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revision 1.255 by heimbach, Wed Feb 18 22:34:52 2004 UTC revision 1.1784 by jmc, Tue Dec 18 01:22:01 2012 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  checkpoint52j_post  o model/src:
8      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
9    o pkg/seaice:
10      - improve description of parameters in seaice_fgmres.F and start
11        cleaning up the code
12      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
13        second argument
14      - add a metric based on grid cell area to SEAICE_SCALPROD; update
15        results of offline_exf_seaice.dyn_jfnk
16      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
17    o pkg/aim_v23:
18      - fix an other bug in dissipation heating (grid-cell area was missing).
19    o model/src + pkg/seaice:
20      - add global (multi-tile) linear solver for pair of tri-diagonal system
21        along X and Y lines, respectively for U and V component.
22        Note: 1) MPI and cube-exchange not yet coded.
23            2) probably not accurate for poorly conditioned / large size problem.
24      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
25        default: not compiled and not used.
26    o pkg/seaice:
27      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
28        introduce bi/bj loops and use global_sum_tile_rl instead of
29        mpi_allreduce in seaice_fgmres.F
30      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
31      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
32      - add a verification experiment for JFNK in offline_exf_seaice
33    o verification:
34      - change (for now, only fwd test) offline_exf_seaice experiment:
35        use a re-entrant channel with idealized costline (trapezoidal shape)
36        at southern boundary to explore seaice dynamics and thermodynamics
37        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
38        secondary test (input.thsice) use thermodynamics only with SST relaxation.
39      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
40    o pkg/exf:
41      - disable "sstExtrapol" when Nr=1
42    o verification:
43      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
44        to test pkg/cheapaml.
45    o pkg/aim_v23 & pkg/shap_filt:
46      - fix dissipation heating (erroneous gravity multiplication factor).
47    o pkg/seaice:
48      - remove unused field pressPre from jfnk solver
49      - rename two subroutines in seaice_preconditioner.F
50    o eesupp/src:
51       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
52    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
53       - remove wrong parts of the rhs and the lhs (were in there
54         because I did not understand the concept of this preconditioner)
55       - add an exchange between u- and v-sweep. This increases communication
56         by a factor of two but improves the convergence of jfnk. Ideally,
57         one would like the u- and v-sweep to be independent. So far within
58         undocumented ifdefs
59       - reorganize the extra computations for printing the residuals
60    o tools/genmake2:
61      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
62        since it's not necessary (and was preventing to use MNC in some cases).
63    
64    checkpoint64a (2012/11/16)
65    o pkg/autodiff:
66      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
67        autodiff_readparms.F no longer depends on calling order (within
68        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
69        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
70        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
71    o pkg/obcs:
72      - adding tidal velocity forcing capability to obcs
73        for usage example, see verification/seaice_obcs/input.tides
74    o pkg/seaice:
75      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
76        SEAICE_LSRrelaxU/V
77      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
78    o pkg/aim_v23:
79      - implement heating from friction (bottom friction and stratospheric drag).
80    o pkg/shap_filt:
81      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
82        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
83    o model/src:
84      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
85        time-constant addMass field from file (addMassFile);
86      - support for heating due to friction (and Kinetic Energy dissipation):
87        add option, run-time switch and 3-D field array + support code ; each pkg
88        or S/R can add heating contribution (if there is a sink of KE); the sum is
89        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
90    o pkg/seaice:
91      - complete merge of ITD code into seaice_growth.F
92        from MITgcm_contrib/torge/itd/code/
93        no verification so far, but Torge Martin tested
94        "1-D test case and Beaufort set up;
95        deliver okay results after 1 model year."
96      - complete merge of SEAICE_SIZE.h into all relevant routines
97      - move computation of eta at Z-points into calc_viscosities
98        + introduce global field etaZ
99        + add different methods for computing etaZ, for now the old
100          method (simple averages of eta to Z-points) is hardwired
101        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
102          seaice_preconditioner
103      - simplify computations for SEAICE_ZETA_SMOOTHREG
104      - seaice_preconditioner:
105        + replace one remaining press by pressLoc (mistake)
106        + adjust printing of residuals
107      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
108        + add (SEAICE.h) and rename some counters (initiliased in
109          seaice_init_fixed.F)
110        + add _BEGIN/END_MASTER (myThid)  around print statements
111        + print total number of iterations and failures over SEAICE_monFreq
112          interval to STDOUT
113      - move control over output-messages by fgmres to seaice_jfnk to save
114        some operations
115      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
116        in order to make restarts with sol .ne. zero (fgmres with restarts)
117        (seaice_jfnk.F, seaice_fgmres.F)
118      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
119        a serious convergence problem when open boundaries are involved
120    o pkg/ggl90: fix computation of control volumes for the case of
121      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
122      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
123    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
124    o pkg/autodiff
125      - Add inAdMode switch for SEAICEuseDYNAMICS:
126        SEAICEuseDYNAMICSinAdMode
127        (extend logic in ADAUTODIFF_INADMODE_SET)
128    o pkg/seaice
129      - Step 1 of merging ice-thickness distribution (ITD) code from
130        MITgcm_contrib/torge/itd/ (author: Torge Martin)
131        The code implements concept laid out in Thorndike et al. (1975);
132        code is enabled via CPP flag SEAICE_ITD
133        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
134        code is not complete yet!!
135      - SEAICE_SIZE.h now included in almost all seaice routines
136    o verification (using seaice):
137      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
138        global_ocean.cs32x15.seaice ; update results.
139      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
140      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
141        offline_exf_seaice (previously compiling B-grid).
142    o pkg/exf:
143      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
144        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
145        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
146    o pkg/layers (adjust changes from Sept 19):
147      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
148        this allows to remove "layers_maxNum" dimension from all layers arrays.
149    o pkg/layers (adjust changes from Sept 19):
150      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
151      - snap-shot extended to all type of layers (not just the 1rst type);
152      - remove layers variables when corresponding CPP option is undef.
153    o pkg/layers:
154      - rename pkg/layers variable and add new output (layer exist & un-weighted
155        velocity in layer)
156    o pkg/seaice:
157      - simplify (?) ocean-drag coefficent computations by using
158        the same routine in all three solvers (saves some code lines)
159      - remove global fields DRAGA and DRAGS from C-grid code and
160        declare them locally in lsr.F (the only place where they are
161        still used)
162      - update AD output of lab_sea.evp (very sensitive anyway).
163    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
164      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
165      and SEAICEuseJFNK=.true. A few things to note:
166      - involves a FGMRES, that is parallel but very inefficient,
167        because of many scalar products (global sums) in the Gram-Schmidt
168        orthogonalization method. Needs to be replaced. Original code
169        from J.-F. Lemieux
170      - preconditioner for FGMRES is a stripped down version of LSOR
171      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
172        preconditioner. For the preconditioner, the default is set to 10.
173      - Jacobian times vector is computed with finite differences
174      - marginally related to JFNK-solver: add a smooth regularization for
175        zeta with tanh that will improve convergence (Lemieux and Tremblay,
176        2009) for any implicit solver (not implemented for EVP because EVP
177        does not need this regularization in the first place). Define
178        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
179    o eesupp/src:
180      - check in genmake2 that intrinsic S/R flush is available.
181      - add S/R to flush IO unit (if intrinsic S/R flush is available)
182      - flush standard & error msg unit before MPI termination
183      - if debugMode, flush IO unit after printing msg
184    o pkg/ctrl:
185      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
186        to ctrl_set_unpack_xyz.
187    
188    checkpoint64 (2012/10/09)
189    o pkg/shelfice
190      - in mom_fluxform.F, mom_vecinv.F:
191        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
192        Bug fix KappaRU -> KappaRV
193        does not change verification/isomip but may change other setups
194        (presumably constant KappaRU=KappaRV)
195      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
196    o pkg/obcs:
197      - fixed some indexing bugs in obcs_seaice_sponge.F
198      - added obcs relaxation subroutines for HSALT and HSNOW
199      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
200    o pkg/seaice:
201      - add "multicategory" parameterization for snow in analogy to ice,
202        default is off for now.
203    o pkg/obcs:
204      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
205        see verification/seaice_obcs/input.seaiceSponge for example application.
206      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
207        index setting by master-thread. This fix multi-threads Pb in previous modifs.
208    o pkg/layers :
209      - add diagnostics to pkg/layers
210      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
211        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
212    o pkg/generic_advdiff/gad_implicit_r.F :
213      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
214    o pkg/seaice/seaice_growth.F:
215      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
216    o pkg/obcs:
217      - change default setting of OBCS_UVICE_OLD from defined to undef;
218      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
219        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
220      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
221      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
222        with Southern & Western OB at a tile edge (at least in a simple set-up).
223    o pkg/obcs:
224      - change settings of OB index in case OB coincides with tile edge (shared by
225        2 tiles), so that common OB location is registered by both tiles (instead of
226        only 1). However, for Southern and Western OB, index value = 0 is not
227        recognized as valid OB index (=default null value) and needs to be fixed.
228      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
229      - new parameter "OB_indexNone" for null index value (for now, still zero)
230        to replace hard-coded null index value of zero.
231    o pkg/exch2:
232      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
233        always check buffer-size (but outside the loop); move checking for valid
234        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
235        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
236    o pkg/ctrl (pack & unpack):
237      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
238        (locally defined) for different variables (+ remove the variable-specific
239        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
240        (to be extended to other local file names in ctrl.h).
241    o pkg/flt:
242      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
243    o pkg/mdsio:
244      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
245    o tools/genmake2:
246      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
247        (added by Alistair in version 1.51 for building without make depend);
248      - remove Header files list (H_SRC_FILES) from the dependence of targets
249         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
250        place in version 1.23): this save going through staf when unrelated header
251        file has been modified.
252       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
253        "make depend" step, still need to do "make links" before "make adtaf".
254    o eesupp/src (+ few pkg src files) & genmake2:
255      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
256      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
257      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
258         upper/lower case ; account for space between "#" and undef/define)
259    o pkg/flt (with exch2):
260      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
261      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
262    
263    checkpoint63s (2012/09/05)
264    o pkg/ecco:
265      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
266      - add more relevant #ifdef ALLOW_SMOOTH ones.
267      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
268    o pkg/ctrl:
269      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
270        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
271      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
272        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
273        ctrlSmoothCorrel3D (new).
274        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
275      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
276      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
277        controls when useAtmWind, and vice versa.
278      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
279      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
280          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
281      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
282          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
283      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
284        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
285    o pkg/smooth:
286      - remove un-necessary includes.
287      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
288        Those CPP options were never defined, and not necessary.
289    o model/src:
290      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
291      - standard treatment of useSMOOTH.
292    o pkg/autodiff:
293      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
294        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
295    o pkg/exch2:
296      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
297        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
298      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
299        and tiles to process mapping.
300      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
301        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
302        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
303        from w2_eeboot.F to w2_readparms.F.
304    o eesupp/src:
305      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
306        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
307        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
308      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
309        is defined (remove condition on usingMPI) to match cases where MPI_INIT
310        has been called.
311      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
312      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
313        (so that on 1 proc, get same myPid independently of usingMPI)
314      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
315        useCubedSphereExchange with EXCH-1 (safer).
316      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
317    o pkg/ggl90:
318      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
319        used in ALLOW_GGL90_SMOOTH code.
320    o pkg/flt:
321      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
322        floats at the Southern end of the domain).
323    o eesupp/inc:
324      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
325        but not used (and not to be used) anywhere, just for documentation.
326    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
327      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
328        a) can damage previously written records in any other multi-record files.
329        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
330    o tools/genmake2:
331      - define variable MAKE within Makefile and use it in place of 'make';
332      - update AD_CONFIG.h (if needed) before building any of the executable
333        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
334        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
335      - always print usual warning comment 'this file is automatically generated'
336        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
337    o pkg/cheapaml:
338      - updated to correspond to the code used in accepted paper (Nico Wienders).
339    o pkg/exf:
340        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
341        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
342        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
343    o pkg/exf, autodiff, ctrl, ecco and seaice:
344        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
345    o pkg/ctrl, ecco:
346        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
347        Depending on useAtmWind, one is inactive, and the other is active (see
348        exf_getffields.F/exf_getsurfacefluxes.F).
349    o tools/genmake2:
350      - improve error msg when failing in 2nd test of check_for_broken_Ff
351      - fix option '-makefile' short-name (-mf according to genmake2 -help)
352      - source local config file "genmake_local" just after processing the genmake2
353        command arguments (previously done before processing arg).
354    o pkg/grdchk:
355      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
356        to this routine from cost_final has been dropped in g_cost_final)
357      - improve printed information (more explicit msg, no longer using "print *,"
358         fix fcpertminus printed value).
359    o model/src:
360      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
361        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
362        this prevents getting cost-funct reset in adinitialise_varia recomputations.
363    o pkg/dic:
364      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
365        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
366    o pkg/grdchk:
367      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
368      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
369    o pkg/autodiff/ctrl/grdchk :
370      - attempt to sort out what works and what does not,
371        with regard to I/O, and to warn/stop accordingly.
372    o pkg/grdchk:
373      - attempt to fix grdchk in the case of useSingleCpuIO.
374      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
375       statements were moved from grdchk_main.F and into
376       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
377      - a global sum is applied to record numbers icvrec/layer
378       out of grdchk_loc so that they be passed to I/O routines.
379    o pkg/smooth:
380      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
381        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
382    o verification/testreport:
383      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
384      - can also use compressed (gzip) reference output file;
385      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
386        to be easier to collect by testreport.
387      - update existing TLM output (half out-of-date by more than 3 yrs).
388      - report NETCDF & LAPACK settings (from genmake2) in output dir.
389      - report run-time in each individual summary (previously only for AD test);
390        for TLM test, add also TAF version.
391      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
392    
393    checkpoint63r (2012/08/15)
394    o tools/genmake2:
395      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
396    o pkg/ecco/ecco_cost_final.F :
397      - fix fc print statements (to stdout and costfunction0000) so
398        that the printed value is always after the global sum.
399    o pkg/seaice/seaice_dynsolver.F :
400      - fix ice strength assymptote at SEAICE_area_max<1
401        (no change for the standard case of SEAICE_area_max=1)
402    o some cleaning:
403      - pkg source files: ensure that all *.F files from each pkg included the
404        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
405        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
406        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
407        includes;
408      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
409      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
410        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
411        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
412      - update option-file CPP_OPTIONS.h of all AD experiments:
413        * no longer include PACKAGES_CONFIG.h ;
414        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
415        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
416          including ECCO_CPPOPTIONS.h).
417    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
418      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
419        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
420        not necessary accurate).
421      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
422        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
423        deliberately break compilation (a remainder that it needs to be customized)
424      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
425      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
426      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
427    o tools/genamke2:
428      - check for lapack.
429    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
430      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
431        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
432        from both packages.
433      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
434      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
435      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
436        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
437    o pkg/cost : add comments to explain special and/or untested setups.
438    o pkg/exf:
439      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
440        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
441    o verification/*/code_ad:
442      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
443      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
444      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
445        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
446    o pkg/seaice :
447      - added possibility to change ice strength/PRESS0 relationship to
448        HEFF, according to the following run time parameters
449        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
450        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
451        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
452    o pkg/ggl90 :
453      - added run time flag mxlSurfFlag to include the code that ensure
454        mixing between first and second level (previously included as a comment)
455    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
456      - add test of newly added dumpAdByRec=T option where
457        we write all records to one file per variable.
458    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
459      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
460        to check that this code is ok with taf and compiles in adjoint.
461    o pkg/autodiff :
462      - added run time param dumpAdByRec : ad dump format switch.
463        If true then write all records to one file per variable.
464        Else write one file per record (remains the default).
465      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
466    o pkg/seaice:
467     - Added SEAICEuseTILT run time switch : if set to
468       false then omit the tilt term in seaice dynamics.
469     - Fix free drift calculation.
470    o pkg/shelfice:
471      When initializing SHELFICEDragQuadratic, set default to be
472      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
473      but retain option to set it independently
474      (inconsistenty spotted by Veronique Dansereau)
475    o eesupp/inc:
476      - in EEPARAMS.h, add real-type constant for some frequently used simple number
477         (0,1,2,1/2), with name explicitly referring to RS/RL type.
478    o model/src:
479      - move balancing of relaxation terms to new S/R balance_relax.F.
480    o pkg/autodiff:
481      re-write active I/O high-level (control) S/R:
482      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
483      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
484      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
485        MDS_READ/WRITE_FIELD); change loops to multi-threads.
486      - update and merge active_file_control_slice.flow into active_file_control.flow
487      - update the calls in lower level S/R (active_file.F, active_file_g.F and
488        active_file_ad.F) keeping the argument list and function unchanged.
489      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
490        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
491      - new low-level active I/O routines, one for each type (RL/RS), for active var
492        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
493        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
494        right type.
495    o autodiff and RS=real*4:
496      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
497        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
498      - change argument type of 3-D mask argument to _RS to match type in the call
499        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
500    o pkg/thsice:
501      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
502      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
503        fresh-water flux: uniform correction or proportional to local precip.
504    o pkg/ctrl:
505      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
506      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
507                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
508      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
509    
510    checkpoint63q (2012/07/30)
511    o pkg/autodiff:
512      note about monitor and snap-shot of ad-variables:
513      a) need to apply ADEXCH before monitor or output of ad-vars to include
514       overlap contributions (was done for adjDump but missing for monitor).
515      b) since ADEXCH implies adding overlap values to interior array, machine
516       truncation error is expected when adding an ADEXCH call in the middle of
517       the time-stepping (although mathematically identical).
518      modifs:
519      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
520        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
521      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
522        apply ADEXCH before monitor or snap-shot of ad-variables:
523           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
524      - implement new method (copy+adexch) for snap-shot and monitor of main model
525        ad-vars (initially not used by default -> output unchanged).
526      - change default (set to 2) to use new method and update few output_adm.txt
527        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
528        and both tutorial_tracer_adjsens tests).
529      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
530        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
531    o pkg/ctrl:
532      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
533      generic control variables via
534      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
535      Only required customization should be S/R ctrl_map_ini_genarr.F
536      (routine in repository contains example)
537    o pkg/exf:
538      - fix and refine checking of surface-relaxation setting when using EXF
539    o verification (adjoint exp):
540      - reduce length of simulation by half for experiment global_ocean.cs32x15
541        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
542    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
543      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
544        of KE that can occur with aggressive optimization
545      + put quadratic bottom drag calculation in separated loops (only done if
546        using bottomDragQuadratic)
547    o model/src: CG2D_NSA
548      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
549         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
550      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
551         change cg2d residual target to be expressed in Wunits (=> do not normalise
552         RHS ; this fix global_max Pb with TAF); update output.
553    o verification/tutorial_tracer_adjsens:
554       improve parameter consistency (and get rid of warnings):
555       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
556       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
557       - use staggerTimeStep (for stability) in som81; use default rotation period.
558    o pkg/exch2:
559      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
560        reset to 0 = 1 long line in X)
561    o pkg/mdsio:
562      - fix reading of dimensions from meta file for large-size domain
563    o model/src:
564      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
565      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
566        Cubed-Sphere Exch with CS-corners inside the domain;
567        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
568        globalArea and to set hasWetCSCorners.
569      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
570        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
571      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
572        useCDscheme and useCubedSphereExchange).
573    o pkg/seaice/seaice_growth.F :
574      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
575        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
576        when the previous code was not correct.
577      - in all cases diagnoze the boundary condition mismatch to SIaaflux
578      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
579        that term to QNET (essentially to set the melt/freeze water to 0degC).
580        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
581    o verification/global_ocean.cs32x15/input.seaice :
582      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
583      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
584      - update results (output.seaice.txt) accordingly.
585    o verification/lab_sea/input/data.seaice :
586      - remove SEAICEheatConsFix, which is now be tested
587        in global_ocean.cs32x15. The presently coded fix
588        is only consistent with real fresh water + nlfs.
589      - update results (output.txt) accordingly.
590    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
591    o AD_CONFIG.h file:
592      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
593      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
594        add it explicitly in each fortran src file where it is needed.
595        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
596        thus introducing potentially wrong dependency; therefore, better to include
597        it only where it's really needed, and after any other included OPTIONS file
598        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
599        or ALLOW_TANGENTLINEAR_RUN).
600    
601    checkpoint63p (2012/07/06)
602    o pkg/autodiff:
603      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
604      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
605        which are now read from new parameter file "data.autodiff" (inAdExact
606        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
607      - add file "data.autodiff" in all verification/*/input_ad/ directories.
608      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
609        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
610    o verification/tutorial_tracer_adjsens/
611      - add extra sub-verification which uses "SOM" advection scheme
612        (2nd Order-Moment Advection Scheme, Prather Limiter) with
613          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
614        and in data:
615          multiDimAdvection=.TRUE.,
616          tempAdvScheme=81,
617          saltAdvScheme=81,
618    o model/src:
619      - introduce ALLOW_BALANCE_RELAX which allow the removal
620       of the global mean of relaxation terms by setting
621       balanceThetaClimRelax and balanceSaltClimRelax
622      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
623       This case is now treated appropriately in seaice_growth.F
624    o pkg/seaice:
625      - do balanceEmPmR and balanceQnet based on the net fluxes
626        (SItflux) that enter the ocean+ice system rather than QNET
627        and EMPMR. Works best in real fresh water.
628      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
629        out of the diagnotics bloc, and stored in global arrays.
630    
631    checkpoint63o (2012/06/29)
632    o vertical mixing schemes:
633      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
634      - replace computation of density (in Function STATE1, opps_calc.F) by a call
635        to S/R FIND_RHO_SCALAR
636      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
637        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
638        affects output (vermix.ggl90) at truncation level.
639    o testreport:
640      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
641        (nSx,nSy) for the number of threads (from eedata.mth)
642    o model/src:
643      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
644        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
645    o verification/tutorial_tracer_adjsens/
646      - compile with ALLOW_CG2D_NSA
647      - run with nonlinFreeSurf=3
648      - update reference output_adm.txt
649    o tools/genmake2:
650      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
651        refine usePROFILES switching off (only when NetCDF is not available).
652    o verification (atmospheric set-up):
653      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
654    o pkg/profiles : refine profiles and files handling.
655    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
656    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
657      - changes to use model/src/the_main_loop.F rather than the ecco version
658        in ecco type adjoint runs.
659    o model/src:
660      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
661      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
662      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
663    o model/src:
664      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
665        update output of test experiment bottom_ctrl_5x5.
666    o pkg/generic_advdiff:
667      - implement vertical bi-harmonic diffusion (for now, only for T & S and
668        only explicitly).
669    o verification/bottom_ctrl_5x5/
670      update reference output (results changed quite some time ago,
671      not sure when; but new reference results look ok in terms of grdchk)
672    o verification/1D_ocean_ice_column/
673      For verification purposes, the exact adjoint rather than an approx.
674      should be used (e.g., to comare against F.D. or TLM).
675      removed autodiff_inadmode*_ad.F routines in code_ad/
676      Update results/ accordingly.
677    o pkg/cal:
678      - change cal_getdate.F so that output date is function of input time only
679        (less ambiguous, not mixed up with input iteration number).
680      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
681    o pkg/diagnostics:
682      - implement calendarDumps also for stats-diags
683      - implement calendarDumps also for snap-shot output (negative freq)
684      - for now, ignores calendarDumps if non-zero phase-lag.
685    
686    checkpoint63n (2012/06/04)
687    o model/src:
688      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
689        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
690      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
691        similar to calc_r_star.F); update results of experiment internal_wave and
692        tutorial_global_oce_in_p (affected @ truncation level).
693    o pkg/shelfice:
694      - add parameterisation of advective-diffusive flux into the ice shelf
695        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
696      - simply eps3/3a computation
697    o eesupp:
698     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
699       between tiles, just fill-in edges assuming locally periodic subdomain) and
700       add corresponding exchange subroutines (EXCH0);
701     - new CG-solver version (_EX0) for disconnected-tiles special case.
702    o model/src (CG-solvers):
703     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
704       (similar final residual output and max-Iter number as with standard version);
705     - allows to store and use lowest-residual solution (standard & _SR versions);
706     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
707     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
708    o eesup/src:
709     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
710       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
711    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
712    
713    checkpoint63m (2012/04/27)
714    o pkg/shelfice:
715     - account for partical cells in surface level below ice-shelf for hydrostatic
716       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
717    o ad test experiments:
718     - update and rename to "ad_optfile.local" local AD-optfile specific to a
719       particular adjoint verification experiment (in verification/*/code_ad/)
720    o pkg/seaice & pkg/exf:
721     - Part two of ECCO-CLIVAR code merges.
722       Completes merge of seaice area relax. code.
723       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
724       to be set in EXF_OPTIONS.h since this pkg controls its I/O
725       (and avoids second CPP option in SEAICE_OPTIONS.h)
726     - change default value of costIceStart & costIceEnd to a valid date.
727     - add snowPrecip to HSNOW in seaice_growth
728    o pkg/ptracers:
729     - move ptracers summary and setup check into separated S/R ; add a check for
730       valid PTRACERS_Iter0 value (error+stop or just warning).
731    o pkg/cal (+ pkg/ecco):
732     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
733       as input; and for AD, unless both are not differentiable (e.g., k index)).
734    o model/src:
735     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
736       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
737       temporary set to usingZCoords value (to be changed to F when using shelfice).
738     - hydrostatic pressure: implement partial cell near the surface also for
739       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
740       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
741    o pkg/ctrl/ctrl_init.F:
742     - add a formal parameter to s/r ctrl_init_rec to print
743       xx_$(ctrl_valiable)_file for easier debugging
744     - move call of cal_* routines into the if-block where they are really
745       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
746       to specify a startdate
747    o pkg/seaice:
748     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
749       global_ocean.cs32x15/code versions).
750     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
751       verification experiment global_ocean.cs32x15.seaice and update results.
752    o pkg/exf:
753     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
754       (according to useExfYearlyFields).
755    o pkg/cal:
756     - move calendar setting & summary (previously in cal_readparams.F) into new
757       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
758       length of the simulation is set (after SET_PARMS call); This is an attempt
759       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
760     - For safety: keep a record of pkg/cal parameter settings status
761               to allow to STOP if one pkg/cal S/R is called too early.
762     - add a stop in all basic pkg/cal subroutines if called before setting is done.
763     - modify cal_getdate.F: stop when nothing was returned;
764       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
765       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
766    
767    checkpoint63l (2012/04/04)
768    o pkg/bbl:
769      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
770        update global_with_exf output.yearly.txt file.
771    o pkg/cal:
772      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
773      - remove 2 unsused and very short (1 line only) functions ;
774      - remove unsused subroutines from AD-Diff list.
775    o model/src:
776      - start to implement clean wait to stop in initialization S/R (config_check.F,
777         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
778    o folowing PRINT_MESSAGE changes:
779      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
780    o pkg/bbl:
781      - modification so it can work with z*
782      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
783      - global_with_exf/input.yearly verification; changes output.yearly.txt
784    o eesupp/src:
785      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
786        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
787      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
788        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
789      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
790      - when using MPI, always set usingMPI=T ; set default accordingly and stop
791        if not consistent.
792      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
793        argument is zero (in case called within single-thread section).
794    o pkg/fizhi:
795        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
796        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
797    o pkg/exch2:
798      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
799        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
800      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
801        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
802        with bad ones coming from a not-yet-updated halo.
803        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
804    o pkg/frazil:
805        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
806        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
807    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
808    o verification/lab_sea
809      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
810      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
811      * nTimeSteps 3 -> 4
812      * changed reference output accordingly
813    o pkg/ctrl:
814      * fix ctrl_get_gen for xx_sst, xx_sss
815    o pkg/fizhi:
816      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
817        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
818      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
819        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
820        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
821    o pkg/gmredi:
822      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
823    o pkg/fizhi:
824      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
825        (old)aces open64 tuv test.
826    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
827    o pkg/mom_vecinv:
828      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
829        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
830        with non-lin free-surf).
831    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
832      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
833      some compilers (gfortran 4.6.0 on MacOS)
834    o momentum:
835      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
836        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
837        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
838    
839    checkpoint63k (2012/03/17)
840    o model/src:
841       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
842         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
843       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
844         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
845    o model/src: solve_*diagonal.F
846       - replace division with multiplication by inverse (similar to original version)
847         update output of AD exp. global_ocean.90x40x15.
848       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
849         to enable the use of the vectorized & differentiable solve_tridiagonal.F
850       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
851         vertical advection (to get solve_tridiagonal tested in AD mode).
852    o pkg/seaice: ECCO-CLIVAR merge:
853      1. seaice AREA relaxation
854         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
855         * runtime flag: SEAICE_tauAreaObsRelax
856      2. modified global mean cost imbalance code: CPP option
857          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
858    o another iteration on solve_*diagonal.F
859       Make choices independent of AUTODIFF
860       Default will be the adjoinable vectorized version.
861       Alternative choices are:
862       * non-adjoinable original version with low memory footprint:
863         #define SOLVE_DIAGONAL_LOWMEMORY
864       * still adjoinable but does not vectorize (k as inner-most loop):
865         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
866    o testreport
867     - add option to use a home made wrapper around "make"
868     - remove MITGCM_IEEE env. variable (no longer active)
869    o pkg/shelfice
870     - improve computation of friction velocity for velocity dependent
871       exchange coefficients: include velocities into SHELFICEBoundaryLayer
872       block to average velocities vertically
873     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
874    o Modify diagonal solvers, now three versions (upon request):
875      #ifndef SOLVE_DIAGONAL_AUTODIFF
876        1. default version (dating back a while ago)
877      #else /* def SOLVE_DIAGONAL_AUTODIFF */
878      # ifdef SOLVE_DIAGONAL_KINNER
879        2. adjoinable version with k-innermost loop (G. Forget)
880      # else
881        3. adjoinable vectorized version of 2.
882      # endif
883      #endif /* SOLVE_DIAGONAL_AUTODIFF */
884      All flags are currently set within routines, but could/should be moved to CPP-options.
885      Array bounds for 1. are as before, for 2.,3. cover the entire domain
886      (could be changed for 1. too).
887    o verification/lab_sea (fwd):
888      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
889        use 7 categories (except hb87), new solve4temp params (except salt_plume),
890        constant salinity (=4) or variable salinity (salt_plume) done through
891        SItracer.
892    o pkg/seaice:
893      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
894      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
895         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
896        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
897        SEAICE_freeze got retired) but already better than previously with
898        SEAICE_freeze=123456.7 deg.C;
899      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
900        (safer multi-threaded setting); always set SEAICEuseEVP;
901      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
902        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
903        stop if multiple specifications for the same coeff; make sure default
904        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
905    o pkg/obcs:
906      - allow to switch to upwind 1rst order advection scheme for the advective
907        flux computation at the open-boundary; disabled for adjoint built.
908    o pkg/ptracers:
909      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
910      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
911      - add parameter to decide when to start a tracer; use internal flag to
912        know which tracer to step-forward; switch this internal flag at the top
913        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
914        for adjoint built.
915    o pkg/seaice:
916      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
917      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
918      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
919    o pkg/ecco:
920      - fix writing of output file DiagnosCost_ClimSalt/Theta
921        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
922    o pkg/seaice:
923      - add missing initialisation of COR_ICE array in dynsolver.F
924      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
925        compiled either way, and is tested in all exps (multidim was only tested
926        in lab_sea ad before).
927      - cosmetic change to prepare for future addition of ITD. no change to results.
928        no defaults change.
929      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
930      - by lack of adequate verification experiments, I further used custom versions
931        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
932        should be correct.
933      - avoid recomputations in ad.
934    o array initialisation in adjoint mode:
935      1) pkg/mom_common/mom_calc_ke.F:
936        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
937        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
938        part this initialisation is gone, resulting in Floating Point Exception
939        (caught by open64 compiler with debug option).
940      2) model/src/convective_weights.F
941        set output convectCount over the full array range (instead of doing
942        an update): this fix a similar issue when called within recomputation (adjoint)
943        which could by-pass the initialisation (normally done in the caller S/R).
944    o pkg/seaice:
945      - final version of turbulent flux params, as agreed at MIT ice meet:
946           SEAICE_mcPheePiston (default is ~ 0.000875)
947           SEAICE_mcPheeTaper (default is 0.)
948           SEAICE_frazilFrac (defualt is 1.)
949           SEAICE_mcPheeStepFunc (default is false)
950      - changes results at trunction error level
951      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
952    o added pkg/frazil:
953      - see frazil_description.tex for details
954      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
955    o pkg/shelfice/shelfice_thermodynamics.F
956      - fix exponents for velocity dependent exchange coefficients: change
957        from 2/3(=0) to 0.66666666666666667
958      - move computation of velocity dependent exchange coefficients into
959        separate loop, so that it applies to both thermodynamics
960      - move some divisions by constants out of loops
961    
962    checkpoint63j (2012/02/16)
963    o pkg/seaice:
964      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
965      - SItracer:  added run time params, and allow coupling to ocn salinity.
966    o pkg/seaice: remove (almost) all divisions by constants within loops
967      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
968      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
969      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
970      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
971    o pkg/seaice :
972      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
973        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
974      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
975      - add permanent SItflux diag that corresponds to TFLUX but includes
976        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
977      - allow activation/testing of a fix for suspected missing term in
978        ocn-ice heat budget (to be confirmed). To test this, you want to
979        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
980        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
981      - no change in results, fwd or ad.
982    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
983      - switch to variable freezing point.
984           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
985      - bug fix : the sublimation term that was missing is now activated.
986           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
987      - bug fix : flooding sign term for SIsal0.NE.0.
988           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
989    o pkg/seaice:
990      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
991        is now the default, and the old default constant freezing point is recovered
992        with SEAICE_tempFrz0    = -1.96,
993             SEAICE_dTempFrz_dS = 0.,
994      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
995      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
996      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
997        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
998      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
999        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1000      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
1001        seaice_growth r149 for legacy branch (no results change).
