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revision 1.1761 by mlosch, Tue Nov 6 13:19:41 2012 UTC revision 1.1980 by mlosch, Wed Apr 23 12:42:19 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: preparations for ridging code and first real ridging code
8      - move most of "PART 1" of S/R seaice_growth into a new and separate
9        S/R seaice_reg_ridge that will both regularize the state variable after
10        advection call the actual ridging routine;
11      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
12        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
13      - remove ridging code from seaice_advdiff
14      - clean up remaining part 1 of seaice_growth in an attempt to make it
15        more readable (this is probably subjective)
16      - call seaice_itd_redist once in the initialisation phase to have the initial
17        conditions in the correct category
18      - finally: add new ridging routine for ITD code
19    
20    checkpoint64v (2014/04/11)
21    o pkg/ecco:
22      - add runtime parameters mdt[start,end]date[1,2]
23      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
24    o pkg/seaice:
25      - make deltaC a global variable, so that it can be used in ridging code
26      - first step towards ridging: introduce new routines that compute
27        ice strength based on ridging parameters
28      - add diagnostic for HSNOWITD
29      - add opnWtrFrac as a global variable (required for ridging scheme)
30    o pkg/salt_plume + pkg/seaice/seaice_growth.F
31      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
32        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
33    o verification/hs94.1x64x5:
34      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
35      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
36    o autodiff:
37      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
38        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
39        For now, only in pkgs used in verification/hs94.1x64x5.
40      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
41        which are specific to TAF/TAMC).
42      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
43        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
44        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
45      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
46        building mitgcmuv_ad (make adAll).
47    o pkg/ecco:
48      - cost_gencost_seaicev4.F:
49         reformulate proxy cost as function of sst and local param SEAICE_freeze
50         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
51      - add stop statement if old names siv4-[sst,vol] are used
52      - add snapshots + cost reports for atmospheric longwave
53      - remove factor 0.1 in front of wtau[u,v]
54      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
55         ALLOW_TMI_SST_COST_CONTRIBUTION
56    o pkg/atm_phys:
57      - add some diagnostics for Short-wave and for convection S/R.
58    o pkg/seaice/seaice_growth:
59      - fix a bug in the lateral melt parameterization for SEAICE_ITD
60        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
61      - rearrange loop order for better vector code in the same code block
62      - rewrite the floeDiameter formula to have fewer divisions
63      -  (miraculously) none of this changes the results of seaice_itd
64    o pkg/smooth:
65      - move param smooth2Ddiffnbt to pkg/ecco
66    o pkg/salt_plume:
67      - salt_plume_frac.F:
68         clean up local param names
69         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
70    o pkg/rw:
71      - add RS version of S/R READ_MFLDS_LEV.
72    o pkg/streamice:
73      - fix the restart test by writing/reading pickup_streamice files.
74    o pkg/seaice:
75      - refine checks for jfnk-related parameters
76      - comment out if statement with SEAICEuseIMEX parameter as long as there
77        is no IMEX code to avoid confusion and surprises
78    
79    checkpoint64u (2014/03/07)
80    o verification/MLAdjust:
81      - rename secondary test suffix:
82         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
83         0.leithD -> AhFlxF  + switch to flux-form
84         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
85         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
86    o pkg/mom_vecinv:
87      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
88        to be before mom_calc_visc.F)
89      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
90      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
91        this is simpler for the adjoint and for diagnostics.
92    o model/src + pkg/momentum:
93      - add input files for  2-D additional Western and Southern cell-edge wall
94         (e.g., to add "thin-wall" where it is =1).
95      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
96        using 2nd hFacZ that is computed from initial (fix domain) hFac
97      - known limitations of thin wall implementation: not yet coded for sigma
98        coords; not working with CD-scheme neither.
99    o pkg/seaice:
100      - rename recently introduced parameters from (wrong name) AB to
101        BDF (backward difference time discretisation)
102      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
103    o tools/adjoint_options:
104      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
105    
106    checkpoint64t (2014/02/01)
107    o pkg/ecco
108      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
109        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
110      - replace hard-coded record number and period which only work for monthly
111        with read-in runtime param that works for other periods (month,day,year)
112    o pkg/thsice
113      - corrected store directive fixes thsice adjoint gradient checks
114    o genmake2 & testreport:
115      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
116        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
117        Update testreport accordingly. No need to set "export OPENAD=true"
118        in adjoint_options/adjoint_oad anymore (will be removed later).
119    o pkg/shelfice:
120      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
121        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
122        so that surface forcing applies to k=kSurf if using pkg/shelfice.
123    o pkg/ctrl, pkg/grdchk, pkg/ecco:
124      - Changes to make GENARR more modular (i.e. invisible if not used)
125    o model/src/temp_integrate.F and salt_integrate.F
126      - re-include store directives that were removed on Dec 27th.
127    o model/src/external_forcing_surf.F
128      - add storage directives for EmPmR and PmEpR to avoid recomputation of
129        seaice_model in the adjoint that is problematic when seaice_model is
130        turned off in the adjoint. The resolved issue dated back to July when
131        EXTERNAL_FORCING_SURF call was moved.
132        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
133    o pkg/exf/exf_check.F
134      - fix a small bug again (originally found by Wentao Liu, now found again)
135      - streamline error output
136    o pkg/streamice and aim_v23:
137      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
138        Apple's /usr/bin/cpp knows what to do:
139        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
140        Target: x86_64-apple-darwin13.0.0
141    
142    checkpoint64s (2014/01/05)
143    o tools/adjoint_options:
144      - switch to fastopt.net TAF server (instead of default fastopt.de) for
145        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
146    o model/src:
147      - remove some unnecessary TAF storage directives in forward_step.F and
148        in dynamics.F (note: not always removed by TAF, e.g., double storage
149        of kappaRU,kappaRV in former version of dynamics.F).
