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revision 1.1234 by jmc, Fri Mar 5 00:44:21 2010 UTC revision 1.1983 by mlosch, Tue Apr 29 14:23:52 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice: remove global variable TICE (not needed)
8      - replace by TICES or local variable where necessary (cost_seaice_test,
9        seaice_diagnostics_state)
10      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
11      - use specific read/write routines for reading and writing individual leves
12        of a multilevel field
13    o pkg/ctrl & model/inc:
14      - move additional anomaly fields of control vars (related to options:
15         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
16        from DYNVARS.h into new header file: CTRL_FIELDS.h
17    o pkg/seaice: some small modifications to the ridging code
18      - make fw2ObyRidge a global variable and add the freshwater flux to
19        seaice_growth
20      - pass actual thickness from seaice_prepare_ridging, so that it is
21        computed only in one place and compute it in the same way as in
22        seaice_growth
23      - initialise more fields in seaice_do_ridging that where cause floating
24        point exceptions over land
25    o pkg/seaice: preparations for ridging code and first real ridging code
26      - move most of "PART 1" of S/R seaice_growth into a new and separate
27        S/R seaice_reg_ridge that will both regularize the state variable after
28        advection call the actual ridging routine;
29      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
30        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
31      - remove ridging code from seaice_advdiff
32      - clean up remaining part 1 of seaice_growth in an attempt to make it
33        more readable (this is probably subjective)
34      - call seaice_itd_redist once in the initialisation phase to have the initial
35        conditions in the correct category
36      - finally: add new ridging routine for ITD code
37    
38    checkpoint64v (2014/04/11)
39    o pkg/ecco:
40      - add runtime parameters mdt[start,end]date[1,2]
41      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
42    o pkg/seaice:
43      - make deltaC a global variable, so that it can be used in ridging code
44      - first step towards ridging: introduce new routines that compute
45        ice strength based on ridging parameters
46      - add diagnostic for HSNOWITD
47      - add opnWtrFrac as a global variable (required for ridging scheme)
48    o pkg/salt_plume + pkg/seaice/seaice_growth.F
49      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
50        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
51    o verification/hs94.1x64x5:
52      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
53      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
54    o autodiff:
55      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
56        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
57        For now, only in pkgs used in verification/hs94.1x64x5.
58      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
59        which are specific to TAF/TAMC).
60      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
61        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
62        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
63      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
64        building mitgcmuv_ad (make adAll).
65    o pkg/ecco:
66      - cost_gencost_seaicev4.F:
67         reformulate proxy cost as function of sst and local param SEAICE_freeze
68         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
69      - add stop statement if old names siv4-[sst,vol] are used
70      - add snapshots + cost reports for atmospheric longwave
71      - remove factor 0.1 in front of wtau[u,v]
72      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
73         ALLOW_TMI_SST_COST_CONTRIBUTION
74    o pkg/atm_phys:
75      - add some diagnostics for Short-wave and for convection S/R.
76    o pkg/seaice/seaice_growth:
77      - fix a bug in the lateral melt parameterization for SEAICE_ITD
78        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
79      - rearrange loop order for better vector code in the same code block
80      - rewrite the floeDiameter formula to have fewer divisions
81      -  (miraculously) none of this changes the results of seaice_itd
82    o pkg/smooth:
83      - move param smooth2Ddiffnbt to pkg/ecco
84    o pkg/salt_plume:
85      - salt_plume_frac.F:
86         clean up local param names
87         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
88    o pkg/rw:
89      - add RS version of S/R READ_MFLDS_LEV.
90    o pkg/streamice:
91      - fix the restart test by writing/reading pickup_streamice files.
92    o pkg/seaice:
93      - refine checks for jfnk-related parameters
94      - comment out if statement with SEAICEuseIMEX parameter as long as there
95        is no IMEX code to avoid confusion and surprises
96    
97    checkpoint64u (2014/03/07)
98    o verification/MLAdjust:
99      - rename secondary test suffix:
100         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
101         0.leithD -> AhFlxF  + switch to flux-form
102         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
103         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
104    o pkg/mom_vecinv:
105      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
106        to be before mom_calc_visc.F)
107      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
108      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
109        this is simpler for the adjoint and for diagnostics.
110    o model/src + pkg/momentum:
111      - add input files for  2-D additional Western and Southern cell-edge wall
112         (e.g., to add "thin-wall" where it is =1).
113      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
114        using 2nd hFacZ that is computed from initial (fix domain) hFac
115      - known limitations of thin wall implementation: not yet coded for sigma
116        coords; not working with CD-scheme neither.
117    o pkg/seaice:
118      - rename recently introduced parameters from (wrong name) AB to
119        BDF (backward difference time discretisation)
120      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
121    o tools/adjoint_options:
122      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
123    
124    checkpoint64t (2014/02/01)
125    o pkg/ecco
126      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
127        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
128      - replace hard-coded record number and period which only work for monthly
129        with read-in runtime param that works for other periods (month,day,year)
130    o pkg/thsice
131      - corrected store directive fixes thsice adjoint gradient checks
132    o genmake2 & testreport:
133      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
134        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
135        Update testreport accordingly. No need to set "export OPENAD=true"
136        in adjoint_options/adjoint_oad anymore (will be removed later).
137    o pkg/shelfice:
138      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
139        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
140        so that surface forcing applies to k=kSurf if using pkg/shelfice.
141    o pkg/ctrl, pkg/grdchk, pkg/ecco:
142      - Changes to make GENARR more modular (i.e. invisible if not used)
143    o model/src/temp_integrate.F and salt_integrate.F
144      - re-include store directives that were removed on Dec 27th.
145    o model/src/external_forcing_surf.F
146      - add storage directives for EmPmR and PmEpR to avoid recomputation of
147        seaice_model in the adjoint that is problematic when seaice_model is
148        turned off in the adjoint. The resolved issue dated back to July when
149        EXTERNAL_FORCING_SURF call was moved.
150        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
151    o pkg/exf/exf_check.F
152      - fix a small bug again (originally found by Wentao Liu, now found again)
153      - streamline error output
154    o pkg/streamice and aim_v23:
155      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
156        Apple's /usr/bin/cpp knows what to do:
157        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
158        Target: x86_64-apple-darwin13.0.0
159    
160    checkpoint64s (2014/01/05)
161    o tools/adjoint_options:
162      - switch to fastopt.net TAF server (instead of default fastopt.de) for
163        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
164    o model/src:
165      - remove some unnecessary TAF storage directives in forward_step.F and
166        in dynamics.F (note: not always removed by TAF, e.g., double storage
167        of kappaRU,kappaRV in former version of dynamics.F).
168    o model/src & pkg/ptracers:
169      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
170        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
171        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
172      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
173      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
174      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
175    o useSingleCpuInput separates single-CPU input from single-CPU output;
176        for now only implemented for in exf_interp_read.F
177    o verification/advect_xy:
178      - fix missing EXCH call in local version of ini_salt.F and update output.
179    o momentum diagnostics:
180      - fix which deltaT is used in Total-Tendency diagnostics.
181      - fix typo in diagnostics for momentum tendency from AB.
182    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
183        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
184    
185    checkpoint64r (2013/12/08)
186    o verification/*/results:
187      - Update reference output of experiments that were passing with just 13 digits
188         (make it easier to detect future changes in results)
189    o model/src & pkg/ptracers:
190      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
191        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
192        to inside ptracers_integrate.F ; remove ptracers_advection.F
193    o coupling interface pkgs:
194        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
195      - change the config check to test the agreement of Ocean Depth
196        with ATM land/sea mask (instead of ATM orography);
197      - send to coupler the number of coupler time-steps to do for this run:
198        this allows to check for consistency and don't need anymore to be
199        specified in parameter file "data";
200      in coupler:
201      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
202      - improve report to log-file of config setting (pass log-file unit to few S/R)
203    o pkg/compon_communic:
204      - add coupling send/receive for non-tiled integer vector;
205      - add S/R to check and stop if any proc has an error (similar to
206        eesupp/src/stop_if_error.F but single thread and across Comm_World).
207    o pkg/exch2:
208      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
209        through list of all tiles my proc owns.
210    o model/src:
211      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
212        from rTrans) to simplify dependencies (no need to store rTrans anymore in
213        calling S/R); this affects AD results at machine truncation level:
214        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
215        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
216    o tools/build_options:
217      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
218    o coupling interface pkgs:
219        [compon_communic, atm_compon_interf & ocn_compon_interf]
220      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
221        to each S/R that needs it; remove un-used variables.
222      - change component tile registration (cpl_register.F in both compon_interf
223        and mitcomponent_tile_register.F) to pass the full list of tiles
224        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
225      - with pkg/exch2: adopt the same convention used for I/O to define mapping
226        towards coupler global array (unless W2_useE2ioLayOut=F):
227         a) can now use different tiling between atm & ocn comp.
228         b) no needs to modify the run-Off map when changing tiling (was needed
229            even if using the same tiling between atm & ocn).
230         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
231            full land tiles); not yet tested.
232      - check for valid mapping from comp. tile to coupler global array
233      - improve report of tile registration results to log file.
234    o pkg/exch2:
235      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
236        tile-registration (CPL_REGISTER);
237      - activate (un-comment) definition and setting of "W2_tileIndex" list to
238        store the local bi,bj indices of each tile;
239      - also print bi,bj in local report to log file;
240      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
241        Jun 2009 modif of pkg/exch2).
242    o testing on baudelaire:
243      - run 2 tests at a time: no significant slow down (since enough cpu) and
244        get the full set of test done earlier
245      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
246    o model/src/thermodynamics.F and routines called from it:
247      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
248        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
249        velocity (outp) by adding bolus velocity.
250      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
251        mass transport from velocity + lateral grid cell area
252      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
253      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
254     in thermodynamics.F
255      - remove k from thermodynamics.F and move it to temp_integrate.F
256        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
257        loop).
258      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
259        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
260        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
261        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
262      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
263        global_ocean.90x40x15, tutorial_global_oce_biogeo and
264        tutorial_tracer_adjsens (+ TLM output).
265    o tools/OAD_support and (verification/*/) code_oad:
266      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
267        module conversion ; remove unneeded CPP_EEOPTIONS.h.
268      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
269        version (closer to model/inc/CPP_OPTIONS.h).
270    o model/src:
271      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
272        retired list of parameters (routine FREEZE has been replace by surface
273        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
274    o pkg/gmredi:
275      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
276        velocity (same scheme but affects machine truncation) for GM_AdvForm.
277      - update output of FWD experiments: front_relax.bvp,
278        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
279    
280    checkpoint64q (2013/11/17)
281    o verification:
282      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
283        tutorial_global_oce_biogeo and global_ocean.90x40x15.
284      - generate new output (growth & melt) for seaice_itd experiment after
285        updating the input pickup_seaice files (previously wrong).
286    o pkg/cost:
287      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
288        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
289        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
290          cannot be applied to var in common block).
291        o allows to get results independent of tile-per-proc setting (if using
292          slower GLOBAL_SUM_SEND_RECV option).
293      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
294        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
295        forward gradients: update output).
296      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
297        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
298    o pkg/mom_common:
299      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
300        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
301        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
302        ensure that all field value that are used are set.
303    o tutorial_deep_convection (smag3d):
304      - add missing scaling in mom_calc_smag_3d.F;
305      - set smag3D_coeff in input.smag3d such that results do not change.
306    o pkg/dic:
307      - change dic_cost.F to compute cost on each tile first and then apply
308        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
309        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
310      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
311    o eesupp/src & pkg/mdsio:
312      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
313        (from pkg/mdsio) since they are no longer used for tape IO.
314      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
315        (+ keep a copy in pkg/atm_ocn_coupler).
316    o verification/isomip:
317      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
318    o tools/build_options:
319      - optfile linux_amd64_ifort11, fast (no ieee) case:
320        to get a working restart for all experiments, add "-fp-model source"
321        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
322    
323    checkpoint64p (2013/10/20)
324    o pkg/autodiff:
325      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
326        criteria, return to simple (default) tape IO format.
327    o pkg/mdsio (+ eesupp/src):
328      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
329        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
330      - fix globalFile and singleCpuIO options using simpler global mapping.
331      - new pairs of scatter/gather vector S/R (one for each type, generated from
332        template) corresponding to simpler global mapping.
333      - adread_write.F: switch to new S/R (but leave old calls commented) and write
334        to globalFile when parameter globalFiles is set to True.
335      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
336    o pkg/autodiff:
337      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
338        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
339        missing, just add a STOP if array type do not match.
340    o pkg/exf:
341      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
342         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
343         and rename array obsSIce to exf_iceFraction.
344    o tutorial_deep_convection:
345      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
346        for now all in this exp. code dir.
347      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
348        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
349    o eesupp/src:
350      - added SINGLE_DISK_IO option because reading of parameter files on
351        very large number of processors did not work with existing set-up
352    
353    checkpoint64o (2013/09/25)
354    o pkg/atm_phys & atm_compon_interf:
355      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
356    o tools/build_options:
357      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
358        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
359        remove CPP setting (was identical to genmake2 default).
360    o pkg/gmredi & model/src: Some updating and work done on the residual model.
361      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
362      - fixed up the calculation of the eddy stress and how it is added to the
363        external forcing via taueddy_external_forcing.F
364      - at the moment, it is very experimental and only works with the variable eddy
365        diffusivity calculated in gmredi_k3d.F
366    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
367        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
368    o testreport (& tools/do_tst_2+2):
369      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
370    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
371      - remove CPP='cpp -traditional -P' (this is genmake2 default)
372      - add switch (for big setups) to use 'medium' memory-model (but leave it
373        commented out for now). Note: needed with FC 19 to compile big setups.
374    o pkg/atm_compon_interf:
375      - regroup per field origin (model & pkgs) the coupling storage routines
376         (which accumalate in time each coupling field)
377      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
378        update accordingly + simplify aim_do_physics.F
379    
380    checkpoint64n (2013/08/26)
381    o pkg/bbl:
382      - update formulation to reduce dispersion of tracer properties in bbl
383      - replaced horizontal and vertical transport parameters with velocities
384      - changes results for verification/global_with_exf.yearly
385    o verification/halfpipe_streamice:
386      - change to matrix construction; update both Fwd & AD output.
387    o verification/tutorial_tracer_adjsens:
388      - OpenAD test: switch to vector-invariant momentum since fluxform with
389        rStar causes problems with OpenAD; update output.
390    o tools:
391      - genmake2: define a common prefix for all temp-file names ; move them
392        to local /tmp disk (but would be easy to move them back);
393      - xmakedepend: apply the same switch for temp-files.
394    o pkg/offline:
395      - changes for use with rStar (NLFS): assume that we continue to provide
396        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
397        output files) and apply r* scaling at each time-step (function of the time
398        varying Eta field); use normal pickup files (needed for restart with NLFS).
399    o adjoint with OpenAD:
400      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
401        package openad.  This package has to be compiled for all runs with OpenAD
402        instead of specifying code_oad_all as a modification directory.
403      - link the fortran templates from tools/OAD_support to the build directory
404        for preprocessing to avoid conflicts between different setups compiled
405        simultaneously and simplify cleanup.
406    o pkg/exf:
407      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
408        main model or other pkgs are exchanged in EXF_MAPFIELDS).
409    o model/src:
410      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
411        (similar to do_fields_blocking_exchanges.F).
412    o tools/genmake2:
413      - remove TAF output src code just before calling staf (when not doing a fresh
414        built, will stop if things go wrong with staf).
415      - fix target "adobj" (left from TAF version-2 transition)
416    o pkg/diagnostics:
417      - add a parameter to track the status of pkg/diagnostics activation;
418        this replace/extend the use of logical param "settingDiags" (to check
419        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
420        New S/R to print error message and stop when pkgStatus is not right.
421      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
422    
423    checkpoint64m (2013/08/13)
424    o model/inc:
425      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
426        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
427    o pkg/kpp & aim_v23:
428      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
429    o pkg/seaice:
430      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
431        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
432      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
433    o eesupp/src:
434      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
435        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
436    o switch to TAF version-2:
437      - add flow directives to "freeze" naming convention for ad-routines that
438        are used in I/O routines of adjoint state and associated common blocks
439        that are used in adcommon.h (backward compatible with version-1)
440      - update all ad-optfiles (in tools/adjoint_options + few local to some
441        verification exp) to switch to latest TAF version (currently 2.5.5);
442        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
443        out except for diva).
444      - the major change with TAF version-2 is that both the differentiated
445        routines and the forward routines (new) are returned as part of the TAF
446        output source code. Update genmake2 accordingly.
447      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
448        with version-2 when compared to TLM or FWD gradient); other experiments
449        output show minor changes (machine truncation level); update the few AD &
450        TLM output with 12 matching digits only (some prior to version-2 switch).
451    
452    checkpoint64l (2013/08/05)
453    o model/src:
454      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
455      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
456        when using TAF but only if using OpenAD.
457    o pkg/mom_common+fluxform+vecinv:
458      - always set horiz. viscosity arrays to background value before calling
459        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
460        only when using variable horiz. viscosity (useVariableVisc=T);
461      - simplify mom_vecinv.F (only 1 block for momViscosity).
462    o pkg/mom_common: variable horiz. viscosity in NH code
463      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
464        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
465      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
466        useBiharmonicVisc & useVariableVisc.
467      - fix old bug (already in 1rst implementation of variable horizontal viscosity
468        in calc_gw.F, version 1.27, 2006/06/20):
469        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
470        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
471      - change background horiz viscosity in vertical momentum (gW) to always be
472        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
473        any type of variable viscosity, e.g., viscAh/4Grid)
474      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
475        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
476        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
477        default viscAh,viscA4 is zero).
478    o model/src:
479      - extend length of drC & recip_drC from Nr to Nr+1.
480    o Divided Adjoint (DIVA) with MPI:
481      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
482      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
483        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
484    
485    checkpoint64k (2013/07/23)
486    o tools/OAD_support:
487      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
488        and remove it from genmake2.
489    o tools/build_options:
490      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
491        MPI_HEADER_FILES list (let genmake2 find the missing headers)
492    o verification/halfpipe_streamice:
493      - change to driving stress formulation; update both Fwd & AD output.
494    o tools/genmake2 and Divided Adjoint with MPI:
495      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
496      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
497      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
498        Makefile, which is set by genmake2, and check which mpi-headers are needed.
499        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
500      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
501    o testreport:
502      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
503        perform additional runs (number of additional runs is "add_DIVA_runs" taken
504        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
505    o verification/lab_sea (AD test):
506      - change to test Divided Adjoint Run in this set-up (both standard AD test
507        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
508    o pkg atm_ & ocn_compon_interf:
509      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
510        staggerTimeStep implementation) and disable (retired) corresponding
511        parameter.
