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revision 1.1901 by jmc, Thu Jul 25 01:12:45 2013 UTC revision 1.2078 by gforget, Mon Oct 6 14:12:28 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/ecco: increase modularity and improve logic
8      - ecco_toolbox.F (new) : basic operations that are often used
9         (for now, ecco_toolbox.F simply contains function ecco_zero).
10      - cost_gencal.F (new) : determine filnames and records.
11      - cost_gendif.F (new) : compute masked model-data difference.
12      - cost_genread.F : use ecco_zero to initialize field to 0s.
13      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
14        and exploit the above functions leading to more compact code.
15      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
16        using_ers, using_gfo, using_mdt is now only defined within gencost)
17    o pkg/ecco: extend generic cost capabilities
18      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
19        capabilities via gencost_preproc (+ _c,_i,_r related params),
20        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
21        gencost_outputlevel arguments to cost_generic
22      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
23        and active_read, making room for gencost_preproc to take effect.
24        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
25      - pkg/ecco/cost_generic.F :
26        compute and store misfit maks*(model-data) in localdif that is
27        then used in cost and for output, output misfit if outlev.GT.0
28      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
29        rather gencost_barfile for deciding whether to write barfile
30      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
31      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
32        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
33      - pkg/ecco/ecco_summary.F : report gencost variables
34      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
35    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
36    o pkg/ecco: internal re-organization
37      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
38        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
39        mv relevant variables definition from ecco_cost.h to ecco.h,
40        make sure gencost routines only include ecco.h)
41      - throughout : add missing CCP switches, rm unused variables,
42        and rm un-necessary CPP switches
43      - throughout gencost routines : replace modelstartdate with
44        gencost_startdate when needed
45      - cost_bp_read.F : use arguments, instead of common blocs
46        so that it can be used also by (new) cost_gencost_bpv4.F
47      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
48      - ecco_phys.F : compute etanFull
49      - ecco_readparms.F : rename using_topex as using_tpj, add
50        bpv4-grace to gencost list, initialize added parameters
51      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
52    
53    checkpoint65e (2014/09/28)
54    o pkg/obcs:
55      - replaced the just-added CPP options with run-time variables
56        (see pkg/obcs/OBCS_PARAMS.h for details)
57    o pkg/obcs:
58      - add additional CPP options for sponge boundary layers
59        (see pkg/obcs/OBCS_OPTIONS.h for details)
60    o pkg/atm_phys:
61      - implement simple (obliquity only, assuming circular planet orbit)
62        seasonal cycle for incoming insolation ; used when run-time parameter
63        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
64    o pkg/exf, pkg/ecco, pkg/ctrl:
65      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
66      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
67      - implement gentim2d for xx_tauu, xx_tauv
68    o pkg/ctrl, pkg/ecco :
69      - fix and complement the generic controls implementation
70    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
71        pkg/shelfice/shelfice_thermodynamics.F,
72        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
73        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
74      - add weight in CTRL_GET_GEN calls
75    o pkg/ctrl :
76      - ctrl_get_gen.F : add weight as input parameter, and apply
77        it directly rather than using smooth_correl2Dw (to be retired).
78      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
79    o pkg/ctrl :
80      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
81        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
82      - re-activate ctrl_summary (call in ctrl_init.F)
83    o pkg/ctrl/ctrl_cost_gen.F :
84      - fix CCP brackets, remove un-necessary myiter, mytime
85    o pkg/ecco, pkg/ctrl :
86      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
87      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
88      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
89      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
90    
91    checkpoint65d (2014/09/15)
92    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
93      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
94        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
95    o pkg/ctrl/ctrl_map_ini_genarr.F :
96      - remove compilation failure
97      - replace hard coded example
98      - use ctrl_map_ini_gen2D, 3D
99    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
100      - on/off switch based upon xx_genarr2d_weight,3d
101    o src/packages_init_variables.F :
102      - regroup pkg/estimation calls
103      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
104        (moved to ctrl_init_variables)
105    o cost/cost_init_varia.F :
106      - remove ecco_cost_init_varia
107        (moved to ecco_init_varia)
108    o ctrl/ctrl_init_variables.F :
109      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
110      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
111    o ctrl/ctrl_map_ini.F :
112      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
113        (moved to ctrl_init_variables)
114    o ctrl/ctrl_map_ini_ecco.F :
115      - remove ECCO_PHYS (mv to ecco_init_varia)
116      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
117    o ecco/ecco_ad_diff.list :
118      - add ecco_init_varia.f
119    o ecco/ecco_init_varia.F
120      - new routine
121    o pkg/streamice:
122      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
123        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
124      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
125    o pkg/generic_advdiff:
126      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
127    o pkg/exf:
128      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
129         xxg_precip capability
130      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
131    o pkg/ctrl:
132      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
133    o model/src/load_fields_driver.F :
134      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
135        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
136    o OpenAD verification experiments:
137      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
138        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
139        for now, only in pkgs used in OpenAD verification experiments.