150    o model/src & pkg/ptracers:
151      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
152        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
153        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
154      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
155      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
156      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
157    o useSingleCpuInput separates single-CPU input from single-CPU output;
158        for now only implemented for in exf_interp_read.F
159    o verification/advect_xy:
160      - fix missing EXCH call in local version of ini_salt.F and update output.
161    o momentum diagnostics:
162      - fix which deltaT is used in Total-Tendency diagnostics.
163      - fix typo in diagnostics for momentum tendency from AB.
164    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
165        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
166    
167    checkpoint64r (2013/12/08)
168    o verification/*/results:
169      - Update reference output of experiments that were passing with just 13 digits
170         (make it easier to detect future changes in results)
171    o model/src & pkg/ptracers:
172      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
173        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
174        to inside ptracers_integrate.F ; remove ptracers_advection.F
175    o coupling interface pkgs:
176        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
177      - change the config check to test the agreement of Ocean Depth
178        with ATM land/sea mask (instead of ATM orography);
179      - send to coupler the number of coupler time-steps to do for this run:
180        this allows to check for consistency and don't need anymore to be
181        specified in parameter file "data";
182      in coupler:
183      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
184      - improve report to log-file of config setting (pass log-file unit to few S/R)
185    o pkg/compon_communic:
186      - add coupling send/receive for non-tiled integer vector;
187      - add S/R to check and stop if any proc has an error (similar to
188        eesupp/src/stop_if_error.F but single thread and across Comm_World).
189    o pkg/exch2:
190      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
191        through list of all tiles my proc owns.
192    o model/src:
193      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
194        from rTrans) to simplify dependencies (no need to store rTrans anymore in
195        calling S/R); this affects AD results at machine truncation level:
196        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
197        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
198    o tools/build_options:
199      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
200    o coupling interface pkgs:
201        [compon_communic, atm_compon_interf & ocn_compon_interf]
202      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
203        to each S/R that needs it; remove un-used variables.
204      - change component tile registration (cpl_register.F in both compon_interf
205        and mitcomponent_tile_register.F) to pass the full list of tiles
206        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
207      - with pkg/exch2: adopt the same convention used for I/O to define mapping
208        towards coupler global array (unless W2_useE2ioLayOut=F):
209         a) can now use different tiling between atm & ocn comp.
210         b) no needs to modify the run-Off map when changing tiling (was needed
211            even if using the same tiling between atm & ocn).
212         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
213            full land tiles); not yet tested.
214      - check for valid mapping from comp. tile to coupler global array
215      - improve report of tile registration results to log file.
216    o pkg/exch2:
217      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
218        tile-registration (CPL_REGISTER);
219      - activate (un-comment) definition and setting of "W2_tileIndex" list to
220        store the local bi,bj indices of each tile;
221      - also print bi,bj in local report to log file;
222      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
223        Jun 2009 modif of pkg/exch2).
224    o testing on baudelaire:
225      - run 2 tests at a time: no significant slow down (since enough cpu) and
226        get the full set of test done earlier
227      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
228    o model/src/thermodynamics.F and routines called from it:
229      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
230        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
231        velocity (outp) by adding bolus velocity.
232      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
233        mass transport from velocity + lateral grid cell area
234      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
235      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
236     in thermodynamics.F
237      - remove k from thermodynamics.F and move it to temp_integrate.F
238        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
239        loop).
240      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
241        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
242        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
243        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
244      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
245        global_ocean.90x40x15, tutorial_global_oce_biogeo and
246        tutorial_tracer_adjsens (+ TLM output).
247    o tools/OAD_support and (verification/*/) code_oad:
248      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
249        module conversion ; remove unneeded CPP_EEOPTIONS.h.
250      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
251        version (closer to model/inc/CPP_OPTIONS.h).
252    o model/src:
253      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
254        retired list of parameters (routine FREEZE has been replace by surface
255        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
256    o pkg/gmredi:
257      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
258        velocity (same scheme but affects machine truncation) for GM_AdvForm.
259      - update output of FWD experiments: front_relax.bvp,
260        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
261    
262    checkpoint64q (2013/11/17)
263    o verification:
264      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
265        tutorial_global_oce_biogeo and global_ocean.90x40x15.
266      - generate new output (growth & melt) for seaice_itd experiment after
267        updating the input pickup_seaice files (previously wrong).
268    o pkg/cost:
269      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
270        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
271        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
272          cannot be applied to var in common block).
273        o allows to get results independent of tile-per-proc setting (if using
274          slower GLOBAL_SUM_SEND_RECV option).
275      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
276        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
277        forward gradients: update output).
278      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
279        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
280    o pkg/mom_common:
281      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
282        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
283        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
284        ensure that all field value that are used are set.
285    o tutorial_deep_convection (smag3d):
286      - add missing scaling in mom_calc_smag_3d.F;
287      - set smag3D_coeff in input.smag3d such that results do not change.
288    o pkg/dic:
289      - change dic_cost.F to compute cost on each tile first and then apply
290        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
291        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
292      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
293    o eesupp/src & pkg/mdsio:
294      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
295        (from pkg/mdsio) since they are no longer used for tape IO.
296      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
297        (+ keep a copy in pkg/atm_ocn_coupler).
298    o verification/isomip:
299      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
300    o tools/build_options:
301      - optfile linux_amd64_ifort11, fast (no ieee) case:
302        to get a working restart for all experiments, add "-fp-model source"
303        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
304    
305    checkpoint64p (2013/10/20)
306    o pkg/autodiff:
307      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
308        criteria, return to simple (default) tape IO format.
