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revision 1.1851 by jmc, Fri Apr 5 21:29:21 2013 UTC revision 1.2011 by mlosch, Wed Jun 25 10:57:05 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
8      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
9        SEAICE_SIZE.h
10      - add a store directive in S/R seaice_calc_viscosities
11    o pkg/seaice (ITD code):
12      - fix definition of Hlimit for multi-threaded case
13      - use double precision arithmetic to compute Hlimit: this affects results;
14        update output of experiment seaice_itd.
15    o replace content of verification/seaice_itd
16      - instead of a 1D column use the configuration of offline_exf_seaice
17        to test the ice thickness distribution code with ridging
18      - this is a first shot at this experiment
19      - change of some defaults of ridging parameters SEAICEhStar (from
20        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
21        and lot of new comments.
22    
23    checkpoint64y (2014/06/20)
24    o pkg/seaice/seaice_reg_ridge.F:
25      - modify the regularization of very small volumes of ice; only check
26        total volume HEFF, and do not apply correction to individual ice
27        classes because that leads to funny patterns in the heat and fw-fluxes
28        into the ocean. Adjust seaice_itd/results/output.txt
29      - replace nITD by SEAICE_multDim in loop-ranges
30    o pkg/exf:
31      - add code to process the case field period = -12. with UV interpolation.
32      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
33        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
34    o verification/global_with_exf:
35      - switch all fields period to -12. (was previously untested) in input/data.exf
36        (but keep secondary test ".yearly" unchanged); update the reference output.
37    o pkg/cal:
38      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
39    o pkg/exf:
40      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
41        to replace logical switch "exf_verbose"
42      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
43    o pkg/sbo:
44      - update from Katherine Quinn: evaluate mass directly from density and SSH
45        (budget using Finite Volume method) instead of from bottom pressure.
46      - allow testreport to collect few selected SBO output ; tested in exp.
47        global_ocean.90x40x15 (after updating the results, to include SBO output).
48      - fix some multi-threading issues (in output part).
49    o model/src & most packages:
50      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
51      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
52        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
53        "data.{pkg}" exist ; and leave the S/R (return) just after.
54      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
55        + call LAND_READPARMS from packages_readparms.F
56    o pkg/seaice:
57      - remove code that resets useThSice in S/R seaice_readparms and
58        replace it by a warning in S/R seaice_check
59      - remove parameter MULTDIM, replace with nITD and runtime
60        parameter SEAICE_multDim (still hard-wired to nITD if
61        SEAICE_ITD is defined)
62    
63    checkpoint64x (2014/05/24)
64    o verification/lab_sea:
65      - update adjoint and TLM output following changes to pkg/salt_plume
66      - un-do the update after putting back local recip_Cp in few places.
67    o pkg/salt_plume: modifications by An Nguyen:
68      - add capability to do brine rejection (salt-plume) as function of
69        volume+tracers (instead of only salinity tracer).
70      - conserve volume by exchanging volume from each kLev to above to
71        accommodate in-coming brine volume
72      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
73      - switch KPP surf buoyancy due to brine forcing to 3-d
74        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
75      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
76      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
77        in East/West Arctic.
78    o pkg/sbo:
79      - incorporate modifications from Katherine Quinn to enable the use of sbo
80        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
81        output for future testreport verification (unfinished).
82    o pkg/atm_phys:
83      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
84        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
85        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
86    o pkg/seaice
87      seaice_calc_ice_strength.F: modify expression to avoid divisions
88        (affects truncation)
89      seaice_do_ridging.F: clean up the insectarium
90      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
91      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
92      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
93      - add some debugging information and error messages (warnings)
94    o model/src: modifications relatd to atmosphere p*:
95      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
96      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
97        of vertical profile tRef in geopotential background and anomaly.
98      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
99        and pkg/atm_phys.
100      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
101        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
102    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
103    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
104        not used right now, but can be used in BGC packages to fix conservation.
105    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
106        other packages too.