140      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
141        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
142        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
143        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
144    o OpenAD verification tests:
145      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
146      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
147        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
148      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
149        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
150    o model/src & generic_advdiff:
151      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
152        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
153        dynamics requires valid tracer forcing only over tile interior but, for
154        some diagnostics, may need to extend it over 1 point in tile halo region.
155      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
156        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
157        setting in temp/salt/ptracer_integrate.F
158    o pkg/dic:
159      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
160        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
161        in gchem_forcing_sep.F
162    o pkg/autodiff & obcs:
163      - add storage of current OB values for U & V (was already done for T & S).
164    
165    checkpoint65c (2014/08/30)
166    o pkg/dic:
167      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
168        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
169        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
170    o verification:
171      - new experiment testing OBCS and DIC pkgs, using params & output from
172        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
173        passage: take OBCS from the last year of a 2 yrs simulation and initial
174        conditions from t=1.yr while keeping the same forcing.
175    o model/src:
176      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
177        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
178    o pkg/diagnostics (Stats-Diags):
179      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
180        a) refine region where stats are computed, excluding where arrhFac=0 ;
181        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
182        c) extend regional stats over the region edges (for U or V pt location).
183    o pkg/gchem:
184      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
185        pkg/dic is currently changing/updating ptracers values beyond the OB).
186    o verification (hs94):
187      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
188        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
189        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
190        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
191    o pkg/ptracers:
192      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
193        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
194      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
195        with AB-2 code (so that it get tested).
196    o model/src:
197      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
198        with AB-2 code (previously only available with AB-3 code).
199        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
200        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
201        there, by calling CYCLE_AB_TRACER).
202    o pkg/generic_advdiff:
203      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
204        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
205        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
206        S/R temp/salt/ptracers_integrate.F
207    o model/src & pkg/ptracers:
208      - remove common block variables gT,gS (in DYNVARS.h), except when
209         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
210      - remove common block variable gPtr.
211    o model/src & pkgs:
212      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
213         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
214         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
215         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
216      + change accordingly all calling S/R.
217      - use local temperature/salinity/ptracer tendency array (without bi,bj)
218        in S/R temp/salt/ptracers_integrate.F
219    o pkg/seaice:
220      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
221        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
222      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
223        in seaice_lsr
224      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
225        in s/r seaice_lsr_calc_coeffs
226    o pkg/mdsio:
227      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
228        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
229        too long (e.g., > MAX_LEN_FNAM/2 )
230    
231    checkpoint65b (2014/08/12)
232    o pkg/matrix:
233      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
234    o model/src:
235      - fix initialisation of geothermalFile; compile geothermal-flux code in
236        natl_box verification experiment.
237    o model/src & pkg/down_slope:
238      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
239      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
240        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
241        results at machine truncation level: update output of experiments
242        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
243    o pkg/diagnostics (Stats-Diags):
244      - do not cumulate the full volume when DIAGNOSTICS_FILL is
245        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
246        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
247        times (but Min,Max and StD are still wrong).
248    o model/src:
249      - add geothermal flux forcing: read in ini_forcing.F as time-constant
250        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
251    o model/src:
252      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
253        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
254        arrays are already updated while adjustments (filters, conv.adjustment) are
255        still applied later, in S/R TRACERS_CORRECTION_STEP.
256    o model/src:
257      - store in common bloc array "rhoInSitu" the virtual potential temperature
258        anomaly that is used to compute geopotential: this make the atmos code
259        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
260    o pkg/seaice/seaice_lsr.F
261      - rename integer variable ilcall to ipass (that's what it is called
262        in the residual diagnostics
263      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
264        default) for improved non-linear convergence of the first few steps
265      - adjust a few comments and add new ones to explain some of the store
266        directives
267    o pkg/generic_advdiff (& ptracers):
268      - re-work the code to check for valid advection scheme and for minimum
269        size of overlap (now stored in local common bloc in gad_advscheme.F)
270    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
271      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
272      - add an auxilliary variable "bet" and fix store directives and keys in
273        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
274        less exact gradients in my tests); but there are still
275        recomputation warning (although gradients are sort of OK), when
276        SEAICE_LSR_VECTORIZE is not defined, so this flag and
277        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
278      - update verification experiments lab_sea.
279      - change some comments in S/R seaice_calc_viscosities
280    o model/src:
281      - if staggerTimeStep=T, always apply exchange to velocity field in
282        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
283        (independent of using multi-dim advection or not); no effect on FWD run
284        but affects AD results (at machine truncation level): update output of
285        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
286        and isomip (oad: 12.d).