309    o pkg/mdsio (+ eesupp/src):
310      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
311        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
312      - fix globalFile and singleCpuIO options using simpler global mapping.
313      - new pairs of scatter/gather vector S/R (one for each type, generated from
314        template) corresponding to simpler global mapping.
315      - adread_write.F: switch to new S/R (but leave old calls commented) and write
316        to globalFile when parameter globalFiles is set to True.
317      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
318    o pkg/autodiff:
319      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
320        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
321        missing, just add a STOP if array type do not match.
322    o pkg/exf:
323      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
324         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
325         and rename array obsSIce to exf_iceFraction.
326    o tutorial_deep_convection:
327      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
328        for now all in this exp. code dir.
329      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
330        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
331    o eesupp/src:
332      - added SINGLE_DISK_IO option because reading of parameter files on
333        very large number of processors did not work with existing set-up
334    
335    checkpoint64o (2013/09/25)
336    o pkg/atm_phys & atm_compon_interf:
337      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
338    o tools/build_options:
339      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
340        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
341        remove CPP setting (was identical to genmake2 default).
342    o pkg/gmredi & model/src: Some updating and work done on the residual model.
343      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
344      - fixed up the calculation of the eddy stress and how it is added to the
345        external forcing via taueddy_external_forcing.F
346      - at the moment, it is very experimental and only works with the variable eddy
347        diffusivity calculated in gmredi_k3d.F
348    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
349        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
350    o testreport (& tools/do_tst_2+2):
351      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
352    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
353      - remove CPP='cpp -traditional -P' (this is genmake2 default)
354      - add switch (for big setups) to use 'medium' memory-model (but leave it
355        commented out for now). Note: needed with FC 19 to compile big setups.
356    o pkg/atm_compon_interf:
357      - regroup per field origin (model & pkgs) the coupling storage routines
358         (which accumalate in time each coupling field)
359      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
360        update accordingly + simplify aim_do_physics.F
361    
362    checkpoint64n (2013/08/26)
363    o pkg/bbl:
364      - update formulation to reduce dispersion of tracer properties in bbl
365      - replaced horizontal and vertical transport parameters with velocities
366      - changes results for verification/global_with_exf.yearly
367    o verification/halfpipe_streamice:
368      - change to matrix construction; update both Fwd & AD output.
369    o verification/tutorial_tracer_adjsens:
370      - OpenAD test: switch to vector-invariant momentum since fluxform with
371        rStar causes problems with OpenAD; update output.
372    o tools:
373      - genmake2: define a common prefix for all temp-file names ; move them
374        to local /tmp disk (but would be easy to move them back);
375      - xmakedepend: apply the same switch for temp-files.
376    o pkg/offline:
377      - changes for use with rStar (NLFS): assume that we continue to provide
378        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
379        output files) and apply r* scaling at each time-step (function of the time
380        varying Eta field); use normal pickup files (needed for restart with NLFS).
381    o adjoint with OpenAD:
382      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
383        package openad.  This package has to be compiled for all runs with OpenAD
384        instead of specifying code_oad_all as a modification directory.
385      - link the fortran templates from tools/OAD_support to the build directory
386        for preprocessing to avoid conflicts between different setups compiled
387        simultaneously and simplify cleanup.
388    o pkg/exf:
389      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
390        main model or other pkgs are exchanged in EXF_MAPFIELDS).
391    o model/src:
392      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
393        (similar to do_fields_blocking_exchanges.F).
394    o tools/genmake2:
395      - remove TAF output src code just before calling staf (when not doing a fresh
396        built, will stop if things go wrong with staf).
397      - fix target "adobj" (left from TAF version-2 transition)
398    o pkg/diagnostics:
399      - add a parameter to track the status of pkg/diagnostics activation;
400        this replace/extend the use of logical param "settingDiags" (to check
401        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
402        New S/R to print error message and stop when pkgStatus is not right.
403      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
404    
405    checkpoint64m (2013/08/13)
406    o model/inc:
407      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
408        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
409    o pkg/kpp & aim_v23:
410      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
411    o pkg/seaice:
412      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
413        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
414      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
415    o eesupp/src:
416      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
417        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
418    o switch to TAF version-2:
419      - add flow directives to "freeze" naming convention for ad-routines that
420        are used in I/O routines of adjoint state and associated common blocks
421        that are used in adcommon.h (backward compatible with version-1)
422      - update all ad-optfiles (in tools/adjoint_options + few local to some
423        verification exp) to switch to latest TAF version (currently 2.5.5);
424        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
425        out except for diva).
426      - the major change with TAF version-2 is that both the differentiated
427        routines and the forward routines (new) are returned as part of the TAF
428        output source code. Update genmake2 accordingly.
429      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
430        with version-2 when compared to TLM or FWD gradient); other experiments
431        output show minor changes (machine truncation level); update the few AD &
432        TLM output with 12 matching digits only (some prior to version-2 switch).
433    
434    checkpoint64l (2013/08/05)
435    o model/src:
436      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
437      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
438        when using TAF but only if using OpenAD.
439    o pkg/mom_common+fluxform+vecinv:
440      - always set horiz. viscosity arrays to background value before calling
441        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
442        only when using variable horiz. viscosity (useVariableVisc=T);
443      - simplify mom_vecinv.F (only 1 block for momViscosity).
444    o pkg/mom_common: variable horiz. viscosity in NH code
445      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
446        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
447      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
448        useBiharmonicVisc & useVariableVisc.
449      - fix old bug (already in 1rst implementation of variable horizontal viscosity
450        in calc_gw.F, version 1.27, 2006/06/20):
451        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
452        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
453      - change background horiz viscosity in vertical momentum (gW) to always be
454        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
455        any type of variable viscosity, e.g., viscAh/4Grid)
456      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
457        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
458        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
459        default viscAh,viscA4 is zero).
