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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.2015 by gforget, Sat Jun 28 22:50:34 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/autodiff :
8      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
9        viscFacInAd : run time parameters allowing for adjoint switches
10        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
11    o pkg/ecco :
12      - introduce cost_gencost_boxmean.F that computes a box mean
13        temperature (for use in adjoint sensitivity studies).
14    o model/src/set_defaults.F : initialize viscFacAdj to 1.
15    o pkg/mom_common/mom_calc_visc.F :
16      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
17    o pkg/seaice/seaice_summary.F :
18      - statement for SEAICEadjMODE now in autodiff_readparms.F
19    o pkg/seaice
20      - remove unnecessary u/vTmp from subroutine call of
21        seaice_lsr_tridiagu/v
22      - remove some store directives and add new ones in an effort to get
23        finally rid off the recomputation warnings. This is successful
24        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
25        defined (i.e. no extensive recomputation warnings left), but there
26        are still too many recomputations on the solver iteration level
27      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
28      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
29        SEAICE_SIZE.h
30      - add a store directive in S/R seaice_calc_viscosities
31    o pkg/seaice (ITD code):
32      - fix definition of Hlimit for multi-threaded case
33      - use double precision arithmetic to compute Hlimit: this affects results;
34        update output of experiment seaice_itd.
35    o replace content of verification/seaice_itd
36      - instead of a 1D column use the configuration of offline_exf_seaice
37        to test the ice thickness distribution code with ridging
38      - this is a first shot at this experiment
39      - change of some defaults of ridging parameters SEAICEhStar (from
40        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
41        and lot of new comments.
42    
43    checkpoint64y (2014/06/20)
44    o pkg/seaice/seaice_reg_ridge.F:
45      - modify the regularization of very small volumes of ice; only check
46        total volume HEFF, and do not apply correction to individual ice
47        classes because that leads to funny patterns in the heat and fw-fluxes
48        into the ocean. Adjust seaice_itd/results/output.txt
49      - replace nITD by SEAICE_multDim in loop-ranges
50    o pkg/exf:
51      - add code to process the case field period = -12. with UV interpolation.
52      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
53        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
54    o verification/global_with_exf:
55      - switch all fields period to -12. (was previously untested) in input/data.exf
56        (but keep secondary test ".yearly" unchanged); update the reference output.
57    o pkg/cal:
58      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
59    o pkg/exf:
60      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
61        to replace logical switch "exf_verbose"
62      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
63    o pkg/sbo:
64      - update from Katherine Quinn: evaluate mass directly from density and SSH
65        (budget using Finite Volume method) instead of from bottom pressure.
66      - allow testreport to collect few selected SBO output ; tested in exp.
67        global_ocean.90x40x15 (after updating the results, to include SBO output).
68      - fix some multi-threading issues (in output part).
69    o model/src & most packages:
70      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
71      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
72        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
73        "data.{pkg}" exist ; and leave the S/R (return) just after.
74      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
75        + call LAND_READPARMS from packages_readparms.F
76    o pkg/seaice:
77      - remove code that resets useThSice in S/R seaice_readparms and
78        replace it by a warning in S/R seaice_check
79      - remove parameter MULTDIM, replace with nITD and runtime
80        parameter SEAICE_multDim (still hard-wired to nITD if
81        SEAICE_ITD is defined)
82    
83    checkpoint64x (2014/05/24)
84    o verification/lab_sea:
85      - update adjoint and TLM output following changes to pkg/salt_plume
86      - un-do the update after putting back local recip_Cp in few places.
87    o pkg/salt_plume: modifications by An Nguyen:
88      - add capability to do brine rejection (salt-plume) as function of
89        volume+tracers (instead of only salinity tracer).
90      - conserve volume by exchanging volume from each kLev to above to
91        accommodate in-coming brine volume
92      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
93      - switch KPP surf buoyancy due to brine forcing to 3-d
94        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
95      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
96      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
97        in East/West Arctic.
