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revision 1.1901 by jmc, Thu Jul 25 01:12:45 2013 UTC revision 1.2033 by mlosch, Tue Jul 29 16:29:56 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      - reduce the number of include files and store directives in
9        S/R seaice_lsr_tridiagu/v
10      - change the order of loops in one case in S/R seaice_lsr_tridiagv
11        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
12        get rid off one store directive (a TAF bug?)
13      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
14        S/R seaice_lsr_tridiagv to change the loop range for consistency
15      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
16      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
17        S/R seaice_lsr_tridiagu/v (requires update of
18        offline_exf_seaice/input.dyn_jfnk)
19    
20    checkpoint65a (2014/07/27)
21    o model/src:
22      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
23        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
24        (topo in p-coords, ice-shelf in z-coords); update output of experiments
25        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
26    o model/src:
27      - collect momentum forcing tendency into local 2-D array (passed as argument
28        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
29        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
30        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
31      - collect T & S forcing tendency into local 2-D array (passed as argument to
32        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
33        affects results at machine truncation level (e.g., ocean: if using
34        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
35        moist correction due to vertical advection).
36      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
37        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
38        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
39        obcs_ctrl (ad & fwd grd @ 12 & 7).
40    o pkg/ptracers & diagnostics:
41      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
42        title (to avoid some unexpected truncation); sort out ptracers diags units.
43      - collect ptracer forcing tendency into local 2-D array (passed as argument
44        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
45    
46    checkpoint65 (2014/07/18)
47    o pkg/fizhi:
48      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
49        affects results at machine truncation level. Update output of experiments
50        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
51    o pkg/seaice: more clean up
52      - rename TAF common block tapes to be more consistent and remove
53        unnecessary duplicates
54      - add store directives to remove more recomputations, but use smaller
55        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
56        The idea behind this flag is to reduce the memory footprint when the
57        adjoint of the LSR is not required. As of now, defining the flag
58        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
59        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
60        For experiment offline_exf_seaice, this means on a linux box with gfortran
61        nearly a factor of 10 (but keep in mind there is mostly seaice code in
62        this experiment):
63        > size mitgcmuv_ad
64        text    data        bss     dec        hex  
65        5100659 1216  220458952  225560827  d71c8fb
66        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
67        but only a moderate increase of 36% for global_ocean.cs32x15:
68        text    data        bss     dec        hex
69        6695027 1648 1014578664 1021275339 3cdf6ccb
70        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
71      - note: there are still recomputations in global_ocean.cs32x15 and
72        offline_exf_seaice and the gradient agreement changes (gets a
73        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
74      - in general, the AD gradients still are wrong
75    o OpenAD
76      - clean up code_oad/ directories somewhat by moving files
77        dontCompile, dontTransform, keepOriginal to OAD_support/
78    o model/src:
79      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
80        (not currently tested): add dissipation terms before NLFS rescaling of
81        tendencies (previously done after).
82    o pkg/diagnostics:
83      - write stats-diags in ascii file with more digits (same as in monitor).
84    o pkg/down_slope:
85      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
86        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
87    o model/src:
88      - new file "apply_forcing.F" containing all the code previously in
89        external_forcing.F, but with new argument list: pass, as new argument,
90        the current level tendency array to update (instead of a direct update
91        of the common bloc array). Change the corresponding calls.
92      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
93        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
94    o pkg/seaice/seaice_lsr, a little bit of clean up
95      - rearrange some code blocks, so that now all calculations for
96        setting up the right-hand-sides done within one single block
97        (I find that easier to read and understand)
98      - rearrange freedrift-code to reduce the number of ifdefs
99      - adjust some indentations and comments
100    
101    checkpoint64z (2014/07/10)
102    o model/src and several pkgs:
103      - change argument list of all S/R called from external_forcing.F and
104        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
105        to pass, as argument, the current level tendency array to update
106        (instead of a direct update of the common bloc array).
