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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1955 by mlosch, Mon Jan 6 14:55:07 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/exf/exf_check.F
8     - fix a small bug again (originally found by Wentao Liu, now found again)
9     - streamline error output
10    o pkg/streamice and aim_v23:
11      replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
12      Apple's /usr/bin/cpp knows what to do:
13      Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
14      Target: x86_64-apple-darwin13.0.0
15    
16    checkpoint64s (2014/01/05)
17    o tools/adjoint_options:
18      - switch to fastopt.net TAF server (instead of default fastopt.de) for
19        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
20    o model/src:
21      - remove some unnecessary TAF storage directives in forward_step.F and
22        in dynamics.F (note: not always removed by TAF, e.g., double storage
23        of kappaRU,kappaRV in former version of dynamics.F).
24    o model/src & pkg/ptracers:
25      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
26        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
27        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
28      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
29      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
30      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
31    o useSingleCpuInput separates single-CPU input from single-CPU output;
32        for now only implemented for in exf_interp_read.F
33    o verification/advect_xy:
34      - fix missing EXCH call in local version of ini_salt.F and update output.
35    o momentum diagnostics:
36      - fix which deltaT is used in Total-Tendency diagnostics.
37      - fix typo in diagnostics for momentum tendency from AB.
38    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
39        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
40    
41    checkpoint64r (2013/12/08)
42    o verification/*/results:
43      - Update reference output of experiments that were passing with just 13 digits
44         (make it easier to detect future changes in results)
45    o model/src & pkg/ptracers:
46      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
47        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
48        to inside ptracers_integrate.F ; remove ptracers_advection.F
49    o coupling interface pkgs:
50        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
51      - change the config check to test the agreement of Ocean Depth
52        with ATM land/sea mask (instead of ATM orography);
53      - send to coupler the number of coupler time-steps to do for this run:
54        this allows to check for consistency and don't need anymore to be
55        specified in parameter file "data";
56      in coupler:
57      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
58      - improve report to log-file of config setting (pass log-file unit to few S/R)
59    o pkg/compon_communic:
60      - add coupling send/receive for non-tiled integer vector;
61      - add S/R to check and stop if any proc has an error (similar to
62        eesupp/src/stop_if_error.F but single thread and across Comm_World).
63    o pkg/exch2:
64      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
65        through list of all tiles my proc owns.
66    o model/src:
67      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
68        from rTrans) to simplify dependencies (no need to store rTrans anymore in
69        calling S/R); this affects AD results at machine truncation level:
70        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
71        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
72    o tools/build_options:
73      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
74    o coupling interface pkgs:
75        [compon_communic, atm_compon_interf & ocn_compon_interf]
76      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
77        to each S/R that needs it; remove un-used variables.
78      - change component tile registration (cpl_register.F in both compon_interf
79        and mitcomponent_tile_register.F) to pass the full list of tiles
80        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
81      - with pkg/exch2: adopt the same convention used for I/O to define mapping
82        towards coupler global array (unless W2_useE2ioLayOut=F):
83         a) can now use different tiling between atm & ocn comp.
84         b) no needs to modify the run-Off map when changing tiling (was needed
85            even if using the same tiling between atm & ocn).
86         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
87            full land tiles); not yet tested.
88      - check for valid mapping from comp. tile to coupler global array
89      - improve report of tile registration results to log file.
90    o pkg/exch2:
91      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
92        tile-registration (CPL_REGISTER);
93      - activate (un-comment) definition and setting of "W2_tileIndex" list to
94        store the local bi,bj indices of each tile;
95      - also print bi,bj in local report to log file;
96      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
97        Jun 2009 modif of pkg/exch2).
98    o testing on baudelaire:
99      - run 2 tests at a time: no significant slow down (since enough cpu) and
100        get the full set of test done earlier
101      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
102    o model/src/thermodynamics.F and routines called from it:
103      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
104        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
105        velocity (outp) by adding bolus velocity.
106      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
107        mass transport from velocity + lateral grid cell area
108      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
109      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
110     in thermodynamics.F
111      - remove k from thermodynamics.F and move it to temp_integrate.F
112        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
113        loop).
114      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
115        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
116        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
117        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
118      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
119        global_ocean.90x40x15, tutorial_global_oce_biogeo and
120        tutorial_tracer_adjsens (+ TLM output).
121    o tools/OAD_support and (verification/*/) code_oad:
122      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
123        module conversion ; remove unneeded CPP_EEOPTIONS.h.
124      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
125        version (closer to model/inc/CPP_OPTIONS.h).
126    o model/src:
127      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
128        retired list of parameters (routine FREEZE has been replace by surface
129        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
130    o pkg/gmredi:
131      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
132        velocity (same scheme but affects machine truncation) for GM_AdvForm.
133      - update output of FWD experiments: front_relax.bvp,
134        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
135    
136    checkpoint64q (2013/11/17)
137    o verification:
138      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
139        tutorial_global_oce_biogeo and global_ocean.90x40x15.
140      - generate new output (growth & melt) for seaice_itd experiment after
141        updating the input pickup_seaice files (previously wrong).
142    o pkg/cost:
143      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
144        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
145        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
146          cannot be applied to var in common block).
147        o allows to get results independent of tile-per-proc setting (if using
148          slower GLOBAL_SUM_SEND_RECV option).
149      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
150        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
151        forward gradients: update output).
152      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
153        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
154    o pkg/mom_common:
155      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
156        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
157        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
158        ensure that all field value that are used are set.
159    o tutorial_deep_convection (smag3d):
160      - add missing scaling in mom_calc_smag_3d.F;
161      - set smag3D_coeff in input.smag3d such that results do not change.
162    o pkg/dic:
163      - change dic_cost.F to compute cost on each tile first and then apply
164        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
165        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
166      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
167    o eesupp/src & pkg/mdsio:
168      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
169        (from pkg/mdsio) since they are no longer used for tape IO.