107    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
108        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
109    o model/src:
110      - since we have several heat capacity (even in model/src), define "recip_Cp"
111        as local variable (no longer in common block) to avoid any confusion.
112      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
113    o pkg/exf:
114      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
115        air density as function of air Temp, Humidity and atm pressure.
116    
117    checkpoint64w (2014/05/02)
118    o verification:
119      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
120        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
121        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
122        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
123        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
124    o model/src: for atmosphere in p* coords:
125      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
126      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
127        but not yet activated.
128    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
129      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
130      - this changes the results (but not for any verification experiment, because
131        none tests this), but avoids having an extra field in the restart files
132    o pkg/seaice: remove global variable TICE (not needed)
133      - replace by TICES or local variable where necessary (cost_seaice_test,
134        seaice_diagnostics_state)
135      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
136      - use specific read/write routines for reading and writing individual leves
137        of a multilevel field
138    o pkg/ctrl & model/inc:
139      - move additional anomaly fields of control vars (related to options:
140         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
141        from DYNVARS.h into new header file: CTRL_FIELDS.h
142    o pkg/seaice: some small modifications to the ridging code
143      - make fw2ObyRidge a global variable and add the freshwater flux to
144        seaice_growth
145      - pass actual thickness from seaice_prepare_ridging, so that it is
146        computed only in one place and compute it in the same way as in
147        seaice_growth
148      - initialise more fields in seaice_do_ridging that where cause floating
149        point exceptions over land
150    o pkg/seaice: preparations for ridging code and first real ridging code
151      - move most of "PART 1" of S/R seaice_growth into a new and separate
152        S/R seaice_reg_ridge that will both regularize the state variable after
153        advection call the actual ridging routine;
154      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
155        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
156      - remove ridging code from seaice_advdiff
157      - clean up remaining part 1 of seaice_growth in an attempt to make it
158        more readable (this is probably subjective)
159      - call seaice_itd_redist once in the initialisation phase to have the initial
160        conditions in the correct category
161      - finally: add new ridging routine for ITD code
162    
163    checkpoint64v (2014/04/11)
164    o pkg/ecco:
165      - add runtime parameters mdt[start,end]date[1,2]
166      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
167    o pkg/seaice:
168      - make deltaC a global variable, so that it can be used in ridging code
169      - first step towards ridging: introduce new routines that compute
170        ice strength based on ridging parameters
171      - add diagnostic for HSNOWITD
172      - add opnWtrFrac as a global variable (required for ridging scheme)
173    o pkg/salt_plume + pkg/seaice/seaice_growth.F
174      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
175        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
176    o verification/hs94.1x64x5:
177      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
178      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
179    o autodiff:
180      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
181        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
182        For now, only in pkgs used in verification/hs94.1x64x5.
183      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
184        which are specific to TAF/TAMC).
185      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
186        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
187        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
188      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
189        building mitgcmuv_ad (make adAll).
190    o pkg/ecco:
191      - cost_gencost_seaicev4.F:
192         reformulate proxy cost as function of sst and local param SEAICE_freeze
193         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
194      - add stop statement if old names siv4-[sst,vol] are used
195      - add snapshots + cost reports for atmospheric longwave
196      - remove factor 0.1 in front of wtau[u,v]
197      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
198         ALLOW_TMI_SST_COST_CONTRIBUTION
199    o pkg/atm_phys:
200      - add some diagnostics for Short-wave and for convection S/R.
201    o pkg/seaice/seaice_growth:
202      - fix a bug in the lateral melt parameterization for SEAICE_ITD
203        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
204      - rearrange loop order for better vector code in the same code block
205      - rewrite the floeDiameter formula to have fewer divisions
206      -  (miraculously) none of this changes the results of seaice_itd
207    o pkg/smooth:
208      - move param smooth2Ddiffnbt to pkg/ecco
209    o pkg/salt_plume:
210      - salt_plume_frac.F:
211         clean up local param names
212         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
213    o pkg/rw:
214      - add RS version of S/R READ_MFLDS_LEV.
215    o pkg/streamice:
216      - fix the restart test by writing/reading pickup_streamice files.
