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revision 1.1901 by jmc, Thu Jul 25 01:12:45 2013 UTC revision 1.2017 by mlosch, Mon Jun 30 15:47:20 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      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
9        generates unnecessary code in seaice_lsr_ad
10      - add more store directives in seaice_lsr to avoid unnecessary code
11        in seaice_lsr_ad
12      - exclude some residual computations in seaice_lsr when
13        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
14        in seaice_lsr_ad
15      - add more storing, a new tape (model/src/the_main_loop.F) and
16        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
17        and klockey should be checked by a specialist)
18      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
19        and update lab_sea after previous changes in pkg/seaice below
20    o pkg/autodiff :
21      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
22        viscFacInAd : run time parameters allowing for adjoint switches
23        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
24    o pkg/ecco :
25      - introduce cost_gencost_boxmean.F that computes a box mean
26        temperature (for use in adjoint sensitivity studies).
27    o model/src/set_defaults.F : initialize viscFacAdj to 1.
28    o pkg/mom_common/mom_calc_visc.F :
29      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
30    o pkg/seaice/seaice_summary.F :
31      - statement for SEAICEadjMODE now in autodiff_readparms.F
32    o pkg/seaice
33      - remove some store directives and add new ones in an effort to get
34        finally rid off the recomputation warnings. This is successful
35        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
36        defined (i.e. no extensive recomputation warnings left), but there
37        are still too many recomputations on the solver iteration level
38      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
39      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
40        SEAICE_SIZE.h
41      - add a store directive in S/R seaice_calc_viscosities
42    o pkg/seaice (ITD code):
43      - fix definition of Hlimit for multi-threaded case
44      - use double precision arithmetic to compute Hlimit: this affects results;
45        update output of experiment seaice_itd.
46    o replace content of verification/seaice_itd
47      - instead of a 1D column use the configuration of offline_exf_seaice
48        to test the ice thickness distribution code with ridging
49      - this is a first shot at this experiment
50      - change of some defaults of ridging parameters SEAICEhStar (from
51        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
52        and lot of new comments.
53    
54    checkpoint64y (2014/06/20)
55    o pkg/seaice/seaice_reg_ridge.F:
56      - modify the regularization of very small volumes of ice; only check
57        total volume HEFF, and do not apply correction to individual ice
58        classes because that leads to funny patterns in the heat and fw-fluxes
59        into the ocean. Adjust seaice_itd/results/output.txt
60      - replace nITD by SEAICE_multDim in loop-ranges
61    o pkg/exf:
62      - add code to process the case field period = -12. with UV interpolation.
63      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
64        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
65    o verification/global_with_exf:
66      - switch all fields period to -12. (was previously untested) in input/data.exf
67        (but keep secondary test ".yearly" unchanged); update the reference output.
68    o pkg/cal:
69      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
70    o pkg/exf:
71      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
72        to replace logical switch "exf_verbose"
73      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
74    o pkg/sbo:
75      - update from Katherine Quinn: evaluate mass directly from density and SSH
76        (budget using Finite Volume method) instead of from bottom pressure.
77      - allow testreport to collect few selected SBO output ; tested in exp.
78        global_ocean.90x40x15 (after updating the results, to include SBO output).
79      - fix some multi-threading issues (in output part).
80    o model/src & most packages:
81      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
82      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
83        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
84        "data.{pkg}" exist ; and leave the S/R (return) just after.
85      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
86        + call LAND_READPARMS from packages_readparms.F
87    o pkg/seaice:
88      - remove code that resets useThSice in S/R seaice_readparms and
89        replace it by a warning in S/R seaice_check
90      - remove parameter MULTDIM, replace with nITD and runtime
91        parameter SEAICE_multDim (still hard-wired to nITD if
92        SEAICE_ITD is defined)
93    
94    checkpoint64x (2014/05/24)
95    o verification/lab_sea:
96      - update adjoint and TLM output following changes to pkg/salt_plume
97      - un-do the update after putting back local recip_Cp in few places.