1002      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1003        from I. Fenty).
1004      - results did not change except for global_ocean.cs32x15, mostly due to the
1005        switch to variable freezing point (see above item for detail).
1006    o pkg/thsice:
1007      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1008        seawater freezing in thsice_calc_thickn (not used).
1009    o pkg/seaice: turbulent flux term specification via run time params.
1010      - replace CPP switches with run time switches to facilitate testing
1011      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1012                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1013      - added runtime parameter : SEAICEturbFluxFormula
1014      - move Mcphee constants to SEAICE_PARAMS.h
1015      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1016                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1017                 remove seaice_summary call (moved to seaice_init_fixed)
1018      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1019        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1020      - seaice_summary.F : add missing report of read turbulent flux term set up
1021                           and SITRACER.
1022      - seaice_check.F : check range; inform and stop if retired CPPs are used
1023                         (incl. SEAICE_AGE).
1024      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1025             CPP switch, same computation as before for the different options.
1026      - change results at the truncation level.
1027    o pkg/seaice:
1028      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1029        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1030        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1031      - update verification/*/input*/data.seaice:
1032        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1033        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1034        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1035        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1036    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1037      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1038        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1039        difference in results only due to machine truncation.
1040      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1041        MaykutPolySatVap; keep MIN_LWDOWN.
1042      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1043      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1044        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1045    o pkg/salt_plume:
1046      - isolate saltPlumeFlux array exch into a specific S/R called from
1047        do_oceanic_phys.F
1048      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1049    o verification:
1050      - move untested set-up to MITgcm_contrib/verification_other.
1051    o pkg/seaice:
1052      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1053    o pkg/seaice:
1054      - seaice_solve4temp.F (keeping results unchanged):
1055        * add 2 future run-time params to select which saturation vapor pressure
1056          formula is used and how post-iteration fluxes are set.
1057          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1058        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1059          the linearized expression to stay consistent with tsurf finding.
1060      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1061        can be < 0.
1062    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1063      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1064        conductive heat flux F_c , and add it explicitly when updating tsurf as
1065        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1066        so that now F_ia has a consistent meaning through the entire routine.
1067        This causes differences at truncation level: update output of fwd exp.
1068        global_ocean.cs32x15.seaice.
1069    o pkg/seaice:
1070      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1071        of arrays, sign/direction of fluxes; no effect on results.
1072      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1073        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1074        note: this should have been done before changing celsius2K default.
1075      - to keep results unchanged, add back old value of celsius2K in verification
1076        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1077      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1078        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1079        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1080        freezing temp is consistent with value in seaice_growth.F ; this causes
1081        differences at machine truncation level: update lab_sea AD output (3/4).
1082    o pkg/seaice:
1083      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1084        and climsst/sss even when using seaice (to prevent calculation that might
1085        use SST on land); does not affect any verification exp.
1086      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1087        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1088    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1089      over land (non-legacy code)
1090    o vectorize salt_plume package:
1091      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1092      - this code computes plumebk everywhere (also over land), thus requires
1093        code to avoid divisions by zero and catch the case of kLev=Nr.
1094      - efficiency of salt_plume_frac is still sub-optimal
1095    o tools (genmake2):
1096      - fix makefile NAME specification (option: -makefile NAME) by adding
1097        "-f $MAKEFILE" in few places where it was missing including makedepend
1098        command (contribution from Paul).
1099    
1100    checkpoint63i (2012/01/24)
1101    o model/src:
1102      - add factorized versions of some EOS code to find_rho.F,
1103        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1104    o model/src:
1105      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1106      - change default celsius2K from 273.16 to 273.15
1107      - to keep results unchanged, add back old value of celsius2K in verification
1108        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1109         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1110    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1111      to make TAF generate vectorizable code
1112    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1113       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1114       have flags that do this more efficiently.
1115    o pkg/diagnostics/diagstats_calc.F
1116      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1117    o pkg/obcs (with exch2):
1118      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1119        and remove code (in obcs_readparms.F) which was based on EXCH of indices
1120        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1121    o pkg/exf and seaice exp:
1122      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1123        so that switching off area & heff advection flags does not affect results.
1124      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1125      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1126        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1127        results of verification experiments: 1D_ocean_ice_column(fwd),
1128        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1129        and offline_exf_seaice (all 4).
1130    o pkg/seaice:
1131      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1132        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
1133      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
1134        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
1135        not multi-dim advection;
1136      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
1137        SHORTWAVE_HEATING #undef.
1138    o optim: make Makefile more robust (?)
1139    o pkg/obcs:
1140      * fix treatment of obcs_read_pickup for TAF
1141    o pkg/shelfice:
1142      * add missing initialisation of num_shifwflx
1143      * new adjoint verification exp. for isomip
1144      * change Prandtl and Schmidt numbers from generic formulations
1145        (in terms of model diffus. and visc.) to separate runtime
1146        parameters, with Holland and Jenkins (1999) default values.
1147    o pkg/exf (interpolation):
1148      - extended input field (2 rows) near the N & S poles:
1149        * fill in with the symetric value (when even Nb of data in longitude)
1150        * add average value at the poles only for scalar quantities ; for vector
1151          component interpolation, skip the averaging and keep duplicated values,
1152          unless the 2 components have same location (uvInterp=T) in which case
1153          interpolate the 2 components together using S/R EXF_INTERP_UV.
1154      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1155        together: this allows to account properly for local orientation when
1156        averaging at N & S pole.
1157      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1158        exf-interpolation near N & S poles. Undef by default.
1159      - add debug check/print on 1rst iter if debugLevel >=2.
1160    o pkg/exf:
1161      - change masking flags definition (no longer "parameter"), put them in
1162        common block and set them in S/R EXF_INIT_FIXED.
1163      - change recognized masking flag from s,u,v to c,w,s since the mask
1164        to use (maskC,W,S) depends on position on model grid and has little to
1165        do with scalar/vector difference; fix masking if using P-coordinates.
1166      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1167        and update results of exp. global_with_exf (x2).
1168      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1169    o pkg/obcs
1170      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1171    o pkg/exf (interpolation):
1172      - assume periodicity in X only if input field cover full longitude range.
1173      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1174        and should vectorise).
1175      - fix input lat of the 2 added row (in case we provide N.pole data).
1176    
1177    checkpoint63h (2011/12/30)
1178    o pkg/seaice:
1179      - change declaration of UVM from _RL to _RS in order to get B-grid
1180        uIce,vIce monitor when _RS = real*4
1181    o pkg/offline:
1182      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1183      - compute vertical velocity if not read from file (switch on exactConserv
1184        & staggerTimeStep);
1185      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1186    o verification:
1187      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1188        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1189        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1190      - update output of exp. global_ocean.cs32x15.viscA4 after changing
1191        grid-file angles (used here for coriolis-3d);
1192      - remove (or gzip) few files not needed to run fizhi-cs experiments.
1193    o pkg/exf (vector interpolation):
1194      - rotate vector component toward local grid-axis orientation using grid-angles
1195        (stored in GRID.h) instead of locally computed rotation angle; keep old code
1196        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1197    o pkg/seaice:
1198      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1199        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1200    o pkg/PKG_OPTIONS.h files:
1201      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1202        outside of the #ifdef ALLOW_THISPKG / #endif block.
1203      - update verification/*/code/PKG_OPTIONS.h files.
1204    o add a verification experiment (offline_exf_seaice/input.seaice) that test
1205      the B-grid LSOR solver
1206    o pkg/seaice: sort out emissivity and long wave radiation step 2:
1207      - add emissivity for snow and ice as new run-time parameters
1208        (unfortunately) that default to the corresponding exf values; this
1209        changes results in most verification experiments so that for backward
1210        compatibility these parameter have to be set explicitly to inconsistent
1211        values (ugly);
1212      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1213        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1214        until we agree how to handle this bug properly
1215    o pkg/exf (interpolation):
1216      - add a set of run-time param ({inputfield}_interpMethod), one for
1217        each interpolated input field, to select the interpolation method
1218        with a value of zero switching off the interpolation;
1219      - print interpolation parameters to standard output;
1220      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1221        (to use instead runoff_interpMethod=0 in data.exf).
1222      - simplify default setting of interpolation parameters (for all fields,
1223        set position to match model grid cell-center position, leading to trivial
1224        interpolation in case of regular Lat-Lon grid) and fix for the case of
1225        non-uniform delY.
1226    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1227       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1228       this factor is absolutely required, because the lw exitance (= out-going
1229       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1230       where the reflectivity rho = 1-emissivity for conservation reasons. Once
1231       this is established, we can remove the CPP-Flag (if we want to).
1232    o pkg/seaice:
1233      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1234        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1235      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1236        what the name implies (and not emissivity*BoltzmannConstant), this means
1237        the old default value of 5.5e-8 now means
1238        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1239        S/R exf_readparms
1240      - FV-discretization of the B-grid LSOR solver, turn on with
1241        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1242        of the calling routine dynsolver, so that B and C-grid code look a
1243        little more alike.
1244      - fix index bugs in ostres.F (B-grid code)
1245    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1246    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1247      default for SEAICE_emissivity, if useEXF; requires setting a wrong
1248      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1249      backward compatiblity
1250    o model/src: use sigmaR in calc_ivdc
1251    
1252    checkpoint63g (2011/12/16)
1253    o pkg/seaice/seaice_growth.F:
1254      fix heat conservation of the coupled ocean-seaice system.
1255      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1256      solid vs liquid water treatment is resolved via QNET.
1257    o pkg/seaice/seaice_growth.F:
1258      add missing term for sublimation in saltFlux, which was breaking conservation.
1259    o pkg/seaice/seaice_model.F:
1260      Remove this patholigical case treatment in evolution branch,
1261      where it is un-necessary and breaks conservation.
1262      Update global_ocean.cs32x15/results accordingly for
1263      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1264    o model/src:
1265      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1266      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1267    o pkg/obcs:
1268      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1269      tendency for temperature and salinity that is then applied to update
1270      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1271      horizontal advection and diffusion contributions on the boundary (in
1272      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1273      removing the mask in S/R timestep_tracer. The advantage of this approach is
1274      that the updated tracer values include contributions from the surface
1275      forcing and vertical diffusion.
1276      This modification changes exp4.stevens because of vertical diffusion.
1277    o model/src:
1278      change non-curvilinear grid setting to also work with exch2 + blank tiles:
1279      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1280        face dimensions.
1281      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1282        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1283        and INI_SPHERICAL_POLAR_GRID.
1284      change test-experiment global_ocean.90x40x15:
1285      - split the domain in many more tiles (9x4 tiles of 10x10 each);
1286      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1287      - update results of both test (std & dwnslp).
1288    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1289       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1290    o model/src:
1291      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1292        and fix initialisation when using sigma-coords.
1293    o model/src:
1294     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1295       to their current value at the beginning of forward_step.F": add a new run-time
1296       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1297     - set doResetHFactors=T in the following test exp:
1298        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1299        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1300        and tutorial_global_oce_in_p (nonLinFS in p)
1301    o pkg/ecco
1302      - added IES cost term
1303    o verification/advect_xz
1304      - scale down the depth by 1/100 (from 200 km to just 2.km)
1305      - add secondary test using divergent flow, r-star and implicit vertical advection.
1306      - add note (check_conserve_TS.txt) and matlab script to check global
1307        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1308    o pkg/rbcs:
1309      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1310    o pkg/obcs (Stevens BCs):
1311      - fix various problems in the phase speed computations of the Stevens
1312        boundary conditions:
1313        - sign error for western and southern boundaries,
1314        - time tendencies were underestimated by factor of dTracerLev and some just
1315          zero (for multidim advection schemes) -> now estimate time tendencies
1316          from difference between previous (n) time level and the one before (n-1);
1317          this requires storing a field per tracer per boundary, also in the pickup
1318          files.
1319        - replace deltaTmom in cflMer/Zon computation with dTracerLev
1320        - set default phase velocity to cflMer/Zon
1321      - update verification experiment exp4.stevens
1322    o pkg/generic_advdiff (implicit_r):
1323      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1324        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1325      - fix implicit vertical diffusion or advection with NonLin FreeSurf
1326        (was using current recip_hFacC instead of future recip_hFacC): set future
1327        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1328        solver S/R ;
1329      - fill diagnostics of vertical advective fluxes (computed from tendency)
1330        when using implicit vert. advection;
1331      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1332         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1333         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1334         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1335    o pkg/diagnostics:
1336      - add diags for T & S tendency which goes through Adams-Bashforth.
1337    
1338    checkpoint63f (2011/11/30)
1339    o pkg/obcs/obcs_calc_stevens.F:
1340      - join some loops to reduce number of if-statements
1341      - fix a bug in code for northern and southern boundaries.
1342    o pkg/seaice/seaice_init_varia.F
1343      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1344        caused zero ice-velocities for the B-grid code
1345    o pkg/seaice/seaice_init_fixed.F
1346      - fix a bug in the initialisation of the second metric terms
1347        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
1348      - this affects all seaice configurations with useCurviLinearGrid = .true.
1349        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
1350        = .true. (default)
1351      - the only verification experiment affected is global_ocean.cs32x15:
1352        icedyn, seaice, and seaice_dynmix (AD)
1353    o pkg/thsice/thsice_diagnostics_state.F
1354      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
1355        not contain garbage that can lead to surprises in diagstats_calc.F
1356    o model/src:
1357      - move bi,bj loops inside INTEGR_CONTINUITY ;
1358      - call INTEGR_CONTINUITY directly from forward_step.F
1359        (previously called from momentum_correction_step.F)
1360      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
1361        forward_step.F and pkg/ecco/the_main_loop.F
1362    o model/src/do_oceanic_phys.F:
1363      - reset addMass to zero only if useICEFRONT ;
1364      - separated k-loop for rhoInSitu calculation ;
1365      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
1366        and at constant T,S (= WdRHOdP);
1367      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
1368        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
1369        transport of locally-referenced potential density);
1370        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
1371    o gluemnc:
1372      - replace ncrcat with ncks when adding variables to *.glob.nc
1373      - change the way variables without record dimensions are handled so that
1374        files that have variables with and without record variables can be glued:
1375        add a record dimension with a new unique name to be able to differentiate
1376        between variable with and without a-prior record dimensions. Remove
1377        this record dimension before adding the variable to the *.glob.nc file.
1378        This procedure automatically works also for grid.*.nc files that do not
1379        have any record dimension.
1380    o verification/cpl_aim+ocn:
1381      - generate new reference output on baudelaire (gfortran, mpich2) (previously
1382        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
1383    o pkg/obcs/obcs_calc_stevens.F:
1384      - add code for northern and southern boundaries.
1385      - reorder some loops to save some operations and so that drFBar can be scalar
1386    o model/src:
1387      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
1388        truncation) and add diagnostics for Adams-Bashforth tendency increment.
1389      - update test-exp. AD output:
1390        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
1391      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
1392        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
1393        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
1394        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
1395        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
1396        tutorial_plume_on_slope.
1397    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
1398      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
1399      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
1400      does not even come with an F77 compiler anymore, this should not be
1401      a limitation
1402    
1403    checkpoint63e (2011/11/06)
1404    o pkg/seaice adjoint of LSR:
1405      - substantially rework STORE dirs.
1406      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
1407        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
1408        and only perform SOLV_MAX_FIXED adjoint iters.
1409        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
1410        always goes to same record, meaning that the last forward field will be
1411        the one used in the adjoint - an approximation.
1412      - now produces non-zero LSR-related gradients, and acceptable gradients for
1413        An's zonal (x-z) test case (to be checked in)
1414      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
1415        (but these are screwed up by the thermodynamics in the first place);
1416        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
1417        output_adm.txt also reflects changes to seaice_lsr
1418      - global_ocean.cs32x15:
1419        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
1420          (output_adm.seaice.txt was updated)
1421        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
1422          (output_adm.seaice_dynmix.txt)
1423    o test-exp. exp4+stevens:
1424      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1425    o pkg/seaice (lsr solver):
1426      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1427        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1428      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1429      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1430        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1431      - compute (with new S/R) and print initial (+ free-driff sol. if available)
1432        and final residual of linearised system.
1433    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1434      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1435    o pkg/obcs: Stevens BCs (still only for east and west)
1436      - fix Stevens BCs by using intermediate velocities of previous
1437        time step as "baroclinic" contribution rather velocity of one grid cell
1438        inside the boundaries; more consistent but makes the entire treatment
1439        more complicated, requires new pickup files and two new S/Rs:
1440        obcs_copy_uv_n and obcs_save_uv_n
1441        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1442        (undefined by default)
1443      - silently move computation of some grid factors into separate loops to
1444        save some recomputations
1445      - add a hack for non-linear free surface
1446      - add a verification experiment to exp4 that tests this code
1447    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1448    
1449    checkpoint63d (2011/10/25)
1450    o pkg/obcs + seaice-dynamics:
1451      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1452        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1453        values (consistent with an implicit method).
1454      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1455        return to older implementation (same results as before); note that none of
1456        the "experimental" OBCS_SEAICE options are implemented in the new version.
1457      - switch test exp. seaice_obcs to use new version (update output).
1458    o pkg/seaice:
1459      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1460      - add parenthesis in Water-Ice drag calculations (evp & lsr);
1461      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1462        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1463      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1464        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1465    o pkg/layers:
1466      - Include potential density as new coordinate (Thanks to David Munday)
1467    o pkg/dic:
1468      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1469        carbonate computation/output to CALC_PCO2_APPROX
1470    o pkg/generic_advdiff
1471      - make TAF generate code that vectorizes:
1472        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1473    o model/src:
1474      - improve vectorization also for adjoint code of
1475        solve_tridiagonal and solve_pentadiagonal. As this requires up to
1476        5 new 3D-fields, this code is only turned on for the combination of
1477        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1478        for singular matrix check (only for TARGET_NEC_SX).
1479      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1480        ALLOW_AUTODIFF. This flag now needs to be set outside of
1481        solve_tri/pentadiagonal.F
1482    o pkg/exf:
1483      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1484        optional namelist EXF_NML_OBCS).
1485      - add many debug-print (to trace down where pkg/cal error msg comes from)
1486    o pkg/mom_vecinv/mom_vi_hdissip.F
1487      - rearrange loops so that vectorization is improved and in particular
1488        the adjoint routine vectorizes. The code is a little longer now, but I
1489        think easier to read.
1490        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1491    o pkg/seaice:
1492      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1493    o pkg/exch2:
1494      - alternative code (without tile x tile matrix) for cumulated (global) sum;
1495        used as default; keep using matrix version in adjustment.cs-32x32x1.
1496    o tools/build_options:
1497      - after merging some MPI and/or multi-threads specific optfiles so that
1498        the modified default optfile support both built (using genmake2 -mpi
1499        for the MPI built, using genmake2 -omp for OpenMP built),
1500        move now obsolete optfiles to tools/build_options/unsupported/
1501       (add copy of email sent to support list in doc/optfiles_changes.txt)
1502    
1503    checkpoint63c (2011/09/28)
1504    o pkg/ebm:
1505      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1506        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1507    o pkg/seaice (SItracer pickup)
1508    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1509      To be done:
1510      - thorough testing of missing fields in S/R seaice_read_pickup
1511      - thorough matching between generic tracers and specific fields used
1512        (e.g. volume-weighted age, area-weighted age, salinity, ...)
1513    o pkg/grdchk:
1514      - all procs calculate and print finite-difference gradient (for testreport)
1515      - change description output used by testreport;
1516      - AD testing: also compare and report Finite-difference gradient;
1517        => update all output_adm*.txt
1518    o test exp. global_ocean_ebm:
1519      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1520        and turn on exactConserve; update (fwd) output.
1521    o pkg/seaice (LSR):
1522      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1523      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1524        * identical results with non-CS topology (but save up to half of EXCH calls)
1525        * no much changes in cs-32 verification tests since no ice at face edges
1526         (differences due to convergence criteria, since nb of iterations changed)
1527        * expect some differences on lat-lon-cap grid.
1528        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1529    o pkg/exch2:
1530      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1531        many tiles); until alternative coding is added, just add a stop.
1532    o pkg/kpp:
1533      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1534        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1535    o optfiles:
1536      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1537        into corresponding standard one, which now support different build:
1538        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1539      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1540    o pkg/obcs (seaice):
1541      - add missing EXCH for uIce,vIce after applying OBCS;
1542      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1543        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1544        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1545      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1546      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1547        and eedata.mth for MPI and mutlti-threaded testing.
1548    o pkg/flt:
1549      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1550      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1551      - fix pickup and trajectories + profiles output with multi-threads;
1552      - add parameter to select group of fields to write along trajectory and
1553        profile (default unchanged);
1554      - only call PORT_RAND* function when flt_noise <> 0;
1555      - add multi-threaded test for verification exp. flt_example.
1556    o eesupp/src:
1557      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1558      - USE_OMP_THREADING: check that number of threads (from eedata) matches
1559        actual number (from env.var. setting).
1560    o pkg/ebm:
1561      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1562      - add multi-threaded test for verification exp. global_ocean_ebm
1563    
1564    checkpoint63b (2011/08/29)
1565    o pkg/ebm:
1566      - fix sign of runoff;
1567      - update directly forcing fields (Qnet,EmPmR) to use standard
1568        external_forcing_surf.F (remove ebm_forcing_surf.F);
1569      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1570      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1571        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1572      - update global_ocean_ebm parameters file data and update output (fwd+ad).
1573    o verification/matrix_example:
1574      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1575        MPI and mutlti-threaded testing.
1576    o pkg/matrix:
1577      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1578      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1579      - fix for multi-threaded (remove DATA statement);
1580      - use standard DIFFERENT_MULTIPLE function;
1581      - add MATRIX_OPTIONS.h
1582    o verification/matrix_example:
1583       To allow to split the domain in several tiles, change the domain size
1584        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1585        Western side) of land points.
1586    o (*_)write_pickup:
1587      - fix few bugs in mypackage_read/write_pickup.F
1588      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1589        array of length 1 (was caught by compiler syntax-check).
1590    o pkg/diagnostics (velocity potential solver):
1591      - fix initialisation of main diagonal matrix (for overlap values)
1592    o tools/build_options:
1593      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1594        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1595      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1596        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1597        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1598        and use "-devel" testreport option for standard testing on baudelaire.
1599    o pkg/grdchk:
1600      - Assume that all gradient-check position are within the same tile
1601        corresponding to global indices (iGloTile,jGloTile) and that
1602        positions (i,j indices or nbeg) are local to this tile;
1603      - set tile local-indices and proc. number according to tile global-indices;
1604      - remove grdchkwhichproc from namelist (retired param);
1605      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1606      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1607    o adding package bbl (Bottom Boundary Layer)
1608      description in MITgcm/pkg/bbl/bbl_description.tex
1609      example/test experiment in MITgcm_contrib/bbl
1610    o adjoint verifications
1611      - changed 5 experiments to multi-tiles
1612        * global_ocean.90x40x15
1613        * obcs_ctrl
1614        * offline_exf_seaice
1615        * tutorial_dic_adjoffline
1616        * tutorial_tracer_adjsens
1617        changed reference output for those that crossed tile boundaries
1618        (changed choices of gradient check positions)
1619      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1620      - temporary bug fix in grdchk_loc.F for obcs
1621    o genmake2 & testreport
1622      - add target "obj" (just for OBJFILES files) to Makefile;
1623      - add option to specify FEXTRAFLAGS on command line.
1624    o pkg/mypackage:
1625      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1626    
1627    checkpoint63a (2011/08/02)
1628    o pkg/diagnostics (velocity potential):
1629      - fix velocity-potential calculation when using OBCS: balance net inflow
1630        at each level (new S/R OBCS_DIAG_BALANCE).
1631      - fix some of the problems with OBCS in stream-function calculation.
1632    o pkg/exf/exf_readparms.F
1633      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1634        EXF_NML_OBCS) more consistent, so that you need not have these lists
1635        in data.exf when they are not used.
1636    o optim/optim_readdata.F:
1637      - add some output about obcs variables that might help debugging
1638      - add a check about nvarlength
1639    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1640    o pkg/diagnostics (velocity potential):
1641      - fix mask for OBCS (still problems in stream-function with OBCS);
1642      - add specific parameter (default = main code CG2D params) for solver;
1643      - in case of poor convergence, use solution corresponding to lowest residual.
1644    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1645      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1646      and should be avoided where possible.
1647    o model/src (rStar):
1648      - include r* effect on reference-state (PhiRef) in totPhiHyd
1649        (so that it's really the potential anomaly at the cell center);
1650        affect solution only if z* with full pressure in EOS.
1651      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1652        update output (because of z* in totPhiHyd and viscA4 changes);
1653      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1654        @ constant r) until interpolation at constant r is implemented.
1655    o pkg/diagnostics
1656      - fix RCENTER diagnostics in case cell center is not at interface middle
1657    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1658      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1659      that THETA and SALT are "conservative temperature" and "absolute
1660      salinity"
1661    o pkg/ctrl
1662      - fix computation of endrec in s/r ctrl_init_rec
1663      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1664    o pkg/seaice/seaice_growth.F
1665      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1666        remove then obsolete STORE directives
1667      - fix STORE directives for tice and tices, so that only the
1668        appropriate part of the fields are stored (and not the entire
1669        field); update global_ocean.cs32x15.seaice AD output.
1670      - cosmetic changes: adjust CPP flags and indentation for better
1671        legibilty
1672    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1673      Chris Wilson)
1674    o pkg/gmredi:
1675       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1676       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1677    
1678    checkpoint63  (2011/07/11)
1679    o pkg/exch2:
1680     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1681     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1682       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1683       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1684    o pkg/diagnostics:
1685     - deal with pairs of post-processed diags which are computed together; in
1686       particular, re-order list of diags within 1 file to save 2nd computation.
1687     - add S/R to compute velocity stream-function (called after velocity-potential
1688       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1689     - add parameter to select grid-point location where PsiVEL == 0.
1690    o eesupp/src:
1691       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1692       (specific S/R needed with exch2 topology - for now, just print an error msg)
1693    o pkg/shelfice
1694     - Implement friction velocity-dependent transfer coefficients following
1695       Holland and Jenkins, JPO, 1999
1696       Original code by M. Losch with small modifs.
1697       Enable with CPP option SHI_ALLOW_GAMMAFRICT
1698       and runtime flag SHELFICEuseGammaFrict
1699    o verification lab_sea & global_ocean.cs32x15:
1700     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1701       does not miss some dependencies (but is slower) and also works with many files
1702       (default makedepend limitation for AD built).
1703     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1704    o pkg/diagnostics:
1705     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1706        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1707       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1708     - Extend the use of "missing_value" setting from data.diagnostics for the case
1709       of counter-diagnostics (where fraction-weight is zero). This applies both to
1710       MNC and MDS output files.
1711    o pkg/seaice/seaice_growth.F:
1712      - add 'a priori' cap of latent heat flux based on actual mass considerations
1713        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1714        non-legacy seaice_solve4temp.
1715      - add diagnostic of the residual sublimation freshwater flux (the freshwater
1716        flux taken from the ocean if the total actual latent heat fluxes exceed
1717        the maximum)
1718      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1719       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1720      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1721       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1722      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1723      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1724    o verification 1D_ocean_ice_column:
1725       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1726       update results
1727    o pkg/diagnostics:
1728     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1729       which are not filled-up but computed from other diags ; In this case, the mate
1730       diag points to the primary (filled-up) diag to used for post processing.
1731     - Update Velocity-potential computation using post-processed diag framework.
1732     ==> Change the ordering of fields and time-periods in MDS output file
1733       when using periodic averaging: now writes one time record with the full set
1734       of fields for this time period, then the next time reccord (it used to be
1735       one field with the full set of time records then the next field).
1736         Note: this is now similar to NetCDF (MNC) output file. <==
1737    
1738    checkpoint62z (2011/06/21)
1739    o adjoint monitor:
1740     - Add adjoint monitor output for packages exf, seaice
1741       and update relevant testreport output
1742    o pkg/seaice:
1743     - re-order diags inits so that they appear in order in available_diagnostics.log
1744     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1745       area/heff/hsnow preceeding thermodynamic growth/melt.
1746     - modified diag: SIdA; output actual effect, as the description states.
1747     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1748     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1749       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1750        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1751     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1752     - added diagnostics for seaice generic tracers (SItr*).
1753     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1754     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1755     I. Fenty: 18-Jun-2011:
1756     Minor changes to seaice package:
1757     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1758        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1759       - Differentiated "regularization variables" from "floor variables"
1760        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1761        * hiceMin became SEAICE_hice_reg (old hiceMin)
1762          (with _reg meaning regularization variable)
1763       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1764        so as to ensure energy conservation when going between phases
1765      - A22 was not used anywhere
1766     2) Changed regularization procedure for heffActual and hsnowActual to ensure
1767        well-boundedness and smooth adjoint in seaice_growth.F
1768     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1769        because the old regularization always set heffActual >= 0.05 cm
1770     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1771        on AREA when HEFF > 0.
1772      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1773        requiring that DISABLE_AREA_FLOOR *not* be defined
1774     Affected verifications:
1775      - 1D_ocean_ice_column (output.txt output_adm.txt)
1776      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1777    o pkg/diagnostics:
1778      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1779      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
1780        (was _RL, now integer) with option = 0 to retrieve all levels.
1781      - add pieces of code to compute velocity potential at each level (new diagnostics
1782        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1783        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
1784      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
1785        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
1786        and in diagnostics_fract_fill.F (do not need a valid pointer for the
1787        diagnostics counter-mate); check that definition of counter-diagnostic
1788        includes a valid counter-mate (in diagnostics_set_levels.F).
1789    o model/src (rStar):
1790      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
1791        affect solution only if z* with full pressure in EOS;
1792        update output of test-exp global_ocean.90x40x15.
1793    o pkg/seaice:
1794      - introduce siEps=1e-5 parameter
1795      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
1796      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
1797      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
1798        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
1799        as well as ice cover age and ridging index (attached to AREA).
1800        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
1801        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
1802        Up to SItrMaxNum=3 tracers can be used simultaneously.
1803    o pkg/salt_plume:
1804      -introduce SPsalFRAC run time parameter that sets the fraction of the
1805       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
1806       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
1807    o model debug options:
1808      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
1809        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
1810      - Refine debug-msg printing selection (3 new levels):
1811        debugMode  : controls printing of debug messages (sequence of S/R calls).
1812        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
1813         debLevZero =  0 ; /* level of disabled aux. msg printing */
1814         debLevA =  1 ; /* level of minimum  aux. msg printing */
1815         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
1816         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
1817         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
1818         debLevE =  5 ; /* level of extensive debug printing */
1819        New debugLevel default: with default debugMode value (=F),
1820          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
1821          and if debugMode=T, default debugLevel = 4 (debLevD).
1822        Relation with previous settings:
1823         debLevB (=2) corresponds to former debLevA (=1)
1824         debLevD (=4) corresponds to former debLevB (=2)
1825        Note:
1826         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
1827         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
1828            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
1829      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
1830        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
1831    o pkg/obcs:
1832      - change OBCSfixTopo default from True to False (should not change the results);
1833        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
1834    o pkg/thsice:
1835      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
1836        2nd layer seaice sublimation (unlikely to happen)
1837      - use Interior mask for OBCS in thsice_advection.F (similar to what is
1838        done in gad_advection & seaice_advection).
1839    o adjoint:
1840      bug fix spotted by Gael Forget:
1841      seaice_advection and thsice_advection still had
1842      legacy CPP options to avoid CS corner updates for adjoint
1843    o pkg/seaice:
1844      => Change some of the defaults (2011/05/29):
1845         - change SEAICEuseFluxForm default (from False to True)
1846         - change DIFF1 default (from 0.004 m/s to 0. m/s)
1847         And print warnings if DIFF1 is not set in data.seaice and centered
1848          avection scheme is used without any diffusion.
1849      also:
1850      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1851      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1852      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1853        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1854        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1855      update results of test exp.:
1856         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1857             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1858             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1859         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1860         seaice_obcs: output (SEAICEuseFluxForm=T)
1861      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1862          for standard fwd & AD lab_sea tests (to keep the same output).
1863    o pkg/seaice/seaice_growth.F:
1864      - use Ian Fenty's capping formulas for actual ice
1865      thickness thoughout EVOLUTION branch.
1866      - put treatment pathological case #2) in CPP brackets
1867      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1868      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1869    o pkg/seaice:
1870      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1871      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1872      also pass fac as a param, which can be 1. (to update the tendency
1873      field) or the time step (to update the field itself).
1874      - seaice_advdiff.F: for multidim, call seaice_diffusion with
1875      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1876      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1877      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1878      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1879    o pkg/seaice:
1880      diffusion with centered advection scheme (diffus.F & advect.F):
1881      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1882        to just compute the laplacian of input-field.
1883      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1884      - fix flux-form version in diffus.F to conserve tracer.
1885      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1886       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1887    
1888    checkpoint62y (2011/05/26)
1889    o pkg/seaice:
1890     - seaice_growth.F : in EVOLUTION branch, always include
1891       a_QSWbyATM_cover in qnet (as it should be).
1892     - verification/global_ocean.cs32x15 : update results accordingly
1893       (output.seaice.txt output_adm.seaice.txt).
1894    o pkg/seaice + obcs:
1895     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1896       equivalent of assuming no tracer gradient outside the OB region.
1897       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
1898     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
1899       after changes above);
1900     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
1901       only at OB location (instead of over a band of OLx width).
1902    o pkg/seaice:
1903     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
1904       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
1905    o pkg/obcs:
1906      - split header file "OBCS.h" into 4 separated files:
1907        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
1908       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
1909         (contain no conditional statement which depends on OBCS options).
1910      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
1911        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
1912    o ctrl, cost, grdchk & autodiff pkgs:
1913      - make options file more standard (like other {PKG}_OPTIONS.h file but
1914        with AD_CONFIG.h); clean-up some of the included header files.
