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revision 1.1889 by dimitri, Mon Jul 1 16:55:57 2013 UTC revision 1.2013 by mlosch, Fri Jun 27 14:48:07 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice
8      - remove unnecessary u/vTmp from subroutine call of
9        seaice_lsr_tridiagu/v
10      - remove some store directives and add new ones in an effort to get
11        finally rid off the recomputation warnings. This is successful
12        for SEAICE_VECTORIZE_LSR defined (i.e. no extensive recomputation
13        warnings left), but there are still too many recomputations on the
14        solver iteration level
15      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
16      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
17        SEAICE_SIZE.h
18      - add a store directive in S/R seaice_calc_viscosities
19    o pkg/seaice (ITD code):
20      - fix definition of Hlimit for multi-threaded case
21      - use double precision arithmetic to compute Hlimit: this affects results;
22        update output of experiment seaice_itd.
23    o replace content of verification/seaice_itd
24      - instead of a 1D column use the configuration of offline_exf_seaice
25        to test the ice thickness distribution code with ridging
26      - this is a first shot at this experiment
27      - change of some defaults of ridging parameters SEAICEhStar (from
28        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
29        and lot of new comments.
30    
31    checkpoint64y (2014/06/20)
32    o pkg/seaice/seaice_reg_ridge.F:
33      - modify the regularization of very small volumes of ice; only check
34        total volume HEFF, and do not apply correction to individual ice
35        classes because that leads to funny patterns in the heat and fw-fluxes
36        into the ocean. Adjust seaice_itd/results/output.txt
37      - replace nITD by SEAICE_multDim in loop-ranges
38    o pkg/exf:
39      - add code to process the case field period = -12. with UV interpolation.
40      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
41        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
42    o verification/global_with_exf:
43      - switch all fields period to -12. (was previously untested) in input/data.exf
44        (but keep secondary test ".yearly" unchanged); update the reference output.
45    o pkg/cal:
46      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
47    o pkg/exf:
48      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
49        to replace logical switch "exf_verbose"
50      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
51    o pkg/sbo:
52      - update from Katherine Quinn: evaluate mass directly from density and SSH
53        (budget using Finite Volume method) instead of from bottom pressure.
54      - allow testreport to collect few selected SBO output ; tested in exp.
55        global_ocean.90x40x15 (after updating the results, to include SBO output).
56      - fix some multi-threading issues (in output part).
57    o model/src & most packages:
58      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
59      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
60        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
61        "data.{pkg}" exist ; and leave the S/R (return) just after.
62      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
63        + call LAND_READPARMS from packages_readparms.F
64    o pkg/seaice:
65      - remove code that resets useThSice in S/R seaice_readparms and
66        replace it by a warning in S/R seaice_check
67      - remove parameter MULTDIM, replace with nITD and runtime
68        parameter SEAICE_multDim (still hard-wired to nITD if
69        SEAICE_ITD is defined)
70    
71    checkpoint64x (2014/05/24)
72    o verification/lab_sea:
73      - update adjoint and TLM output following changes to pkg/salt_plume
74      - un-do the update after putting back local recip_Cp in few places.
75    o pkg/salt_plume: modifications by An Nguyen:
76      - add capability to do brine rejection (salt-plume) as function of
77        volume+tracers (instead of only salinity tracer).
78      - conserve volume by exchanging volume from each kLev to above to
79        accommodate in-coming brine volume
80      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
81      - switch KPP surf buoyancy due to brine forcing to 3-d
82        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
83      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
84      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
85        in East/West Arctic.
86    o pkg/sbo:
87      - incorporate modifications from Katherine Quinn to enable the use of sbo
88        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
89        output for future testreport verification (unfinished).
90    o pkg/atm_phys:
91      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
92        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
93        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
94    o pkg/seaice
95      seaice_calc_ice_strength.F: modify expression to avoid divisions
96        (affects truncation)
97      seaice_do_ridging.F: clean up the insectarium
98      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
99      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
100      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
101      - add some debugging information and error messages (warnings)
102    o model/src: modifications relatd to atmosphere p*:
103      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
104      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
105        of vertical profile tRef in geopotential background and anomaly.
106      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
107        and pkg/atm_phys.
108      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
109        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
110    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
111    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
112        not used right now, but can be used in BGC packages to fix conservation.