98    o pkg/salt_plume: modifications by An Nguyen:
99      - add capability to do brine rejection (salt-plume) as function of
100        volume+tracers (instead of only salinity tracer).
101      - conserve volume by exchanging volume from each kLev to above to
102        accommodate in-coming brine volume
103      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
104      - switch KPP surf buoyancy due to brine forcing to 3-d
105        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
106      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
107      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
108        in East/West Arctic.
109    o pkg/sbo:
110      - incorporate modifications from Katherine Quinn to enable the use of sbo
111        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
112        output for future testreport verification (unfinished).
113    o pkg/atm_phys:
114      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
115        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
116        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
117    o pkg/seaice
118      seaice_calc_ice_strength.F: modify expression to avoid divisions
119        (affects truncation)
120      seaice_do_ridging.F: clean up the insectarium
121      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
122      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
123      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
124      - add some debugging information and error messages (warnings)
125    o model/src: modifications relatd to atmosphere p*:
126      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
127      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
128        of vertical profile tRef in geopotential background and anomaly.
129      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
130        and pkg/atm_phys.
131      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
132        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
133    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
134    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
135        not used right now, but can be used in BGC packages to fix conservation.
136    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
137        other packages too.
138    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
139        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
140    o model/src:
141      - since we have several heat capacity (even in model/src), define "recip_Cp"
142        as local variable (no longer in common block) to avoid any confusion.
143      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
144    o pkg/exf:
145      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
146        air density as function of air Temp, Humidity and atm pressure.
147    
148    checkpoint64w (2014/05/02)
149    o verification:
150      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
151        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
152        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
153        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
154        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
155    o model/src: for atmosphere in p* coords:
156      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
157      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
158        but not yet activated.
159    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
160      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
161      - this changes the results (but not for any verification experiment, because
162        none tests this), but avoids having an extra field in the restart files
163    o pkg/seaice: remove global variable TICE (not needed)
164      - replace by TICES or local variable where necessary (cost_seaice_test,
165        seaice_diagnostics_state)
166      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
167      - use specific read/write routines for reading and writing individual leves
168        of a multilevel field
169    o pkg/ctrl & model/inc:
170      - move additional anomaly fields of control vars (related to options:
171         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
172        from DYNVARS.h into new header file: CTRL_FIELDS.h
173    o pkg/seaice: some small modifications to the ridging code
174      - make fw2ObyRidge a global variable and add the freshwater flux to
175        seaice_growth
176      - pass actual thickness from seaice_prepare_ridging, so that it is
177        computed only in one place and compute it in the same way as in
178        seaice_growth
179      - initialise more fields in seaice_do_ridging that where cause floating
180        point exceptions over land
181    o pkg/seaice: preparations for ridging code and first real ridging code
182      - move most of "PART 1" of S/R seaice_growth into a new and separate
183        S/R seaice_reg_ridge that will both regularize the state variable after
184        advection call the actual ridging routine;
185      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
186        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
187      - remove ridging code from seaice_advdiff
188      - clean up remaining part 1 of seaice_growth in an attempt to make it
189        more readable (this is probably subjective)
190      - call seaice_itd_redist once in the initialisation phase to have the initial
191        conditions in the correct category
192      - finally: add new ridging routine for ITD code
193    
194    checkpoint64v (2014/04/11)
195    o pkg/ecco:
196      - add runtime parameters mdt[start,end]date[1,2]
197      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
198    o pkg/seaice:
199      - make deltaC a global variable, so that it can be used in ridging code
200      - first step towards ridging: introduce new routines that compute
201        ice strength based on ridging parameters
202      - add diagnostic for HSNOWITD
203      - add opnWtrFrac as a global variable (required for ridging scheme)
204    o pkg/salt_plume + pkg/seaice/seaice_growth.F
205      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
206        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
207    o verification/hs94.1x64x5:
208      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
209      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
210    o autodiff:
211      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
212        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
213        For now, only in pkgs used in verification/hs94.1x64x5.
214      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
215        which are specific to TAF/TAMC).
216      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
217        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
218        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
219      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
220        building mitgcmuv_ad (make adAll).