1915    o pkg/obcs:
1916      - do not mask tracer when applying OB (tracer == 0 could generate problems)
1917      - apply tracer OB values to tracer field only at OB location (instead of
1918        over a band of OLx width)
1919      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1920      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1921        obcs_apply_tloc.F & obcs_apply_sloc.F
1922    o obcs in model/src:
1923      - call OBCS_APPLY_W only if NonHydrostatic.
1924      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1925      - reset dEtaHdt and wVel to zero outside OB interior region ;
1926      - leave tracer unchanged outside OB interior region: This has no effect
1927        on the solution but just to prevent unrealistic tracer value outside OB.
1928      - zero out velocity outside OB interior region: This has no effect on
1929        the solution but just to prevent unrealistic velocity outside OB.
1930    o obcs and non-lin free-surf:
1931       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1932       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1933       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1934       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1935       update results of test-exp. exp4(nlfs).
1936    o exp4 (nlfs) test-exp:
1937       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1938       with NonLin-FreeSurf); update output.nlfs.txt
1939    o obcs and 2d/3d solver norm:
1940       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1941       and outside OB interior region (will allow to place OB further inside the
1942       domain). Depending on the domain, can affects cg2d-Norm (previous
1943       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1944       and cg3d-Norm (previous Norm was computed before canceling OB terms),
1945       e.g. in tutorial_plume_on_slope.
1946      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1947    o pkg rbcs:
1948      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1949      - add capability to apply relaxation to horizontal velocity uVel & vVel.
1950    o pkg/grdchk: add gradient check for control variable xx_shifwflx
1951    o pkg/shelfice/shelfice_init_fixed.F
1952      fix CPP-flag combinations
1953    o pkg/seaice: Merge iceage code of Pierre Rampal
1954      * update/change/correct ice age calculations
1955      * add age updates for pathological cases
1956      Probably needs more testing...
1957    
1958    checkpoint62x (2011/05/13)
1959    o pkg/mom_vecinv:
1960       high-order vorticity scheme: use interior masks (maskInW & S)
1961       to zero-out (outside OB) gradient of vorticity.
1962    o verification exp.:
1963       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1964       hs94.128x64x5 and seaice_obcs ; update results.
1965    o pkg/obcs:
1966      fix bug in OBeta for YZ sections in obcs_exf_load.F
1967    o pkg/ctrl, pkg/shelfice, and optim:
1968      - add new control variable xx_shifwflx (fresh water flux underneath ice
1969        shelves). This is almost as tedious as obcs-ctrl, because the
1970        variables needs its own mask.
1971      - add a cost function term that penalizes the deviation of xx_shifwflx
1972        from the first guess (zero) in analogy to other control variables
1973    o pkg/shelfice:
1974      - start basic adjoint
1975    o pkg/ctrl:
1976      - remove extra 2D field "for good measure" when initializing in
1977        ctrl_set_globfld_[xy/xz/yz].F
1978      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1979      - improve error messages in ctrl_set_unpack_*
1980    o OBC implementation in momentum:
1981       use interior masks (maskInC,W & S) in momentum S/R:
1982       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1983       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1984       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1985       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1986       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1987        (and also with Leith/Smagorinsky harmonic-viscosity).
1988       Update output of experiment dome and exp4 (+nlfs).
1989    o exp4 test-exp:
1990      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1991        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1992        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1993        time-varying OB at Western-side for wVel (NonHyd); update output.
1994      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1995        and biharmonic-viscosity ; also use prescribed time varying OB.
1996    o pkg/obcs:
1997      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1998    o model/src:
1999      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
2000      - initialise startTime & nIter0 with unlikely values: allows to set one
2001        from the other without ambiguity.
2002    o seaice_obcs test-exp.:
2003      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
2004    o pkg/obcs:
2005      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
2006        no longer needed with maskInC,W,S in pkg/generic_advdiff.
2007    o pkg/seaice:
2008      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
2009        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
2010      - fixed bug in the initialization of sea ice salinity variable HSALT
2011        in seaice_init_varia.F  (removed dependence on ICE2WATR)
2012    o fizhi-cs test exp.:
2013       switch reference output convention for these 2 non-standard test-exp,
2014        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
2015          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
2016       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
2017    o model/inc:
2018      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
2019        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
2020    o pkg/seaice:
2021      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
2022    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
2023      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
2024        and initial HSALT
2025    
2026    checkpoint62w (2011/04/26)
2027    o pkg/mom_fluxform:
2028      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
2029      - use parameter "sideDragFactor" in no-slip BC side-drag part.
2030      - update output of exp. global_ocean.90x40x15
2031    o pkg/mom_vecinv:
2032      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
2033    o update seaice exp.:
2034      use more consistent parameter values (remove "backward compatability only":
2035       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
2036      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
2037       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
2038    o update test-exp global_ocean.90x40x15:
2039      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
2040      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
2041      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
2042      o turn on zStar & viscA4 in standard set-up (dir input/)
2043        and update output files: output.txt & output.dwnslp.txt
2044    o new AD-test experiment: obcs_ctrl
2045      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
2046    o pkg/dic:
2047      fix two bugs in handling water vapour pressure in carbonate chemistry
2048      and air-sea fluxes. Found by Val Bennington and Galen McKinley
2049      (add DIC Option = WATERVAP_BUG to recover old results)
2050      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
2051    o adding allowInteriorFreezing option to check for water below freezing point
2052      at depth and bring the negative heat anomaly to the surface level
2053    o pkgs _fields_load:
2054      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
2055      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
2056        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
2057        rbcs to get interpolation weights and time reccord number.
2058      - fix multi-threading in aim_fields_load.F
2059      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
2060    o external_fields_load:
2061      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
2062       interpolation weights) to use in a periodic time-series ; do not divide by
2063       time-step to convert to integer:
2064       - this fixes case where externForcingPeriod is not multiple of time-step
2065          (Thanks to Christopher L. Wolfe)
2066       - this fixes case where externForcingPeriod is an odd multiple of time-step
2067         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
2068      store index of time-record which is currently loaded:
2069       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
2070       - needed for the adjoint but not yet used because of extensive recomputations;
2071         (to be fixed soon)
2072    
2073    checkpoint62v (2011/04/02)
2074    o verification/1D_ocean_ice_column added to test Ian Fenty's
2075      pkg/seaice_growth.F modifications for improving sea ice code differentiability
2076    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
2077      (new velocity statistics after changing maskInW & maskInS definition)
2078    o pkg/generic_advdiff with OBCS:
2079      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
2080      equivalent to assumption of no tracer gradient outside the OB region.
2081      This will affect the results if using obcs+biharmonic diffusion.
2082      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
2083    o pkg/obcs:
2084      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
2085      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
2086      in Interior region. No impact on solution but affects Velocity monitor stats.
2087    o pkg/ptracers (adjoint)
2088      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
2089      tape file for each tracer
2090    o model/inc/src and pkg/autodiff: add parameters that allow to turn
2091      of parts of the adjoint code at run time. For now, there are only
2092      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
2093      parameters are set in data.pkg.
2094      This is the lazy coward's version of doing this, but still useful for
2095      debugging. In order to do it right, everything needs to be moved to
2096      pkg/autodiff.
2097    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
2098      the end; this fixes the adjoint balancing code for open boundaries.
2099    o pkg/ctrl:
2100      - change behavior of xx_${varname}period to be analogous to exf-conventions:
2101        xx_${varname}period =   0.,  means time-independent control part
2102        xx_${varname}period = -12., means one-year-periodic monthly control part
2103      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
2104        clean up ctrl_init a little, remove unused variables
2105      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
2106      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
2107    
2108    checkpoint62u (2011/03/15)
2109    o model/src:
2110      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
2111        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
2112      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
2113        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
2114    o pkg/ctrl/obcs/ecco:
2115      - remove obsolete, unused, and partially broken code:
2116        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
2117        ALLOW_CTRL_OBCS_BALANCE
2118      - put a stop statement into ecco/cost_obcsvol.F, but also add
2119        cost_obcsvol to ecco_ad_diff.list
2120    o pkg/ecco: fix counting cost function contributions for obcs (code
2121      by Matt M.) and diffkr for diagnostics
2122    o pkg/ecco, pkg/ctrl, pkg/grdchk:
2123      add cost penalty terms for initial uvel, vvel, eta controls
2124      and I/O for prior error files
2125    o pkg/mdsio:
2126       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
2127       (new argument) to check for tiled file in mdsioLocalDir : this fix the
2128       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
2129    o pkg/ctrl:
2130     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
2131       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
2132       unused and superfluous variables
2133     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
2134    o pkg/ecco
2135     - enable adjoint of Stevens OB
2136    o pkg/ctrl/ecco/grdchk:
2137      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
2138        Fortunately, we do not have any tests for the numerous cpp-flagged
2139        option of "obcs as control parameters" so we will never know
2140        if this is an improvement (but at least now things compile).
2141      - remove an obsolete initialization from ecco_cost_init_barfiles.F
2142      - fix some problems within never used ifdefs to make the code compile
2143    o pkg/obcs:
2144     - Refine Interior mask definition to work with more complex OB (e.g.
2145       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2146       read in Interior mask from file. Check if Interior mask is consistent
2147       with OB list of indices.
2148    o pkg/seaice
2149     - beginning code for a seaice tracer package,
2150       but currently only used for seaice age: SEAICE_AGE
2151       SEAICE_num = 4
2152       iTracer = 1: area-weighted ice age
2153               = 2: volume-weighted ice age
2154               = 3, 4: template for one-year vs. multi-year ice
2155       data.seaice has new namelist SEAICE_PARM03 for arrays related to
2156       SEAICE_num
2157    
2158    checkpoint62t (2011/03/05)
2159    o pkg/obcs:
2160     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2161       then normal component. This ensures that the normal component is set
2162       correctly even when it conficts with tangential setting from an other OB.
2163       Affects results of test-experiment seaice_obcs: update the output.txt
2164    o pkg/obcs:
2165     - add code to monitor statistics of dynamical fields at OB.
2166     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2167       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2168       - change default: balance the Net inflow through all OB (instead of balancing
2169         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2170     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2171       to match Nortern OB inflow (OBCS_balanceFacN=0).
2172    o pkg/seaice:
2173     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2174    o pkg/seaice (seaice_growth v 1.113):
2175     - reverting seaice_growth to v 1.111 in order to have code with exact bit
2176       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2177       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2178       runtime flag SEAICEareaFormula is kept but is inactive
2179    o model/src:
2180     - add new param to scale curvilinear grid distance and area when using
2181       a different sphere radius from the grid-files.
2182     - test/check multi-threads EXCH applied to local variable (cg2d_x)
2183    o adjoint:
2184     - enable adjoint of Stevens OB
2185     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2186       (a bit delicate because of potentially modified adj. common block structure;
2187       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2188    
2189    checkpoint62s (2011/02/15)
2190    o pkg/seaice (seaice_growth v 1.112):
2191     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2192       computing the ice cover tendency from effective thickness tendencies. Include
2193       Ian Fenty's formula.
2194     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2195       SEAICEareaFormula.
2196     - simplify notations for the various d_HEFF/d_AREA terms.
2197    o pkg/gmredi:
2198     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
2199       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
2200       add a verification test-run (front_relax.bvp) to test GM_useBVP.
2201    o pkg/seaice (seaice_growth v 1.111):
2202     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
2203     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
2204       also melt ice.
2205    o pkg/seaice:
2206     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
2207     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
2208    o pkg/cheapaml:
2209     - from Nico Wienders: New version of this package.
2210    o pkg/flt:
2211     - add CPP options to prevent floats to re-enter the opposite side of
2212       a periodic domain (default: keep periodicity)
2213    o pkg/gmredi:
2214     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
2215       (needed for multi-dim advection).
2216     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2217    o model/src:
2218     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2219    o tutorial_tracer_adjsens
2220     - extend to NLFS and replace maskC by hFacC
2221       (change reference output accordingly)
2222    
2223    checkpoint62r (2011/01/24)
2224    o testreport:
2225     - add option -deloutp (-do) to remove output file after successful run
2226     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2227       extract exact list of procs from this file ; adjust COMMAND by
2228       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2229    o pkg/ecco: replace old ineffective way of penalizing deviations from
2230      first guess (of obcs) with code by Matt Mazloff
2231    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2232      exf/cal
2233      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2234        and handle case of obcs?period == 0
2235        Not affected by these changes: There is still an inconsistency in
2236        the computation of start/endrec for the obcs variables for ALLOW_CAL
2237        defined (see comment by Menemenlis, 7-Mar-2003)
2238      - make S/R ctrl_get_gen_rec return something meaningful even if
2239        ALLOW_CAL is not defined
2240      - ctrl_getobcs?: simplify code so that it does not need to use
2241                       S/R exf_swapfields
2242    o testreport:
2243       allow to test MPI with different number of processors for each experiment:
2244       create file "SIZE.h.mpi" in each build dir.
2245       Note: update of "-command" argument not yet implemented.
2246    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2247      alleviate the need for additional 3D tapes when using
2248      the non-inear free surface in the adjoint. This is done
2249      by adding an 'update' of hfacc etc. to their current
2250      value at the beginning of forward_step.F.
2251    o pkg/seaice
2252      seaice_lsr: move stress-divergence computations out of outer pseudo-
2253      timestepping loop
2254    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2255      up, so that the calls of the ctrl_* subroutines are really at the end
2256      of the routine.
2257    o pkg/gmredi:
2258      allow to specify a 2-D horizontal map and a 1-D vertical profil
2259      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2260    o pkg/seaice:
2261      move lsr iterations from seaice_dynsolver to seaice_lsr.
2262    o pkg/seaice:
2263      reduce memory footprint of seaice mutldim advection tapes,
2264      by using a 2D tape independent of the generic_advdiff ones,
2265      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2266    
2267    checkpoint62q (2010/12/29)
2268    o model/src:
2269      - check horizontal grid-spacing for unset or zero/negative values.
2270      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2271    o pkg/flt:
2272      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
2273      - precision of input and output files set according to readBinaryPrec
2274        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
2275      - initial float position from tiled file was not converted to index space
2276        (looks like a bug): fixed to make it similar to initial pos. global file.
2277    o global_ocean.cs32x15:
2278       change SIZE.h of AD set-up to get same tiling as with MPI.
2279       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
2280    o model/src:
2281       add flag to control printing of domain fields (bathymetry, hFac ...) in
2282       ini_mask_etc (call to plot_fieds_xy*).
2283    o pkg/thsice:
2284       if useEXF, some forcing fields are not valid in overlap: fixed by computing
2285       over the interior only + apply EXCH at the end (like with SEAICE advection).
2286    o pkg/mdsio:
2287      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
2288        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
2289      - change barrier call for safe multi-threads access to 3-D shared buffer.
2290      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
2291      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
2292        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
2293    o pkg/flt:
2294      - add fourth-order Runge-Kutta integration
2295      - add basic exch2 support (only 1 facet supported so far!)
2296    o pkg/mdsio+rw:
2297      new S/R to read local (or tile independent) vector (read counterpart of
2298       mds_writevec_loc, and front-end write_glvec_rl/rs).
2299    o global_ocean.cs32x15: additional input_ad.seaice experiment
2300        that uses pkg/seaice rather than pkg/thsice.
2301        (using multidim advection for seaice)
2302    o towards more F95 syntax for array specification in namelist:
2303      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
2304        of all verification experiments.
2305           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
2306          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
2307      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
2308    o global_ocean.cs32x15: additional input.seaice experiment
2309        that uses pkg/seaice rather than pkg/thsice.
2310    
2311    checkpoint62p (2010/12/17)
2312    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
2313        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
2314    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
2315        allow for use of multim. advection in seaice adjoint.
2316    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
2317      - first attempt to close budgets by taking into account the freshwater
2318        flux implied by the sublimation of snow and ice. So far only the
2319        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
2320        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
2321    o eesupp/src:
2322      new S/R with new option (NML_EXTENDED_F77) to change array specification
2323      from F95 standard to commonly accepted extended F77 form.
2324      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
2325      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
2326      for less tolerant f77 compiler (e.g., pgf77, g77).
2327    o globalFiles:
2328      commented out in parameter file "data" since it's not safe with MPI
2329      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
2330      in this case); no longer commented out in restart test (tst_2+2).
2331    o add adTapeDir to specify a special directory where adjoint tapes are
2332      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
2333      and cannot be used together with mdsioLocalDir.
2334    o nesting pkgs:
2335      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
2336      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2337      - add parameter files + utils dir + output from short run on beagle.
2338    o pkg/seaice:
2339        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
2340    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
2341      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
2342    
2343    checkpoint62o (2010/11/25)
2344    o pkg/exf:
2345      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
2346    o pkg/seaice:
2347      - seaice_ocean_stress: split a loop for better vectorization of the
2348        adjoint code
2349      - seaice_growth.F: fix bug in conservation of freshwater connected to
2350        capping of heff, put contribution into d_HEFFbyNEG
2351      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
2352        by something more sensible (parameters that are what their name implies)
2353      - change some defaults, so that by default exf-parameters are used for
2354        things like rhoAir, cpAir,latent/sensible heat parameters, in order
2355        to reproduce the old results, many data.seaice now contain funny values
2356        for cpAir and latent heat of sublimation
2357    o packages_readparms.F: move exf_readparms up in line so that
2358        exf-parameters are visible for other packages (e.g. seaice)
2359    o debugMode & debugLevel=2:
2360      - differentiate between debugMode & debugLevel=2:
2361        debugMode: controls printing of debug messages (sequence of S/R calls).
2362        debugLevel: controls printing of algorithm intermediate results and stats.
2363      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
2364        => allows to print debug-stats without all sequence of call messages.
2365      - switch control of debug print from debugLevel to debugMode in many S/R.
2366    o pkg/obcs (obcs-sponge):
2367        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
2368        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
2369    o pkg/generic_advdiff:
2370      - record overlap minimum size for each advection scheme;
2371      - refine criteria on overlap minimum size;
2372      - check and stop (in gad_check) if overlap size is too small.
2373    o pkg/obcs:
2374      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
2375        once, in ptracers_implicit.F)
2376      - with seaice: remove test on empty file name in obcs_apply_seaice (always
2377        apply OB values when tile has OB)
2378    o model/src, coriolis setting:
2379      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
2380        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
2381        files (selectCoriMap=3) with any grid.
2382      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
2383    o pkg/seaice/seaice_growth.F:
2384        a few cosmetic changes that reduce the number of lines of code
2385    o pkg/obcs: add boundary conditions following Stevens (1990)
2386      - the code follows old MOM/NAOSIM code
2387      - so far it is only implemented for the eastern and western boundaries
2388        and NOT for pTracers
2389    o pkg/rbcs:
2390      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
2391        beginning of the first rbcs forcing period.
2392      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
2393        offline package, i.e., one file per time, labeled by iteration number;
2394        deltaTrbcs sets the timestep with which the data was generated;
2395        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
2396      - rbcsForcingCycle=0 makes forcing non-cyclic.
2397      - make arithmetic safe for negative times and odd forcing periods.
2398    
2399    checkpoint62n (2010/11/09)
2400    o pkg/seaice:
2401        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
2402    o pkg/obcs:
2403       New S/R to copy tracer value from the OB location to narrow band region
2404        (width = same as overlap) beyond the OB: preserve OB value (needed for
2405        high-order scheme) which were overwritten by EXCH call if in overlap
2406        region. Applied to theta, salt, ptracer and advected seaice variables.
2407       With seaice: use maskInC in similar way as in gad_advection.F,
2408        in seaice_advection.F and advect.F.
2409       Update output of experiment seaice_obcs and change exp4 to test OBCS with
2410        4th order Adv.Scheme. for pasive salt and ptracer.
2411    o tools/genmake2:
2412      - when looking for an optfile (not specified), only search for Fortran compiler
2413        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
2414      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
2415        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
2416      - set default for CPP to "cpp -traditional -P" (was the case without specifying
2417        an optfile, but otherwise default was just "cpp".
2418      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
2419      - when "CC" is not set in the optfile, look for possible C compiler
2420        (instead of just setting CC=cc)
2421      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
2422        => add a ".F" to ".o" rule for source files with no "#include" (such as
2423           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
2424      - move gfortran before g77 in list of possible Fortran compiler (consistent
2425        with reference compiler switch from g77 to gfortran)
2426    o pkg/seaice:
2427      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
2428        seaice_check that stops the model, when the CPP flag is used.
2429      o seaice_growth.F: make capping of ice volume conserving by returning the
2430        capped ice as freshwater to EmPmR. This does not change the verification
2431        experiments but will change runs where the capping is acutally active
2432    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
2433      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
2434         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
2435         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
2436    o tools/genmake2:
2437      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
2438      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
2439      - clean previous genmake log files before anything else.
2440      - change Makefile to remove testreport log files (*.tr_log) and genmake log
2441        files only with "CLEAN" target (instead of "Clean");
2442    o pkg/generic_advdiff:
2443      Change OBCS in multiDim advection (gad_advection.F):
2444       Use maskInC to prevent intermediate update of tracer-field in OB regions,
2445       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
2446       which were applying future time-step OB values.
2447      This way, all explicit calculations use current-time-step OB values
2448       (simpler and more consistent).
2449      Affects results when set-up uses time-varying OBC and multi-dim advection;
2450       update output of experiment seaice_obcs.
2451    o pkg/seaice:
2452      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
2453       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
2454         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
2455      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
2456       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
2457       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
2458    o pkg aim (2010/10/26):
2459      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
2460        formulation with obliquity, eccentricity, ... as run-time parameters,
2461      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
2462        upward shortwave radition at the surface (all-sky and clear-sky).
2463    o pkg/obcs:
2464      - writing sections with globalFiles=T does not work: switch to tiled-files
2465        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
2466      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
2467      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
2468    
2469    checkpoint62m (2010/10/21)
2470    o pkg/seaice: vectorize seaice_solve4temp.F
2471      - move iterations loops outside of i/j-loops
2472      - requires 2D arrays for TB and effConduct
2473      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
2474        modified in this routine
2475      - a little bit of clean up, adjusting indentation, etc.
2476      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
2477        performance and '**TWO' by '**2' (because TWO is a float),
2478        replaced ONE, ZERO
2479    o eesupp/src:
2480       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
2481    o pkg/seaice/seaice_growth.F
2482      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
2483      merging process. The merged routine has two branches, and one activates the 'evolution'
2484      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
2485      In summary, here is what the '10/10 revision' did consist of
2486        part 1: seaice_growth.F revisions 1.71 to 1.75
2487          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2488            The emphasis here was on improving readability (e.g. by trying to use meaningful
2489            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2490        part 1.5:
2491          - revising the lab_sea experiment to make it a more useful (i.e. stable
2492            and representative of an actual model run). This was done by generating a
2493            (winter) pickup to start from, switching back the main experiment dynamic
2494            solver from evp to lsr, having one of the experiments use the free drift solution.
2495        part 2: seaice_growth.F revisions 1.76 to 1.85
2496          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2497          - Sorting out the various fields units and sign (set early on and reset at the end)
2498            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
2499            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
2500          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
2501            and simplifying logical expressions to further improve readibility.
2502        part 3: seaice_growth.F revisions 1.86 to 1.89
2503          - Re-organize the blocks of code more logically.
2504          - Merging the '_if.F' pieces that add something new.
2505    o pkg/thsice:
2506      - vectorize thsice_solve4temp and thsice_get_exf.
2507        Problem: thsice_solve4temp has an unvectorizable statement that
2508        might also be problematic for TAF
2509      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
2510        does not change the verifcation experiment, but will change all
2511        experiments that have this flag undefined (not tested in verification);
2512        a little reorganization to save a few 2D fields and recomputations
2513      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
2514      - 2nd step:  fix some store dirs
2515        o seems to work somewhat, i.e. using ifort but not g77
2516        o likely cause are incomplete init. or recomputation
2517        o start verification/global_ocean.cs32x15/input_ad.thsice
2518    o pkg/obcs: add support for exch2
2519      - the position of the boundary and prescribed values are specified using
2520        a global domain with exch2 facets stacked
2521        - in x for N,S boundaries (like W2_mapIO=-1)
2522        - in y for E,W boundaries (so E,W boundaries do not overlap)
2523    o pkg/mdsio: add support for writing global sections with exch2
2524        file layout is as for obcs described above:
2525        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
2526        - for y-z sections, facets are stacked in y
2527    o pkg/thsice:
2528       - change a few routines for better vectorization: thsice_albedo.F,
2529         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
2530         not affected, but in particular the latter routine has changed
2531         dramatically (not necessarily easier to read now).
2532       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
2533       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
2534    o verification/lab_sea:
2535      - overhaul of the forward model experiments. The main motivation
2536        for this revision is that lab_sea has proven quite fragile (when
2537        changing the sea-ice code, and switching platforms) to a point
2538        when failures were very hard to attribute to specific code problems.
2539      - the suspected reason for this fragility is noise amplification by evp so,
2540        to start with, we decided to replace evp with lsr in the main experiment.
2541      - the input.lsr experiment thus became obsolete and was removed.
2542      - it was replaced with the input.fd experiment that uses an
2543        analytical "free drift" solution as the ice velocity field.
2544      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
2545        will hopefully allow us to discriminate problems due to dynamic solvers
2546        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
2547        us to test additional options, along with the salt plume package.
2548      - Finally a pickup was generated (at the end of a one year run) to
2549        make the tests more representative of an actual model run. Previously
2550        the tests starting point was a 1m thickness of ice everywhere.
2551    o pkg/seaice:
2552      - introducing S\R seaice_freedrift.F that compute the
2553        analytical solution to an approximate ice momentum
2554        equation (i.e. the simple stress/coriolis balance).
2555      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2556        of the free drift velocity field, and enable its use.
2557        To actually use the free drift solution as the model ice
2558        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
2559    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
2560    
2561    checkpoint62l (2010/10/04)
2562    o pkg/seaice:
2563      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
2564      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
2565       version (with USE_ORIGINAL_SBI undef);
2566    o add hooks for new packages OASIS, the package will follow
2567      (hooks exclude the seaice pkg for now)
2568    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
2569      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
2570      rather than mdsio_readvector.F/mdsio_writevector.F, within
2571      adread_adwrite.F to read/write adjoint-related tapes to disk.
2572    o eesupp and pkg/mdsio: ALLOW_WHIO
2573      Option to write/read 2D fields to files including tiles halos.
2574      The main purpose is for adjoint related "tape I/O".
2575      The secondary purpose is for debugging phases.
2576      A word on those rather specifically intended purposes.
2577      The code was meant to be stripped down to the bare minimum.
2578      Typically, there is a unique and basic mapping to the global
2579      buffer (tile by tile, then proc by proc, then level by level), and
2580      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
2581      meant to generate user friendly outputs of various shapes and forms.
2582      Rather it is intended, for the knowledgeabale developers,
2583      to be largely independent of the many mdsio options, to allow
2584      outputs of tiles+halos in debugging phases and in adjoint runs,
2585      and to allow some flexibility in tuning (adoint) I/O depending on each
2586      file system behavior. With regard to tuning, most of the potential knobs
2587      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
2588      to specify directories, to specify the typical size of I/O calls, etc.)
2589      are not yet included, and will be added if they prove useful.
2590    o pkg/seaice:
2591       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
2592    o pkg/seaice:
2593       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
2594       code (seaice_budget_ice_if.F) which enable to recover old standard
2595       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
2596       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
2597    o model/src (rStar):
2598       use simple average (not area weighted) of rStarFac at U,V point when using
2599       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
2600       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
2601    
2602    checkpoint62k (2010/09/17)
2603    o adjoint
2604       * changed verification/global_ocean.cs32x15 ; adjoint now tests
2605         Adams-Bashforth 3 + NLFS + RSTAR
2606       * some more modifs required for ECCO-GODAE v4
2607    o pkg/seaice
2608       add SEAICE_AGE_VOL option to use volume instead of area for
2609       integrating SEAICE_AGE
2610    o model/src:
2611       first check-in of sigma & hybrid-sigma coordinate code ; also includes
2612       non-linear free-surface parts ; but pressure-gradient not yet coded.
2613    o pkg/ptracers:
2614       option for ptracer to convert Salt Relax into additional EmP.
2615        tested in exp. global_ocean.90x40x15.dwnslp (update output)
2616    
2617    checkpoint62j (2010/08/25)
2618    o pkg/ggl90:
2619       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
2620    o pkg/dic: car_flux.F, phos_flux.F
2621      - reduce number of exp-calls in order to improve performance
2622      - clean up a little (replace fields by their macros, etc., fix
2623        typo in CPP-flag)
2624    o pkg/ggl90: minor changes
2625      - GGL90diffKrS was removed --> always use GGL90diffKr
2626      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
2627      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
2628        (commented out for now)
2629      - change in max/min operations to ensure that smoothing is ok
2630      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
2631      - always use diffKrNrT as background profile (i.e. never use diffKr field)
2632    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
2633    o pkg/dic:
2634      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
2635        vectorization
2636      - small bug fix in insol for the unlikely case of a cartesian grid
2637      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
2638        + now vectorize, which also removes adjoint recomputations;
2639        + replace integer maksp1 by _RL maskp1
2640        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
2641    
2642    checkpoint62i (2010/07/21)
2643    o pkg/flt:
2644      - with OBCS: stop floats which enter the OB region
2645    o model/src:
2646      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
2647        for implicit vertical advection.
2648    o pkg/seaice:
2649     - account for melting in seaice age evolution.
2650     - remove double counting of seaice ridging effect on seaice age.
2651    
2652    checkpoint62h (2010/06/18)
2653    o pkg/exch2:
2654     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
2655    o tools/genmake2
2656      - remove "-pdefault" option: redundant with the use of "packages.conf";
2657      - remove file pkg/pkg_default : set the default as a pkg group
2658        ("default_pkg_list") defined in pkg/pkg_groups;
2659      - fix for case pkg/pkg_depend is missing (was hanging before);
2660      - add option "-pgroups" to specify a different pkg_groups than the default.
2661    o verification/adjustment.cs-32x32x1:
2662       add a "minimal" set-up test (code_min & input_min) which only compiles
2663       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
2664    o tools/genmake2
2665      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
2666      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
2667    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
2668      files are nearly the same anyway.
2669      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
2670       - redefinition of tau(i,i) (by a factor of ustar)
2671       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
2672       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
2673       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
2674       - replace
2675         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
2676         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
2677         by
2678         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
2679         (changes results)
2680       -> exf_bulkformulae v1.22,
2681          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
2682          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
2683                    output.txt 1.63
2684           offline_exf_seaice: output.seaicetd.txt 1.7
2685           seaice_obcs: output.txt 1.10)
2686      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
2687       -> exf_bulkformulae v1.23,
2688          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
2689          and global_ocean.cs32x15.icedyn (only 11 matching digits)
2690      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
2691    o adjoint of exch-1:
2692     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
2693       (note: was already like this when using EXCH-2) and remove flow dir
2694       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
2695     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
2696     - update pkg/exch2 diff list.
2697    
2698    checkpoint62g (2010/05/19)
2699    o eesupp/src (exch-1):
2700     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
2701       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
2702       (renamed to exch1_*rx_cube.F).
2703     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
2704       to call new exch1 S/R ; update Makefile and .cvsignore.
2705     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
2706       exch2_xy_rx later)
2707      Note: after updating your code, need to run "make clean" in eesupp/src
2708    o test experiment bottom_ctrl_5x5:
2709       new output_adm.txt with fewer grdchk & less monitor output.
2710    o model/src:
2711      remove the call to ini_cori in initialise_varia.F (just keep the usual one
2712       in initialise_fixed.F). More consistent with coriolis & horizontal grid
2713       beeing treated in the same way (ini_grid is not called a 2nd time).
2714    o pkg/exf:
2715      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
2716      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
2717      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
2718      - cosmetic changes to exf_bulkformulae.F to make it look more like
2719        exf_bulk_largeyeager04.F
2720    o eesupp/src (exch-1):
2721      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
2722      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
2723        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
2724        (even without using MPI).
2725      - Message mode: move RecvAck setting (indicator of buffer being ready)
2726        from send_put to recv_get S/R (was useless before, but not sure if
2727        it's much more useful now);
2728      - Switch the order of sync: MPI-proc 1rst and then threads;
2729      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
2730      - fix AD code for communication mode ='get' (but not used).
2731    o model/src:
2732      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
2733      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
2734    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
2735    o pkg/ctrl: require a specific set of control variables and exf-flags for
2736      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
2737    o model/src:
2738     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
2739       1rst forward sweep, to avoid over-writing output files during recomputations
2740       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
2741     b) 2nd version:
2742      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
2743      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
2744         writePickupAtEnd) + seaice & ptracers output;
2745      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
2746    o model/src:
2747      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
2748    o pkg/exch2:
2749      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
2750      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
2751    o pkg/autodiff & exch2:
2752      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
2753      (for now, only if ALLOW_EXCH2 is defined).
2754    o pkg/autodiff:
2755      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
2756        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
2757       + clean-up comments (_RS is not always real*4)
2758      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
2759      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
2760        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
2761    o testreport (AD-tests):
2762      no longer link files from dir "../input" (1rst link files from
2763      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
2764    
2765    checkpoint62f (2010/04/29)
2766    o model/src/the_main_loop.F:
2767      adjust store directives for seaice evp and multicategory according to
2768      pkg/ecco/the_main_loop.F
2769    o adjoint:
2770      global_sum_ad was incomplete (noted many times by many people ;)
2771      nice description by Jean U. as follows:
2772      * allreduce(var) in global_sum.F can be interpreted as
2773        reduce(sum) followed by broadcast of sum.