460    o model/src:
461      - extend length of drC & recip_drC from Nr to Nr+1.
462    o Divided Adjoint (DIVA) with MPI:
463      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
464      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
465        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
466    
467    checkpoint64k (2013/07/23)
468    o tools/OAD_support:
469      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
470        and remove it from genmake2.
471    o tools/build_options:
472      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
473        MPI_HEADER_FILES list (let genmake2 find the missing headers)
474    o verification/halfpipe_streamice:
475      - change to driving stress formulation; update both Fwd & AD output.
476    o tools/genmake2 and Divided Adjoint with MPI:
477      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
478      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
479      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
480        Makefile, which is set by genmake2, and check which mpi-headers are needed.
481        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
482      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
483    o testreport:
484      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
485        perform additional runs (number of additional runs is "add_DIVA_runs" taken
486        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
487    o verification/lab_sea (AD test):
488      - change to test Divided Adjoint Run in this set-up (both standard AD test
489        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
490    o pkg atm_ & ocn_compon_interf:
491      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
492        staggerTimeStep implementation) and disable (retired) corresponding
493        parameter.
494    o pkg/offline:
495      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
496      - add S/R OFFLINE_CHECK to print offline parameter summary
497        and stop if loading a file that is not used;
498      - enable to calculate GMRedi tensor, KPP mixing and convective index
499        when the corresponding file(s) is/are not specified (but pkg is used).
500      - comment out resetting of monitorFreq (to endTime) since it still useful
501        for monitoring CFL numbers and checking offline fields.
502    o OpenAD:
503      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
504        smaller standard output) and generate new (smaller) output (on baudelaire
505        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
506    o model/src:
507      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
508        (where external_forcing_adjust was called) and change list of arguments;
509      - merge external_forcing_adjust.F into external_forcing_surf.F
510      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
511        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
512        previously in file "balance_relax.F", now removed); remove corresponding
513        arrays in FFIELDS.h.
514      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
515        a hack for getting back surfaceForcingS (loaded from file) when using
516        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
517      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
518        (was getting only 11 digits for AD-grad, due to different truncation
519         error in AD code).
520    
521    checkpoint64j (2013/07/04)
522    o pkg/offline:
523      - to enable the use of other features with pkg offline (e.g., obcs),
524        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
525      - comment out "allowFreezing" (now active) in 2 offline testing exp.
526    o pkg/exf ALLOW_RUNOFTEMP
527      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
528      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
529      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
530    o pkg/atm_phys:
531      - allows to add some damping on uVel,vVel (strength only function of k).
532    o verification, ad-tests:
533      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
534        global_ocean_ebm and offline_exf_seaice.thsice.
535    o verification/halfpipe_streamice:
536      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
537        flux input boundary conditions to be ignored; a fix for this bug changed
538        verification results for forward test.
539      - add adjoint test.
540    o pkg/ptracers:
541      - allow to restart without SOM pickup (resetting SOM to zero).
542    o pkg/gmredi:
543      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
544      - It uses mixing length theory and suppression by steering level effects to
545        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
546        to JPO, for more details).
547      - It also uses the diffusivity to calculate an eddy induced streamfunction
548        based on a PV closure (rather than a buoyancy closure as in GM).
549      - New files added to pkg/gmredi:
550        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
551          induced overturning streamfunction (called from gmredi_calc_tensor)
552        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
553          for use in gmredi_k3d
554        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
555          the eddy diffusivity
556    
557    checkpoint64i (2013/06/18)
558    o pkg/cheapaml:
559      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
560        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
561        with pkg/cheapaml.
562    o utils/python: add subpackage for cubed sphere function, first example is
563        simple cs.pcol to plot 2D fields on a map
564    o pkg/streamice:
565      - This is a new package in MITgcm, which solves dynamic equations for ice
566         sheets and ice streams
567      - At the moment it is independent of atmosphere/ocean dynamics, or any
568        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
569        ed that this will change)
570      - There is a new verification exercise that tests it, halfpipe_streamice,
571        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
572        rectangular embayment
573      - halfpipe_streamice is forward-only for now, will have TAF test soon
574      - for questions, email dgoldber@mit.edu
575    o pkg/thsice:
576      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
577        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
578      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
579         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
580      - allow precip from pkg/cheapaml to make snow over seaice.
581    o pkg/cfc:
582      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
583      - remove atmos CFC 2-D arrays from common bloc (now local variables)
584      - change some hard-coded constant to run time parameter for reading and
585        and interpolating atmospheric CFC ; keep same default as previously.
586      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
587      - put arguments in standard order: myTime, myIter, myThid
588      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
589        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
590      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
591      - new routine to print summary of CFC params and check for consistency.
592    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
593      similar to thsice_advdiff.
594      Note that for the B-grid case the routine parameters uc/vc are overwritten.
595    o pkg/cfc:
596      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
597        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
598      - fix interpolation of atmphspheric CFC between Sorthern and Northern
599        hemisphere value.
600    o pkg/seaice:
601      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
602    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
603                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
604      - requires an additional time level that is stored in the pickup
605      - you can start with AB2 from a pickup without this time level with
606        pickupStrictlyMatch = .false.
607    
608    checkpoint64h (2013/05/26)
609    o pkg/cheapaml:
610      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
611        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
612      - consistent treatment of uWind,vWind location: assume everywhere in
613        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
614        (Note: was already the case for Tair,Qair advection);
615        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
616      - compute diabatic forcing only in the interior (excluding overlap regions)
617      - fill in array "Qsw" (for short-wave heating);
618      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
619        before any update (consistent with MITgcm state var diagnostics);
620      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
621        non periodic ; + adjusted for uWind,vWind (C-grid).