107      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
108      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
109    o pkg/seaice/seaice_lsr.F
110      - always initialize local arrays in seaice_lsr_tridiagu/v
111      - add more local tapes to seaice_lsr_tridiagu/v
112      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
113        keep it in bi/bj loop; this seems to be essential
114      - gradients are still wrong but only by 4-7 orders of magnitude
115        instead of 15 orders of magnitude, lab_sea improves a little
116    o pkg/seaice
117      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
118        generates unnecessary code in seaice_lsr_ad
119      - add more store directives in seaice_lsr to avoid unnecessary code
120        in seaice_lsr_ad
121      - exclude some residual computations in seaice_lsr when
122        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
123        in seaice_lsr_ad
124      - add more storing, a new tape (model/src/the_main_loop.F) and
125        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
126        and klockey should be checked by a specialist)
127      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
128        and update lab_sea after previous changes in pkg/seaice below
129    o pkg/autodiff:
130      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
131        viscFacInAd : run time parameters allowing for adjoint switches
132        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
133    o pkg/ecco:
134      - introduce cost_gencost_boxmean.F that computes a box mean
135        temperature (for use in adjoint sensitivity studies).
136    o model/src/set_defaults.F : initialize viscFacAdj to 1.
137    o pkg/mom_common/mom_calc_visc.F:
138      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
139    o pkg/seaice/seaice_summary.F:
140      - statement for SEAICEadjMODE now in autodiff_readparms.F
141    o pkg/seaice:
142      - remove some store directives and add new ones in an effort to get
143        finally rid off the recomputation warnings. This is successful
144        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
145        defined (i.e. no extensive recomputation warnings left), but there
146        are still too many recomputations on the solver iteration level
147      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
148      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
149        SEAICE_SIZE.h
150      - add a store directive in S/R seaice_calc_viscosities
151    o pkg/seaice (ITD code):
152      - fix definition of Hlimit for multi-threaded case
153      - use double precision arithmetic to compute Hlimit: this affects results;
154        update output of experiment seaice_itd.
155    o replace content of verification/seaice_itd
156      - instead of a 1D column use the configuration of offline_exf_seaice
157        to test the ice thickness distribution code with ridging
158      - this is a first shot at this experiment
159      - change of some defaults of ridging parameters SEAICEhStar (from
160        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
161        and lot of new comments.
162    
163    checkpoint64y (2014/06/20)
164    o pkg/seaice/seaice_reg_ridge.F:
165      - modify the regularization of very small volumes of ice; only check
166        total volume HEFF, and do not apply correction to individual ice
167        classes because that leads to funny patterns in the heat and fw-fluxes
168        into the ocean. Adjust seaice_itd/results/output.txt
169      - replace nITD by SEAICE_multDim in loop-ranges
170    o pkg/exf:
171      - add code to process the case field period = -12. with UV interpolation.
172      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
173        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
174    o verification/global_with_exf:
175      - switch all fields period to -12. (was previously untested) in input/data.exf
176        (but keep secondary test ".yearly" unchanged); update the reference output.
177    o pkg/cal:
178      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
179    o pkg/exf:
180      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
181        to replace logical switch "exf_verbose"
182      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
183    o pkg/sbo:
184      - update from Katherine Quinn: evaluate mass directly from density and SSH
185        (budget using Finite Volume method) instead of from bottom pressure.
186      - allow testreport to collect few selected SBO output ; tested in exp.
187        global_ocean.90x40x15 (after updating the results, to include SBO output).
188      - fix some multi-threading issues (in output part).
189    o model/src & most packages:
190      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
191      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
192        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
193        "data.{pkg}" exist ; and leave the S/R (return) just after.
194      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
195        + call LAND_READPARMS from packages_readparms.F
196    o pkg/seaice:
197      - remove code that resets useThSice in S/R seaice_readparms and
198        replace it by a warning in S/R seaice_check
199      - remove parameter MULTDIM, replace with nITD and runtime
200        parameter SEAICE_multDim (still hard-wired to nITD if
201        SEAICE_ITD is defined)
202    
203    checkpoint64x (2014/05/24)
204    o verification/lab_sea:
205      - update adjoint and TLM output following changes to pkg/salt_plume
206      - un-do the update after putting back local recip_Cp in few places.
