
286    o eesupp/inc:
287      - in EEPARAMS.h, add real-type constant for some frequently used simple number
288         (0,1,2,1/2), with name explicitly referring to RS/RL type.
289    o model/src:
290      - move balancing of relaxation terms to new S/R balance_relax.F.
291    o pkg/autodiff:
292      re-write active I/O high-level (control) S/R:
293      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
294      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
295      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
296        MDS_READ/WRITE_FIELD); change loops to multi-threads.
297      - update and merge active_file_control_slice.flow into active_file_control.flow
298      - update the calls in lower level S/R (active_file.F, active_file_g.F and
299        active_file_ad.F) keeping the argument list and function unchanged.
300      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
301        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
302      - new low-level active I/O routines, one for each type (RL/RS), for active var
303        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
304        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
305        right type.
306    o autodiff and RS=real*4:
307      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
308        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
309      - change argument type of 3-D mask argument to _RS to match type in the call
310        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
311    o pkg/thsice:
312      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
313      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
314        fresh-water flux: uniform correction or proportional to local precip.
315    o pkg/ctrl:
316      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
317      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
318                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
319      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
320    
321    checkpoint63q (2012/07/30)
322    o pkg/autodiff:
323      note about monitor and snap-shot of ad-variables:
324      a) need to apply ADEXCH before monitor or output of ad-vars to include
325       overlap contributions (was done for adjDump but missing for monitor).
326      b) since ADEXCH implies adding overlap values to interior array, machine
327       truncation error is expected when adding an ADEXCH call in the middle of
328       the time-stepping (although mathematically identical).
329      modifs:
330      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
331        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
332      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
333        apply ADEXCH before monitor or snap-shot of ad-variables:
334           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
335      - implement new method (copy+adexch) for snap-shot and monitor of main model
336        ad-vars (initially not used by default -> output unchanged).
337      - change default (set to 2) to use new method and update few output_adm.txt
338        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
339        and both tutorial_tracer_adjsens tests).
340      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
341        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
342    o pkg/ctrl:
343      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
344      generic control variables via
345      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
346      Only required customization should be S/R ctrl_map_ini_genarr.F
347      (routine in repository contains example)
348    o pkg/exf:
349      - fix and refine checking of surface-relaxation setting when using EXF
350    o verification (adjoint exp):
351      - reduce length of simulation by half for experiment global_ocean.cs32x15
352        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
353    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
354      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
355        of KE that can occur with aggressive optimization
356      + put quadratic bottom drag calculation in separated loops (only done if
357        using bottomDragQuadratic)
358    o model/src: CG2D_NSA
359      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
360         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
361      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
362         change cg2d residual target to be expressed in Wunits (=> do not normalise
363         RHS ; this fix global_max Pb with TAF); update output.
364    o verification/tutorial_tracer_adjsens:
365       improve parameter consistency (and get rid of warnings):
366       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
367       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
368       - use staggerTimeStep (for stability) in som81; use default rotation period.
369    o pkg/exch2:
370      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
371        reset to 0 = 1 long line in X)
372    o pkg/mdsio:
373      - fix reading of dimensions from meta file for large-size domain
374    o model/src:
375      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
376      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
377        Cubed-Sphere Exch with CS-corners inside the domain;
378        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
379        globalArea and to set hasWetCSCorners.
380      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
381        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
382      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
383        useCDscheme and useCubedSphereExchange).
384    o pkg/seaice/seaice_growth.F :
385      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
386        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
387        when the previous code was not correct.
388      - in all cases diagnoze the boundary condition mismatch to SIaaflux
389      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
390        that term to QNET (essentially to set the melt/freeze water to 0degC).
391        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
392    o verification/global_ocean.cs32x15/input.seaice :
393      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
394      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
395      - update results (output.seaice.txt) accordingly.
396    o verification/lab_sea/input/data.seaice :
397      - remove SEAICEheatConsFix, which is now be tested
398        in global_ocean.cs32x15. The presently coded fix
399        is only consistent with real fresh water + nlfs.
400      - update results (output.txt) accordingly.
401    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
402    o AD_CONFIG.h file:
403      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
404      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
405        add it explicitly in each fortran src file where it is needed.