113    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
114        other packages too.
115    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
116        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
117    o model/src:
118      - since we have several heat capacity (even in model/src), define "recip_Cp"
119        as local variable (no longer in common block) to avoid any confusion.
120      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
121    o pkg/exf:
122      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
123        air density as function of air Temp, Humidity and atm pressure.
124    
125    checkpoint64w (2014/05/02)
126    o verification:
127      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
128        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
129        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
130        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
131        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
132    o model/src: for atmosphere in p* coords:
133      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
134      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
135        but not yet activated.
136    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
137      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
138      - this changes the results (but not for any verification experiment, because
139        none tests this), but avoids having an extra field in the restart files
140    o pkg/seaice: remove global variable TICE (not needed)
141      - replace by TICES or local variable where necessary (cost_seaice_test,
142        seaice_diagnostics_state)
143      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
144      - use specific read/write routines for reading and writing individual leves
145        of a multilevel field
146    o pkg/ctrl & model/inc:
147      - move additional anomaly fields of control vars (related to options:
148         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
149        from DYNVARS.h into new header file: CTRL_FIELDS.h
150    o pkg/seaice: some small modifications to the ridging code
151      - make fw2ObyRidge a global variable and add the freshwater flux to
152        seaice_growth
153      - pass actual thickness from seaice_prepare_ridging, so that it is
154        computed only in one place and compute it in the same way as in
155        seaice_growth
156      - initialise more fields in seaice_do_ridging that where cause floating
157        point exceptions over land
158    o pkg/seaice: preparations for ridging code and first real ridging code
159      - move most of "PART 1" of S/R seaice_growth into a new and separate
160        S/R seaice_reg_ridge that will both regularize the state variable after
161        advection call the actual ridging routine;
162      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
163        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
164      - remove ridging code from seaice_advdiff
165      - clean up remaining part 1 of seaice_growth in an attempt to make it
166        more readable (this is probably subjective)
167      - call seaice_itd_redist once in the initialisation phase to have the initial
168        conditions in the correct category
169      - finally: add new ridging routine for ITD code
170    
171    checkpoint64v (2014/04/11)
172    o pkg/ecco:
173      - add runtime parameters mdt[start,end]date[1,2]
174      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
175    o pkg/seaice:
176      - make deltaC a global variable, so that it can be used in ridging code
177      - first step towards ridging: introduce new routines that compute
178        ice strength based on ridging parameters
179      - add diagnostic for HSNOWITD
180      - add opnWtrFrac as a global variable (required for ridging scheme)
181    o pkg/salt_plume + pkg/seaice/seaice_growth.F
182      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
183        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
184    o verification/hs94.1x64x5:
185      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
186      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
187    o autodiff:
188      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
189        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
190        For now, only in pkgs used in verification/hs94.1x64x5.
191      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
192        which are specific to TAF/TAMC).
193      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
194        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
195        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
196      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
197        building mitgcmuv_ad (make adAll).
198    o pkg/ecco:
199      - cost_gencost_seaicev4.F:
200         reformulate proxy cost as function of sst and local param SEAICE_freeze
201         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
202      - add stop statement if old names siv4-[sst,vol] are used
203      - add snapshots + cost reports for atmospheric longwave
204      - remove factor 0.1 in front of wtau[u,v]
205      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
206         ALLOW_TMI_SST_COST_CONTRIBUTION
207    o pkg/atm_phys:
208      - add some diagnostics for Short-wave and for convection S/R.
209    o pkg/seaice/seaice_growth:
210      - fix a bug in the lateral melt parameterization for SEAICE_ITD
211        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
212      - rearrange loop order for better vector code in the same code block
213      - rewrite the floeDiameter formula to have fewer divisions
214      -  (miraculously) none of this changes the results of seaice_itd
215    o pkg/smooth:
216      - move param smooth2Ddiffnbt to pkg/ecco
217    o pkg/salt_plume:
218      - salt_plume_frac.F:
219         clean up local param names
220         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
221    o pkg/rw:
222      - add RS version of S/R READ_MFLDS_LEV.
223    o pkg/streamice:
224      - fix the restart test by writing/reading pickup_streamice files.