207    o pkg/salt_plume: modifications by An Nguyen:
208      - add capability to do brine rejection (salt-plume) as function of
209        volume+tracers (instead of only salinity tracer).
210      - conserve volume by exchanging volume from each kLev to above to
211        accommodate in-coming brine volume
212      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
213      - switch KPP surf buoyancy due to brine forcing to 3-d
214        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
215      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
216      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
217        in East/West Arctic.
218    o pkg/sbo:
219      - incorporate modifications from Katherine Quinn to enable the use of sbo
220        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
221        output for future testreport verification (unfinished).
222    o pkg/atm_phys:
223      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
224        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
225        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
226    o pkg/seaice
227      seaice_calc_ice_strength.F: modify expression to avoid divisions
228        (affects truncation)
229      seaice_do_ridging.F: clean up the insectarium
230      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
231      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
232      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
233      - add some debugging information and error messages (warnings)
234    o model/src: modifications relatd to atmosphere p*:
235      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
236      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
237        of vertical profile tRef in geopotential background and anomaly.
238      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
239        and pkg/atm_phys.
240      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
241        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
242    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
243    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
244        not used right now, but can be used in BGC packages to fix conservation.
245    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
246        other packages too.
247    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
248        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
249    o model/src:
250      - since we have several heat capacity (even in model/src), define "recip_Cp"
251        as local variable (no longer in common block) to avoid any confusion.
252      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
253    o pkg/exf:
254      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
255        air density as function of air Temp, Humidity and atm pressure.
256    
257    checkpoint64w (2014/05/02)
258    o verification:
259      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
260        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
261        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
262        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
263        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
264    o model/src: for atmosphere in p* coords:
265      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
266      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
267        but not yet activated.
268    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
269      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
270      - this changes the results (but not for any verification experiment, because
271        none tests this), but avoids having an extra field in the restart files
272    o pkg/seaice: remove global variable TICE (not needed)
273      - replace by TICES or local variable where necessary (cost_seaice_test,
274        seaice_diagnostics_state)
275      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
276      - use specific read/write routines for reading and writing individual leves
277        of a multilevel field
278    o pkg/ctrl & model/inc:
279      - move additional anomaly fields of control vars (related to options:
280         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
281        from DYNVARS.h into new header file: CTRL_FIELDS.h
282    o pkg/seaice: some small modifications to the ridging code
283      - make fw2ObyRidge a global variable and add the freshwater flux to
284        seaice_growth
285      - pass actual thickness from seaice_prepare_ridging, so that it is
286        computed only in one place and compute it in the same way as in
287        seaice_growth
288      - initialise more fields in seaice_do_ridging that where cause floating
289        point exceptions over land
290    o pkg/seaice: preparations for ridging code and first real ridging code
291      - move most of "PART 1" of S/R seaice_growth into a new and separate
292        S/R seaice_reg_ridge that will both regularize the state variable after
293        advection call the actual ridging routine;
294      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
295        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
296      - remove ridging code from seaice_advdiff
297      - clean up remaining part 1 of seaice_growth in an attempt to make it
298        more readable (this is probably subjective)
299      - call seaice_itd_redist once in the initialisation phase to have the initial
300        conditions in the correct category
301      - finally: add new ridging routine for ITD code
302    
303    checkpoint64v (2014/04/11)
304    o pkg/ecco:
305      - add runtime parameters mdt[start,end]date[1,2]
306      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
307    o pkg/seaice:
308      - make deltaC a global variable, so that it can be used in ridging code
309      - first step towards ridging: introduce new routines that compute
310        ice strength based on ridging parameters
311      - add diagnostic for HSNOWITD
312      - add opnWtrFrac as a global variable (required for ridging scheme)
313    o pkg/salt_plume + pkg/seaice/seaice_growth.F
314      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
315        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
316    o verification/hs94.1x64x5:
317      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
318      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
319    o autodiff:
320      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
321        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
322        For now, only in pkgs used in verification/hs94.1x64x5.
323      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
324        which are specific to TAF/TAMC).