406        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
407        thus introducing potentially wrong dependency; therefore, better to include
408        it only where it's really needed, and after any other included OPTIONS file
409        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
410        or ALLOW_TANGENTLINEAR_RUN).
411    
412    checkpoint63p (2012/07/06)
413    o pkg/autodiff:
414      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
415      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
416        which are now read from new parameter file "data.autodiff" (inAdExact
417        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
418      - add file "data.autodiff" in all verification/*/input_ad/ directories.
419      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
420        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
421    o verification/tutorial_tracer_adjsens/
422      - add extra sub-verification which uses "SOM" advection scheme
423        (2nd Order-Moment Advection Scheme, Prather Limiter) with
424          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
425        and in data:
426          multiDimAdvection=.TRUE.,
427          tempAdvScheme=81,
428          saltAdvScheme=81,
429    o model/src:
430      - introduce ALLOW_BALANCE_RELAX which allow the removal
431       of the global mean of relaxation terms by setting
432       balanceThetaClimRelax and balanceSaltClimRelax
433      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
434       This case is now treated appropriately in seaice_growth.F
435    o pkg/seaice:
436      - do balanceEmPmR and balanceQnet based on the net fluxes
437        (SItflux) that enter the ocean+ice system rather than QNET
438        and EMPMR. Works best in real fresh water.
439      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
440        out of the diagnotics bloc, and stored in global arrays.
441    
442    checkpoint63o (2012/06/29)
443    o vertical mixing schemes:
444      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
445      - replace computation of density (in Function STATE1, opps_calc.F) by a call
446        to S/R FIND_RHO_SCALAR
447      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
448        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
449        affects output (vermix.ggl90) at truncation level.
450    o testreport:
451      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
452        (nSx,nSy) for the number of threads (from eedata.mth)
453    o model/src:
454      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
455        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
456    o verification/tutorial_tracer_adjsens/
457      - compile with ALLOW_CG2D_NSA
458      - run with nonlinFreeSurf=3
459      - update reference output_adm.txt
460    o tools/genmake2:
461      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
462        refine usePROFILES switching off (only when NetCDF is not available).
463    o verification (atmospheric set-up):
464      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
465    o pkg/profiles : refine profiles and files handling.
466    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
467    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
468      - changes to use model/src/the_main_loop.F rather than the ecco version
469        in ecco type adjoint runs.
470    o model/src:
471      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
472      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
473      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
474    o model/src:
475      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
476        update output of test experiment bottom_ctrl_5x5.
477    o pkg/generic_advdiff:
478      - implement vertical bi-harmonic diffusion (for now, only for T & S and
479        only explicitly).
480    o verification/bottom_ctrl_5x5/
481      update reference output (results changed quite some time ago,
482      not sure when; but new reference results look ok in terms of grdchk)
483    o verification/1D_ocean_ice_column/
484      For verification purposes, the exact adjoint rather than an approx.
485      should be used (e.g., to comare against F.D. or TLM).
486      removed autodiff_inadmode*_ad.F routines in code_ad/
487      Update results/ accordingly.
488    o pkg/cal:
489      - change cal_getdate.F so that output date is function of input time only
490        (less ambiguous, not mixed up with input iteration number).
491      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
492    o pkg/diagnostics:
493      - implement calendarDumps also for stats-diags
494      - implement calendarDumps also for snap-shot output (negative freq)
495      - for now, ignores calendarDumps if non-zero phase-lag.
496    
497    checkpoint63n (2012/06/04)
498    o model/src:
499      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
500        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
501      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
502        similar to calc_r_star.F); update results of experiment internal_wave and
503        tutorial_global_oce_in_p (affected @ truncation level).
504    o pkg/shelfice:
505      - add parameterisation of advective-diffusive flux into the ice shelf
506        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
507      - simply eps3/3a computation
508    o eesupp:
509     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
510       between tiles, just fill-in edges assuming locally periodic subdomain) and
511       add corresponding exchange subroutines (EXCH0);
512     - new CG-solver version (_EX0) for disconnected-tiles special case.