622    o pkg/seaice:
623      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
624        add explicitly pkg/exf in experiments that currently use pkg/seaice.
625      - allows to compile pkg/seaice without pkg/exf.
626    o tools/OAD_support:
627      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
628        of array "ourStepOf" in function rvNextAction (revolve.F90).
629    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
630      - change pkg name (to be used with other atmospheric physics pkg)
631        but by-pass CVS when making the new pkg so that we keep the CVS history.
632    o pkg/offline:
633      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
634        (previously called from pkg/dic_surfforcing_init.F)
635    o model/src:
636      - re-order sequence of calls within packages_init_variables.F, using
637        standard order, except for:
638         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
639         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
640    o new pkg: atm_phys
641      - add entry point and source code (previously in contrib
642          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
643        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
644      - re-order sequence of calls within packages_readparms.F,
645         packages_init_fixed.F and packages_write_pickup.F
646        (but skip packages_init_variables.F because of TAF issues).
647      - update contrib/*/atm_gray/ experiment.
648    o pkg/seaice (ITD code):
649      - simplify and fix the writing of pickup-files for ITD case
650    o pkg/seaice (ITD code):
651      - introduce floe size dependent lateral melt for ITD case;
652      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
653      - update seaice_itd experiment main output.
654    o pkg/thsice:
655      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
656        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
657        changed accordingly pkg/atm2d.
658    
659    checkpoint64g (2013/05/01)
660    o pkg/exf ALLOW_RUNOFTEMP
661      - if defined,  river and glacier runoff temperature can be read-in from
662        runoftempfile; runoftempfile needs to have same format as runofffile
663    o pkg/thsice (& pkg/bulk_force):
664      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
665        for energy content of Precip + RunOff & Evap (like with pkg/exf).
666      - change computation domain to always be the interior (without overlap).
667      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
668    o verification/tutorial_global_oce_biogeo:
669      - add preliminary OpenAD setup (still has problems)
670    o pkg/seaice:
671      - turn some parameters for choosing the convergence criterion of
672        the inexact Newton method (JFNK) into runtime parameters for convenience
673      - clean up seaice_calc_viscosities.F: remove/retire two options for
674        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
675        the results of lab_sea/input because a division has been replaced by
676        a multiplication with the reciprocal (sumNorm)
677      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
678        convergence of solver (changes results, of course), and to test some
679        new features
680    o model/src:
681      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
682      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
683      - move forcing adjustment (balancing surface forcing) in specific S/R
684        where might also be applied exchanges (if needed) to forcing arrays.
685    o pkg/shelfice:
686      - allow to specify the Ice-Shelf mass per unit area (instead of
687        shelficeLoadAnomaly) and do the conversion from one to the other
688      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
689        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
690        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
691        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
692      - update isomip experiment forward output (get machine truncation error
693        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
694    o verification/offline_exf_seaice:
695      revise data.seaice in input.thermo and input_ad and update results accordingly
696        HO = 0.2, SEAICE_areaLossFormula = 2,
697        SEAICE_growMeltByConv = .TRUE.,
698        SEAICE_doOpenWaterMelt = .TRUE.,
699      Improve consistency with input.thsice and fix the spurious 500m ice corners
700    o verification/global_ocean.cs32x15:
701      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
702        in icedyn (thsice+seaice-dyn) test and update output.
703    o verification/offline_exf_seaice:
704      - adjust list of tested variables (with testreport) and update
705        standard test output with better slection of monitored fields.
706    o pkg/cd_code:
707      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
708        experiment lab_sea.hb87
709    o tools/genmake2:
710      - change default makedepend from the system default to tools/xmakedepend:
711        When no makedepend is specified, select tools/xmakedepend it the test pass,
712        otherwise select the system default (if exist and pass the test) or
713        try to build cyrus-makedepend ; stop if none of the 3 works.
714    o pkg/exf & pkg/thsice:
715      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
716        for energy content of Precip + RunOff & Evap. Assumes:
717       1) Rain has same temp as Air.
718       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
719       3) Run-Off comes at the temp of surface water (with same Cp)
720       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
721        put directly into Latent Heat flux & should use water-vapor heat capacity.
722       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
723        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
724    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
725        (compile when SEAICE_ALLOW_JFNK is defined)
726    o pkg/thsice:
727      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
728        implementation): move THSICE_AVE call after the advection (called directly
729        from thsice_do_advect.F).
730    o verification/global_ocean.90x40x15 and OpenAD:
731      New experiment for OpenAD is identical to the one in input_ad except that
732        multiDimAdvection=.FALSE.,
733      There is still an issue with this.
734    o pkg/thsice:
735      - account for ice velocity (ocean relative velocity) in turbulent heat flux
736        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
737        and offline_exf_seaice (main test).
738    
739    checkpoint64f (2013/03/31)
740    o verification/OpenAD:
741      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
742    o verification/isomip, pkg/shelfice and OpenAD:
743      - add OpenAD setup to this exp and make shelfice package work with OpenAD
744    o verification/tutorial_global_oce_biogeo:
745      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
746    o verification/offline_exf_seaice:
747      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
748    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
749      - add OpenAD setup to this exp and make ptracers package work with OpenAD
750    o pkg/seaice/seaice_evp.F:
751       mask the asymmetric contribution of the ice-ocean stress (when
752       the turningAngle is non-zero) over open water to avoid stripes
753       in the EVP-solutions after many EVP-substeps. This does not change
754       the verification experiment (because turningAngle=0 in that experiment),
755       but will affect other EVP solutions with turningAngle.ne.0
756    o verification, AD & TLM output:
757      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
758        additions and multiplications which affect results at machine truncation
759        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
760        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
761        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
762        digits of matching.