325      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
326        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
327        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
328      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
329        building mitgcmuv_ad (make adAll).
330    o pkg/ecco:
331      - cost_gencost_seaicev4.F:
332         reformulate proxy cost as function of sst and local param SEAICE_freeze
333         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
334      - add stop statement if old names siv4-[sst,vol] are used
335      - add snapshots + cost reports for atmospheric longwave
336      - remove factor 0.1 in front of wtau[u,v]
337      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
338         ALLOW_TMI_SST_COST_CONTRIBUTION
339    o pkg/atm_phys:
340      - add some diagnostics for Short-wave and for convection S/R.
341    o pkg/seaice/seaice_growth:
342      - fix a bug in the lateral melt parameterization for SEAICE_ITD
343        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
344      - rearrange loop order for better vector code in the same code block
345      - rewrite the floeDiameter formula to have fewer divisions
346      -  (miraculously) none of this changes the results of seaice_itd
347    o pkg/smooth:
348      - move param smooth2Ddiffnbt to pkg/ecco
349    o pkg/salt_plume:
350      - salt_plume_frac.F:
351         clean up local param names
352         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
353    o pkg/rw:
354      - add RS version of S/R READ_MFLDS_LEV.
355    o pkg/streamice:
356      - fix the restart test by writing/reading pickup_streamice files.
357    o pkg/seaice:
358      - refine checks for jfnk-related parameters
359      - comment out if statement with SEAICEuseIMEX parameter as long as there
360        is no IMEX code to avoid confusion and surprises
361    
362    checkpoint64u (2014/03/07)
363    o verification/MLAdjust:
364      - rename secondary test suffix:
365         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
366         0.leithD -> AhFlxF  + switch to flux-form
367         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
368         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
369    o pkg/mom_vecinv:
370      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
371        to be before mom_calc_visc.F)
372      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
373      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
374        this is simpler for the adjoint and for diagnostics.
375    o model/src + pkg/momentum:
376      - add input files for  2-D additional Western and Southern cell-edge wall
377         (e.g., to add "thin-wall" where it is =1).
378      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
379        using 2nd hFacZ that is computed from initial (fix domain) hFac
380      - known limitations of thin wall implementation: not yet coded for sigma
381        coords; not working with CD-scheme neither.
382    o pkg/seaice:
383      - rename recently introduced parameters from (wrong name) AB to
384        BDF (backward difference time discretisation)
385      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
386    o tools/adjoint_options:
387      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
388    
389    checkpoint64t (2014/02/01)
390    o pkg/ecco
391      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
392        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
393      - replace hard-coded record number and period which only work for monthly
394        with read-in runtime param that works for other periods (month,day,year)
395    o pkg/thsice
396      - corrected store directive fixes thsice adjoint gradient checks
397    o genmake2 & testreport:
398      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
399        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
400        Update testreport accordingly. No need to set "export OPENAD=true"
401        in adjoint_options/adjoint_oad anymore (will be removed later).
402    o pkg/shelfice:
403      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
404        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
405        so that surface forcing applies to k=kSurf if using pkg/shelfice.
406    o pkg/ctrl, pkg/grdchk, pkg/ecco:
407      - Changes to make GENARR more modular (i.e. invisible if not used)
408    o model/src/temp_integrate.F and salt_integrate.F
409      - re-include store directives that were removed on Dec 27th.
410    o model/src/external_forcing_surf.F
411      - add storage directives for EmPmR and PmEpR to avoid recomputation of
412        seaice_model in the adjoint that is problematic when seaice_model is
413        turned off in the adjoint. The resolved issue dated back to July when
414        EXTERNAL_FORCING_SURF call was moved.
415        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
416    o pkg/exf/exf_check.F
417      - fix a small bug again (originally found by Wentao Liu, now found again)
418      - streamline error output
419    o pkg/streamice and aim_v23:
420      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
421        Apple's /usr/bin/cpp knows what to do:
422        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
423        Target: x86_64-apple-darwin13.0.0
424    
425    checkpoint64s (2014/01/05)
426    o tools/adjoint_options:
427      - switch to fastopt.net TAF server (instead of default fastopt.de) for
428        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
429    o model/src:
430      - remove some unnecessary TAF storage directives in forward_step.F and
431        in dynamics.F (note: not always removed by TAF, e.g., double storage
432        of kappaRU,kappaRV in former version of dynamics.F).