512    o pkg/offline:
513      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
514      - add S/R OFFLINE_CHECK to print offline parameter summary
515        and stop if loading a file that is not used;
516      - enable to calculate GMRedi tensor, KPP mixing and convective index
517        when the corresponding file(s) is/are not specified (but pkg is used).
518      - comment out resetting of monitorFreq (to endTime) since it still useful
519        for monitoring CFL numbers and checking offline fields.
520    o OpenAD:
521      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
522        smaller standard output) and generate new (smaller) output (on baudelaire
523        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
524    o model/src:
525      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
526        (where external_forcing_adjust was called) and change list of arguments;
527      - merge external_forcing_adjust.F into external_forcing_surf.F
528      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
529        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
530        previously in file "balance_relax.F", now removed); remove corresponding
531        arrays in FFIELDS.h.
532      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
533        a hack for getting back surfaceForcingS (loaded from file) when using
534        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
535      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
536        (was getting only 11 digits for AD-grad, due to different truncation
537         error in AD code).
538    
539    checkpoint64j (2013/07/04)
540    o pkg/offline:
541      - to enable the use of other features with pkg offline (e.g., obcs),
542        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
543      - comment out "allowFreezing" (now active) in 2 offline testing exp.
544    o pkg/exf ALLOW_RUNOFTEMP
545      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
546      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
547      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
548    o pkg/atm_phys:
549      - allows to add some damping on uVel,vVel (strength only function of k).
550    o verification, ad-tests:
551      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
552        global_ocean_ebm and offline_exf_seaice.thsice.
553    o verification/halfpipe_streamice:
554      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
555        flux input boundary conditions to be ignored; a fix for this bug changed
556        verification results for forward test.
557      - add adjoint test.
558    o pkg/ptracers:
559      - allow to restart without SOM pickup (resetting SOM to zero).
560    o pkg/gmredi:
561      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
562      - It uses mixing length theory and suppression by steering level effects to
563        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
564        to JPO, for more details).
565      - It also uses the diffusivity to calculate an eddy induced streamfunction
566        based on a PV closure (rather than a buoyancy closure as in GM).
567      - New files added to pkg/gmredi:
568        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
569          induced overturning streamfunction (called from gmredi_calc_tensor)
570        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
571          for use in gmredi_k3d
572        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
573          the eddy diffusivity
574    
575    checkpoint64i (2013/06/18)
576    o pkg/cheapaml:
577      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
578        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
579        with pkg/cheapaml.
580    o utils/python: add subpackage for cubed sphere function, first example is
581        simple cs.pcol to plot 2D fields on a map
582    o pkg/streamice:
583      - This is a new package in MITgcm, which solves dynamic equations for ice
584         sheets and ice streams
585      - At the moment it is independent of atmosphere/ocean dynamics, or any
586        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
587        ed that this will change)
588      - There is a new verification exercise that tests it, halfpipe_streamice,
589        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
590        rectangular embayment
591      - halfpipe_streamice is forward-only for now, will have TAF test soon
592      - for questions, email dgoldber@mit.edu
593    o pkg/thsice:
594      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
595        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
596      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
597         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
598      - allow precip from pkg/cheapaml to make snow over seaice.
599    o pkg/cfc:
600      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
601      - remove atmos CFC 2-D arrays from common bloc (now local variables)
602      - change some hard-coded constant to run time parameter for reading and
603        and interpolating atmospheric CFC ; keep same default as previously.
604      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
605      - put arguments in standard order: myTime, myIter, myThid
606      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
607        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
608      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
609      - new routine to print summary of CFC params and check for consistency.
610    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
611      similar to thsice_advdiff.
612      Note that for the B-grid case the routine parameters uc/vc are overwritten.
613    o pkg/cfc:
614      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
615        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
616      - fix interpolation of atmphspheric CFC between Sorthern and Northern
617        hemisphere value.
618    o pkg/seaice:
619      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
620    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
621                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
622      - requires an additional time level that is stored in the pickup
623      - you can start with AB2 from a pickup without this time level with
624        pickupStrictlyMatch = .false.
625    
626    checkpoint64h (2013/05/26)
627    o pkg/cheapaml:
628      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
629        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
630      - consistent treatment of uWind,vWind location: assume everywhere in
631        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
632        (Note: was already the case for Tair,Qair advection);
633        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
634      - compute diabatic forcing only in the interior (excluding overlap regions)
635      - fill in array "Qsw" (for short-wave heating);
636      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
637        before any update (consistent with MITgcm state var diagnostics);
638      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
639        non periodic ; + adjusted for uWind,vWind (C-grid).
640    o pkg/seaice:
641      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
642        add explicitly pkg/exf in experiments that currently use pkg/seaice.
643      - allows to compile pkg/seaice without pkg/exf.
644    o tools/OAD_support:
645      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
646        of array "ourStepOf" in function rvNextAction (revolve.F90).
647    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
648      - change pkg name (to be used with other atmospheric physics pkg)
649        but by-pass CVS when making the new pkg so that we keep the CVS history.
650    o pkg/offline:
651      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
652        (previously called from pkg/dic_surfforcing_init.F)
653    o model/src:
654      - re-order sequence of calls within packages_init_variables.F, using
655        standard order, except for:
656         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
657         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
658    o new pkg: atm_phys
659      - add entry point and source code (previously in contrib
660          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
661        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
662      - re-order sequence of calls within packages_readparms.F,
663         packages_init_fixed.F and packages_write_pickup.F
664        (but skip packages_init_variables.F because of TAF issues).
665      - update contrib/*/atm_gray/ experiment.
666    o pkg/seaice (ITD code):
667      - simplify and fix the writing of pickup-files for ITD case
668    o pkg/seaice (ITD code):
669      - introduce floe size dependent lateral melt for ITD case;
670      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
671      - update seaice_itd experiment main output.
672    o pkg/thsice:
673      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
674        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
675        changed accordingly pkg/atm2d.
676    
677    checkpoint64g (2013/05/01)
678    o pkg/exf ALLOW_RUNOFTEMP
679      - if defined,  river and glacier runoff temperature can be read-in from
680        runoftempfile; runoftempfile needs to have same format as runofffile
681    o pkg/thsice (& pkg/bulk_force):
682      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
683        for energy content of Precip + RunOff & Evap (like with pkg/exf).
684      - change computation domain to always be the interior (without overlap).
685      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
686    o verification/tutorial_global_oce_biogeo:
687      - add preliminary OpenAD setup (still has problems)
688    o pkg/seaice:
689      - turn some parameters for choosing the convergence criterion of
690        the inexact Newton method (JFNK) into runtime parameters for convenience
691      - clean up seaice_calc_viscosities.F: remove/retire two options for
692        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
693        the results of lab_sea/input because a division has been replaced by
694        a multiplication with the reciprocal (sumNorm)
695      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
696        convergence of solver (changes results, of course), and to test some
697        new features
698    o model/src:
699      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
700      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
701      - move forcing adjustment (balancing surface forcing) in specific S/R
702        where might also be applied exchanges (if needed) to forcing arrays.
703    o pkg/shelfice:
704      - allow to specify the Ice-Shelf mass per unit area (instead of
705        shelficeLoadAnomaly) and do the conversion from one to the other
706      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
707        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
708        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
709        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
710      - update isomip experiment forward output (get machine truncation error
711        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
712    o verification/offline_exf_seaice:
713      revise data.seaice in input.thermo and input_ad and update results accordingly
714        HO = 0.2, SEAICE_areaLossFormula = 2,
715        SEAICE_growMeltByConv = .TRUE.,
716        SEAICE_doOpenWaterMelt = .TRUE.,
717      Improve consistency with input.thsice and fix the spurious 500m ice corners
718    o verification/global_ocean.cs32x15:
719      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
720        in icedyn (thsice+seaice-dyn) test and update output.
721    o verification/offline_exf_seaice:
722      - adjust list of tested variables (with testreport) and update
723        standard test output with better slection of monitored fields.
724    o pkg/cd_code:
725      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
726        experiment lab_sea.hb87
727    o tools/genmake2:
728      - change default makedepend from the system default to tools/xmakedepend:
729        When no makedepend is specified, select tools/xmakedepend it the test pass,
730        otherwise select the system default (if exist and pass the test) or
731        try to build cyrus-makedepend ; stop if none of the 3 works.
732    o pkg/exf & pkg/thsice:
733      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
734        for energy content of Precip + RunOff & Evap. Assumes:
735       1) Rain has same temp as Air.
736       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
737       3) Run-Off comes at the temp of surface water (with same Cp)
738       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
739        put directly into Latent Heat flux & should use water-vapor heat capacity.
740       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
741        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
742    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
743        (compile when SEAICE_ALLOW_JFNK is defined)
744    o pkg/thsice:
745      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
746        implementation): move THSICE_AVE call after the advection (called directly
747        from thsice_do_advect.F).
748    o verification/global_ocean.90x40x15 and OpenAD:
749      New experiment for OpenAD is identical to the one in input_ad except that
750        multiDimAdvection=.FALSE.,
751      There is still an issue with this.
752    o pkg/thsice:
753      - account for ice velocity (ocean relative velocity) in turbulent heat flux
754        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
755        and offline_exf_seaice (main test).
756    
757    checkpoint64f (2013/03/31)
758    o verification/OpenAD:
759      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
760    o verification/isomip, pkg/shelfice and OpenAD:
761      - add OpenAD setup to this exp and make shelfice package work with OpenAD
762    o verification/tutorial_global_oce_biogeo:
763      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
764    o verification/offline_exf_seaice:
765      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
766    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
767      - add OpenAD setup to this exp and make ptracers package work with OpenAD
768    o pkg/seaice/seaice_evp.F:
769       mask the asymmetric contribution of the ice-ocean stress (when
770       the turningAngle is non-zero) over open water to avoid stripes
771       in the EVP-solutions after many EVP-substeps. This does not change
772       the verification experiment (because turningAngle=0 in that experiment),
773       but will affect other EVP solutions with turningAngle.ne.0
774    o verification, AD & TLM output:
775      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
776        additions and multiplications which affect results at machine truncation
777        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
778        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
779        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
780        digits of matching.
781    o pkg/seaice:
782       modify lsr-algorithm so that it vectorizes AND converges by using a
783       "zebra" method: split vector loop into two with step size 2; this
784       solves a general convergence problem for the JFNK solver on a vector
785       computer. It has the potential to even improve convergence for
786       non-vector machines, but it does change the results so it is turned
787       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
788       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
789    
790    checkpoint64e (2013/03/05)
791    o pkg/ecco and several verification experiments:
792       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
793       from ecco package, and revert to unified routine in model/src/
794       Adjust verification experiments accordingly, especially gloal_oce_llc90
795       Should conclude long-standing work by Gael to reconsile the_main_loop with
796       ECCO and will enable OpenAD's revolve loop in ECCO setup.
797    o pkg/generic_advdiff:
798      - implement compressible flow method for multi-dim advection (similar to
799        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
800        TAF generates many recomputations) to use it; no yet coded with implicit
801        vertical advection.
802      - change experiment advect_cs (new output) and advect_xy (same output)
803        to test compressible flow multi-dim advection.
804    o pkg/generic_advdiff:
805      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
806        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
807    o pkg/seaice:
808      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
809        bug affects two verification experiments (lab_sea and lab_sea.hb87),
810        recover old (wrong) results by setting noSlipFac = 2. in
811        seaice_calc_strainrates.F;
812      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
813      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
814        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
815      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
816    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
817      - new subroutines seaice_lsr_tridiagu/v
818      - introduce loop bounds i/jmin/max to be able to use a restricted
819        additive Schwarz method, but not used for now.
820      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
821      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
822    o OpenAD support
823       Reorganize S/R call for overall time-stepping loop to facilitate
824       OpenAD revolve loop replacement
825       (new S/R main_do_loop.F)
826    o model/src:
827      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
828      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
829        ADAMS_BASHFORTH2.
830    o pkg/cheapaml:
831      - add new parameter (default=F, same as before) to disable full domain
832        (including land) periodicity in X & Y dir.
833      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
834        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
835        into single S/R CHEAPAML_TIMESTEP.
836    
837    checkpoint64d (2013/02/17)
838    o pkg/monitor (angular momentum):
839      - do not add Eta contribution to the total AM if using rigid-lid;
840      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
841      - horizontal discretisation: compute Zonal wind contribution separately for
842        each component (instead of from cell centered averaged) and use the 4
843        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
844      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
845        FreeSurf) if using vectorInvariant momentum.
846    o model/src (horizontal grid):
847      - move initialisation of all horizontal grid arrays to null value
848        from specific horizontal grid S/R to main S/R INI_GRID;
849      - add 2 new arrays to project model C-grid velocity on to zonal direction
850        (similar to AngleCosC & -AngleSinC but at U and V point location) and
851        compute them in S/R CALC_GRID_ANGLES.
852    o pkg/seaice: replace a hard coded parameter by a runtime parameter
853        SEAICE_JFNK_tolIter
854    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
855        preconditioner for JFNK (run LSR into the overlaps as far as possible,
856        i.e OLx/y-2, but overwrite the solution in the overlaps)
857      - extend loop range in seaice_calc_viscosity
858      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
859      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
860      - slightly modify loops in tridiagonal solver lsr-preconditioner
861      - by default remove the extra exchange in seaice_preconditioner with a
862        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
863      - modify offline_exf_seaice so that old results without RAS are reproduced
864        for output.dyn_jfnk.txt
865      in seaice_fgmres.F (unrelated to RAS)
866      - add a cpp-flag option for a re-ordered mapping (potentially more
867        efficient), but because this changes the results, turn it off by
868        default
869      - replace the save statement by local common blocks
870    o utils/matlab:
871      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
872      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
873        instead of local script "load_cs.m".
874    o pkg/seaice:
875      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
876        to the scalarProductMetric and the unrolling. By chance this does not
877        change the verification experiment, because of the particular domain
878        decomposition
879    o pkg/diagnostics:
880      - change default missing_value from UNSET_RL to -999.
881    o pkg/layers: improve vectorization of layers_fluxcalc.F
882      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
883        time spent in this routine by more than a factor of 3 on an NEC-SX8
884      - step 2: replace search algorithm by a bisection algorithm found in
885        Press et al. Numerical Recipes in Fortran. This algorithm can be
886        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
887        For now, use this algorithm only for TARGET_NEC_SX defined.
888      - moved the search algorithm into a separate subroutine, that is kept
889        within the same file for automatic inlining.
890      - modified catching potential errors
891    o pkg/ecco:
892      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
893    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
894      - modifications for ALLOW_GENTIM2D_CONTROL
895      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
896      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
897      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
898      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
899    o model/src:
900      - account for moist thermodynamics in (dry) potential temperature equation;
901        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
902        and cpl_aim+ocn.
903      - also switch to standard compiler (gfortran, was using ifort previously)
904        for fizhi-cs experiments reference output.
905    o pkg/ctrl:
906      - 1st step toward generic time-varying control variable (2D) via CPP option
907        ALLOW_GENTIM2D_CONTROL
908      - note new namelist ctrl_nml_genarr in data.ctrl
909    o verification/global_ocean.cs32x15:
910      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
911        thsice calling sequence and update "output.icedyn.txt" output file.
912    o pkg/ptracers:
913      - from Ryan A.: code to allow to restart a tracer at regular time interval
914        specifying a reset frequency and a reset-phase (for each tracers).
915    o pkg/thsice:
916      - implement new sequence of calls for thsice+seaice:
917          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
918          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
919      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
920        in CPP_OPTIONS.h) to recover old sequence;
921      - update diagnostics for Intermediate State thsice diagnostics: now filled
922        just before advection (instead of just after advection in old sequence);
923      - update output of experiment offline_exf_seaice (standard test);
924      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
925        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
926    o pkg/aim_v23:
927      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
928      - use standard pkg/mdsio routines to read & write CO2 pickup file;
929      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
930      - Implement new sequence of calls for seaice advection (with thsice and
931        seaice diffusion): do ice advection after ice-Thermodynamic (previously
932        was done before); change aim_do_physics.F (split the bi,bj loops block);
933      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
934    o pkg/thsice:
935      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
936        where just seaice diffusion is used without seaice-dynamics.
937    
938    checkpoint64c (2013/01/18)
939    o pkg/seaice:
940      - add a parameter JFNKres_tFac that can replace JFNKres_t
941        (= JFNKres_tFac*JFNKresidual before JFNK solver)
942      - add a line search option to the JFNK solver
943      - move update of u/vIce and computation of initial residual into a separate
944        routine (same file); makes the code a little easier to read (?)
945      - the line search requires computation of the residual and for some reason
946        I cannot do the update of u/vIce at the beginning of the Newton loop
947        without changing the results, so we move computation of the new residual
948        also to the end of the Newton loop, even without the line search
949    o pkg/mdsio:
950      - write missing value (corresponding to undefined array value) to meta files;
951        skip this if missing value is one (UNSET_RL would be a better value for the
952        case of undefined missing value but it's current the default missing-value);
953        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
954    o pkg/exf & thsice:
955      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
956        diagnostics) even when SHORTWAVE_HEATING is #undef;
957    o verification/cfc_example:
958      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
959        illustrate how to use it).
960    o verification/offline_exf_seaice:
961      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
962        files to only one time-record.
963      in input.thermo: narrow the 2 bands of low initial ice-concentration near
964        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
965        snapshot output; same mcPheePiston value as in thsice with
966        surf-current=0.2m/s.
967      in input.thsice: similar set-up as in input.thermo (channel with same seaice
968        initial conditions).
969    o verification/cfc_example:
970      - update file "data" with more standard choice (default rotationPeriod,
971        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
972        set deltaTFreeSurf to deltaTtracer) and update the output.
973    o pkg/layers:
974      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
975      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
976    o verification/offline_exf_seaice:
977      - set all {field}period to zero for constant-in-time forcing (not tested
978        anywhere else).
979    o verification/offline_exf_seaice:
980      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
981      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
982    o model/src:
983      - implement Finite-Volume method for (hydrostatic) presure gradient
984        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
985    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
986      - In order to be compatible with the default EVP code, this requires changing
987        the EVP code around a little; and because any small change immediately
988        breaks the lab_sea.hb87 verification experiment, the reference output is
989        updated two times (each time the remaining aggrement was only 2 digits):
990        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
991        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
992        The adjoint test lab_sea.evp also needed to be updated.
993      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
994        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
995        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
996        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
997        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
998        kept obscure, because I need to test it a little more.