513    o model/src (CG-solvers):
514     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
515       (similar final residual output and max-Iter number as with standard version);
516     - allows to store and use lowest-residual solution (standard & _SR versions);
517     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
518     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
519    o eesup/src:
520     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
521       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
522    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
523    
524    checkpoint63m (2012/04/27)
525    o pkg/shelfice:
526     - account for partical cells in surface level below ice-shelf for hydrostatic
527       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
528    o ad test experiments:
529     - update and rename to "ad_optfile.local" local AD-optfile specific to a
530       particular adjoint verification experiment (in verification/*/code_ad/)
531    o pkg/seaice & pkg/exf:
532     - Part two of ECCO-CLIVAR code merges.
533       Completes merge of seaice area relax. code.
534       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
535       to be set in EXF_OPTIONS.h since this pkg controls its I/O
536       (and avoids second CPP option in SEAICE_OPTIONS.h)
537     - change default value of costIceStart & costIceEnd to a valid date.
538     - add snowPrecip to HSNOW in seaice_growth
539    o pkg/ptracers:
540     - move ptracers summary and setup check into separated S/R ; add a check for
541       valid PTRACERS_Iter0 value (error+stop or just warning).
542    o pkg/cal (+ pkg/ecco):
543     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
544       as input; and for AD, unless both are not differentiable (e.g., k index)).
545    o model/src:
546     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
547       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
548       temporary set to usingZCoords value (to be changed to F when using shelfice).
549     - hydrostatic pressure: implement partial cell near the surface also for
550       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
551       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
552    o pkg/ctrl/ctrl_init.F:
553     - add a formal parameter to s/r ctrl_init_rec to print
554       xx_$(ctrl_valiable)_file for easier debugging
555     - move call of cal_* routines into the if-block where they are really
556       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
557       to specify a startdate
558    o pkg/seaice:
559     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
560       global_ocean.cs32x15/code versions).
561     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
562       verification experiment global_ocean.cs32x15.seaice and update results.
563    o pkg/exf:
564     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
565       (according to useExfYearlyFields).
566    o pkg/cal:
567     - move calendar setting & summary (previously in cal_readparams.F) into new
568       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
569       length of the simulation is set (after SET_PARMS call); This is an attempt
570       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
571     - For safety: keep a record of pkg/cal parameter settings status
572               to allow to STOP if one pkg/cal S/R is called too early.
573     - add a stop in all basic pkg/cal subroutines if called before setting is done.
574     - modify cal_getdate.F: stop when nothing was returned;
575       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
576       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
577    
578    checkpoint63l (2012/04/04)
579    o pkg/bbl:
580      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
581        update global_with_exf output.yearly.txt file.
582    o pkg/cal:
583      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
584      - remove 2 unsused and very short (1 line only) functions ;
585      - remove unsused subroutines from AD-Diff list.
586    o model/src:
587      - start to implement clean wait to stop in initialization S/R (config_check.F,
588         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
589    o folowing PRINT_MESSAGE changes:
590      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
591    o pkg/bbl:
592      - modification so it can work with z*
593      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
594      - global_with_exf/input.yearly verification; changes output.yearly.txt
595    o eesupp/src:
596      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
597        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
598      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
599        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
600      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
601      - when using MPI, always set usingMPI=T ; set default accordingly and stop
602        if not consistent.
603      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
604        argument is zero (in case called within single-thread section).
605    o pkg/fizhi:
606        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
607        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
608    o pkg/exch2:
609      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
610        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
611      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
612        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
613        with bad ones coming from a not-yet-updated halo.
614        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
615    o pkg/frazil:
616        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
617        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
618    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
619    o verification/lab_sea
620      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
621      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
622      * nTimeSteps 3 -> 4
623      * changed reference output accordingly
624    o pkg/ctrl:
625      * fix ctrl_get_gen for xx_sst, xx_sss
626    o pkg/fizhi:
627      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
628        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
629      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
630        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
631        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
632    o pkg/gmredi:
633      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
634    o pkg/fizhi:
635      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
636        (old)aces open64 tuv test.
637    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
638    o pkg/mom_vecinv:
639      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
640        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
641        with non-lin free-surf).