287    o pkg/generic_advdiff:
288      - stop if doAB_onGtGs is set to FALSE but ignored
289      - refine warning related to stability of tracer time-stepping
290        regarding internal wave dynamics.
291      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
292        on staggerTimeStep & implicitIntGravWave (will now get a warning
293        if potentially unstable).
294    o pkg/kl10:
295      - add new pkg "kl10" for mixing due to internal wave breaking, from
296        http://www.sciencedirect.com/science/article/pii/S1463500310000144
297        (contribution from Jody Klymak), tested in verification experiment
298        verification/internal_wave/input.kl10/
299    o isomip experiment:
300      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
301        (input.htd) and update the output.
302    o cd_code experiments:
303      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
304        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
305        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
306        update the corresponding output.
307    o pkg/seaice:
308      - reduce the number of include files and store directives in
309        S/R seaice_lsr_tridiagu/v
310      - change the order of loops in one case in S/R seaice_lsr_tridiagv
311        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
312        get rid off one store directive (a TAF bug?)
313      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
314        S/R seaice_lsr_tridiagv to change the loop range for consistency
315      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
316      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
317        S/R seaice_lsr_tridiagu/v (requires update of
318        offline_exf_seaice/input.dyn_jfnk)
319    
320    checkpoint65a (2014/07/27)
321    o model/src:
322      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
323        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
324        (topo in p-coords, ice-shelf in z-coords); update output of experiments
325        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
326    o model/src:
327      - collect momentum forcing tendency into local 2-D array (passed as argument
328        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
329        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
330        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
331      - collect T & S forcing tendency into local 2-D array (passed as argument to
332        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
333        affects results at machine truncation level (e.g., ocean: if using
334        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
335        correction due to vertical advection).
336      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
337        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
338        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
339        obcs_ctrl (ad & fwd grd @ 12 & 7).
340    o pkg/ptracers & diagnostics:
341      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
342        title (to avoid some unexpected truncation); sort out ptracers diags units.
343      - collect ptracer forcing tendency into local 2-D array (passed as argument
344        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
345    
346    checkpoint65 (2014/07/18)
347    o pkg/fizhi:
348      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
349        affects results at machine truncation level. Update output of experiments
350        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
351    o pkg/seaice: more clean up
352      - rename TAF common block tapes to be more consistent and remove
353        unnecessary duplicates
354      - add store directives to remove more recomputations, but use smaller
355        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
356        The idea behind this flag is to reduce the memory footprint when the
357        adjoint of the LSR is not required. As of now, defining the flag
358        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
359        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
360        For experiment offline_exf_seaice, this means on a linux box with gfortran
361        nearly a factor of 10 (but keep in mind there is mostly seaice code in
362        this experiment):
363        > size mitgcmuv_ad
364        text    data        bss     dec        hex  
365        5100659 1216  220458952  225560827  d71c8fb
366        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
367        but only a moderate increase of 36% for global_ocean.cs32x15:
368        text    data        bss     dec        hex
369        6695027 1648 1014578664 1021275339 3cdf6ccb
370        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
371      - note: there are still recomputations in global_ocean.cs32x15 and
372        offline_exf_seaice and the gradient agreement changes (gets a
373        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
374      - in general, the AD gradients still are wrong
375    o OpenAD
376      - clean up code_oad/ directories somewhat by moving files
377        dontCompile, dontTransform, keepOriginal to OAD_support/
378    o model/src:
379      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
380        (not currently tested): add dissipation terms before NLFS rescaling of
381        tendencies (previously done after).
382    o pkg/diagnostics:
383      - write stats-diags in ascii file with more digits (same as in monitor).
384    o pkg/down_slope:
385      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
386        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
387    o model/src:
388      - new file "apply_forcing.F" containing all the code previously in
389        external_forcing.F, but with new argument list: pass, as new argument,
390        the current level tendency array to update (instead of a direct update
391        of the common bloc array). Change the corresponding calls.
392      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
393        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
394    o pkg/seaice/seaice_lsr, a little bit of clean up
395      - rearrange some code blocks, so that now all calculations for
396        setting up the right-hand-sides done within one single block
397        (I find that easier to read and understand)
398      - rearrange freedrift-code to reduce the number of ifdefs
399      - adjust some indentations and comments
400    
401    checkpoint64z (2014/07/10)
402    o model/src and several pkgs:
403      - change argument list of all S/R called from external_forcing.F and
404        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
405        to pass, as argument, the current level tendency array to update
406        (instead of a direct update of the common bloc array).