999    o pkg/cheapaml:
1000      - fix few incorrect type (_RL/_RS) in subroutine calls.
1001    o pkg/seaice:
1002      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
1003        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
1004    o model/src:
1005      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
1006        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
1007        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
1008    o pkg/cheapaml:
1009      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
1010        update output of experiment cheapAML_box.
1011      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
1012        and set them only in one place (cheapaml_readparms.F).
1013      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
1014      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
1015        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
1016    o model/src/the_main_loop.F:
1017      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
1018    o pkg/seaice:
1019      - remove legacy branch code.
1020      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
1021    o verification/*/code*/SEAICE_OPTIONS.h:
1022      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
1023        SEAICE_CAP_HEFF).
1024    o pkg/cheapaml:
1025      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
1026        to load new forcing fields.
1027      - add missing "_d 0" where it's needed; + some editing (improve indentation).
1028      - remove switch to "-r8" compiler option (no longer needed) in verification
1029        cheapAML_box, keep same output (small trucation error differences).
1030    o verification/offline_exf_seaice:
1031      - add thermodynamics only test.
1032    o verification/cheapAML_box:
1033      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
1034        keep same output (same 14 digits for cg2d).
1035      - switch on "-r8" compiler option (some numerical values are missing
1036        the "_d 0") and update output (only 6 digits for cg2d were preserved).
1037    
1038    checkpoint64b (2012/12/24)
1039    o pkg/cheapaml:
1040      - remove un-used variables (Qnet,EmPmR) from pickup files.
1041      - store tendency of advected variables into cheapaml pickup file
1042        and fix the AB-2 restart.
1043    o verification/offline_exf_seaice and lab_sea adjoint:
1044      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
1045      - switch to 4 time steps in offline, consistent with lab_sea.
1046      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
1047      - update results after change of experiment seaice.
1048    o pkg/seaice:
1049      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
1050        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
1051        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
1052        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
1053    o model/src:
1054      - add run-time parameter to select CG2D solver minimum-residual solution
1055        (in case of a poor convergence).
1056    o pkg/seaice/seaice_lsr.F
1057      - move calculation of matrix coefficients into new
1058        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
1059        file; the main purpose of this change is to be able to reuse the code
1060        in S/R SEAICE_PRECONDITIONER
1061      - modify the computation of the residual so that the mass of sea-ice
1062        is not used twice; this simplifies the calculations, but since
1063        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
1064        not tested in testreport---this does not affect the testreport results.
1065    o verification/seaice_obcs:
1066      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
1067        verification/lab_sea/input.salt_plume; changes results/output.txt*
1068    o model/src:
1069      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
1070    o pkg/seaice:
1071      - improve description of parameters in seaice_fgmres.F and start
1072        cleaning up the code
1073      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
1074        second argument
1075      - add a metric based on grid cell area to SEAICE_SCALPROD; update
1076        results of offline_exf_seaice.dyn_jfnk
1077      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
1078    o pkg/aim_v23:
1079      - fix an other bug in dissipation heating (grid-cell area was missing).
1080    o model/src + pkg/seaice:
1081      - add global (multi-tile) linear solver for pair of tri-diagonal system
1082        along X and Y lines, respectively for U and V component.
1083        Note: 1) MPI and cube-exchange not yet coded.
1084            2) probably not accurate for poorly conditioned / large size problem.
1085      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
1086        default: not compiled and not used.
1087    o pkg/seaice:
1088      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
1089        introduce bi/bj loops and use global_sum_tile_rl instead of
1090        mpi_allreduce in seaice_fgmres.F
1091      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
1092      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
1093      - add a verification experiment for JFNK in offline_exf_seaice
1094    o verification:
1095      - change (for now, only fwd test) offline_exf_seaice experiment:
1096        use a re-entrant channel with idealized coastline (trapezoidal shape)
1097        at southern boundary to explore seaice dynamics and thermodynamics
1098        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
1099        secondary test (input.thsice) use thermodynamics only with SST relaxation.
1100      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
1101    o pkg/exf:
1102      - disable "sstExtrapol" when Nr=1
1103    o verification:
1104      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
1105        to test pkg/cheapaml.
1106    o pkg/aim_v23 & pkg/shap_filt:
1107      - fix dissipation heating (erroneous gravity multiplication factor).
1108    o pkg/seaice:
1109      - remove unused field pressPre from jfnk solver
1110      - rename two subroutines in seaice_preconditioner.F
1111    o eesupp/src:
1112       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
1113    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
1114       - remove wrong parts of the rhs and the lhs (were in there
1115         because I did not understand the concept of this preconditioner)
1116       - add an exchange between u- and v-sweep. This increases communication
1117         by a factor of two but improves the convergence of jfnk. Ideally,
1118         one would like the u- and v-sweep to be independent. So far within
1119         undocumented ifdefs
1120       - reorganize the extra computations for printing the residuals
1121    o tools/genmake2:
1122      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
1123        since it's not necessary (and was preventing to use MNC in some cases).
1124    
1125    checkpoint64a (2012/11/16)
1126    o pkg/autodiff:
1127      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
1128        autodiff_readparms.F no longer depends on calling order (within
1129        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
1130        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
1131        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
1132    o pkg/obcs:
1133      - adding tidal velocity forcing capability to obcs
1134        for usage example, see verification/seaice_obcs/input.tides
1135    o pkg/seaice:
1136      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
1137        SEAICE_LSRrelaxU/V
1138      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
1139    o pkg/aim_v23:
1140      - implement heating from friction (bottom friction and stratospheric drag).
1141    o pkg/shap_filt:
1142      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
1143        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
1144    o model/src:
1145      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
1146        time-constant addMass field from file (addMassFile);
1147      - support for heating due to friction (and Kinetic Energy dissipation):
1148        add option, run-time switch and 3-D field array + support code ; each pkg
1149        or S/R can add heating contribution (if there is a sink of KE); the sum is
1150        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
1151    o pkg/seaice:
1152      - complete merge of ITD code into seaice_growth.F
1153        from MITgcm_contrib/torge/itd/code/
1154        no verification so far, but Torge Martin tested
1155        "1-D test case and Beaufort set up;
1156        deliver okay results after 1 model year."
1157      - complete merge of SEAICE_SIZE.h into all relevant routines
1158      - move computation of eta at Z-points into calc_viscosities
1159        + introduce global field etaZ
1160        + add different methods for computing etaZ, for now the old
1161          method (simple averages of eta to Z-points) is hardwired
1162        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
1163          seaice_preconditioner
1164      - simplify computations for SEAICE_ZETA_SMOOTHREG
1165      - seaice_preconditioner:
1166        + replace one remaining press by pressLoc (mistake)
1167        + adjust printing of residuals
1168      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
1169        + add (SEAICE.h) and rename some counters (initiliased in
1170          seaice_init_fixed.F)
1171        + add _BEGIN/END_MASTER (myThid)  around print statements
1172        + print total number of iterations and failures over SEAICE_monFreq
1173          interval to STDOUT
1174      - move control over output-messages by fgmres to seaice_jfnk to save
1175        some operations
1176      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
1177        in order to make restarts with sol .ne. zero (fgmres with restarts)
1178        (seaice_jfnk.F, seaice_fgmres.F)
1179      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
1180        a serious convergence problem when open boundaries are involved
1181    o pkg/ggl90: fix computation of control volumes for the case of
1182      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
1183      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
1184    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
1185    o pkg/autodiff
1186      - Add inAdMode switch for SEAICEuseDYNAMICS:
1187        SEAICEuseDYNAMICSinAdMode
1188        (extend logic in ADAUTODIFF_INADMODE_SET)
1189    o pkg/seaice
1190      - Step 1 of merging ice-thickness distribution (ITD) code from
1191        MITgcm_contrib/torge/itd/ (author: Torge Martin)
1192        The code implements concept laid out in Thorndike et al. (1975);
1193        code is enabled via CPP flag SEAICE_ITD
1194        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
1195        code is not complete yet!!
1196      - SEAICE_SIZE.h now included in almost all seaice routines
1197    o verification (using seaice):
1198      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
1199        global_ocean.cs32x15.seaice ; update results.
1200      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
1201      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
1202        offline_exf_seaice (previously compiling B-grid).
1203    o pkg/exf:
1204      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
1205        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
1206        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
1207    o pkg/layers (adjust changes from Sept 19):
1208      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
1209        this allows to remove "layers_maxNum" dimension from all layers arrays.
1210    o pkg/layers (adjust changes from Sept 19):
1211      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
1212      - snap-shot extended to all type of layers (not just the 1rst type);
1213      - remove layers variables when corresponding CPP option is undef.
1214    o pkg/layers:
1215      - rename pkg/layers variable and add new output (layer exist & un-weighted
1216        velocity in layer)
1217    o pkg/seaice:
1218      - simplify (?) ocean-drag coefficent computations by using
1219        the same routine in all three solvers (saves some code lines)
1220      - remove global fields DRAGA and DRAGS from C-grid code and
1221        declare them locally in lsr.F (the only place where they are
1222        still used)
1223      - update AD output of lab_sea.evp (very sensitive anyway).
1224    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
1225      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
1226      and SEAICEuseJFNK=.true. A few things to note:
1227      - involves a FGMRES, that is parallel but very inefficient,
1228        because of many scalar products (global sums) in the Gram-Schmidt
1229        orthogonalization method. Needs to be replaced. Original code
1230        from J.-F. Lemieux
1231      - preconditioner for FGMRES is a stripped down version of LSOR
1232      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
1233        preconditioner. For the preconditioner, the default is set to 10.
1234      - Jacobian times vector is computed with finite differences
1235      - marginally related to JFNK-solver: add a smooth regularization for
1236        zeta with tanh that will improve convergence (Lemieux and Tremblay,
1237        2009) for any implicit solver (not implemented for EVP because EVP
1238        does not need this regularization in the first place). Define
1239        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
1240    o eesupp/src:
1241      - check in genmake2 that intrinsic S/R flush is available.
1242      - add S/R to flush IO unit (if intrinsic S/R flush is available)
1243      - flush standard & error msg unit before MPI termination
1244      - if debugMode, flush IO unit after printing msg
1245    o pkg/ctrl:
1246      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
1247        to ctrl_set_unpack_xyz.
1248    
1249    checkpoint64 (2012/10/09)
1250    o pkg/shelfice
1251      - in mom_fluxform.F, mom_vecinv.F:
1252        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
1253        Bug fix KappaRU -> KappaRV
1254        does not change verification/isomip but may change other setups
1255        (presumably constant KappaRU=KappaRV)
1256      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
1257    o pkg/obcs:
1258      - fixed some indexing bugs in obcs_seaice_sponge.F
1259      - added obcs relaxation subroutines for HSALT and HSNOW
1260      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
1261    o pkg/seaice:
1262      - add "multicategory" parameterization for snow in analogy to ice,
1263        default is off for now.
1264    o pkg/obcs:
1265      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
1266        see verification/seaice_obcs/input.seaiceSponge for example application.
1267      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
1268        index setting by master-thread. This fix multi-threads Pb in previous modifs.
1269    o pkg/layers :
1270      - add diagnostics to pkg/layers
1271      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
1272        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
1273    o pkg/generic_advdiff/gad_implicit_r.F :
1274      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
1275    o pkg/seaice/seaice_growth.F:
1276      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
1277    o pkg/obcs:
1278      - change default setting of OBCS_UVICE_OLD from defined to undef;
1279      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
1280        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
1281      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
1282      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
1283        with Southern & Western OB at a tile edge (at least in a simple set-up).
1284    o pkg/obcs:
1285      - change settings of OB index in case OB coincides with tile edge (shared by
1286        2 tiles), so that common OB location is registered by both tiles (instead of
1287        only 1). However, for Southern and Western OB, index value = 0 is not
1288        recognized as valid OB index (=default null value) and needs to be fixed.
1289      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
1290      - new parameter "OB_indexNone" for null index value (for now, still zero)
1291        to replace hard-coded null index value of zero.
1292    o pkg/exch2:
1293      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
1294        always check buffer-size (but outside the loop); move checking for valid
1295        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
1296        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
1297    o pkg/ctrl (pack & unpack):
1298      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
1299        (locally defined) for different variables (+ remove the variable-specific
1300        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
1301        (to be extended to other local file names in ctrl.h).
1302    o pkg/flt:
1303      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
1304    o pkg/mdsio:
1305      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
1306    o tools/genmake2:
1307      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
1308        (added by Alistair in version 1.51 for building without make depend);
1309      - remove Header files list (H_SRC_FILES) from the dependence of targets
1310         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
1311        place in version 1.23): this save going through staf when unrelated header
1312        file has been modified.
1313       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
1314        "make depend" step, still need to do "make links" before "make adtaf".
1315    o eesupp/src (+ few pkg src files) & genmake2:
1316      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
1317      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
1318      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
1319         upper/lower case ; account for space between "#" and undef/define)
1320    o pkg/flt (with exch2):
1321      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
1322      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
1323    
1324    checkpoint63s (2012/09/05)
1325    o pkg/ecco:
1326      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
1327      - add more relevant #ifdef ALLOW_SMOOTH ones.
1328      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
1329    o pkg/ctrl:
1330      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
1331        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
1332      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
1333        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
1334        ctrlSmoothCorrel3D (new).
1335        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
1336      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
1337      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
1338        controls when useAtmWind, and vice versa.
1339      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
1340      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
1341          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
1342      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
1343          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
1344      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
1345        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
1346    o pkg/smooth:
1347      - remove un-necessary includes.
1348      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
1349        Those CPP options were never defined, and not necessary.
1350    o model/src:
1351      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
1352      - standard treatment of useSMOOTH.
1353    o pkg/autodiff:
1354      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
1355        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
1356    o pkg/exch2:
1357      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
1358        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
1359      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
1360        and tiles to process mapping.
1361      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
1362        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
1363        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
1364        from w2_eeboot.F to w2_readparms.F.
1365    o eesupp/src:
1366      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
1367        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
1368        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
1369      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
1370        is defined (remove condition on usingMPI) to match cases where MPI_INIT
1371        has been called.
1372      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
1373      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
1374        (so that on 1 proc, get same myPid independently of usingMPI)
1375      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
1376        useCubedSphereExchange with EXCH-1 (safer).
1377      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
1378    o pkg/ggl90:
1379      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
1380        used in ALLOW_GGL90_SMOOTH code.
1381    o pkg/flt:
1382      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
1383        floats at the Southern end of the domain).
1384    o eesupp/inc:
1385      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
1386        but not used (and not to be used) anywhere, just for documentation.
1387    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
1388      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
1389        a) can damage previously written records in any other multi-record files.
1390        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
1391    o tools/genmake2:
1392      - define variable MAKE within Makefile and use it in place of 'make';
1393      - update AD_CONFIG.h (if needed) before building any of the executable
1394        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
1395        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
1396      - always print usual warning comment 'this file is automatically generated'
1397        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
1398    o pkg/cheapaml:
1399      - updated to correspond to the code used in accepted paper (Nico Wienders).
1400    o pkg/exf:
1401        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
1402        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
1403        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
1404    o pkg/exf, autodiff, ctrl, ecco and seaice:
1405        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
1406    o pkg/ctrl, ecco:
1407        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
1408        Depending on useAtmWind, one is inactive, and the other is active (see
1409        exf_getffields.F/exf_getsurfacefluxes.F).
1410    o tools/genmake2:
1411      - improve error msg when failing in 2nd test of check_for_broken_Ff
1412      - fix option '-makefile' short-name (-mf according to genmake2 -help)
1413      - source local config file "genmake_local" just after processing the genmake2
1414        command arguments (previously done before processing arg).
1415    o pkg/grdchk:
1416      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
1417        to this routine from cost_final has been dropped in g_cost_final)
1418      - improve printed information (more explicit msg, no longer using "print *,"
1419         fix fcpertminus printed value).
1420    o model/src:
1421      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
1422        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
1423        this prevents getting cost-funct reset in adinitialise_varia recomputations.
1424    o pkg/dic:
1425      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
1426        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
1427    o pkg/grdchk:
1428      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
1429      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
1430    o pkg/autodiff/ctrl/grdchk :
1431      - attempt to sort out what works and what does not,
1432        with regard to I/O, and to warn/stop accordingly.
1433    o pkg/grdchk:
1434      - attempt to fix grdchk in the case of useSingleCpuIO.
1435      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
1436       statements were moved from grdchk_main.F and into
1437       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
1438      - a global sum is applied to record numbers icvrec/layer
1439       out of grdchk_loc so that they be passed to I/O routines.
1440    o pkg/smooth:
1441      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
1442        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
1443    o verification/testreport:
1444      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
1445      - can also use compressed (gzip) reference output file;
1446      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
1447        to be easier to collect by testreport.
1448      - update existing TLM output (half out-of-date by more than 3 yrs).
1449      - report NETCDF & LAPACK settings (from genmake2) in output dir.
1450      - report run-time in each individual summary (previously only for AD test);
1451        for TLM test, add also TAF version.
1452      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
1453    
1454    checkpoint63r (2012/08/15)
1455    o tools/genmake2:
1456      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
1457    o pkg/ecco/ecco_cost_final.F :
1458      - fix fc print statements (to stdout and costfunction0000) so
1459        that the printed value is always after the global sum.
1460    o pkg/seaice/seaice_dynsolver.F :
1461      - fix ice strength assymptote at SEAICE_area_max<1
1462        (no change for the standard case of SEAICE_area_max=1)
1463    o some cleaning:
1464      - pkg source files: ensure that all *.F files from each pkg included the
1465        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
1466        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
1467        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
1468        includes;
1469      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
1470      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
1471        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
1472        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
1473      - update option-file CPP_OPTIONS.h of all AD experiments:
1474        * no longer include PACKAGES_CONFIG.h ;
1475        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
1476        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
1477          including ECCO_CPPOPTIONS.h).
1478    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
1479      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
1480        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
1481        not necessary accurate).
1482      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
1483        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
1484        deliberately break compilation (a remainder that it needs to be customized)
1485      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
1486      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
1487      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
1488    o tools/genamke2:
1489      - check for lapack.
1490    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
1491      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
1492        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
1493        from both packages.
1494      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
1495      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
1496      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
1497        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
1498    o pkg/cost : add comments to explain special and/or untested setups.