170      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
171        (+ keep a copy in pkg/atm_ocn_coupler).
172    o verification/isomip:
173      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
174    o tools/build_options:
175      - optfile linux_amd64_ifort11, fast (no ieee) case:
176        to get a working restart for all experiments, add "-fp-model source"
177        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
178    
179    checkpoint64p (2013/10/20)
180    o pkg/autodiff:
181      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
182        criteria, return to simple (default) tape IO format.
183    o pkg/mdsio (+ eesupp/src):
184      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
185        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
186      - fix globalFile and singleCpuIO options using simpler global mapping.
187      - new pairs of scatter/gather vector S/R (one for each type, generated from
188        template) corresponding to simpler global mapping.
189      - adread_write.F: switch to new S/R (but leave old calls commented) and write
190        to globalFile when parameter globalFiles is set to True.
191      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
192    o pkg/autodiff:
193      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
194        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
195        missing, just add a STOP if array type do not match.
196    o pkg/exf:
197      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
198         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
199         and rename array obsSIce to exf_iceFraction.
200    o tutorial_deep_convection:
201      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
202        for now all in this exp. code dir.
203      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
204        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
205    o eesupp/src:
206      - added SINGLE_DISK_IO option because reading of parameter files on
207        very large number of processors did not work with existing set-up
208    
209    checkpoint64o (2013/09/25)
210    o pkg/atm_phys & atm_compon_interf:
211      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
212    o tools/build_options:
213      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
214        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
215        remove CPP setting (was identical to genmake2 default).
216    o pkg/gmredi & model/src: Some updating and work done on the residual model.
217      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
218      - fixed up the calculation of the eddy stress and how it is added to the
219        external forcing via taueddy_external_forcing.F
220      - at the moment, it is very experimental and only works with the variable eddy
221        diffusivity calculated in gmredi_k3d.F
222    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
223        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
224    o testreport (& tools/do_tst_2+2):
225      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
226    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
227      - remove CPP='cpp -traditional -P' (this is genmake2 default)
228      - add switch (for big setups) to use 'medium' memory-model (but leave it
229        commented out for now). Note: needed with FC 19 to compile big setups.
230    o pkg/atm_compon_interf:
231      - regroup per field origin (model & pkgs) the coupling storage routines
232         (which accumalate in time each coupling field)
233      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
234        update accordingly + simplify aim_do_physics.F
235    
236    checkpoint64n (2013/08/26)
237    o pkg/bbl:
238      - update formulation to reduce dispersion of tracer properties in bbl
239      - replaced horizontal and vertical transport parameters with velocities
240      - changes results for verification/global_with_exf.yearly
241    o verification/halfpipe_streamice:
242      - change to matrix construction; update both Fwd & AD output.
243    o verification/tutorial_tracer_adjsens:
244      - OpenAD test: switch to vector-invariant momentum since fluxform with
245        rStar causes problems with OpenAD; update output.
246    o tools:
247      - genmake2: define a common prefix for all temp-file names ; move them
248        to local /tmp disk (but would be easy to move them back);
249      - xmakedepend: apply the same switch for temp-files.
250    o pkg/offline:
251      - changes for use with rStar (NLFS): assume that we continue to provide
252        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
253        output files) and apply r* scaling at each time-step (function of the time
254        varying Eta field); use normal pickup files (needed for restart with NLFS).
255    o adjoint with OpenAD:
256      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
257        package openad.  This package has to be compiled for all runs with OpenAD
258        instead of specifying code_oad_all as a modification directory.
259      - link the fortran templates from tools/OAD_support to the build directory
260        for preprocessing to avoid conflicts between different setups compiled
261        simultaneously and simplify cleanup.
262    o pkg/exf:
263      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
264        main model or other pkgs are exchanged in EXF_MAPFIELDS).
265    o model/src:
266      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
267        (similar to do_fields_blocking_exchanges.F).
268    o tools/genmake2:
269      - remove TAF output src code just before calling staf (when not doing a fresh
270        built, will stop if things go wrong with staf).
271      - fix target "adobj" (left from TAF version-2 transition)
272    o pkg/diagnostics:
273      - add a parameter to track the status of pkg/diagnostics activation;
274        this replace/extend the use of logical param "settingDiags" (to check
275        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
276        New S/R to print error message and stop when pkgStatus is not right.
277      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
278    
279    checkpoint64m (2013/08/13)
280    o model/inc:
281      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
282        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
283    o pkg/kpp & aim_v23:
284      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
285    o pkg/seaice:
286      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
287        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
288      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
289    o eesupp/src:
290      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
291        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
292    o switch to TAF version-2:
293      - add flow directives to "freeze" naming convention for ad-routines that
294        are used in I/O routines of adjoint state and associated common blocks
295        that are used in adcommon.h (backward compatible with version-1)
296      - update all ad-optfiles (in tools/adjoint_options + few local to some
297        verification exp) to switch to latest TAF version (currently 2.5.5);
298        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
299        out except for diva).
300      - the major change with TAF version-2 is that both the differentiated
301        routines and the forward routines (new) are returned as part of the TAF
302        output source code. Update genmake2 accordingly.
303      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
304        with version-2 when compared to TLM or FWD gradient); other experiments
305        output show minor changes (machine truncation level); update the few AD &
306        TLM output with 12 matching digits only (some prior to version-2 switch).
307    
308    checkpoint64l (2013/08/05)
309    o model/src:
310      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
311      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
312        when using TAF but only if using OpenAD.
313    o pkg/mom_common+fluxform+vecinv:
314      - always set horiz. viscosity arrays to background value before calling
315        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
316        only when using variable horiz. viscosity (useVariableVisc=T);
317      - simplify mom_vecinv.F (only 1 block for momViscosity).
318    o pkg/mom_common: variable horiz. viscosity in NH code
319      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
320        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
321      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
322        useBiharmonicVisc & useVariableVisc.