217    o pkg/seaice:
218      - refine checks for jfnk-related parameters
219      - comment out if statement with SEAICEuseIMEX parameter as long as there
220        is no IMEX code to avoid confusion and surprises
221    
222    checkpoint64u (2014/03/07)
223    o verification/MLAdjust:
224      - rename secondary test suffix:
225         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
226         0.leithD -> AhFlxF  + switch to flux-form
227         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
228         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
229    o pkg/mom_vecinv:
230      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
231        to be before mom_calc_visc.F)
232      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
233      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
234        this is simpler for the adjoint and for diagnostics.
235    o model/src + pkg/momentum:
236      - add input files for  2-D additional Western and Southern cell-edge wall
237         (e.g., to add "thin-wall" where it is =1).
238      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
239        using 2nd hFacZ that is computed from initial (fix domain) hFac
240      - known limitations of thin wall implementation: not yet coded for sigma
241        coords; not working with CD-scheme neither.
242    o pkg/seaice:
243      - rename recently introduced parameters from (wrong name) AB to
244        BDF (backward difference time discretisation)
245      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
246    o tools/adjoint_options:
247      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
248    
249    checkpoint64t (2014/02/01)
250    o pkg/ecco
251      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
252        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
253      - replace hard-coded record number and period which only work for monthly
254        with read-in runtime param that works for other periods (month,day,year)
255    o pkg/thsice
256      - corrected store directive fixes thsice adjoint gradient checks
257    o genmake2 & testreport:
258      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
259        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
260        Update testreport accordingly. No need to set "export OPENAD=true"
261        in adjoint_options/adjoint_oad anymore (will be removed later).
262    o pkg/shelfice:
263      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
264        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
265        so that surface forcing applies to k=kSurf if using pkg/shelfice.
266    o pkg/ctrl, pkg/grdchk, pkg/ecco:
267      - Changes to make GENARR more modular (i.e. invisible if not used)
268    o model/src/temp_integrate.F and salt_integrate.F
269      - re-include store directives that were removed on Dec 27th.
270    o model/src/external_forcing_surf.F
271      - add storage directives for EmPmR and PmEpR to avoid recomputation of
272        seaice_model in the adjoint that is problematic when seaice_model is
273        turned off in the adjoint. The resolved issue dated back to July when
274        EXTERNAL_FORCING_SURF call was moved.
275        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
276    o pkg/exf/exf_check.F
277      - fix a small bug again (originally found by Wentao Liu, now found again)
278      - streamline error output
279    o pkg/streamice and aim_v23:
280      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
281        Apple's /usr/bin/cpp knows what to do:
282        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
283        Target: x86_64-apple-darwin13.0.0
284    
285    checkpoint64s (2014/01/05)
286    o tools/adjoint_options:
287      - switch to fastopt.net TAF server (instead of default fastopt.de) for
288        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
289    o model/src:
290      - remove some unnecessary TAF storage directives in forward_step.F and
291        in dynamics.F (note: not always removed by TAF, e.g., double storage
292        of kappaRU,kappaRV in former version of dynamics.F).
293    o model/src & pkg/ptracers:
294      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
295        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
296        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
297      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
298      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
299      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
300    o useSingleCpuInput separates single-CPU input from single-CPU output;
301        for now only implemented for in exf_interp_read.F
302    o verification/advect_xy:
303      - fix missing EXCH call in local version of ini_salt.F and update output.
304    o momentum diagnostics:
305      - fix which deltaT is used in Total-Tendency diagnostics.
306      - fix typo in diagnostics for momentum tendency from AB.
