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revision 1.1641 by dimitri, Mon Apr 2 04:34:07 2012 UTC revision 1.1749 by mlosch, Tue Oct 16 07:08:56 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: add Jacobian-free Newton Krylov solver for ice dynamics
8      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
9      and SEAICEuseJFNK=.true. A few things to note:
10      - involves a FGMRES, that is parallel but very inefficient,
11        because of many scalar products (global sums) in the Gram-Schmidt
12        orthogonalization method. Needs to be replaced. Original code
13        from J.-F. Lemieux
14      - preconditioner for FGMRES is a stripped down version of LSOR
15      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
16        preconditioner. For the preconditioner, the default is set to 10.
17      - Jacobian times vector is computed with finite differences
18      - marginally related to JFNK-solver: add a smooth regularization for
19        zeta with tanh that will improve convergence (Lemieux and Tremblay,
20        2009) for any implicit solver (not implemented for EVP because EVP
21        does not need this regularization in the first place). Define
22        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
23    o eesupp/src:
24      - check in genmake2 that intrinsic S/R flush is available.
25      - add S/R to flush IO unit (if intrinsic S/R flush is available)
26      - flush standard & error msg unit before MPI termination
27      - if debugMode, flush IO unit after printing msg
28    o pkg/ctrl:
29      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
30        to ctrl_set_unpack_xyz.
31    
32    checkpoint64 (2012/10/09)
33    o pkg/shelfice
34      - in mom_fluxform.F, mom_vecinv.F:
35        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
36        Bug fix KappaRU -> KappaRV
37        does not change verification/isomip but may change other setups
38        (presumably constant KappaRU=KappaRV)
39      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
40    o pkg/obcs:
41      - fixed some indexing bugs in obcs_seaice_sponge.F
42      - added obcs relaxation subroutines for HSALT and HSNOW
43      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
44    o pkg/seaice:
45      - add "multicategory" parameterization for snow in analogy to ice,
46        default is off for now.
47    o pkg/obcs:
48      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
49        see verification/seaice_obcs/input.seaiceSponge for example application.
50      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
51        index setting by master-thread. This fix multi-threads Pb in previous modifs.
52    o pkg/layers :
53      - add diagnostics to pkg/layers
54      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
55        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
56    o pkg/generic_advdiff/gad_implicit_r.F :
57      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
58    o pkg/seaice/seaice_growth.F:
59      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
60    o pkg/obcs:
61      - change default setting of OBCS_UVICE_OLD from defined to undef;
62      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
63        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
64      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
65      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
66        with Southern & Western OB at a tile edge (at least in a simple set-up).
67    o pkg/obcs:
68      - change settings of OB index in case OB coincides with tile edge (shared by
69        2 tiles), so that common OB location is registered by both tiles (instead of
70        only 1). However, for Southern and Western OB, index value = 0 is not
71        recognized as valid OB index (=default null value) and needs to be fixed.
72      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
73      - new parameter "OB_indexNone" for null index value (for now, still zero)
74        to replace hard-coded null index value of zero.
75    o pkg/exch2:
76      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
77        always check buffer-size (but outside the loop); move checking for valid
78        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
79        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
80    o pkg/ctrl (pack & unpack):
81      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
82        (locally defined) for different variables (+ remove the variable-specific
83        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
84        (to be extended to other local file names in ctrl.h).
85    o pkg/flt:
86      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
87    o pkg/mdsio:
88      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
89    o tools/genmake2:
90      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
91        (added by Alistair in version 1.51 for building without make depend);
92      - remove Header files list (H_SRC_FILES) from the dependence of targets
93         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
94        place in version 1.23): this save going through staf when unrelated header
95        file has been modified.
96       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
97        "make depend" step, still need to do "make links" before "make adtaf".
98    o eesupp/src (+ few pkg src files) & genmake2:
99      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
100      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
101      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
102         upper/lower case ; account for space between "#" and undef/define)
103    o pkg/flt (with exch2):
104      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
105      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
106    
107    checkpoint63s (2012/09/05)
108    o pkg/ecco:
109      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
110      - add more relevant #ifdef ALLOW_SMOOTH ones.
111      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
112    o pkg/ctrl:
113      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
114        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
115      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
116        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
117        ctrlSmoothCorrel3D (new).
118        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
119      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
120      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
121        controls when useAtmWind, and vice versa.