1499    o pkg/exf:
1500      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
1501        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
1502    o verification/*/code_ad:
1503      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
1504      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
1505      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
1506        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
1507    o pkg/seaice :
1508      - added possibility to change ice strength/PRESS0 relationship to
1509        HEFF, according to the following run time parameters
1510        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
1511        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
1512        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
1513    o pkg/ggl90 :
1514      - added run time flag mxlSurfFlag to include the code that ensure
1515        mixing between first and second level (previously included as a comment)
1516    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
1517      - add test of newly added dumpAdByRec=T option where
1518        we write all records to one file per variable.
1519    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
1520      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
1521        to check that this code is ok with taf and compiles in adjoint.
1522    o pkg/autodiff :
1523      - added run time param dumpAdByRec : ad dump format switch.
1524        If true then write all records to one file per variable.
1525        Else write one file per record (remains the default).
1526      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
1527    o pkg/seaice:
1528     - Added SEAICEuseTILT run time switch : if set to
1529       false then omit the tilt term in seaice dynamics.
1530     - Fix free drift calculation.
1531    o pkg/shelfice:
1532      When initializing SHELFICEDragQuadratic, set default to be
1533      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
1534      but retain option to set it independently
1535      (inconsistenty spotted by Veronique Dansereau)
1536    o eesupp/inc:
1537      - in EEPARAMS.h, add real-type constant for some frequently used simple number
1538         (0,1,2,1/2), with name explicitly referring to RS/RL type.
1539    o model/src:
1540      - move balancing of relaxation terms to new S/R balance_relax.F.
1541    o pkg/autodiff:
1542      re-write active I/O high-level (control) S/R:
1543      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
1544      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
1545      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
1546        MDS_READ/WRITE_FIELD); change loops to multi-threads.
1547      - update and merge active_file_control_slice.flow into active_file_control.flow
1548      - update the calls in lower level S/R (active_file.F, active_file_g.F and
1549        active_file_ad.F) keeping the argument list and function unchanged.
1550      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
1551        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
1552      - new low-level active I/O routines, one for each type (RL/RS), for active var
1553        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
1554        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
1555        right type.
1556    o autodiff and RS=real*4:
1557      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
1558        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
1559      - change argument type of 3-D mask argument to _RS to match type in the call
1560        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
1561    o pkg/thsice:
1562      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
1563      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
1564        fresh-water flux: uniform correction or proportional to local precip.
1565    o pkg/ctrl:
1566      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
1567      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
1568                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
1569      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
1570    
1571    checkpoint63q (2012/07/30)
1572    o pkg/autodiff:
1573      note about monitor and snap-shot of ad-variables:
1574      a) need to apply ADEXCH before monitor or output of ad-vars to include
1575       overlap contributions (was done for adjDump but missing for monitor).
1576      b) since ADEXCH implies adding overlap values to interior array, machine
1577       truncation error is expected when adding an ADEXCH call in the middle of
1578       the time-stepping (although mathematically identical).
1579      modifs:
1580      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
1581        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
1582      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
1583        apply ADEXCH before monitor or snap-shot of ad-variables:
1584           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
1585      - implement new method (copy+adexch) for snap-shot and monitor of main model
1586        ad-vars (initially not used by default -> output unchanged).
1587      - change default (set to 2) to use new method and update few output_adm.txt
1588        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
1589        and both tutorial_tracer_adjsens tests).
1590      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
1591        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
1592    o pkg/ctrl:
1593      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
1594      generic control variables via
1595      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
1596      Only required customization should be S/R ctrl_map_ini_genarr.F
1597      (routine in repository contains example)
1598    o pkg/exf:
1599      - fix and refine checking of surface-relaxation setting when using EXF
1600    o verification (adjoint exp):
1601      - reduce length of simulation by half for experiment global_ocean.cs32x15
1602        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
1603    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
1604      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
1605        of KE that can occur with aggressive optimization
1606      + put quadratic bottom drag calculation in separated loops (only done if
1607        using bottomDragQuadratic)
1608    o model/src: CG2D_NSA
1609      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
1610         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
1611      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
1612         change cg2d residual target to be expressed in Wunits (=> do not normalise
1613         RHS ; this fix global_max Pb with TAF); update output.
1614    o verification/tutorial_tracer_adjsens:
1615       improve parameter consistency (and get rid of warnings):
1616       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
1617       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
1618       - use staggerTimeStep (for stability) in som81; use default rotation period.
1619    o pkg/exch2:
1620      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
1621        reset to 0 = 1 long line in X)
1622    o pkg/mdsio:
1623      - fix reading of dimensions from meta file for large-size domain
1624    o model/src:
1625      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
1626      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
1627        Cubed-Sphere Exch with CS-corners inside the domain;
1628        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
1629        globalArea and to set hasWetCSCorners.
1630      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
1631        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
1632      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
1633        useCDscheme and useCubedSphereExchange).
1634    o pkg/seaice/seaice_growth.F :
1635      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
1636        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
1637        when the previous code was not correct.
1638      - in all cases diagnoze the boundary condition mismatch to SIaaflux
1639      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
1640        that term to QNET (essentially to set the melt/freeze water to 0degC).
1641        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
1642    o verification/global_ocean.cs32x15/input.seaice :
1643      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
1644      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
1645      - update results (output.seaice.txt) accordingly.
1646    o verification/lab_sea/input/data.seaice :
1647      - remove SEAICEheatConsFix, which is now be tested
1648        in global_ocean.cs32x15. The presently coded fix
1649        is only consistent with real fresh water + nlfs.
1650      - update results (output.txt) accordingly.
1651    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
1652    o AD_CONFIG.h file:
1653      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
1654      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
1655        add it explicitly in each fortran src file where it is needed.
1656        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
1657        thus introducing potentially wrong dependency; therefore, better to include
1658        it only where it's really needed, and after any other included OPTIONS file
1659        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
1660        or ALLOW_TANGENTLINEAR_RUN).
1661    
1662    checkpoint63p (2012/07/06)
1663    o pkg/autodiff:
1664      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
1665      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
1666        which are now read from new parameter file "data.autodiff" (inAdExact
1667        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
1668      - add file "data.autodiff" in all verification/*/input_ad/ directories.
1669      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
1670        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
1671    o verification/tutorial_tracer_adjsens/
1672      - add extra sub-verification which uses "SOM" advection scheme
1673        (2nd Order-Moment Advection Scheme, Prather Limiter) with
1674          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
1675        and in data:
1676          multiDimAdvection=.TRUE.,
1677          tempAdvScheme=81,
1678          saltAdvScheme=81,
1679    o model/src:
1680      - introduce ALLOW_BALANCE_RELAX which allow the removal
1681       of the global mean of relaxation terms by setting
1682       balanceThetaClimRelax and balanceSaltClimRelax
1683      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
1684       This case is now treated appropriately in seaice_growth.F
1685    o pkg/seaice:
1686      - do balanceEmPmR and balanceQnet based on the net fluxes
1687        (SItflux) that enter the ocean+ice system rather than QNET
1688        and EMPMR. Works best in real fresh water.
1689      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
1690        out of the diagnotics bloc, and stored in global arrays.
1691    
1692    checkpoint63o (2012/06/29)
1693    o vertical mixing schemes:
1694      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
1695      - replace computation of density (in Function STATE1, opps_calc.F) by a call
1696        to S/R FIND_RHO_SCALAR
1697      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
1698        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
1699        affects output (vermix.ggl90) at truncation level.
1700    o testreport:
1701      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
1702        (nSx,nSy) for the number of threads (from eedata.mth)
1703    o model/src:
1704      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
1705        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
1706    o verification/tutorial_tracer_adjsens/
1707      - compile with ALLOW_CG2D_NSA
1708      - run with nonlinFreeSurf=3
1709      - update reference output_adm.txt
1710    o tools/genmake2:
1711      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
1712        refine usePROFILES switching off (only when NetCDF is not available).
1713    o verification (atmospheric set-up):
1714      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
1715    o pkg/profiles : refine profiles and files handling.
1716    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
1717    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
1718      - changes to use model/src/the_main_loop.F rather than the ecco version
1719        in ecco type adjoint runs.
1720    o model/src:
1721      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
1722      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
1723      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
1724    o model/src:
1725      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
1726        update output of test experiment bottom_ctrl_5x5.
1727    o pkg/generic_advdiff:
1728      - implement vertical bi-harmonic diffusion (for now, only for T & S and
1729        only explicitly).
1730    o verification/bottom_ctrl_5x5/
1731      update reference output (results changed quite some time ago,
1732      not sure when; but new reference results look ok in terms of grdchk)
1733    o verification/1D_ocean_ice_column/
1734      For verification purposes, the exact adjoint rather than an approx.
1735      should be used (e.g., to comare against F.D. or TLM).
1736      removed autodiff_inadmode*_ad.F routines in code_ad/
1737      Update results/ accordingly.
1738    o pkg/cal:
1739      - change cal_getdate.F so that output date is function of input time only
1740        (less ambiguous, not mixed up with input iteration number).
1741      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
1742    o pkg/diagnostics:
1743      - implement calendarDumps also for stats-diags
1744      - implement calendarDumps also for snap-shot output (negative freq)
1745      - for now, ignores calendarDumps if non-zero phase-lag.
1746    
1747    checkpoint63n (2012/06/04)
1748    o model/src:
1749      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
1750        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
1751      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
1752        similar to calc_r_star.F); update results of experiment internal_wave and
1753        tutorial_global_oce_in_p (affected @ truncation level).
1754    o pkg/shelfice:
1755      - add parameterisation of advective-diffusive flux into the ice shelf
1756        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1757      - simply eps3/3a computation
1758    o eesupp:
1759     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
1760       between tiles, just fill-in edges assuming locally periodic subdomain) and
1761       add corresponding exchange subroutines (EXCH0);
1762     - new CG-solver version (_EX0) for disconnected-tiles special case.
1763    o model/src (CG-solvers):
1764     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
1765       (similar final residual output and max-Iter number as with standard version);
1766     - allows to store and use lowest-residual solution (standard & _SR versions);
1767     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
1768     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
1769    o eesup/src:
1770     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
1771       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
1772    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
1773    
1774    checkpoint63m (2012/04/27)
1775    o pkg/shelfice:
1776     - account for partical cells in surface level below ice-shelf for hydrostatic
1777       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
1778    o ad test experiments:
1779     - update and rename to "ad_optfile.local" local AD-optfile specific to a
1780       particular adjoint verification experiment (in verification/*/code_ad/)
1781    o pkg/seaice & pkg/exf:
1782     - Part two of ECCO-CLIVAR code merges.
1783       Completes merge of seaice area relax. code.
1784       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
1785       to be set in EXF_OPTIONS.h since this pkg controls its I/O
1786       (and avoids second CPP option in SEAICE_OPTIONS.h)
1787     - change default value of costIceStart & costIceEnd to a valid date.
1788     - add snowPrecip to HSNOW in seaice_growth
1789    o pkg/ptracers:
1790     - move ptracers summary and setup check into separated S/R ; add a check for
1791       valid PTRACERS_Iter0 value (error+stop or just warning).
1792    o pkg/cal (+ pkg/ecco):
1793     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
1794       as input; and for AD, unless both are not differentiable (e.g., k index)).
1795    o model/src:
1796     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
1797       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
1798       temporary set to usingZCoords value (to be changed to F when using shelfice).
1799     - hydrostatic pressure: implement partial cell near the surface also for
1800       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
1801       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
1802    o pkg/ctrl/ctrl_init.F:
1803     - add a formal parameter to s/r ctrl_init_rec to print
1804       xx_$(ctrl_valiable)_file for easier debugging
1805     - move call of cal_* routines into the if-block where they are really
1806       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1807       to specify a startdate
1808    o pkg/seaice:
1809     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1810       global_ocean.cs32x15/code versions).
1811     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1812       verification experiment global_ocean.cs32x15.seaice and update results.
1813    o pkg/exf:
1814     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1815       (according to useExfYearlyFields).
1816    o pkg/cal:
1817     - move calendar setting & summary (previously in cal_readparams.F) into new
1818       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1819       length of the simulation is set (after SET_PARMS call); This is an attempt
1820       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1821     - For safety: keep a record of pkg/cal parameter settings status
1822               to allow to STOP if one pkg/cal S/R is called too early.
1823     - add a stop in all basic pkg/cal subroutines if called before setting is done.
1824     - modify cal_getdate.F: stop when nothing was returned;
1825       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1826       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1827    
1828    checkpoint63l (2012/04/04)
1829    o pkg/bbl:
1830      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1831        update global_with_exf output.yearly.txt file.
1832    o pkg/cal:
1833      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1834      - remove 2 unsused and very short (1 line only) functions ;
1835      - remove unsused subroutines from AD-Diff list.
1836    o model/src:
1837      - start to implement clean wait to stop in initialization S/R (config_check.F,
1838         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1839    o folowing PRINT_MESSAGE changes:
1840      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1841    o pkg/bbl:
1842      - modification so it can work with z*
1843      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1844      - global_with_exf/input.yearly verification; changes output.yearly.txt
1845    o eesupp/src:
1846      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1847        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1848      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1849        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1850      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1851      - when using MPI, always set usingMPI=T ; set default accordingly and stop
1852        if not consistent.
1853      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1854        argument is zero (in case called within single-thread section).
1855    o pkg/fizhi:
1856        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1857        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1858    o pkg/exch2:
1859      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1860        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1861      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1862        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1863        with bad ones coming from a not-yet-updated halo.
1864        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1865    o pkg/frazil:
1866        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1867        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1868    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1869    o verification/lab_sea
1870      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1871      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1872      * nTimeSteps 3 -> 4
1873      * changed reference output accordingly
1874    o pkg/ctrl:
1875      * fix ctrl_get_gen for xx_sst, xx_sss
1876    o pkg/fizhi:
1877      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1878        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1879      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1880        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1881        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1882    o pkg/gmredi:
1883      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1884    o pkg/fizhi:
1885      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1886        (old)aces open64 tuv test.
1887    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1888    o pkg/mom_vecinv:
1889      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1890        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1891        with non-lin free-surf).
1892    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1893      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1894      some compilers (gfortran 4.6.0 on MacOS)
1895    o momentum:
1896      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1897        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1898        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1899    
1900    checkpoint63k (2012/03/17)
1901    o model/src:
1902       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1903         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1904       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1905         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1906    o model/src: solve_*diagonal.F
1907       - replace division with multiplication by inverse (similar to original version)
1908         update output of AD exp. global_ocean.90x40x15.
1909       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1910         to enable the use of the vectorized & differentiable solve_tridiagonal.F
1911       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1912         vertical advection (to get solve_tridiagonal tested in AD mode).
1913    o pkg/seaice: ECCO-CLIVAR merge:
1914      1. seaice AREA relaxation
1915         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1916         * runtime flag: SEAICE_tauAreaObsRelax
1917      2. modified global mean cost imbalance code: CPP option
1918          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1919    o another iteration on solve_*diagonal.F
1920       Make choices independent of AUTODIFF
1921       Default will be the adjoinable vectorized version.
1922       Alternative choices are:
1923       * non-adjoinable original version with low memory footprint:
1924         #define SOLVE_DIAGONAL_LOWMEMORY
1925       * still adjoinable but does not vectorize (k as inner-most loop):
1926         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1927    o testreport
1928     - add option to use a home made wrapper around "make"
1929     - remove MITGCM_IEEE env. variable (no longer active)
1930    o pkg/shelfice
1931     - improve computation of friction velocity for velocity dependent
1932       exchange coefficients: include velocities into SHELFICEBoundaryLayer
1933       block to average velocities vertically
1934     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1935    o Modify diagonal solvers, now three versions (upon request):
1936      #ifndef SOLVE_DIAGONAL_AUTODIFF
1937        1. default version (dating back a while ago)
1938      #else /* def SOLVE_DIAGONAL_AUTODIFF */
1939      # ifdef SOLVE_DIAGONAL_KINNER
1940        2. adjoinable version with k-innermost loop (G. Forget)
1941      # else
1942        3. adjoinable vectorized version of 2.
1943      # endif
1944      #endif /* SOLVE_DIAGONAL_AUTODIFF */
1945      All flags are currently set within routines, but could/should be moved to CPP-options.
1946      Array bounds for 1. are as before, for 2.,3. cover the entire domain
1947      (could be changed for 1. too).
1948    o verification/lab_sea (fwd):
1949      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1950        use 7 categories (except hb87), new solve4temp params (except salt_plume),
1951        constant salinity (=4) or variable salinity (salt_plume) done through
1952        SItracer.
1953    o pkg/seaice:
1954      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1955      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1956         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1957        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1958        SEAICE_freeze got retired) but already better than previously with
1959        SEAICE_freeze=123456.7 deg.C;
1960      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1961        (safer multi-threaded setting); always set SEAICEuseEVP;
1962      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1963        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1964        stop if multiple specifications for the same coeff; make sure default
1965        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1966    o pkg/obcs:
1967      - allow to switch to upwind 1rst order advection scheme for the advective
1968        flux computation at the open-boundary; disabled for adjoint built.
1969    o pkg/ptracers:
1970      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1971      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1972      - add parameter to decide when to start a tracer; use internal flag to
1973        know which tracer to step-forward; switch this internal flag at the top
1974        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1975        for adjoint built.
1976    o pkg/seaice:
1977      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1978      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1979      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1980    o pkg/ecco:
1981      - fix writing of output file DiagnosCost_ClimSalt/Theta
1982        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1983    o pkg/seaice:
1984      - add missing initialisation of COR_ICE array in dynsolver.F
1985      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1986        compiled either way, and is tested in all exps (multidim was only tested
1987        in lab_sea ad before).
1988      - cosmetic change to prepare for future addition of ITD. no change to results.
1989        no defaults change.
1990      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1991      - by lack of adequate verification experiments, I further used custom versions
1992        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1993        should be correct.
1994      - avoid recomputations in ad.
1995    o array initialisation in adjoint mode:
1996      1) pkg/mom_common/mom_calc_ke.F:
1997        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1998        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1999        part this initialisation is gone, resulting in Floating Point Exception
2000        (caught by open64 compiler with debug option).
2001      2) model/src/convective_weights.F
2002        set output convectCount over the full array range (instead of doing
2003        an update): this fix a similar issue when called within recomputation (adjoint)
2004        which could by-pass the initialisation (normally done in the caller S/R).