98    o pkg/sbo:
99      - incorporate modifications from Katherine Quinn to enable the use of sbo
100        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
101        output for future testreport verification (unfinished).
102    o pkg/atm_phys:
103      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
104        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
105        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
106    o pkg/seaice
107      seaice_calc_ice_strength.F: modify expression to avoid divisions
108        (affects truncation)
109      seaice_do_ridging.F: clean up the insectarium
110      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
111      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
112      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
113      - add some debugging information and error messages (warnings)
114    o model/src: modifications relatd to atmosphere p*:
115      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
116      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
117        of vertical profile tRef in geopotential background and anomaly.
118      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
119        and pkg/atm_phys.
120      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
121        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
122    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
123    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
124        not used right now, but can be used in BGC packages to fix conservation.
125    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
126        other packages too.
127    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
128        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
129    o model/src:
130      - since we have several heat capacity (even in model/src), define "recip_Cp"
131        as local variable (no longer in common block) to avoid any confusion.
132      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
133    o pkg/exf:
134      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
135        air density as function of air Temp, Humidity and atm pressure.
136    
137    checkpoint64w (2014/05/02)
138    o verification:
139      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
140        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
141        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
142        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
143        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
144    o model/src: for atmosphere in p* coords:
145      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
146      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
147        but not yet activated.
148    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
149      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
150      - this changes the results (but not for any verification experiment, because
151        none tests this), but avoids having an extra field in the restart files
152    o pkg/seaice: remove global variable TICE (not needed)
153      - replace by TICES or local variable where necessary (cost_seaice_test,
154        seaice_diagnostics_state)
155      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
156      - use specific read/write routines for reading and writing individual leves
157        of a multilevel field
158    o pkg/ctrl & model/inc:
159      - move additional anomaly fields of control vars (related to options:
160         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
161        from DYNVARS.h into new header file: CTRL_FIELDS.h
162    o pkg/seaice: some small modifications to the ridging code
163      - make fw2ObyRidge a global variable and add the freshwater flux to
164        seaice_growth
165      - pass actual thickness from seaice_prepare_ridging, so that it is
166        computed only in one place and compute it in the same way as in
167        seaice_growth
168      - initialise more fields in seaice_do_ridging that where cause floating
169        point exceptions over land
170    o pkg/seaice: preparations for ridging code and first real ridging code
171      - move most of "PART 1" of S/R seaice_growth into a new and separate
172        S/R seaice_reg_ridge that will both regularize the state variable after
173        advection call the actual ridging routine;
174      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
175        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
176      - remove ridging code from seaice_advdiff
177      - clean up remaining part 1 of seaice_growth in an attempt to make it
178        more readable (this is probably subjective)
179      - call seaice_itd_redist once in the initialisation phase to have the initial
180        conditions in the correct category
181      - finally: add new ridging routine for ITD code
182    
183    checkpoint64v (2014/04/11)
184    o pkg/ecco:
185      - add runtime parameters mdt[start,end]date[1,2]
186      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
187    o pkg/seaice:
188      - make deltaC a global variable, so that it can be used in ridging code
189      - first step towards ridging: introduce new routines that compute
190        ice strength based on ridging parameters
191      - add diagnostic for HSNOWITD
192      - add opnWtrFrac as a global variable (required for ridging scheme)
193    o pkg/salt_plume + pkg/seaice/seaice_growth.F
194      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
195        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
196    o verification/hs94.1x64x5:
197      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
198      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
199    o autodiff:
200      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
201        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
202        For now, only in pkgs used in verification/hs94.1x64x5.
203      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
204        which are specific to TAF/TAMC).
205      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
206        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
207        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
208      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
209        building mitgcmuv_ad (make adAll).