221    o pkg/ecco:
222      - cost_gencost_seaicev4.F:
223         reformulate proxy cost as function of sst and local param SEAICE_freeze
224         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
225      - add stop statement if old names siv4-[sst,vol] are used
226      - add snapshots + cost reports for atmospheric longwave
227      - remove factor 0.1 in front of wtau[u,v]
228      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
229         ALLOW_TMI_SST_COST_CONTRIBUTION
230    o pkg/atm_phys:
231      - add some diagnostics for Short-wave and for convection S/R.
232    o pkg/seaice/seaice_growth:
233      - fix a bug in the lateral melt parameterization for SEAICE_ITD
234        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
235      - rearrange loop order for better vector code in the same code block
236      - rewrite the floeDiameter formula to have fewer divisions
237      -  (miraculously) none of this changes the results of seaice_itd
238    o pkg/smooth:
239      - move param smooth2Ddiffnbt to pkg/ecco
240    o pkg/salt_plume:
241      - salt_plume_frac.F:
242         clean up local param names
243         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
244    o pkg/rw:
245      - add RS version of S/R READ_MFLDS_LEV.
246    o pkg/streamice:
247      - fix the restart test by writing/reading pickup_streamice files.
248    o pkg/seaice:
249      - refine checks for jfnk-related parameters
250      - comment out if statement with SEAICEuseIMEX parameter as long as there
251        is no IMEX code to avoid confusion and surprises
252    
253    checkpoint64u (2014/03/07)
254    o verification/MLAdjust:
255      - rename secondary test suffix:
256         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
257         0.leithD -> AhFlxF  + switch to flux-form
258         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
259         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
260    o pkg/mom_vecinv:
261      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
262        to be before mom_calc_visc.F)
263      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
264      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
265        this is simpler for the adjoint and for diagnostics.
266    o model/src + pkg/momentum:
267      - add input files for  2-D additional Western and Southern cell-edge wall
268         (e.g., to add "thin-wall" where it is =1).
269      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
270        using 2nd hFacZ that is computed from initial (fix domain) hFac
271      - known limitations of thin wall implementation: not yet coded for sigma
272        coords; not working with CD-scheme neither.
273    o pkg/seaice:
274      - rename recently introduced parameters from (wrong name) AB to
275        BDF (backward difference time discretisation)
276      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
277    o tools/adjoint_options:
278      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
279    
280    checkpoint64t (2014/02/01)
281    o pkg/ecco
282      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
283        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
284      - replace hard-coded record number and period which only work for monthly
285        with read-in runtime param that works for other periods (month,day,year)
286    o pkg/thsice
287      - corrected store directive fixes thsice adjoint gradient checks
288    o genmake2 & testreport:
289      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
290        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
291        Update testreport accordingly. No need to set "export OPENAD=true"
292        in adjoint_options/adjoint_oad anymore (will be removed later).
293    o pkg/shelfice:
294      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
295        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
296        so that surface forcing applies to k=kSurf if using pkg/shelfice.
297    o pkg/ctrl, pkg/grdchk, pkg/ecco:
298      - Changes to make GENARR more modular (i.e. invisible if not used)
299    o model/src/temp_integrate.F and salt_integrate.F
300      - re-include store directives that were removed on Dec 27th.
301    o model/src/external_forcing_surf.F
302      - add storage directives for EmPmR and PmEpR to avoid recomputation of
303        seaice_model in the adjoint that is problematic when seaice_model is
304        turned off in the adjoint. The resolved issue dated back to July when
305        EXTERNAL_FORCING_SURF call was moved.
306        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
307    o pkg/exf/exf_check.F
308      - fix a small bug again (originally found by Wentao Liu, now found again)
309      - streamline error output
310    o pkg/streamice and aim_v23:
311      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
312        Apple's /usr/bin/cpp knows what to do:
313        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
314        Target: x86_64-apple-darwin13.0.0
315    
316    checkpoint64s (2014/01/05)
317    o tools/adjoint_options:
318      - switch to fastopt.net TAF server (instead of default fastopt.de) for
319        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
320    o model/src:
321      - remove some unnecessary TAF storage directives in forward_step.F and
322        in dynamics.F (note: not always removed by TAF, e.g., double storage
323        of kappaRU,kappaRV in former version of dynamics.F).