225    o pkg/seaice:
226      - refine checks for jfnk-related parameters
227      - comment out if statement with SEAICEuseIMEX parameter as long as there
228        is no IMEX code to avoid confusion and surprises
229    
230    checkpoint64u (2014/03/07)
231    o verification/MLAdjust:
232      - rename secondary test suffix:
233         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
234         0.leithD -> AhFlxF  + switch to flux-form
235         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
236         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
237    o pkg/mom_vecinv:
238      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
239        to be before mom_calc_visc.F)
240      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
241      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
242        this is simpler for the adjoint and for diagnostics.
243    o model/src + pkg/momentum:
244      - add input files for  2-D additional Western and Southern cell-edge wall
245         (e.g., to add "thin-wall" where it is =1).
246      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
247        using 2nd hFacZ that is computed from initial (fix domain) hFac
248      - known limitations of thin wall implementation: not yet coded for sigma
249        coords; not working with CD-scheme neither.
250    o pkg/seaice:
251      - rename recently introduced parameters from (wrong name) AB to
252        BDF (backward difference time discretisation)
253      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
254    o tools/adjoint_options:
255      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
256    
257    checkpoint64t (2014/02/01)
258    o pkg/ecco
259      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
260        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
261      - replace hard-coded record number and period which only work for monthly
262        with read-in runtime param that works for other periods (month,day,year)
263    o pkg/thsice
264      - corrected store directive fixes thsice adjoint gradient checks
265    o genmake2 & testreport:
266      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
267        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
268        Update testreport accordingly. No need to set "export OPENAD=true"
269        in adjoint_options/adjoint_oad anymore (will be removed later).
270    o pkg/shelfice:
271      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
272        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
273        so that surface forcing applies to k=kSurf if using pkg/shelfice.
274    o pkg/ctrl, pkg/grdchk, pkg/ecco:
275      - Changes to make GENARR more modular (i.e. invisible if not used)
276    o model/src/temp_integrate.F and salt_integrate.F
277      - re-include store directives that were removed on Dec 27th.
278    o model/src/external_forcing_surf.F
279      - add storage directives for EmPmR and PmEpR to avoid recomputation of
280        seaice_model in the adjoint that is problematic when seaice_model is
281        turned off in the adjoint. The resolved issue dated back to July when
282        EXTERNAL_FORCING_SURF call was moved.
283        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
284    o pkg/exf/exf_check.F
285      - fix a small bug again (originally found by Wentao Liu, now found again)
286      - streamline error output
287    o pkg/streamice and aim_v23:
288      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
289        Apple's /usr/bin/cpp knows what to do:
290        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
291        Target: x86_64-apple-darwin13.0.0
292    
293    checkpoint64s (2014/01/05)
294    o tools/adjoint_options:
295      - switch to fastopt.net TAF server (instead of default fastopt.de) for
296        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
297    o model/src:
298      - remove some unnecessary TAF storage directives in forward_step.F and
299        in dynamics.F (note: not always removed by TAF, e.g., double storage
300        of kappaRU,kappaRV in former version of dynamics.F).
301    o model/src & pkg/ptracers:
302      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
303        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
304        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
305      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
306      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
307      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
308    o useSingleCpuInput separates single-CPU input from single-CPU output;
309        for now only implemented for in exf_interp_read.F
310    o verification/advect_xy:
311      - fix missing EXCH call in local version of ini_salt.F and update output.
312    o momentum diagnostics:
313      - fix which deltaT is used in Total-Tendency diagnostics.
314      - fix typo in diagnostics for momentum tendency from AB.
315    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
316        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
317    
318    checkpoint64r (2013/12/08)
319    o verification/*/results:
320      - Update reference output of experiments that were passing with just 13 digits
321         (make it easier to detect future changes in results)
322    o model/src & pkg/ptracers:
323      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
324        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
325        to inside ptracers_integrate.F ; remove ptracers_advection.F
326    o coupling interface pkgs:
327        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
328      - change the config check to test the agreement of Ocean Depth
329        with ATM land/sea mask (instead of ATM orography);
330      - send to coupler the number of coupler time-steps to do for this run:
331        this allows to check for consistency and don't need anymore to be
332        specified in parameter file "data";
333      in coupler:
334      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
335      - improve report to log-file of config setting (pass log-file unit to few S/R)
336    o pkg/compon_communic:
337      - add coupling send/receive for non-tiled integer vector;
338      - add S/R to check and stop if any proc has an error (similar to
339        eesupp/src/stop_if_error.F but single thread and across Comm_World).