210    o pkg/ecco:
211      - cost_gencost_seaicev4.F:
212         reformulate proxy cost as function of sst and local param SEAICE_freeze
213         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
214      - add stop statement if old names siv4-[sst,vol] are used
215      - add snapshots + cost reports for atmospheric longwave
216      - remove factor 0.1 in front of wtau[u,v]
217      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
218         ALLOW_TMI_SST_COST_CONTRIBUTION
219    o pkg/atm_phys:
220      - add some diagnostics for Short-wave and for convection S/R.
221    o pkg/seaice/seaice_growth:
222      - fix a bug in the lateral melt parameterization for SEAICE_ITD
223        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
224      - rearrange loop order for better vector code in the same code block
225      - rewrite the floeDiameter formula to have fewer divisions
226      -  (miraculously) none of this changes the results of seaice_itd
227    o pkg/smooth:
228      - move param smooth2Ddiffnbt to pkg/ecco
229    o pkg/salt_plume:
230      - salt_plume_frac.F:
231         clean up local param names
232         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
233    o pkg/rw:
234      - add RS version of S/R READ_MFLDS_LEV.
235    o pkg/streamice:
236      - fix the restart test by writing/reading pickup_streamice files.
237    o pkg/seaice:
238      - refine checks for jfnk-related parameters
239      - comment out if statement with SEAICEuseIMEX parameter as long as there
240        is no IMEX code to avoid confusion and surprises
241    
242    checkpoint64u (2014/03/07)
243    o verification/MLAdjust:
244      - rename secondary test suffix:
245         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
246         0.leithD -> AhFlxF  + switch to flux-form
247         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
248         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
249    o pkg/mom_vecinv:
250      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
251        to be before mom_calc_visc.F)
252      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
253      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
254        this is simpler for the adjoint and for diagnostics.
255    o model/src + pkg/momentum:
256      - add input files for  2-D additional Western and Southern cell-edge wall
257         (e.g., to add "thin-wall" where it is =1).
258      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
259        using 2nd hFacZ that is computed from initial (fix domain) hFac
260      - known limitations of thin wall implementation: not yet coded for sigma
261        coords; not working with CD-scheme neither.
262    o pkg/seaice:
263      - rename recently introduced parameters from (wrong name) AB to
264        BDF (backward difference time discretisation)
265      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
266    o tools/adjoint_options:
267      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
268    
269    checkpoint64t (2014/02/01)
270    o pkg/ecco
271      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
272        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
273      - replace hard-coded record number and period which only work for monthly
274        with read-in runtime param that works for other periods (month,day,year)
275    o pkg/thsice
276      - corrected store directive fixes thsice adjoint gradient checks
277    o genmake2 & testreport:
278      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
279        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
280        Update testreport accordingly. No need to set "export OPENAD=true"
281        in adjoint_options/adjoint_oad anymore (will be removed later).
282    o pkg/shelfice:
283      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
284        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
285        so that surface forcing applies to k=kSurf if using pkg/shelfice.
286    o pkg/ctrl, pkg/grdchk, pkg/ecco:
287      - Changes to make GENARR more modular (i.e. invisible if not used)
288    o model/src/temp_integrate.F and salt_integrate.F
289      - re-include store directives that were removed on Dec 27th.
290    o model/src/external_forcing_surf.F
291      - add storage directives for EmPmR and PmEpR to avoid recomputation of
292        seaice_model in the adjoint that is problematic when seaice_model is
293        turned off in the adjoint. The resolved issue dated back to July when
294        EXTERNAL_FORCING_SURF call was moved.
295        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
296    o pkg/exf/exf_check.F
297      - fix a small bug again (originally found by Wentao Liu, now found again)
298      - streamline error output
299    o pkg/streamice and aim_v23:
300      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
301        Apple's /usr/bin/cpp knows what to do:
302        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
303        Target: x86_64-apple-darwin13.0.0
304    
305    checkpoint64s (2014/01/05)
306    o tools/adjoint_options:
307      - switch to fastopt.net TAF server (instead of default fastopt.de) for
308        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
309    o model/src:
310      - remove some unnecessary TAF storage directives in forward_step.F and
311        in dynamics.F (note: not always removed by TAF, e.g., double storage
312        of kappaRU,kappaRV in former version of dynamics.F).