323      - fix old bug (already in 1rst implementation of variable horizontal viscosity
324        in calc_gw.F, version 1.27, 2006/06/20):
325        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
326        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
327      - change background horiz viscosity in vertical momentum (gW) to always be
328        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
329        any type of variable viscosity, e.g., viscAh/4Grid)
330      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
331        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
332        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
333        default viscAh,viscA4 is zero).
334    o model/src:
335      - extend length of drC & recip_drC from Nr to Nr+1.
336    o Divided Adjoint (DIVA) with MPI:
337      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
338      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
339        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
340    
341    checkpoint64k (2013/07/23)
342    o tools/OAD_support:
343      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
344        and remove it from genmake2.
345    o tools/build_options:
346      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
347        MPI_HEADER_FILES list (let genmake2 find the missing headers)
348    o verification/halfpipe_streamice:
349      - change to driving stress formulation; update both Fwd & AD output.
350    o tools/genmake2 and Divided Adjoint with MPI:
351      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
352      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
353      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
354        Makefile, which is set by genmake2, and check which mpi-headers are needed.
355        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
356      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
357    o testreport:
358      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
359        perform additional runs (number of additional runs is "add_DIVA_runs" taken
360        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
361    o verification/lab_sea (AD test):
362      - change to test Divided Adjoint Run in this set-up (both standard AD test
363        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
364    o pkg atm_ & ocn_compon_interf:
365      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
366        staggerTimeStep implementation) and disable (retired) corresponding
367        parameter.
368    o pkg/offline:
369      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
370      - add S/R OFFLINE_CHECK to print offline parameter summary
371        and stop if loading a file that is not used;
372      - enable to calculate GMRedi tensor, KPP mixing and convective index
373        when the corresponding file(s) is/are not specified (but pkg is used).
374      - comment out resetting of monitorFreq (to endTime) since it still useful
375        for monitoring CFL numbers and checking offline fields.
376    o OpenAD:
377      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
378        smaller standard output) and generate new (smaller) output (on baudelaire
379        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
380    o model/src:
381      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
382        (where external_forcing_adjust was called) and change list of arguments;
383      - merge external_forcing_adjust.F into external_forcing_surf.F
384      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
385        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
386        previously in file "balance_relax.F", now removed); remove corresponding
387        arrays in FFIELDS.h.
388      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
389        a hack for getting back surfaceForcingS (loaded from file) when using
390        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
391      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
392        (was getting only 11 digits for AD-grad, due to different truncation
393         error in AD code).
394    
395    checkpoint64j (2013/07/04)
396    o pkg/offline:
397      - to enable the use of other features with pkg offline (e.g., obcs),
398        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
399      - comment out "allowFreezing" (now active) in 2 offline testing exp.
400    o pkg/exf ALLOW_RUNOFTEMP
401      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
402      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
403      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
404    o pkg/atm_phys:
405      - allows to add some damping on uVel,vVel (strength only function of k).
406    o verification, ad-tests:
407      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
408        global_ocean_ebm and offline_exf_seaice.thsice.
409    o verification/halfpipe_streamice:
410      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
411        flux input boundary conditions to be ignored; a fix for this bug changed
412        verification results for forward test.
413      - add adjoint test.
414    o pkg/ptracers:
415      - allow to restart without SOM pickup (resetting SOM to zero).
416    o pkg/gmredi:
417      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
418      - It uses mixing length theory and suppression by steering level effects to
419        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
420        to JPO, for more details).
421      - It also uses the diffusivity to calculate an eddy induced streamfunction
422        based on a PV closure (rather than a buoyancy closure as in GM).
423      - New files added to pkg/gmredi:
424        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
425          induced overturning streamfunction (called from gmredi_calc_tensor)
426        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
427          for use in gmredi_k3d
428        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
429          the eddy diffusivity
430    
431    checkpoint64i (2013/06/18)
432    o pkg/cheapaml:
433      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
434        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
435        with pkg/cheapaml.
436    o utils/python: add subpackage for cubed sphere function, first example is
437        simple cs.pcol to plot 2D fields on a map
438    o pkg/streamice:
439      - This is a new package in MITgcm, which solves dynamic equations for ice
440         sheets and ice streams
441      - At the moment it is independent of atmosphere/ocean dynamics, or any
442        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
443        ed that this will change)
444      - There is a new verification exercise that tests it, halfpipe_streamice,
445        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
446        rectangular embayment
447      - halfpipe_streamice is forward-only for now, will have TAF test soon
448      - for questions, email dgoldber@mit.edu
449    o pkg/thsice:
450      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
451        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
452      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
453         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
454      - allow precip from pkg/cheapaml to make snow over seaice.
455    o pkg/cfc:
456      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
457      - remove atmos CFC 2-D arrays from common bloc (now local variables)
458      - change some hard-coded constant to run time parameter for reading and
459        and interpolating atmospheric CFC ; keep same default as previously.
460      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
461      - put arguments in standard order: myTime, myIter, myThid
462      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
463        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
464      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
465      - new routine to print summary of CFC params and check for consistency.
466    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
467      similar to thsice_advdiff.
468      Note that for the B-grid case the routine parameters uc/vc are overwritten.
469    o pkg/cfc:
470      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
471        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
472      - fix interpolation of atmphspheric CFC between Sorthern and Northern
473        hemisphere value.
474    o pkg/seaice:
475      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
476    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
477                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
478      - requires an additional time level that is stored in the pickup
479      - you can start with AB2 from a pickup without this time level with
480        pickupStrictlyMatch = .false.
481    
482    checkpoint64h (2013/05/26)
483    o pkg/cheapaml:
484      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
485        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
486      - consistent treatment of uWind,vWind location: assume everywhere in
487        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
488        (Note: was already the case for Tair,Qair advection);
489        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
490      - compute diabatic forcing only in the interior (excluding overlap regions)
491      - fill in array "Qsw" (for short-wave heating);
492      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
493        before any update (consistent with MITgcm state var diagnostics);
494      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
495        non periodic ; + adjusted for uWind,vWind (C-grid).