407      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
408      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
409    o pkg/seaice/seaice_lsr.F
410      - always initialize local arrays in seaice_lsr_tridiagu/v
411      - add more local tapes to seaice_lsr_tridiagu/v
412      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
413        keep it in bi/bj loop; this seems to be essential
414      - gradients are still wrong but only by 4-7 orders of magnitude
415        instead of 15 orders of magnitude, lab_sea improves a little
416    o pkg/seaice
417      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
418        generates unnecessary code in seaice_lsr_ad
419      - add more store directives in seaice_lsr to avoid unnecessary code
420        in seaice_lsr_ad
421      - exclude some residual computations in seaice_lsr when
422        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
423        in seaice_lsr_ad
424      - add more storing, a new tape (model/src/the_main_loop.F) and
425        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
426        and klockey should be checked by a specialist)
427      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
428        and update lab_sea after previous changes in pkg/seaice below
429    o pkg/autodiff:
430      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
431        viscFacInAd : run time parameters allowing for adjoint switches
432        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
433    o pkg/ecco:
434      - introduce cost_gencost_boxmean.F that computes a box mean
435        temperature (for use in adjoint sensitivity studies).
436    o model/src/set_defaults.F : initialize viscFacAdj to 1.
437    o pkg/mom_common/mom_calc_visc.F:
438      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
439    o pkg/seaice/seaice_summary.F:
440      - statement for SEAICEadjMODE now in autodiff_readparms.F
441    o pkg/seaice:
442      - remove some store directives and add new ones in an effort to get
443        finally rid off the recomputation warnings. This is successful
444        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
445        defined (i.e. no extensive recomputation warnings left), but there
446        are still too many recomputations on the solver iteration level
447      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
448      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
449        SEAICE_SIZE.h
450      - add a store directive in S/R seaice_calc_viscosities
451    o pkg/seaice (ITD code):
452      - fix definition of Hlimit for multi-threaded case
453      - use double precision arithmetic to compute Hlimit: this affects results;
454        update output of experiment seaice_itd.
455    o replace content of verification/seaice_itd
456      - instead of a 1D column use the configuration of offline_exf_seaice
457        to test the ice thickness distribution code with ridging
458      - this is a first shot at this experiment
459      - change of some defaults of ridging parameters SEAICEhStar (from
460        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
461        and lot of new comments.
462    
463    checkpoint64y (2014/06/20)
464    o pkg/seaice/seaice_reg_ridge.F:
465      - modify the regularization of very small volumes of ice; only check
466        total volume HEFF, and do not apply correction to individual ice
467        classes because that leads to funny patterns in the heat and fw-fluxes
468        into the ocean. Adjust seaice_itd/results/output.txt
469      - replace nITD by SEAICE_multDim in loop-ranges
470    o pkg/exf:
471      - add code to process the case field period = -12. with UV interpolation.
472      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
473        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
474    o verification/global_with_exf:
475      - switch all fields period to -12. (was previously untested) in input/data.exf
476        (but keep secondary test ".yearly" unchanged); update the reference output.
477    o pkg/cal:
478      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
479    o pkg/exf:
480      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
481        to replace logical switch "exf_verbose"
482      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
483    o pkg/sbo:
484      - update from Katherine Quinn: evaluate mass directly from density and SSH
485        (budget using Finite Volume method) instead of from bottom pressure.
486      - allow testreport to collect few selected SBO output ; tested in exp.
487        global_ocean.90x40x15 (after updating the results, to include SBO output).
488      - fix some multi-threading issues (in output part).
489    o model/src & most packages:
490      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
491      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
492        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
493        "data.{pkg}" exist ; and leave the S/R (return) just after.
494      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
495        + call LAND_READPARMS from packages_readparms.F
496    o pkg/seaice:
497      - remove code that resets useThSice in S/R seaice_readparms and
498        replace it by a warning in S/R seaice_check
499      - remove parameter MULTDIM, replace with nITD and runtime
500        parameter SEAICE_multDim (still hard-wired to nITD if
501        SEAICE_ITD is defined)
502    
503    checkpoint64x (2014/05/24)
504    o verification/lab_sea:
505      - update adjoint and TLM output following changes to pkg/salt_plume
506      - un-do the update after putting back local recip_Cp in few places.
507    o pkg/salt_plume: modifications by An Nguyen:
508      - add capability to do brine rejection (salt-plume) as function of
509        volume+tracers (instead of only salinity tracer).
510      - conserve volume by exchanging volume from each kLev to above to
511        accommodate in-coming brine volume
512      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
513      - switch KPP surf buoyancy due to brine forcing to 3-d
514        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
515      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
516      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
517        in East/West Arctic.
518    o pkg/sbo:
519      - incorporate modifications from Katherine Quinn to enable the use of sbo
520        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
521        output for future testreport verification (unfinished).
522    o pkg/atm_phys:
523      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
524        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
525        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
526    o pkg/seaice
527      seaice_calc_ice_strength.F: modify expression to avoid divisions
528        (affects truncation)
529      seaice_do_ridging.F: clean up the insectarium
530      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
531      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
532      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
533      - add some debugging information and error messages (warnings)
534    o model/src: modifications relatd to atmosphere p*:
535      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
536      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
537        of vertical profile tRef in geopotential background and anomaly.