122      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
123      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
124          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
125      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
126          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
127      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
128        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
129    o pkg/smooth:
130      - remove un-necessary includes.
131      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
132        Those CPP options were never defined, and not necessary.
133    o model/src:
134      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
135      - standard treatment of useSMOOTH.
136    o pkg/autodiff:
137      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
138        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
139    o pkg/exch2:
140      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
141        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
142      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
143        and tiles to process mapping.
144      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
145        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
146        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
147        from w2_eeboot.F to w2_readparms.F.
148    o eesupp/src:
149      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
150        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
151        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
152      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
153        is defined (remove condition on usingMPI) to match cases where MPI_INIT
154        has been called.
155      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
156      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
157        (so that on 1 proc, get same myPid independently of usingMPI)
158      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
159        useCubedSphereExchange with EXCH-1 (safer).
160      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
161    o pkg/ggl90:
162      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
163        used in ALLOW_GGL90_SMOOTH code.
164    o pkg/flt:
165      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
166        floats at the Southern end of the domain).
167    o eesupp/inc:
168      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
169        but not used (and not to be used) anywhere, just for documentation.
170    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
171      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
172        a) can damage previously written records in any other multi-record files.
173        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
174    o tools/genmake2:
175      - define variable MAKE within Makefile and use it in place of 'make';
176      - update AD_CONFIG.h (if needed) before building any of the executable
177        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
178        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
179      - always print usual warning comment 'this file is automatically generated'
180        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
181    o pkg/cheapaml:
182      - updated to correspond to the code used in accepted paper (Nico Wienders).
183    o pkg/exf:
184        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
185        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
186        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
187    o pkg/exf, autodiff, ctrl, ecco and seaice:
188        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
189    o pkg/ctrl, ecco:
190        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
191        Depending on useAtmWind, one is inactive, and the other is active (see
192        exf_getffields.F/exf_getsurfacefluxes.F).
193    o tools/genmake2:
194      - improve error msg when failing in 2nd test of check_for_broken_Ff
195      - fix option '-makefile' short-name (-mf according to genmake2 -help)
196      - source local config file "genmake_local" just after processing the genmake2
197        command arguments (previously done before processing arg).
198    o pkg/grdchk:
199      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
200        to this routine from cost_final has been dropped in g_cost_final)
201      - improve printed information (more explicit msg, no longer using "print *,"
202         fix fcpertminus printed value).
203    o model/src:
204      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
205        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
206        this prevents getting cost-funct reset in adinitialise_varia recomputations.
207    o pkg/dic:
208      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
209        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
210    o pkg/grdchk:
211      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
212      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
213    o pkg/autodiff/ctrl/grdchk :
214      - attempt to sort out what works and what does not,
215        with regard to I/O, and to warn/stop accordingly.
216    o pkg/grdchk:
217      - attempt to fix grdchk in the case of useSingleCpuIO.
218      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
219       statements were moved from grdchk_main.F and into
220       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
221      - a global sum is applied to record numbers icvrec/layer
222       out of grdchk_loc so that they be passed to I/O routines.
223    o pkg/smooth:
224      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
225        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
226    o verification/testreport:
227      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
228      - can also use compressed (gzip) reference output file;
229      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
230        to be easier to collect by testreport.
231      - update existing TLM output (half out-of-date by more than 3 yrs).
232      - report NETCDF & LAPACK settings (from genmake2) in output dir.
233      - report run-time in each individual summary (previously only for AD test);
234        for TLM test, add also TAF version.
235      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
236    
237    checkpoint63r (2012/08/15)
238    o tools/genmake2:
239      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
240    o pkg/ecco/ecco_cost_final.F :
241      - fix fc print statements (to stdout and costfunction0000) so
242        that the printed value is always after the global sum.
243    o pkg/seaice/seaice_dynsolver.F :
244      - fix ice strength assymptote at SEAICE_area_max<1
245        (no change for the standard case of SEAICE_area_max=1)
246    o some cleaning:
247      - pkg source files: ensure that all *.F files from each pkg included the
248        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
249        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
250        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
251        includes;
252      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
253      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
254        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
255        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
256      - update option-file CPP_OPTIONS.h of all AD experiments:
257        * no longer include PACKAGES_CONFIG.h ;
258        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
259        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
260          including ECCO_CPPOPTIONS.h).