642    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
643      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
644      some compilers (gfortran 4.6.0 on MacOS)
645    o momentum:
646      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
647        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
648        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
649    
650    checkpoint63k (2012/03/17)
651    o model/src:
652       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
653         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
654       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
655         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
656    o model/src: solve_*diagonal.F
657       - replace division with multiplication by inverse (similar to original version)
658         update output of AD exp. global_ocean.90x40x15.
659       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
660         to enable the use of the vectorized & differentiable solve_tridiagonal.F
661       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
662         vertical advection (to get solve_tridiagonal tested in AD mode).
663    o pkg/seaice: ECCO-CLIVAR merge:
664      1. seaice AREA relaxation
665         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
666         * runtime flag: SEAICE_tauAreaObsRelax
667      2. modified global mean cost imbalance code: CPP option
668          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
669    o another iteration on solve_*diagonal.F
670       Make choices independent of AUTODIFF
671       Default will be the adjoinable vectorized version.
672       Alternative choices are:
673       * non-adjoinable original version with low memory footprint:
674         #define SOLVE_DIAGONAL_LOWMEMORY
675       * still adjoinable but does not vectorize (k as inner-most loop):
676         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
677    o testreport
678     - add option to use a home made wrapper around "make"
679     - remove MITGCM_IEEE env. variable (no longer active)
680    o pkg/shelfice
681     - improve computation of friction velocity for velocity dependent
682       exchange coefficients: include velocities into SHELFICEBoundaryLayer
683       block to average velocities vertically
684     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
685    o Modify diagonal solvers, now three versions (upon request):
686      #ifndef SOLVE_DIAGONAL_AUTODIFF
687        1. default version (dating back a while ago)
688      #else /* def SOLVE_DIAGONAL_AUTODIFF */
689      # ifdef SOLVE_DIAGONAL_KINNER
690        2. adjoinable version with k-innermost loop (G. Forget)
691      # else
692        3. adjoinable vectorized version of 2.
693      # endif
694      #endif /* SOLVE_DIAGONAL_AUTODIFF */
695      All flags are currently set within routines, but could/should be moved to CPP-options.
696      Array bounds for 1. are as before, for 2.,3. cover the entire domain
697      (could be changed for 1. too).
698    o verification/lab_sea (fwd):
699      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
700        use 7 categories (except hb87), new solve4temp params (except salt_plume),
701        constant salinity (=4) or variable salinity (salt_plume) done through
702        SItracer.
703    o pkg/seaice:
704      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
705      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
706         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
707        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
708        SEAICE_freeze got retired) but already better than previously with
709        SEAICE_freeze=123456.7 deg.C;
710      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
711        (safer multi-threaded setting); always set SEAICEuseEVP;
712      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
713        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
714        stop if multiple specifications for the same coeff; make sure default
715        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
716    o pkg/obcs:
717      - allow to switch to upwind 1rst order advection scheme for the advective
718        flux computation at the open-boundary; disabled for adjoint built.
719    o pkg/ptracers:
720      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
721      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
722      - add parameter to decide when to start a tracer; use internal flag to
723        know which tracer to step-forward; switch this internal flag at the top
724        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
725        for adjoint built.
726    o pkg/seaice:
727      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
728      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
729      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
730    o pkg/ecco:
731      - fix writing of output file DiagnosCost_ClimSalt/Theta
732        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
733    o pkg/seaice:
734      - add missing initialisation of COR_ICE array in dynsolver.F
735      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
736        compiled either way, and is tested in all exps (multidim was only tested
737        in lab_sea ad before).
738      - cosmetic change to prepare for future addition of ITD. no change to results.
739        no defaults change.
740      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
741      - by lack of adequate verification experiments, I further used custom versions
742        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
743        should be correct.
744      - avoid recomputations in ad.
745    o array initialisation in adjoint mode:
746      1) pkg/mom_common/mom_calc_ke.F:
747        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
748        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
749        part this initialisation is gone, resulting in Floating Point Exception
750        (caught by open64 compiler with debug option).
751      2) model/src/convective_weights.F
752        set output convectCount over the full array range (instead of doing
753        an update): this fix a similar issue when called within recomputation (adjoint)
754        which could by-pass the initialisation (normally done in the caller S/R).