307    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
308        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
309    
310    checkpoint64r (2013/12/08)
311    o verification/*/results:
312      - Update reference output of experiments that were passing with just 13 digits
313         (make it easier to detect future changes in results)
314    o model/src & pkg/ptracers:
315      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
316        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
317        to inside ptracers_integrate.F ; remove ptracers_advection.F
318    o coupling interface pkgs:
319        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
320      - change the config check to test the agreement of Ocean Depth
321        with ATM land/sea mask (instead of ATM orography);
322      - send to coupler the number of coupler time-steps to do for this run:
323        this allows to check for consistency and don't need anymore to be
324        specified in parameter file "data";
325      in coupler:
326      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
327      - improve report to log-file of config setting (pass log-file unit to few S/R)
328    o pkg/compon_communic:
329      - add coupling send/receive for non-tiled integer vector;
330      - add S/R to check and stop if any proc has an error (similar to
331        eesupp/src/stop_if_error.F but single thread and across Comm_World).
332    o pkg/exch2:
333      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
334        through list of all tiles my proc owns.
335    o model/src:
336      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
337        from rTrans) to simplify dependencies (no need to store rTrans anymore in
338        calling S/R); this affects AD results at machine truncation level:
339        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
340        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
341    o tools/build_options:
342      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
343    o coupling interface pkgs:
344        [compon_communic, atm_compon_interf & ocn_compon_interf]
345      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
346        to each S/R that needs it; remove un-used variables.
347      - change component tile registration (cpl_register.F in both compon_interf
348        and mitcomponent_tile_register.F) to pass the full list of tiles
349        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
350      - with pkg/exch2: adopt the same convention used for I/O to define mapping
351        towards coupler global array (unless W2_useE2ioLayOut=F):
352         a) can now use different tiling between atm & ocn comp.
353         b) no needs to modify the run-Off map when changing tiling (was needed
354            even if using the same tiling between atm & ocn).
355         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
356            full land tiles); not yet tested.
357      - check for valid mapping from comp. tile to coupler global array
358      - improve report of tile registration results to log file.
359    o pkg/exch2:
360      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
361        tile-registration (CPL_REGISTER);
362      - activate (un-comment) definition and setting of "W2_tileIndex" list to
363        store the local bi,bj indices of each tile;
364      - also print bi,bj in local report to log file;
365      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
366        Jun 2009 modif of pkg/exch2).
367    o testing on baudelaire:
368      - run 2 tests at a time: no significant slow down (since enough cpu) and
369        get the full set of test done earlier
370      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
371    o model/src/thermodynamics.F and routines called from it:
372      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
373        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
374        velocity (outp) by adding bolus velocity.
375      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
376        mass transport from velocity + lateral grid cell area
377      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
378      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
379     in thermodynamics.F
380      - remove k from thermodynamics.F and move it to temp_integrate.F
381        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
382        loop).
383      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
384        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
385        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
386        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
387      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
388        global_ocean.90x40x15, tutorial_global_oce_biogeo and
389        tutorial_tracer_adjsens (+ TLM output).
390    o tools/OAD_support and (verification/*/) code_oad:
391      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
392        module conversion ; remove unneeded CPP_EEOPTIONS.h.
393      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
394        version (closer to model/inc/CPP_OPTIONS.h).
395    o model/src:
396      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
397        retired list of parameters (routine FREEZE has been replace by surface
398        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
399    o pkg/gmredi:
400      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
401        velocity (same scheme but affects machine truncation) for GM_AdvForm.
402      - update output of FWD experiments: front_relax.bvp,
403        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
404    
405    checkpoint64q (2013/11/17)
406    o verification:
407      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
408        tutorial_global_oce_biogeo and global_ocean.90x40x15.
409      - generate new output (growth & melt) for seaice_itd experiment after
410        updating the input pickup_seaice files (previously wrong).
411    o pkg/cost:
412      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
413        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
414        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
415          cannot be applied to var in common block).
416        o allows to get results independent of tile-per-proc setting (if using
417          slower GLOBAL_SUM_SEND_RECV option).
418      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
419        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
420        forward gradients: update output).
421      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
422        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
423    o pkg/mom_common:
424      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
425        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
426        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
427        ensure that all field value that are used are set.
428    o tutorial_deep_convection (smag3d):
429      - add missing scaling in mom_calc_smag_3d.F;
430      - set smag3D_coeff in input.smag3d such that results do not change.