2774      * The adjoint of that is
2775        sum(adjoint) followed by broadcast(summed adjoint value)
2776        or in other words, allreduce(sum, adjoint vars)
2777      We were missing the sum(adjoint)!
2778      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
2779      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
2780      The fix should produce 16-digit accuracy between
2781      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
2782      multi-CPU single-tile (e.g. nSx=1, nPx-2)
2783      We'll probably change this yet again shortly
2784    o eesupp/src:
2785      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
2786    o pkg/icefront
2787      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
2788        specification of addmass array based on a 2D field, which is added
2789        at bottommost wet level at each horizontal location.
2790    o model/src:
2791     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
2792     layout; (not always compatible with delX,delY setting; commented out for now).
2793    o pkg/exch2:
2794     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
2795     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
2796    
2797    checkpoint62e (2010/04/15)
2798    o pkg/obcs:
2799      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
2800    o pkg/dic:
2801      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
2802        (note: not presently tested in any forward verification exp.)
2803       update tutorial_global_oce_biogeo AD output file.
2804    o pkg/exf:
2805      - account for the variation of albedo as a function of zenith angle
2806        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
2807    o build_options:
2808     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
2809    o pkg/dic:
2810      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
2811      - use binary pickup file for restart;
2812      - initialise atmos-CO2 box from dic_pCO2 parameter;
2813      - fix multi-threaded.
2814    o pkg/rbcs:
2815     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
2816       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
2817     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
2818       and update output.txt
2819    o pkg/kpp:
2820     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
2821     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
2822       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
2823       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
2824     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
2825       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
2826    o pkg/offline:
2827      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
2828      (bug was added in version 1.10 on 2007-08-23).
2829    o pkg/offline:
2830      - no need to specify periodicExternalForcing, etc ... to use offline pack
2831      - offline input files no longer just single prec --> parameter offlineLoadPrec
2832    o verification/lab_sea:
2833      change AD test to multi-tile setup and update all 4 AD output.
2834      NOTE: while cost function values remain very similar,
2835      gradients are very different, although gradient checks are self-consistent
2836      Should try to get to the bottom of this (cost function summation order?)
2837    o pkg/dic:
2838      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
2839      a weakness of TAF that drops part of double precision in log10 derivative.
2840      <= changes removed since problem has been fixed in current TAF version 1.9.71
2841      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
2842    o pkg/ecco:
2843      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
2844      update all 4 lab_sea AD output.
2845    
2846    checkpoint62d (2010/03/22)
2847    o build_options:
2848      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
2849    o remove unbalanced quote (single or double) in commented line of source code
2850      (may cause some warning with some preprocessor/makedepend versions).
2851    o pkg/seaice:
2852      fix seaice_model.F for adjoint (gael) and update AD results of experiments
2853       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
2854    o testreport:
2855      add option '-runonly' (short: '-ro') to just do the run part (without make).
2856    o eesupp: remove JAM communication code (obsolete).
2857    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
2858      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
2859      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
2860      (update also the output).
2861    
2862    checkpoint62c (2010/03/02)
2863    o tools/build_options :
2864       move (some) old optfiles from build_options/ to build_options/unsupported/
2865    o model/src and pkg/exf
2866       surface relaxation -- separating data and data.exf options
2867       The point is to ensure that we specify the surface relaxation
2868       either in data or in data.exf (but not half and half) and to
2869       avoid an accidental relaxation to 0 (which happened if a time
2870       scale was specified but the file name was left empty)
2871    o model/src model/inc and pkg/mom_common
2872       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
2873       => addition to the viscosity field as computed by others schemes
2874    o tools/build_options:
2875      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
2876        but keep the former optfile for few weeks for smooth transition
2877    o pkg/ecco
2878      - allow user defined cost function contributions
2879         CPP: ALLOW_USERCOST_CONTRIBUTION
2880         USAGE: compute contributions in cost_usercost_all.F
2881      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
2882          the two options are complementary.
2883    o pkg/smooth
2884      - migration from contrib to the main repository
2885    
2886    checkpoint62b (2010/01/26)
2887    o pkg/monitor:
2888      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
2889        (in case someone forgot to update customized pieces of code)
2890    o nonHydrostatic:
2891      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
2892      - add a simple 2-D experiment (short_surf_wave) to test it.
2893    o pkg/icefront:
2894       adding the shell of, and the hooks to, a new package that
2895       will model melting and freezing of vertical glacier ice fronts
2896    o momentum:
2897      add diagnostics of momentum tendency from Hydrostatic pressure gradient
2898       (without surf.pressure term: would need a 2nd filling since implicit term).
2899    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
2900      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
2901      cannot deal with the former
2902    o cleaning:
2903      - remove all (except OpenAD) old TLM output from results_ad dirs.
2904      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
2905      - comment out maskH definition (replaced by maskInC)
2906    o pkg/monitor:
2907      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
2908        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
2909    
2910    checkpoint62a (2010/01/15)
2911    o model/src:
2912      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
2913    o pkg/diagnostics:
2914      - add optional level number diagnostics (i.e., level number to be define
2915        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
2916      - strictly check for valid parser-code(10) ;
2917      - check if adding diag to the list from the right place.
2918    o pkg/longstep:
2919      - change parameters and fix tracer conservation with rstar/nonlinear free surface
2920    o diagnostics:
2921     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
2922       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
2923    o pkg/diagnostics:
2924     - Add option for writing vertical integral (sum of selected levels) of an output
2925        field instead of writing output field levels. Activate this option on a per
2926        output-file basis, by setting the 2nd character of fileflag to 'I'.
2927     - Add field-specific information relative to level integral in 3rd postion
2928        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
2929        vertically (x level-thickness x hFac), "r"=same but without hFac.
2930    o do_the_model_io:
2931      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
2932        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
2933        writing pickups and stopping.
2934    o pkg/diagnostics (for now, only with mdsio):
2935      - write time information to meta file (and modify accordingly rdmds.m) :
2936        time-averaged diagnostics output: write starting and ending time of the
2937        time-averaging interval ; snap-shot diagnostics output remains unchanged;
2938    o pkg/timeave:
2939      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
2940        always Nr), now assumed to be equal to number of levels of averaged field;
2941        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
2942    o pkg/sbo:
2943      - fix ocean bottom pressure global-average & 2-D time-ave output (was
2944        neither initialised nor filled).
2945      - add starting iteration in suffix of global-average output file
2946        (to avoid over-writing the file after a restart)
2947      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
2948    o time-average:
2949      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
2950        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
2951         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
2952        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
2953      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
2954      - fix missing accumulation for pkg/opps.
2955      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
2956         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
2957      - fix initialisation of time-ave vars and do only full time-step increment
2958        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
2959    o pkg/layers:
2960      - use standard RW pkg S/R to write the output
2961        and remove local write_fld version (which had a problem).
2962      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
2963      - fix LAYERS_CALC argument list.
2964    o pkg/timeave:
2965      - store cumulative-time in a simple tiled array (drop the level index)
2966      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
2967    o pkg/ocn,aim_compon_interf
2968      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
2969    
2970    checkpoint62  (2009/12/23)
2971    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
2972        (was not previously tested in any other exp.)
2973    o pkg/monitor:
2974      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
2975        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
2976        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
2977      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
2978      - change del2 calculation.
2979      - use interior masks (instead of maskH, <- to be remove).
2980      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
2981    o mask & obcs:
2982      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
2983      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
2984        (called after packages_init_fixed)
2985    o pkg/obcs:
2986      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
2987        Fixes bug in obcs+exf with nSx*nSy.GT.1
2988      - fix multi-tile handling in obcs balance code
2989    o nonHydrostatic:
2990      - Implement AB-3 for non-hydrostatic vertical momentum ;
2991        (change ordering of var. stored in pickup file when using NH)
2992      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
2993      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
2994        (in prep. for new NH free surface form).
2995    o pkg/obcs:
2996      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
2997    o model/src:
2998      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
2999    
3000    checkpoint61z (2009/12/01)
3001    o nonHydrostatic:
3002      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
3003        a spurious source of energy in simple baroclinic adjusment test case.
3004      Update all non-hydrostatic exp output.
3005    o model/src (3-d solver):
3006      Change again 3-D solver free-surface RHS term when exactConserv=T:
3007        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
3008        (which was not the case with previous formulation).
3009      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
3010      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
3011    o nonHydrostatic:
3012      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
3013        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
3014      - change 3-D solver to work with r* (for now, only with linear free-surf.)
3015      - add few debug diagnostics (cg3d_x, residual)
3016    o model/src:
3017      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
3018        update output of exp. global_ocean.cs32x15.viscA4
3019    o update output of exp. global_ocean.cs32x15.icedyn after removing
3020      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
3021    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3022    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
3023      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
3024    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
3025      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
3026      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
3027      to test this code
3028    o pkg/cd_code:
3029      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
3030       C-grid momentum. D-grid velocity used to be stepped forward in time with
3031       Adams-Bashforth only on surface pressure term. Tests show that using AB on
3032       D-grid coriolis term improves stability (as expected from CD-scheme paper).
3033      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
3034      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
3035       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
3036       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
3037      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
3038           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
3039    o pkg/obcs:
3040     - fix bug in initialisation (broken since Oct 1rst modification)
3041       for useOBCSprescribe without useEXF.
3042    
3043    checkpoint61y (2009/11/15)
3044    o pkg/seaice
3045     - change (once again) the discretization for the evp solver: rather than
3046       squaring the averages of strain rates, average the squares to give
3047       a better approximation to VP behavior (in simple test); this breaks
3048       verification experiments that use EVP (lab_sea and lab_sea.hb87)
3049        --> update outputs
3050    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
3051      to improve vectorization of adjoint code on TARGET_NEC_SX
3052    o verification/vermix:
3053      - change vermix to a more "classical" 1d column with high vertical
3054        resolution, seasonal heat flux forcing and constant wind forcing
3055        --> update outputs
3056    o pkg/seaice
3057     - fix diagnostics of principal stress components for EVP
3058     - add optional diagnostics of non-linear convergence for LSOR solver
3059     - make maximum zeta a runtime parameter
3060    o model/src (3-d solver):
3061      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
3062       which consisted in removing the Surf. Non-Hydrostatic pressure from the
3063       whole column and adding it to Eta (inspired from Casualli, 1999):
3064       Only affects 3-D solver initial guess and only if using ExactConserv,
3065       but tests did show a degradation of solver convergence. For this reason,
3066       decide to disable this piece of code.
3067       to recover previous version, just set zeroPsNH = exactConserv (line 78).
3068      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
3069    o pkg/ggl90:
3070     - fix previous modif (unfortunatly has not been documented here).
3071    o pkg/seaice/autodiff:
3072     - add CPP flag to include clipping of zeta in EVP code;
3073       although clipping of zeta is not necessary for EVP and not recommended
3074       it was done by default, now clipping is disabled by default
3075     - modify computation and store zetaC/Z in seaice_evp for TAF
3076     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
3077     - change seaice_calc_viscosities/strainrates for better
3078       vectorization after AD by TAF
3079     - rearrange common blocks in SEAICE.h once again for easier dumps of
3080       adjoint output, adjust adcommon.h and g_common.h
3081     - change flux form of default advection scheme for better vectorization
3082       of adjoint code
3083     - modify lab_sea/input.lsr to test the flux form of default advection
3084       scheme
3085    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
3086      transition in checkpoint61r)
3087    
3088    checkpoint61x (2009/10/19)
3089    o adjoint: adding two new verification experiments
3090      * tutorial_global_biogeo: an online dic sensitivity experiment
3091        (work with G. Forget)
3092      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
3093        (an update of the Dutkiewicz et al., 2006 paper)
3094      Both use the same CO2FLUX cost function, but different controls
3095      Gradient checks look good, but some recomp. could still be traightened out
3096      Should add xx_dic control variable to test at some point
3097    o model/src:
3098      add run-time parameters to check and/or mask initial Temp & Salt
3099    o pkg/ptracers:
3100      apply zonal filter (if used) to all passive tracers
3101    
3102    checkpoint61w (2009/10/12)
3103    o adjoint:
3104      * update and finish work on adjoint of dic package (G. Forget)
3105      * start adjoint of offline package
3106      * bug fix for cube-sphere TLM code (active_file_g.F)
3107    o tutorial_global_oce_optim:
3108      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
3109      and add SIZE.h_mpi for MPI testing
3110    o pkg autodiff
3111     - fix bug in autodiff_restore
3112     - make genmake2 remove comments and empty lines from ad_input_code.f in
3113       order to reduce file size (new script file remove_comments_sed)
3114    o allows to specify vertical profile of vertical viscosity (viscArNr)
3115    o pkg autodiff
3116      autodiff_ini_model_io: comment out writing of grid information to netcdf
3117      files, because at this time the grid fields are a bunch of zeros
3118      (this is analogous to ini_mnc_vars.F)
3119    o pkg seaice/autodiff:
3120     left-over from removing the 3-time-level fields:
3121     - small rearrangement of common blocks (SEAICE.h)
3122     - fix field declaration in order to get meaningful output in
3123       adseaice.*.nc (adcommon.h)
3124    o pkg obcs:
3125     - go through NH code only if nonHydrostatic=T
3126     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
3127     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
3128       => Update output of experiment seaice_obcs
3129     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
3130     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
3131     - fix restart for useOBCSprescribe + useEXF
3132    o pkg ctrl
3133     - make obcs as control parameter work also with useSingleCPUio
3134     - replace a few sny and snx by Ny and Nx to be consistent with
3135       ctrl_set_globfld_x/yz.F
3136    o pkg seaice
3137     - re-introduce global field frWtrAtm for the case of
3138       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
3139     - catch the case of an empty filename in seaice_cost_init_fixed.F
3140    o pkg ecco:
3141     - small bug fixes in the_main_loop
3142      . fix order of monitor arguments
3143      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
3144      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
3145        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
3146     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
3147       imbalance diagnostics for wmean_h/sflux = 0
3148     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
3149     - catch the case of empty filenames in ecco_cost_init_fixed.F
3150       and ecco_readparms.F
3151     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
3152       to make this statement meaningfull in ecco_cost_weights.F
3153    o pkg zonal_filt:
3154      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
3155      - when using rStar, filter uVel*hFacW instead of uVel
3156       (tested without topography: fix a Pb of growing instability with NLFS)
3157    o pkg/aim/thsice:
3158     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
3159      (works as SST restoring)
3160    o pkg/thsice:
3161     -add specific parameter for salt restoring in slab mixed-layer
3162       (by default equal to the temperature restoring)
3163    
3164    checkpoint61v (2009/09/21)
3165    o pkg/kpp:
3166     -add double diffusive contributions as a hack, turned off by default
3167      for now, and the code can be excluded with a CPP-flag
3168      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
3169     -add a verification experiments to "vermix" to test this code
3170    o pkg/mom_common:
3171      Move computation of length scales to mom_init_fixed.F (avoid recomputation
3172      at each time-steps*levels).
3173    o pkg/layers:
3174      Created a new package for computing volume fluxes in temperature or
3175      [not yet implemented] density layers, e.g. for calculating residual
3176      overturning circulations.
3177    o pkg/diagnostics:
3178      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
3179    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
3180    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
3181      To avoid mixing type (RS/RL) of input/output array argument,
3182      replace single mixed-type array with a pair from each type (RS/RL).
3183    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
3184      is now implemented for all pkgs (previously only done for the main pickup)
3185    
3186    checkpoint61u (2009/08/25)
3187    o pkg/obcs:
3188      - change OB?eta from _RS to _RL and put them into a separate commen block
3189      - add code to read OB?eta from a file via obcs_prescribe_read: the code
3190        compiles and does not destroy any other experiments, the data is read
3191        properly, but the code is not tested in actual applications
3192    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
3193      create a meaningful unit attribute for the time coordinate variable
3194    o pkg/ebm: add plenty of missing "_d 0" ;
3195       update results of experiment global_ocean_ebm (fwd + adjoint tests)
3196      Notes: several pieces of code only works for (very) specific set up
3197       (domain size, lat range, etc ...); should be documented & stop if one
3198       of those assumptions is not meet.
3199    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
3200       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
3201          and offline_exf_seaice (seaicetd + adjoint).
3202    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
3203       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
3204        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
3205    o few changes to pass when compiling with strick checking of arguments
3206       across S/R (allow to find few bugs in S/R calls).
3207    o pkg/seaice:
3208     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
3209       2d-fields, for slightly better performance
3210    
3211    checkpoint61t (2009/07/22)
3212    o pkg/seaice:
3213     - remove unused variables in seaice_evp
3214     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
3215    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
3216       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
3217       each processor opens a different file (a fix from Matt).
3218    o cg2d:
3219       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
3220       this reduces number of EXCH calls by 2 when using exch2.
3221       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
3222       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
3223    o pkg/thsice:
3224       add code for Near Infra-Red albedo (from Jeff)
3225       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
3226    o ini_model_io:
3227       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
3228       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
3229       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
3230    
3231    checkpoint61s (2009/06/30)
3232    o pkg/exch2 (exch2_rxN_cube*):
3233       remove last BARRIER (no need to synchronise after getting data from shared
3234       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
3235    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
3236      and generate new output (for the 2 tests) using default rotationPeriod.
3237    o pkg/exch2:
3238      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
3239        (was already the case with AUTODIFF_EXCH2 defined)
3240      - add bj in exch2 arrays and S/R.
3241      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
3242        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
3243    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
3244      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
3245        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
3246      - verification experiment natl_box.longstep
3247    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
3248      allow different versions of ifort (8 or 9) and different versions
3249       of mpi (mpich or mpich2) to be used with the same optfile.
3250      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
3251       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
3252    o pkg/seaice:
3253      fix previous modif (3-level field removed) for old-pickup reading
3254    
3255    checkpoint61r (2009/06/25)
3256    o pkg/seaice:
3257     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
3258      1. introduce fields for time step (N-1)
3259      2. do not use levels 2 and 3 anymore (but keep them)
3260      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
3261         includes changes to pkg/thsice/thsice_get_velocity.F,
3262         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
3263         pkg/obcs/obcs_apply_uvice.F.
3264     - completely remove code for leap-frog time stepping for second order
3265       advection
3266     - adjusted adjoint accordingly;
3267       gradient checks have improved by an order of magnitude!
3268    
3269    checkpoint61q (2009/06/22)
3270    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
3271     - the boundary conditions along open boundaries are unclear, because the
3272       associated masks are set to zero and are thus treated as closed when
3273       applying the slip-boundary conditions.
3274     - move initialisation of grid variables from seaice_init_varia to _fixed
3275    o adding doc/diags_changes.txt
3276    o model/src:
3277      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
3278       to avoid "_diags" naming if no relation to pkg/diagnostics.
3279      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
3280       file and only call PLOT_FIELD_XYZ if debugMode=T.
3281      remove few PLOT_FIELD_XY calls outside initialisation.
3282      remove few unnecessary BARRIER.
3283    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
3284      of salt_plume package in Southern Ocean
3285    o pkg/thsice:
3286     - fix hOceMxL in overlap (needed for sea-ice advection);
3287       update output of experiment global_ocean.cs32x15.icedyn.
3288    o pkg/seaice:
3289     - make the (placeholder-)tracer IceAge a little more meaningful
3290      by avoiding ridging of age due to convergent ice flow
3291     - add diagnostics for surface temperature, atmospheric and oceanic
3292       heat flux, and atmospheric and oceanic ice growth
3293    
3294    checkpoint61p (2009/06/10)
3295    o eesupp (global_max & global_sum):
3296     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
3297     - remove starting & endding barrier (no longer needed)
3298    o pkg/mdsio, writelocal:
3299       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
3300       (remove the STOP): uses shared buffer IO to store data from all threads
3301       and then let master-thread write nThreads tiles.
3302    o pkg/mdsio (read/write field):
3303     - tiled IO done in 1 piece (all levels at a time);
3304     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
3305     - multi-threaded: allow to read/write local (non-shared) array
3306       (was already working with singleCpuIO ; now works also without);
3307       => no longer needs barrier call after reading a file (added inside
3308       mds_read/write field).
3309     - move barrier calls outside gather/scatter_2d to mds_read/write_field
3310    o pkg/obcs/exf
3311      - exf_getffieldrec.F: add a few ". _d 0" and
3312                            add code to catch the case fldperiod = 0.  
3313      - obcs_precribe_read.F: change if statements so that they match
3314                              the variable type (_RL)
3315      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
3316        exf_iprec) as part of namelist EXF_NML_01
3317    o pkg/mdsio:
3318      - read/write tiled (local) files: read/write 1-level tile chunk at a time
3319        (instead of segment of length sNx); expected to speed up tiled IO.
3320    o pkg/exch2:
3321      - take buffer copy from/to array out of S/R exch2_send/recv into new
3322        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
3323        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
3324      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
3325      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
3326        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
3327        including Topology header file (and common blocks).
3328      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
3329        remove 2nd exch call in exch2_s3d_rx (no longer needed).
3330      - document S/R arg. list (+ update some comments)
3331    o pkg/seaice:
3332      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
3333        temperature and humidity over sea ice based on climatological values.
3334      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
3335        of LSR (this change is expected to change the results slightly because now
3336        it uses slightly difference moduli from the second last LSR solution, but
3337        that is more consistent with the stress computations; this part of the code
3338        is not tested in the verification experiments)
3339      - fix diagnostics for flux of ice in case of B-grid
3340      - turn strain rates eij and press into global fields within global
3341        common block in SEAICE.h for more straighforward diagnostics
3342      - fix diagnostics for principal stress components, press, zeta, eta
3343        to give something meaning full
3344    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
3345      new output (all 4 tests) using default rotationPeriod.
3346    o pkg KPP:
3347      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
3348      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
3349        and normal grid from 1 to Nr)
3350    o Fix computations of L4rdt in mom_calc_visc.F
3351    o eesupp:
3352      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
3353      should be called before a "stop" if we know that all process are going
3354      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
3355    
3356    checkpoint61o (2009/05/26)
3357    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
3358    o model/src/ini_curvilinear_grid.F:
3359       compute angleSin/CosC when they are not read from a file
3360    o pkg/seaice:
3361       add pseudo time stepping for LSOR
3362    o pkg/exch2:
3363       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
3364    o pkg/seaice:
3365       Adding separate sea ice albedo, drag coefficients, and HO in Southern
3366       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
3367    o SingleCpuIO:
3368       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
3369    o pkg/seaice:
3370       put exchanged variable in (local) common block for MPI+Multi-Threads
3371       to work (necessary with exch1, and for now with exch2 too).
3372    o verification: to get more experiments tested with mpi, mth and mpi+mth,
3373      change tiling of:
3374       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
3375       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
3376      update output of exp:
3377       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
3378       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
3379      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
3380                       (note: output.txt generated on faulks using only 1 tile)
3381    o eesupp & mdsio (SingleCpuIO):
3382     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
3383       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
3384       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
3385     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
3386     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
3387       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
3388    o pkg/exch2:
3389     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
3390       read parameter file "data.exch2" if it exists; otherwise try default regular
3391       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
3392     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
3393       with new code (not to be used, just as a backup solution).
3394     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
3395       in utils/exch2/input.
3396    
3397    checkpoint61n (2009/05/12)
3398    o eesupp & mdsio (SingleCpuIO):
3399      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
3400        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
3401        receive real*4 array (instead of real*8) to read/write 32.bit files.
3402        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
3403         and remove new mapping S/R)
3404    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
3405      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
3406        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
3407        when using exch2. Add S/R to map global io-buffer to global model array.
3408      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
3409    
3410    checkpoint61m (2009/04/29)
3411    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
3412      and add 3 other S/R for other types (R4,R8,RS).
3413      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
3414    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
3415     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
3416     - reduce number of macro definitions (keep only those which are used);
3417       can always call directly the corrresponding S/R if needed.
3418     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
3419       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
3420     Fixed wrong type of arg in:
3421       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
3422       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
3423     To fix: global_sum of var in common block is wrong (multi-threaded) in:
3424       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
3425     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
3426    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
3427      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
3428    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
3429    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
3430      edges are closed (zero depth); might happen with "blank tiles";
3431      for now, disabled if using OBCS.
3432    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
3433      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
3434    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
3435      to reduce length of 1.D array print in STDOUT.
3436    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
3437      + use 48 tiles (16x8): this will allow to test "blank tiles".
3438    o start to test MPI + multi-threaded (change testreport to skip tests
3439      where number of tiles do not match).
3440    o genmake2: add option "-omp" to turn on Open-MP ;
3441      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
3442    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
3443      and keep the original tile numbering. Note: compatible with old
3444      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
3445    
3446    checkpoint61l (2009/04/07)
3447    o Overlaps had been forgotten in calculating ijk keys : fixed
3448    o fix cyrus makedepend for gcc 4.4
3449    o experiment fizhi-cs-aqualev20:
3450      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
3451      and generate new output. Note: new output is much closer to the old
3452      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
3453      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
3454    o pkg/fizhi:
3455     - change to avoid indices going deliberately over array-bounds
3456     - remove unnecessary MPI stuff
3457     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
3458     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
3459       does not go over array-bounds and therefore returns reliable output.
3460     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
3461       this S/R has 4 output arguments, which are used inside "get_alarm";
3462       when it is called with the same variable "ndum" in place of several
3463       output arguments, this produces weird side effect inside "get_alarm"
3464      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
3465       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
3466       address) and produces error.
3467    o tools/gemake2: (March 27-29 2009)
3468      with option "-mpi": link *_mpi files from "MODS" dir (this is what
3469      testreport does).
3470    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
3471    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
3472       update lab_sea.lsr & lab_sea.salt_plume results
3473    o pkg/seaice:
3474      Major overhaul of the LSOR solver: change discretization from original
3475      finite differences to finite volume. The old routine is still in the
3476      file seaice_lsr.F and can be turned on with the CPP-flag
3477      SEAICE_OLD_AND_BAD_DISCRETIZATION
3478      Along with this change, the discretization of the strain rates is changed.
3479      The same flag turns on the old discretization in seaice_calc_strainrates.F
3480      All verification experiments with seaice are affected (except for
3481      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
3482      results by setting the above flag.
3483      Further changes involve changes in defaults:
3484      - ALLOW_FLOODING is defined and turned on by default
3485      - SEAICEadvSnow = .true. is now the default
3486      - SEAICEadvSalt = .true. is now the default
3487      - SEAICEadvAge  = .true. is now the default
3488      - SEAICE_clipVelocities  = .false. is now the default
3489                                         (as per J. Zhang's recommendation)
3490      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
3491        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
3492      - seaice_growth: replace computation of UG by a simple copy from wspeed
3493    
3494    checkpoint61k (2009/03/18)
3495    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
3496      seaice_lsr: fixed a few metric terms,
3497                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
3498                  add more debugging diagnostics
3499      seaice_evp: removed superfluous many metric terms of FV discretization
3500                  of stress divergence
3501                  affects lab_sea, lab_sea.hb87
3502      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
3503                  of stress divergence for non-evp solver
3504                  (this part is not tested anywhere)
3505      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
3506                  they were effectively only half slip
3507                  affects lab_sea.hb87
3508      updated all relevant verification experiments (except lab_sea//output_adm.txt
3509        which was left over, but fails at level 7 & 6)
3510    
3511    checkpoint61j (2009/03/17)
3512    o pkg/seaice: turn a few hard wired parameters into run time parameters
3513    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
3514      time in seconds as promised by the usints in seaice_monitor and exf_monitor
3515    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
3516      that are not cubed-sphere grids
3517    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
3518    o pkg/ctrl:
3519      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
3520    o non-hydrostatic (calc_gw.F):
3521      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
3522      update output of exp. global_ocean.cs32x15.viscA4
3523    o remove backward compatibility for thetaMin,phiMin
3524      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
3525    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
3526      interpolated wind field not only for curvilineargrid=.true., but also
3527      for a rotated grid (rotateGrid=.true.)
3528    o pkg/exf: add capability to bypass interpolation for runoff
3529      by setting yet another CPP-flag
3530    o eesupp/src, B-grid exchange:
3531      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
3532    o autodiff
3533      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
3534      allows to switch to single-prec common blocks;
3535      corresponding switch occurs in tamc.h, integer isbyte
3536      TAF store directivs "byte" and "kind" seem equivalent;
3537      Most tamc.h have been updated correspondingly.
3538    
3539    checkpoint61i (2009/02/13)
3540    o autodiff:
3541      fix autodiff_sore/_restore indices for obcs
3542      (spotted by I. Hoteit, M. Mazloff)
3543    o pkg/autodiff, pkg/ctrl:
3544      Add flag to reduce all tapelev I/O to single-prec.
3545      In data.ctrl set
3546        doSinglePrecTapelev = .TRUE.
3547    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
3548      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
3549    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
3550      real fresh water flux (not yet)
3551    o pkg/mdsio & rw:
3552     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
3553     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
3554    o pkg/flt:
3555     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
3556       init_fixed & ini_varia.
3557     - clean-up & simplify linear interpolation S/R:
3558       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
3559     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
3560     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
3561     - add vert. coordinate & horiz. indices to output files.
3562     - change vertical position in initial condition, from index to depth [m].
3563     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
3564       (easier to get to a curvilinear grid) ; delX,delY no longer used.
3565    o pkg/ggl90: a few modifications:
3566     - fix bottom boundary condition, and interpolation of KappaE
3567       near top and bottom
3568     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
3569     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
3570     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
3571    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
3572      (maintain temporary backward compatibility, until next checkpoint)
3573    
3574    checkpoint61h (2009/01/27)
3575    o pkg/diagnostics with "periodic averaging diagnostics":
3576      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
3577    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
3578    o pkg/obcs: fix loop ranges for balancing code
3579    o pkg/flt:
3580     - improve criteria for finding which tile owns a float.
3581     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
3582    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
3583      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
3584      with ocean biogeo)
3585    o pkg/flt:
3586     - do some cleaning and fix the restart ;
3587     - add output.txt in flt_example/results to get this pkg tested.
3588    o genmake2: add an EXTENDED_SRC option and flag.
3589       for now, cannot be turned on on command line (only through genmake_local)
3590    o pkg/mdsio: read/write vector:
3591     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
3592     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
3593       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
3594     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
3595      (drop to 4 digits matching for grad). But this test does not look very
3596      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
3597    
3598    checkpoint61g (2008/12/29)
3599    o pkg/flt:
3600      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
3601       + make OPTIONS file more standard.
3602      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
3603      - fix _BYTESWAPIO CPP-Flag
3604      - standard reading of file-parameter "data.flt"
3605      - fix argument list of S/R FLT_RESTART
3606      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
3607    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
3608    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
3609      a still unfixed compiler/optimization bug
3610    
3611    checkpoint61f (2008/11/21)
3612    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
3613      update results of global_ocean.cs32x15.icedyn test.
3614    o move getcon.F from model/src to pkg/fizhi.
3615    o pkg/exf: add parameter for extrapolation of temp up to the surface
3616       and option to prevent negative evap (in bulk_largeyeager04 only).
3617    o Prather Advection scheme: fix tracer conservation for divergent flow
3618      (e.g., when using NonLin Free-Surface).
3619    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
3620    o gmredi (Visbeck-variable-K):
3621     - add more parameters to Visbeck-variable-K.
3622     - use a 5 points average for dSigmaR in Visbeck-K calculation
3623       (more "homogenous": same stencil and same weights as in dSigmaH)
3624     - update output of ideal_2D_oce experiment.
3625    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
3626      (#undef REAL4_IS_SLOW)
3627     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
3628       coordinate variable
3629     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
3630       (surface forcing fields), removes some of the functionality
3631     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
3632     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
3633       probably not all: copy _RS surface flux fields to RL field before
3634       calling DIAGNOSTICS_FILL
3635     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
3636       real*4 (CALL EXCH_*_RS) versions.
3637     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
3638       (generate new output).
3639    
3640    checkpoint61e (2008/10/23)
3641    o gmredi (Visbeck-variable-K):
3642      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
3643      - change computation of Visbeck-K where Slope > Smax :        
3644        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
3645        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
3646    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
3647      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
3648    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
3649    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
3650      does not become too large (to avoid precision problems in implicit-diffusion
3651      solver); update ideal_2D_oce output.
3652    o pkg ggl90:
3653      - in ggl90_cal.F: compute only one set of visc/diff, used to
3654        step forward TKE/T/S/momentum
3655      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
3656        have Prandlt =1)
3657    o gmredi (fm07):
3658      - add lower limit on Transition layer thickness + lower limit on 1/lambda
3659      - allow to set few more params from data.gmredi
3660    o pkg ggl90:
3661          - add missing sqrt(2) factor in computation of mixing length
3662            scale in ggl90_calc.F
3663            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
3664    
3665    checkpoint61d (2008/09/25)
3666    o adjoint modifs
3667      - adapt to new field rhoInSitu
3668      - allow to revert from StoreDynVars2D, StoreDynVars3D
3669        to individual fields
3670        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
3671    o store 3-D (in-situ) density in commom block (DYNVARS.h)
3672     - save 1 rho computation.
3673     - no longer modify T & S inland when using down_slope pkg.
3674    o gad_som : allow to switch to SOM advection for T & S without corresponding
3675      pickup files (using new S/R: MDS_CHECK4FILE).
3676    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
3677      (for useSingleCpuIO to work in multi-threaded)
3678    o pkg/shelfice:
3679     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
3680       with SHELFICEtopoFile in data.shelfice
3681     - move code for reading ice shelf topography and modifying hFacC into separate
3682       subroutines of the shelfice package
3683     - separate initialisation of "fixed" and "variable" variables
3684     - kTopC is not (yet) replaced by kSurfC, although this is possible
3685    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
3686    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
3687      and rename:
3688      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
3689      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
3690    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
3691    
3692    checkpoint61c (2008/08/30)
3693    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
3694      to add mass source/sink of fluid in the interior (3-D generalisation
3695      of oceanic real-fresh water flux).
3696    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
3697    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
3698    o new pkg: down_slope
3699      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
3700      - presently, modify T & S inland (dwnslp_calc_rho.F).
3701        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
3702      - implementation for ocean in P-coords not tested.