763    o pkg/seaice:
764       modify lsr-algorithm so that it vectorizes AND converges by using a
765       "zebra" method: split vector loop into two with step size 2; this
766       solves a general convergence problem for the JFNK solver on a vector
767       computer. It has the potential to even improve convergence for
768       non-vector machines, but it does change the results so it is turned
769       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
770       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
771    
772    checkpoint64e (2013/03/05)
773    o pkg/ecco and several verification experiments:
774       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
775       from ecco package, and revert to unified routine in model/src/
776       Adjust verification experiments accordingly, especially gloal_oce_llc90
777       Should conclude long-standing work by Gael to reconsile the_main_loop with
778       ECCO and will enable OpenAD's revolve loop in ECCO setup.
779    o pkg/generic_advdiff:
780      - implement compressible flow method for multi-dim advection (similar to
781        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
782        TAF generates many recomputations) to use it; no yet coded with implicit
783        vertical advection.
784      - change experiment advect_cs (new output) and advect_xy (same output)
785        to test compressible flow multi-dim advection.
786    o pkg/generic_advdiff:
787      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
788        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
789    o pkg/seaice:
790      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
791        bug affects two verification experiments (lab_sea and lab_sea.hb87),
792        recover old (wrong) results by setting noSlipFac = 2. in
793        seaice_calc_strainrates.F;
794      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
795      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
796        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
797      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
798    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
799      - new subroutines seaice_lsr_tridiagu/v
800      - introduce loop bounds i/jmin/max to be able to use a restricted
801        additive Schwarz method, but not used for now.
802      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
803      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
804    o OpenAD support
805       Reorganize S/R call for overall time-stepping loop to facilitate
806       OpenAD revolve loop replacement
807       (new S/R main_do_loop.F)
808    o model/src:
809      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
810      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
811        ADAMS_BASHFORTH2.
812    o pkg/cheapaml:
813      - add new parameter (default=F, same as before) to disable full domain
814        (including land) periodicity in X & Y dir.
815      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
816        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
817        into single S/R CHEAPAML_TIMESTEP.
818    
819    checkpoint64d (2013/02/17)
820    o pkg/monitor (angular momentum):
821      - do not add Eta contribution to the total AM if using rigid-lid;
822      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
823      - horizontal discretisation: compute Zonal wind contribution separately for
824        each component (instead of from cell centered averaged) and use the 4
825        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
826      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
827        FreeSurf) if using vectorInvariant momentum.
828    o model/src (horizontal grid):
829      - move initialisation of all horizontal grid arrays to null value
830        from specific horizontal grid S/R to main S/R INI_GRID;
831      - add 2 new arrays to project model C-grid velocity on to zonal direction
832        (similar to AngleCosC & -AngleSinC but at U and V point location) and
833        compute them in S/R CALC_GRID_ANGLES.
834    o pkg/seaice: replace a hard coded parameter by a runtime parameter
835        SEAICE_JFNK_tolIter
836    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
837        preconditioner for JFNK (run LSR into the overlaps as far as possible,
838        i.e OLx/y-2, but overwrite the solution in the overlaps)
839      - extend loop range in seaice_calc_viscosity
840      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
841      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
842      - slightly modify loops in tridiagonal solver lsr-preconditioner
843      - by default remove the extra exchange in seaice_preconditioner with a
844        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
845      - modify offline_exf_seaice so that old results without RAS are reproduced
846        for output.dyn_jfnk.txt
847      in seaice_fgmres.F (unrelated to RAS)
848      - add a cpp-flag option for a re-ordered mapping (potentially more
849        efficient), but because this changes the results, turn it off by
850        default
851      - replace the save statement by local common blocks
852    o utils/matlab:
853      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
854      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
855        instead of local script "load_cs.m".
856    o pkg/seaice:
857      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
858        to the scalarProductMetric and the unrolling. By chance this does not
859        change the verification experiment, because of the particular domain
860        decomposition
861    o pkg/diagnostics:
862      - change default missing_value from UNSET_RL to -999.
863    o pkg/layers: improve vectorization of layers_fluxcalc.F
864      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
865        time spent in this routine by more than a factor of 3 on an NEC-SX8
866      - step 2: replace search algorithm by a bisection algorithm found in
867        Press et al. Numerical Recipes in Fortran. This algorithm can be
868        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
869        For now, use this algorithm only for TARGET_NEC_SX defined.
870      - moved the search algorithm into a separate subroutine, that is kept
871        within the same file for automatic inlining.
872      - modified catching potential errors
873    o pkg/ecco:
874      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
875    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
876      - modifications for ALLOW_GENTIM2D_CONTROL
877      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
878      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
879      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
880      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
881    o model/src:
882      - account for moist thermodynamics in (dry) potential temperature equation;
883        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
884        and cpl_aim+ocn.
885      - also switch to standard compiler (gfortran, was using ifort previously)
886        for fizhi-cs experiments reference output.
887    o pkg/ctrl:
888      - 1st step toward generic time-varying control variable (2D) via CPP option
889        ALLOW_GENTIM2D_CONTROL
890      - note new namelist ctrl_nml_genarr in data.ctrl
891    o verification/global_ocean.cs32x15:
892      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
893        thsice calling sequence and update "output.icedyn.txt" output file.
894    o pkg/ptracers:
895      - from Ryan A.: code to allow to restart a tracer at regular time interval
896        specifying a reset frequency and a reset-phase (for each tracers).