324    o model/src & pkg/ptracers:
325      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
326        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
327        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
328      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
329      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
330      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
331    o useSingleCpuInput separates single-CPU input from single-CPU output;
332        for now only implemented for in exf_interp_read.F
333    o verification/advect_xy:
334      - fix missing EXCH call in local version of ini_salt.F and update output.
335    o momentum diagnostics:
336      - fix which deltaT is used in Total-Tendency diagnostics.
337      - fix typo in diagnostics for momentum tendency from AB.
338    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
339        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
340    
341    checkpoint64r (2013/12/08)
342    o verification/*/results:
343      - Update reference output of experiments that were passing with just 13 digits
344         (make it easier to detect future changes in results)
345    o model/src & pkg/ptracers:
346      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
347        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
348        to inside ptracers_integrate.F ; remove ptracers_advection.F
349    o coupling interface pkgs:
350        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
351      - change the config check to test the agreement of Ocean Depth
352        with ATM land/sea mask (instead of ATM orography);
353      - send to coupler the number of coupler time-steps to do for this run:
354        this allows to check for consistency and don't need anymore to be
355        specified in parameter file "data";
356      in coupler:
357      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
358      - improve report to log-file of config setting (pass log-file unit to few S/R)
359    o pkg/compon_communic:
360      - add coupling send/receive for non-tiled integer vector;
361      - add S/R to check and stop if any proc has an error (similar to
362        eesupp/src/stop_if_error.F but single thread and across Comm_World).
363    o pkg/exch2:
364      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
365        through list of all tiles my proc owns.
366    o model/src:
367      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
368        from rTrans) to simplify dependencies (no need to store rTrans anymore in
369        calling S/R); this affects AD results at machine truncation level:
370        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
371        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
372    o tools/build_options:
373      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
374    o coupling interface pkgs:
375        [compon_communic, atm_compon_interf & ocn_compon_interf]
376      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
377        to each S/R that needs it; remove un-used variables.
378      - change component tile registration (cpl_register.F in both compon_interf
379        and mitcomponent_tile_register.F) to pass the full list of tiles
380        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
381      - with pkg/exch2: adopt the same convention used for I/O to define mapping
382        towards coupler global array (unless W2_useE2ioLayOut=F):
383         a) can now use different tiling between atm & ocn comp.
384         b) no needs to modify the run-Off map when changing tiling (was needed
385            even if using the same tiling between atm & ocn).
386         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
387            full land tiles); not yet tested.
388      - check for valid mapping from comp. tile to coupler global array
389      - improve report of tile registration results to log file.
390    o pkg/exch2:
391      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
392        tile-registration (CPL_REGISTER);
393      - activate (un-comment) definition and setting of "W2_tileIndex" list to
394        store the local bi,bj indices of each tile;
395      - also print bi,bj in local report to log file;
396      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
397        Jun 2009 modif of pkg/exch2).
398    o testing on baudelaire:
399      - run 2 tests at a time: no significant slow down (since enough cpu) and
400        get the full set of test done earlier
401      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
402    o model/src/thermodynamics.F and routines called from it:
403      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
404        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
405        velocity (outp) by adding bolus velocity.
406      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
407        mass transport from velocity + lateral grid cell area
408      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
409      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
410     in thermodynamics.F
411      - remove k from thermodynamics.F and move it to temp_integrate.F
412        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
413        loop).
414      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
415        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
416        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
417        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
418      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
419        global_ocean.90x40x15, tutorial_global_oce_biogeo and
420        tutorial_tracer_adjsens (+ TLM output).
421    o tools/OAD_support and (verification/*/) code_oad:
422      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
423        module conversion ; remove unneeded CPP_EEOPTIONS.h.
424      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
425        version (closer to model/inc/CPP_OPTIONS.h).