538      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
539        and pkg/atm_phys.
540      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
541        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
542    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
543    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
544        not used right now, but can be used in BGC packages to fix conservation.
545    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
546        other packages too.
547    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
548        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
549    o model/src:
550      - since we have several heat capacity (even in model/src), define "recip_Cp"
551        as local variable (no longer in common block) to avoid any confusion.
552      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
553    o pkg/exf:
554      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
555        air density as function of air Temp, Humidity and atm pressure.
556    
557    checkpoint64w (2014/05/02)
558    o verification:
559      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
560        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
561        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
562        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
563        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
564    o model/src: for atmosphere in p* coords:
565      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
566      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
567        but not yet activated.
568    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
569      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
570      - this changes the results (but not for any verification experiment, because
571        none tests this), but avoids having an extra field in the restart files
572    o pkg/seaice: remove global variable TICE (not needed)
573      - replace by TICES or local variable where necessary (cost_seaice_test,
574        seaice_diagnostics_state)
575      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
576      - use specific read/write routines for reading and writing individual leves
577        of a multilevel field
578    o pkg/ctrl & model/inc:
579      - move additional anomaly fields of control vars (related to options:
580         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
581        from DYNVARS.h into new header file: CTRL_FIELDS.h
582    o pkg/seaice: some small modifications to the ridging code
583      - make fw2ObyRidge a global variable and add the freshwater flux to
584        seaice_growth
585      - pass actual thickness from seaice_prepare_ridging, so that it is
586        computed only in one place and compute it in the same way as in
587        seaice_growth
588      - initialise more fields in seaice_do_ridging that where cause floating
589        point exceptions over land
590    o pkg/seaice: preparations for ridging code and first real ridging code
591      - move most of "PART 1" of S/R seaice_growth into a new and separate
592        S/R seaice_reg_ridge that will both regularize the state variable after
593        advection call the actual ridging routine;
594      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
595        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
596      - remove ridging code from seaice_advdiff
597      - clean up remaining part 1 of seaice_growth in an attempt to make it
598        more readable (this is probably subjective)
599      - call seaice_itd_redist once in the initialisation phase to have the initial
600        conditions in the correct category
601      - finally: add new ridging routine for ITD code
602    
603    checkpoint64v (2014/04/11)
604    o pkg/ecco:
605      - add runtime parameters mdt[start,end]date[1,2]
606      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
607    o pkg/seaice:
608      - make deltaC a global variable, so that it can be used in ridging code
609      - first step towards ridging: introduce new routines that compute
610        ice strength based on ridging parameters
611      - add diagnostic for HSNOWITD
612      - add opnWtrFrac as a global variable (required for ridging scheme)
613    o pkg/salt_plume + pkg/seaice/seaice_growth.F
614      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
615        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
616    o verification/hs94.1x64x5:
617      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
618      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
619    o autodiff:
620      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
621        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
622        For now, only in pkgs used in verification/hs94.1x64x5.
623      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
624        which are specific to TAF/TAMC).
625      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
626        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
627        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
628      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
629        building mitgcmuv_ad (make adAll).
630    o pkg/ecco:
631      - cost_gencost_seaicev4.F:
632         reformulate proxy cost as function of sst and local param SEAICE_freeze
633         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
634      - add stop statement if old names siv4-[sst,vol] are used
635      - add snapshots + cost reports for atmospheric longwave
636      - remove factor 0.1 in front of wtau[u,v]
637      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
638         ALLOW_TMI_SST_COST_CONTRIBUTION
639    o pkg/atm_phys:
640      - add some diagnostics for Short-wave and for convection S/R.
641    o pkg/seaice/seaice_growth:
642      - fix a bug in the lateral melt parameterization for SEAICE_ITD
643        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
644      - rearrange loop order for better vector code in the same code block
645      - rewrite the floeDiameter formula to have fewer divisions
646      -  (miraculously) none of this changes the results of seaice_itd
647    o pkg/smooth:
648      - move param smooth2Ddiffnbt to pkg/ecco
649    o pkg/salt_plume:
650      - salt_plume_frac.F:
651         clean up local param names
652         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
653    o pkg/rw:
654      - add RS version of S/R READ_MFLDS_LEV.
655    o pkg/streamice:
656      - fix the restart test by writing/reading pickup_streamice files.
657    o pkg/seaice:
658      - refine checks for jfnk-related parameters
659      - comment out if statement with SEAICEuseIMEX parameter as long as there
660        is no IMEX code to avoid confusion and surprises
661    
662    checkpoint64u (2014/03/07)
663    o verification/MLAdjust:
664      - rename secondary test suffix:
665         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
666         0.leithD -> AhFlxF  + switch to flux-form
667         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
668         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
669    o pkg/mom_vecinv:
670      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
671        to be before mom_calc_visc.F)
672      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
673      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
674        this is simpler for the adjoint and for diagnostics.