755    o pkg/seaice:
756      - final version of turbulent flux params, as agreed at MIT ice meet:
757           SEAICE_mcPheePiston (default is ~ 0.000875)
758           SEAICE_mcPheeTaper (default is 0.)
759           SEAICE_frazilFrac (defualt is 1.)
760           SEAICE_mcPheeStepFunc (default is false)
761      - changes results at trunction error level
762      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
763    o added pkg/frazil:
764      - see frazil_description.tex for details
765      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
766    o pkg/shelfice/shelfice_thermodynamics.F
767      - fix exponents for velocity dependent exchange coefficients: change
768        from 2/3(=0) to 0.66666666666666667
769      - move computation of velocity dependent exchange coefficients into
770        separate loop, so that it applies to both thermodynamics
771      - move some divisions by constants out of loops
772    
773    checkpoint63j (2012/02/16)
774    o pkg/seaice:
775      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
776      - SItracer:  added run time params, and allow coupling to ocn salinity.
777    o pkg/seaice: remove (almost) all divisions by constants within loops
778      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
779      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
780      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
781      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
782    o pkg/seaice :
783      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
784        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
785      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
786      - add permanent SItflux diag that corresponds to TFLUX but includes
787        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
788      - allow activation/testing of a fix for suspected missing term in
789        ocn-ice heat budget (to be confirmed). To test this, you want to
790        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
791        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
792      - no change in results, fwd or ad.
793    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
794      - switch to variable freezing point.
795           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
796      - bug fix : the sublimation term that was missing is now activated.
797           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
798      - bug fix : flooding sign term for SIsal0.NE.0.
799           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
800    o pkg/seaice:
801      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
802        is now the default, and the old default constant freezing point is recovered
803        with SEAICE_tempFrz0    = -1.96,
804             SEAICE_dTempFrz_dS = 0.,
805      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
806      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
807      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
808        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
809      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
810        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
811      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
812        seaice_growth r149 for legacy branch (no results change).
813      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
814        from I. Fenty).
815      - results did not change except for global_ocean.cs32x15, mostly due to the
816        switch to variable freezing point (see above item for detail).
817    o pkg/thsice:
818      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
819        seawater freezing in thsice_calc_thickn (not used).
820    o pkg/seaice: turbulent flux term specification via run time params.
821      - replace CPP switches with run time switches to facilitate testing
822      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
823                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
824      - added runtime parameter : SEAICEturbFluxFormula
825      - move Mcphee constants to SEAICE_PARAMS.h
826      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
827                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
828                 remove seaice_summary call (moved to seaice_init_fixed)
829      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
830        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
831      - seaice_summary.F : add missing report of read turbulent flux term set up
832                           and SITRACER.
833      - seaice_check.F : check range; inform and stop if retired CPPs are used
834                         (incl. SEAICE_AGE).
835      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
836             CPP switch, same computation as before for the different options.
837      - change results at the truncation level.
838    o pkg/seaice:
839      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
840        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
841        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
842      - update verification/*/input*/data.seaice:
843        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
844        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
845        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
846        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
847    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
848      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
849        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
850        difference in results only due to machine truncation.
851      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
852        MaykutPolySatVap; keep MIN_LWDOWN.
853      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
854      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
855        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
856    o pkg/salt_plume:
857      - isolate saltPlumeFlux array exch into a specific S/R called from
858        do_oceanic_phys.F
859      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
860    o verification:
861      - move untested set-up to MITgcm_contrib/verification_other.
862    o pkg/seaice:
863      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
864    o pkg/seaice:
865      - seaice_solve4temp.F (keeping results unchanged):
866        * add 2 future run-time params to select which saturation vapor pressure
867          formula is used and how post-iteration fluxes are set.
868          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
869        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
870          the linearized expression to stay consistent with tsurf finding.
871      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
872        can be < 0.
873    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
874      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
875        conductive heat flux F_c , and add it explicitly when updating tsurf as
876        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
877        so that now F_ia has a consistent meaning through the entire routine.
878        This causes differences at truncation level: update output of fwd exp.
879        global_ocean.cs32x15.seaice.
880    o pkg/seaice:
881      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
882        of arrays, sign/direction of fluxes; no effect on results.
883      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
884        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
885        note: this should have been done before changing celsius2K default.