426    o model/src:
427      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
428        retired list of parameters (routine FREEZE has been replace by surface
429        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
430    o pkg/gmredi:
431      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
432        velocity (same scheme but affects machine truncation) for GM_AdvForm.
433      - update output of FWD experiments: front_relax.bvp,
434        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
435    
436    checkpoint64q (2013/11/17)
437    o verification:
438      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
439        tutorial_global_oce_biogeo and global_ocean.90x40x15.
440      - generate new output (growth & melt) for seaice_itd experiment after
441        updating the input pickup_seaice files (previously wrong).
442    o pkg/cost:
443      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
444        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
445        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
446          cannot be applied to var in common block).
447        o allows to get results independent of tile-per-proc setting (if using
448          slower GLOBAL_SUM_SEND_RECV option).
449      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
450        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
451        forward gradients: update output).
452      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
453        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
454    o pkg/mom_common:
455      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
456        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
457        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
458        ensure that all field value that are used are set.
459    o tutorial_deep_convection (smag3d):
460      - add missing scaling in mom_calc_smag_3d.F;
461      - set smag3D_coeff in input.smag3d such that results do not change.
462    o pkg/dic:
463      - change dic_cost.F to compute cost on each tile first and then apply
464        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
465        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
466      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
467    o eesupp/src & pkg/mdsio:
468      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
469        (from pkg/mdsio) since they are no longer used for tape IO.
470      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
471        (+ keep a copy in pkg/atm_ocn_coupler).
472    o verification/isomip:
473      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
474    o tools/build_options:
475      - optfile linux_amd64_ifort11, fast (no ieee) case:
476        to get a working restart for all experiments, add "-fp-model source"
477        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
478    
479    checkpoint64p (2013/10/20)
480    o pkg/autodiff:
481      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
482        criteria, return to simple (default) tape IO format.
483    o pkg/mdsio (+ eesupp/src):
484      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
485        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
486      - fix globalFile and singleCpuIO options using simpler global mapping.
487      - new pairs of scatter/gather vector S/R (one for each type, generated from
488        template) corresponding to simpler global mapping.
489      - adread_write.F: switch to new S/R (but leave old calls commented) and write
490        to globalFile when parameter globalFiles is set to True.
491      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
492    o pkg/autodiff:
493      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
494        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
495        missing, just add a STOP if array type do not match.
496    o pkg/exf:
497      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
498         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
499         and rename array obsSIce to exf_iceFraction.
500    o tutorial_deep_convection:
501      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
502        for now all in this exp. code dir.
503      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
504        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
505    o eesupp/src:
506      - added SINGLE_DISK_IO option because reading of parameter files on
507        very large number of processors did not work with existing set-up
508    
509    checkpoint64o (2013/09/25)
510    o pkg/atm_phys & atm_compon_interf:
511      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
512    o tools/build_options:
513      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
514        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
515        remove CPP setting (was identical to genmake2 default).
516    o pkg/gmredi & model/src: Some updating and work done on the residual model.
517      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
518      - fixed up the calculation of the eddy stress and how it is added to the
519        external forcing via taueddy_external_forcing.F
520      - at the moment, it is very experimental and only works with the variable eddy
521        diffusivity calculated in gmredi_k3d.F
522    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
523        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
524    o testreport (& tools/do_tst_2+2):
525      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
526    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
527      - remove CPP='cpp -traditional -P' (this is genmake2 default)
528      - add switch (for big setups) to use 'medium' memory-model (but leave it
529        commented out for now). Note: needed with FC 19 to compile big setups.
530    o pkg/atm_compon_interf:
531      - regroup per field origin (model & pkgs) the coupling storage routines
532         (which accumalate in time each coupling field)
533      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
534        update accordingly + simplify aim_do_physics.F
535    
536    checkpoint64n (2013/08/26)
537    o pkg/bbl:
538      - update formulation to reduce dispersion of tracer properties in bbl
539      - replaced horizontal and vertical transport parameters with velocities
540      - changes results for verification/global_with_exf.yearly
541    o verification/halfpipe_streamice:
542      - change to matrix construction; update both Fwd & AD output.