496    o pkg/seaice:
497      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
498        add explicitly pkg/exf in experiments that currently use pkg/seaice.
499      - allows to compile pkg/seaice without pkg/exf.
500    o tools/OAD_support:
501      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
502        of array "ourStepOf" in function rvNextAction (revolve.F90).
503    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
504      - change pkg name (to be used with other atmospheric physics pkg)
505        but by-pass CVS when making the new pkg so that we keep the CVS history.
506    o pkg/offline:
507      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
508        (previously called from pkg/dic_surfforcing_init.F)
509    o model/src:
510      - re-order sequence of calls within packages_init_variables.F, using
511        standard order, except for:
512         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
513         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
514    o new pkg: atm_phys
515      - add entry point and source code (previously in contrib
516          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
517        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
518      - re-order sequence of calls within packages_readparms.F,
519         packages_init_fixed.F and packages_write_pickup.F
520        (but skip packages_init_variables.F because of TAF issues).
521      - update contrib/*/atm_gray/ experiment.
522    o pkg/seaice (ITD code):
523      - simplify and fix the writing of pickup-files for ITD case
524    o pkg/seaice (ITD code):
525      - introduce floe size dependent lateral melt for ITD case;
526      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
527      - update seaice_itd experiment main output.
528    o pkg/thsice:
529      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
530        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
531        changed accordingly pkg/atm2d.
532    
533    checkpoint64g (2013/05/01)
534    o pkg/exf ALLOW_RUNOFTEMP
535      - if defined,  river and glacier runoff temperature can be read-in from
536        runoftempfile; runoftempfile needs to have same format as runofffile
537    o pkg/thsice (& pkg/bulk_force):
538      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
539        for energy content of Precip + RunOff & Evap (like with pkg/exf).
540      - change computation domain to always be the interior (without overlap).
541      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
542    o verification/tutorial_global_oce_biogeo:
543      - add preliminary OpenAD setup (still has problems)
544    o pkg/seaice:
545      - turn some parameters for choosing the convergence criterion of
546        the inexact Newton method (JFNK) into runtime parameters for convenience
547      - clean up seaice_calc_viscosities.F: remove/retire two options for
548        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
549        the results of lab_sea/input because a division has been replaced by
550        a multiplication with the reciprocal (sumNorm)
551      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
552        convergence of solver (changes results, of course), and to test some
553        new features
554    o model/src:
555      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
556      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
557      - move forcing adjustment (balancing surface forcing) in specific S/R
558        where might also be applied exchanges (if needed) to forcing arrays.
559    o pkg/shelfice:
560      - allow to specify the Ice-Shelf mass per unit area (instead of
561        shelficeLoadAnomaly) and do the conversion from one to the other
562      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
563        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
564        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
565        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
566      - update isomip experiment forward output (get machine truncation error
567        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
568    o verification/offline_exf_seaice:
569      revise data.seaice in input.thermo and input_ad and update results accordingly
570        HO = 0.2, SEAICE_areaLossFormula = 2,
571        SEAICE_growMeltByConv = .TRUE.,
572        SEAICE_doOpenWaterMelt = .TRUE.,
573      Improve consistency with input.thsice and fix the spurious 500m ice corners
574    o verification/global_ocean.cs32x15:
575      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
576        in icedyn (thsice+seaice-dyn) test and update output.
577    o verification/offline_exf_seaice:
578      - adjust list of tested variables (with testreport) and update
579        standard test output with better slection of monitored fields.
580    o pkg/cd_code:
581      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
582        experiment lab_sea.hb87
583    o tools/genmake2:
584      - change default makedepend from the system default to tools/xmakedepend:
585        When no makedepend is specified, select tools/xmakedepend it the test pass,
586        otherwise select the system default (if exist and pass the test) or
587        try to build cyrus-makedepend ; stop if none of the 3 works.
588    o pkg/exf & pkg/thsice:
589      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
590        for energy content of Precip + RunOff & Evap. Assumes:
591       1) Rain has same temp as Air.
592       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
593       3) Run-Off comes at the temp of surface water (with same Cp)
594       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
595        put directly into Latent Heat flux & should use water-vapor heat capacity.
596       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
597        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
598    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
599        (compile when SEAICE_ALLOW_JFNK is defined)
600    o pkg/thsice:
601      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
602        implementation): move THSICE_AVE call after the advection (called directly
603        from thsice_do_advect.F).
604    o verification/global_ocean.90x40x15 and OpenAD:
605      New experiment for OpenAD is identical to the one in input_ad except that
606        multiDimAdvection=.FALSE.,
607      There is still an issue with this.
608    o pkg/thsice:
609      - account for ice velocity (ocean relative velocity) in turbulent heat flux
610        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
611        and offline_exf_seaice (main test).
612    
613    checkpoint64f (2013/03/31)
614    o verification/OpenAD:
615      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
616    o verification/isomip, pkg/shelfice and OpenAD:
617      - add OpenAD setup to this exp and make shelfice package work with OpenAD
618    o verification/tutorial_global_oce_biogeo:
619      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
620    o verification/offline_exf_seaice:
621      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
622    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
623      - add OpenAD setup to this exp and make ptracers package work with OpenAD
624    o pkg/seaice/seaice_evp.F:
625       mask the asymmetric contribution of the ice-ocean stress (when
626       the turningAngle is non-zero) over open water to avoid stripes
627       in the EVP-solutions after many EVP-substeps. This does not change
628       the verification experiment (because turningAngle=0 in that experiment),
629       but will affect other EVP solutions with turningAngle.ne.0
630    o verification, AD & TLM output:
631      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
632        additions and multiplications which affect results at machine truncation
633        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
634        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
635        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
636        digits of matching.