313    o model/src & pkg/ptracers:
314      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
315        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
316        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
317      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
318      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
319      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
320    o useSingleCpuInput separates single-CPU input from single-CPU output;
321        for now only implemented for in exf_interp_read.F
322    o verification/advect_xy:
323      - fix missing EXCH call in local version of ini_salt.F and update output.
324    o momentum diagnostics:
325      - fix which deltaT is used in Total-Tendency diagnostics.
326      - fix typo in diagnostics for momentum tendency from AB.
327    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
328        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
329    
330    checkpoint64r (2013/12/08)
331    o verification/*/results:
332      - Update reference output of experiments that were passing with just 13 digits
333         (make it easier to detect future changes in results)
334    o model/src & pkg/ptracers:
335      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
336        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
337        to inside ptracers_integrate.F ; remove ptracers_advection.F
338    o coupling interface pkgs:
339        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
340      - change the config check to test the agreement of Ocean Depth
341        with ATM land/sea mask (instead of ATM orography);
342      - send to coupler the number of coupler time-steps to do for this run:
343        this allows to check for consistency and don't need anymore to be
344        specified in parameter file "data";
345      in coupler:
346      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
347      - improve report to log-file of config setting (pass log-file unit to few S/R)
348    o pkg/compon_communic:
349      - add coupling send/receive for non-tiled integer vector;
350      - add S/R to check and stop if any proc has an error (similar to
351        eesupp/src/stop_if_error.F but single thread and across Comm_World).
352    o pkg/exch2:
353      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
354        through list of all tiles my proc owns.
355    o model/src:
356      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
357        from rTrans) to simplify dependencies (no need to store rTrans anymore in
358        calling S/R); this affects AD results at machine truncation level:
359        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
360        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
361    o tools/build_options:
362      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
363    o coupling interface pkgs:
364        [compon_communic, atm_compon_interf & ocn_compon_interf]
365      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
366        to each S/R that needs it; remove un-used variables.
367      - change component tile registration (cpl_register.F in both compon_interf
368        and mitcomponent_tile_register.F) to pass the full list of tiles
369        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
370      - with pkg/exch2: adopt the same convention used for I/O to define mapping
371        towards coupler global array (unless W2_useE2ioLayOut=F):
372         a) can now use different tiling between atm & ocn comp.
373         b) no needs to modify the run-Off map when changing tiling (was needed
374            even if using the same tiling between atm & ocn).
375         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
376            full land tiles); not yet tested.
377      - check for valid mapping from comp. tile to coupler global array
378      - improve report of tile registration results to log file.
379    o pkg/exch2:
380      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
381        tile-registration (CPL_REGISTER);
382      - activate (un-comment) definition and setting of "W2_tileIndex" list to
383        store the local bi,bj indices of each tile;
384      - also print bi,bj in local report to log file;
385      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
386        Jun 2009 modif of pkg/exch2).
387    o testing on baudelaire:
388      - run 2 tests at a time: no significant slow down (since enough cpu) and
389        get the full set of test done earlier
390      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
391    o model/src/thermodynamics.F and routines called from it:
392      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
393        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
394        velocity (outp) by adding bolus velocity.
395      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
396        mass transport from velocity + lateral grid cell area
397      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
398      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
399     in thermodynamics.F
400      - remove k from thermodynamics.F and move it to temp_integrate.F
401        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
402        loop).
403      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
404        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
405        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
406        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
407      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
408        global_ocean.90x40x15, tutorial_global_oce_biogeo and
409        tutorial_tracer_adjsens (+ TLM output).