897    o pkg/thsice:
898      - implement new sequence of calls for thsice+seaice:
899          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
900          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
901      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
902        in CPP_OPTIONS.h) to recover old sequence;
903      - update diagnostics for Intermediate State thsice diagnostics: now filled
904        just before advection (instead of just after advection in old sequence);
905      - update output of experiment offline_exf_seaice (standard test);
906      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
907        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
908    o pkg/aim_v23:
909      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
910      - use standard pkg/mdsio routines to read & write CO2 pickup file;
911      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
912      - Implement new sequence of calls for seaice advection (with thsice and
913        seaice diffusion): do ice advection after ice-Thermodynamic (previously
914        was done before); change aim_do_physics.F (split the bi,bj loops block);
915      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
916    o pkg/thsice:
917      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
918        where just seaice diffusion is used without seaice-dynamics.
919    
920    checkpoint64c (2013/01/18)
921    o pkg/seaice:
922      - add a parameter JFNKres_tFac that can replace JFNKres_t
923        (= JFNKres_tFac*JFNKresidual before JFNK solver)
924      - add a line search option to the JFNK solver
925      - move update of u/vIce and computation of initial residual into a separate
926        routine (same file); makes the code a little easier to read (?)
927      - the line search requires computation of the residual and for some reason
928        I cannot do the update of u/vIce at the beginning of the Newton loop
929        without changing the results, so we move computation of the new residual
930        also to the end of the Newton loop, even without the line search
931    o pkg/mdsio:
932      - write missing value (corresponding to undefined array value) to meta files;
933        skip this if missing value is one (UNSET_RL would be a better value for the
934        case of undefined missing value but it's current the default missing-value);
935        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
936    o pkg/exf & thsice:
937      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
938        diagnostics) even when SHORTWAVE_HEATING is #undef;
939    o verification/cfc_example:
940      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
941        illustrate how to use it).
942    o verification/offline_exf_seaice:
943      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
944        files to only one time-record.
945      in input.thermo: narrow the 2 bands of low initial ice-concentration near
946        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
947        snapshot output; same mcPheePiston value as in thsice with
948        surf-current=0.2m/s.
949      in input.thsice: similar set-up as in input.thermo (channel with same seaice
950        initial conditions).
951    o verification/cfc_example:
952      - update file "data" with more standard choice (default rotationPeriod,
953        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
954        set deltaTFreeSurf to deltaTtracer) and update the output.
955    o pkg/layers:
956      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
957      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
958    o verification/offline_exf_seaice:
959      - set all {field}period to zero for constant-in-time forcing (not tested
960        anywhere else).
961    o verification/offline_exf_seaice:
962      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
963      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
964    o model/src:
965      - implement Finite-Volume method for (hydrostatic) presure gradient
966        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
967    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
968      - In order to be compatible with the default EVP code, this requires changing
969        the EVP code around a little; and because any small change immediately
970        breaks the lab_sea.hb87 verification experiment, the reference output is
971        updated two times (each time the remaining aggrement was only 2 digits):
972        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
973        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
974        The adjoint test lab_sea.evp also needed to be updated.
975      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
976        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
977        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
978        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
979        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
980        kept obscure, because I need to test it a little more.
981    o pkg/cheapaml:
982      - fix few incorrect type (_RL/_RS) in subroutine calls.
983    o pkg/seaice:
984      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
985        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
986    o model/src:
987      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
988        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
989        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
990    o pkg/cheapaml:
991      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
992        update output of experiment cheapAML_box.
993      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
994        and set them only in one place (cheapaml_readparms.F).
995      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
996      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
997        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
998    o model/src/the_main_loop.F:
999      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
1000    o pkg/seaice:
1001      - remove legacy branch code.
1002      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
1003    o verification/*/code*/SEAICE_OPTIONS.h:
1004      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
1005        SEAICE_CAP_HEFF).
1006    o pkg/cheapaml:
1007      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
1008        to load new forcing fields.
1009      - add missing "_d 0" where it's needed; + some editing (improve indentation).
1010      - remove switch to "-r8" compiler option (no longer needed) in verification
1011        cheapAML_box, keep same output (small trucation error differences).
1012    o verification/offline_exf_seaice:
1013      - add thermodynamics only test.
1014    o verification/cheapAML_box:
1015      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
1016        keep same output (same 14 digits for cg2d).
1017      - switch on "-r8" compiler option (some numerical values are missing
1018        the "_d 0") and update output (only 6 digits for cg2d were preserved).
1019    
1020    checkpoint64b (2012/12/24)
1021    o pkg/cheapaml:
1022      - remove un-used variables (Qnet,EmPmR) from pickup files.
1023      - store tendency of advected variables into cheapaml pickup file
1024        and fix the AB-2 restart.
1025    o verification/offline_exf_seaice and lab_sea adjoint:
1026      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
1027      - switch to 4 time steps in offline, consistent with lab_sea.
1028      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
1029      - update results after change of experiment seaice.
1030    o pkg/seaice:
1031      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
1032        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
1033        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
1034        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
1035    o model/src:
1036      - add run-time parameter to select CG2D solver minimum-residual solution
1037        (in case of a poor convergence).
1038    o pkg/seaice/seaice_lsr.F
1039      - move calculation of matrix coefficients into new
1040        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
1041        file; the main purpose of this change is to be able to reuse the code
1042        in S/R SEAICE_PRECONDITIONER
1043      - modify the computation of the residual so that the mass of sea-ice
1044        is not used twice; this simplifies the calculations, but since
1045        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
1046        not tested in testreport---this does not affect the testreport results.
1047    o verification/seaice_obcs:
1048      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
1049        verification/lab_sea/input.salt_plume; changes results/output.txt*
1050    o model/src:
1051      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
1052    o pkg/seaice:
1053      - improve description of parameters in seaice_fgmres.F and start
1054        cleaning up the code
1055      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
1056        second argument
1057      - add a metric based on grid cell area to SEAICE_SCALPROD; update
1058        results of offline_exf_seaice.dyn_jfnk
1059      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
1060    o pkg/aim_v23:
1061      - fix an other bug in dissipation heating (grid-cell area was missing).