261    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
262      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
263        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
264        not necessary accurate).
265      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
266        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
267        deliberately break compilation (a remainder that it needs to be customized)
268      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
269      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
270      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
271    o tools/genamke2:
272      - check for lapack.
273    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
274      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
275        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
276        from both packages.
277      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
278      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
279      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
280        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
281    o pkg/cost : add comments to explain special and/or untested setups.
282    o pkg/exf:
283      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
284        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
285    o verification/*/code_ad:
286      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
287      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
288      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
289        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
290    o pkg/seaice :
291      - added possibility to change ice strength/PRESS0 relationship to
292        HEFF, according to the following run time parameters
293        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
294        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
295        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
296    o pkg/ggl90 :
297      - added run time flag mxlSurfFlag to include the code that ensure
298        mixing between first and second level (previously included as a comment)
299    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
300      - add test of newly added dumpAdByRec=T option where
301        we write all records to one file per variable.
302    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
303      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
304        to check that this code is ok with taf and compiles in adjoint.
305    o pkg/autodiff :
306      - added run time param dumpAdByRec : ad dump format switch.
307        If true then write all records to one file per variable.
308        Else write one file per record (remains the default).
309      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
310    o pkg/seaice:
311     - Added SEAICEuseTILT run time switch : if set to
312       false then omit the tilt term in seaice dynamics.
313     - Fix free drift calculation.
314    o pkg/shelfice:
315      When initializing SHELFICEDragQuadratic, set default to be
316      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
317      but retain option to set it independently
318      (inconsistenty spotted by Veronique Dansereau)
319    o eesupp/inc:
320      - in EEPARAMS.h, add real-type constant for some frequently used simple number
321         (0,1,2,1/2), with name explicitly referring to RS/RL type.
322    o model/src:
323      - move balancing of relaxation terms to new S/R balance_relax.F.
324    o pkg/autodiff:
325      re-write active I/O high-level (control) S/R:
326      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
327      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
328      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
329        MDS_READ/WRITE_FIELD); change loops to multi-threads.
330      - update and merge active_file_control_slice.flow into active_file_control.flow
331      - update the calls in lower level S/R (active_file.F, active_file_g.F and
332        active_file_ad.F) keeping the argument list and function unchanged.
333      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
334        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
335      - new low-level active I/O routines, one for each type (RL/RS), for active var
336        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
337        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
338        right type.
339    o autodiff and RS=real*4:
340      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
341        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
342      - change argument type of 3-D mask argument to _RS to match type in the call
343        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
344    o pkg/thsice:
345      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
346      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
347        fresh-water flux: uniform correction or proportional to local precip.
348    o pkg/ctrl:
349      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
350      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
351                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
352      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
353    
354    checkpoint63q (2012/07/30)
355    o pkg/autodiff:
356      note about monitor and snap-shot of ad-variables:
357      a) need to apply ADEXCH before monitor or output of ad-vars to include
358       overlap contributions (was done for adjDump but missing for monitor).
359      b) since ADEXCH implies adding overlap values to interior array, machine
360       truncation error is expected when adding an ADEXCH call in the middle of
361       the time-stepping (although mathematically identical).
362      modifs:
363      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
364        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
365      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
366        apply ADEXCH before monitor or snap-shot of ad-variables:
367           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
368      - implement new method (copy+adexch) for snap-shot and monitor of main model
369        ad-vars (initially not used by default -> output unchanged).
370      - change default (set to 2) to use new method and update few output_adm.txt
371        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
372        and both tutorial_tracer_adjsens tests).
373      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
374        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
375    o pkg/ctrl:
376      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
377      generic control variables via
378      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
379      Only required customization should be S/R ctrl_map_ini_genarr.F
380      (routine in repository contains example)
381    o pkg/exf:
382      - fix and refine checking of surface-relaxation setting when using EXF
383    o verification (adjoint exp):
384      - reduce length of simulation by half for experiment global_ocean.cs32x15
385        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
386    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
387      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
388        of KE that can occur with aggressive optimization
389      + put quadratic bottom drag calculation in separated loops (only done if
390        using bottomDragQuadratic)
391    o model/src: CG2D_NSA
392      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
393         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
394      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
395         change cg2d residual target to be expressed in Wunits (=> do not normalise
396         RHS ; this fix global_max Pb with TAF); update output.
397    o verification/tutorial_tracer_adjsens:
398       improve parameter consistency (and get rid of warnings):
399       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
400       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
401       - use staggerTimeStep (for stability) in som81; use default rotation period.