340    o pkg/exch2:
341      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
342        through list of all tiles my proc owns.
343    o model/src:
344      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
345        from rTrans) to simplify dependencies (no need to store rTrans anymore in
346        calling S/R); this affects AD results at machine truncation level:
347        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
348        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
349    o tools/build_options:
350      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
351    o coupling interface pkgs:
352        [compon_communic, atm_compon_interf & ocn_compon_interf]
353      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
354        to each S/R that needs it; remove un-used variables.
355      - change component tile registration (cpl_register.F in both compon_interf
356        and mitcomponent_tile_register.F) to pass the full list of tiles
357        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
358      - with pkg/exch2: adopt the same convention used for I/O to define mapping
359        towards coupler global array (unless W2_useE2ioLayOut=F):
360         a) can now use different tiling between atm & ocn comp.
361         b) no needs to modify the run-Off map when changing tiling (was needed
362            even if using the same tiling between atm & ocn).
363         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
364            full land tiles); not yet tested.
365      - check for valid mapping from comp. tile to coupler global array
366      - improve report of tile registration results to log file.
367    o pkg/exch2:
368      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
369        tile-registration (CPL_REGISTER);
370      - activate (un-comment) definition and setting of "W2_tileIndex" list to
371        store the local bi,bj indices of each tile;
372      - also print bi,bj in local report to log file;
373      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
374        Jun 2009 modif of pkg/exch2).
375    o testing on baudelaire:
376      - run 2 tests at a time: no significant slow down (since enough cpu) and
377        get the full set of test done earlier
378      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
379    o model/src/thermodynamics.F and routines called from it:
380      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
381        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
382        velocity (outp) by adding bolus velocity.
383      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
384        mass transport from velocity + lateral grid cell area
385      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
386      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
387     in thermodynamics.F
388      - remove k from thermodynamics.F and move it to temp_integrate.F
389        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
390        loop).
391      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
392        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
393        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
394        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
395      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
396        global_ocean.90x40x15, tutorial_global_oce_biogeo and
397        tutorial_tracer_adjsens (+ TLM output).
398    o tools/OAD_support and (verification/*/) code_oad:
399      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
400        module conversion ; remove unneeded CPP_EEOPTIONS.h.
401      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
402        version (closer to model/inc/CPP_OPTIONS.h).
403    o model/src:
404      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
405        retired list of parameters (routine FREEZE has been replace by surface
406        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
407    o pkg/gmredi:
408      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
409        velocity (same scheme but affects machine truncation) for GM_AdvForm.
410      - update output of FWD experiments: front_relax.bvp,
411        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
412    
413    checkpoint64q (2013/11/17)
414    o verification:
415      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
416        tutorial_global_oce_biogeo and global_ocean.90x40x15.
417      - generate new output (growth & melt) for seaice_itd experiment after
418        updating the input pickup_seaice files (previously wrong).
419    o pkg/cost:
420      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
421        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
422        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
423          cannot be applied to var in common block).
424        o allows to get results independent of tile-per-proc setting (if using
425          slower GLOBAL_SUM_SEND_RECV option).
426      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
427        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
428        forward gradients: update output).
429      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
430        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
431    o pkg/mom_common:
432      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
433        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
434        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
435        ensure that all field value that are used are set.
436    o tutorial_deep_convection (smag3d):
437      - add missing scaling in mom_calc_smag_3d.F;
438      - set smag3D_coeff in input.smag3d such that results do not change.
439    o pkg/dic:
440      - change dic_cost.F to compute cost on each tile first and then apply
441        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
442        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
443      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
444    o eesupp/src & pkg/mdsio:
445      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
446        (from pkg/mdsio) since they are no longer used for tape IO.
447      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
448        (+ keep a copy in pkg/atm_ocn_coupler).
449    o verification/isomip:
450      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
451    o tools/build_options:
452      - optfile linux_amd64_ifort11, fast (no ieee) case:
453        to get a working restart for all experiments, add "-fp-model source"
454        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
455    
456    checkpoint64p (2013/10/20)
457    o pkg/autodiff:
458      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
459        criteria, return to simple (default) tape IO format.