433    o model/src & pkg/ptracers:
434      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
435        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
436        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
437      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
438      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
439      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
440    o useSingleCpuInput separates single-CPU input from single-CPU output;
441        for now only implemented for in exf_interp_read.F
442    o verification/advect_xy:
443      - fix missing EXCH call in local version of ini_salt.F and update output.
444    o momentum diagnostics:
445      - fix which deltaT is used in Total-Tendency diagnostics.
446      - fix typo in diagnostics for momentum tendency from AB.
447    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
448        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
449    
450    checkpoint64r (2013/12/08)
451    o verification/*/results:
452      - Update reference output of experiments that were passing with just 13 digits
453         (make it easier to detect future changes in results)
454    o model/src & pkg/ptracers:
455      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
456        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
457        to inside ptracers_integrate.F ; remove ptracers_advection.F
458    o coupling interface pkgs:
459        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
460      - change the config check to test the agreement of Ocean Depth
461        with ATM land/sea mask (instead of ATM orography);
462      - send to coupler the number of coupler time-steps to do for this run:
463        this allows to check for consistency and don't need anymore to be
464        specified in parameter file "data";
465      in coupler:
466      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
467      - improve report to log-file of config setting (pass log-file unit to few S/R)
468    o pkg/compon_communic:
469      - add coupling send/receive for non-tiled integer vector;
470      - add S/R to check and stop if any proc has an error (similar to
471        eesupp/src/stop_if_error.F but single thread and across Comm_World).
472    o pkg/exch2:
473      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
474        through list of all tiles my proc owns.
475    o model/src:
476      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
477        from rTrans) to simplify dependencies (no need to store rTrans anymore in
478        calling S/R); this affects AD results at machine truncation level:
479        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
480        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
481    o tools/build_options:
482      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
483    o coupling interface pkgs:
484        [compon_communic, atm_compon_interf & ocn_compon_interf]
485      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
486        to each S/R that needs it; remove un-used variables.
487      - change component tile registration (cpl_register.F in both compon_interf
488        and mitcomponent_tile_register.F) to pass the full list of tiles
489        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
490      - with pkg/exch2: adopt the same convention used for I/O to define mapping
491        towards coupler global array (unless W2_useE2ioLayOut=F):
492         a) can now use different tiling between atm & ocn comp.
493         b) no needs to modify the run-Off map when changing tiling (was needed
494            even if using the same tiling between atm & ocn).
495         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
496            full land tiles); not yet tested.
497      - check for valid mapping from comp. tile to coupler global array
498      - improve report of tile registration results to log file.
499    o pkg/exch2:
500      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
501        tile-registration (CPL_REGISTER);
502      - activate (un-comment) definition and setting of "W2_tileIndex" list to
503        store the local bi,bj indices of each tile;
504      - also print bi,bj in local report to log file;
505      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
506        Jun 2009 modif of pkg/exch2).
507    o testing on baudelaire:
508      - run 2 tests at a time: no significant slow down (since enough cpu) and
509        get the full set of test done earlier
510      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
511    o model/src/thermodynamics.F and routines called from it:
512      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
513        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
514        velocity (outp) by adding bolus velocity.
515      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
516        mass transport from velocity + lateral grid cell area
517      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
518      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
519     in thermodynamics.F
520      - remove k from thermodynamics.F and move it to temp_integrate.F
521        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
522        loop).
523      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
524        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
525        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
526        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
527      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
528        global_ocean.90x40x15, tutorial_global_oce_biogeo and
529        tutorial_tracer_adjsens (+ TLM output).
530    o tools/OAD_support and (verification/*/) code_oad:
531      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
532        module conversion ; remove unneeded CPP_EEOPTIONS.h.