3703      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
3704    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
3705      (to facilitate conversion of oceanic pkg to p-coordinate).
3706    o change FIND_RHO to FIND_RHO_2D :
3707      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
3708    o new pkg: cheapaml
3709    
3710    checkpoint61b (2008/08/05)
3711    o exch2:
3712      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
3713      - no longer depend on the order sequence (N,S,E,W).
3714      - 3rd exchange no longer needed (tested with 24 tiles).
3715      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
3716      - exch_UV_A-grid readily available (but not yet tested).
3717      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
3718      (both are no longer needed) in exch_uv: no effect in forward run; but
3719       get truncation error differences with adjoint exch.
3720    o exch2:
3721     - change index-bounds storage (moved from target to local tile,
3722       more intuitive this way) ; rename/remove some variables.
3723     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
3724    
3725    checkpoint61a (2008/07/29)
3726    o exch2/matlab-topology-generator:
3727      fix bug in index bounds for N-S internal exchange (hard to tell if this
3728      had any effect on the solution).
3729    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
3730      is exceeded
3731    o testreport: modify syntax of awk, so that it works also with
3732      awk, and not only with nawk and gawk
3733    
3734    checkpoint61 (2008/06/24)
3735    o autodiff
3736      Change default for TAF usage by removing argument '-nonew_arg'
3737      This changes TAF subroutine argument list (ordering of active var.)
3738      Omission of this flag leads to incompatibility w.r.t. TAMC
3739      To restore TAMC-compatibility, need following modifs:
3740      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
3741      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
3742      Tested TAF version is 1.9.22
3743      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
3744    
3745    checkpoint60 (2008/06/19)
3746    --->>> This is the last checkpoint for which generating the adjoint
3747    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
3748    --->>> by default.
3749    --->>> Future checkpoints will ommit this flag by default.
3750    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
3751    o pkg/grdchk: Add gradient check to etan0 perturbations.
3752    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
3753    o pkg/autodiff: more flexibility in zeroadj.
3754      model/src: modifying do_oceanic_phys.F accordingly.
3755    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
3756    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
3757      special setup of gmredi for which the adjoint is stable
3758      enough for parameter optimization.
3759    o bridging the gap between eddy stress and GM.
3760      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
3761          along with a change in CPP option (now ALLOW_EDDYPSI).
3762      -> when using GM w/ GM_AdvForm:
3763          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
3764          is applied either in the tracer Eq. or in momentum Eq.
3765          depending on data.gmredi (intro. GM_InMomAsStress).
3766      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
3767      The key modifications are in model/src/taueddy_external_forcing.F
3768      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
3769    
3770    checkpoint59r (2008/05/29)
3771    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
3772      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
3773      fix option to read coriolis(@ cell-corner) from files with CS-grid.
3774    o pkg/mnc: add some attributes to standard 1D-coordinate variables
3775    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
3776      mass points, when using mnc for output
3777      - add runtime parameter (missing_value, missing_value_int) to override
3778        default (which is the value of getcon('UNDEF'))
3779    o pkg/mnc: prepare mnc for the actual use of missing values with the
3780      diagnostics package: small fix in mnc_cw_readwrite.template and more
3781      initialisation of never used fields
3782      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
3783      versions
3784    o pkg/thsice/thsice_ini_vars.F added default initial values so that
3785      thermodynamics sea ice solver does not blow up when some initial fields
3786      are missing.
3787    o move from external_forcing_surf.F to ini_forcing.F
3788      the p-coord. hack consisting in using pLoad to set phi0surf ;
3789      update output of tutorial_global_oce_in_p (affected @ truncation level).
3790    o Freshen up a bit hs94.1x64x5, notably:
3791      remove rotationPeriod and tRef=5*0. (adjoint only), and add
3792      exactConserv=.TRUE.
3793    o pkg/generic_advdiff:
3794      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
3795      applies to files where Temperature & Salinity 2nd Order moments are used.
3796    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
3797      this uses a dynamically allocated internal state data structure
3798      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
3799      and requires a fortran 90 compiler
3800    
3801    checkpoint59q (2008/05/06)
3802    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
3803       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
3804    o Refresh tutorial_global_oce_biogeo, notably:
3805      - change bathymetry (put back seamounts in ACC, use hFacs)
3806      - change EOS (POLY3 --> JMD95Z)
3807      - use Bryan-Lewis vertical diffusivity
3808      - use multidimensional advection
3809      - remove old virtual virtual in dic pkg, now done through ptracer pkg
3810      - change a couple of parameters in dic pkg
3811    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
3812    o pkg/obcs: change default to OBCSfixTopo = .true.,
3813      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
3814      - replace "debugMode" with "debugLevel .GE. debLevB"
3815    o implementation of TAF directives for gchem,cfc,dic
3816    o remove "exp5" (replaced by tutorial_deep_convection).
3817    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
3818      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
3819      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
3820      --> changes results in exp4, seaice_obcs
3821    o tutorial_deep_convection :
3822      update the set-up and increase resolution and domain size ; start
3823      from pseudo initial conditions = output at t=120mn in order to see
3824      something happening when running testreport.
3825    o pkg/seaice: add os7mp as an advection scheme
3826                  add check for advection schemes
3827                  add a flag for restoring T and S underneath sea ice
3828    o pkg/my82: add netcdf-support and diagnostics
3829    o thsice pkg:
3830      - Now hsMax limits snow height by turning it into ice following
3831        flooding scheme (and now conserving energy)
3832      - Slight rewriting of the formula in thsice_calc_thick.F
3833      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
3834      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
3835    
3836    checkpoint59p (2008/04/10)
3837    o gchem / dic / cfc :
3838      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
3839      - add new parameter files: "data.dic" & "data.cfc" ;
3840      - various re-arrangement in initialisation & header file ;
3841      - fix tutorial_global_oce_biogeo for multi-threaded test.
3842    o pkg/dic: test for "pickup_dic" file when restarting ;
3843      if no pickup-file, can restart with a re-initialised pH (same as it did
3844      before) providing pickupStrictlyMatch is set to False.
3845    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
3846      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
3847    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
3848      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
3849    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
3850     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
3851       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
3852    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
3853       scheme to use for vorticty-term ;
3854     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
3855       (with default selectVortScheme, return to original discretisation)
3856     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
3857    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
3858    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
3859      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
3860      also fix diagnostics VISCAHW & VISCA4W.
3861    
3862    checkpoint59o (2008/03/07)
3863    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
3864    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
3865      move a few statemens out the main loop into separate loops
3866    o pkg/shelfice:
3867      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
3868        (kg/m^2/s), does not break tests, because in verification/isomip,
3869        rhoConstFresh=rhoConst (by accident)
3870      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
3871      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
3872        new file model/src/seawater.F, so that they are available for all pkgs.
3873      - convert potential temperature into in-situ temperature. This changes the
3874        isomip tests => update tests
3875    o add a flag writePickupAtEnd (default=true) to be able to suppress
3876      writing a pickup at the last timestep
3877    o tools/mpack-1.6 :
3878      - disable automake (not working) and autoconf (not needed).
3879      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
3880        also cleaner with much less compilation warnings.
3881    o pkg/profiles:
3882      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
3883      (for "less than 32 characters name" compiler requirement)
3884    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
3885      conditions that have a different sampling frequency than S/T/U/V obcs
3886    o pkg/diagnostics (stats-diags):
3887      - fix global Min/Max in case 1 processor get only empty tiles
3888    o genmake2: replace (4 times)
3889         make genmake_tc_1.o >> genmake_warnings 2>&1
3890      with
3891         COMM="$CC $CFLAGS -c genmake_tc_1.c"
3892         echo $COMM >> genmake_warnings
3893         $COMM >> genmake_warnings 2>&1
3894      to make genmake2 always see the value of CC as specified in the optfile.
3895    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
3896      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
3897      - modify verification advect_cs test to test SOM-advection on CS-grid.
3898    o pkg/ctrl:
3899      - Rewrite of ctrl_map_ini_ecco.F,
3900        introducing a generic routine (ctrl_map_ini_gen.F).
3901      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
3902    
3903    checkpoint59n (2008/02/09)
3904    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
3905      number in dedicate array "hdiag":
3906      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
3907        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
3908      - many small changes (integer format) for large number of diagnostics
3909      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
3910        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
3911    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
3912      usingSphericalGrid, this allows to define the rotated grid coordinates
3913      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
3914      geographical coordinates according to the inverse of the rotation defined
3915      by the Euler angles, so that Coriolis parameter and online-interpolation by
3916      exf works with the geographical coordinates on XC/YC/XG/YG.
3917      Naturally, this feature does not work with all packages, so some
3918      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
3919      profiles), because there the coordinates are assumed to be regular
3920      spherical grid coordinates.
3921    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
3922      - introduce isopycnal diffusion coefficient control.
3923    o tools/adjoint_options:
3924      - additional control vector components.
3925    o pkg/mnc: have mnc create marginally meaning full coordinate variables
3926      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
3927    o pkg/mypackage:
3928      - add example of read/write pickup for state-var ;
3929      - add entry points to the main code for state-vars diags & write-pickup.
3930    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
3931      transitions for useExfYearlyFields
3932      - add new subroutine that determines the file to read from for
3933        use*YearlyFields = .TRUE. and .FALSE.
3934      - add a verification experiment to global_with_exf that tests
3935        useExfYearlyFields with USE_EXF_INTERPOLATION defined
3936    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
3937      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
3938      subroutines (which could be generated from a template, because they are
3939      almost identical), for now they are included in obcs_prescribe_read.F for
3940      simplicity
3941    o pkg/exf:
3942      - add a little more diagnostic to exf_interp_read (in analogy to
3943        mds_read_field, can be turned off with debugLevel < debugLevA=1)
3944      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
3945        ugly but fast by unrolling short inner loops, inserting a unroll=8
3946        directive in routine lagran, and splitting a loop and making do while the
3947        outermost loop (the latter requires the intoduction of index arrays)
3948    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
3949    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
3950      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
3951    o verification/seaice_obcs: updated for restart test and latest options
3952    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
3953      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
3954      for now this is only available for the C-grid code and also within
3955      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
3956    
3957    checkpoint59m (2008/01/14)
3958    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
3959      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
3960    o gad_som : fix flux output (& diagnostics) to have same units as other  
3961      advection scheme fluxes (was previously multiplied by deltaT).  
3962    o added verification/seaice_obcs both to test seaice open boundaries
3963      and to provide an example matlab scrpt for generating them
3964    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
3965    o pkg/salt_plume: clean up salt_plume_frac.F to
3966      remove redundancy in PlumeMethod 1 and 4
3967    o pkg/kpp: added saltplume diagnostics
3968    o pkg/obcs and pkg/seaice:
3969      - do not set uice and vice to zero when OB*icefile are unspecified
3970      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
3971      - moved seaice tracer obcs after call to seaice_growth
3972    o pkg/salt_plume: added various options for salt plume depth
3973      criterion and for vertical distribution of the salt
3974    
3975    checkpoint59l (2007/12/18)
3976    o pkg/ptracers: new version of ptracers pickup:
3977      read meta file and write only fields which are needed to restart.
3978      ( same logic as main pickup file ; also using pickupStrictlyMatch )
3979    o pkg/seaice:
3980      - add timescale for melting due to warm mixed layer as a means of
3981        setting SEAICE_availHeatFrac more conveniently
3982      - add a CPP-flag/runtime parameter check for flooding algorithm
3983      - reformulated availHeat in seaice_growth.F to be independent of AREA
3984    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
3985      unit changes
3986    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
3987    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
3988      SX vector computer.
3989    o pkg/seaice:
3990      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
3991        seaice forcing fields can now be read only through pkg/exf
3992      - removed some unused halos
3993    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
3994    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
3995      or U/VICE from U/VWIND before computing U/VSTRESS
3996    
3997    checkpoint59k (2007/11/30)
3998    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
3999      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
4000    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
4001      all experiments pass when compile with un-initialised var. checking option.
4002    o added pkg/salt_plume
4003    o script to test restart (for now, in MITgcm_contrib/jmc_script)
4004    o pkg/seaice: new read/write pickup version.
4005      read meta file and write only fields which are needed to restart.
4006      ( same logic as main pickup file ; also using pickupStrictlyMatch )
4007    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
4008    o lab_sea.hb87: modify the domain & update output.hb87.txt :
4009      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
4010      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
4011      process. Fixed here by closing the domain at the Northern boundary.
4012    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
4013    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
4014      a set of consecutive levels in/from a 3-D array.
4015    o pkg/ptracers:
4016      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
4017      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
4018    
4019    checkpoint59j (2007/11/09)
4020    o in pkgs: dic, obcs, offline, rbcs:
4021      standard way to compute coeff. for time interpolation between 2 time reccords
4022      which retains full precision (& make results less dependent on compiler).
4023      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
4024    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
4025      packages instead of reading ice cover and wind speed separately
4026    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
4027     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
4028      to allow to compile customized code before the update)
4029    o cleaning-up:
4030      - fix CPP instruction syntax in pkg/obcs
4031      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
4032        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
4033      - fix some threads issue in IO parts.
4034    o pkg/dic:
4035      - add tons of "_d 0" (--> much better testreports !)
4036       and then update outputs of tutorial_global_oce_biogeo
4037    o pkg/mom_fluxform:
4038      add a special version of momentum advection intended to conserve momentum
4039      next to a bathymetry step or a coastline edge. (default = off = #undef)
4040    o new read/write pickup version:
4041      - for now, only implemented for main (mdsio) pickup file.
4042      - write out only what is needed to restart; merge pickup_nh , pickup_ph
4043        and main pickup together.
4044      - read meta file; read only what is needed to restart; stop if a field
4045        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
4046        if it make sense (even if the restart is not perfect).
4047      - if no meta file, assume that pickup to read corresponds exactly to
4048        a pickup that would currently be written.
4049      - read pickup written in the old format (until checkpoint59i) if it
4050        recognizes an old meta file (no field-list).
4051      - add a meta file in exp. which starts from a pickup: 2 cases:
4052        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
4053         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
4054        b) a meta file describing the content of the associated pickup file
4055         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
4056    o pkg/mdsio & pkg/rw:
4057      - new routine to read a meta file ; new set of routine to read
4058        Multiple-fields file (with meta file).
4059    o added open boundary conditions capability for seaice
4060        HSNOW, HSALT, UICE, and VICE
4061    
4062    checkpoint59i (2007/10/21)
4063    o adjoint:
4064      * fix multiDimAdvection adjoint
4065        (partial recomputation problem by TAF for fVerT(:,:,kDown)
4066        and comlev1 size definition (maxpass vs. max. number of tracers)
4067      * verification/global_ocean.90x45x15 adjoint now tests
4068        NLFS and multiDimAdvection using DST3 (=30)
4069      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
4070    o pkg/kpp: add "_d 0" to real constant (if missing);
4071      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
4072      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
4073    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
4074      for internal parameters related to restart process (formerly from PARAMS.h)
4075      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
4076    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
4077      as argument. (only atm2d & obcs write_pickup have not yet been updated)
4078    o pkg/monitor:
4079      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
4080      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
4081      - account for deep Atmosphere factor and density factor (anelastic)
4082    o added open boundary conditions capability for seaice HEFF and AREA
4083    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
4084      thermodynamics
4085      - requires a little reorganization, which affects the testreport results
4086        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
4087        so that now the conservative form is tested
4088      - add a few comments
4089    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
4090    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
4091    o add new diagnostics to seaice: advective, diffusive fluxes (only for
4092      multidim-advection, for scheme 2 they are not filled) and transports,
4093      thermodynamic growth rates
4094    o change units of EmPmR (inside the code, + within coupling interface)
4095      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
4096      Affects results @ truncation level (cg2d match) and update output of
4097       experiments: lab_sea(6), global_ocean.90x40x15(10),
4098      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
4099      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
4100      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
4101      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
4102    
4103    checkpoint59h (2007/09/29)
4104    o pkg/exf:
4105      - improve vectorization by moving if-statement out of loops in
4106        exf_mapfields, exf_radiation
4107      - exf_bulkformulae.F: introduce 2D fields and vectorize code
4108    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
4109    o testreport:
4110      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
4111        monitor & update offline_exf_seaice exp. output.
4112      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
4113    o pkg/seaice:
4114      - bug fix in the evp solver: boundary conditions were affected be
4115        masking of zMax/zMin (changes results)
4116      - minor bug fix in boundary conditions in seaice_calc_strainrates
4117        (changes results for no_slip)
4118      - seaice_lsr.F: make interpolation of eta dependent on boundaries
4119      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
4120      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
4121        stress formulation and no-slip boundary conditions
4122    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
4123      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
4124    o pkg/seaice: a first HSALT time stepping equation has been checked in
4125    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
4126      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
4127      without requiring DO-IF statements
4128    o pkg/thsice:
4129      use continuous power-law function for partition of energy between lateral
4130      melting/freezing and thinning/thickening ; old code using step function
4131      still available with #undef THSICE_FRACEN_POWERLAW
4132      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
4133    o testreport: change AD testing : check against results/output_adm.txt
4134      using same scripts as for forward test.
4135    
4136    checkpoint59g (2007/09/17)
4137    o adjoint testing: in preparation for changing testreport:
4138      - output format: cost and grad written on separated lines
4139      - ad output results in directory "results" (instead of "results_ad")
4140    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
4141    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
4142    o pkg/ecco: allow user defined cost function contributions
4143    o testreport:
4144      Allow to choose (per experiment) the list of tested output variables
4145       and the main variable (used to issue a pass/FAIL ) ;
4146      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
4147      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
4148      Also modify printing of summary:
4149       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
4150       b) echo the list of tested variables in the individual summary.txt of
4151          each experiment.
4152    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
4153      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
4154      (but still depend on the tile decompostion of the domain).
4155    o pkg/seaice: change a discretization detail to make the B-grid code
4156      "more symmetric". This change is likely to remove all "ridges/leads" that
4157      where quasi-aligned with the grid in B-grid solutions. It may also be
4158      the solution to the stress coupling issues with the B-grid.
4159    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
4160      remove .cvsignore from input dir. (since testreport no longer run here).
4161    o pkg/thsice:
4162     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
4163     - fix reshaping of sea-ice just after advection:
4164       melt all the ice only if ice-volume is too small.
4165     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
4166       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
4167     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
4168    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
4169      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
4170    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
4171      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
4172      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
4173      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
4174      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
4175      -> update output.txt
4176    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
4177     this affects truncation error: -> update output.txt of exp:
4178      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
4179      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
4180    
4181    checkpoint59f (2007/08/21)
4182    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
4183    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
4184      a bounded range (in forward mode)
4185    o pkg/ecco, ctrl, autodiff and mom_common:
4186     internal parameter controls, completements of implementations
4187    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
4188    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
4189      (not seem any difference in testing results).
4190    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
4191       at face corners.
4192    o pkg/generic_advdiff:
4193     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
4194      loop range indices for computing vertical advection tendency
4195      and do the calculation in the interior only (no overlap) ;
4196      for now, only implemented for SOM advection (to save CPU time).
4197     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
4198    o exch2 adjoint
4199      First set of changes:
4200      - add exch2 hand-written adjoint templates
4201      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
4202        This will require cleanup in pkg/autodiff/*.F
4203        (changed routines currently kept separate in verif. code/)
4204      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
4205        that used to hide exch2 or cubed-sphere specific code
4206        (commented via 'cph-exch2')
4207    o pkg/seaice
4208      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
4209    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
4210       output of global_ocean.cs32x15.thsice .
4211    
4212    checkpoint59e (2007/07/26)
4213    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
4214      for B-grid vector (not yet tested) and C-grid vector (<- only used
4215      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
4216    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
4217      (#ifdef ALLOW_SALT_PLUME)
4218    o gather_2d/scatter_2d: removed halo regions
4219    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
4220      scheme and the corresponding test case (under front_relax dir). For now,
4221      only available with Skew-flux form and not yet tested in realistic set-up.
4222      adjoint: store directives updated, but gradient checks deteriorated,
4223      so maybe GM/Redi adjoint is now broken.
4224    o seaice adjoint
4225      * add AREA, HEFF, HSNOW as control variable
4226        (should not change lab_sea results)
4227      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
4228    o pkg/seaice:
4229      * added computation of saltFlux in seaice_growth;
4230        For time being, sea ice salinity is assumed constant
4231        contribution of snow flooding to freshening of sea ice is neglected.
4232        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
4233        defaults to 0.0 in order to maintain backward compatibility.
4234        Typical values for SEAICE_salinity are 4 to 10 g/kg.
4235      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
4236      * added SEAICE_availHeatFrac, which specifies fraction of surface level
4237        heat content used to melt or grow ice
4238      * commented out cap of HICE: it helps keep ice thinner
4239      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
4240      * applied OBCS T/S mask to HEFFM sea ice mask
4241    
4242    checkpoint59d (2007/06/21)
4243    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
4244     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
4245     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
4246    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
4247     and change default value of parameter "GM_Small_Number";
4248     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
4249       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
4250       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
4251    o pkg/ecco: cost function when applying pkg/smooth to controls
4252    o pkg/ctrl: add forcingPrecond run time parameter
4253    o pkg/seaice:
4254     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
4255     - fix bug in metric terms of u-equation in LSR solver (implicit part),
4256       changes verification/lab_sea
4257     - rearrange implicit part of u-equation in LSR solver to make it easier to
4258       read, understand, and debug. This causes changes at the truncation level.
4259     - fix (serious) bug in the boundary conditions (sign error in the implicit
4260       part) of the LSR solver. Changes all LSR results.
4261     - fixed problem with HSNOW initialization to avoid thick snow when AREA
4262       is initilized with small values - does not change lab_sea results.
4263     - added HsnowFile initialization capability
4264    o pkg/smooth: addition to model/src and pkg/ctrl so allow
4265     initialization of pkg/smooth and application to control vector
4266    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
4267    o dependencies: pkg/profiles requires pkg/cal
4268    o pkg/profiles:
4269     - added option ALLOW_PROFILES_GENERICGRID
4270         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
4271         that interpolation information (grid points and coefficients) is provided
4272         within the netcdf input files.
4273         -> sample matlab scripts can be found in MITgcm_contrib/gael
4274         that allow you to prepare netcdf input files.
4275     - also modified: cleaner include statements, cleaner error print statements,
4276       cleaner stops when error, and more tests of the netcdf input files consistency.
4277    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
4278    o pkg/seaice:
4279     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
4280       requires a new routine: seaice_diagnostics_fill.F
4281     - make sure that seaice does not move if not forced (pressure replacement
4282       method, Hibler and Ip, 1995), changes results
4283     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
4284     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
4285       It is turned off by default (=-1.), because it changes the results.
4286     - make it possible to read AREA from a file, too.
4287    
4288    checkpoint59c (2007/06/04)
4289    o add S/R and diagnostics for oceanic mixed-layer depth
4290    o move GMRedi call after all vertical mixing schemes (including KPP)
4291    o pkg/thsice:
4292     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
4293      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
4294    o pkg/obcs:
4295     - bug fix for balance code
4296    o pkg/seaice:
4297      - allow values of SEAICE_elasticParm > 1
4298      - add new parameter SEAICE_evpTauRelax as an alternative
4299        to SEAICE_elasticParm
4300      - make lsr boundary conditions free slip (by default), changes result
4301      - add code for no slip boundary conditions for lsr
4302      - set minimum of zeta to zero (and not 4e8) (changes results)
4303      - add a cap on AREA after advecting AREA if seaice_growth is not called
4304    o change calculation of Visbeck K:
4305      - no longer depend on tapering scheme; instead, compute slope (limited
4306        by GM_maxSlope). this is equivalent to what was comuted before with
4307        clipping or linear tappering.
4308      - fix vertical averaging (wrong by 1/2 level)
4309      - leave the old version (but will not be maintained) within
4310        #ifdef OLD_VISBECK_CALC / #endif
4311      - update output of exp. ideal_2D_oce
4312    o change error catch in calc_r_star to improve vectorization
4313    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
4314      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
4315    o adjoint:
4316      Re-organized adjoint checkpointing according to Matt Mazloff
4317      (but with modifs/completions/cleanups)
4318      Storing is now bundled into large arrays to optimized I/O
4319      (and second step in cleanup of the_main_loop)
4320    
4321    checkpoint59b (2007/05/16)
4322    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
4323      - export/import (between ocean & coupler) fields needed for ocean DIC.
4324    o pkg/seaice:
4325      - get rid of three more exchanges seaice_calc_viscosities (required
4326        different loop boundaries in seaice_lsr and seaice_ocean_stress)
4327      - bug fix in seaice_ocean_stress (update of lab_sea required)
4328      - reduce loop boundaries to necessary minimum also in seaice_evp
4329      - go back to the old way of computing deltaC/Z as the adjoint likes that
4330        better
4331    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
4332      passive tracer to an Age Tracer) + update output.txt
4333    o pkg/exf:
4334      - implement A-grid / C-grid selection for wind-stress input files.
4335      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
4336      for now, in exf_bulk_largeyeager04.F only :
4337      - change implementation for case where windspeed + 2. components wind-stress
4338        are read-in. AND use rhoConstFresh to convert evap.
4339    o pkg/seaice:
4340      - use correct EXCH_UV for wind-forcing (on A-grid).
4341      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
4342        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
4343    o pkg/exf:
4344      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
4345      EXF_INTERPOLATION:
4346      - merge global_with_exf/code version of exf_interp_read.F
4347        to the main code ;
4348      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
4349        reading the file ; Important: This options needs to be defined to recover
4350        previous code.
4351        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
4352      - no longer loose real*8 precision along the way when using exf_iprec=64.
4353    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
4354      - change discretisation of evp-solver in order to avoid another exchange
4355        (changes lab_sea) and clean up a little
4356      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
4357        help the adjoint (this also changes the results slightly)
4358      - add a few "_d 0" where they had been missing in seaice_evp.F
4359      - cleaning up: remove unused seaice_calc_rhs.F
4360    o pkg/exf: some cleaning-up:
4361      - change various "constants" into runtime parameters
4362      - cleaned-up Large&Yeager04 routine which should eventually
4363        replace exf_bulkformulae.F (changed names of S/R and CPP)
4364        and merged various ALLOW_ATM_WIND options
4365     only used with thsice pkg (in thsice_get_exf.F):
4366      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
4367        which are used when useStabilityFct_overIce=TRUE (= the default)
4368      - change default values of ice & snow emissivity and scale downward LW
4369        by ice & snow emissivity.
4370    o pkg/thsice:
4371     fix few little problems, in thsice_calc_thickn.F:
4372      - growth vertically (and not laterally) if iceFrac == iceMaskMax
4373      - melt only laterally if hIce < hThinIce (as the comments say)
4374      and in thsice_extend.F:
4375      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
4376      - start to form ice as soon as the minimum ice-volume is reachable.
4377     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
4378      and cpl_aim+ocn
4379    o pkg/kpp
4380     - move computation of surface related input fields to KPP into a new
4381       subroutine kpp_forcing_surf.F
4382     - remove wrong (within bi,bj loops) EXCH calls.
4383     - little cleaning (add argument myThid in last position, cvs header ...)
4384     - for now, fix conservation problem by exchanging KPPviscAz (may not
4385       be the best fix)
4386    o pkg/seaice
4387     - check for inconsistent evp parameter/cpp-flag combination
4388     - remove leftover errIO flat for obsolete name list error handling
4389    o OpenAD
4390     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
4391    
4392    checkpoint59a (2007/05/01)
4393    o pkg/seaice: some parameter clarifications and a little bit of clean up
4394    o pkg/thsice: rename run-time parameters:
4395       himin       -> hIceMin
4396       himin0      -> hThinIce
4397       hihig       -> hThickIce
4398       i0          -> i0swFrac
4399       transCoef   -> bMeltCoef
4400       frac_energy -> fracMelting
4401      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
4402       with default values (for now) that do not change the results.
4403      remove old version of thsice vars advection in pkg/seaice.
4404    o in FFIELDS.h:
4405      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
4406      - make pLoad & sIceLoad always available (but still only used if
4407         ATMOSPHERIC_LOADING is #define).
4408    o pkg/kpp: replaced _KPP_RL with _RL
4409    o bug fixes for vertical diffusivity computations when both KPP and
4410        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
4411        are no longer updating the vertical diffusivity array
4412        (passed as argument) but are (re-) setting those arrays.
4413    o pkg/seaice: fix bug in evp solver, while doing that
4414      - change (improve?) discretization of stress computations for both
4415        cgrid-lsr and evp solver
4416      - add a new routine to compute strain rates
4417      - the above changes lab_sea results
4418      - add no slip conditions for evp solver (off by default), lsr-version
4419        may follow
4420      - fix exchange for shear at Z-points (does not change lab_sea)
4421      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
4422        (to force the user to pick a time step since there is not "safe" way
4423        of choosing it)
4424      - add principal stress diagnostics
4425      - rearrange fields for evp a little to avoid having to call a: too many
4426        exchanges and b: exchanges for stress trensor components which we do
4427        not have.
4428      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
4429        of evp, complete rewrite for lsr case (latter is does not yet work
4430        in all cases)
4431    o pkg/kpp: add code to have mixing in shelf ice caverns
4432      - add myThid to all kpp routines (long overdue)
4433    
4434    checkpoint59 (2007/04/19)
4435    o pkg/exf:
4436      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
4437        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
4438      - move exf header files from lower_case.h to UPPER_CASE.h ;
4439        add missing cvs Header & Name
4440      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
4441      - add namelist param. selectStressGridPosition, exf_monFreq
4442      - retire many _CLIM routines, and remove data.exf_clim
4443        + params moved to data.exf
4444        + climsst, climsss now handled by exf_set_gen, i.e.
4445          climss?period=0 refers to constant field,
4446          climss?period=-12 to monthly forcing
4447      - split up namelists in data.exf
4448    o pkg/seaice:
4449      - remove seaice_exch and seaice_exch_uv
4450      - remove superfluous exchange of theta
4451      - add myThid to seaice_budget_ocean/ice
4452      - add new interface for atmospheric wind forcing (C-grid only)
4453        + new routine
4454        + two new field (taux, tauy for stress over ice)
4455        + removed one global field (DAIRN) for C-grid case only
4456    o pkg/thsise
4457      - 2nd set of modifs for thsice adjoint in conjunction with exf
4458    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
4459    
4460    checkpoint58y_post (2007/04/15)
4461    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
4462      vertical diffusivity, similar to that in MOM4; turned on using
4463      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
4464      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
4465    o Added capability for 3D specification of background vertical diffusion
4466      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
4467      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
4468      "data" file that contains the 3D vertical diffusivity coefficients.
4469    o ice dynamics (pkg/seaice) with thsice thermodynamics:
4470      - add code within pkg thsice to advect & diffuse sea-ice fields
4471      similar to (and will replace) what has been added in  seaice_advdiff.F,
4472      but: - conserving Mass, Heat & Salt.
4473           - better when using non-linear advection scheme (not yet fully tested)
4474           - can also be used in atmospheric set-up (for now, only the diffusion).
4475    
4476    checkpoint58x_post (2007/04/04)
4477    o IO option for global-file compact format:
4478      - add options when generating topology (utils/exch2/matlab-topology-generator)
4479      - add I/O capability (pkg/mdsio).
4480      - adapt utils/matlab/rdmds.m to read this format.
4481      for now long-line format not yet supported by pkg/mdsio (& exch2).
4482    o shelfice: add a few diagnostics
4483    
4484    checkpoint58w_post (2007/03/13)
4485    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
4486      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
4487      (and replace horiVertRatio in NH code).
4488      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
4489                         and tutorial_plume_on_slope (sensitive to truncation)
4490    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
4491      directly to drive seaice model (C-grid only)
4492    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
4493     - reintroduce computation of wind from stress,
4494     - compute tau (in exf_bulkformulae.F) from windstress averaged to
4495       mass points to avoid tau = 0
4496     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
4497    o rdmnc.m: make it work with "global" files created with gluemnc
4498    o rdmnc.m : some improvements in dealing with singleton dimension
4499      (tested on all testreport mnc output files).
4500    o genmake2: disable pkg/profiles if netcdf test fails.
4501    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
4502    o move call to cal_readparms up to make calendar parameters/variable available
4503      to all packages
4504    
4505    checkpoint58v_post (2007/02/08)
4506    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
4507      useDynP_inEos_Zc tested.
4508    o pkg/exf: changes to properly interpolate/mask/scale initial fields
4509    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
4510      and portions thereof.  See read_cs.txt for description and examples.
4511    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
4512      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
4513      following the great-circle arc between those 2 points.
4514    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
4515      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
4516    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
4517     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
4518     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
4519     - still needs work (not working with some options ; efficiency to improve)
4520       and serious testing.
4521     - use this scheme for temperature & salinity in 2 advection test exp.:
4522       advect_xy & advect_xz, respectively.
4523    
4524    checkpoint58u_post (2007/01/12)
4525    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
4526    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
4527    o testreport: add option "-skipdir" to skip some test.
4528    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
4529      momentum calculation.
4530    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
4531    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
4532      remove checkpoint.F and the_correction_step.F (no longer used);
4533      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
4534    o add option (linFSConserveTr) to correct for tracer source/sink due to
4535      Linear Free surface
4536    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
4537    o pkg/thsice: fix reading mnc-pickups
4538    
4539    checkpoint58t_post (2006/12/30)
4540    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
4541    o pkg/mdsio:
4542     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
4543       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
4544       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
4545     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
4546     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
4547       either MDS_READ_FIELD or MDS_WRITE_FIELD )
4548     - new S/R (to replace MDSWRITEMETA), which allows to write more
4549       informations (variable names, time ...) to meta files.
4550     - modify rdmds.m to give back the meta file content.
4551    o pkg/diagnostics: change vertical interpolation to be safer, and more
4552       flexible (define p-levels to interpolate to in data.diagnostics);
4553      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
4554       diagnostic pointer.