637    o pkg/seaice:
638       modify lsr-algorithm so that it vectorizes AND converges by using a
639       "zebra" method: split vector loop into two with step size 2; this
640       solves a general convergence problem for the JFNK solver on a vector
641       computer. It has the potential to even improve convergence for
642       non-vector machines, but it does change the results so it is turned
643       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
644       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
645    
646    checkpoint64e (2013/03/05)
647    o pkg/ecco and several verification experiments:
648       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
649       from ecco package, and revert to unified routine in model/src/
650       Adjust verification experiments accordingly, especially gloal_oce_llc90
651       Should conclude long-standing work by Gael to reconsile the_main_loop with
652       ECCO and will enable OpenAD's revolve loop in ECCO setup.
653    o pkg/generic_advdiff:
654      - implement compressible flow method for multi-dim advection (similar to
655        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
656        TAF generates many recomputations) to use it; no yet coded with implicit
657        vertical advection.
658      - change experiment advect_cs (new output) and advect_xy (same output)
659        to test compressible flow multi-dim advection.
660    o pkg/generic_advdiff:
661      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
662        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
663    o pkg/seaice:
664      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
665        bug affects two verification experiments (lab_sea and lab_sea.hb87),
666        recover old (wrong) results by setting noSlipFac = 2. in
667        seaice_calc_strainrates.F;
668      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
669      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
670        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
671      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
672    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
673      - new subroutines seaice_lsr_tridiagu/v
674      - introduce loop bounds i/jmin/max to be able to use a restricted
675        additive Schwarz method, but not used for now.
676      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
677      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
678    o OpenAD support
679       Reorganize S/R call for overall time-stepping loop to facilitate
680       OpenAD revolve loop replacement
681       (new S/R main_do_loop.F)
682    o model/src:
683      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
684      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
685        ADAMS_BASHFORTH2.
686    o pkg/cheapaml:
687      - add new parameter (default=F, same as before) to disable full domain
688        (including land) periodicity in X & Y dir.
689      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
690        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
691        into single S/R CHEAPAML_TIMESTEP.
692    
693    checkpoint64d (2013/02/17)
694    o pkg/monitor (angular momentum):
695      - do not add Eta contribution to the total AM if using rigid-lid;
696      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
697      - horizontal discretisation: compute Zonal wind contribution separately for
698        each component (instead of from cell centered averaged) and use the 4
699        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
700      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
701        FreeSurf) if using vectorInvariant momentum.
702    o model/src (horizontal grid):
703      - move initialisation of all horizontal grid arrays to null value
704        from specific horizontal grid S/R to main S/R INI_GRID;
705      - add 2 new arrays to project model C-grid velocity on to zonal direction
706        (similar to AngleCosC & -AngleSinC but at U and V point location) and
707        compute them in S/R CALC_GRID_ANGLES.
708    o pkg/seaice: replace a hard coded parameter by a runtime parameter
709        SEAICE_JFNK_tolIter
710    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
711        preconditioner for JFNK (run LSR into the overlaps as far as possible,
712        i.e OLx/y-2, but overwrite the solution in the overlaps)
713      - extend loop range in seaice_calc_viscosity
714      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
715      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
716      - slightly modify loops in tridiagonal solver lsr-preconditioner
717      - by default remove the extra exchange in seaice_preconditioner with a
718        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
719      - modify offline_exf_seaice so that old results without RAS are reproduced
720        for output.dyn_jfnk.txt
721      in seaice_fgmres.F (unrelated to RAS)
722      - add a cpp-flag option for a re-ordered mapping (potentially more
723        efficient), but because this changes the results, turn it off by
724        default
725      - replace the save statement by local common blocks
726    o utils/matlab:
727      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
728      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
729        instead of local script "load_cs.m".
730    o pkg/seaice:
731      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
732        to the scalarProductMetric and the unrolling. By chance this does not
733        change the verification experiment, because of the particular domain
734        decomposition
735    o pkg/diagnostics:
736      - change default missing_value from UNSET_RL to -999.
737    o pkg/layers: improve vectorization of layers_fluxcalc.F
738      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
739        time spent in this routine by more than a factor of 3 on an NEC-SX8
740      - step 2: replace search algorithm by a bisection algorithm found in
741        Press et al. Numerical Recipes in Fortran. This algorithm can be
742        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
743        For now, use this algorithm only for TARGET_NEC_SX defined.
744      - moved the search algorithm into a separate subroutine, that is kept
745        within the same file for automatic inlining.
746      - modified catching potential errors
747    o pkg/ecco:
748      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
749    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
750      - modifications for ALLOW_GENTIM2D_CONTROL
751      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
752      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
753      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
754      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
755    o model/src:
756      - account for moist thermodynamics in (dry) potential temperature equation;
757        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
758        and cpl_aim+ocn.
759      - also switch to standard compiler (gfortran, was using ifort previously)
760        for fizhi-cs experiments reference output.
761    o pkg/ctrl:
762      - 1st step toward generic time-varying control variable (2D) via CPP option
763        ALLOW_GENTIM2D_CONTROL
764      - note new namelist ctrl_nml_genarr in data.ctrl
765    o verification/global_ocean.cs32x15:
766      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
767        thsice calling sequence and update "output.icedyn.txt" output file.
768    o pkg/ptracers:
769      - from Ryan A.: code to allow to restart a tracer at regular time interval
770        specifying a reset frequency and a reset-phase (for each tracers).
771    o pkg/thsice:
772      - implement new sequence of calls for thsice+seaice:
773          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
774          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
775      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
776        in CPP_OPTIONS.h) to recover old sequence;
777      - update diagnostics for Intermediate State thsice diagnostics: now filled
778        just before advection (instead of just after advection in old sequence);
779      - update output of experiment offline_exf_seaice (standard test);
780      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
781        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
782    o pkg/aim_v23:
783      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
784      - use standard pkg/mdsio routines to read & write CO2 pickup file;
785      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
786      - Implement new sequence of calls for seaice advection (with thsice and
787        seaice diffusion): do ice advection after ice-Thermodynamic (previously
788        was done before); change aim_do_physics.F (split the bi,bj loops block);
789      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
790    o pkg/thsice:
791      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
792        where just seaice diffusion is used without seaice-dynamics.