533      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
534        version (closer to model/inc/CPP_OPTIONS.h).
535    o model/src:
536      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
537        retired list of parameters (routine FREEZE has been replace by surface
538        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
539    o pkg/gmredi:
540      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
541        velocity (same scheme but affects machine truncation) for GM_AdvForm.
542      - update output of FWD experiments: front_relax.bvp,
543        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
544    
545    checkpoint64q (2013/11/17)
546    o verification:
547      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
548        tutorial_global_oce_biogeo and global_ocean.90x40x15.
549      - generate new output (growth & melt) for seaice_itd experiment after
550        updating the input pickup_seaice files (previously wrong).
551    o pkg/cost:
552      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
553        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
554        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
555          cannot be applied to var in common block).
556        o allows to get results independent of tile-per-proc setting (if using
557          slower GLOBAL_SUM_SEND_RECV option).
558      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
559        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
560        forward gradients: update output).
561      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
562        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
563    o pkg/mom_common:
564      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
565        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
566        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
567        ensure that all field value that are used are set.
568    o tutorial_deep_convection (smag3d):
569      - add missing scaling in mom_calc_smag_3d.F;
570      - set smag3D_coeff in input.smag3d such that results do not change.
571    o pkg/dic:
572      - change dic_cost.F to compute cost on each tile first and then apply
573        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
574        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
575      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
576    o eesupp/src & pkg/mdsio:
577      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
578        (from pkg/mdsio) since they are no longer used for tape IO.
579      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
580        (+ keep a copy in pkg/atm_ocn_coupler).
581    o verification/isomip:
582      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
583    o tools/build_options:
584      - optfile linux_amd64_ifort11, fast (no ieee) case:
585        to get a working restart for all experiments, add "-fp-model source"
586        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
587    
588    checkpoint64p (2013/10/20)
589    o pkg/autodiff:
590      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
591        criteria, return to simple (default) tape IO format.
592    o pkg/mdsio (+ eesupp/src):
593      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
594        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
595      - fix globalFile and singleCpuIO options using simpler global mapping.
596      - new pairs of scatter/gather vector S/R (one for each type, generated from
597        template) corresponding to simpler global mapping.
598      - adread_write.F: switch to new S/R (but leave old calls commented) and write
599        to globalFile when parameter globalFiles is set to True.
600      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
601    o pkg/autodiff:
602      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
603        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
604        missing, just add a STOP if array type do not match.
605    o pkg/exf:
606      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
607         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
608         and rename array obsSIce to exf_iceFraction.
609    o tutorial_deep_convection:
610      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
611        for now all in this exp. code dir.
612      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
613        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
614    o eesupp/src:
615      - added SINGLE_DISK_IO option because reading of parameter files on
616        very large number of processors did not work with existing set-up
617    
618    checkpoint64o (2013/09/25)
619    o pkg/atm_phys & atm_compon_interf:
620      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
621    o tools/build_options:
622      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
623        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
624        remove CPP setting (was identical to genmake2 default).
625    o pkg/gmredi & model/src: Some updating and work done on the residual model.
626      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
627      - fixed up the calculation of the eddy stress and how it is added to the
628        external forcing via taueddy_external_forcing.F
629      - at the moment, it is very experimental and only works with the variable eddy
630        diffusivity calculated in gmredi_k3d.F
631    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
632        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
633    o testreport (& tools/do_tst_2+2):
634      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
635    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
636      - remove CPP='cpp -traditional -P' (this is genmake2 default)
637      - add switch (for big setups) to use 'medium' memory-model (but leave it
638        commented out for now). Note: needed with FC 19 to compile big setups.
639    o pkg/atm_compon_interf:
640      - regroup per field origin (model & pkgs) the coupling storage routines
641         (which accumalate in time each coupling field)
642      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
643        update accordingly + simplify aim_do_physics.F
644    
645    checkpoint64n (2013/08/26)
646    o pkg/bbl:
647      - update formulation to reduce dispersion of tracer properties in bbl
648      - replaced horizontal and vertical transport parameters with velocities
649      - changes results for verification/global_with_exf.yearly
650    o verification/halfpipe_streamice:
651      - change to matrix construction; update both Fwd & AD output.