675    o model/src + pkg/momentum:
676      - add input files for  2-D additional Western and Southern cell-edge wall
677         (e.g., to add "thin-wall" where it is =1).
678      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
679        using 2nd hFacZ that is computed from initial (fix domain) hFac
680      - known limitations of thin wall implementation: not yet coded for sigma
681        coords; not working with CD-scheme neither.
682    o pkg/seaice:
683      - rename recently introduced parameters from (wrong name) AB to
684        BDF (backward difference time discretisation)
685      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
686    o tools/adjoint_options:
687      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
688    
689    checkpoint64t (2014/02/01)
690    o pkg/ecco
691      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
692        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
693      - replace hard-coded record number and period which only work for monthly
694        with read-in runtime param that works for other periods (month,day,year)
695    o pkg/thsice
696      - corrected store directive fixes thsice adjoint gradient checks
697    o genmake2 & testreport:
698      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
699        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
700        Update testreport accordingly. No need to set "export OPENAD=true"
701        in adjoint_options/adjoint_oad anymore (will be removed later).
702    o pkg/shelfice:
703      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
704        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
705        so that surface forcing applies to k=kSurf if using pkg/shelfice.
706    o pkg/ctrl, pkg/grdchk, pkg/ecco:
707      - Changes to make GENARR more modular (i.e. invisible if not used)
708    o model/src/temp_integrate.F and salt_integrate.F
709      - re-include store directives that were removed on Dec 27th.
710    o model/src/external_forcing_surf.F
711      - add storage directives for EmPmR and PmEpR to avoid recomputation of
712        seaice_model in the adjoint that is problematic when seaice_model is
713        turned off in the adjoint. The resolved issue dated back to July when
714        EXTERNAL_FORCING_SURF call was moved.
715        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
716    o pkg/exf/exf_check.F
717      - fix a small bug again (originally found by Wentao Liu, now found again)
718      - streamline error output
719    o pkg/streamice and aim_v23:
720      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
721        Apple's /usr/bin/cpp knows what to do:
722        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
723        Target: x86_64-apple-darwin13.0.0
724    
725    checkpoint64s (2014/01/05)
726    o tools/adjoint_options:
727      - switch to fastopt.net TAF server (instead of default fastopt.de) for
728        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
729    o model/src:
730      - remove some unnecessary TAF storage directives in forward_step.F and
731        in dynamics.F (note: not always removed by TAF, e.g., double storage
732        of kappaRU,kappaRV in former version of dynamics.F).
733    o model/src & pkg/ptracers:
734      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
735        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
736        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
737      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
738      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
739      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
740    o useSingleCpuInput separates single-CPU input from single-CPU output;
741        for now only implemented for in exf_interp_read.F
742    o verification/advect_xy:
743      - fix missing EXCH call in local version of ini_salt.F and update output.
744    o momentum diagnostics:
745      - fix which deltaT is used in Total-Tendency diagnostics.
746      - fix typo in diagnostics for momentum tendency from AB.
747    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
748        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
749    
750    checkpoint64r (2013/12/08)
751    o verification/*/results:
752      - Update reference output of experiments that were passing with just 13 digits
753         (make it easier to detect future changes in results)
754    o model/src & pkg/ptracers:
755      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
756        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
757        to inside ptracers_integrate.F ; remove ptracers_advection.F
758    o coupling interface pkgs:
759        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
760      - change the config check to test the agreement of Ocean Depth
761        with ATM land/sea mask (instead of ATM orography);
762      - send to coupler the number of coupler time-steps to do for this run:
763        this allows to check for consistency and don't need anymore to be
764        specified in parameter file "data";
765      in coupler:
766      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
767      - improve report to log-file of config setting (pass log-file unit to few S/R)
768    o pkg/compon_communic:
769      - add coupling send/receive for non-tiled integer vector;
770      - add S/R to check and stop if any proc has an error (similar to
771        eesupp/src/stop_if_error.F but single thread and across Comm_World).
772    o pkg/exch2:
773      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
774        through list of all tiles my proc owns.
775    o model/src:
776      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
777        from rTrans) to simplify dependencies (no need to store rTrans anymore in
778        calling S/R); this affects AD results at machine truncation level:
779        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
780        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
781    o tools/build_options:
782      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
783    o coupling interface pkgs:
784        [compon_communic, atm_compon_interf & ocn_compon_interf]
785      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
786        to each S/R that needs it; remove un-used variables.
787      - change component tile registration (cpl_register.F in both compon_interf
788        and mitcomponent_tile_register.F) to pass the full list of tiles
789        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
790      - with pkg/exch2: adopt the same convention used for I/O to define mapping
791        towards coupler global array (unless W2_useE2ioLayOut=F):
792         a) can now use different tiling between atm & ocn comp.