402    o pkg/exch2:
403      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
404        reset to 0 = 1 long line in X)
405    o pkg/mdsio:
406      - fix reading of dimensions from meta file for large-size domain
407    o model/src:
408      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
409      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
410        Cubed-Sphere Exch with CS-corners inside the domain;
411        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
412        globalArea and to set hasWetCSCorners.
413      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
414        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
415      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
416        useCDscheme and useCubedSphereExchange).
417    o pkg/seaice/seaice_growth.F :
418      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
419        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
420        when the previous code was not correct.
421      - in all cases diagnoze the boundary condition mismatch to SIaaflux
422      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
423        that term to QNET (essentially to set the melt/freeze water to 0degC).
424        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
425    o verification/global_ocean.cs32x15/input.seaice :
426      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
427      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
428      - update results (output.seaice.txt) accordingly.
429    o verification/lab_sea/input/data.seaice :
430      - remove SEAICEheatConsFix, which is now be tested
431        in global_ocean.cs32x15. The presently coded fix
432        is only consistent with real fresh water + nlfs.
433      - update results (output.txt) accordingly.
434    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
435    o AD_CONFIG.h file:
436      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
437      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
438        add it explicitly in each fortran src file where it is needed.
439        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
440        thus introducing potentially wrong dependency; therefore, better to include
441        it only where it's really needed, and after any other included OPTIONS file
442        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
443        or ALLOW_TANGENTLINEAR_RUN).
444    
445    checkpoint63p (2012/07/06)
446    o pkg/autodiff:
447      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
448      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
449        which are now read from new parameter file "data.autodiff" (inAdExact
450        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
451      - add file "data.autodiff" in all verification/*/input_ad/ directories.
452      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
453        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
454    o verification/tutorial_tracer_adjsens/
455      - add extra sub-verification which uses "SOM" advection scheme
456        (2nd Order-Moment Advection Scheme, Prather Limiter) with
457          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
458        and in data:
459          multiDimAdvection=.TRUE.,
460          tempAdvScheme=81,
461          saltAdvScheme=81,
462    o model/src:
463      - introduce ALLOW_BALANCE_RELAX which allow the removal
464       of the global mean of relaxation terms by setting
465       balanceThetaClimRelax and balanceSaltClimRelax
466      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
467       This case is now treated appropriately in seaice_growth.F
468    o pkg/seaice:
469      - do balanceEmPmR and balanceQnet based on the net fluxes
470        (SItflux) that enter the ocean+ice system rather than QNET
471        and EMPMR. Works best in real fresh water.
472      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
473        out of the diagnotics bloc, and stored in global arrays.
474    
475    checkpoint63o (2012/06/29)
476    o vertical mixing schemes:
477      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
478      - replace computation of density (in Function STATE1, opps_calc.F) by a call
479        to S/R FIND_RHO_SCALAR
480      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
481        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
482        affects output (vermix.ggl90) at truncation level.
483    o testreport:
484      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
485        (nSx,nSy) for the number of threads (from eedata.mth)
486    o model/src:
487      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
488        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
489    o verification/tutorial_tracer_adjsens/
490      - compile with ALLOW_CG2D_NSA
491      - run with nonlinFreeSurf=3
492      - update reference output_adm.txt
493    o tools/genmake2:
494      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
495        refine usePROFILES switching off (only when NetCDF is not available).
496    o verification (atmospheric set-up):
497      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
498    o pkg/profiles : refine profiles and files handling.
499    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
500    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
501      - changes to use model/src/the_main_loop.F rather than the ecco version
502        in ecco type adjoint runs.
503    o model/src:
504      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
505      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
506      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
507    o model/src:
508      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
509        update output of test experiment bottom_ctrl_5x5.
510    o pkg/generic_advdiff:
511      - implement vertical bi-harmonic diffusion (for now, only for T & S and
512        only explicitly).
513    o verification/bottom_ctrl_5x5/
514      update reference output (results changed quite some time ago,
515      not sure when; but new reference results look ok in terms of grdchk)
516    o verification/1D_ocean_ice_column/
517      For verification purposes, the exact adjoint rather than an approx.
518      should be used (e.g., to comare against F.D. or TLM).