431    o pkg/dic:
432      - change dic_cost.F to compute cost on each tile first and then apply
433        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
434        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
435      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
436    o eesupp/src & pkg/mdsio:
437      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
438        (from pkg/mdsio) since they are no longer used for tape IO.
439      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
440        (+ keep a copy in pkg/atm_ocn_coupler).
441    o verification/isomip:
442      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
443    o tools/build_options:
444      - optfile linux_amd64_ifort11, fast (no ieee) case:
445        to get a working restart for all experiments, add "-fp-model source"
446        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
447    
448    checkpoint64p (2013/10/20)
449    o pkg/autodiff:
450      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
451        criteria, return to simple (default) tape IO format.
452    o pkg/mdsio (+ eesupp/src):
453      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
454        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
455      - fix globalFile and singleCpuIO options using simpler global mapping.
456      - new pairs of scatter/gather vector S/R (one for each type, generated from
457        template) corresponding to simpler global mapping.
458      - adread_write.F: switch to new S/R (but leave old calls commented) and write
459        to globalFile when parameter globalFiles is set to True.
460      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
461    o pkg/autodiff:
462      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
463        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
464        missing, just add a STOP if array type do not match.
465    o pkg/exf:
466      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
467         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
468         and rename array obsSIce to exf_iceFraction.
469    o tutorial_deep_convection:
470      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
471        for now all in this exp. code dir.
472      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
473        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
474    o eesupp/src:
475      - added SINGLE_DISK_IO option because reading of parameter files on
476        very large number of processors did not work with existing set-up
477    
478    checkpoint64o (2013/09/25)
479    o pkg/atm_phys & atm_compon_interf:
480      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
481    o tools/build_options:
482      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
483        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
484        remove CPP setting (was identical to genmake2 default).
485    o pkg/gmredi & model/src: Some updating and work done on the residual model.
486      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
487      - fixed up the calculation of the eddy stress and how it is added to the
488        external forcing via taueddy_external_forcing.F
489      - at the moment, it is very experimental and only works with the variable eddy
490        diffusivity calculated in gmredi_k3d.F
491    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
492        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
493    o testreport (& tools/do_tst_2+2):
494      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
495    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
496      - remove CPP='cpp -traditional -P' (this is genmake2 default)
497      - add switch (for big setups) to use 'medium' memory-model (but leave it
498        commented out for now). Note: needed with FC 19 to compile big setups.
499    o pkg/atm_compon_interf:
500      - regroup per field origin (model & pkgs) the coupling storage routines
501         (which accumalate in time each coupling field)
502      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
503        update accordingly + simplify aim_do_physics.F
504    
505    checkpoint64n (2013/08/26)
506    o pkg/bbl:
507      - update formulation to reduce dispersion of tracer properties in bbl
508      - replaced horizontal and vertical transport parameters with velocities
509      - changes results for verification/global_with_exf.yearly
510    o verification/halfpipe_streamice:
511      - change to matrix construction; update both Fwd & AD output.
512    o verification/tutorial_tracer_adjsens:
513      - OpenAD test: switch to vector-invariant momentum since fluxform with
514        rStar causes problems with OpenAD; update output.
515    o tools:
516      - genmake2: define a common prefix for all temp-file names ; move them
517        to local /tmp disk (but would be easy to move them back);
518      - xmakedepend: apply the same switch for temp-files.
519    o pkg/offline:
520      - changes for use with rStar (NLFS): assume that we continue to provide
521        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
522        output files) and apply r* scaling at each time-step (function of the time
523        varying Eta field); use normal pickup files (needed for restart with NLFS).
524    o adjoint with OpenAD:
525      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
526        package openad.  This package has to be compiled for all runs with OpenAD
527        instead of specifying code_oad_all as a modification directory.
528      - link the fortran templates from tools/OAD_support to the build directory
529        for preprocessing to avoid conflicts between different setups compiled
530        simultaneously and simplify cleanup.
531    o pkg/exf:
532      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
533        main model or other pkgs are exchanged in EXF_MAPFIELDS).