793    
794    checkpoint64c (2013/01/18)
795    o pkg/seaice:
796      - add a parameter JFNKres_tFac that can replace JFNKres_t
797        (= JFNKres_tFac*JFNKresidual before JFNK solver)
798      - add a line search option to the JFNK solver
799      - move update of u/vIce and computation of initial residual into a separate
800        routine (same file); makes the code a little easier to read (?)
801      - the line search requires computation of the residual and for some reason
802        I cannot do the update of u/vIce at the beginning of the Newton loop
803        without changing the results, so we move computation of the new residual
804        also to the end of the Newton loop, even without the line search
805    o pkg/mdsio:
806      - write missing value (corresponding to undefined array value) to meta files;
807        skip this if missing value is one (UNSET_RL would be a better value for the
808        case of undefined missing value but it's current the default missing-value);
809        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
810    o pkg/exf & thsice:
811      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
812        diagnostics) even when SHORTWAVE_HEATING is #undef;
813    o verification/cfc_example:
814      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
815        illustrate how to use it).
816    o verification/offline_exf_seaice:
817      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
818        files to only one time-record.
819      in input.thermo: narrow the 2 bands of low initial ice-concentration near
820        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
821        snapshot output; same mcPheePiston value as in thsice with
822        surf-current=0.2m/s.
823      in input.thsice: similar set-up as in input.thermo (channel with same seaice
824        initial conditions).
825    o verification/cfc_example:
826      - update file "data" with more standard choice (default rotationPeriod,
827        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
828        set deltaTFreeSurf to deltaTtracer) and update the output.
829    o pkg/layers:
830      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
831      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
832    o verification/offline_exf_seaice:
833      - set all {field}period to zero for constant-in-time forcing (not tested
834        anywhere else).
835    o verification/offline_exf_seaice:
836      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
837      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
838    o model/src:
839      - implement Finite-Volume method for (hydrostatic) presure gradient
840        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
841    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
842      - In order to be compatible with the default EVP code, this requires changing
843        the EVP code around a little; and because any small change immediately
844        breaks the lab_sea.hb87 verification experiment, the reference output is
845        updated two times (each time the remaining aggrement was only 2 digits):
846        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
847        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
848        The adjoint test lab_sea.evp also needed to be updated.
849      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
850        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
851        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
852        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
853        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
854        kept obscure, because I need to test it a little more.
855    o pkg/cheapaml:
856      - fix few incorrect type (_RL/_RS) in subroutine calls.
857    o pkg/seaice:
858      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
859        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
860    o model/src:
861      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
862        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
863        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
864    o pkg/cheapaml:
865      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
866        update output of experiment cheapAML_box.
867      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
868        and set them only in one place (cheapaml_readparms.F).
869      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
870      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
871        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
872    o model/src/the_main_loop.F:
873      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
874    o pkg/seaice:
875      - remove legacy branch code.
876      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
877    o verification/*/code*/SEAICE_OPTIONS.h:
878      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
879        SEAICE_CAP_HEFF).
880    o pkg/cheapaml:
881      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
882        to load new forcing fields.
883      - add missing "_d 0" where it's needed; + some editing (improve indentation).
884      - remove switch to "-r8" compiler option (no longer needed) in verification
885        cheapAML_box, keep same output (small trucation error differences).
886    o verification/offline_exf_seaice:
887      - add thermodynamics only test.
888    o verification/cheapAML_box:
889      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
890        keep same output (same 14 digits for cg2d).
891      - switch on "-r8" compiler option (some numerical values are missing
892        the "_d 0") and update output (only 6 digits for cg2d were preserved).
893    
894    checkpoint64b (2012/12/24)
895    o pkg/cheapaml:
896      - remove un-used variables (Qnet,EmPmR) from pickup files.
897      - store tendency of advected variables into cheapaml pickup file
898        and fix the AB-2 restart.
899    o verification/offline_exf_seaice and lab_sea adjoint:
900      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
901      - switch to 4 time steps in offline, consistent with lab_sea.
902      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
903      - update results after change of experiment seaice.
904    o pkg/seaice:
905      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
906        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
907        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
908        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
909    o model/src:
910      - add run-time parameter to select CG2D solver minimum-residual solution
911        (in case of a poor convergence).
912    o pkg/seaice/seaice_lsr.F
913      - move calculation of matrix coefficients into new
914        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
915        file; the main purpose of this change is to be able to reuse the code
916        in S/R SEAICE_PRECONDITIONER
917      - modify the computation of the residual so that the mass of sea-ice
918        is not used twice; this simplifies the calculations, but since
919        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
920        not tested in testreport---this does not affect the testreport results.
921    o verification/seaice_obcs:
922      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
923        verification/lab_sea/input.salt_plume; changes results/output.txt*
924    o model/src:
925      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
926    o pkg/seaice:
927      - improve description of parameters in seaice_fgmres.F and start
928        cleaning up the code
929      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
930        second argument
931      - add a metric based on grid cell area to SEAICE_SCALPROD; update
932        results of offline_exf_seaice.dyn_jfnk
933      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
934    o pkg/aim_v23:
935      - fix an other bug in dissipation heating (grid-cell area was missing).
936    o model/src + pkg/seaice:
937      - add global (multi-tile) linear solver for pair of tri-diagonal system
938        along X and Y lines, respectively for U and V component.
939        Note: 1) MPI and cube-exchange not yet coded.
940            2) probably not accurate for poorly conditioned / large size problem.
941      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
942        default: not compiled and not used.