1062    o model/src + pkg/seaice:
1063      - add global (multi-tile) linear solver for pair of tri-diagonal system
1064        along X and Y lines, respectively for U and V component.
1065        Note: 1) MPI and cube-exchange not yet coded.
1066            2) probably not accurate for poorly conditioned / large size problem.
1067      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
1068        default: not compiled and not used.
1069    o pkg/seaice:
1070      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
1071        introduce bi/bj loops and use global_sum_tile_rl instead of
1072        mpi_allreduce in seaice_fgmres.F
1073      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
1074      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
1075      - add a verification experiment for JFNK in offline_exf_seaice
1076    o verification:
1077      - change (for now, only fwd test) offline_exf_seaice experiment:
1078        use a re-entrant channel with idealized coastline (trapezoidal shape)
1079        at southern boundary to explore seaice dynamics and thermodynamics
1080        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
1081        secondary test (input.thsice) use thermodynamics only with SST relaxation.
1082      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
1083    o pkg/exf:
1084      - disable "sstExtrapol" when Nr=1
1085    o verification:
1086      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
1087        to test pkg/cheapaml.
1088    o pkg/aim_v23 & pkg/shap_filt:
1089      - fix dissipation heating (erroneous gravity multiplication factor).
1090    o pkg/seaice:
1091      - remove unused field pressPre from jfnk solver
1092      - rename two subroutines in seaice_preconditioner.F
1093    o eesupp/src:
1094       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
1095    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
1096       - remove wrong parts of the rhs and the lhs (were in there
1097         because I did not understand the concept of this preconditioner)
1098       - add an exchange between u- and v-sweep. This increases communication
1099         by a factor of two but improves the convergence of jfnk. Ideally,
1100         one would like the u- and v-sweep to be independent. So far within
1101         undocumented ifdefs
1102       - reorganize the extra computations for printing the residuals
1103    o tools/genmake2:
1104      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
1105        since it's not necessary (and was preventing to use MNC in some cases).
1106    
1107    checkpoint64a (2012/11/16)
1108    o pkg/autodiff:
1109      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
1110        autodiff_readparms.F no longer depends on calling order (within
1111        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
1112        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
1113        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
1114    o pkg/obcs:
1115      - adding tidal velocity forcing capability to obcs
1116        for usage example, see verification/seaice_obcs/input.tides
1117    o pkg/seaice:
1118      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
1119        SEAICE_LSRrelaxU/V
1120      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
1121    o pkg/aim_v23:
1122      - implement heating from friction (bottom friction and stratospheric drag).
1123    o pkg/shap_filt:
1124      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
1125        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
1126    o model/src:
1127      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
1128        time-constant addMass field from file (addMassFile);
1129      - support for heating due to friction (and Kinetic Energy dissipation):
1130        add option, run-time switch and 3-D field array + support code ; each pkg
1131        or S/R can add heating contribution (if there is a sink of KE); the sum is
1132        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
1133  o pkg/seaice:  o pkg/seaice:
1134      - complete merge of ITD code into seaice_growth.F
1135        from MITgcm_contrib/torge/itd/code/
1136        no verification so far, but Torge Martin tested
1137        "1-D test case and Beaufort set up;
1138        deliver okay results after 1 model year."
1139      - complete merge of SEAICE_SIZE.h into all relevant routines
1140      - move computation of eta at Z-points into calc_viscosities
1141        + introduce global field etaZ
1142        + add different methods for computing etaZ, for now the old
1143          method (simple averages of eta to Z-points) is hardwired
1144        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
1145          seaice_preconditioner
1146      - simplify computations for SEAICE_ZETA_SMOOTHREG
1147      - seaice_preconditioner:
1148        + replace one remaining press by pressLoc (mistake)
1149        + adjust printing of residuals
1150      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
1151        + add (SEAICE.h) and rename some counters (initiliased in
1152          seaice_init_fixed.F)
1153        + add _BEGIN/END_MASTER (myThid)  around print statements
1154        + print total number of iterations and failures over SEAICE_monFreq
1155          interval to STDOUT
1156      - move control over output-messages by fgmres to seaice_jfnk to save
1157        some operations
1158    - move resetting initial guess for fgmres outside of seaice_fgmres_driver    - move resetting initial guess for fgmres outside of seaice_fgmres_driver
1159      in order to make restarts with sol .ne. zero (fgmres with restarts)      in order to make restarts with sol .ne. zero (fgmres with restarts)
1160      (seaice_jfnk.F, seaice_fgmres.F)      (seaice_jfnk.F, seaice_fgmres.F)
1161    - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes    - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
1162      a serious convergence problem when open boundaries are involved      a serious convergence problem when open boundaries are involved
1163  o pkg/ggl90: fix computation of control volumes for the case of  o pkg/ggl90: fix computation of control volumes for the case of
1164    ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes    ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
1165    up half a grid cell from C-centered to W-centered (pointed out by C. Eden)    up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
1166  o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC  o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
1167  o pkg/autodiff  o pkg/autodiff
1168    - Add inAdMode switch for SEAICEuseDYNAMICS:    - Add inAdMode switch for SEAICEuseDYNAMICS:
1169      SEAICEuseDYNAMICSinAdMode      SEAICEuseDYNAMICSinAdMode
1170      (extend logic in ADAUTODIFF_INADMODE_SET)      (extend logic in ADAUTODIFF_INADMODE_SET)
1171  o pkg/seaice  o pkg/seaice
1172    - Step 1 of merging ice-thickness distribution (ITD) code from    - Step 1 of merging ice-thickness distribution (ITD) code from
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