534    o model/src:
535      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
536        (similar to do_fields_blocking_exchanges.F).
537    o tools/genmake2:
538      - remove TAF output src code just before calling staf (when not doing a fresh
539        built, will stop if things go wrong with staf).
540      - fix target "adobj" (left from TAF version-2 transition)
541    o pkg/diagnostics:
542      - add a parameter to track the status of pkg/diagnostics activation;
543        this replace/extend the use of logical param "settingDiags" (to check
544        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
545        New S/R to print error message and stop when pkgStatus is not right.
546      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
547    
548    checkpoint64m (2013/08/13)
549    o model/inc:
550      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
551        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
552    o pkg/kpp & aim_v23:
553      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
554    o pkg/seaice:
555      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
556        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
557      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
558    o eesupp/src:
559      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
560        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
561    o switch to TAF version-2:
562      - add flow directives to "freeze" naming convention for ad-routines that
563        are used in I/O routines of adjoint state and associated common blocks
564        that are used in adcommon.h (backward compatible with version-1)
565      - update all ad-optfiles (in tools/adjoint_options + few local to some
566        verification exp) to switch to latest TAF version (currently 2.5.5);
567        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
568        out except for diva).
569      - the major change with TAF version-2 is that both the differentiated
570        routines and the forward routines (new) are returned as part of the TAF
571        output source code. Update genmake2 accordingly.
572      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
573        with version-2 when compared to TLM or FWD gradient); other experiments
574        output show minor changes (machine truncation level); update the few AD &
575        TLM output with 12 matching digits only (some prior to version-2 switch).
576    
577    checkpoint64l (2013/08/05)
578    o model/src:
579      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
580      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
581        when using TAF but only if using OpenAD.
582    o pkg/mom_common+fluxform+vecinv:
583      - always set horiz. viscosity arrays to background value before calling
584        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
585        only when using variable horiz. viscosity (useVariableVisc=T);
586      - simplify mom_vecinv.F (only 1 block for momViscosity).
587    o pkg/mom_common: variable horiz. viscosity in NH code
588      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
589        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
590      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
591        useBiharmonicVisc & useVariableVisc.
592      - fix old bug (already in 1rst implementation of variable horizontal viscosity
593        in calc_gw.F, version 1.27, 2006/06/20):
594        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
595        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
596      - change background horiz viscosity in vertical momentum (gW) to always be
597        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
598        any type of variable viscosity, e.g., viscAh/4Grid)
599      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
600        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
601        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
602        default viscAh,viscA4 is zero).
603    o model/src:
604      - extend length of drC & recip_drC from Nr to Nr+1.
605    o Divided Adjoint (DIVA) with MPI:
606      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
607      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
608        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
609    
610    checkpoint64k (2013/07/23)
611    o tools/OAD_support:
612      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
613        and remove it from genmake2.
614    o tools/build_options:
615      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
616        MPI_HEADER_FILES list (let genmake2 find the missing headers)
617    o verification/halfpipe_streamice:
618      - change to driving stress formulation; update both Fwd & AD output.
619    o tools/genmake2 and Divided Adjoint with MPI:
620      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
621      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
622      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
623        Makefile, which is set by genmake2, and check which mpi-headers are needed.
624        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
625      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
626    o testreport:
627      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
628        perform additional runs (number of additional runs is "add_DIVA_runs" taken
629        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
630    o verification/lab_sea (AD test):
631      - change to test Divided Adjoint Run in this set-up (both standard AD test
632        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
633    o pkg atm_ & ocn_compon_interf:
634      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
635        staggerTimeStep implementation) and disable (retired) corresponding
636        parameter.
637    o pkg/offline:
638      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
639      - add S/R OFFLINE_CHECK to print offline parameter summary
640        and stop if loading a file that is not used;
641      - enable to calculate GMRedi tensor, KPP mixing and convective index
642        when the corresponding file(s) is/are not specified (but pkg is used).
643      - comment out resetting of monitorFreq (to endTime) since it still useful
644        for monitoring CFL numbers and checking offline fields.