4555    o pkg/seaice: more cleaning up of seaice_growth, added many comments
4556    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
4557    o fix multi-category seaice:
4558     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
4559       SEAICE_MULTICATEGORY
4560     - fix short wave heat flux
4561    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
4562       and allow to use EVP solver. Change forward lab_sea: test both EVP
4563       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
4564    o Initial check-in of lab_sea adjoint
4565      (very similar to natl_box_adjoint/code_seaice)
4566      * used C-grid and EVP solver
4567      * used KPP, GM/Redi
4568      * uses inAdExact=.TRUE.
4569      * gradient checks fail for both ADM and TLM
4570        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
4571        f.d. gradients actually seem more problematic than ADM, TLM gradients;
4572        issue is related to forward mismatch between g77 an ifort
4573    o pkg/seaice: overhaul of thermodynamics
4574     - growth.F and groatb.F are replaced by new routine seaice_growth.F
4575     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
4576     - move a few global fields out of SEAICE.h into seaice_growth.F and
4577       make them 2D (FICE/QNETO/ ...)
4578     - remove FO (it is the same as QNETO)
4579     - introduce a few local fields to avoid modifying external fields such
4580       as atemp, etc.
4581    
4582    checkpoint58s_post (2006/12/11)
4583    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
4584      changed exf_set_gen.F so that
4585        genperiod=0 means input file is one time-constant field and
4586        genperiod=-12 means input file contains 12 monthly means
4587    o CG2D: use pre-computed solver main-diagonal (stored in common block);
4588      this affects truncation error ; generate new output file for exp. which
4589      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
4590        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
4591        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
4592        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
4593        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
4594        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
4595    o start implementation of deep-atmosphere and anelastic formulation
4596    o verification: remove 2nd copy of input files and use script "prepare_run"
4597      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
4598    o mom_common/vecinv/fluxform: fix a few initialisation isssues
4599    o profiles: fix for multithreaded case
4600    
4601    o diagnostics: rename few diags:
4602      s/'PRESSURE'/'RCENTER '/g
4603      s/'TICE    '/'oceFreez'/g
4604      s/'TAUX    '/'oceTAUX '/g
4605      s/'TAUY    '/'oceTAUY '/g
4606      s/'SWFLUX  '/'oceQsw  '/g
4607      s/DIFx/DFxE/g
4608      s/DIFy/DFyE/g
4609      and add few ocean-forcing diagnostics:
4610      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
4611    o modifications to pkg/seaice/growth.F and budget.F, which change results of
4612      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
4613      as actual snow thickness.  It now refers everywhere to effective snow
4614      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
4615    
4616    checkpoint58r_post (2006/11/17)
4617    o modifications to pkg/seaice/growth.F, which change results of
4618      lab_sea experiment: fixes pertain to melting snow over open water, to
4619      masking EVAP under sea ice, and to using the correct AREA variable for
4620      computations of EVAP, PRECIP, HSNOW, and GHEFF
4621    o add ability to read bathy, salt, and theta using MNC (off by def)
4622    o add flooding algorithm and advection of HSNOW for pkg/seaice;
4623      both are turned off by default and do no change any results
4624    o seaice advection with pkg/thsice: a step toward the use of non-linear
4625      advection scheme, but #ifdef or commented out for now (requires more EXCH).
4626    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
4627      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
4628      in natl_box (affects results @ truncation level: update output.txt)
4629    o multi-threading and IO:
4630      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
4631      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
4632        (needed to work with SingleCpuIO): tested in all verif. exp.
4633    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
4634      affects the results (but none of the verification test uses this scheme).
4635    o Adding some pkg/diagnostics capability to pkg/seaice
4636      (will certainly be subject to changes)
4637    o ctrl: adding new control variables:
4638      lwflux, lwdown, evap, snowprecip, apressure, runoff
4639    
4640    checkpoint58q_post (2006/10/20)
4641    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
4642      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
4643      high_res_cube configuration by 4% on Columbia.
4644    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
4645      add (in global_with_exf/code) a version of EXF_INTERP_READ without
4646      dynamical allocation (seems to work in multi-threaded).
4647    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
4648      single CPU io) so that TAF does not have to see EESUPPORT.h
4649    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
4650    
4651    checkpoint58p_post (2006/09/08)
4652    o obcs: stop if obcs is used with useCDscheme = .true.
4653    o shelfice:
4654     - fix a sign error so that no slip at shelfice interface works
4655     - remove stop for combination non-hydrostatic code and shelfice. That does
4656       not mean, that the results are correct, but at least they are numerically
4657       stable
4658    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
4659    o added adjoint exch routined for all exch*3d* routines
4660      and updated flow directives
4661    
4662    checkpoint58o_post (2006/08/28)
4663    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
4664      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
4665    o change controling S/R for writing pickup file (new S/R do_write_pickup)
4666      and clean-up reading/writing of pickup files.
4667    o fix local version of read/write pickup (NH part) in rotating_tank/code
4668    o simplify EXCH interface:
4669     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
4670     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
4671    o added the regrid package
4672    o shelfice:
4673     - add a simple boundary layer scheme to reduce noise
4674     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
4675    
4676    checkpoint58n_post (2006/08/14)
4677    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
4678       local variable (not in common block).
4679    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
4680      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
4681      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
4682        to work with SingleCpuIO.
4683    o add "_d 0" to real constant of pkg/cfc subroutines ;
4684       update exp. cfc_exemple & tutorial_cfc_offline output files.
4685    o multi-threading and IO:
4686      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
4687        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
4688      - barrier before and after reading.
4689      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
4690      - avoid using MDS_WRITELOCAL for LAND pkg output.
4691      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
4692        common-block variables ; Allows multi-threading with master-thread IO.
4693    o change default MAX_NO_THREADS from 32 to 4 ;
4694      and stop cleanly when MAX_NO_THREADS is too small.
4695    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
4696    
4697    checkpoint58m_post (2006/07/17)
4698    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
4699       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
4700    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
4701       keep global_ocean.90x40x15 (for AD testing) with former secondary test
4702       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
4703    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
4704        add MITgcm_tutorials (= code + all the tutorials)
4705    o ecco, option to compute cost for total ssh (mean+anom)
4706    o consistent with addition of ptracer and ssh in pkg/profiles
4707    o profiles: adding ptracer and ssh
4708    o testreport: change multi-test output-file name
4709      (from output.txt.{name} to output.{name}.txt)
4710    o profiles: now ok for mutli-tiles case
4711    o seaice: add 4 parameters for different advection schemes for area,
4712      (effective) seaice thickness, enthalphy, and snow height. Their default
4713      is the standard parameter SEAICEadvScheme
4714    o calc_gw:
4715     - add cosFacU in zonal viscous flux (harmonic.visc.).
4716     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
4717       of tutorial_plume_on_slope.
4718    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
4719    o calc_gw: true flux-form, account for horizontal grid spacing.
4720      update rotating_tank results, but not plume_on_slope (affected at
4721      truncation level, 11 digits).
4722    
4723    checkpoint58l_post (2006/07/12)
4724    o calc_gw:
4725     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
4726     - remove side-drag for now (need to fix it); update plume_on_slope results.
4727     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
4728    o commit code to make SST/SSS weights spatially variable
4729      (based on either variable in-situ or variable initial T/S weights)
4730    o pkg/ecco:
4731      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
4732        now based on horizontally varying weights wthetaLev, wsaltLev
4733      * cost_averagesflags now returns year indices in addition to day, month
4734      * sflux balance is performed on annual basis
4735        (sflxumm, sfluxmm2, bal_sfluxmm)
4736      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
4737        including separate counting and multipliers
4738    o pkg/rbcs
4739      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
4740    
4741    checkpoint58k_post (2006/07/06)
4742    o testreport:
4743     - always build in dir. "build" (if not there, mkdir build instead of building
4744       & running in input)
4745     - run in dir run (if it exists), in build otherwise.
4746     - call prepare_run (if input/prepare_run exists)
4747     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
4748    o pkg/exf modifications to interpolation and rotation routines for more
4749       reasonable treatment of North Pole singularity: for tracers North Pole
4750       value is set to northernmost zonal-mean value, for zonal velocity it is
4751       set to zero, and for meridional velocity it is set to northernmost value.
4752    o pkg/exf/exf_check_range.F
4753     - add tile index to diagnostics and move stop statement to the very
4754       end of the routine.
4755    o pkg/diagnostics: (diagnostics_main_init.F)
4756      define title of isomorphic variables according to the current config.
4757    o pkg/thsice with pkg/seaice dynamics:
4758    - fix domain of computation (interior only, required for exf) and do exchanges
4759    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
4760    o towards a standard way of dealing with multi-threading in MONITOR
4761      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
4762    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
4763       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
4764    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
4765    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
4766    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
4767       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
4768    o tracer advection:
4769     - clean-up and simplify calc_common_factors.F
4770     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
4771       advection subroutine (but still not used within DST advection S/R)
4772    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
4773    
4774    checkpoint58j_post (2006/06/15)
4775    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
4776      from file (collects calls previously in FORWARD_STEP)
4777    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
4778    o adjoint store dir. adjusted accordingly
4779    o genmake2
4780      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
4781    
4782    checkpoint58i_post (2006/06/14)
4783    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
4784      on wind stress (SEAICEstressFactor defaults to 1.)
4785    o Total number of Timers is finite (<=40): comment out 2 non-essential one
4786      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
4787    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
4788      on CS-grid: no longer loosing mass.
4789    o exf & curvilinear-grid: no longer modify longitude xC & xG.
4790    o pkg/ggl90: fix sloppy output and fix a bug
4791    o pkg/seaice: added SEAICEuseEVPpickup parameter
4792      - Set to false in order to start EVP solver with
4793        non-EVP pickup files when using SEAICEuseEVP
4794      - fix sign error in diffusion in seaice_calc_rhs
4795    
4796    checkpoint58h_post (2006/06/07)
4797    * Modifications for bottom topography control
4798      o replace hFacC by _hFacC at various places
4799      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
4800      o add non-self-adjoint cg2d_nsa
4801      o update autodiff support routines
4802      o re-initialise hfac after ctrl_depth_ini
4803      o works for 5x5 box, doesnt work for global_ocean.90x40x15
4804    * Adding verification for 5x5 box (4-layer) bottom topography control
4805    
4806    checkpoint58g_post (2006/06/07)
4807    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
4808       used for mean seasonal cycle, mean diurnal cycle); add an example
4809       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
4810    o pkg/ggl90:
4811      - add parameter (minimum surface kinetic energy)
4812      - fix bug (avoiding division by zero)
4813    o couple pkg/thsice to pkg/seaice:
4814      - modify advection in seaice to accomodate new scalar fields to be advected
4815      - only muliDimAdection scheme work with seaice/thsice
4816      - mapping of thsice-variables to seaice-variables, back and forth
4817      - does not break the verification experiments, but does not give the
4818        desired results either
4819    o pkg/seaice
4820      - make (default) second order advection a bit less confusing?
4821    
4822    checkpoint58f_post (2006/06/05)
4823    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
4824      to pkg/seaice):
4825      - new routines thsice_map_exf and thsice_get_exf provide the interface
4826      - add an additional formal parameter to thsice_solve4temp
4827    o pkg/exf:
4828      - add new fields wspeed, snowprecip (to be able to couple to thsice)
4829      - correct Stefan-Boltzmann constant
4830      - new parameter for longwave surface emittance
4831      - separate some stuff from exf_bulkformulae into new routines  
4832        exf_radiation, exf_wind
4833      - add new parameters and constants: longwave emissivity for ocean, ice
4834        and snow, evaporation parameters over ice
4835      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
4836        either wind from stress or stress from wind
4837    o pkg/thSIce:
4838    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
4839    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
4840       and THSICE_CALC_THICKN
4841    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
4842    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
4843      to make debugging easier.
4844    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
4845    o pkg/bulk_force:
4846      - clean-up comments and parameters ;
4847      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
4848    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
4849      generate new output for test-experiment: aim.5l_cs.thSI
4850    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
4851      testreport accordingly
4852    
4853    checkpoint58e_post (2006/05/17)
4854    o SEAICE_CGRID adjoint done
4855    o R_STAR adjoint implemented.
4856      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
4857      * need to sort out init. of h0facc, etc.
4858    o Make pkg/profile fully independent of ecco,cost, etc. stuff
4859      to be able to use it in pure forward.
4860    
4861    checkpoint58d_post (2006/04/21)
4862    o upgrade simple test-experiment to tutorial example:
4863     step.1: duplicate the experiment and (step.2) will remove the old copy.
4864      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
4865      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
4866      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
4867      tutorial_global_oce_biogeo    <- copy of dic_example
4868      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
4869      tutorial_plume_on_slope       <- copy of plume_on_slope
4870      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
4871      tutorial_global_oce_optim     <- empty for now (David ?)
4872      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
4873     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
4874    o correct a sign problem in cost_scat.F
4875    o obcs and ptracers: fix boundary conditions for advections schemes
4876      with larger stencil
4877    o thsice adjoint: start
4878    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
4879      completeness
4880    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
4881      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
4882    o ptracers adjoint:
4883      * avoid extensive recomputatations
4884      * fix missing re-init. of gptr (missed by TAF)
4885    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
4886      me to turn off the excessive output to STDOUT that this package produces
4887    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
4888      and add those terms in Vector-Invariant formulation.
4889    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
4890      if the control period (xx_hfluxperiod etc) is 0
4891    o in profiles pkg, clean routines and fix details
4892    o in ecco pkg, reading ssh data:
4893      fix problem in case the model does not start at iter0=0
4894    o fix mnc-pickup/restart for ptracers
4895    o new package prifiles:
4896      code to compute profile-based cost by Gael Forget
4897      (modifs in ecco, ctrl, autodiff)
4898    o Benign bug fix in initialization (spotted by M. Mazloff) of
4899      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
4900    
4901    checkpoint58c_post (2006/03/23)
4902    o adjoint: finish NLFS adjoint and provide reference output in
4903      verification/global_ocean.90x40x15/results_ad_nlfs
4904    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
4905      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
4906      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
4907      with SEAICE_CGRID defined.
4908    o move calendarDumps from "data" to "data.cal" and clean-up the code
4909      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
4910    o add useEXF & useCAL flags (for now, set in hard-coded way)
4911    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
4912      (were missing in NH mode, and wrong in quasihydrostatic mode).
4913      waiting for Chris updated version of calc_gw to add those CALLs.
4914    o fix bug in quasihydrostatic S/R ;
4915      add a test for this option: global_ocean.90x40x15.qshyd
4916    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
4917      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
4918    o add on/off flag useOffLine for package OFFLINE
4919    o seaice:
4920      - modify advection so that it works also on the C-grid
4921      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
4922        problem in multi-tile runs with C-grid
4923      - add flags for clipping ice velocities and/or masking solver forcing
4924      - fix drag (ocean on ice) formulation and a bug that caused noise in the
4925        C-grid solver
4926      - added a few comments to seaice_diffusion.F
4927      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
4928        are now exclusive)
4929      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
4930        required re-ordering the code a little:
4931       + make DAIRN global variable (defined in SEAICE)
4932       + move computation of the viscosities eta and zeta into a new separate
4933         routine (because I need to recompute them in seaice_ocean_stress.F)
4934    
4935    checkpoint58b_post (2006/03/13)
4936    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
4937      update output.txt of exp. aim.5l_cs.thSI
4938    o various mnc cleanups and improvements:
4939      + shrink lookup tables by factor of ~4
4940      + better error reporting when running out of lookup space
4941      + able to handle longer path/file names (up to 500 chars)
4942    o adjoint:
4943      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
4944      - TBD: "hidden" mom_vecinv recomp. in dynamics
4945    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
4946     (allow to differentiate between forcing components using new integer flags:
4947      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
4948     and add new flag to put Dissipation tendency out of Adams-Bashforth.
4949    o ecco
4950      - enable trend removal from SSH anomaly obs.
4951    o adjoint
4952      - a fix for PmEpR when #undef EXACT_CONSERV
4953      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
4954      - try to fix "hidden" recomp. in forward_step for NLFS
4955        (NLFS seems broken sometimes after I checked it in)
4956    o seaice:
4957     - add c-grid version of the dynamic solver:
4958       + three new routines that are the c-grid substitute lsr, dynsolver
4959         and ostres
4960       + put a few fields that were local to dynsolver into global common
4961         blocks, so that I can move the computation of stresses etc into
4962         seaice_lsr (saves coding but may break the adjoint).
4963     - replace more hardwired parameters by runtime parameters
4964     - add ice masks that mask the rhs of the implicit solvers where there
4965       is no ice (commented out in seaice_dynsolver, because i am not sure
4966       if this works properly), eventually this should replace the clipping
4967       of ice velocities in seaice_dynsolver to +/-40cm/s.
4968    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
4969      include it only where its needed
4970    o move balancing of fluxes before the call of external_forcing_surf
4971    o seaice:
4972      - correct units of turning angles (now they are really in degrees)
4973      - move computation of GWATX/Y out of main routine into dynsolver
4974      - initialize GWATX/Y in seaice_init
4975    o Apply mask on Fresh-Water flux (needed for SSH forcing).
4976      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
4977    o seaice: add runtime flags for turning angles (default to zero)
4978    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
4979      and trend from exf forcing and ctrl control adjustments
4980    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
4981      (since checkpoint57x_post)
4982    o change the default rotation period to 86164.s = the Earth rotation
4983    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
4984      and based on a reference stratification. Tested within hs94.cs-32x32x5.
4985    o seaice advection: add code for choosing between the default (2nd order
4986      central differences) and multiDim advection schemes provided by
4987      pkg/generic_advdiff
4988    o seaice:
4989      - removed all references to SEAICE_GRID.h fields from
4990        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
4991        (cubed-sphere configuration will change a little)
4992      - grid computations in seaice_init are obsolete now.
4993      - cleaned up code a little so that is easier to read (hopefully).
4994      - added new (better?) discretizations of default advection and diffusion
4995        (turn on with SEAICEuseFluxForm)
4996      - replace 1 in 3d global fields by kSurface in growth.F
4997      
4998    checkpoint58a_post (2006/02/13)
4999    o seaice:
5000      - bug fix in advect.F
5001    o shelfice:
5002      - separate shelfice load anomaly from pload (breaks with time
5003        dependent forcing), => introduce constant field shelficeLoadAnomaly.
5004        Its default is 0., but it may be computed more cleverly from (unknown)
5005        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
5006        done offline. A good approximation of the pressure load anomaly is
5007        necessary to avoid large initial adjustment processes underneath
5008        deep-reaching shelfice.
5009      - small fix in ISOMIP shelfice_thermodynamics
5010      - add more sophisticated thermodynamics of Hellmer (1989), this is
5011        now the default
5012      - give a few constants more intuitive names
5013    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
5014      if bulk formulae are used in long integration (especially EmPmR). Turn
5015      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
5016      if balancePrintMean, the imbalance that is substracted is printed to
5017      STDOUT.
5018    o fix bug (typo) in obcs_apply_eta.F
5019    o add a new package shelfice which enables us to model the circulation
5020      underneath shelf-ice with draughts of hundreds of meters.
5021     - works
5022     - to do: + include improved thermodynamics
5023              + check whether kSurfC (from model/inc/SURFACE.h) can be used
5024                instead of new field kTopC
5025              + can we use topoFile, Ro_surf and existing code in ini_depth.F
5026                instead of new field R_shelfIce and new code in ini_depth.F
5027                and ini_mask_etc.F?
5028              + adjust vertical mixing schemes?
5029    o seaice pkg:
5030     - add a cpp-flag to include a simple formula for a salinity dependent
5031       freezing point of sea water at the surface
5032     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
5033       meridional stresses are now different (and hopefully correct)
5034    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
5035       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
5036       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
5037    o pkg/diagnostics: add options and parameters for regional-statistics
5038       diagnostics ; define regions by reading a region-mask from a file
5039       (might add other options later)
5040    o pkg/bulk_force:
5041     - add option and parameters to use AIM surface-flux formulae.
5042     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
5043       others forcing fields (defined in PARM05, parameter file "data") are loaded
5044       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
5045     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
5046     - use the right EXCH call for uwind,vwind (to work on CS-grid).
5047     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
5048       and parameters (note: calcWindStress replaces .NOT.readwindstress).
5049     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
5050    
5051    checkpoint58 (2006/01/12)
5052    o add "--embed-source" option to genmake2 which, when the supporting
5053      tools can be compiled (as determined by genmake2) will turn on the
5054      embed_files package which then embeds the entire MITgcm source code
5055      (*.[fFhc] + Makefile) used for the build within the executable
5056      - requested by CNH but off by default
5057      - adds a paltry <9MB to the mitgcmuv executable in most cases
5058      - only writes the output when useEMBEDSRC in eedata is true
5059    o clean up 3-dim. relaxation codes:
5060      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
5061      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
5062      * Thanks to Tom Haine for testing!
5063    
5064    checkpoint57z_post (2005/12/31)
5065    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
5066      affects output (@ truncation level) of exp. plume_on_slope ; updated.
5067    o fix the pickup behavior for obcs in combination with ptracers
5068    o fix a bug in ptracers_external_fields_load
5069    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
5070      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
5071    o transfered surface NH pressure to eta field (if exactConserv).
5072    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
5073         and update lab_sea output.txt file.
5074    o completing 3-dim. relaxation code: additional term
5075         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
5076      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
5077      * At compile time, in "EXF_OPTIONS.h" set
5078          #define  ALLOW_CLIMTEMP_RELAXATION
5079          #define  ALLOW_CLIMSALT_RELAXATION
5080      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
5081          tauThetaClimRelax3Dim = 15552000.0,
5082          tauSaltClimRelax3Dim  = 15552000.0,
5083      * 3 cases:
5084          1) Use a constant-in-time 3-dim. field
5085          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
5086          3) Real-time relax. to time-evolving prescribed field
5087    o Adding Laplacian-type smoothness constraint on
5088      initial and boundary (forcing) controls (ic, bc)
5089      * enable at compile-time via
5090        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
5091      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
5092      * Absolute scale somewhat unclear so far
5093      * no area weighting was included since no other cost term does so far
5094    
5095    checkpoint57y_post (2005/12/08)
5096    First step for a NLFS adjoint
5097    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
5098    o new init. routines for calc_r_star, calc_surf_dr
5099    o still need to deal with ini_masks_etc
5100    o testreport seemed happy
5101    checkpoint57y_pre (2005/12/08)
5102    
5103    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
5104    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
5105    o add new offset feature to offline pkg (plus minor cleanup)
5106    o cfc fixes for final year of integration
5107    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
5108      be in GCHEM_OPTIONS).
5109    
5110    checkpoint57x_post (2005/12/04)
5111    o fix testreport Pb in multiple test experiment.
5112    o cleanup our namelist syntax in verification:
5113      - make it more F95 standards compliant (some work still needed)
5114      - allows the vast majority of our tests to work with gfortran
5115    o Non-Hydrostatic:
5116     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
5117     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
5118    o Allow to apply AB on T,S rather than on AB(gT,gS):
5119     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
5120     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
5121       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
5122     - need a "clever" read_pickup to restart from the other AB formulation
5123    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
5124    o remove some unused variables (reduces number of compiler warnings)
5125    o adjoint
5126      * Disable useVariableViscosity for adjoint for time being
5127        (there are a number of extensive recomputations)
5128      * Initialize certain variables needed for adjoint
5129    
5130    checkpoint57w_post (2005/11/03)
5131    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
5132                 fix the singleCpuIO RS version of MDSWRITEFIELD
5133       and add a WARNING if using globalFiles=T with multi-processors.
5134    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
5135      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
5136    o tracer advection scheme:
5137      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
5138       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
5139       was not very convenient).
5140      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
5141       (further tests needed for the implicit DST & Flux-Limiter schemes).
5142    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
5143      and sRef for convenience, handy, when you want to initialize
5144      ptracers in a large domain with a constant non-zero value. Also,
5145      untangle ptracers_init.F a little.
5146    
5147    checkpoint57v_post (2005/10/13)
5148    o change dome exp. to use variable viscosity in side-drag terms.
5149    o remove all the files from the cfc_offline test since they are now
5150      incorporated into tutorial_cfc_offline which has been producing
5151      identical results for a few days of testing
5152    o add new parameter: sideDragFactor to enable half-slip-side BC
5153      and change side-drag S/R to use viscosity from mom_calc_visc
5154      (can switch back by setting sideDragFactor=0.); affects results at
5155      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
5156       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
5157    o vorticity & strain are now computed without masking, to account for
5158      no-slip-side BC in variable viscosity calculation ; mask is applied
5159      anyway later on, before computing advection/coriolis terms.
5160    o modify exp4 to test new obcs support for reading from external files
5161      and for passive tracers
5162    o fix behavior of ptracers_monitor when monitor output is written to a
5163      netcdf-file; still not independent of monitor.F (writes in the same
5164      file).
5165    o change default value of tRef (put a uniform, meaningful value for ocean
5166      & atmos) and initialize sRef (was missing, as Martin mentioned).
5167    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
5168      to be proportional to enstrophy dissipation length.  Thus,
5169       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
5170      This is now consistent with Smagorinsky and with the manual.
5171    
5172    checkpoint57u_post
5173    o OBCS and PTRACERS: add open boundary support for passive tracers
5174      - either use homogenous (pseudo) v.Neumann conditions or prescribe
5175        OB-values from file; this is not different from the way theta and salinity
5176        are treated
5177      - however, Orlanski-radiation conditions are not supported, and the model
5178        will stop if you use pTracers and Orlanski at the same time.
5179      - beefed up the rountine obcs_external_fields_load: now only those open
5180        boundary values are overwritten with values from files for which there
5181        are really files, otherwise the OB-fields remain untouched. This makes
5182        it possible to use different OBs at different ends of the domain (as
5183        with EXF)
5184    o reduce number of exch calls in shap_filt (s2).
5185    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
5186      truncation level) 4/5 MLAdjust test results (11&12 digits match).
5187    
5188    checkpoint57t_post (2005/10/03)
5189    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
5190    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
5191      same truncation, independent of the face number: affects affects several
5192      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
5193    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
5194      note that biharmonic viscosity + no-slip was not tested in any experiment.
5195    o fix bug in non-linear free-surf side-drag ; generate new output for
5196      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
5197    o make mnc honor the writeBinaryPrec flag for most kinds of output
5198    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
5199    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
5200      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
5201    o add brackets in multi-terms sum to get same truncation, independent of
5202      the face number (manage to get exactly same value of gU,gV at the cs-edge)
5203      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
5204    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
5205      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
5206      a maximum grid-scale Reynolds number.  Also, changes all length calculations
5207      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
5208      Suggested values of viscosity parameters found in mom_calc_visc.
5209      Many new viscosity diagnostics available.
5210    
5211    checkpoint57s_post (2005/09/20)
5212    o Add clearing-house for viscosity calculations, mom_calc_visc and
5213      correct numerous bugs in LeithD and Smagorinsky discretizations.  
5214      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
5215      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
5216      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
5217      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
5218      The Strain-Tension form is now called with useStrainTensonVisc=.true.
5219      ViscAhStrain and viscAhTension are now retired.
5220    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
5221    o In response to JMC's bug report, genmake2 now ignores any soft-links
5222      that it finds in the *current* directory when searching for files.
5223      Soft-links found in any other source directories will still work as
5224      they did before.
5225    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
5226      a C routine to unlimit the stack size
5227    o mnc-ify pkg/aim snapshot vars
5228    o mnc-ify pkg/land as requested by Daniel
5229    o various changes to mnc including:
5230      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
5231      - output can now be grouped so that all files within a group
5232          change the ITER portion of their names in lock-step together
5233      - can now read ("global") PER-FACE (in addition to PER-TILE) files
5234          and works with both EXCH1 and EXCH2 (but needs more testing)
5235      - writing works for all verification test cases w/ g77 on Linux
5236    
5237    checkpoint57r_post (2005/09/07)
5238    o make MNC variable initialization happen earlier
5239    o add diagnostics for (almost) each term of the momentum Eq.
5240    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
5241    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
5242    o remove MINIMAL_TAVE_OUTPUT option ;
5243      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
5244    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
5245      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5246    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
5247    o add time-dependent SST, SSS control
5248    o cost terms in ecco/ modularized (new cost_generic.F)
5249    o cost_averages routines are modularized (new cost_averagesgeneric.F)
5250    o new infrastructure for seaice model vs. obs misfits in seaice/
5251      * driver from the_main_loop.F is seaice_cost_driver.F
5252      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
5253      * gradient check in Exp. 6a of natl_box_adjoint/
5254    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
5255      (see README file)
5256    
5257    checkpoint57q_post (2005/08/19)
5258    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
5259    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
5260      - bug was reported by Jean-Michel and Ian Fenty
5261    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
5262      update exp. cpl_aim+ocn output.
5263    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
5264      Needed for high-res. runs with large global files
5265      to be able to limit tapelev size
5266    o Changed some tests for adjoint:
5267      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
5268      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
5269      * global_ocean.90x40x15/ back to default 3-level checkpointing
5270    o Modifications to enable scripted COMMON to MODULE conversion
5271      * verification/OpenAD/code/ has necessary scripts and description;
5272      * converts, compiles and runs successfully;
5273    
5274    checkpoint57p_post (2005/08/01)
5275    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
5276    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
5277      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
5278    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
5279    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
5280      (was already the case for dissipation with mom_vecinv,
5281       and also the case for grad.PhiHyd when staggered-timeStep)
5282      This will allow to put dissipation out-off the AB time-stepping.
5283     Unfortunately, affects truncation error. Update output of exp. that "fails"
5284      (cg2d matching number) and leave the others for later: front_relax(10),
5285      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
5286      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
5287    
5288    checkpoint57o_post (2005/07/30)
5289    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
5290      (2) its ready to be documented during the 20050801 DocFest
5291    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
5292      for ideal_2D_oce and lab_sea on linux_ia32_g77
5293    o set to #undef CTRL_SET_OLD_MAXCVARS_30
5294      in global1x1_tot/code_seaice_adj to access indices 32, 33
5295      (worth another tag)
5296    
5297    checkpoint57n_post (2005/07/29)
5298    o adding precip control xx_precip 32
5299    o adding swflux control xx_swflux 33
5300    o Replacing 10 forcing penalty cost routines by 1 generic.
5301    o Implementing partitioning in time-mean and variable adjustment
5302      for atmos. state.
5303    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
5304    o in natl_box_adjoint:
5305      * updated exp 1 to 10
5306        (but does not have time-mean vs. variable split results yet)
5307    o updated global1x1/*_seaice_adj/
5308      to incorporate latest changes
5309    o enable useSingleCpuIO for mdsio vector routines
5310      (applies in particular to tapelev I/O)
5311    o removed inefficient K-loop in all active_file*control*.F
5312    
5313    checkpoint57m_post (2005/07/28)
5314    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
5315      and advect_cs (use EXCH-2 and standard cs-32 grid files).
5316    o pkg/exch2: filling of face-corner halo regions is optional
5317      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
5318    
5319    checkpoint57l_post (2005/07/14)
5320     tag before updating tutorials (pre-release-2)
5321    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
5322       for output and interpolation of input fields onto model grid)
5323    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
5324       Affects results of exp. rotating_tank ; update output.txt.
5325    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
5326          and taking the square quantity and/or using a fraction-weight field.
5327    o fix aim_diagnostics_init.F mate numbers.
5328    o add mnc output capability to diagnostics/diagstat and update
5329      our cvsignore files for the ACSII output generated
5330    
5331    checkpoint57k_post (2005/07/02)
5332    o lab_sea now uses diagnostics package and provides a suite of
5333      new EXF diagnostics output.
5334    
5335    checkpoint57j_post (2005/06/30)
5336    o exf
5337      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
5338        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
5339        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
5340      * extended diagnostics output
5341        - now includes all EXF variables
5342        - hs, hl moved to common block
5343        - separate S/R for diagnostics, called after ctrl vector is added
5344        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
5345        - EXFqnet contains true Qnet (i.e. includes qsw)
5346      * updated verif. lab_sea, global_with_exf
5347      * Rearranging hflux (exf_mapfields -> exf_getforcing)
5348        to ensure that diagnostics sees a true EXFqnet
5349    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
5350    o diagnostics pkg: change pointers so that 1 diagnostic can be used
5351      several times with different frequencies.
5352    o mnc-ify the thsice package as requested by Daniel Enderton
5353      - the monitor--MNC output needs work
5354      - many attributes need to be added (most are currently blank)
5355    o mnc-ify theaim_v23 package as requested by Daniel Enderton
5356      - many attributes need to be added (most are currently blank)
5357    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
5358    o add Sadourny like discretization to the 4th.O vorticity advection scheme
5359    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
5360      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
5361         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
5362    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
5363     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
5364    
5365    checkpoint57i_post (2005/06/19)
5366    o Diagnostics package was changed: diagnostic allocation is now deactivated
5367      by setting an empty file name in the namelist (used to be by setting 0 frequency)
5368    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
5369      add 1rst Order upwind vertical Shear.
5370    o add a quick fix for A/B checkpointing in OFFLINE mode
5371    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
5372      end-run around the C/Fortran linking horror in eesup/src/timers.F
5373    o added pkg/runclock: allows user to terminate run based on wall clock
5374    o added non-hydrostatic scaling parameter: nh_am2
5375    o pkg/my82: futile attempt to make results compiler-independent by adding
5376      some "_d 0", etc. no effect.
5377    o for mnc output, fill the 'T' coordinate var with myTime and create a
5378      separate 'iter' variable for iteration count
5379    o pkg/diagnostics:
5380      add new capability: output of Global/Regional & per-level statistics ;
5381      tested against monitor output (including land & thSIce) on various exp.
5382    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
5383    
5384    checkpoint57h_done (2005/05/19)
5385      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
5386      data.diagnostics, data.gchem, data.ptracers) is done.