410    o tools/OAD_support and (verification/*/) code_oad:
411      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
412        module conversion ; remove unneeded CPP_EEOPTIONS.h.
413      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
414        version (closer to model/inc/CPP_OPTIONS.h).
415    o model/src:
416      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
417        retired list of parameters (routine FREEZE has been replace by surface
418        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
419    o pkg/gmredi:
420      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
421        velocity (same scheme but affects machine truncation) for GM_AdvForm.
422      - update output of FWD experiments: front_relax.bvp,
423        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
424    
425    checkpoint64q (2013/11/17)
426    o verification:
427      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
428        tutorial_global_oce_biogeo and global_ocean.90x40x15.
429      - generate new output (growth & melt) for seaice_itd experiment after
430        updating the input pickup_seaice files (previously wrong).
431    o pkg/cost:
432      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
433        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
434        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
435          cannot be applied to var in common block).
436        o allows to get results independent of tile-per-proc setting (if using
437          slower GLOBAL_SUM_SEND_RECV option).
438      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
439        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
440        forward gradients: update output).
441      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
442        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
443    o pkg/mom_common:
444      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
445        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
446        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
447        ensure that all field value that are used are set.
448    o tutorial_deep_convection (smag3d):
449      - add missing scaling in mom_calc_smag_3d.F;
450      - set smag3D_coeff in input.smag3d such that results do not change.
451    o pkg/dic:
452      - change dic_cost.F to compute cost on each tile first and then apply
453        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
454        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
455      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
456    o eesupp/src & pkg/mdsio:
457      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
458        (from pkg/mdsio) since they are no longer used for tape IO.
459      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
460        (+ keep a copy in pkg/atm_ocn_coupler).
461    o verification/isomip:
462      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
463    o tools/build_options:
464      - optfile linux_amd64_ifort11, fast (no ieee) case:
465        to get a working restart for all experiments, add "-fp-model source"
466        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
467    
468    checkpoint64p (2013/10/20)
469    o pkg/autodiff:
470      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
471        criteria, return to simple (default) tape IO format.
472    o pkg/mdsio (+ eesupp/src):
473      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
474        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
475      - fix globalFile and singleCpuIO options using simpler global mapping.
476      - new pairs of scatter/gather vector S/R (one for each type, generated from
477        template) corresponding to simpler global mapping.
478      - adread_write.F: switch to new S/R (but leave old calls commented) and write
479        to globalFile when parameter globalFiles is set to True.
480      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
481    o pkg/autodiff:
482      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
483        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
484        missing, just add a STOP if array type do not match.
485    o pkg/exf:
486      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
487         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
488         and rename array obsSIce to exf_iceFraction.
489    o tutorial_deep_convection:
490      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
491        for now all in this exp. code dir.
492      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
493        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
494    o eesupp/src:
495      - added SINGLE_DISK_IO option because reading of parameter files on
496        very large number of processors did not work with existing set-up
497    
498    checkpoint64o (2013/09/25)
499    o pkg/atm_phys & atm_compon_interf:
500      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
501    o tools/build_options:
502      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
503        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
504        remove CPP setting (was identical to genmake2 default).
505    o pkg/gmredi & model/src: Some updating and work done on the residual model.
506      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
507      - fixed up the calculation of the eddy stress and how it is added to the
508        external forcing via taueddy_external_forcing.F
509      - at the moment, it is very experimental and only works with the variable eddy
510        diffusivity calculated in gmredi_k3d.F
511    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
512        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
513    o testreport (& tools/do_tst_2+2):
514      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
515    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
516      - remove CPP='cpp -traditional -P' (this is genmake2 default)
517      - add switch (for big setups) to use 'medium' memory-model (but leave it
518        commented out for now). Note: needed with FC 19 to compile big setups.