793         b) no needs to modify the run-Off map when changing tiling (was needed
794            even if using the same tiling between atm & ocn).
795         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
796            full land tiles); not yet tested.
797      - check for valid mapping from comp. tile to coupler global array
798      - improve report of tile registration results to log file.
799    o pkg/exch2:
800      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
801        tile-registration (CPL_REGISTER);
802      - activate (un-comment) definition and setting of "W2_tileIndex" list to
803        store the local bi,bj indices of each tile;
804      - also print bi,bj in local report to log file;
805      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
806        Jun 2009 modif of pkg/exch2).
807    o testing on baudelaire:
808      - run 2 tests at a time: no significant slow down (since enough cpu) and
809        get the full set of test done earlier
810      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
811    o model/src/thermodynamics.F and routines called from it:
812      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
813        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
814        velocity (outp) by adding bolus velocity.
815      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
816        mass transport from velocity + lateral grid cell area
817      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
818      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
819     in thermodynamics.F
820      - remove k from thermodynamics.F and move it to temp_integrate.F
821        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
822        loop).
823      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
824        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
825        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
826        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
827      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
828        global_ocean.90x40x15, tutorial_global_oce_biogeo and
829        tutorial_tracer_adjsens (+ TLM output).
830    o tools/OAD_support and (verification/*/) code_oad:
831      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
832        module conversion ; remove unneeded CPP_EEOPTIONS.h.
833      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
834        version (closer to model/inc/CPP_OPTIONS.h).
835    o model/src:
836      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
837        retired list of parameters (routine FREEZE has been replace by surface
838        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
839    o pkg/gmredi:
840      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
841        velocity (same scheme but affects machine truncation) for GM_AdvForm.
842      - update output of FWD experiments: front_relax.bvp,
843        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
844    
845    checkpoint64q (2013/11/17)
846    o verification:
847      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
848        tutorial_global_oce_biogeo and global_ocean.90x40x15.
849      - generate new output (growth & melt) for seaice_itd experiment after
850        updating the input pickup_seaice files (previously wrong).
851    o pkg/cost:
852      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
853        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
854        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
855          cannot be applied to var in common block).
856        o allows to get results independent of tile-per-proc setting (if using
857          slower GLOBAL_SUM_SEND_RECV option).
858      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
859        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
860        forward gradients: update output).
861      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
862        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
863    o pkg/mom_common:
864      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
865        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
866        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
867        ensure that all field value that are used are set.
868    o tutorial_deep_convection (smag3d):
869      - add missing scaling in mom_calc_smag_3d.F;
870      - set smag3D_coeff in input.smag3d such that results do not change.
871    o pkg/dic:
872      - change dic_cost.F to compute cost on each tile first and then apply
873        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
874        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
875      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
876    o eesupp/src & pkg/mdsio:
877      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
878        (from pkg/mdsio) since they are no longer used for tape IO.
879      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
880        (+ keep a copy in pkg/atm_ocn_coupler).
881    o verification/isomip:
882      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
883    o tools/build_options:
884      - optfile linux_amd64_ifort11, fast (no ieee) case:
885        to get a working restart for all experiments, add "-fp-model source"
886        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
887    
888    checkpoint64p (2013/10/20)
889    o pkg/autodiff:
890      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
891        criteria, return to simple (default) tape IO format.
892    o pkg/mdsio (+ eesupp/src):
893      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
894        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
895      - fix globalFile and singleCpuIO options using simpler global mapping.
896      - new pairs of scatter/gather vector S/R (one for each type, generated from
897        template) corresponding to simpler global mapping.
898      - adread_write.F: switch to new S/R (but leave old calls commented) and write
899        to globalFile when parameter globalFiles is set to True.
900      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
901    o pkg/autodiff:
902      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
903        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
904        missing, just add a STOP if array type do not match.
905    o pkg/exf:
906      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
907         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
908         and rename array obsSIce to exf_iceFraction.
909    o tutorial_deep_convection:
910      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
911        for now all in this exp. code dir.
912      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
913        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
914    o eesupp/src:
915      - added SINGLE_DISK_IO option because reading of parameter files on
916        very large number of processors did not work with existing set-up
917    
918    checkpoint64o (2013/09/25)
919    o pkg/atm_phys & atm_compon_interf:
920      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
921    o tools/build_options:
922      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
923        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
924        remove CPP setting (was identical to genmake2 default).
925    o pkg/gmredi & model/src: Some updating and work done on the residual model.