645    o OpenAD:
646      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
647        smaller standard output) and generate new (smaller) output (on baudelaire
648        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
649    o model/src:
650      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
651        (where external_forcing_adjust was called) and change list of arguments;
652      - merge external_forcing_adjust.F into external_forcing_surf.F
653      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
654        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
655        previously in file "balance_relax.F", now removed); remove corresponding
656        arrays in FFIELDS.h.
657      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
658        a hack for getting back surfaceForcingS (loaded from file) when using
659        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
660      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
661        (was getting only 11 digits for AD-grad, due to different truncation
662         error in AD code).
663    
664    checkpoint64j (2013/07/04)
665    o pkg/offline:
666      - to enable the use of other features with pkg offline (e.g., obcs),
667        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
668      - comment out "allowFreezing" (now active) in 2 offline testing exp.
669    o pkg/exf ALLOW_RUNOFTEMP
670      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
671      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
672      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
673    o pkg/atm_phys:
674      - allows to add some damping on uVel,vVel (strength only function of k).
675    o verification, ad-tests:
676      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
677        global_ocean_ebm and offline_exf_seaice.thsice.
678    o verification/halfpipe_streamice:
679      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
680        flux input boundary conditions to be ignored; a fix for this bug changed
681        verification results for forward test.
682      - add adjoint test.
683    o pkg/ptracers:
684      - allow to restart without SOM pickup (resetting SOM to zero).
685    o pkg/gmredi:
686      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
687      - It uses mixing length theory and suppression by steering level effects to
688        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
689        to JPO, for more details).
690      - It also uses the diffusivity to calculate an eddy induced streamfunction
691        based on a PV closure (rather than a buoyancy closure as in GM).
692      - New files added to pkg/gmredi:
693        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
694          induced overturning streamfunction (called from gmredi_calc_tensor)
695        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
696          for use in gmredi_k3d
697        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
698          the eddy diffusivity
699    
700    checkpoint64i (2013/06/18)
701    o pkg/cheapaml:
702      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
703        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
704        with pkg/cheapaml.
705    o utils/python: add subpackage for cubed sphere function, first example is
706        simple cs.pcol to plot 2D fields on a map
707    o pkg/streamice:
708      - This is a new package in MITgcm, which solves dynamic equations for ice
709         sheets and ice streams
710      - At the moment it is independent of atmosphere/ocean dynamics, or any
711        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
712        ed that this will change)
713      - There is a new verification exercise that tests it, halfpipe_streamice,
714        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
715        rectangular embayment
716      - halfpipe_streamice is forward-only for now, will have TAF test soon
717      - for questions, email dgoldber@mit.edu
718    o pkg/thsice:
719      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
720        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
721      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
722         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
723      - allow precip from pkg/cheapaml to make snow over seaice.
724    o pkg/cfc:
725      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
726      - remove atmos CFC 2-D arrays from common bloc (now local variables)
727      - change some hard-coded constant to run time parameter for reading and
728        and interpolating atmospheric CFC ; keep same default as previously.
729      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
730      - put arguments in standard order: myTime, myIter, myThid
731      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
732        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
733      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
734      - new routine to print summary of CFC params and check for consistency.
735    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
736      similar to thsice_advdiff.
737      Note that for the B-grid case the routine parameters uc/vc are overwritten.
738    o pkg/cfc:
739      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
740        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
741      - fix interpolation of atmphspheric CFC between Sorthern and Northern
742        hemisphere value.
743    o pkg/seaice:
744      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
745    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
746                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
747      - requires an additional time level that is stored in the pickup
748      - you can start with AB2 from a pickup without this time level with
749        pickupStrictlyMatch = .false.
750    
751    checkpoint64h (2013/05/26)
752    o pkg/cheapaml:
753      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
754        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
755      - consistent treatment of uWind,vWind location: assume everywhere in
756        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
757        (Note: was already the case for Tair,Qair advection);
758        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
759      - compute diabatic forcing only in the interior (excluding overlap regions)
760      - fill in array "Qsw" (for short-wave heating);
761      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
762        before any update (consistent with MITgcm state var diagnostics);
763      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
764        non periodic ; + adjusted for uWind,vWind (C-grid).