652    o verification/tutorial_tracer_adjsens:
653      - OpenAD test: switch to vector-invariant momentum since fluxform with
654        rStar causes problems with OpenAD; update output.
655    o tools:
656      - genmake2: define a common prefix for all temp-file names ; move them
657        to local /tmp disk (but would be easy to move them back);
658      - xmakedepend: apply the same switch for temp-files.
659    o pkg/offline:
660      - changes for use with rStar (NLFS): assume that we continue to provide
661        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
662        output files) and apply r* scaling at each time-step (function of the time
663        varying Eta field); use normal pickup files (needed for restart with NLFS).
664    o adjoint with OpenAD:
665      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
666        package openad.  This package has to be compiled for all runs with OpenAD
667        instead of specifying code_oad_all as a modification directory.
668      - link the fortran templates from tools/OAD_support to the build directory
669        for preprocessing to avoid conflicts between different setups compiled
670        simultaneously and simplify cleanup.
671    o pkg/exf:
672      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
673        main model or other pkgs are exchanged in EXF_MAPFIELDS).
674    o model/src:
675      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
676        (similar to do_fields_blocking_exchanges.F).
677    o tools/genmake2:
678      - remove TAF output src code just before calling staf (when not doing a fresh
679        built, will stop if things go wrong with staf).
680      - fix target "adobj" (left from TAF version-2 transition)
681    o pkg/diagnostics:
682      - add a parameter to track the status of pkg/diagnostics activation;
683        this replace/extend the use of logical param "settingDiags" (to check
684        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
685        New S/R to print error message and stop when pkgStatus is not right.
686      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
687    
688    checkpoint64m (2013/08/13)
689    o model/inc:
690      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
691        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
692    o pkg/kpp & aim_v23:
693      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
694    o pkg/seaice:
695      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
696        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
697      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
698    o eesupp/src:
699      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
700        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
701    o switch to TAF version-2:
702      - add flow directives to "freeze" naming convention for ad-routines that
703        are used in I/O routines of adjoint state and associated common blocks
704        that are used in adcommon.h (backward compatible with version-1)
705      - update all ad-optfiles (in tools/adjoint_options + few local to some
706        verification exp) to switch to latest TAF version (currently 2.5.5);
707        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
708        out except for diva).
709      - the major change with TAF version-2 is that both the differentiated
710        routines and the forward routines (new) are returned as part of the TAF
711        output source code. Update genmake2 accordingly.
712      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
713        with version-2 when compared to TLM or FWD gradient); other experiments
714        output show minor changes (machine truncation level); update the few AD &
715        TLM output with 12 matching digits only (some prior to version-2 switch).
716    
717    checkpoint64l (2013/08/05)
718    o model/src:
719      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
720      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
721        when using TAF but only if using OpenAD.
722    o pkg/mom_common+fluxform+vecinv:
723      - always set horiz. viscosity arrays to background value before calling
724        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
725        only when using variable horiz. viscosity (useVariableVisc=T);
726      - simplify mom_vecinv.F (only 1 block for momViscosity).
727    o pkg/mom_common: variable horiz. viscosity in NH code
728      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
729        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
730      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
731        useBiharmonicVisc & useVariableVisc.
732      - fix old bug (already in 1rst implementation of variable horizontal viscosity
733        in calc_gw.F, version 1.27, 2006/06/20):
734        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
735        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
736      - change background horiz viscosity in vertical momentum (gW) to always be
737        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
738        any type of variable viscosity, e.g., viscAh/4Grid)
739      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
740        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
741        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
742        default viscAh,viscA4 is zero).
743    o model/src:
744      - extend length of drC & recip_drC from Nr to Nr+1.
745  o Divided Adjoint (DIVA) with MPI:  o Divided Adjoint (DIVA) with MPI:
746    - 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.
747    - 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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