886      - to keep results unchanged, add back old value of celsius2K in verification
887        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
888      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
889        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
890        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
891        freezing temp is consistent with value in seaice_growth.F ; this causes
892        differences at machine truncation level: update lab_sea AD output (3/4).
893    o pkg/seaice:
894      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
895        and climsst/sss even when using seaice (to prevent calculation that might
896        use SST on land); does not affect any verification exp.
897      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
898        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
899    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
900      over land (non-legacy code)
901    o vectorize salt_plume package:
902      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
903      - this code computes plumebk everywhere (also over land), thus requires
904        code to avoid divisions by zero and catch the case of kLev=Nr.
905      - efficiency of salt_plume_frac is still sub-optimal
906    o tools (genmake2):
907      - fix makefile NAME specification (option: -makefile NAME) by adding
908        "-f $MAKEFILE" in few places where it was missing including makedepend
909        command (contribution from Paul).
910    
911    checkpoint63i (2012/01/24)
912    o model/src:
913      - add factorized versions of some EOS code to find_rho.F,
914        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
915    o model/src:
916      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
917      - change default celsius2K from 273.16 to 273.15
918      - to keep results unchanged, add back old value of celsius2K in verification
919        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
920         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
921    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
922      to make TAF generate vectorizable code
923    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
924       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
925       have flags that do this more efficiently.
926    o pkg/diagnostics/diagstats_calc.F
927      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
928    o pkg/obcs (with exch2):
929      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
930        and remove code (in obcs_readparms.F) which was based on EXCH of indices
931        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
932    o pkg/exf and seaice exp:
933      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
934        so that switching off area & heff advection flags does not affect results.
935      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
936      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
937        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
938        results of verification experiments: 1D_ocean_ice_column(fwd),
939        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
940        and offline_exf_seaice (all 4).
941    o pkg/seaice:
942      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
943        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
944      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
945        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
946        not multi-dim advection;
947      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
948        SHORTWAVE_HEATING #undef.
949    o optim: make Makefile more robust (?)
950    o pkg/obcs:
951      * fix treatment of obcs_read_pickup for TAF
952    o pkg/shelfice:
953      * add missing initialisation of num_shifwflx
954      * new adjoint verification exp. for isomip
955      * change Prandtl and Schmidt numbers from generic formulations
956        (in terms of model diffus. and visc.) to separate runtime
957        parameters, with Holland and Jenkins (1999) default values.
958    o pkg/exf (interpolation):
959      - extended input field (2 rows) near the N & S poles:
960        * fill in with the symetric value (when even Nb of data in longitude)
961        * add average value at the poles only for scalar quantities ; for vector
962          component interpolation, skip the averaging and keep duplicated values,
963          unless the 2 components have same location (uvInterp=T) in which case
964          interpolate the 2 components together using S/R EXF_INTERP_UV.
965      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
966        together: this allows to account properly for local orientation when
967        averaging at N & S pole.
968      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
969        exf-interpolation near N & S poles. Undef by default.
970      - add debug check/print on 1rst iter if debugLevel >=2.
971    o pkg/exf:
972      - change masking flags definition (no longer "parameter"), put them in
973        common block and set them in S/R EXF_INIT_FIXED.
974      - change recognized masking flag from s,u,v to c,w,s since the mask
975        to use (maskC,W,S) depends on position on model grid and has little to
976        do with scalar/vector difference; fix masking if using P-coordinates.
977      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
978        and update results of exp. global_with_exf (x2).
979      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
980    o pkg/obcs
981      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
982    o pkg/exf (interpolation):
983      - assume periodicity in X only if input field cover full longitude range.
984      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
985        and should vectorise).
986      - fix input lat of the 2 added row (in case we provide N.pole data).
987    
988    checkpoint63h (2011/12/30)
989    o pkg/seaice:
990      - change declaration of UVM from _RL to _RS in order to get B-grid
991        uIce,vIce monitor when _RS = real*4
992    o pkg/offline:
993      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
994      - compute vertical velocity if not read from file (switch on exactConserv
995        & staggerTimeStep);
996      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
997    o verification:
998      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
999        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1000        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1001      - update output of exp. global_ocean.cs32x15.viscA4 after changing
1002        grid-file angles (used here for coriolis-3d);
1003      - remove (or gzip) few files not needed to run fizhi-cs experiments.