519    o pkg/atm_compon_interf:
520      - regroup per field origin (model & pkgs) the coupling storage routines
521         (which accumalate in time each coupling field)
522      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
523        update accordingly + simplify aim_do_physics.F
524    
525    checkpoint64n (2013/08/26)
526    o pkg/bbl:
527      - update formulation to reduce dispersion of tracer properties in bbl
528      - replaced horizontal and vertical transport parameters with velocities
529      - changes results for verification/global_with_exf.yearly
530    o verification/halfpipe_streamice:
531      - change to matrix construction; update both Fwd & AD output.
532    o verification/tutorial_tracer_adjsens:
533      - OpenAD test: switch to vector-invariant momentum since fluxform with
534        rStar causes problems with OpenAD; update output.
535    o tools:
536      - genmake2: define a common prefix for all temp-file names ; move them
537        to local /tmp disk (but would be easy to move them back);
538      - xmakedepend: apply the same switch for temp-files.
539    o pkg/offline:
540      - changes for use with rStar (NLFS): assume that we continue to provide
541        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
542        output files) and apply r* scaling at each time-step (function of the time
543        varying Eta field); use normal pickup files (needed for restart with NLFS).
544    o adjoint with OpenAD:
545      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
546        package openad.  This package has to be compiled for all runs with OpenAD
547        instead of specifying code_oad_all as a modification directory.
548      - link the fortran templates from tools/OAD_support to the build directory
549        for preprocessing to avoid conflicts between different setups compiled
550        simultaneously and simplify cleanup.
551    o pkg/exf:
552      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
553        main model or other pkgs are exchanged in EXF_MAPFIELDS).
554    o model/src:
555      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
556        (similar to do_fields_blocking_exchanges.F).
557    o tools/genmake2:
558      - remove TAF output src code just before calling staf (when not doing a fresh
559        built, will stop if things go wrong with staf).
560      - fix target "adobj" (left from TAF version-2 transition)
561    o pkg/diagnostics:
562      - add a parameter to track the status of pkg/diagnostics activation;
563        this replace/extend the use of logical param "settingDiags" (to check
564        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
565        New S/R to print error message and stop when pkgStatus is not right.
566      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
567    
568    checkpoint64m (2013/08/13)
569    o model/inc:
570      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
571        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
572    o pkg/kpp & aim_v23:
573      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
574    o pkg/seaice:
575      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
576        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
577      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
578    o eesupp/src:
579      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
580        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
581    o switch to TAF version-2:
582      - add flow directives to "freeze" naming convention for ad-routines that
583        are used in I/O routines of adjoint state and associated common blocks
584        that are used in adcommon.h (backward compatible with version-1)
585      - update all ad-optfiles (in tools/adjoint_options + few local to some
586        verification exp) to switch to latest TAF version (currently 2.5.5);
587        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
588        out except for diva).
589      - the major change with TAF version-2 is that both the differentiated
590        routines and the forward routines (new) are returned as part of the TAF
591        output source code. Update genmake2 accordingly.
592      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
593        with version-2 when compared to TLM or FWD gradient); other experiments
594        output show minor changes (machine truncation level); update the few AD &
595        TLM output with 12 matching digits only (some prior to version-2 switch).
596    
597    checkpoint64l (2013/08/05)
598    o model/src:
599      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
600      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
601        when using TAF but only if using OpenAD.
602    o pkg/mom_common+fluxform+vecinv:
603      - always set horiz. viscosity arrays to background value before calling
604        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
605        only when using variable horiz. viscosity (useVariableVisc=T);
606      - simplify mom_vecinv.F (only 1 block for momViscosity).
607    o pkg/mom_common: variable horiz. viscosity in NH code
608      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
609        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
610      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
611        useBiharmonicVisc & useVariableVisc.
612      - fix old bug (already in 1rst implementation of variable horizontal viscosity
613        in calc_gw.F, version 1.27, 2006/06/20):
614        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
615        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
616      - change background horiz viscosity in vertical momentum (gW) to always be
617        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
618        any type of variable viscosity, e.g., viscAh/4Grid)
619      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
620        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
621        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
622        default viscAh,viscA4 is zero).