543    o verification/tutorial_tracer_adjsens:
544      - OpenAD test: switch to vector-invariant momentum since fluxform with
545        rStar causes problems with OpenAD; update output.
546    o tools:
547      - genmake2: define a common prefix for all temp-file names ; move them
548        to local /tmp disk (but would be easy to move them back);
549      - xmakedepend: apply the same switch for temp-files.
550    o pkg/offline:
551      - changes for use with rStar (NLFS): assume that we continue to provide
552        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
553        output files) and apply r* scaling at each time-step (function of the time
554        varying Eta field); use normal pickup files (needed for restart with NLFS).
555    o adjoint with OpenAD:
556      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
557        package openad.  This package has to be compiled for all runs with OpenAD
558        instead of specifying code_oad_all as a modification directory.
559      - link the fortran templates from tools/OAD_support to the build directory
560        for preprocessing to avoid conflicts between different setups compiled
561        simultaneously and simplify cleanup.
562    o pkg/exf:
563      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
564        main model or other pkgs are exchanged in EXF_MAPFIELDS).
565    o model/src:
566      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
567        (similar to do_fields_blocking_exchanges.F).
568    o tools/genmake2:
569      - remove TAF output src code just before calling staf (when not doing a fresh
570        built, will stop if things go wrong with staf).
571      - fix target "adobj" (left from TAF version-2 transition)
572    o pkg/diagnostics:
573      - add a parameter to track the status of pkg/diagnostics activation;
574        this replace/extend the use of logical param "settingDiags" (to check
575        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
576        New S/R to print error message and stop when pkgStatus is not right.
577      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
578    
579    checkpoint64m (2013/08/13)
580    o model/inc:
581      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
582        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
583    o pkg/kpp & aim_v23:
584      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
585    o pkg/seaice:
586      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
587        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
588      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
589    o eesupp/src:
590      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
591        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
592    o switch to TAF version-2:
593      - add flow directives to "freeze" naming convention for ad-routines that
594        are used in I/O routines of adjoint state and associated common blocks
595        that are used in adcommon.h (backward compatible with version-1)
596      - update all ad-optfiles (in tools/adjoint_options + few local to some
597        verification exp) to switch to latest TAF version (currently 2.5.5);
598        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
599        out except for diva).
600      - the major change with TAF version-2 is that both the differentiated
601        routines and the forward routines (new) are returned as part of the TAF
602        output source code. Update genmake2 accordingly.
603      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
604        with version-2 when compared to TLM or FWD gradient); other experiments
605        output show minor changes (machine truncation level); update the few AD &
606        TLM output with 12 matching digits only (some prior to version-2 switch).
607    
608    checkpoint64l (2013/08/05)
609    o model/src:
610      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
611      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
612        when using TAF but only if using OpenAD.
613    o pkg/mom_common+fluxform+vecinv:
614      - always set horiz. viscosity arrays to background value before calling
615        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
616        only when using variable horiz. viscosity (useVariableVisc=T);
617      - simplify mom_vecinv.F (only 1 block for momViscosity).
618    o pkg/mom_common: variable horiz. viscosity in NH code
619      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
620        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
621      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
622        useBiharmonicVisc & useVariableVisc.
623      - fix old bug (already in 1rst implementation of variable horizontal viscosity
624        in calc_gw.F, version 1.27, 2006/06/20):
625        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
626        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
627      - change background horiz viscosity in vertical momentum (gW) to always be
628        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
629        any type of variable viscosity, e.g., viscAh/4Grid)
630      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
631        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
632        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
633        default viscAh,viscA4 is zero).
634    o model/src:
635      - extend length of drC & recip_drC from Nr to Nr+1.
636  o Divided Adjoint (DIVA) with MPI:  o Divided Adjoint (DIVA) with MPI:
637    - genmake2: do not create local ./mpi_headers dir when no file to copy into.    - genmake2: do not create local ./mpi_headers dir when no file to copy into.
638    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT

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