943    o pkg/seaice:
944      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
945        introduce bi/bj loops and use global_sum_tile_rl instead of
946        mpi_allreduce in seaice_fgmres.F
947      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
948      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
949      - add a verification experiment for JFNK in offline_exf_seaice
950    o verification:
951      - change (for now, only fwd test) offline_exf_seaice experiment:
952        use a re-entrant channel with idealized coastline (trapezoidal shape)
953        at southern boundary to explore seaice dynamics and thermodynamics
954        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
955        secondary test (input.thsice) use thermodynamics only with SST relaxation.
956      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
957    o pkg/exf:
958      - disable "sstExtrapol" when Nr=1
959    o verification:
960      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
961        to test pkg/cheapaml.
962    o pkg/aim_v23 & pkg/shap_filt:
963      - fix dissipation heating (erroneous gravity multiplication factor).
964    o pkg/seaice:
965      - remove unused field pressPre from jfnk solver
966      - rename two subroutines in seaice_preconditioner.F
967    o eesupp/src:
968       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
969    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
970       - remove wrong parts of the rhs and the lhs (were in there
971         because I did not understand the concept of this preconditioner)
972       - add an exchange between u- and v-sweep. This increases communication
973         by a factor of two but improves the convergence of jfnk. Ideally,
974         one would like the u- and v-sweep to be independent. So far within
975         undocumented ifdefs
976       - reorganize the extra computations for printing the residuals
977    o tools/genmake2:
978      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
979        since it's not necessary (and was preventing to use MNC in some cases).
980    
981    checkpoint64a (2012/11/16)
982    o pkg/autodiff:
983      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
984        autodiff_readparms.F no longer depends on calling order (within
985        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
986        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
987        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
988    o pkg/obcs:
989      - adding tidal velocity forcing capability to obcs
990        for usage example, see verification/seaice_obcs/input.tides
991    o pkg/seaice:
992      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
993        SEAICE_LSRrelaxU/V
994      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
995    o pkg/aim_v23:
996      - implement heating from friction (bottom friction and stratospheric drag).
997    o pkg/shap_filt:
998      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
999        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
1000    o model/src:
1001      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
1002        time-constant addMass field from file (addMassFile);
1003      - support for heating due to friction (and Kinetic Energy dissipation):
1004        add option, run-time switch and 3-D field array + support code ; each pkg
1005        or S/R can add heating contribution (if there is a sink of KE); the sum is
1006        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
1007    o pkg/seaice:
1008      - complete merge of ITD code into seaice_growth.F
1009        from MITgcm_contrib/torge/itd/code/
1010        no verification so far, but Torge Martin tested
1011        "1-D test case and Beaufort set up;
1012        deliver okay results after 1 model year."
1013      - complete merge of SEAICE_SIZE.h into all relevant routines
1014      - move computation of eta at Z-points into calc_viscosities
1015        + introduce global field etaZ
1016        + add different methods for computing etaZ, for now the old
1017          method (simple averages of eta to Z-points) is hardwired
1018        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
1019          seaice_preconditioner
1020      - simplify computations for SEAICE_ZETA_SMOOTHREG
1021      - seaice_preconditioner:
1022        + replace one remaining press by pressLoc (mistake)
1023        + adjust printing of residuals
1024      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
1025        + add (SEAICE.h) and rename some counters (initiliased in
1026          seaice_init_fixed.F)
1027        + add _BEGIN/END_MASTER (myThid)  around print statements
1028        + print total number of iterations and failures over SEAICE_monFreq
1029          interval to STDOUT
1030      - move control over output-messages by fgmres to seaice_jfnk to save
1031        some operations
1032      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
1033        in order to make restarts with sol .ne. zero (fgmres with restarts)
1034        (seaice_jfnk.F, seaice_fgmres.F)
1035      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
1036        a serious convergence problem when open boundaries are involved
1037    o pkg/ggl90: fix computation of control volumes for the case of
1038      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
1039      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
1040    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
1041    o pkg/autodiff
1042      - Add inAdMode switch for SEAICEuseDYNAMICS:
1043        SEAICEuseDYNAMICSinAdMode
1044        (extend logic in ADAUTODIFF_INADMODE_SET)
1045    o pkg/seaice
1046      - Step 1 of merging ice-thickness distribution (ITD) code from
1047        MITgcm_contrib/torge/itd/ (author: Torge Martin)
1048        The code implements concept laid out in Thorndike et al. (1975);
1049        code is enabled via CPP flag SEAICE_ITD
1050        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
1051        code is not complete yet!!
1052      - SEAICE_SIZE.h now included in almost all seaice routines
1053    o verification (using seaice):
1054      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
1055        global_ocean.cs32x15.seaice ; update results.
1056      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
1057      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
1058        offline_exf_seaice (previously compiling B-grid).
1059    o pkg/exf:
1060      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
1061        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
1062        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
1063    o pkg/layers (adjust changes from Sept 19):
1064      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
1065        this allows to remove "layers_maxNum" dimension from all layers arrays.
1066    o pkg/layers (adjust changes from Sept 19):
1067      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
1068      - snap-shot extended to all type of layers (not just the 1rst type);
1069      - remove layers variables when corresponding CPP option is undef.
1070    o pkg/layers:
1071      - rename pkg/layers variable and add new output (layer exist & un-weighted
1072        velocity in layer)
1073    o pkg/seaice:
1074      - simplify (?) ocean-drag coefficent computations by using
1075        the same routine in all three solvers (saves some code lines)
1076      - remove global fields DRAGA and DRAGS from C-grid code and
1077        declare them locally in lsr.F (the only place where they are
1078        still used)
1079      - update AD output of lab_sea.evp (very sensitive anyway).
1080    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
1081      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
1082      and SEAICEuseJFNK=.true. A few things to note:
1083      - involves a FGMRES, that is parallel but very inefficient,
1084        because of many scalar products (global sums) in the Gram-Schmidt
1085        orthogonalization method. Needs to be replaced. Original code
1086        from J.-F. Lemieux
1087      - preconditioner for FGMRES is a stripped down version of LSOR
1088      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
1089        preconditioner. For the preconditioner, the default is set to 10.