1004    o pkg/exf (vector interpolation):
1005      - rotate vector component toward local grid-axis orientation using grid-angles
1006        (stored in GRID.h) instead of locally computed rotation angle; keep old code
1007        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1008    o pkg/seaice:
1009      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1010        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1011    o pkg/PKG_OPTIONS.h files:
1012      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1013        outside of the #ifdef ALLOW_THISPKG / #endif block.
1014      - update verification/*/code/PKG_OPTIONS.h files.
1015    o add a verification experiment (offline_exf_seaice/input.seaice) that test
1016      the B-grid LSOR solver
1017    o pkg/seaice: sort out emissivity and long wave radiation step 2:
1018      - add emissivity for snow and ice as new run-time parameters
1019        (unfortunately) that default to the corresponding exf values; this
1020        changes results in most verification experiments so that for backward
1021        compatibility these parameter have to be set explicitly to inconsistent
1022        values (ugly);
1023      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1024        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1025        until we agree how to handle this bug properly
1026    o pkg/exf (interpolation):
1027      - add a set of run-time param ({inputfield}_interpMethod), one for
1028        each interpolated input field, to select the interpolation method
1029        with a value of zero switching off the interpolation;
1030      - print interpolation parameters to standard output;
1031      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1032        (to use instead runoff_interpMethod=0 in data.exf).
1033      - simplify default setting of interpolation parameters (for all fields,
1034        set position to match model grid cell-center position, leading to trivial
1035        interpolation in case of regular Lat-Lon grid) and fix for the case of
1036        non-uniform delY.
1037    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1038       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1039       this factor is absolutely required, because the lw exitance (= out-going
1040       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1041       where the reflectivity rho = 1-emissivity for conservation reasons. Once
1042       this is established, we can remove the CPP-Flag (if we want to).
1043    o pkg/seaice:
1044      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1045        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1046      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1047        what the name implies (and not emissivity*BoltzmannConstant), this means
1048        the old default value of 5.5e-8 now means
1049        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1050        S/R exf_readparms
1051      - FV-discretization of the B-grid LSOR solver, turn on with
1052        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1053        of the calling routine dynsolver, so that B and C-grid code look a
1054        little more alike.
1055      - fix index bugs in ostres.F (B-grid code)
1056    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1057    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1058      default for SEAICE_emissivity, if useEXF; requires setting a wrong
1059      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1060      backward compatiblity
1061    o model/src: use sigmaR in calc_ivdc
1062    
1063    checkpoint63g (2011/12/16)
1064    o pkg/seaice/seaice_growth.F:
1065      fix heat conservation of the coupled ocean-seaice system.
1066      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1067      solid vs liquid water treatment is resolved via QNET.
1068    o pkg/seaice/seaice_growth.F:
1069      add missing term for sublimation in saltFlux, which was breaking conservation.
1070    o pkg/seaice/seaice_model.F:
1071      Remove this patholigical case treatment in evolution branch,
1072      where it is un-necessary and breaks conservation.
1073      Update global_ocean.cs32x15/results accordingly for
1074      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1075    o model/src:
1076      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1077      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1078    o pkg/obcs:
1079      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1080      tendency for temperature and salinity that is then applied to update
1081      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1082      horizontal advection and diffusion contributions on the boundary (in
1083      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1084      removing the mask in S/R timestep_tracer. The advantage of this approach is
1085      that the updated tracer values include contributions from the surface
1086      forcing and vertical diffusion.
1087      This modification changes exp4.stevens because of vertical diffusion.
1088    o model/src:
1089      change non-curvilinear grid setting to also work with exch2 + blank tiles:
1090      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1091        face dimensions.
1092      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1093        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1094        and INI_SPHERICAL_POLAR_GRID.
1095      change test-experiment global_ocean.90x40x15:
1096      - split the domain in many more tiles (9x4 tiles of 10x10 each);
1097      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1098      - update results of both test (std & dwnslp).
1099    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1100       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1101  o model/src:  o model/src:
1102    - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS    - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1103      and fix initialisation when using sigma-coords.      and fix initialisation when using sigma-coords.
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