765    o pkg/seaice:
766      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
767        add explicitly pkg/exf in experiments that currently use pkg/seaice.
768      - allows to compile pkg/seaice without pkg/exf.
769    o tools/OAD_support:
770      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
771        of array "ourStepOf" in function rvNextAction (revolve.F90).
772    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
773      - change pkg name (to be used with other atmospheric physics pkg)
774        but by-pass CVS when making the new pkg so that we keep the CVS history.
775    o pkg/offline:
776      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
777        (previously called from pkg/dic_surfforcing_init.F)
778    o model/src:
779      - re-order sequence of calls within packages_init_variables.F, using
780        standard order, except for:
781         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
782         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
783    o new pkg: atm_phys
784      - add entry point and source code (previously in contrib
785          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
786        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
787      - re-order sequence of calls within packages_readparms.F,
788         packages_init_fixed.F and packages_write_pickup.F
789        (but skip packages_init_variables.F because of TAF issues).
790      - update contrib/*/atm_gray/ experiment.
791    o pkg/seaice (ITD code):
792      - simplify and fix the writing of pickup-files for ITD case
793    o pkg/seaice (ITD code):
794      - introduce floe size dependent lateral melt for ITD case;
795      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
796      - update seaice_itd experiment main output.
797    o pkg/thsice:
798      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
799        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
800        changed accordingly pkg/atm2d.
801    
802    checkpoint64g (2013/05/01)
803    o pkg/exf ALLOW_RUNOFTEMP
804      - if defined,  river and glacier runoff temperature can be read-in from
805        runoftempfile; runoftempfile needs to have same format as runofffile
806    o pkg/thsice (& pkg/bulk_force):
807      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
808        for energy content of Precip + RunOff & Evap (like with pkg/exf).
809      - change computation domain to always be the interior (without overlap).
810      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
811    o verification/tutorial_global_oce_biogeo:
812      - add preliminary OpenAD setup (still has problems)
813    o pkg/seaice:
814      - turn some parameters for choosing the convergence criterion of
815        the inexact Newton method (JFNK) into runtime parameters for convenience
816      - clean up seaice_calc_viscosities.F: remove/retire two options for
817        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
818        the results of lab_sea/input because a division has been replaced by
819        a multiplication with the reciprocal (sumNorm)
820      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
821        convergence of solver (changes results, of course), and to test some
822        new features
823    o model/src:
824      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
825      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
826      - move forcing adjustment (balancing surface forcing) in specific S/R
827        where might also be applied exchanges (if needed) to forcing arrays.
828    o pkg/shelfice:
829      - allow to specify the Ice-Shelf mass per unit area (instead of
830        shelficeLoadAnomaly) and do the conversion from one to the other
831      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
832        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
833        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
834        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
835      - update isomip experiment forward output (get machine truncation error
836        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
837    o verification/offline_exf_seaice:
838      revise data.seaice in input.thermo and input_ad and update results accordingly
839        HO = 0.2, SEAICE_areaLossFormula = 2,
840        SEAICE_growMeltByConv = .TRUE.,
841        SEAICE_doOpenWaterMelt = .TRUE.,
842      Improve consistency with input.thsice and fix the spurious 500m ice corners
843    o verification/global_ocean.cs32x15:
844      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
845        in icedyn (thsice+seaice-dyn) test and update output.
846    o verification/offline_exf_seaice:
847      - adjust list of tested variables (with testreport) and update
848        standard test output with better slection of monitored fields.
849    o pkg/cd_code:
850      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
851        experiment lab_sea.hb87
852  o tools/genmake2:  o tools/genmake2:
853    - change default makedepend from the system default to tools/xmakedepend:    - change default makedepend from the system default to tools/xmakedepend:
854      When no makedepend is specified, select tools/xmakedepend it the test pass,      When no makedepend is specified, select tools/xmakedepend it the test pass,
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