1090      - Jacobian times vector is computed with finite differences
1091      - marginally related to JFNK-solver: add a smooth regularization for
1092        zeta with tanh that will improve convergence (Lemieux and Tremblay,
1093        2009) for any implicit solver (not implemented for EVP because EVP
1094        does not need this regularization in the first place). Define
1095        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
1096    o eesupp/src:
1097      - check in genmake2 that intrinsic S/R flush is available.
1098      - add S/R to flush IO unit (if intrinsic S/R flush is available)
1099      - flush standard & error msg unit before MPI termination
1100      - if debugMode, flush IO unit after printing msg
1101    o pkg/ctrl:
1102      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
1103        to ctrl_set_unpack_xyz.
1104    
1105    checkpoint64 (2012/10/09)
1106    o pkg/shelfice
1107      - in mom_fluxform.F, mom_vecinv.F:
1108        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
1109        Bug fix KappaRU -> KappaRV
1110        does not change verification/isomip but may change other setups
1111        (presumably constant KappaRU=KappaRV)
1112      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
1113    o pkg/obcs:
1114      - fixed some indexing bugs in obcs_seaice_sponge.F
1115      - added obcs relaxation subroutines for HSALT and HSNOW
1116      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
1117    o pkg/seaice:
1118      - add "multicategory" parameterization for snow in analogy to ice,
1119        default is off for now.
1120    o pkg/obcs:
1121      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
1122        see verification/seaice_obcs/input.seaiceSponge for example application.
1123      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
1124        index setting by master-thread. This fix multi-threads Pb in previous modifs.
1125    o pkg/layers :
1126      - add diagnostics to pkg/layers
1127      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
1128        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
1129    o pkg/generic_advdiff/gad_implicit_r.F :
1130      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
1131    o pkg/seaice/seaice_growth.F:
1132      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
1133    o pkg/obcs:
1134      - change default setting of OBCS_UVICE_OLD from defined to undef;
1135      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
1136        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
1137      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
1138      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
1139        with Southern & Western OB at a tile edge (at least in a simple set-up).
1140    o pkg/obcs:
1141      - change settings of OB index in case OB coincides with tile edge (shared by
1142        2 tiles), so that common OB location is registered by both tiles (instead of
1143        only 1). However, for Southern and Western OB, index value = 0 is not
1144        recognized as valid OB index (=default null value) and needs to be fixed.
1145      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
1146      - new parameter "OB_indexNone" for null index value (for now, still zero)
1147        to replace hard-coded null index value of zero.
1148    o pkg/exch2:
1149      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
1150        always check buffer-size (but outside the loop); move checking for valid
1151        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
1152        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
1153    o pkg/ctrl (pack & unpack):
1154      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
1155        (locally defined) for different variables (+ remove the variable-specific
1156        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
1157        (to be extended to other local file names in ctrl.h).
1158    o pkg/flt:
1159      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
1160    o pkg/mdsio:
1161      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
1162    o tools/genmake2:
1163      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
1164        (added by Alistair in version 1.51 for building without make depend);
1165      - remove Header files list (H_SRC_FILES) from the dependence of targets
1166         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
1167        place in version 1.23): this save going through staf when unrelated header
1168        file has been modified.
1169       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
1170        "make depend" step, still need to do "make links" before "make adtaf".
1171    o eesupp/src (+ few pkg src files) & genmake2:
1172      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
1173      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
1174      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
1175         upper/lower case ; account for space between "#" and undef/define)
1176    o pkg/flt (with exch2):
1177      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
1178      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
1179    
1180    checkpoint63s (2012/09/05)
1181    o pkg/ecco:
1182      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
1183      - add more relevant #ifdef ALLOW_SMOOTH ones.
1184      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
1185    o pkg/ctrl:
1186      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
1187        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
1188      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
1189        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
1190        ctrlSmoothCorrel3D (new).
1191        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
1192      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
1193      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
1194        controls when useAtmWind, and vice versa.
1195      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
1196      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
1197          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
1198      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
1199          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
1200      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
1201        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
1202    o pkg/smooth:
1203      - remove un-necessary includes.
1204      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
1205        Those CPP options were never defined, and not necessary.
1206    o model/src:
1207      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
1208      - standard treatment of useSMOOTH.
1209    o pkg/autodiff:
1210      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
1211        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
1212    o pkg/exch2:
1213      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
1214        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
1215      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
1216        and tiles to process mapping.
1217      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
1218        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
1219        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
1220        from w2_eeboot.F to w2_readparms.F.
1221    o eesupp/src:
1222      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
1223        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
1224        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
1225      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
1226        is defined (remove condition on usingMPI) to match cases where MPI_INIT
1227        has been called.
1228      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
1229      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
1230        (so that on 1 proc, get same myPid independently of usingMPI)
1231      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
1232        useCubedSphereExchange with EXCH-1 (safer).
1233      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
1234    o pkg/ggl90:
1235      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
1236        used in ALLOW_GGL90_SMOOTH code.
1237    o pkg/flt:
1238      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
1239        floats at the Southern end of the domain).
1240    o eesupp/inc:
1241      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
1242        but not used (and not to be used) anywhere, just for documentation.
1243    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
1244      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
1245        a) can damage previously written records in any other multi-record files.
1246        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
1247  o tools/genmake2:  o tools/genmake2:
1248    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
1249    - update AD_CONFIG.h (if needed) before building any of the executable    - update AD_CONFIG.h (if needed) before building any of the executable
# Line 11  o tools/genmake2: Line 1251  o tools/genmake2:
1251      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
1252    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
1253      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
1254    o pkg/cheapaml:
1255      - updated to correspond to the code used in accepted paper (Nico Wienders).
1256  o pkg/exf:  o pkg/exf:
1257      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
1258      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
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