460    o pkg/mdsio (+ eesupp/src):
461      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
462        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
463      - fix globalFile and singleCpuIO options using simpler global mapping.
464      - new pairs of scatter/gather vector S/R (one for each type, generated from
465        template) corresponding to simpler global mapping.
466      - adread_write.F: switch to new S/R (but leave old calls commented) and write
467        to globalFile when parameter globalFiles is set to True.
468      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
469    o pkg/autodiff:
470      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
471        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
472        missing, just add a STOP if array type do not match.
473    o pkg/exf:
474      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
475         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
476         and rename array obsSIce to exf_iceFraction.
477    o tutorial_deep_convection:
478      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
479        for now all in this exp. code dir.
480      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
481        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
482    o eesupp/src:
483      - added SINGLE_DISK_IO option because reading of parameter files on
484        very large number of processors did not work with existing set-up
485    
486    checkpoint64o (2013/09/25)
487    o pkg/atm_phys & atm_compon_interf:
488      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
489    o tools/build_options:
490      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
491        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
492        remove CPP setting (was identical to genmake2 default).
493    o pkg/gmredi & model/src: Some updating and work done on the residual model.
494      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
495      - fixed up the calculation of the eddy stress and how it is added to the
496        external forcing via taueddy_external_forcing.F
497      - at the moment, it is very experimental and only works with the variable eddy
498        diffusivity calculated in gmredi_k3d.F
499    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
500        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
501    o testreport (& tools/do_tst_2+2):
502      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
503    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
504      - remove CPP='cpp -traditional -P' (this is genmake2 default)
505      - add switch (for big setups) to use 'medium' memory-model (but leave it
506        commented out for now). Note: needed with FC 19 to compile big setups.
507    o pkg/atm_compon_interf:
508      - regroup per field origin (model & pkgs) the coupling storage routines
509         (which accumalate in time each coupling field)
510      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
511        update accordingly + simplify aim_do_physics.F
512    
513    checkpoint64n (2013/08/26)
514    o pkg/bbl:
515      - update formulation to reduce dispersion of tracer properties in bbl
516      - replaced horizontal and vertical transport parameters with velocities
517      - changes results for verification/global_with_exf.yearly
518    o verification/halfpipe_streamice:
519      - change to matrix construction; update both Fwd & AD output.
520    o verification/tutorial_tracer_adjsens:
521      - OpenAD test: switch to vector-invariant momentum since fluxform with
522        rStar causes problems with OpenAD; update output.
523    o tools:
524      - genmake2: define a common prefix for all temp-file names ; move them
525        to local /tmp disk (but would be easy to move them back);
526      - xmakedepend: apply the same switch for temp-files.
527    o pkg/offline:
528      - changes for use with rStar (NLFS): assume that we continue to provide
529        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
530        output files) and apply r* scaling at each time-step (function of the time
531        varying Eta field); use normal pickup files (needed for restart with NLFS).
532    o adjoint with OpenAD:
533      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
534        package openad.  This package has to be compiled for all runs with OpenAD
535        instead of specifying code_oad_all as a modification directory.
536      - link the fortran templates from tools/OAD_support to the build directory
537        for preprocessing to avoid conflicts between different setups compiled
538        simultaneously and simplify cleanup.
539    o pkg/exf:
540      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
541        main model or other pkgs are exchanged in EXF_MAPFIELDS).
542    o model/src:
543      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
544        (similar to do_fields_blocking_exchanges.F).
545    o tools/genmake2:
546      - remove TAF output src code just before calling staf (when not doing a fresh
547        built, will stop if things go wrong with staf).
548      - fix target "adobj" (left from TAF version-2 transition)
549    o pkg/diagnostics:
550      - add a parameter to track the status of pkg/diagnostics activation;
551        this replace/extend the use of logical param "settingDiags" (to check
552        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
553        New S/R to print error message and stop when pkgStatus is not right.
554      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
555    
556    checkpoint64m (2013/08/13)
557    o model/inc:
558      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
559        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
560    o pkg/kpp & aim_v23:
561      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
562    o pkg/seaice:
563      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
564        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
565      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
566    o eesupp/src:
567      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
568        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
569    o switch to TAF version-2:
570      - add flow directives to "freeze" naming convention for ad-routines that
571        are used in I/O routines of adjoint state and associated common blocks
572        that are used in adcommon.h (backward compatible with version-1)
573      - update all ad-optfiles (in tools/adjoint_options + few local to some
574        verification exp) to switch to latest TAF version (currently 2.5.5);
575        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
576        out except for diva).