926      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
927      - fixed up the calculation of the eddy stress and how it is added to the
928        external forcing via taueddy_external_forcing.F
929      - at the moment, it is very experimental and only works with the variable eddy
930        diffusivity calculated in gmredi_k3d.F
931    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
932        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
933    o testreport (& tools/do_tst_2+2):
934      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
935    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
936      - remove CPP='cpp -traditional -P' (this is genmake2 default)
937      - add switch (for big setups) to use 'medium' memory-model (but leave it
938        commented out for now). Note: needed with FC 19 to compile big setups.
939    o pkg/atm_compon_interf:
940      - regroup per field origin (model & pkgs) the coupling storage routines
941         (which accumalate in time each coupling field)
942      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
943        update accordingly + simplify aim_do_physics.F
944    
945    checkpoint64n (2013/08/26)
946    o pkg/bbl:
947      - update formulation to reduce dispersion of tracer properties in bbl
948      - replaced horizontal and vertical transport parameters with velocities
949      - changes results for verification/global_with_exf.yearly
950    o verification/halfpipe_streamice:
951      - change to matrix construction; update both Fwd & AD output.
952    o verification/tutorial_tracer_adjsens:
953      - OpenAD test: switch to vector-invariant momentum since fluxform with
954        rStar causes problems with OpenAD; update output.
955    o tools:
956      - genmake2: define a common prefix for all temp-file names ; move them
957        to local /tmp disk (but would be easy to move them back);
958      - xmakedepend: apply the same switch for temp-files.
959    o pkg/offline:
960      - changes for use with rStar (NLFS): assume that we continue to provide
961        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
962        output files) and apply r* scaling at each time-step (function of the time
963        varying Eta field); use normal pickup files (needed for restart with NLFS).
964    o adjoint with OpenAD:
965      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
966        package openad.  This package has to be compiled for all runs with OpenAD
967        instead of specifying code_oad_all as a modification directory.
968      - link the fortran templates from tools/OAD_support to the build directory
969        for preprocessing to avoid conflicts between different setups compiled
970        simultaneously and simplify cleanup.
971    o pkg/exf:
972      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
973        main model or other pkgs are exchanged in EXF_MAPFIELDS).
974    o model/src:
975      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
976        (similar to do_fields_blocking_exchanges.F).
977    o tools/genmake2:
978      - remove TAF output src code just before calling staf (when not doing a fresh
979        built, will stop if things go wrong with staf).
980      - fix target "adobj" (left from TAF version-2 transition)
981    o pkg/diagnostics:
982      - add a parameter to track the status of pkg/diagnostics activation;
983        this replace/extend the use of logical param "settingDiags" (to check
984        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
985        New S/R to print error message and stop when pkgStatus is not right.
986      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
987    
988    checkpoint64m (2013/08/13)
989    o model/inc:
990      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
991        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
992    o pkg/kpp & aim_v23:
993      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
994    o pkg/seaice:
995      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
996        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
997      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
998    o eesupp/src:
999      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
1000        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
1001    o switch to TAF version-2:
1002      - add flow directives to "freeze" naming convention for ad-routines that
1003        are used in I/O routines of adjoint state and associated common blocks
1004        that are used in adcommon.h (backward compatible with version-1)
1005      - update all ad-optfiles (in tools/adjoint_options + few local to some
1006        verification exp) to switch to latest TAF version (currently 2.5.5);
1007        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
1008        out except for diva).
1009      - the major change with TAF version-2 is that both the differentiated
1010        routines and the forward routines (new) are returned as part of the TAF
1011        output source code. Update genmake2 accordingly.
1012      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
1013        with version-2 when compared to TLM or FWD gradient); other experiments
1014        output show minor changes (machine truncation level); update the few AD &
1015        TLM output with 12 matching digits only (some prior to version-2 switch).
1016    
1017    checkpoint64l (2013/08/05)
1018    o model/src:
1019      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
1020      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1021        when using TAF but only if using OpenAD.
1022    o pkg/mom_common+fluxform+vecinv:
1023      - always set horiz. viscosity arrays to background value before calling
1024        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1025        only when using variable horiz. viscosity (useVariableVisc=T);
1026      - simplify mom_vecinv.F (only 1 block for momViscosity).
1027    o pkg/mom_common: variable horiz. viscosity in NH code
1028      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1029        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1030      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1031        useBiharmonicVisc & useVariableVisc.
1032      - fix old bug (already in 1rst implementation of variable horizontal viscosity
1033        in calc_gw.F, version 1.27, 2006/06/20):
1034        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1035        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1036      - change background horiz viscosity in vertical momentum (gW) to always be
1037        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1038        any type of variable viscosity, e.g., viscAh/4Grid)
1039      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1040        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1041        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1042        default viscAh,viscA4 is zero).
1043    o model/src:
1044      - extend length of drC & recip_drC from Nr to Nr+1.
1045  o Divided Adjoint (DIVA) with MPI:  o Divided Adjoint (DIVA) with MPI:
1046    - 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.
1047    - 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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