5387    
5388    o pkg/diagnostics: prepare for Global/Regional statistics.
5389      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
5390    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
5391      and rename it: DIFFERENT_MULTIPLE
5392    
5393    checkpoint57h_post (2005/05/14)
5394    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
5395    o pkg/diagnostics: change output frequency, now in seconds (instead
5396      of Nb of iterations). This requires to change data.diagnostics.
5397    checkpoint57h_pre (2005/05/12)
5398    
5399    o in mnc, let the user create the output dir if both mnc_outdir_date
5400      and mnc_outdir_num are false
5401    o add fflags() to pkg/diagnostics which allows one to specify, on a
5402      per-file basis, the file precision [default behavior is unchanged]
5403    o added diagnostics to pkg/kpp, including computation of mixed layer
5404      depth based on a temperature/density criterion
5405    o updated verification/natl_box to test the new pkg/kpp diagnostics
5406    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
5407    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
5408    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
5409      not mnc -- this mistake was found by JMC and is now corrected
5410    
5411    checkpoint57g_post (2005/04/15)
5412    o add Adams-Bashforth 3rd Order time stepping:
5413      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
5414      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
5415    checkpoint57g_pre (2005/04/15)
5416    
5417    o make lambda[Theta,Salt]ClimRelax spatially varying
5418      (default remains spatially uniform constant based on tau)
5419    o added new control variables
5420      * init. uVel, vVel, etanN
5421      * lambda[Theta,Salt]ClimRelax
5422    o separate masks used for ctrl_pack/unpack 'from write_grid' output
5423      (suggested by G. Forget)
5424    
5425    checkpoint57f_post (2005/04/06)
5426    o add parameter "baseTime" = model base time = time at iteration zero
5427      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
5428      account for baseTime shift
5429    o move Coriolis arrays from PARAMS.h to GRID.h
5430    checkpoint57f_pre (2005/04/06)
5431    
5432    o mnc-ifying the seaice package
5433    o introduced an alternative length scale calculation for use in the limiting
5434      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
5435    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
5436    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
5437      as well as grad(vort3).  Made it compatible with both approximate form
5438      for the cubed sphere and full form of these gradients.  Added flag
5439      useFullLeith to select between approximate and full form.  
5440    o add "d0" in getcon.F to reduce differences between compilers/platforms
5441      update output.txt of exp. fizhi-gridalt-hs
5442    o change port_rand funtion to allow to set the seed.
5443    o fix obscure MNC bug involving conversion between reals and integers
5444      - it caused no problems with certain (eg. gcc, ifc) compilers but the
5445        new version is now more standards-compliant
5446    o adjoint-related modifications
5447      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
5448      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
5449      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
5450    
5451    checkpoint57e_post (2005/02/28)
5452    o Adding eddy stress controls a la Ferreira et al.
5453    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
5454    
5455    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
5456      update output.txt of exp. fizhi-gridalt-hs
5457    o add more "Z" dimensions and associated coordinate vars to MNC
5458    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
5459    o parameter calendarDumps: when set, approximate months (30-31 days) and years
5460      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
5461      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
5462      months and years.  Requires pkg/cal.
5463    o diagnostics: add pickup functionality
5464      - off by default for backwards compatibility
5465      - current version only uses MDSIO -- MNC will be added
5466    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
5467    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
5468    
5469    checkpoint57d_post (2005/02/11)
5470    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
5471    o modify verification/ideal_2D_oce so that it tests the creation of mnc
5472      output from the diagnostics package
5473    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
5474    o make genmake2 more portable by using ".$FS" instead of ".f" for more
5475      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
5476    o add coordinate variables to the MNC output from the diagnostics package
5477    o change MNC-flags default value: true when useMNC=TRUE
5478    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
5479      the ability (off by default) to read the grid information using MNC
5480    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
5481    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
5482    o do snap-shot diagnostics at the middle of the time-interval (instead of
5483      at the end).
5484    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
5485      new test for AIM with thSIce + slab-ocean
5486    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
5487    o move state variable diagnostics to the beginning of the time step ;
5488      (note: still needs some work specially for snap-shot diagnostics)
5489      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
5490    
5491    checkpoint57c_post (2005/01/27)
5492    o Change testing option (-ieee) to get closer agreement between g77 & ifort
5493    o generate new output.txt files on faulks with g77 & the new -ieee option
5494    checkpoint57c_pre (2005/01/27)
5495    
5496    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
5497      update output.txt of exp. global_ocean.90x40x15
5498    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
5499      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
5500    o add saltFlux(+File) forcing capability with periodicExternalForcing
5501    o allow to use pkg diagnostics for GM-Redi & ThSIce output
5502    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
5503    o improvements for the MNC output from DIAGNOSTICS:
5504      - correct handling of the unlimitied dimension
5505      - all dims now have associated coordinate variables
5506      - variables located at U, V, and Corner ("Z") points are now written
5507        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
5508        *all* data points are output
5509    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
5510    o added pkg/seaice/seaice_monitor.F
5511    o mdsio_readfield.F can now read files visible only to master MPI process.
5512    o pkg/seaice: some test code for ice-modified ocean stress
5513    o exf_getffields interpolation defaults to bilinear for all scalar forcing
5514      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
5515      spurious negative numbers for precipitation and humidity.  Will cause
5516      some small numerical differences for integrations using pkg/exf/exf_interp.F.
5517    o pkg/ctrl/
5518      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
5519        May be enabled via doPackDiag
5520      *  introduce z-scaling of
5521         + gradient (doZscalePack) and
5522         + control (doZscaleUnpack)
5523    o pkg/mdsio/
5524      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
5525      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
5526    
5527    checkpoint57b_post (2004/12/20)
5528    o simplify options in diagnostics_fill arguments (remove weird combinations)
5529    o fix MNC coordinate variables so that they now contain per-face index
5530      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
5531      general, EXCH2 grids are only aligned to a "local" coordinate system
5532    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
5533    o Implement instantaneous output within pkg diagnostics:
5534      setting a negative frequency in data.diagnostics produces
5535     "snap-shot" output (as opposed to time-average if freq > 0)
5536    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
5537      NOTE: change ptracer diagnostics name: use 2 characters to work with
5538            more than 9 tracers. Add also diagnostics of advect & diffus flux.
5539    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
5540      becomes the coordinate variable for the 'T' dimension
5541    o add CF-style coordinate variables to MNC
5542      - just a first cut:  numbers are meaningless on the cubesphere and
5543        missing along the T axis but otherwise it works!
5544    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
5545    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
5546    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
5547      this is based directly on what the model compute, so that the content of
5548      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
5549    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
5550    o clean up build options files for SunOS, in particular
5551      - remove -traditional from xmakedepend
5552      - change -xarch=v9 to -xarch=native for f77
5553      - restore use of make (not gmake)
5554      - add CC=gcc if using g77
5555    o changes per discussion of AM, JMC, & EH3 today:
5556      - move redundant "grid" variables out of "state" -- in preparation of
5557        creating proper CF-style coordinate variables and in recognition
5558        that any/all grid variables can be easily copied (eg. w/NCO) from
5559        the grid files into any of the other NetCDF files
5560      - *always* output grid variables with MDSIO (this will eventually be
5561        changed)
5562      - output MNC grid file if useMNC is true
5563    o every instance of _END_MASTER() has been found and replaced with
5564      _END_MASTER( myThid ) in order to satisfy certain picky Sun
5565      preprocessors
5566    o re-arrange diagnostics pkg initialisation:
5567     - allow each package to extend the available diagnostics list
5568     - add some checking and fix small problems (multi-threaded, ...)
5569     - new S/R diagnostics_fill (replace fill_diagnostics):
5570       look through the short list of active diag. (instead of the long list)
5571       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
5572    
5573    checkpoint57a_post (2004/12/10)
5574    o this set of changes restores TAMC compatibility
5575      tested for global_ocean.90x40x15 adjoint on trough
5576      (what a pain)
5577    
5578    checkpoint57a_pre (2004/12/10)
5579    o some modifs in tools/build_options for sunos
5580    o call ctrl_pack for ctrl at end for optimcycle=0
5581    
5582    checkpoint57 (2004/12/09)
5583    o add horizontal bi-harmonic viscosity for vertical velocity
5584      - new parameter viscA4W (defaults to viscA4)
5585      - affects only non-hydrostatic code
5586      - to be done: no-slip lateral boundary conditions
5587    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
5588    o implement Implicit Vertical advection for pTracers
5589    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
5590      (implemented also for implicit vertical diffusion & advection)
5591    o OBCS: extend application of tracer open boundary conditions
5592      to a strip beyond the boundary of width Olx/Oly
5593    o add call monitor to TAF set of required calls (flow directives)
5594      and include in natl_box_adjoint
5595    o untangle a few ifdefs related to cost, ctrl, autodiff
5596      untangel a few ALLOW_ECCO_OPTIMIZATION
5597    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
5598      (theta2, salt2 in ecco_cost_weights)
5599    
5600    checkpoint56c_post (2004/12/03)
5601    o OBCS as control variables
5602      - update ctrl_ad_diff.list, obcs_ad_diff.list
5603      - remove balance of obcs controls from default
5604      - fix index bug nobcs in ctrl_init
5605      - fix dummy fields filen in ctrl_pack
5606      - add dummy weights for obcs
5607    o lsopt: comment out fort.94 output
5608    o optim:
5609      - remove unnecessary header files
5610      - adjusted namelists
5611      - add xerbla.F to Makefile
5612    o exf:
5613      - multiple modifications of exf_check_range
5614      - unit change in exf_init_runoff from [m/year] to [m/s]
5615    o mdsio:
5616      - i/o-vector change debugLevel from debLevA to debLevB
5617    
5618    checkpoint56b_post (2004/12/01)
5619    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
5620      is called from DO_THE_MODEL_IO
5621      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
5622      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
5623      - clean up PTRACERS_WRITE_TIMEAVE a little
5624    o add another verification experiment that tests both the cfc-pkg and
5625      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
5626      reactive tendencies treated inline with regular timestepping
5627    o testreport previously did a lousy job of comparing small numbers, so
5628      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
5629      implemented in the little c-progam tmp_cmpnum.c which is embedded in
5630      testreport.
5631    o ptracers_monitor: bug fix for MPI
5632    
5633    checkpoint56a_post (2004/11/28)
5634    o GCHEM: finish reorganizating the package
5635      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
5636        (introduces another 3D-array for each passive tracer, but only if
5637        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
5638        gchemTendency is not needed because the timestep is done separately)
5639      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
5640      - GCHEM is now---more or less cleanly---separate from PTRACERS
5641      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
5642        so clear to me how that should be done in a general way.
5643    o CFC: improve formatting of output in CFC_ATMOS
5644    o PTRACERS:
5645      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
5646        that ALL experiments with ptracers enable can be checked. This makes
5647        GCHEM_MONITOR obsolete.
5648      - include a runtime parameter PTRACERS_monitorFreq that defaults to
5649        monitorFreq
5650      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
5651    o add PTRACERS (PTR0[1-5]) to testreport output
5652    o exf_check_range:
5653      * default changed to .TRUE.
5654      * will check values for niter0 if debLevA, every timestep if debLevB
5655      * STOP in exf_check_range if 'out of range'
5656      * range chosen generous to allow for potential extema
5657      TBD: a version with stricter range
5658           permitted range would be runtime parameters
5659    o GMredi:
5660      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
5661      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
5662      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
5663    o GCHEM:
5664      - move call to GCHEM_FORCING_SEP, so that it is now called before
5665        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
5666      - introduced a useGCHEM runtime flag and applied it everywhere.
5667      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
5668        this flag is now only visible within GCHEM-pkg routines.
5669      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
5670        be replaced by a 3D array that is computed before thermodynamics; for
5671        this, the tracer ID iTracer had to be included into the parameter list
5672        of ptracers_forcing
5673      - set up forward_step to call gchem_forcing, that will replace
5674        gchem_forcing_int in ptracers_forcing
5675      - cleaning up
5676    o small cleaning of exch2: remove files that are also in eesupp/src
5677    
5678    checkpoint56 (2004/11/17)
5679    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
5680    o mnc: cleanup "full" files--fixes out-of-memory problem
5681    o ECCO-GODAE
5682      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
5683      * fully merged and updated from SIO code
5684        windstress sign change affects
5685        - exf_inscal_[u/v]stress
5686        - sign of xx_tau[u/v] adjustments
5687        - signs in cost_scat
5688      * ctrl_get_gen: avoid update of tau[u/v] for first few days
5689      * natl_box_adjoint updated and compressed
5690      * 2-level checkpoint switch added
5691        (tested in EXP. 1 of natl_box_adjoint)
5692      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
5693    o SVD
5694      * first complete, non-hacked version for SVD calculations
5695      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
5696        performed via direct access files admtlm_vector.it????
5697        (via ctrl_[un]pack)
5698      * optimcycle is used for ARPACK iteration counter
5699        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
5700      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
5701        and add linear transforms where necessary
5702      * controls are initial/final SST, SSS (can be extended; need to check
5703        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
5704    o mdsio: filename info to both stderr, stdout
5705    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
5706      from sign change
5707    
5708    checkpoint55j_post (2004/11/10)
5709    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
5710      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5711    o add consistent build directories and .cvsignore files to verification
5712    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
5713    o make all subroutines 30 or less characters in length for certain older
5714      compilers to work (a thorough search only turns up two routines in
5715      pkg/ptracers)
5716    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
5717      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5718    
5719    checkpoint55i_post (2004/10/28)
5720    o change arrays for total vertical diffusivity (2.D if explicit,
5721      3.D if implicit) ; each ptracer uses its own background value.
5722    o added mnc/NetCDF output capability to ocn_compon_interf
5723      - added bits to verification/cpl_aim+ocn so that it can run on
5724        ITRDA and other clusters without the mpirun "-wd" option
5725    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
5726      configuration
5727    o give MNC the ability to create additional files rather than
5728      exceeding a specified file size limit "MNC_MAX_FILESIZE"
5729      - the default is just less than 2GB which is a practical limit
5730        on many systems
5731    o Compute the non-local term using either KPP vertical diffusivity (=default)
5732       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
5733    
5734    checkpoint55h_post (2004/10/20)
5735    o add verification test "vermix"
5736    o remove all the *_ioinc flags and replace with the single global
5737      outputTypesInclusive flag
5738    o allow to set a vertical profile of vertical diffusivity for T & S
5739    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
5740    o useMNC moved from data.mnc to data.pkg
5741    
5742    checkpoint55g_post (2004/10/14)
5743    o Renaming carbon AD experiments to comply with testreport conventions
5744    o Updating adjoint of Held-Suarez hs94.1x64x5
5745    o Fixing directives for non-ECCO forward_step, after ECCO directives
5746      have been fixed to avoid recomp. of do_oceanic_phys
5747      Works well for global_ocean.90x40x15,
5748      but recomp. issue remains for carbon
5749    o Updating adjoint output for natl_box_adjoint after
5750      pkg/ecco has been modified (see taga c55d_post)
5751    
5752    checkpoint55f_post (2004/10/13)
5753    o rename to timeave_init_fixed
5754    
5755    checkpoint55e_post (2004/10/13)
5756    o some delicate re-shuffle of store directives to avoid one
5757      extra call of do_oceanic_physics
5758      affects ecco_the_main_loop.F, do_oceanic_physics.F
5759      checkpoint_lev1_directives.h
5760    o NB: this may break global_ocean adjoint temporarily,
5761      but it is clear how to fix it. Will do later, need this now.
5762    
5763    checkpoint55d_post (2004/10/11)
5764    o ECCO specific cost function terms (up-to-date with 1x1 runs)
5765    o ecco_cost_weights is modified to 1x1 runs
5766    o modifs to allow observations to be read in as
5767      single file or yearly files
5768    o enable to read exf forcing fields as either
5769      single file or yearly files (flag useExfYearlyFields)
5770    checkpoint55d_pre (2004/10/08)
5771    
5772    o switch between 2-level and 3-level checkpointing
5773    o add ability of MNC to write local and "partial" (eg. 2D slices where
5774      the full 3D field is never actually stored) arrays to NetCDF files
5775      with the correct (that is, the complete multi-dimensional) set of
5776      array indicies
5777      - used in mom_vecinv() to write the diagFreq output
5778      - tested (demonstrated) in verification/aim.5l_cs
5779    o further mnc-ification
5780      - add verification/lab_sea to the list with mnc setups
5781      - fix undefined mnc v-names in cd_code
5782      - add kpp to mnc output (both snapshot and timeave)
5783    o non-hydrostatic code
5784      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
5785        in calc_gw.F
5786      - defaults to viscAh
5787      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
5788        friction or Leith) in non-hydrostatic mode, as long as there is
5789        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
5790    o pkg/cost
5791      extend simple cost functions to treat time mean quantities
5792      (T,U,V) via cost_accumulate_state from cost_tile
5793    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
5794        be 2 times larger than the minimum size the advection scheme requires.
5795        now get a perfect conservation of salt in advect_cs test-exp (updated)
5796    o GGL90 (Gaspar's TKE mixed layer)
5797      - add horizontal diffusion of TKE, requires exchanges in
5798        do_fields_blocking_exchanges, horizontal diffusivity is zero by
5799        default. In OPA there is no horizontal diffusion of TKE but the
5800        mixing coefficients are computed from a horizontal average of TKE of
5801        6 points or so. I think that diffusion has a little more physical
5802        justification.
5803      - clean up ggl90_calc in the hope of reducing memory usage (this hope
5804        was in vain)
5805      - mask tke-variable in ggl90_init
5806    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
5807    o fix biharmonic diffusion on CS-grid.
5808    o more obcs stuff
5809      - added obcs_external_fields_load as an alternative to the EXF-pkg option
5810        for reading boundary values. This routine is called from
5811        obcs_prescribe_read
5812      - updated obcs_check
5813      - changed sponge layer relaxation parameter units for days to seconds
5814      - turned off sponge layer by default
5815      - changed argument list of OBCS_CALC to myTime+deltaTclock
5816      - fixed about 35 bugs in obcs_external_fields_load
5817    
5818    checkpoint55c_post (2004/09/23)
5819    o obcs stuff
5820      - new runtime flags useOBCSprescribe, useOBCSbalance
5821      - re-arranged obcs_calc
5822      - moved exf_getobcs to obcs_prescibe_read
5823        obcs_prescibe_read is called after ORLANSKI stuff
5824        and independent of it (executable can contain all).
5825      - updated obcs_check
5826      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
5827        These may be necessary only if tangential velocities are
5828        prescribed at OB, not sure, needs testing.
5829    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
5830      which simplifies the calls and passes the ifc check-bounds test
5831    
5832    checkpoint55b_post (2004/09/22)
5833    o add a 2D scalar, Z location, exchange_2 routine.
5834    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
5835      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
5836      affects advect_cs results (for the wrong reason): update output.txt
5837    o use a more standard discretization for biharmonic viscosity ;
5838     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
5839      affects results of dome set-up: update output.txt
5840    o fix gad_advection.F (CubedSphere part), back to version 1.23
5841    o fix bug in mom_vi_del2uv.F (CubedSphere part).
5842    
5843    checkpoint55a_post (2004/09/20)
5844    o merged code to
5845      * prescribe/read time-dependent open boundaries
5846        (works in conjunction with exf, cal)
5847      * sponge layer code for open boundaries
5848      * each boundary N/S/E/W now has its own CPP option
5849        (healthy for the adjoint)
5850    
5851    checkpoint55 (2004/09/17)
5852    o up-to-date adjoint of previous breaks
5853      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
5854      - global_ocean_ebm: adjoint still needs fix (TLM ok)
5855      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
5856      - carbon: * remove tr1-related adjoint verification
5857                * add ptracer as control variable
5858    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
5859      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
5860    
5861    checkpoint54f_post (2004/09/16)
5862    o in verification/carbin/ remove experiment related to
5863      ALLOW_PASSIVE_TRACER (array tr1 etc)
5864      code_ad/ input_ad/ results_ad
5865    
5866    o add two new packages
5867      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
5868        + subject to optimization (memory)
5869      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
5870        + subject to reordering (many GOTOs in the original code)
5871        + so far opps is called for every (i,j) point, and then operates in
5872          the vertical; one may want to reorder the scheme in order operate in
5873          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
5874          fields)
5875    o overhaul of IO so that we now have flags for MDSIO and/or MNC
5876      - all verification tests compile and run with linux_ia32_g77
5877      - defaults are compatible with current input files--nothing
5878        should change if you were not previously using MNC
5879      - MNC output has been added in numerous places (eg. timeave)
5880        but there are still a few writes not yet do-able with MNC
5881        (this is in progress)
5882      - flags now allow for either/or/both use of MDSIO and MNC and
5883        documentation will soon follow
5884      - numerous small formatting cleanups for ProTeX
5885    o add version info (via BUILD_INFO.h) to MNC and stdout
5886    
5887    checkpoint54e_post (2004/09/02)
5888    o add two new packages
5889      - pp81 (Packanowski and Philander, 1981), Richardson number and
5890        stratification dependent mixing
5891      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
5892      - these scheme operate in a similar manner as KPP (without ghat, of
5893        course), however there is only one diffusivity that is used for both
5894        temperature and salinity (and passive tracers)
5895    o add offline package
5896    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
5897      provided by Stephanie Dutkiewicz
5898    o genmake2: add ability to search for C compilers and cleanup test output
5899      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
5900    
5901    checkpoint54d_post (2004/07/27)
5902    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
5903    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
5904      leading to additional shift by 5 days each year of integration
5905       (i.e. leading to considerable offset over the years)
5906    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
5907    o start with no AB and no initial filtering (staggerTimeStep):
5908      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
5909    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
5910      (external loading & cpl import/export stay in forward_step.F)
5911    o update coupling interface to work with new staggerTimeStep
5912    o change MDSIO ptracers_pickup.
5913    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
5914    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
5915    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
5916    
5917    checkpoint54c_post (2004/07/18)
5918    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
5919      this affects (truncation error) output.txt of test-exp:
5920       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
5921    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
5922    o change Qnet to always be the net heat flux, (+upward).
5923      affects (truncation error) output of natl_box exp.: updated
5924    o define the max number of passive tracers in PTRACERS_SIZE.h
5925    o start to test mnc routinely in exp0
5926    o add sea-ice loading (sIceLoad) as a new forcing field.
5927    
5928    checkpoint54b_post (2004/07/08)
5929    o add testreport "-j JOBS" option for parallel builds (tested and pretty
5930       impressive on Altix and Opteron systems)
5931    o diagnostics can now write NetCDF files through the mnc package
5932    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
5933    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
5934    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
5935      affects (truncation error) output of lab_sea & natl_box exp.: updated
5936    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
5937    
5938    checkpoint54a_post (2004/07/06)
5939    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
5940    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
5941    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
5942    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
5943      + internal_wave (shift in writing cg2d_ini_res)
5944    checkpoint54a_pre (2004/07/05)
5945    
5946    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
5947      - modified verification/lab_sea and natl_box_adjoint accordingly
5948    
5949    checkpoint54 (2004/07/02)
5950    checkpoint53g_post (2004/07/02)
5951    o prepare splitting of thermodynamics: store convect.counter in common block
5952    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
5953      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
5954    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
5955    o new parameter "nShapS": allow to treat differently S from T (nShapT)
5956    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
5957    o restore adjointability
5958    
5959    checkpoint53f_post (2004/06/25)
5960    o modifications that affect AIM experiment results (update output.txt):
5961      - no advection of S at top interface Nr (pkg/generic_advdiff)
5962      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
5963    o AIM pkg:
5964      - include stability function into surf.Flux derivative relative to Tsurf
5965      - calculate clear-sky radiation & surface temp. change (for diagnostics)
5966    
5967    checkpoint53e_post
5968    o merged cylindrical coord configuration
5969    o added rotating_tank experiment
5970    checkpoint53e_pre
5971    
5972    checkpoint53d_post (2004/06/14)
5973    o faulks upgraded: re-generate output.txt that have changed:
5974       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
5975    o Added Bryan and Lewis, 1979, vertical diffusivity profile
5976    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
5977    o added Sadourny discretization of Coriolis
5978      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
5979      - re-enabled use of omega3 (useAbsVorticity)
5980    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
5981      vector-invariant equations
5982      - note: does *NOT* yet use same variable visc. for no-slip BC's.
5983    o recoded the lateral boundary conditions for non-hydrostatic w, this time
5984      hopefully without new bugs
5985      - still to do: biharmonic friction for non-hydrostatic w
5986    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
5987    o regenerated output for global_ocean_ebm (using -ieee)
5988    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
5989      of mom_common/
5990      - simple re-arrangement of instructions within computing loop
5991    checkpoint53d_pre (2004/05/21)
5992    
5993    checkpoint53c_post (2004/05/21)
5994    o new version of coupler for AIM+thSIce and Ocean models
5995     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
5996     - land: change Evaporation of snow
5997     - aim with thSIce: fix bug in snow-precip.
5998    o changes to calc_gw.F
5999     - bug fix for w^2 term near the bottom boundary
6000     - (hopefully) improve the lateral slip boundary condtions for use with
6001        partial/looped cells
6002      - because the bug fix changes two verification experiments anyway (exp5
6003        and plume on slope), change the lateral boundary condition from half slip
6004        to the value of no_slip_sides
6005    o ebm package wasnt quite up to the parallel task. Fixed that.
6006    o Adjoint of EBM package + verification
6007      * TLM OK
6008      * ADM not sufficient accuracy yet (needs further testing)
6009    
6010    checkpoint53b_post (2004/05/14)
6011    o Commiting new energy balance model to repository
6012      * package is pkg/ebm
6013      * verif. is verification/global_ocean_ebm
6014      * references are in ebm_driver.F
6015    C      * X. Wang, P. Stone and J. Marotzke, 1999:
6016    C        Global thermohaline circulation. Part I:
6017    C        Sensitivity to atmospheric moisture transport.
6018    C        J. Climate 12(1), 71-82
6019    C      * X. Wang, P. Stone and J. Marotzke, 1999:
6020    C        Global thermohaline circulation. Part II:
6021    C        Sensitivity with interactive transport.
6022    C        J. Climate 12(1), 83-91
6023    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
6024    C        Destabilization of the thermohaline circulation
6025    C        by atmospheric eddy transports.
6026    C        J. Climate 7(12), 1870-1882
6027    o Will need long integration testing.
6028    checkpoint53b_pre (2004/05/14)
6029    
6030    o created pkg/mom_common in preparation for variable viscosity code
6031    o renamed and split ini_mnc_io
6032    o pkg/land: only liquid water can diffuse or run-off
6033    o AIM using land: soil wetness availability account for snow
6034    o added printMapIncludesZeros to EEPARMS namelist
6035    
6036    checkpoint53a_post (2004/05/11)
6037    o restore TAMC compatiility for exf_constants.h
6038      (no usage of _d in .h)
6039    o Additional storing in KPP in an attempt to fix
6040      TAMC problem with adjoint of KPP code.
6041      (no success...)
6042      Identical code works fine with TAF.
6043    o Fixed verification/natl_box_adjoint experiments.
6044      Initial conditions for Experiments 4 and 5 are now
6045      set to "SEAICE_initialHEFF=0", which is more reasonable,
6046      and hence gives results closer to that of Experiment 2.
6047      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
6048    
6049    checkpoint53 (2004/05/06)
6050    o stable checkpoint with up to date adjoint
6051      TLM tests only run for 1st grdchk at the moment. Its unclear if
6052      this is a code problem or a problem with resetting code for g_
6053      variables that is being autogenerated wrong.
6054      Otherwise:
6055       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
6056       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
6057         are both still in chaos following their security messes.
6058    
6059    checkpoint52n_post (2004/05/06)
6060    o various build (mostly genmake2) changes including:
6061      - ability to build/run more easily within Cygwin and MacOS X
6062      - more complicated Makefiles with a stronger dependence on Gnu Make
6063    o pkg/seaice modifications
6064      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
6065        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
6066        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
6067      - changed proxy for geostrophic velocity and updated
6068        verification/lab_sea/results/* accordingly
6069      - removed ADI dynamic solver from pkg/seaice
6070      - replaced all occurrences of 1/CSTICE or 1/CSUICE
6071        they caused a segmentation fault under certain circumstances
6072      - removed unused field WATR
6073    o bug fix in exf-package:
6074      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
6075         now reflect that.
6076    o small fixes in the cal-package:
6077      - set reference date to first of January for the 'model'-calendar
6078      - failing of cal_CheckDate in cal_FullDate now actually results in a
6079        warning
6080    o small modifications in exf-package to increase flexibility:
6081      - change climtempfreeze from a constant to a runtime parameter that
6082        is specified in data.exf_clim (default = -1.9)
6083      - introduce runtime parameter windstressmax (default = 2.0) that is
6084        specified in data.exf
6085    o fix in pkg/thsice:
6086      - update Evap (Tsf changes) to be consistent with Latent heat flux
6087      - maintain snow precipitation unchanged (even if Tsf >=0).
6088     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
6089    
6090    checkpoint52m_post (2004/04/18)
6091    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
6092      this does not change any of the results, because myIter=0 in swfrac always
6093      lead to jwtype=2 (the default anyway), but the call makes little sense
6094      as a default
6095    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
6096    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
6097      atmospheric model (AIM) to use it ; add a "slab ocean" component.
6098    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
6099    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
6100    o extending useSingleCpuIO option to work with new exch2 I/O format
6101      - old-style, missing-tile I/O is still accessible by defining CPP
6102        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
6103    o monitor package can write to NetCDF files and/or STDOUT
6104    o fix re-definition bug in MNC_GRID_INIT_ALL()
6105    o doc/api_reference added
6106      - a framework for building an API Reference Manual using all
6107        the "protex" comments embedded in the code
6108      - see pkg/generic_advdiff, pkg/mnc for examples
6109    o MNC:
6110      - make myThid the last argument for all subroutines
6111      - new default for the grid files: NO halos
6112      - add useMNC and other run-time flags
6113      - separate per-file-group handling of the unlimited dimension
6114      - early initialization of MNC w/ flags read at the eeboot stage
6115        and lookup tables set in initialize_fixed
6116      - write all MNC output to a freshly-created directory
6117    o thermodynamics sea-ice (thsice) is now tested with testreport.
6118    o test exp. advect_cs: use the standard cs32 grid ; update output.
6119    o Added functionality to grdchk:
6120      pick global i,j,k position (or nearest wet) where to perform check.
6121    
6122    checkpoint52l_post (2004/03/11)
6123    o new land formulation:
6124      a) use ground enthalpy as prognostic variable to ensure exact
6125         energy conservation.
6126      b) account for water temperature and for latent heat of freezing
6127         in all processes (rain, run-off, ground storage)
6128      c) compute surface and ground temperature implicitly.
6129    o aim_v23 modification for new land model:
6130      a) Treat separately land / ocean / sea-ice surface fluxes
6131         to allow implicit computation of land & sea-ice surface temp.
6132      b) add snow precipitation.
6133    checkpoint52l_pre (2004/03/11)
6134    
6135    o fix problem (when 1 tile is empty) in min/max monitor.
6136    o fix bug in timeAve (u,vZetatave in common block)
6137    o no restoring terms under ice for pkg/seaice
6138    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
6139    o bug fix for pkg/seaice pickups
6140    o change MNC call locations and add coordinate attributes
6141    o mask vorticity at the corner ; affects global_ocean.cs output
6142    o fix ini_curvilinear_grid ; test CS experiments with mpi
6143    o aim.5l_cs: modify sea-ice fraction input file ; update output
6144    o exf: Adding simple range check routine for exf fields after read
6145    
6146    checkpoint52k_post (2004/02/23)
6147    o removed top-level directory "diags"
6148      - we migrated these functions to pkg/timeave a long time ago
6149    o fixed bug introduced in pkg/monitor
6150    o accuracy ctrlprec = 32 insuffient for gradient checks using
6151      averaged fields (I/O via cost_averages)
6152      -> use ctrl.h in active_file*.F to control I/O precision.
6153    o paramter list of CALL ADTHE_MAIN_LOOP
6154    o added initial do_the_model_io to ecco
6155    o set all ...Freq to zero after cost_final
6156      taveFreq, dumpFreq, pChkptFreq
6157    o MAIN and ECCO differentiability restored
6158    
6159    checkpoint52j_post (2004/02/18)
6160  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
6161  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
6162  o Really weird thing!  o Really weird thing!
# Line 11  o Really weird thing! Line 6164  o Really weird thing!
6164    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
6165    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
6166    after cost_final call which should not be there!    after cost_final call which should not be there!
6167  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
6168    
6169  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
6170    error messages    error messages
# Line 28  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 6181  o merged mom_vi_calc_relvort3.F, mom_vi_
6181    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
6182  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
6183    
6184  checkpoint52i_post  checkpoint52i_post (2004/01/21)
6185  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
6186  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
6187  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
6188    
6189  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
6190    the old pkg/aim).    the old pkg/aim).