577      - the major change with TAF version-2 is that both the differentiated
578        routines and the forward routines (new) are returned as part of the TAF
579        output source code. Update genmake2 accordingly.
580      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
581        with version-2 when compared to TLM or FWD gradient); other experiments
582        output show minor changes (machine truncation level); update the few AD &
583        TLM output with 12 matching digits only (some prior to version-2 switch).
584    
585    checkpoint64l (2013/08/05)
586    o model/src:
587      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
588      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
589        when using TAF but only if using OpenAD.
590    o pkg/mom_common+fluxform+vecinv:
591      - always set horiz. viscosity arrays to background value before calling
592        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
593        only when using variable horiz. viscosity (useVariableVisc=T);
594      - simplify mom_vecinv.F (only 1 block for momViscosity).
595    o pkg/mom_common: variable horiz. viscosity in NH code
596      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
597        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
598      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
599        useBiharmonicVisc & useVariableVisc.
600      - fix old bug (already in 1rst implementation of variable horizontal viscosity
601        in calc_gw.F, version 1.27, 2006/06/20):
602        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
603        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
604      - change background horiz viscosity in vertical momentum (gW) to always be
605        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
606        any type of variable viscosity, e.g., viscAh/4Grid)
607      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
608        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
609        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
610        default viscAh,viscA4 is zero).
611    o model/src:
612      - extend length of drC & recip_drC from Nr to Nr+1.
613    o Divided Adjoint (DIVA) with MPI:
614      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
615      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
616        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
617    
618    checkpoint64k (2013/07/23)
619    o tools/OAD_support:
620      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
621        and remove it from genmake2.
622    o tools/build_options:
623      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
624        MPI_HEADER_FILES list (let genmake2 find the missing headers)
625    o verification/halfpipe_streamice:
626      - change to driving stress formulation; update both Fwd & AD output.
627    o tools/genmake2 and Divided Adjoint with MPI:
628      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
629      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
630      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
631        Makefile, which is set by genmake2, and check which mpi-headers are needed.
632        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
633      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
634    o testreport:
635      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
636        perform additional runs (number of additional runs is "add_DIVA_runs" taken
637        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
638    o verification/lab_sea (AD test):
639      - change to test Divided Adjoint Run in this set-up (both standard AD test
640        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
641    o pkg atm_ & ocn_compon_interf:
642      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
643        staggerTimeStep implementation) and disable (retired) corresponding
644        parameter.
645    o pkg/offline:
646      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
647      - add S/R OFFLINE_CHECK to print offline parameter summary
648        and stop if loading a file that is not used;
649      - enable to calculate GMRedi tensor, KPP mixing and convective index
650        when the corresponding file(s) is/are not specified (but pkg is used).
651      - comment out resetting of monitorFreq (to endTime) since it still useful
652        for monitoring CFL numbers and checking offline fields.
653    o OpenAD:
654      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
655        smaller standard output) and generate new (smaller) output (on baudelaire
656        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
657    o model/src:
658      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
659        (where external_forcing_adjust was called) and change list of arguments;
660      - merge external_forcing_adjust.F into external_forcing_surf.F
661      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
662        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
663        previously in file "balance_relax.F", now removed); remove corresponding
664        arrays in FFIELDS.h.
665      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
666        a hack for getting back surfaceForcingS (loaded from file) when using
667        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
668      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
669        (was getting only 11 digits for AD-grad, due to different truncation
670         error in AD code).
671    
672    checkpoint64j (2013/07/04)
673    o pkg/offline:
674      - to enable the use of other features with pkg offline (e.g., obcs),
675        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
676      - comment out "allowFreezing" (now active) in 2 offline testing exp.
677  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
678    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
679    - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice    - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
680    - changes verification/global_ocean.cs32x15/results/output.seaice.txt    - changes verification/global_ocean.cs32x15/results/output.seaice.txt
681  o pkg/atm_phys:  o pkg/atm_phys:
682    - allows to add some damping on uVel,vVel (strength only function of k).    - allows to add some damping on uVel,vVel (strength only function of k).
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