2005    o pkg/seaice:
2006      - final version of turbulent flux params, as agreed at MIT ice meet:
2007           SEAICE_mcPheePiston (default is ~ 0.000875)
2008           SEAICE_mcPheeTaper (default is 0.)
2009           SEAICE_frazilFrac (defualt is 1.)
2010           SEAICE_mcPheeStepFunc (default is false)
2011      - changes results at trunction error level
2012      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
2013    o added pkg/frazil:
2014      - see frazil_description.tex for details
2015      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
2016    o pkg/shelfice/shelfice_thermodynamics.F
2017      - fix exponents for velocity dependent exchange coefficients: change
2018        from 2/3(=0) to 0.66666666666666667
2019      - move computation of velocity dependent exchange coefficients into
2020        separate loop, so that it applies to both thermodynamics
2021      - move some divisions by constants out of loops
2022    
2023    checkpoint63j (2012/02/16)
2024    o pkg/seaice:
2025      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
2026      - SItracer:  added run time params, and allow coupling to ocn salinity.
2027    o pkg/seaice: remove (almost) all divisions by constants within loops
2028      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
2029      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
2030      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
2031      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
2032    o pkg/seaice :
2033      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
2034        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
2035      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
2036      - add permanent SItflux diag that corresponds to TFLUX but includes
2037        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
2038      - allow activation/testing of a fix for suspected missing term in
2039        ocn-ice heat budget (to be confirmed). To test this, you want to
2040        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
2041        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
2042      - no change in results, fwd or ad.
2043    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
2044      - switch to variable freezing point.
2045           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
2046      - bug fix : the sublimation term that was missing is now activated.
2047           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
2048      - bug fix : flooding sign term for SIsal0.NE.0.
2049           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
2050    o pkg/seaice:
2051      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
2052        is now the default, and the old default constant freezing point is recovered
2053        with SEAICE_tempFrz0    = -1.96,
2054             SEAICE_dTempFrz_dS = 0.,
2055      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
2056      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
2057      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
2058        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
2059      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
2060        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
2061      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
2062        seaice_growth r149 for legacy branch (no results change).
2063      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
2064        from I. Fenty).
2065      - results did not change except for global_ocean.cs32x15, mostly due to the
2066        switch to variable freezing point (see above item for detail).
2067    o pkg/thsice:
2068      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
2069        seawater freezing in thsice_calc_thickn (not used).
2070    o pkg/seaice: turbulent flux term specification via run time params.
2071      - replace CPP switches with run time switches to facilitate testing
2072      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
2073                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
2074      - added runtime parameter : SEAICEturbFluxFormula
2075      - move Mcphee constants to SEAICE_PARAMS.h
2076      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
2077                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
2078                 remove seaice_summary call (moved to seaice_init_fixed)
2079      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
2080        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
2081      - seaice_summary.F : add missing report of read turbulent flux term set up
2082                           and SITRACER.
2083      - seaice_check.F : check range; inform and stop if retired CPPs are used
2084                         (incl. SEAICE_AGE).
2085      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
2086             CPP switch, same computation as before for the different options.
2087      - change results at the truncation level.
2088    o pkg/seaice:
2089      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
2090        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
2091        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
2092      - update verification/*/input*/data.seaice:
2093        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
2094        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
2095        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
2096        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
2097    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
2098      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
2099        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
2100        difference in results only due to machine truncation.
2101      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
2102        MaykutPolySatVap; keep MIN_LWDOWN.
2103      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
2104      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
2105        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
2106    o pkg/salt_plume:
2107      - isolate saltPlumeFlux array exch into a specific S/R called from
2108        do_oceanic_phys.F
2109      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
2110    o verification:
2111      - move untested set-up to MITgcm_contrib/verification_other.
2112    o pkg/seaice:
2113      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
2114    o pkg/seaice:
2115      - seaice_solve4temp.F (keeping results unchanged):
2116        * add 2 future run-time params to select which saturation vapor pressure
2117          formula is used and how post-iteration fluxes are set.
2118          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
2119        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
2120          the linearized expression to stay consistent with tsurf finding.
2121      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
2122        can be < 0.
2123    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
2124      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
2125        conductive heat flux F_c , and add it explicitly when updating tsurf as
2126        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
2127        so that now F_ia has a consistent meaning through the entire routine.
2128        This causes differences at truncation level: update output of fwd exp.
2129        global_ocean.cs32x15.seaice.
2130    o pkg/seaice:
2131      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
2132        of arrays, sign/direction of fluxes; no effect on results.
2133      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
2134        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
2135        note: this should have been done before changing celsius2K default.
2136      - to keep results unchanged, add back old value of celsius2K in verification
2137        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
2138      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
2139        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
2140        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
2141        freezing temp is consistent with value in seaice_growth.F ; this causes
2142        differences at machine truncation level: update lab_sea AD output (3/4).
2143    o pkg/seaice:
2144      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
2145        and climsst/sss even when using seaice (to prevent calculation that might
2146        use SST on land); does not affect any verification exp.
2147      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
2148        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
2149    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
2150      over land (non-legacy code)
2151    o vectorize salt_plume package:
2152      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
2153      - this code computes plumebk everywhere (also over land), thus requires
2154        code to avoid divisions by zero and catch the case of kLev=Nr.
2155      - efficiency of salt_plume_frac is still sub-optimal
2156    o tools (genmake2):
2157      - fix makefile NAME specification (option: -makefile NAME) by adding
2158        "-f $MAKEFILE" in few places where it was missing including makedepend
2159        command (contribution from Paul).
2160    
2161    checkpoint63i (2012/01/24)
2162    o model/src:
2163      - add factorized versions of some EOS code to find_rho.F,
2164        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
2165    o model/src:
2166      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
2167      - change default celsius2K from 273.16 to 273.15
2168      - to keep results unchanged, add back old value of celsius2K in verification
2169        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
2170         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
2171    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
2172      to make TAF generate vectorizable code
2173    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
2174       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
2175       have flags that do this more efficiently.
2176    o pkg/diagnostics/diagstats_calc.F
2177      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
2178    o pkg/obcs (with exch2):
2179      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
2180        and remove code (in obcs_readparms.F) which was based on EXCH of indices
2181        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
2182    o pkg/exf and seaice exp:
2183      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
2184        so that switching off area & heff advection flags does not affect results.
2185      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
2186      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
2187        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
2188        results of verification experiments: 1D_ocean_ice_column(fwd),
2189        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
2190        and offline_exf_seaice (all 4).
2191    o pkg/seaice:
2192      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
2193        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
2194      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
2195        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
2196        not multi-dim advection;
2197      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
2198        SHORTWAVE_HEATING #undef.
2199    o optim: make Makefile more robust (?)
2200    o pkg/obcs:
2201      * fix treatment of obcs_read_pickup for TAF
2202    o pkg/shelfice:
2203      * add missing initialisation of num_shifwflx
2204      * new adjoint verification exp. for isomip
2205      * change Prandtl and Schmidt numbers from generic formulations
2206        (in terms of model diffus. and visc.) to separate runtime
2207        parameters, with Holland and Jenkins (1999) default values.
2208    o pkg/exf (interpolation):
2209      - extended input field (2 rows) near the N & S poles:
2210        * fill in with the symetric value (when even Nb of data in longitude)
2211        * add average value at the poles only for scalar quantities ; for vector
2212          component interpolation, skip the averaging and keep duplicated values,
2213          unless the 2 components have same location (uvInterp=T) in which case
2214          interpolate the 2 components together using S/R EXF_INTERP_UV.
2215      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
2216        together: this allows to account properly for local orientation when
2217        averaging at N & S pole.
2218      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
2219        exf-interpolation near N & S poles. Undef by default.
2220      - add debug check/print on 1rst iter if debugLevel >=2.
2221    o pkg/exf:
2222      - change masking flags definition (no longer "parameter"), put them in
2223        common block and set them in S/R EXF_INIT_FIXED.
2224      - change recognized masking flag from s,u,v to c,w,s since the mask
2225        to use (maskC,W,S) depends on position on model grid and has little to
2226        do with scalar/vector difference; fix masking if using P-coordinates.
2227      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
2228        and update results of exp. global_with_exf (x2).
2229      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
2230    o pkg/obcs
2231      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
2232    o pkg/exf (interpolation):
2233      - assume periodicity in X only if input field cover full longitude range.
2234      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
2235        and should vectorise).
2236      - fix input lat of the 2 added row (in case we provide N.pole data).
2237    
2238    checkpoint63h (2011/12/30)
2239    o pkg/seaice:
2240      - change declaration of UVM from _RL to _RS in order to get B-grid
2241        uIce,vIce monitor when _RS = real*4
2242    o pkg/offline:
2243      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
2244      - compute vertical velocity if not read from file (switch on exactConserv
2245        & staggerTimeStep);
2246      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
2247    o verification:
2248      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
2249        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
2250        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
2251      - update output of exp. global_ocean.cs32x15.viscA4 after changing
2252        grid-file angles (used here for coriolis-3d);
2253      - remove (or gzip) few files not needed to run fizhi-cs experiments.
2254    o pkg/exf (vector interpolation):
2255      - rotate vector component toward local grid-axis orientation using grid-angles
2256        (stored in GRID.h) instead of locally computed rotation angle; keep old code
2257        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
2258    o pkg/seaice:
2259      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
2260        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
2261    o pkg/PKG_OPTIONS.h files:
2262      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
2263        outside of the #ifdef ALLOW_THISPKG / #endif block.
2264      - update verification/*/code/PKG_OPTIONS.h files.
2265    o add a verification experiment (offline_exf_seaice/input.seaice) that test
2266      the B-grid LSOR solver
2267    o pkg/seaice: sort out emissivity and long wave radiation step 2:
2268      - add emissivity for snow and ice as new run-time parameters
2269        (unfortunately) that default to the corresponding exf values; this
2270        changes results in most verification experiments so that for backward
2271        compatibility these parameter have to be set explicitly to inconsistent
2272        values (ugly);
2273      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
2274        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
2275        until we agree how to handle this bug properly
2276    o pkg/exf (interpolation):
2277      - add a set of run-time param ({inputfield}_interpMethod), one for
2278        each interpolated input field, to select the interpolation method
2279        with a value of zero switching off the interpolation;
2280      - print interpolation parameters to standard output;
2281      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
2282        (to use instead runoff_interpMethod=0 in data.exf).
2283      - simplify default setting of interpolation parameters (for all fields,
2284        set position to match model grid cell-center position, leading to trivial
2285        interpolation in case of regular Lat-Lon grid) and fix for the case of
2286        non-uniform delY.
2287    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
2288       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
2289       this factor is absolutely required, because the lw exitance (= out-going
2290       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
2291       where the reflectivity rho = 1-emissivity for conservation reasons. Once
2292       this is established, we can remove the CPP-Flag (if we want to).
2293    o pkg/seaice:
2294      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
2295        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
2296      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
2297        what the name implies (and not emissivity*BoltzmannConstant), this means
2298        the old default value of 5.5e-8 now means
2299        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
2300        S/R exf_readparms
2301      - FV-discretization of the B-grid LSOR solver, turn on with
2302        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
2303        of the calling routine dynsolver, so that B and C-grid code look a
2304        little more alike.
2305      - fix index bugs in ostres.F (B-grid code)
2306    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
2307    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
2308      default for SEAICE_emissivity, if useEXF; requires setting a wrong
2309      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
2310      backward compatiblity
2311    o model/src: use sigmaR in calc_ivdc
2312    
2313    checkpoint63g (2011/12/16)
2314    o pkg/seaice/seaice_growth.F:
2315      fix heat conservation of the coupled ocean-seaice system.
2316      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
2317      solid vs liquid water treatment is resolved via QNET.
2318    o pkg/seaice/seaice_growth.F:
2319      add missing term for sublimation in saltFlux, which was breaking conservation.
2320    o pkg/seaice/seaice_model.F:
2321      Remove this patholigical case treatment in evolution branch,
2322      where it is un-necessary and breaks conservation.
2323      Update global_ocean.cs32x15/results accordingly for
2324      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
2325    o model/src:
2326      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
2327      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
2328    o pkg/obcs:
2329      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
2330      tendency for temperature and salinity that is then applied to update
2331      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
2332      horizontal advection and diffusion contributions on the boundary (in
2333      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
2334      removing the mask in S/R timestep_tracer. The advantage of this approach is
2335      that the updated tracer values include contributions from the surface
2336      forcing and vertical diffusion.
2337      This modification changes exp4.stevens because of vertical diffusion.
2338    o model/src:
2339      change non-curvilinear grid setting to also work with exch2 + blank tiles:
2340      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
2341        face dimensions.
2342      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
2343        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
2344        and INI_SPHERICAL_POLAR_GRID.
2345      change test-experiment global_ocean.90x40x15:
2346      - split the domain in many more tiles (9x4 tiles of 10x10 each);
2347      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
2348      - update results of both test (std & dwnslp).
2349    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
2350       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
2351    o model/src:
2352      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
2353        and fix initialisation when using sigma-coords.
2354    o model/src:
2355     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
2356       to their current value at the beginning of forward_step.F": add a new run-time
2357       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
2358     - set doResetHFactors=T in the following test exp:
2359        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
2360        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
2361        and tutorial_global_oce_in_p (nonLinFS in p)
2362    o pkg/ecco
2363      - added IES cost term
2364    o verification/advect_xz
2365      - scale down the depth by 1/100 (from 200 km to just 2.km)
2366      - add secondary test using divergent flow, r-star and implicit vertical advection.
2367      - add note (check_conserve_TS.txt) and matlab script to check global
2368        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
2369    o pkg/rbcs:
2370      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
2371    o pkg/obcs (Stevens BCs):
2372      - fix various problems in the phase speed computations of the Stevens
2373        boundary conditions:
2374        - sign error for western and southern boundaries,
2375        - time tendencies were underestimated by factor of dTracerLev and some just
2376          zero (for multidim advection schemes) -> now estimate time tendencies
2377          from difference between previous (n) time level and the one before (n-1);
2378          this requires storing a field per tracer per boundary, also in the pickup
2379          files.
2380        - replace deltaTmom in cflMer/Zon computation with dTracerLev
2381        - set default phase velocity to cflMer/Zon
2382      - update verification experiment exp4.stevens
2383    o pkg/generic_advdiff (implicit_r):
2384      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
2385        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
2386      - fix implicit vertical diffusion or advection with NonLin FreeSurf
2387        (was using current recip_hFacC instead of future recip_hFacC): set future
2388        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
2389        solver S/R ;
2390      - fill diagnostics of vertical advective fluxes (computed from tendency)
2391        when using implicit vert. advection;
2392      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
2393         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
2394         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
2395         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
2396    o pkg/diagnostics:
2397      - add diags for T & S tendency which goes through Adams-Bashforth.
2398    
2399    checkpoint63f (2011/11/30)
2400    o pkg/obcs/obcs_calc_stevens.F:
2401      - join some loops to reduce number of if-statements
2402      - fix a bug in code for northern and southern boundaries.
2403    o pkg/seaice/seaice_init_varia.F
2404      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
2405        caused zero ice-velocities for the B-grid code
2406    o pkg/seaice/seaice_init_fixed.F
2407      - fix a bug in the initialisation of the second metric terms
2408        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
2409      - this affects all seaice configurations with useCurviLinearGrid = .true.
2410        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
2411        = .true. (default)
2412      - the only verification experiment affected is global_ocean.cs32x15:
2413        icedyn, seaice, and seaice_dynmix (AD)
2414    o pkg/thsice/thsice_diagnostics_state.F
2415      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
2416        not contain garbage that can lead to surprises in diagstats_calc.F
2417    o model/src:
2418      - move bi,bj loops inside INTEGR_CONTINUITY ;
2419      - call INTEGR_CONTINUITY directly from forward_step.F
2420        (previously called from momentum_correction_step.F)
2421      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
2422        forward_step.F and pkg/ecco/the_main_loop.F
2423    o model/src/do_oceanic_phys.F:
2424      - reset addMass to zero only if useICEFRONT ;
2425      - separated k-loop for rhoInSitu calculation ;
2426      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
2427        and at constant T,S (= WdRHOdP);
2428      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
2429        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
2430        transport of locally-referenced potential density);
2431        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
2432    o gluemnc:
2433      - replace ncrcat with ncks when adding variables to *.glob.nc
2434      - change the way variables without record dimensions are handled so that
2435        files that have variables with and without record variables can be glued:
2436        add a record dimension with a new unique name to be able to differentiate
2437        between variable with and without a-prior record dimensions. Remove
2438        this record dimension before adding the variable to the *.glob.nc file.
2439        This procedure automatically works also for grid.*.nc files that do not
2440        have any record dimension.
2441    o verification/cpl_aim+ocn:
2442      - generate new reference output on baudelaire (gfortran, mpich2) (previously
2443        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
2444    o pkg/obcs/obcs_calc_stevens.F:
2445      - add code for northern and southern boundaries.
2446      - reorder some loops to save some operations and so that drFBar can be scalar
2447    o model/src:
2448      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
2449        truncation) and add diagnostics for Adams-Bashforth tendency increment.
2450      - update test-exp. AD output:
2451        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
2452      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
2453        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
2454        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
2455        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
2456        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
2457        tutorial_plume_on_slope.
2458    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
2459      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
2460      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
2461      does not even come with an F77 compiler anymore, this should not be
2462      a limitation
2463    
2464    checkpoint63e (2011/11/06)
2465    o pkg/seaice adjoint of LSR:
2466      - substantially rework STORE dirs.
2467      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
2468        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
2469        and only perform SOLV_MAX_FIXED adjoint iters.
2470        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
2471        always goes to same record, meaning that the last forward field will be
2472        the one used in the adjoint - an approximation.
2473      - now produces non-zero LSR-related gradients, and acceptable gradients for
2474        An's zonal (x-z) test case (to be checked in)
2475      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
2476        (but these are screwed up by the thermodynamics in the first place);
2477        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
2478        output_adm.txt also reflects changes to seaice_lsr
2479      - global_ocean.cs32x15:
2480        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
2481          (output_adm.seaice.txt was updated)
2482        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
2483          (output_adm.seaice_dynmix.txt)
2484    o test-exp. exp4+stevens:
2485      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
2486    o pkg/seaice (lsr solver):
2487      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
2488        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
2489      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
2490      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
2491        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
2492      - compute (with new S/R) and print initial (+ free-driff sol. if available)
2493        and final residual of linearised system.