519      removed autodiff_inadmode*_ad.F routines in code_ad/
520      Update results/ accordingly.
521    o pkg/cal:
522      - change cal_getdate.F so that output date is function of input time only
523        (less ambiguous, not mixed up with input iteration number).
524      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
525    o pkg/diagnostics:
526      - implement calendarDumps also for stats-diags
527      - implement calendarDumps also for snap-shot output (negative freq)
528      - for now, ignores calendarDumps if non-zero phase-lag.
529    
530    checkpoint63n (2012/06/04)
531    o model/src:
532      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
533        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
534      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
535        similar to calc_r_star.F); update results of experiment internal_wave and
536        tutorial_global_oce_in_p (affected @ truncation level).
537    o pkg/shelfice:
538      - add parameterisation of advective-diffusive flux into the ice shelf
539        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
540      - simply eps3/3a computation
541    o eesupp:
542     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
543       between tiles, just fill-in edges assuming locally periodic subdomain) and
544       add corresponding exchange subroutines (EXCH0);
545     - new CG-solver version (_EX0) for disconnected-tiles special case.
546    o model/src (CG-solvers):
547     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
548       (similar final residual output and max-Iter number as with standard version);
549     - allows to store and use lowest-residual solution (standard & _SR versions);
550     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
551     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
552    o eesup/src:
553     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
554       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
555    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
556    
557    checkpoint63m (2012/04/27)
558    o pkg/shelfice:
559     - account for partical cells in surface level below ice-shelf for hydrostatic
560       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
561    o ad test experiments:
562     - update and rename to "ad_optfile.local" local AD-optfile specific to a
563       particular adjoint verification experiment (in verification/*/code_ad/)
564    o pkg/seaice & pkg/exf:
565     - Part two of ECCO-CLIVAR code merges.
566       Completes merge of seaice area relax. code.
567       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
568       to be set in EXF_OPTIONS.h since this pkg controls its I/O
569       (and avoids second CPP option in SEAICE_OPTIONS.h)
570     - change default value of costIceStart & costIceEnd to a valid date.
571     - add snowPrecip to HSNOW in seaice_growth
572    o pkg/ptracers:
573     - move ptracers summary and setup check into separated S/R ; add a check for
574       valid PTRACERS_Iter0 value (error+stop or just warning).
575    o pkg/cal (+ pkg/ecco):
576     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
577       as input; and for AD, unless both are not differentiable (e.g., k index)).
578    o model/src:
579     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
580       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
581       temporary set to usingZCoords value (to be changed to F when using shelfice).
582     - hydrostatic pressure: implement partial cell near the surface also for
583       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
584       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
585    o pkg/ctrl/ctrl_init.F:
586     - add a formal parameter to s/r ctrl_init_rec to print
587       xx_$(ctrl_valiable)_file for easier debugging
588     - move call of cal_* routines into the if-block where they are really
589       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
590       to specify a startdate
591    o pkg/seaice:
592     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
593       global_ocean.cs32x15/code versions).
594     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
595       verification experiment global_ocean.cs32x15.seaice and update results.
596    o pkg/exf:
597     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
598       (according to useExfYearlyFields).
599    o pkg/cal:
600     - move calendar setting & summary (previously in cal_readparams.F) into new
601       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
602       length of the simulation is set (after SET_PARMS call); This is an attempt
603       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
604     - For safety: keep a record of pkg/cal parameter settings status
605               to allow to STOP if one pkg/cal S/R is called too early.
606     - add a stop in all basic pkg/cal subroutines if called before setting is done.
607     - modify cal_getdate.F: stop when nothing was returned;
608       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
609       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
610    
611    checkpoint63l (2012/04/04)
612    o pkg/bbl:
613      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
614        update global_with_exf output.yearly.txt file.
615    o pkg/cal:
616      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
617      - remove 2 unsused and very short (1 line only) functions ;
618      - remove unsused subroutines from AD-Diff list.
619    o model/src:
620      - start to implement clean wait to stop in initialization S/R (config_check.F,
621         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
622    o folowing PRINT_MESSAGE changes:
623      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
624  o pkg/bbl:  o pkg/bbl:
625    - modification so it can work with z*    - modification so it can work with z*
626    - replace deltaT with dTtracerLev(k) for asynchronous time stepping    - replace deltaT with dTtracerLev(k) for asynchronous time stepping

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