6191    
6192  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
6193  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
6194  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
6195  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 47  o added temporary hack for sea-ice dynam Line 6200  o added temporary hack for sea-ice dynam
6200    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
6201    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
6202    
6203  checkpoint52f_post  checkpoint52f_post (2004/01/09)
6204  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
6205  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
6206  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
6207  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
6208    
6209  checkpoint52e_post  checkpoint52e_post (2004/01/07)
6210  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
6211    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
6212  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 61  o step.1 : rewrite (as in MultiDimAdvec) Line 6214  o step.1 : rewrite (as in MultiDimAdvec)
6214  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
6215  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
6216   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
6217  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
6218    
6219  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
6220  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 72  o added exf_offset_atemp for Celsius to Line 6225  o added exf_offset_atemp for Celsius to
6225  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
6226  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
6227    
6228  checkpoint52d_post  checkpoint52d_post (2003/12/16)
6229  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
6230    - updated output accordingly    - updated output accordingly
6231    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 101  o check-in the first version of the coup Line 6254  o check-in the first version of the coup
6254  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
6255     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
6256    
6257  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
6258  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
6259  o add call to AIM pendant S/R in external_forcing & external_fields_load.F  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
6260    
6261  checkpoint52c_post  checkpoint52c_post (2003/11/25)
6262  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
6263    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
6264    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 119  o Removed all CPP options for cal packag Line 6272  o Removed all CPP options for cal packag
6272  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
6273  o corrected key comp. for passkey  o corrected key comp. for passkey
6274    
6275  checkpoint52b_post  checkpoint52b_post (2003/11/23)
6276  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
6277   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
6278   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 127  o new version: "thsice" of thermodynamic Line 6280  o new version: "thsice" of thermodynamic
6280   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
6281     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
6282  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
6283  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
6284    
6285  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
6286  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
# Line 137  o missing PTRACERS headers in some routi Line 6290  o missing PTRACERS headers in some routi
6290  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
6291    to ensure proper customization    to ensure proper customization
6292    
6293  checkpoint52a_post  checkpoint52a_post (2003/11/17)
6294  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
6295    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
6296    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 152  o fix problem with ECCO-related divided Line 6305  o fix problem with ECCO-related divided
6305    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
6306    but no warning issued by TAF    but no warning issued by TAF
6307    
6308  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
6309  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
6310    
6311  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
6312  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
6313    
6314  checkpoint51u_post  checkpoint51u_post (2003/11/06)
6315  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
6316    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
6317  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 173  o top level routines the_main_loop, forw Line 6326  o top level routines the_main_loop, forw
6326    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
6327  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
6328    
6329  checkpoint51t_post  checkpoint51t_post (2003/11/04)
6330  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
6331    
6332  checkpoint51s_post  checkpoint51s_post (2003/11/04)
6333  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
6334  o pkg/grdchk  o pkg/grdchk
6335    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 185  o pkg/grdchk Line 6338  o pkg/grdchk
6338    - additional high-precision output for testreport    - additional high-precision output for testreport
6339      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
6340    
6341  checkpoint51r_post  checkpoint51r_post (2003/11/03)
6342  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
6343  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
6344    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
6345    
6346  checkpoint51q_post  checkpoint51q_post (2003/10/30)
6347  o cd_code:  o cd_code:
6348    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
6349    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 206  o ctrl package totally restructured Line 6359  o ctrl package totally restructured
6359    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
6360  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
6361    
6362  checkpoint51p_post  checkpoint51p_post (2003/10/30)
6363  o create initial cd_code package  o create initial cd_code package
6364    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
6365      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 221  o create initial cd_code package Line 6374  o create initial cd_code package
6374  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
6375  o cleanup testreport  o cleanup testreport
6376    
6377  checkpoint51o_post  checkpoint51o_post (2003/10/27)
6378  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
6379    - carbon/    - carbon/
6380    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 242  o Correcting initialisations for fVerU, Line 6395  o Correcting initialisations for fVerU,
6395  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
6396    fVerU, fVerV    fVerU, fVerV
6397  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
6398  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
6399    
6400  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
6401  o added the [#include "AD_CONFIG.h"] statement to all files that need  o added the [#include "AD_CONFIG.h"] statement to all files that need
# Line 250  o added the [#include "AD_CONFIG.h"] sta Line 6403  o added the [#include "AD_CONFIG.h"] sta
6403   o re-worked the build logic in genmake2 to support AD_CONFIG.h   o re-worked the build logic in genmake2 to support AD_CONFIG.h
6404   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
6405    
6406  checkpoint51n_post  checkpoint51n_post (2003/10/23)
6407  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
6408    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
6409    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 259  o modifications to make FREEZE flux visi Line 6412  o modifications to make FREEZE flux visi
6412       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
6413  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
6414    
6415  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
6416  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
6417  o added [#include "AD_CONFIG.h"] to all files that use the following  o added [#include "AD_CONFIG.h"] to all files that use the following
6418    defines:    defines:
# Line 267  o added [#include "AD_CONFIG.h"] to all Line 6420  o added [#include "AD_CONFIG.h"] to all
6420    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
6421    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
6422    
6423  checkpoint51m_post  checkpoint51m_post (2003/10/21)
6424  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
6425    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
6426    - various cleanups related to package handling    - various cleanups related to package handling
6427    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
6428    
6429  checkpoint51l_post  checkpoint51l_post (2003/10/20)
6430  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
6431   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
6432   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
6433   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
6434     model integration time     model integration time
6435    
6436  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
6437  o add salt flux to forcing fields (used when salty sea-ice forms or melts)  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
6438  o enable to apply restoring on S & T only in a latitude band.  o enable to apply restoring on S & T only in a latitude band.
6439  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
6440     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
6441    
6442  checkpoint51k_post  checkpoint51k_post (2003/10/16)
6443  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
6444   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
6445     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
# Line 300  o added an include barrier to the defaul Line 6453  o added an include barrier to the defaul
6453    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
6454  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
6455    
6456  checkpoint51j_post  checkpoint51j_post (2003/10/10)
6457  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
6458  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
6459  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 314  o Moving pkg-specific flow directives to Line 6467  o Moving pkg-specific flow directives to
6467         - pkg_ad_diff.list         - pkg_ad_diff.list
6468         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
6469    
6470  checkpoint51i_post  checkpoint51i_post (2003/10/09)
6471  o merge of the branch-genmake2  o merge of the branch-genmake2
6472    - knowingly breaks the older genmake    - knowingly breaks the older genmake
6473    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
6474    - new testreport supersedes older testscript    - new testreport supersedes older testscript
6475  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
6476  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
6477    
6478  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
6479  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 332  o modify gchem pkg to be more versatile Line 6485  o modify gchem pkg to be more versatile
6485  o modifications to clean up dic pkg  o modifications to clean up dic pkg
6486  o add pkg/cfc  o add pkg/cfc
6487    
6488  checkpoint51g_post  checkpoint51g_post (2003/10/02)
6489  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
6490  o start removing verification/vero/  o start removing verification/vero/
6491  o update AD-related stuff  o update AD-related stuff
# Line 340  o update AD-related stuff Line 6493  o update AD-related stuff
6493  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
6494    vector invariant setup    vector invariant setup
6495    
6496  checkpoint51f_post  checkpoint51f_post (2003/10/02)
6497  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
6498  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
6499    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
6500    
6501  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
6502  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
6503      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
6504    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 357  o Bug fix to pkg/ptracers, pkg/generic_a Line 6510  o Bug fix to pkg/ptracers, pkg/generic_a
6510      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
6511      non-local transport term.      non-local transport term.
6512    
6513  checkpoint51e_post  checkpoint51e_post (2003/08/03)
6514  o pkg/mom_vecinv:  o pkg/mom_vecinv:
6515    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
6516    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 367  o atmospheric geopotential: - include wa Line 6520  o atmospheric geopotential: - include wa
6520  o land pkg: read initial state from files.  o land pkg: read initial state from files.
6521  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
6522    
6523  checkpoint51d_post  checkpoint51d_post (2003/07/18)
6524  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
6525    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
6526  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
# Line 380  o Use cluster local disks for purely loc Line 6533  o Use cluster local disks for purely loc
6533    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
6534    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
6535    
6536  checkpoint51c_post  checkpoint51c_post (2003/07/08)
6537  o introducing integer flag debugLevel  o introducing integer flag debugLevel
6538    - debLevZero: suppress all output    - debLevZero: suppress all output
6539    - debLevA: standard    - debLevA: standard
# Line 403  o added verification for adjoint with pt Line 6556  o added verification for adjoint with pt
6556    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
6557  <<<checkpoint51b_pre  <<<checkpoint51b_pre
6558    
6559  checkpoint51a_post  checkpoint51a_post (2003/06/25)
6560  o added code for biogeochemistry package  o added code for biogeochemistry package
6561    - new pkgs: dic, gchem    - new pkgs: dic, gchem
6562    - new subroutine in ptracers    - new subroutine in ptracers
6563  o modify code for biogeo packages  o modify code for biogeo packages
6564    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
6565    
6566  checkpoint51  checkpoint51 (2003/06/24)
6567  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
6568    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
6569    kept separate packages    kept separate packages
# Line 418  o merged improved packages from ecco-bra Line 6571  o merged improved packages from ecco-bra
6571  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
6572    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
6573    
6574  checkpoint50i_post  checkpoint50i_post (2003/06/23)
6575  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
6576    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
6577    - 1st step: this one is differentiable    - 1st step: this one is differentiable
6578    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
6579                from ecco-branch)                from ecco-branch)
6580    
6581  checkpoint50h_post  checkpoint50h_post (2003/06/20)
6582  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
6583  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
6584  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
# Line 434  o New variable in PARM03 for more flexib Line 6587  o New variable in PARM03 for more flexib
6587  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
6588    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
6589    
6590  checkpoint50g_post  checkpoint50g_post (2003/05/23)
6591  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
6592    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
6593    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
6594      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
6595    
6596  checkpoint50f_post  checkpoint50f_post (2003/05/23)
6597  o exf totally restructured  o exf totally restructured
6598    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
6599      and made sure it's still differentiable      and made sure it's still differentiable
# Line 448  o exf totally restructured Line 6601  o exf totally restructured
6601    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
6602    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
6603    
6604  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
6605   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
6606        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
6607   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 458  checkpoint50f_pre Line 6611  checkpoint50f_pre
6611   o new fn in pkg/monitor to stop model if solution grows too big   o new fn in pkg/monitor to stop model if solution grows too big
6612   o removed lots of single quotes from comments   o removed lots of single quotes from comments
6613    
6614  checkpoint50e_post  checkpoint50e_post (2003/05/14)
6615  o make KPP work with PTRACERS  o make KPP work with PTRACERS
6616   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
6617     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
6618   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
6619     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
6620  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
6621  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
6622    
6623  checkpoint50d_post  checkpoint50d_post (2003/05/13)
6624  o change kpp output from multiple-record state files to single-record state  o change kpp output from multiple-record state files to single-record state
6625    files analogous to write_state.F    files analogous to write_state.F
6626  o reduce the output frequency of cg3d-related stuff to the monitor frequency,  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
6627    analogous to the cg2d-related output.    analogous to the cg2d-related output.
6628  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
6629    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
6630  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
6631    
6632  checkpoint50c_post  checkpoint50c_post (2003/05/12)
6633  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
6634  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
6635  o add time-average diagnostic of U*V and vertical diffusive flux for theta.  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
6636  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
6637  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
6638    
6639  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
6640  Merging from release1_p13:  Merging from release1_p13:
6641  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
6642  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
6643    
6644  checkpoint50b_post  checkpoint50b_post (2003/04/17)
6645  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
6646  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
6647    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 497  o new flag "useCDscheme" (default=F); re Line 6650  o new flag "useCDscheme" (default=F); re
6650  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
6651     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
6652    
6653  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
6654  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
6655  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
6656    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
6657    
6658  checkpoint50a_post  checkpoint50a_post (2003/03/21)
6659  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
6660    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
6661    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
6662    in contradiction with new key itdkey.    in contradiction with new key itdkey.
6663    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
6664    
6665  checkpoint50  checkpoint50 (2003/03/08)
6666  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
6667    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
6668  - bug fix in find_alpha  - bug fix in find_alpha
# Line 517  checkpoint50 Line 6670  checkpoint50
6670  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
6671  - merged some sliced AD support routines  - merged some sliced AD support routines
6672    
6673  checkpoint49  checkpoint49 (2003/03/06)
6674  merged from ecco-branch:  merged from ecco-branch:
6675  o exf:  o exf:
6676    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 555  o DIVA: Line 6708  o DIVA:
6708    (see MITgcm manual).    (see MITgcm manual).
6709  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
6710    
6711  checkpoint48i_post  checkpoint48i_post (2003/03/05)
6712  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
6713    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
6714    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 573  o Modif. for DIVA: Line 6726  o Modif. for DIVA:
6726    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
6727    only relevant for ecco-branch)    only relevant for ecco-branch)
6728    
6729  checkpoint48h_post  checkpoint48h_post (2003/02/28)
6730  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
6731  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
6732  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
6733  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
6734    
6735  checkpoint48g_post  checkpoint48g_post (2003/02/18)
6736  --- EOS:  --- EOS:
6737  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
6738    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 593  o accurate phiHyd when using interface-W Line 6746  o accurate phiHyd when using interface-W
6746   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
6747  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
6748    
6749  checkpoint48f_post  checkpoint48f_post (2003/02/18)
6750  Merging from release1_p12:  Merging from release1_p12:
6751  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
6752    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 621  o pkg/seaice: Line 6774  o pkg/seaice:
6774    - adjoint-friendly modifications    - adjoint-friendly modifications
6775    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
6776    
6777  checkpoint48e_post  checkpoint48e_post (2003/02/12)
6778  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
6779  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
6780    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
# Line 632  o following exp works with Olx=Oly=2 (an Line 6785  o following exp works with Olx=Oly=2 (an
6785      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
6786    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
6787    
6788  checkpoint48d_post  checkpoint48d_post (2003/02/09)
6789  o in preparation for r*:  o in preparation for r*:
6790   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
6791      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
# Line 640  o in preparation for r*: Line 6793  o in preparation for r*:
6793      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
6794    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
6795    
6796  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
6797  o in preparation for r*:  o in preparation for r*:
6798    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
6799    pass the 2 comp. of the grad. as arguments to momentum S/R.    pass the 2 comp. of the grad. as arguments to momentum S/R.
6800    but for the moment, only used if it does not change the results.    but for the moment, only used if it does not change the results.
6801  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
6802    
6803  checkpoint48c_post  checkpoint48c_post (2003/02/06)
6804  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
6805  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
6806    
6807  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
6808  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
6809  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
6810    
6811  checkpoint48b_post  checkpoint48b_post (2003/01/27)
6812  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
6813   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
6814  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
6815    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
6816    
6817  checkpoint48a_post  checkpoint48a_post (2003/01/24)
6818  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
6819     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
6820    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
6821                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
6822    
6823  checkpoint48  checkpoint48 (2003/01/23)
6824  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
6825    
6826  checkpoint47j_post  checkpoint47j_post (2003/01/21)
6827  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
6828  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
6829  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 689  o Yet more changes in gmredi: Line 6842  o Yet more changes in gmredi:
6842      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
6843  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
6844    
6845  checkpoint47i_post  checkpoint47i_post (2003/01/13)
6846  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
6847  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
6848    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
# Line 705  o case GM_BOLUS_ADVEC should be cleaned Line 6858  o case GM_BOLUS_ADVEC should be cleaned
6858    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
6859  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
6860    
6861  checkpoint47g_post  checkpoint47g_post (2003/01/10)
6862  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
6863    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
6864  o After TAF bug fix:  o After TAF bug fix:
# Line 731  Gradient checks OK for Line 6884  Gradient checks OK for
6884  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
6885  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
6886    
6887  checkpoint47f_post  checkpoint47f_post (2002/12/28)
6888  Merging from release1_p10:  Merging from release1_p10:
6889  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
6890    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 743  o modifications for using pkg/exf with p Line 6896  o modifications for using pkg/exf with p
6896    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
6897      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
6898    
6899  checkpoint47e_post  checkpoint47e_post (2002/12/27)
6900  o created a tag prior to creating a branch  o created a tag prior to creating a branch
6901    
6902  checkpoint47d_post  checkpoint47d_post (2002/12/16)
6903  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
6904    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
6905  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
6906    oceanic pressure coordinates code    oceanic pressure coordinates code
6907  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
6908    also described in the tutorial section of the manual    also described in the tutorial section of the manual
6909  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
6910    
6911  checkpoint47c_post  checkpoint47c_post (2002/12/16)
6912  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
6913    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
6914    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 767  o OCEANICP & realFreshWater: include P-E Line 6920  o OCEANICP & realFreshWater: include P-E
6920    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
6921  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
6922    
6923  checkpoint47b_post  checkpoint47b_post (2002/12/05)
6924  Merging from release1_p9:  Merging from release1_p9:
6925  o pkg/seaice  o pkg/seaice
6926    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 784  o verification/lab_sea Line 6937  o verification/lab_sea
6937    - added missing matlab routines    - added missing matlab routines
6938    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
6939    
6940  checkpoint47a_post  checkpoint47a_post (2002/11/23)
6941  o new pkg: aim_v23  o new pkg: aim_v23
6942   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
6943     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 801  o bulk_force and therm_seaice Line 6954  o bulk_force and therm_seaice
6954  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
6955     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
6956    
6957  checkpoint47  checkpoint47 (2002/11/15)
6958  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
6959  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
6960  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 830  o Updated verification/carbon/ Line 6983  o Updated verification/carbon/
6983    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
6984    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
6985    
6986  checkpoint46n_post  checkpoint46n_post (2002/11/12)
6987  Merging from release1_p8:  Merging from release1_p8:
6988  o verification/natl_box:  o verification/natl_box:
6989    updating new external_fields_load routine    updating new external_fields_load routine
# Line 884  o Adding new verification experiment glo Line 7037  o Adding new verification experiment glo
7037    the exf (and cal) package instead of the    the exf (and cal) package instead of the
7038    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
7039    
7040  checkpoint46m_post  checkpoint46m_post (2002/11/07)
7041  o modified testscript to return -- when there are no lines of "%MON" output  o modified testscript to return -- when there are no lines of "%MON" output
7042  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
7043    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 897  o introduced flag for controllin non-hyd Line 7050  o introduced flag for controllin non-hyd
7050  o removed gravitySign from PARM04  o removed gravitySign from PARM04
7051  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
7052    
7053  checkpoint46l_post  checkpoint46l_post (2002/11/01)
7054  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
7055   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
7056     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 910  o made convective adjustment work with p Line 7063  o made convective adjustment work with p
7063     at the beginning of find_rho, find_alpha, and find_beta, does a     at the beginning of find_rho, find_alpha, and find_beta, does a
7064     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
7065     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
7066  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
7067    
7068  checkpoint46k_post  checkpoint46k_post (2002/10/23)
7069  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
7070   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
7071   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 926  o S/R aim_initialise.F replace S/R aim_i Line 7079  o S/R aim_initialise.F replace S/R aim_i
7079   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
7080   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
7081    
7082  checkpoint46j_post  checkpoint46j_post (2002/10/07)
7083  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
7084  o move wVel computation at the end of the time step, in S/R integr_continuity  o move wVel computation at the end of the time step, in S/R integr_continuity
7085  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
7086  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
7087  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
7088    
7089  checkpoint46i_post  checkpoint46i_post (2002/09/25)
7090  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
7091    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
7092    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
7093    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
7094    
7095  checkpoint46h_post  checkpoint46h_post (2002/09/25)
7096  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
7097    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
7098      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
# Line 949  o introduced new parameter rhoConstFresh Line 7102  o introduced new parameter rhoConstFresh
7102    value is 999.8 kg/m^3    value is 999.8 kg/m^3
7103  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
7104    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
7105  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
7106    
7107   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
7108   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
7109   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
7110    
7111  checkpoint46g_post  checkpoint46g_post (2002/09/18)
7112  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
7113    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
7114    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 973  o cleaned up find_rho Line 7126  o cleaned up find_rho
7126    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
7127  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
7128    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
7129  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
7130    
7131  checkpoint46f_post  checkpoint46f_post (2002/09/16)
7132  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
7133    - extended active file handling to g_... files    - extended active file handling to g_... files
7134    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 983  o Enable tangent linear (forward mode) g Line 7136  o Enable tangent linear (forward mode) g
7136  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
7137  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
7138    
7139  checkpoint46e_post  checkpoint46e_post (2002/09/05)
7140  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
7141    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
7142    - caveat: the equation of state is only valid for a smaller (more    - caveat: the equation of state is only valid for a smaller (more
# Line 992  o Added new equation of state -> MDJWF Line 7145  o Added new equation of state -> MDJWF
7145    - added more check values for density in check_eos (ini_eos.F), some of    - added more check values for density in check_eos (ini_eos.F), some of
7146      the old check values are out of the range of the MDJWF-eos, so don't      the old check values are out of the range of the MDJWF-eos, so don't
7147      expect perfect matches for those      expect perfect matches for those
7148  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
7149    
7150  checkpoint46d_post  checkpoint46d_post (2002/08/19)
7151  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
7152    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
7153    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
7154    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
7155  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
7156    in find_alpha/beta.    in find_alpha/beta.
7157  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
7158    
7159  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
7160    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
7161    
7162  checkpoint46c_post  checkpoint46c_post (2002/08/15)
7163  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
7164   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
7165   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
7166      the factor dRdZ which I added when we first switched to R coordinates).      the factor dRdZ which I added when we first switched to R coordinates).
7167   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
7168   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
7169  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
7170    
7171  checkpoint46b_post  checkpoint46b_post (2002/08/07)
7172  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
7173    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
7174    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 1024  o Added UNESCO EOS, but not recommended Line 7177  o Added UNESCO EOS, but not recommended
7177    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
7178  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
7179    unesco.f to be used with POLY3    unesco.f to be used with POLY3
7180  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
7181    
7182  checkpoint46a_post  checkpoint46a_post (2002/07/31)
7183  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
7184    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
7185    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
7186  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
7187  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
7188  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
7189    
7190  checkpoint46  checkpoint46 (2002/07/13)
7191  further merges from release1_p5  further merges from release1_p5
7192  o new ctrl package  o new ctrl package
7193    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 1061  o added hooks for Eliassen Palm fluxes ( Line 7214  o added hooks for Eliassen Palm fluxes (
7214  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
7215  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
7216    
7217  checkpoint45d_post  checkpoint45d_post (2002/07/12)
7218  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7219  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
7220    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 1075  o add new flags: Line 7228  o add new flags:
7228   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
7229  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
7230    
7231  checkpoint45c_post  checkpoint45c_post (2002/05/30)
7232  o Removed f90 comments ("!")  o Removed f90 comments ("!")
7233  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
7234    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 1083  o modifications to gradient check packag Line 7236  o modifications to gradient check packag
7236    - enable centered differences    - enable centered differences
7237    - modified format of standard output    - modified format of standard output
7238    
7239  checkpoint45b_post  checkpoint45b_post (2002/05/30)
7240  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
7241  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
7242  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1095  o in initialise_varia, moved call packag Line 7248  o in initialise_varia, moved call packag
7248    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
7249  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
7250    
7251  checkpoint45a_post  checkpoint45a_post (2002/05/01)
7252  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
7253  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
7254  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
# Line 1115  o errorMessageUnit set non-equal zero in Line 7268  o errorMessageUnit set non-equal zero in
7268    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
7269  o modified carbon verif.  o modified carbon verif.
7270    
7271  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
7272  o vertical grid option: allow to put the Interface at the middle between  o vertical grid option: allow to put the Interface at the middle between
7273    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
7274  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
7275    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
7276    
7277  checkpoint44g_post  checkpoint44g_post (2002/03/05)
7278  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
7279    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
7280    
# Line 1186  o merge of relevant stuff from the ecco- Line 7339  o merge of relevant stuff from the ecco-
7339  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
7340  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
7341    
7342  checkpoint44  checkpoint44 (2002/01/18)
7343  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
7344  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
7345  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 1194  o update AIM experiments (NCEP input fil Line 7347  o update AIM experiments (NCEP input fil
7347  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
7348  o added some stuff for AD  o added some stuff for AD
7349    
7350  checkpoint43  checkpoint43 (2001/09/28)
7351  o added two new advection tests  o added two new advection tests
7352  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
7353  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
7354  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
7355    
7356  checkpoint42  checkpoint42 (2001/09/27)
7357    Fixed AD-related problems:    Fixed AD-related problems:
7358  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
7359    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1212  o Modified store directives for split of Line 7365  o Modified store directives for split of
7365    for the case ALLOW_KPP    for the case ALLOW_KPP
7366  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
7367    
7368  checkpoint41  checkpoint41 (2001/09/27)
7369  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
7370    to work with protex    to work with protex
7371    
7372  checkpoint40  checkpoint40 (2001/09/27)
7373  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
7374  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
7375  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1225  o more mods for non-linear free-surface Line 7378  o more mods for non-linear free-surface
7378  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
7379  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
7380    
7381  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
7382  o added DST advection schemes  o added DST advection schemes
7383  o fix MPI bug on SGI's  o fix MPI bug on SGI's
7384  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1235  o changes to commenting of arguments for Line 7388  o changes to commenting of arguments for
7388  o added/updated many matlab scripts  o added/updated many matlab scripts
7389  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
7390        
7391  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
7392  o new package rw/  o new package rw/
7393    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
7394    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1254  o TAMC-related update to cope with mom_f Line 7407  o TAMC-related update to cope with mom_f
7407    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
7408    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
7409    
7410  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
7411  o bug fix in dynamics.F  o bug fix in dynamics.F
7412    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
7413  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
7414  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
7415    related to TAF    related to TAF
7416    
7417  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
7418  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
7419  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
7420    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1269  o corresponding split of calc_diffusivit Line 7422  o corresponding split of calc_diffusivit
7422  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
7423  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
7424    
7425  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
7426  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
7427    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
7428  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 1283  o added new expt "solid-body.cs-32x32x1" Line 7436  o added new expt "solid-body.cs-32x32x1"
7436    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
7437      is not necessarily any better than the current one...      is not necessarily any better than the current one...
7438    
7439  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
7440  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
7441    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
7442  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1291  o extended iMin,jMin range for calc_comm Line 7444  o extended iMin,jMin range for calc_comm
7444  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
7445  o a few minor updates and fixes  o a few minor updates and fixes
7446    
7447  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
7448  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
7449  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
7450  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
7451    
7452  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
7453  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
7454  o Added gradient check package  o Added gradient check package
7455  o Added routines for passive tracer handling  o Added routines for passive tracer handling
7456  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
7457    
7458  checkpoint39  checkpoint39 (2001/05/14)
7459   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
7460     (mainly missing or wrong directives)     (mainly missing or wrong directives)
7461   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 1316  checkpoint39 Line 7469  checkpoint39
7469           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
7470   o disabled some packages by default in genmake   o disabled some packages by default in genmake
7471    
7472  checkpoint38  checkpoint38 (2001/04/10)
7473   o see notes_c37_adj.txt   o see notes_c37_adj.txt
7474   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
7475   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1324  checkpoint38 Line 7477  checkpoint38
7477     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
7478   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
7479    
7480  checkpoint37  checkpoint37 (2001/03/13)
7481   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
7482     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
7483      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1341  checkpoint37 Line 7494  checkpoint37
7494   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
7495   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
7496    
7497  checkpoint36  checkpoint36 (2001/02/20)
7498   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
7499   o recover Time-Average diagnostics   o recover Time-Average diagnostics
7500   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
7501   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
7502    
7503  checkpoint35  checkpoint35 (2001/02/08)
7504   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
7505   o allows staggered time-stepping   o allows staggered time-stepping
7506   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
7507   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
7508    
7509  checkpoint34  checkpoint34 (2001/01/30)
7510   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
7511   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
7512     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1364  checkpoint34 Line 7517  checkpoint34
7517   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
7518   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
7519    
7520  checkpoint33  checkpoint33 (2000/11/30)
7521   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
7522   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
7523     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1382  checkpoint33 Line 7535  checkpoint33
7535       possibly use them.       possibly use them.
7536   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
7537    
7538  checkpoint32  checkpoint32 (2000/11/13)
7539   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
7540     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
7541   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1393  checkpoint32 Line 7546  checkpoint32
7546   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
7547   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
7548    
7549  checkpoint31  checkpoint31 (2000/09/11)
7550   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
7551     -> new routines packages_...F     -> new routines packages_...F
7552     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1410  checkpoint31 Line 7563  checkpoint31
7563     - not yet tested for GMRedi.     - not yet tested for GMRedi.
7564     - not yet tested for KPP.     - not yet tested for KPP.
7565    
7566  checkpoint30  checkpoint30 (2000/07/13)
7567   o Updates for OBCs   o Updates for OBCs
7568   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
7569   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1419  checkpoint30 Line 7572  checkpoint30
7572   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
7573     and entry for T90 in genmake     and entry for T90 in genmake
7574    
7575  checkpoint29  checkpoint29 (2000/06/21)
7576   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
7577    
7578  checkpoint28  checkpoint28 (2000/06/09)
7579   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
7580   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
7581   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 1435  checkpoint28 Line 7588  checkpoint28
7588     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
7589   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
7590    
7591  checkpoint27  checkpoint27 (2000/04/10)
7592   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
7593     formulation works properly with variable resolution.     formulation works properly with variable resolution.
7594   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 1443  checkpoint27 Line 7596  checkpoint27
7596   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
7597     in new routine ini_psurf()     in new routine ini_psurf()
7598    
7599  checkpoint26  checkpoint26 (2000/04/05)
7600   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
7601     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
7602   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 1453  checkpoint26 Line 7606  checkpoint26
7606     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
7607   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
7608    
7609  checkpoint25  checkpoint25 (2000/03/15)
7610   o updates for OBCs and NH   o updates for OBCs and NH
7611   o dramatically reduced memory usage   o dramatically reduced memory usage
7612   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 1464  checkpoint25 Line 7617  checkpoint25
7617      an explicit free-surface option)      an explicit free-surface option)
7618   o initial state input files for U and V   o initial state input files for U and V
7619    
7620  checkpoint24  checkpoint24 (1999/08/02)
7621   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
7622   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
7623   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
7624    
7625  checkpoint23  checkpoint23 (1999/05/26)
7626   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
7627   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
7628    
7629  checkpoint22  checkpoint22 (1999/05/18)
7630   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
7631   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
7632    
7633  checkpoint21  checkpoint21 (1999/05/18)
7634   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
7635   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
7636   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
7637   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
7638    
7639  checkpoint20  checkpoint20 (1999/03/22)
7640   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
7641   o Added non-hydrostatic code   o Added non-hydrostatic code
7642   o Fixed some input data   o Fixed some input data
7643   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
7644    
7645  checkpoint19  checkpoint19 (1998/12/15)
7646   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
7647   o Added new code for open boundaries.   o Added new code for open boundaries.
7648   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 1497  checkpoint19 Line 7650  checkpoint19
7650   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
7651   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
7652    
7653  checkpoint18  checkpoint18 (1998/11/30)
7654   o Further changes for optional code generation with   o Further changes for optional code generation with
7655     CPP - ugh!     CPP - ugh!
7656    
7657  checkpoint17  checkpoint17 (1998/11/03)
7658   o Beginning to incorporating modularity   o Beginning to incorporating modularity
7659     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
7660   o Small changes for TAMC complinace   o Small changes for TAMC complinace
7661   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
7662     configuration "exp0".     configuration "exp0".
7663    
7664  checkpoint16  checkpoint16 (1998/10/28)
7665   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
7666     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
7667     assignment is an addition.     assignment is an addition.
# Line 1516  checkpoint16 Line 7669  checkpoint16
7669     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
7670     limit ).     limit ).
7671    
7672  checkpoint15  checkpoint15 (1998/09/29)
7673   Rewrote exchange routines to allow   Rewrote exchange routines to allow
7674   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
7675   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 1525  checkpoint15 Line 7678  checkpoint15
7678     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
7679     communication method.     communication method.
7680    
7681  checkpoint14  checkpoint14 (1998/09/09)
7682   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
7683   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
7684    
7685  checkpoint13  checkpoint13 (1998/07/17)
7686   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
7687   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
7688   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 1544  branch-point-rdot Line 7697  branch-point-rdot
7697   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
7698   we've actually tested it...   we've actually tested it...
7699    
7700  checkpoint12  checkpoint12 (1998/07/08)
7701   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
7702   configure script).   configure script).
7703   Released to testers.   Released to testers.
7704    
7705  checkpoint11  checkpoint11 (1998/07/02)
7706   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
7707   and ini_masks_etc().   and ini_masks_etc().
7708    
7709  checkpoint10  checkpoint10 (1998/07/01)
7710   Introduced the configure script.   Introduced the configure script.
7711   Separated out the diags package.   Separated out the diags package.
7712   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
7713   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
7714    
7715  checkpoint9  checkpoint9 (1998/06/22)
7716   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
7717   General tidy-up.   General tidy-up.
7718   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
7719    
7720  checkpoint8  checkpoint8 (1998/06/22)
7721   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
7722   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
7723    
# Line 1574  checkpoint7-4degree-ref Line 7727  checkpoint7-4degree-ref
7727   model etc..   model etc..
7728   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
7729    
7730  checkpoint7  checkpoint7 (1998/06/15)
7731   Created by cnh   Created by cnh
7732   Simple 4 degree global simulation   Simple 4 degree global simulation
7733   configuration.   configuration.
# Line 1582  checkpoint7 Line 7735  checkpoint7
7735   hydrography, bathymetry etc   hydrography, bathymetry etc
7736   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
7737    
7738  checkpoint6  checkpoint6 (1998/06/08)
7739   Created by cnh   Created by cnh
7740   merged checkpoint5 with CD and   merged checkpoint5 with CD and
7741   spherical polar code.   spherical polar code.
7742   Still some problems with GM Redi   Still some problems with GM Redi
7743   abd full topography.   abd full topography.
7744    
7745  checkpoint5  checkpoint5 (1998/06/08)
7746   Created by AJA   Created by AJA
7747   contains updates to GM Redi   contains updates to GM Redi
7748   and reordered timestepping loop   and reordered timestepping loop
7749   for Implicit Diffusion.   for Implicit Diffusion.
7750    
7751  checkpoint4  checkpoint4 (1998/05/30)
7752   Created by cnh   Created by cnh
7753   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
7754   grid variations are limited.   grid variations are limited.
7755   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
7756   for generation.   for generation.
7757    
7758  checkpoint3  checkpoint3 (1998/05/26)
7759   Created by cnh   Created by cnh
7760   Added extra flags for runtime options   Added extra flags for runtime options
7761   Added this file   Added this file

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