2494    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
2495      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
2496    o pkg/obcs: Stevens BCs (still only for east and west)
2497      - fix Stevens BCs by using intermediate velocities of previous
2498        time step as "baroclinic" contribution rather velocity of one grid cell
2499        inside the boundaries; more consistent but makes the entire treatment
2500        more complicated, requires new pickup files and two new S/Rs:
2501        obcs_copy_uv_n and obcs_save_uv_n
2502        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
2503        (undefined by default)
2504      - silently move computation of some grid factors into separate loops to
2505        save some recomputations
2506      - add a hack for non-linear free surface
2507      - add a verification experiment to exp4 that tests this code
2508    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
2509    
2510    checkpoint63d (2011/10/25)
2511    o pkg/obcs + seaice-dynamics:
2512      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
2513        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
2514        values (consistent with an implicit method).
2515      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
2516        return to older implementation (same results as before); note that none of
2517        the "experimental" OBCS_SEAICE options are implemented in the new version.
2518      - switch test exp. seaice_obcs to use new version (update output).
2519    o pkg/seaice:
2520      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
2521      - add parenthesis in Water-Ice drag calculations (evp & lsr);
2522      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
2523        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
2524      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
2525        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
2526    o pkg/layers:
2527      - Include potential density as new coordinate (Thanks to David Munday)
2528    o pkg/dic:
2529      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
2530        carbonate computation/output to CALC_PCO2_APPROX
2531    o pkg/generic_advdiff
2532      - make TAF generate code that vectorizes:
2533        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
2534    o model/src:
2535      - improve vectorization also for adjoint code of
2536        solve_tridiagonal and solve_pentadiagonal. As this requires up to
2537        5 new 3D-fields, this code is only turned on for the combination of
2538        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
2539        for singular matrix check (only for TARGET_NEC_SX).
2540      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
2541        ALLOW_AUTODIFF. This flag now needs to be set outside of
2542        solve_tri/pentadiagonal.F
2543    o pkg/exf:
2544      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
2545        optional namelist EXF_NML_OBCS).
2546      - add many debug-print (to trace down where pkg/cal error msg comes from)
2547    o pkg/mom_vecinv/mom_vi_hdissip.F
2548      - rearrange loops so that vectorization is improved and in particular
2549        the adjoint routine vectorizes. The code is a little longer now, but I
2550        think easier to read.
2551        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
2552    o pkg/seaice:
2553      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
2554    o pkg/exch2:
2555      - alternative code (without tile x tile matrix) for cumulated (global) sum;
2556        used as default; keep using matrix version in adjustment.cs-32x32x1.
2557    o tools/build_options:
2558      - after merging some MPI and/or multi-threads specific optfiles so that
2559        the modified default optfile support both built (using genmake2 -mpi
2560        for the MPI built, using genmake2 -omp for OpenMP built),
2561        move now obsolete optfiles to tools/build_options/unsupported/
2562       (add copy of email sent to support list in doc/optfiles_changes.txt)
2563    
2564    checkpoint63c (2011/09/28)
2565    o pkg/ebm:
2566      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
2567        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
2568    o pkg/seaice (SItracer pickup)
2569    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
2570      To be done:
2571      - thorough testing of missing fields in S/R seaice_read_pickup
2572      - thorough matching between generic tracers and specific fields used
2573        (e.g. volume-weighted age, area-weighted age, salinity, ...)
2574    o pkg/grdchk:
2575      - all procs calculate and print finite-difference gradient (for testreport)
2576      - change description output used by testreport;
2577      - AD testing: also compare and report Finite-difference gradient;
2578        => update all output_adm*.txt
2579    o test exp. global_ocean_ebm:
2580      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
2581        and turn on exactConserve; update (fwd) output.
2582    o pkg/seaice (LSR):
2583      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
2584      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
2585        * identical results with non-CS topology (but save up to half of EXCH calls)
2586        * no much changes in cs-32 verification tests since no ice at face edges
2587         (differences due to convergence criteria, since nb of iterations changed)
2588        * expect some differences on lat-lon-cap grid.
2589        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
2590    o pkg/exch2:
2591      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
2592        many tiles); until alternative coding is added, just add a stop.
2593    o pkg/kpp:
2594      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
2595        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
2596    o optfiles:
2597      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
2598        into corresponding standard one, which now support different build:
2599        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
2600      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
2601    o pkg/obcs (seaice):
2602      - add missing EXCH for uIce,vIce after applying OBCS;
2603      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
2604        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
2605        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
2606      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
2607      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
2608        and eedata.mth for MPI and mutlti-threaded testing.
2609    o pkg/flt:
2610      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
2611      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
2612      - fix pickup and trajectories + profiles output with multi-threads;
2613      - add parameter to select group of fields to write along trajectory and
2614        profile (default unchanged);
2615      - only call PORT_RAND* function when flt_noise <> 0;
2616      - add multi-threaded test for verification exp. flt_example.
2617    o eesupp/src:
2618      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
2619      - USE_OMP_THREADING: check that number of threads (from eedata) matches
2620        actual number (from env.var. setting).
2621    o pkg/ebm:
2622      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
2623      - add multi-threaded test for verification exp. global_ocean_ebm
2624    
2625    checkpoint63b (2011/08/29)
2626    o pkg/ebm:
2627      - fix sign of runoff;
2628      - update directly forcing fields (Qnet,EmPmR) to use standard
2629        external_forcing_surf.F (remove ebm_forcing_surf.F);
2630      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
2631      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
2632        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
2633      - update global_ocean_ebm parameters file data and update output (fwd+ad).
2634    o verification/matrix_example:
2635      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
2636        MPI and mutlti-threaded testing.
2637    o pkg/matrix:
2638      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
2639      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
2640      - fix for multi-threaded (remove DATA statement);
2641      - use standard DIFFERENT_MULTIPLE function;
2642      - add MATRIX_OPTIONS.h
2643    o verification/matrix_example:
2644       To allow to split the domain in several tiles, change the domain size
2645        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
2646        Western side) of land points.
2647    o (*_)write_pickup:
2648      - fix few bugs in mypackage_read/write_pickup.F
2649      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
2650        array of length 1 (was caught by compiler syntax-check).
2651    o pkg/diagnostics (velocity potential solver):
2652      - fix initialisation of main diagonal matrix (for overlap values)
2653    o tools/build_options:
2654      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
2655        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
2656      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
2657        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
2658        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
2659        and use "-devel" testreport option for standard testing on baudelaire.
2660    o pkg/grdchk:
2661      - Assume that all gradient-check position are within the same tile
2662        corresponding to global indices (iGloTile,jGloTile) and that
2663        positions (i,j indices or nbeg) are local to this tile;
2664      - set tile local-indices and proc. number according to tile global-indices;
2665      - remove grdchkwhichproc from namelist (retired param);
2666      - send adjoint gradient to all procs so that all procs print it to STDOUT;
2667      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
2668    o adding package bbl (Bottom Boundary Layer)
2669      description in MITgcm/pkg/bbl/bbl_description.tex
2670      example/test experiment in MITgcm_contrib/bbl
2671    o adjoint verifications
2672      - changed 5 experiments to multi-tiles
2673        * global_ocean.90x40x15
2674        * obcs_ctrl
2675        * offline_exf_seaice
2676        * tutorial_dic_adjoffline
2677        * tutorial_tracer_adjsens
2678        changed reference output for those that crossed tile boundaries
2679        (changed choices of gradient check positions)
2680      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
2681      - temporary bug fix in grdchk_loc.F for obcs
2682    o genmake2 & testreport
2683      - add target "obj" (just for OBJFILES files) to Makefile;
2684      - add option to specify FEXTRAFLAGS on command line.
2685    o pkg/mypackage:
2686      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
2687    
2688    checkpoint63a (2011/08/02)
2689    o pkg/diagnostics (velocity potential):
2690      - fix velocity-potential calculation when using OBCS: balance net inflow
2691        at each level (new S/R OBCS_DIAG_BALANCE).
2692      - fix some of the problems with OBCS in stream-function calculation.
2693    o pkg/exf/exf_readparms.F
2694      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
2695        EXF_NML_OBCS) more consistent, so that you need not have these lists
2696        in data.exf when they are not used.
2697    o optim/optim_readdata.F:
2698      - add some output about obcs variables that might help debugging
2699      - add a check about nvarlength
2700    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
2701    o pkg/diagnostics (velocity potential):
2702      - fix mask for OBCS (still problems in stream-function with OBCS);
2703      - add specific parameter (default = main code CG2D params) for solver;
2704      - in case of poor convergence, use solution corresponding to lowest residual.
2705    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
2706      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
2707      and should be avoided where possible.
2708    o model/src (rStar):
2709      - include r* effect on reference-state (PhiRef) in totPhiHyd
2710        (so that it's really the potential anomaly at the cell center);
2711        affect solution only if z* with full pressure in EOS.
2712      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
2713        update output (because of z* in totPhiHyd and viscA4 changes);
2714      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
2715        @ constant r) until interpolation at constant r is implemented.
2716    o pkg/diagnostics
2717      - fix RCENTER diagnostics in case cell center is not at interface middle
2718    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
2719      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
2720      that THETA and SALT are "conservative temperature" and "absolute
2721      salinity"
2722    o pkg/ctrl
2723      - fix computation of endrec in s/r ctrl_init_rec
2724      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
2725    o pkg/seaice/seaice_growth.F
2726      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
2727        remove then obsolete STORE directives
2728      - fix STORE directives for tice and tices, so that only the
2729        appropriate part of the fields are stored (and not the entire
2730        field); update global_ocean.cs32x15.seaice AD output.
2731      - cosmetic changes: adjust CPP flags and indentation for better
2732        legibilty
2733    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
2734      Chris Wilson)
2735    o pkg/gmredi:
2736       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
2737       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
2738    
2739    checkpoint63  (2011/07/11)
2740    o pkg/exch2:
2741     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
2742     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
2743       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
2744       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
2745    o pkg/diagnostics:
2746     - deal with pairs of post-processed diags which are computed together; in
2747       particular, re-order list of diags within 1 file to save 2nd computation.
2748     - add S/R to compute velocity stream-function (called after velocity-potential
2749       calculation) from divergence free transport -> new diagnostics "PsiVEL".
2750     - add parameter to select grid-point location where PsiVEL == 0.
2751    o eesupp/src:
2752       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
2753       (specific S/R needed with exch2 topology - for now, just print an error msg)
2754    o pkg/shelfice
2755     - Implement friction velocity-dependent transfer coefficients following
2756       Holland and Jenkins, JPO, 1999
2757       Original code by M. Losch with small modifs.
2758       Enable with CPP option SHI_ALLOW_GAMMAFRICT
2759       and runtime flag SHELFICEuseGammaFrict
2760    o verification lab_sea & global_ocean.cs32x15:
2761     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
2762       does not miss some dependencies (but is slower) and also works with many files
2763       (default makedepend limitation for AD built).
2764     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
2765    o pkg/diagnostics:
2766     - add run-time parameter "useMissingValue" (def=False) to fill land-point
2767        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
2768       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
2769     - Extend the use of "missing_value" setting from data.diagnostics for the case
2770       of counter-diagnostics (where fraction-weight is zero). This applies both to
2771       MNC and MDS output files.
2772    o pkg/seaice/seaice_growth.F:
2773      - add 'a priori' cap of latent heat flux based on actual mass considerations
2774        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
2775        non-legacy seaice_solve4temp.
2776      - add diagnostic of the residual sublimation freshwater flux (the freshwater
2777        flux taken from the ocean if the total actual latent heat fluxes exceed
2778        the maximum)
2779      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
2780       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
2781      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
2782       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
2783      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
2784      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
2785    o verification 1D_ocean_ice_column:
2786       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
2787       update results
2788    o pkg/diagnostics:
2789     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
2790       which are not filled-up but computed from other diags ; In this case, the mate
2791       diag points to the primary (filled-up) diag to used for post processing.
2792     - Update Velocity-potential computation using post-processed diag framework.
2793     ==> Change the ordering of fields and time-periods in MDS output file
2794       when using periodic averaging: now writes one time record with the full set
2795       of fields for this time period, then the next time reccord (it used to be
2796       one field with the full set of time records then the next field).
2797         Note: this is now similar to NetCDF (MNC) output file. <==
2798    
2799    checkpoint62z (2011/06/21)
2800    o adjoint monitor:
2801     - Add adjoint monitor output for packages exf, seaice
2802       and update relevant testreport output
2803    o pkg/seaice:
2804     - re-order diags inits so that they appear in order in available_diagnostics.log
2805     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
2806       area/heff/hsnow preceeding thermodynamic growth/melt.
2807     - modified diag: SIdA; output actual effect, as the description states.
2808     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
2809     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
2810       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
2811        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
2812     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
2813     - added diagnostics for seaice generic tracers (SItr*).
2814     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
2815     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
2816     I. Fenty: 18-Jun-2011:
2817     Minor changes to seaice package:
2818     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
2819        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
2820       - Differentiated "regularization variables" from "floor variables"
2821        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
2822        * hiceMin became SEAICE_hice_reg (old hiceMin)
2823          (with _reg meaning regularization variable)
2824       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
2825        so as to ensure energy conservation when going between phases
2826      - A22 was not used anywhere
2827     2) Changed regularization procedure for heffActual and hsnowActual to ensure
2828        well-boundedness and smooth adjoint in seaice_growth.F
2829     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
2830        because the old regularization always set heffActual >= 0.05 cm
2831     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
2832        on AREA when HEFF > 0.
2833      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
2834        requiring that DISABLE_AREA_FLOOR *not* be defined
2835     Affected verifications:
2836      - 1D_ocean_ice_column (output.txt output_adm.txt)
2837      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
2838    o pkg/diagnostics:
2839      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
2840      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
2841        (was _RL, now integer) with option = 0 to retrieve all levels.
2842      - add pieces of code to compute velocity potential at each level (new diagnostics
2843        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
2844        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
2845      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
2846        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
2847        and in diagnostics_fract_fill.F (do not need a valid pointer for the
2848        diagnostics counter-mate); check that definition of counter-diagnostic
2849        includes a valid counter-mate (in diagnostics_set_levels.F).
2850    o model/src (rStar):
2851      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
2852        affect solution only if z* with full pressure in EOS;
2853        update output of test-exp global_ocean.90x40x15.
2854    o pkg/seaice:
2855      - introduce siEps=1e-5 parameter
2856      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
2857      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
2858      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
2859        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
2860        as well as ice cover age and ridging index (attached to AREA).
2861        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
2862        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
2863        Up to SItrMaxNum=3 tracers can be used simultaneously.
2864    o pkg/salt_plume:
2865      -introduce SPsalFRAC run time parameter that sets the fraction of the
2866       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
2867       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
2868    o model debug options:
2869      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
2870        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
2871      - Refine debug-msg printing selection (3 new levels):
2872        debugMode  : controls printing of debug messages (sequence of S/R calls).
2873        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
2874         debLevZero =  0 ; /* level of disabled aux. msg printing */
2875         debLevA =  1 ; /* level of minimum  aux. msg printing */
2876         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
2877         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
2878         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
2879         debLevE =  5 ; /* level of extensive debug printing */
2880        New debugLevel default: with default debugMode value (=F),
2881          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
2882          and if debugMode=T, default debugLevel = 4 (debLevD).
2883        Relation with previous settings:
2884         debLevB (=2) corresponds to former debLevA (=1)
2885         debLevD (=4) corresponds to former debLevB (=2)
2886        Note:
2887         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
2888         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
2889            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
2890      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
2891        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
2892    o pkg/obcs:
2893      - change OBCSfixTopo default from True to False (should not change the results);
2894        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
2895    o pkg/thsice:
2896      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
2897        2nd layer seaice sublimation (unlikely to happen)
2898      - use Interior mask for OBCS in thsice_advection.F (similar to what is
2899        done in gad_advection & seaice_advection).
2900    o adjoint:
2901      bug fix spotted by Gael Forget:
2902      seaice_advection and thsice_advection still had
2903      legacy CPP options to avoid CS corner updates for adjoint
2904    o pkg/seaice:
2905      => Change some of the defaults (2011/05/29):
2906         - change SEAICEuseFluxForm default (from False to True)
2907         - change DIFF1 default (from 0.004 m/s to 0. m/s)
2908         And print warnings if DIFF1 is not set in data.seaice and centered
2909          avection scheme is used without any diffusion.
2910      also:
2911      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
2912      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
2913      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
2914        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
2915        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
2916      update results of test exp.:
2917         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
2918             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
2919             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
2920         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
2921         seaice_obcs: output (SEAICEuseFluxForm=T)
2922      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
2923          for standard fwd & AD lab_sea tests (to keep the same output).
2924    o pkg/seaice/seaice_growth.F:
2925      - use Ian Fenty's capping formulas for actual ice
2926      thickness thoughout EVOLUTION branch.
2927      - put treatment pathological case #2) in CPP brackets
2928      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
2929      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
2930    o pkg/seaice:
2931      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
2932      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
2933      also pass fac as a param, which can be 1. (to update the tendency
2934      field) or the time step (to update the field itself).
2935      - seaice_advdiff.F: for multidim, call seaice_diffusion with
2936      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
2937      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
2938      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
2939      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
2940    o pkg/seaice:
2941      diffusion with centered advection scheme (diffus.F & advect.F):
2942      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
2943        to just compute the laplacian of input-field.
2944      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
2945      - fix flux-form version in diffus.F to conserve tracer.
2946      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
2947       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
2948    
2949    checkpoint62y (2011/05/26)
2950    o pkg/seaice:
2951     - seaice_growth.F : in EVOLUTION branch, always include
2952       a_QSWbyATM_cover in qnet (as it should be).
2953     - verification/global_ocean.cs32x15 : update results accordingly
2954       (output.seaice.txt output_adm.seaice.txt).
2955    o pkg/seaice + obcs:
2956     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
2957       equivalent of assuming no tracer gradient outside the OB region.
2958       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
2959     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
2960       after changes above);
2961     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
2962       only at OB location (instead of over a band of OLx width).
2963    o pkg/seaice:
2964     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
2965       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
2966    o pkg/obcs:
2967      - split header file "OBCS.h" into 4 separated files:
2968        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
2969       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
2970         (contain no conditional statement which depends on OBCS options).
2971      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
2972        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
2973    o ctrl, cost, grdchk & autodiff pkgs:
2974      - make options file more standard (like other {PKG}_OPTIONS.h file but
2975        with AD_CONFIG.h); clean-up some of the included header files.
2976    o pkg/obcs:
2977      - do not mask tracer when applying OB (tracer == 0 could generate problems)
2978      - apply tracer OB values to tracer field only at OB location (instead of
2979        over a band of OLx width)
2980      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
2981      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
2982        obcs_apply_tloc.F & obcs_apply_sloc.F
2983    o obcs in model/src:
2984      - call OBCS_APPLY_W only if NonHydrostatic.