623    o model/src:
624      - extend length of drC & recip_drC from Nr to Nr+1.
625    o Divided Adjoint (DIVA) with MPI:
626      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
627      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
628        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
629    
630    checkpoint64k (2013/07/23)
631    o tools/OAD_support:
632      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
633        and remove it from genmake2.
634    o tools/build_options:
635      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
636        MPI_HEADER_FILES list (let genmake2 find the missing headers)
637    o verification/halfpipe_streamice:
638      - change to driving stress formulation; update both Fwd & AD output.
639    o tools/genmake2 and Divided Adjoint with MPI:
640      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
641      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
642      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
643        Makefile, which is set by genmake2, and check which mpi-headers are needed.
644        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
645      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
646    o testreport:
647      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
648        perform additional runs (number of additional runs is "add_DIVA_runs" taken
649        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
650    o verification/lab_sea (AD test):
651      - change to test Divided Adjoint Run in this set-up (both standard AD test
652        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
653    o pkg atm_ & ocn_compon_interf:
654      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
655        staggerTimeStep implementation) and disable (retired) corresponding
656        parameter.
657    o pkg/offline:
658      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
659      - add S/R OFFLINE_CHECK to print offline parameter summary
660        and stop if loading a file that is not used;
661      - enable to calculate GMRedi tensor, KPP mixing and convective index
662        when the corresponding file(s) is/are not specified (but pkg is used).
663      - comment out resetting of monitorFreq (to endTime) since it still useful
664        for monitoring CFL numbers and checking offline fields.
665    o OpenAD:
666      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
667        smaller standard output) and generate new (smaller) output (on baudelaire
668        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
669    o model/src:
670      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
671        (where external_forcing_adjust was called) and change list of arguments;
672      - merge external_forcing_adjust.F into external_forcing_surf.F
673      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
674        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
675        previously in file "balance_relax.F", now removed); remove corresponding
676        arrays in FFIELDS.h.
677      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
678        a hack for getting back surfaceForcingS (loaded from file) when using
679        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
680      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
681        (was getting only 11 digits for AD-grad, due to different truncation
682         error in AD code).
683    
684    checkpoint64j (2013/07/04)
685    o pkg/offline:
686      - to enable the use of other features with pkg offline (e.g., obcs),
687        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
688      - comment out "allowFreezing" (now active) in 2 offline testing exp.
689    o pkg/exf ALLOW_RUNOFTEMP
690      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
691      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
692      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
693    o pkg/atm_phys:
694      - allows to add some damping on uVel,vVel (strength only function of k).
695    o verification, ad-tests:
696      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
697        global_ocean_ebm and offline_exf_seaice.thsice.
698    o verification/halfpipe_streamice:
699      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
700        flux input boundary conditions to be ignored; a fix for this bug changed
701        verification results for forward test.
702      - add adjoint test.
703    o pkg/ptracers:
704      - allow to restart without SOM pickup (resetting SOM to zero).
705    o pkg/gmredi:
706      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
707      - It uses mixing length theory and suppression by steering level effects to
708        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
709        to JPO, for more details).
710      - It also uses the diffusivity to calculate an eddy induced streamfunction
711        based on a PV closure (rather than a buoyancy closure as in GM).
712      - New files added to pkg/gmredi:
713        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
714          induced overturning streamfunction (called from gmredi_calc_tensor)
715        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
716          for use in gmredi_k3d
717        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
718          the eddy diffusivity
719    
720  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
721  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 752  o pkg/cfc:
752      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
753    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
754    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
755    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
756      similar to thsice_advdiff.
757      Note that for the B-grid case the routine parameters uc/vc are overwritten.
758  o pkg/cfc:  o pkg/cfc:
759    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
760      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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