2985      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
2986      - reset dEtaHdt and wVel to zero outside OB interior region ;
2987      - leave tracer unchanged outside OB interior region: This has no effect
2988        on the solution but just to prevent unrealistic tracer value outside OB.
2989      - zero out velocity outside OB interior region: This has no effect on
2990        the solution but just to prevent unrealistic velocity outside OB.
2991    o obcs and non-lin free-surf:
2992       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
2993       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
2994       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
2995       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
2996       update results of test-exp. exp4(nlfs).
2997    o exp4 (nlfs) test-exp:
2998       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
2999       with NonLin-FreeSurf); update output.nlfs.txt
3000    o obcs and 2d/3d solver norm:
3001       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
3002       and outside OB interior region (will allow to place OB further inside the
3003       domain). Depending on the domain, can affects cg2d-Norm (previous
3004       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
3005       and cg3d-Norm (previous Norm was computed before canceling OB terms),
3006       e.g. in tutorial_plume_on_slope.
3007      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
3008    o pkg rbcs:
3009      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
3010      - add capability to apply relaxation to horizontal velocity uVel & vVel.
3011    o pkg/grdchk: add gradient check for control variable xx_shifwflx
3012    o pkg/shelfice/shelfice_init_fixed.F
3013      fix CPP-flag combinations
3014    o pkg/seaice: Merge iceage code of Pierre Rampal
3015      * update/change/correct ice age calculations
3016      * add age updates for pathological cases
3017      Probably needs more testing...
3018    
3019    checkpoint62x (2011/05/13)
3020    o pkg/mom_vecinv:
3021       high-order vorticity scheme: use interior masks (maskInW & S)
3022       to zero-out (outside OB) gradient of vorticity.
3023    o verification exp.:
3024       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
3025       hs94.128x64x5 and seaice_obcs ; update results.
3026    o pkg/obcs:
3027      fix bug in OBeta for YZ sections in obcs_exf_load.F
3028    o pkg/ctrl, pkg/shelfice, and optim:
3029      - add new control variable xx_shifwflx (fresh water flux underneath ice
3030        shelves). This is almost as tedious as obcs-ctrl, because the
3031        variables needs its own mask.
3032      - add a cost function term that penalizes the deviation of xx_shifwflx
3033        from the first guess (zero) in analogy to other control variables
3034    o pkg/shelfice:
3035      - start basic adjoint
3036    o pkg/ctrl:
3037      - remove extra 2D field "for good measure" when initializing in
3038        ctrl_set_globfld_[xy/xz/yz].F
3039      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
3040      - improve error messages in ctrl_set_unpack_*
3041    o OBC implementation in momentum:
3042       use interior masks (maskInC,W & S) in momentum S/R:
3043       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
3044       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
3045       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
3046       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
3047       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
3048        (and also with Leith/Smagorinsky harmonic-viscosity).
3049       Update output of experiment dome and exp4 (+nlfs).
3050    o exp4 test-exp:
3051      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
3052        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
3053        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
3054        time-varying OB at Western-side for wVel (NonHyd); update output.
3055      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
3056        and biharmonic-viscosity ; also use prescribed time varying OB.
3057    o pkg/obcs:
3058      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
3059    o model/src:
3060      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
3061      - initialise startTime & nIter0 with unlikely values: allows to set one
3062        from the other without ambiguity.
3063    o seaice_obcs test-exp.:
3064      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
3065    o pkg/obcs:
3066      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
3067        no longer needed with maskInC,W,S in pkg/generic_advdiff.
3068    o pkg/seaice:
3069      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
3070        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
3071      - fixed bug in the initialization of sea ice salinity variable HSALT
3072        in seaice_init_varia.F  (removed dependence on ICE2WATR)
3073    o fizhi-cs test exp.:
3074       switch reference output convention for these 2 non-standard test-exp,
3075        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
3076          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
3077       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
3078    o model/inc:
3079      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
3080        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
3081    o pkg/seaice:
3082      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
3083    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
3084      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
3085        and initial HSALT
3086    
3087    checkpoint62w (2011/04/26)
3088    o pkg/mom_fluxform:
3089      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
3090      - use parameter "sideDragFactor" in no-slip BC side-drag part.
3091      - update output of exp. global_ocean.90x40x15
3092    o pkg/mom_vecinv:
3093      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
3094    o update seaice exp.:
3095      use more consistent parameter values (remove "backward compatability only":
3096       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
3097      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
3098       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
3099    o update test-exp global_ocean.90x40x15:
3100      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
3101      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
3102      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
3103      o turn on zStar & viscA4 in standard set-up (dir input/)
3104        and update output files: output.txt & output.dwnslp.txt
3105    o new AD-test experiment: obcs_ctrl
3106      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
3107    o pkg/dic:
3108      fix two bugs in handling water vapour pressure in carbonate chemistry
3109      and air-sea fluxes. Found by Val Bennington and Galen McKinley
3110      (add DIC Option = WATERVAP_BUG to recover old results)
3111      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
3112    o adding allowInteriorFreezing option to check for water below freezing point
3113      at depth and bring the negative heat anomaly to the surface level
3114    o pkgs _fields_load:
3115      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
3116      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
3117        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
3118        rbcs to get interpolation weights and time reccord number.
3119      - fix multi-threading in aim_fields_load.F
3120      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
3121    o external_fields_load:
3122      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
3123       interpolation weights) to use in a periodic time-series ; do not divide by
3124       time-step to convert to integer:
3125       - this fixes case where externForcingPeriod is not multiple of time-step
3126          (Thanks to Christopher L. Wolfe)
3127       - this fixes case where externForcingPeriod is an odd multiple of time-step
3128         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
3129      store index of time-record which is currently loaded:
3130       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
3131       - needed for the adjoint but not yet used because of extensive recomputations;
3132         (to be fixed soon)
3133    
3134    checkpoint62v (2011/04/02)
3135    o verification/1D_ocean_ice_column added to test Ian Fenty's
3136      pkg/seaice_growth.F modifications for improving sea ice code differentiability
3137    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
3138      (new velocity statistics after changing maskInW & maskInS definition)
3139    o pkg/generic_advdiff with OBCS:
3140      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
3141      equivalent to assumption of no tracer gradient outside the OB region.
3142      This will affect the results if using obcs+biharmonic diffusion.
3143      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
3144    o pkg/obcs:
3145      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
3146      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
3147      in Interior region. No impact on solution but affects Velocity monitor stats.
3148    o pkg/ptracers (adjoint)
3149      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
3150      tape file for each tracer
3151    o model/inc/src and pkg/autodiff: add parameters that allow to turn
3152      of parts of the adjoint code at run time. For now, there are only
3153      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
3154      parameters are set in data.pkg.
3155      This is the lazy coward's version of doing this, but still useful for
3156      debugging. In order to do it right, everything needs to be moved to
3157      pkg/autodiff.
3158    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
3159      the end; this fixes the adjoint balancing code for open boundaries.
3160    o pkg/ctrl:
3161      - change behavior of xx_${varname}period to be analogous to exf-conventions:
3162        xx_${varname}period =   0.,  means time-independent control part
3163        xx_${varname}period = -12., means one-year-periodic monthly control part
3164      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
3165        clean up ctrl_init a little, remove unused variables
3166      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
3167      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
3168    
3169    checkpoint62u (2011/03/15)
3170    o model/src:
3171      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
3172        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
3173      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
3174        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
3175    o pkg/ctrl/obcs/ecco:
3176      - remove obsolete, unused, and partially broken code:
3177        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
3178        ALLOW_CTRL_OBCS_BALANCE
3179      - put a stop statement into ecco/cost_obcsvol.F, but also add
3180        cost_obcsvol to ecco_ad_diff.list
3181    o pkg/ecco: fix counting cost function contributions for obcs (code
3182      by Matt M.) and diffkr for diagnostics
3183    o pkg/ecco, pkg/ctrl, pkg/grdchk:
3184      add cost penalty terms for initial uvel, vvel, eta controls
3185      and I/O for prior error files
3186    o pkg/mdsio:
3187       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
3188       (new argument) to check for tiled file in mdsioLocalDir : this fix the
3189       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
3190    o pkg/ctrl:
3191     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
3192       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
3193       unused and superfluous variables
3194     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
3195    o pkg/ecco
3196     - enable adjoint of Stevens OB
3197    o pkg/ctrl/ecco/grdchk:
3198      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
3199        Fortunately, we do not have any tests for the numerous cpp-flagged
3200        option of "obcs as control parameters" so we will never know
3201        if this is an improvement (but at least now things compile).
3202      - remove an obsolete initialization from ecco_cost_init_barfiles.F
3203      - fix some problems within never used ifdefs to make the code compile
3204    o pkg/obcs:
3205     - Refine Interior mask definition to work with more complex OB (e.g.
3206       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
3207       read in Interior mask from file. Check if Interior mask is consistent
3208       with OB list of indices.
3209    o pkg/seaice
3210     - beginning code for a seaice tracer package,
3211       but currently only used for seaice age: SEAICE_AGE
3212       SEAICE_num = 4
3213       iTracer = 1: area-weighted ice age
3214               = 2: volume-weighted ice age
3215               = 3, 4: template for one-year vs. multi-year ice
3216       data.seaice has new namelist SEAICE_PARM03 for arrays related to
3217       SEAICE_num
3218    
3219    checkpoint62t (2011/03/05)
3220    o pkg/obcs:
3221     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
3222       then normal component. This ensures that the normal component is set
3223       correctly even when it conficts with tangential setting from an other OB.
3224       Affects results of test-experiment seaice_obcs: update the output.txt
3225    o pkg/obcs:
3226     - add code to monitor statistics of dynamical fields at OB.
3227     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
3228       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
3229       - change default: balance the Net inflow through all OB (instead of balancing
3230         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
3231     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
3232       to match Nortern OB inflow (OBCS_balanceFacN=0).
3233    o pkg/seaice:
3234     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
3235    o pkg/seaice (seaice_growth v 1.113):
3236     - reverting seaice_growth to v 1.111 in order to have code with exact bit
3237       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
3238       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
3239       runtime flag SEAICEareaFormula is kept but is inactive
3240    o model/src:
3241     - add new param to scale curvilinear grid distance and area when using
3242       a different sphere radius from the grid-files.
3243     - test/check multi-threads EXCH applied to local variable (cg2d_x)
3244    o adjoint:
3245     - enable adjoint of Stevens OB
3246     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
3247       (a bit delicate because of potentially modified adj. common block structure;
3248       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
3249    
3250    checkpoint62s (2011/02/15)
3251    o pkg/seaice (seaice_growth v 1.112):
3252     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
3253       computing the ice cover tendency from effective thickness tendencies. Include
3254       Ian Fenty's formula.
3255     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
3256       SEAICEareaFormula.
3257     - simplify notations for the various d_HEFF/d_AREA terms.
3258    o pkg/gmredi:
3259     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
3260       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
3261       add a verification test-run (front_relax.bvp) to test GM_useBVP.
3262    o pkg/seaice (seaice_growth v 1.111):
3263     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
3264     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
3265       also melt ice.
3266    o pkg/seaice:
3267     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
3268     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
3269    o pkg/cheapaml:
3270     - from Nico Wienders: New version of this package.
3271    o pkg/flt:
3272     - add CPP options to prevent floats to re-enter the opposite side of
3273       a periodic domain (default: keep periodicity)
3274    o pkg/gmredi:
3275     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
3276       (needed for multi-dim advection).
3277     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
3278    o model/src:
3279     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
3280    o tutorial_tracer_adjsens
3281     - extend to NLFS and replace maskC by hFacC
3282       (change reference output accordingly)
3283    
3284    checkpoint62r (2011/01/24)
3285    o testreport:
3286     - add option -deloutp (-do) to remove output file after successful run
3287     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
3288       extract exact list of procs from this file ; adjust COMMAND by
3289       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
3290    o pkg/ecco: replace old ineffective way of penalizing deviations from
3291      first guess (of obcs) with code by Matt Mazloff
3292    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
3293      exf/cal
3294      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
3295        and handle case of obcs?period == 0
3296        Not affected by these changes: There is still an inconsistency in
3297        the computation of start/endrec for the obcs variables for ALLOW_CAL
3298        defined (see comment by Menemenlis, 7-Mar-2003)
3299      - make S/R ctrl_get_gen_rec return something meaningful even if
3300        ALLOW_CAL is not defined
3301      - ctrl_getobcs?: simplify code so that it does not need to use
3302                       S/R exf_swapfields
3303    o testreport:
3304       allow to test MPI with different number of processors for each experiment:
3305       create file "SIZE.h.mpi" in each build dir.
3306       Note: update of "-command" argument not yet implemented.
3307    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
3308      alleviate the need for additional 3D tapes when using
3309      the non-inear free surface in the adjoint. This is done
3310      by adding an 'update' of hfacc etc. to their current
3311      value at the beginning of forward_step.F.
3312    o pkg/seaice
3313      seaice_lsr: move stress-divergence computations out of outer pseudo-
3314      timestepping loop
3315    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
3316      up, so that the calls of the ctrl_* subroutines are really at the end
3317      of the routine.
3318    o pkg/gmredi:
3319      allow to specify a 2-D horizontal map and a 1-D vertical profil
3320      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
3321    o pkg/seaice:
3322      move lsr iterations from seaice_dynsolver to seaice_lsr.
3323    o pkg/seaice:
3324      reduce memory footprint of seaice mutldim advection tapes,
3325      by using a 2D tape independent of the generic_advdiff ones,
3326      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
3327    
3328    checkpoint62q (2010/12/29)
3329    o model/src:
3330      - check horizontal grid-spacing for unset or zero/negative values.
3331      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
3332    o pkg/flt:
3333      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
3334      - precision of input and output files set according to readBinaryPrec
3335        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
3336      - initial float position from tiled file was not converted to index space
3337        (looks like a bug): fixed to make it similar to initial pos. global file.
3338    o global_ocean.cs32x15:
3339       change SIZE.h of AD set-up to get same tiling as with MPI.
3340       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
3341    o model/src:
3342       add flag to control printing of domain fields (bathymetry, hFac ...) in
3343       ini_mask_etc (call to plot_fieds_xy*).
3344    o pkg/thsice:
3345       if useEXF, some forcing fields are not valid in overlap: fixed by computing
3346       over the interior only + apply EXCH at the end (like with SEAICE advection).
3347    o pkg/mdsio:
3348      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
3349        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
3350      - change barrier call for safe multi-threads access to 3-D shared buffer.
3351      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
3352      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
3353        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
3354    o pkg/flt:
3355      - add fourth-order Runge-Kutta integration
3356      - add basic exch2 support (only 1 facet supported so far!)
3357    o pkg/mdsio+rw:
3358      new S/R to read local (or tile independent) vector (read counterpart of
3359       mds_writevec_loc, and front-end write_glvec_rl/rs).
3360    o global_ocean.cs32x15: additional input_ad.seaice experiment
3361        that uses pkg/seaice rather than pkg/thsice.
3362        (using multidim advection for seaice)
3363    o towards more F95 syntax for array specification in namelist:
3364      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
3365        of all verification experiments.
3366           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
3367          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
3368      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
3369    o global_ocean.cs32x15: additional input.seaice experiment
3370        that uses pkg/seaice rather than pkg/thsice.
3371    
3372    checkpoint62p (2010/12/17)
3373    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
3374        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
3375    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
3376        allow for use of multim. advection in seaice adjoint.
3377    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
3378      - first attempt to close budgets by taking into account the freshwater
3379        flux implied by the sublimation of snow and ice. So far only the
3380        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
3381        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
3382    o eesupp/src:
3383      new S/R with new option (NML_EXTENDED_F77) to change array specification
3384      from F95 standard to commonly accepted extended F77 form.
3385      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
3386      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
3387      for less tolerant f77 compiler (e.g., pgf77, g77).
3388    o globalFiles:
3389      commented out in parameter file "data" since it's not safe with MPI
3390      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
3391      in this case); no longer commented out in restart test (tst_2+2).
3392    o add adTapeDir to specify a special directory where adjoint tapes are
3393      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
3394      and cannot be used together with mdsioLocalDir.
3395    o nesting pkgs:
3396      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
3397      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3398      - add parameter files + utils dir + output from short run on beagle.
3399    o pkg/seaice:
3400        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
3401    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
3402      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
3403    
3404    checkpoint62o (2010/11/25)
3405    o pkg/exf:
3406      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
3407    o pkg/seaice:
3408      - seaice_ocean_stress: split a loop for better vectorization of the
3409        adjoint code
3410      - seaice_growth.F: fix bug in conservation of freshwater connected to
3411        capping of heff, put contribution into d_HEFFbyNEG
3412      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
3413        by something more sensible (parameters that are what their name implies)
3414      - change some defaults, so that by default exf-parameters are used for
3415        things like rhoAir, cpAir,latent/sensible heat parameters, in order
3416        to reproduce the old results, many data.seaice now contain funny values
3417        for cpAir and latent heat of sublimation
3418    o packages_readparms.F: move exf_readparms up in line so that
3419        exf-parameters are visible for other packages (e.g. seaice)
3420    o debugMode & debugLevel=2:
3421      - differentiate between debugMode & debugLevel=2:
3422        debugMode: controls printing of debug messages (sequence of S/R calls).
3423        debugLevel: controls printing of algorithm intermediate results and stats.
3424      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
3425        => allows to print debug-stats without all sequence of call messages.
3426      - switch control of debug print from debugLevel to debugMode in many S/R.
3427    o pkg/obcs (obcs-sponge):
3428        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
3429        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
3430    o pkg/generic_advdiff:
3431      - record overlap minimum size for each advection scheme;
3432      - refine criteria on overlap minimum size;
3433      - check and stop (in gad_check) if overlap size is too small.
3434    o pkg/obcs:
3435      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
3436        once, in ptracers_implicit.F)
3437      - with seaice: remove test on empty file name in obcs_apply_seaice (always
3438        apply OB values when tile has OB)
3439    o model/src, coriolis setting:
3440      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
3441        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
3442        files (selectCoriMap=3) with any grid.
3443      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
3444    o pkg/seaice/seaice_growth.F:
3445        a few cosmetic changes that reduce the number of lines of code
3446    o pkg/obcs: add boundary conditions following Stevens (1990)
3447      - the code follows old MOM/NAOSIM code
3448      - so far it is only implemented for the eastern and western boundaries
3449        and NOT for pTracers
3450    o pkg/rbcs:
3451      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
3452        beginning of the first rbcs forcing period.
3453      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
3454        offline package, i.e., one file per time, labeled by iteration number;
3455        deltaTrbcs sets the timestep with which the data was generated;
3456        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
3457      - rbcsForcingCycle=0 makes forcing non-cyclic.
3458      - make arithmetic safe for negative times and odd forcing periods.
3459    
3460    checkpoint62n (2010/11/09)
3461    o pkg/seaice:
3462        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
3463    o pkg/obcs:
3464       New S/R to copy tracer value from the OB location to narrow band region
3465        (width = same as overlap) beyond the OB: preserve OB value (needed for
3466        high-order scheme) which were overwritten by EXCH call if in overlap
3467        region. Applied to theta, salt, ptracer and advected seaice variables.
3468       With seaice: use maskInC in similar way as in gad_advection.F,
3469        in seaice_advection.F and advect.F.
3470       Update output of experiment seaice_obcs and change exp4 to test OBCS with
3471        4th order Adv.Scheme. for pasive salt and ptracer.
3472    o tools/genmake2:
3473      - when looking for an optfile (not specified), only search for Fortran compiler
3474        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
3475      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
3476        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
3477      - set default for CPP to "cpp -traditional -P" (was the case without specifying
3478        an optfile, but otherwise default was just "cpp".
3479      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
3480      - when "CC" is not set in the optfile, look for possible C compiler
3481        (instead of just setting CC=cc)
3482      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
3483        => add a ".F" to ".o" rule for source files with no "#include" (such as
3484           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
3485      - move gfortran before g77 in list of possible Fortran compiler (consistent
3486        with reference compiler switch from g77 to gfortran)
3487    o pkg/seaice:
3488      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
3489        seaice_check that stops the model, when the CPP flag is used.
3490      o seaice_growth.F: make capping of ice volume conserving by returning the
3491        capped ice as freshwater to EmPmR. This does not change the verification
3492        experiments but will change runs where the capping is acutally active
3493    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
3494      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
3495         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
3496         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
3497    o tools/genmake2:
3498      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
3499      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
3500      - clean previous genmake log files before anything else.
3501      - change Makefile to remove testreport log files (*.tr_log) and genmake log
3502        files only with "CLEAN" target (instead of "Clean");
3503    o pkg/generic_advdiff:
3504      Change OBCS in multiDim advection (gad_advection.F):
3505       Use maskInC to prevent intermediate update of tracer-field in OB regions,
3506       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
3507       which were applying future time-step OB values.
3508      This way, all explicit calculations use current-time-step OB values
3509       (simpler and more consistent).
3510      Affects results when set-up uses time-varying OBC and multi-dim advection;
3511       update output of experiment seaice_obcs.
3512    o pkg/seaice:
3513      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
3514       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
3515         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
3516      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
3517       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
3518       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
3519    o pkg aim (2010/10/26):
3520      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
3521        formulation with obliquity, eccentricity, ... as run-time parameters,
3522      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
3523        upward shortwave radition at the surface (all-sky and clear-sky).
3524    o pkg/obcs:
3525      - writing sections with globalFiles=T does not work: switch to tiled-files
3526        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
3527      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
3528      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
3529    
3530    checkpoint62m (2010/10/21)
3531    o pkg/seaice: vectorize seaice_solve4temp.F
3532      - move iterations loops outside of i/j-loops
3533      - requires 2D arrays for TB and effConduct
3534      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
3535        modified in this routine
3536      - a little bit of clean up, adjusting indentation, etc.
3537      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
3538        performance and '**TWO' by '**2' (because TWO is a float),
3539        replaced ONE, ZERO
3540    o eesupp/src:
3541       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
3542    o pkg/seaice/seaice_growth.F
3543      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
3544      merging process. The merged routine has two branches, and one activates the 'evolution'
3545      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
3546      In summary, here is what the '10/10 revision' did consist of
3547        part 1: seaice_growth.F revisions 1.71 to 1.75
3548          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
3549            The emphasis here was on improving readability (e.g. by trying to use meaningful
3550            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
3551        part 1.5:
3552          - revising the lab_sea experiment to make it a more useful (i.e. stable
3553            and representative of an actual model run). This was done by generating a
3554            (winter) pickup to start from, switching back the main experiment dynamic
3555            solver from evp to lsr, having one of the experiments use the free drift solution.
3556        part 2: seaice_growth.F revisions 1.76 to 1.85
3557          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
3558          - Sorting out the various fields units and sign (set early on and reset at the end)
3559            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
3560            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
3561          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
3562            and simplifying logical expressions to further improve readibility.
3563        part 3: seaice_growth.F revisions 1.86 to 1.89
3564          - Re-organize the blocks of code more logically.
3565          - Merging the '_if.F' pieces that add something new.
3566    o pkg/thsice:
3567      - vectorize thsice_solve4temp and thsice_get_exf.
3568        Problem: thsice_solve4temp has an unvectorizable statement that
3569        might also be problematic for TAF
3570      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
3571        does not change the verifcation experiment, but will change all
3572        experiments that have this flag undefined (not tested in verification);
3573        a little reorganization to save a few 2D fields and recomputations
3574      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
3575      - 2nd step:  fix some store dirs
3576        o seems to work somewhat, i.e. using ifort but not g77
3577        o likely cause are incomplete init. or recomputation
3578        o start verification/global_ocean.cs32x15/input_ad.thsice
3579    o pkg/obcs: add support for exch2
3580      - the position of the boundary and prescribed values are specified using
3581        a global domain with exch2 facets stacked
3582        - in x for N,S boundaries (like W2_mapIO=-1)
3583        - in y for E,W boundaries (so E,W boundaries do not overlap)
3584    o pkg/mdsio: add support for writing global sections with exch2
3585        file layout is as for obcs described above:
3586        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
3587        - for y-z sections, facets are stacked in y
3588    o pkg/thsice:
3589       - change a few routines for better vectorization: thsice_albedo.F,
3590         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
3591         not affected, but in particular the latter routine has changed
3592         dramatically (not necessarily easier to read now).
3593       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
3594       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
3595    o verification/lab_sea:
3596      - overhaul of the forward model experiments. The main motivation
3597        for this revision is that lab_sea has proven quite fragile (when
3598        changing the sea-ice code, and switching platforms) to a point
3599        when failures were very hard to attribute to specific code problems.
3600      - the suspected reason for this fragility is noise amplification by evp so,
3601        to start with, we decided to replace evp with lsr in the main experiment.
3602      - the input.lsr experiment thus became obsolete and was removed.
3603      - it was replaced with the input.fd experiment that uses an
3604        analytical "free drift" solution as the ice velocity field.
3605      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
3606        will hopefully allow us to discriminate problems due to dynamic solvers
3607        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
3608        us to test additional options, along with the salt plume package.
3609      - Finally a pickup was generated (at the end of a one year run) to
3610        make the tests more representative of an actual model run. Previously
3611        the tests starting point was a 1m thickness of ice everywhere.
3612    o pkg/seaice:
3613      - introducing S\R seaice_freedrift.F that compute the
3614        analytical solution to an approximate ice momentum
3615        equation (i.e. the simple stress/coriolis balance).
3616      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
3617        of the free drift velocity field, and enable its use.
3618        To actually use the free drift solution as the model ice
3619        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
3620    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
3621    
3622    checkpoint62l (2010/10/04)
3623    o pkg/seaice:
3624      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
3625      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
3626       version (with USE_ORIGINAL_SBI undef);
3627    o add hooks for new packages OASIS, the package will follow
3628      (hooks exclude the seaice pkg for now)
3629    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
3630      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
3631      rather than mdsio_readvector.F/mdsio_writevector.F, within
3632      adread_adwrite.F to read/write adjoint-related tapes to disk.
3633    o eesupp and pkg/mdsio: ALLOW_WHIO
3634      Option to write/read 2D fields to files including tiles halos.
3635      The main purpose is for adjoint related "tape I/O".
3636      The secondary purpose is for debugging phases.
3637      A word on those rather specifically intended purposes.
3638      The code was meant to be stripped down to the bare minimum.
3639      Typically, there is a unique and basic mapping to the global
3640      buffer (tile by tile, then proc by proc, then level by level), and
3641      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
3642      meant to generate user friendly outputs of various shapes and forms.
3643      Rather it is intended, for the knowledgeabale developers,
3644      to be largely independent of the many mdsio options, to allow
3645      outputs of tiles+halos in debugging phases and in adjoint runs,
3646      and to allow some flexibility in tuning (adoint) I/O depending on each
3647      file system behavior. With regard to tuning, most of the potential knobs
3648      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
3649      to specify directories, to specify the typical size of I/O calls, etc.)
3650      are not yet included, and will be added if they prove useful.
3651    o pkg/seaice:
3652       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
3653    o pkg/seaice:
3654       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
3655       code (seaice_budget_ice_if.F) which enable to recover old standard
3656       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
3657       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
3658    o model/src (rStar):
3659       use simple average (not area weighted) of rStarFac at U,V point when using
3660       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
3661       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
3662    
3663    checkpoint62k (2010/09/17)
3664    o adjoint
3665       * changed verification/global_ocean.cs32x15 ; adjoint now tests
3666         Adams-Bashforth 3 + NLFS + RSTAR
3667       * some more modifs required for ECCO-GODAE v4
3668    o pkg/seaice
3669       add SEAICE_AGE_VOL option to use volume instead of area for
3670       integrating SEAICE_AGE
3671    o model/src:
3672       first check-in of sigma & hybrid-sigma coordinate code ; also includes
3673       non-linear free-surface parts ; but pressure-gradient not yet coded.
3674    o pkg/ptracers:
3675       option for ptracer to convert Salt Relax into additional EmP.
3676        tested in exp. global_ocean.90x40x15.dwnslp (update output)
3677    
3678    checkpoint62j (2010/08/25)
3679    o pkg/ggl90:
3680       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
3681    o pkg/dic: car_flux.F, phos_flux.F
3682      - reduce number of exp-calls in order to improve performance
3683      - clean up a little (replace fields by their macros, etc., fix
3684        typo in CPP-flag)
3685    o pkg/ggl90: minor changes
3686      - GGL90diffKrS was removed --> always use GGL90diffKr
3687      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
3688      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
3689        (commented out for now)
3690      - change in max/min operations to ensure that smoothing is ok
3691      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
3692      - always use diffKrNrT as background profile (i.e. never use diffKr field)
3693    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
3694    o pkg/dic:
3695      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
3696        vectorization
3697      - small bug fix in insol for the unlikely case of a cartesian grid
3698      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
3699        + now vectorize, which also removes adjoint recomputations;
3700        + replace integer maksp1 by _RL maskp1
3701        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
3702    
3703    checkpoint62i (2010/07/21)
3704    o pkg/flt:
3705      - with OBCS: stop floats which enter the OB region
3706    o model/src:
3707      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
3708        for implicit vertical advection.
3709    o pkg/seaice:
3710     - account for melting in seaice age evolution.
3711     - remove double counting of seaice ridging effect on seaice age.
3712    
3713    checkpoint62h (2010/06/18)
3714    o pkg/exch2:
3715     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
3716    o tools/genmake2
3717      - remove "-pdefault" option: redundant with the use of "packages.conf";
3718      - remove file pkg/pkg_default : set the default as a pkg group
3719        ("default_pkg_list") defined in pkg/pkg_groups;
3720      - fix for case pkg/pkg_depend is missing (was hanging before);
3721      - add option "-pgroups" to specify a different pkg_groups than the default.
3722    o verification/adjustment.cs-32x32x1:
3723       add a "minimal" set-up test (code_min & input_min) which only compiles
3724       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
3725    o tools/genmake2
3726      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
3727      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
3728    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
3729      files are nearly the same anyway.
3730      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
3731       - redefinition of tau(i,i) (by a factor of ustar)
3732       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
3733       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
3734       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
3735       - replace
3736         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
3737         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
3738         by
3739         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
3740         (changes results)
3741       -> exf_bulkformulae v1.22,
3742          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
3743          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
3744                    output.txt 1.63
3745           offline_exf_seaice: output.seaicetd.txt 1.7
3746           seaice_obcs: output.txt 1.10)
3747      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
3748       -> exf_bulkformulae v1.23,
3749          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
3750          and global_ocean.cs32x15.icedyn (only 11 matching digits)
3751      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
3752    o adjoint of exch-1:
3753     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
3754       (note: was already like this when using EXCH-2) and remove flow dir
3755       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
3756     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
3757     - update pkg/exch2 diff list.
3758    
3759    checkpoint62g (2010/05/19)
3760    o eesupp/src (exch-1):
3761     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
3762       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
3763       (renamed to exch1_*rx_cube.F).
3764     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
3765       to call new exch1 S/R ; update Makefile and .cvsignore.
3766     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
3767       exch2_xy_rx later)
3768      Note: after updating your code, need to run "make clean" in eesupp/src
3769    o test experiment bottom_ctrl_5x5:
3770       new output_adm.txt with fewer grdchk & less monitor output.
3771    o model/src:
3772      remove the call to ini_cori in initialise_varia.F (just keep the usual one
3773       in initialise_fixed.F). More consistent with coriolis & horizontal grid
3774       beeing treated in the same way (ini_grid is not called a 2nd time).
3775    o pkg/exf:
3776      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
3777      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
3778      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
3779      - cosmetic changes to exf_bulkformulae.F to make it look more like
3780        exf_bulk_largeyeager04.F
3781    o eesupp/src (exch-1):
3782      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
3783      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
3784        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
3785        (even without using MPI).
3786      - Message mode: move RecvAck setting (indicator of buffer being ready)
3787        from send_put to recv_get S/R (was useless before, but not sure if
3788        it's much more useful now);
3789      - Switch the order of sync: MPI-proc 1rst and then threads;
3790      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
3791      - fix AD code for communication mode ='get' (but not used).
3792    o model/src:
3793      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
3794      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
3795    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
3796    o pkg/ctrl: require a specific set of control variables and exf-flags for
3797      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
3798    o model/src:
3799     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
3800       1rst forward sweep, to avoid over-writing output files during recomputations
3801       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
3802     b) 2nd version:
3803      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
3804      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
3805         writePickupAtEnd) + seaice & ptracers output;
3806      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
3807    o model/src:
3808      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
3809    o pkg/exch2:
3810      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
3811      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
3812    o pkg/autodiff & exch2:
3813      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
3814      (for now, only if ALLOW_EXCH2 is defined).
3815    o pkg/autodiff:
3816      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
3817        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
3818       + clean-up comments (_RS is not always real*4)
3819      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
3820      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
3821        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
3822    o testreport (AD-tests):
3823      no longer link files from dir "../input" (1rst link files from
3824      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
3825    
3826    checkpoint62f (2010/04/29)
3827    o model/src/the_main_loop.F:
3828      adjust store directives for seaice evp and multicategory according to
3829      pkg/ecco/the_main_loop.F
3830    o adjoint:
3831      global_sum_ad was incomplete (noted many times by many people ;)
3832      nice description by Jean U. as follows:
3833      * allreduce(var) in global_sum.F can be interpreted as
3834        reduce(sum) followed by broadcast of sum.
3835      * The adjoint of that is
3836        sum(adjoint) followed by broadcast(summed adjoint value)
3837        or in other words, allreduce(sum, adjoint vars)
3838      We were missing the sum(adjoint)!
3839      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
3840      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
3841      The fix should produce 16-digit accuracy between
3842      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
3843      multi-CPU single-tile (e.g. nSx=1, nPx-2)
3844      We'll probably change this yet again shortly
3845    o eesupp/src:
3846      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
3847    o pkg/icefront
3848      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
3849        specification of addmass array based on a 2D field, which is added
3850        at bottommost wet level at each horizontal location.
3851    o model/src:
3852     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
3853     layout; (not always compatible with delX,delY setting; commented out for now).
3854    o pkg/exch2:
3855     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
3856     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
3857    
3858    checkpoint62e (2010/04/15)
3859    o pkg/obcs:
3860      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
3861    o pkg/dic:
3862      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
3863        (note: not presently tested in any forward verification exp.)
3864       update tutorial_global_oce_biogeo AD output file.
3865    o pkg/exf:
3866      - account for the variation of albedo as a function of zenith angle
3867        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
3868    o build_options:
3869     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
3870    o pkg/dic:
3871      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
3872      - use binary pickup file for restart;
3873      - initialise atmos-CO2 box from dic_pCO2 parameter;
3874      - fix multi-threaded.
3875    o pkg/rbcs:
3876     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
3877       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
3878     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
3879       and update output.txt
3880    o pkg/kpp:
3881     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
3882     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
3883       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
3884       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
3885     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
3886       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
3887    o pkg/offline:
3888      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
3889      (bug was added in version 1.10 on 2007-08-23).
3890    o pkg/offline:
3891      - no need to specify periodicExternalForcing, etc ... to use offline pack
3892      - offline input files no longer just single prec --> parameter offlineLoadPrec
3893    o verification/lab_sea:
3894      change AD test to multi-tile setup and update all 4 AD output.
3895      NOTE: while cost function values remain very similar,
3896      gradients are very different, although gradient checks are self-consistent
3897      Should try to get to the bottom of this (cost function summation order?)
3898    o pkg/dic:
3899      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
3900      a weakness of TAF that drops part of double precision in log10 derivative.
3901      <= changes removed since problem has been fixed in current TAF version 1.9.71
3902      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
3903    o pkg/ecco:
3904      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
3905      update all 4 lab_sea AD output.
3906    
3907    checkpoint62d (2010/03/22)
3908    o build_options:
3909      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
3910    o remove unbalanced quote (single or double) in commented line of source code
3911      (may cause some warning with some preprocessor/makedepend versions).
3912    o pkg/seaice:
3913      fix seaice_model.F for adjoint (gael) and update AD results of experiments
3914       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3915    o testreport:
3916      add option '-runonly' (short: '-ro') to just do the run part (without make).
3917    o eesupp: remove JAM communication code (obsolete).
3918  o add option to genmake2 & testreport to switch "_RS" type to "real*4"  o add option to genmake2 & testreport to switch "_RS" type to "real*4"
3919    (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return    (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
3920    to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1    to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
# Line 26  o tools/build_options: Line 3937  o tools/build_options:
3937      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
3938  o pkg/ecco  o pkg/ecco
3939    - allow user defined cost function contributions    - allow user defined cost function contributions
3940          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
3941          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
3942    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
3943        the two options are complementary.        the two options are complementary.
3944  o pkg/smooth  o pkg/smooth

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