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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.2077 by gforget, Mon Oct 6 12:05:00 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, gencost_posproc, gencost_nrecperiod,
20        gencost_outputlevel, gencost_scalefile arguments to cost_generic
21      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
22        and active_read, making room for gencost_preproc to take effect.
23        Added preproc code ('climmon ') to replace GENERIC_BAR_MONTH.
24      - pkg/ecco/cost_generic.F :
25        compute and store misfit maks*(model-data) in localdif that is
26        then used in cost and for output, output misfit if outlev.GT.0
27      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
28        rather gencost_barfile for deciding whether to write barfile
29      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
30      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
31        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
32      - pkg/ecco/ecco_summary.F : report gencost variables
33      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
34    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
35    o pkg/ecco: internal re-organization
36      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
37        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
38        mv relevant variables definition from ecco_cost.h to ecco.h,
39        make sure gencost routines only include ecco.h)
40      - throughout : add missing CCP switches, rm unused variables,
41        and rm un-necessary CPP switches
42      - throughout gencost routines : replace modelstartdate with
43        gencost_startdate when needed
44      - cost_bp_read.F : use arguments, instead of common blocs
45        so that it can be used also by (new) cost_gencost_bpv4.F
46      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
47      - ecco_phys.F : compute etanFull
48      - ecco_readparms.F : rename using_topex as using_tpj, add
49        bpv4-grace to gencost list, initialize added parameters
50      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
51    
52    checkpoint65e (2014/09/28)
53    o pkg/obcs:
54      - replaced the just-added CPP options with run-time variables
55        (see pkg/obcs/OBCS_PARAMS.h for details)
56    o pkg/obcs:
57      - add additional CPP options for sponge boundary layers
58        (see pkg/obcs/OBCS_OPTIONS.h for details)
59    o pkg/atm_phys:
60      - implement simple (obliquity only, assuming circular planet orbit)
61        seasonal cycle for incoming insolation ; used when run-time parameter
62        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
63    o pkg/exf, pkg/ecco, pkg/ctrl:
64      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
65      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
66      - implement gentim2d for xx_tauu, xx_tauv
67    o pkg/ctrl, pkg/ecco :
68      - fix and complement the generic controls implementation
69    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
70        pkg/shelfice/shelfice_thermodynamics.F,
71        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
72        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
73      - add weight in CTRL_GET_GEN calls
74    o pkg/ctrl :
75      - ctrl_get_gen.F : add weight as input parameter, and apply
76        it directly rather than using smooth_correl2Dw (to be retired).
77      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
78    o pkg/ctrl :
79      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
80        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
81      - re-activate ctrl_summary (call in ctrl_init.F)
82    o pkg/ctrl/ctrl_cost_gen.F :
83      - fix CCP brackets, remove un-necessary myiter, mytime
84    o pkg/ecco, pkg/ctrl :
85      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
86      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
87      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
88      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
89    
90    checkpoint65d (2014/09/15)
91    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
92      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
93        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
94    o pkg/ctrl/ctrl_map_ini_genarr.F :
95      - remove compilation failure
96      - replace hard coded example
97      - use ctrl_map_ini_gen2D, 3D
98    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
99      - on/off switch based upon xx_genarr2d_weight,3d
100    o src/packages_init_variables.F :
101      - regroup pkg/estimation calls
102      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
103        (moved to ctrl_init_variables)
104    o cost/cost_init_varia.F :
105      - remove ecco_cost_init_varia
106        (moved to ecco_init_varia)
107    o ctrl/ctrl_init_variables.F :
108      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
109      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
110    o ctrl/ctrl_map_ini.F :
111      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
112        (moved to ctrl_init_variables)
113    o ctrl/ctrl_map_ini_ecco.F :
114      - remove ECCO_PHYS (mv to ecco_init_varia)
115      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
116    o ecco/ecco_ad_diff.list :
117      - add ecco_init_varia.f
118    o ecco/ecco_init_varia.F
119      - new routine
120    o pkg/streamice:
121      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
122        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
123      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
124    o pkg/generic_advdiff:
125      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
126    o pkg/exf:
127      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
128         xxg_precip capability
129      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
130    o pkg/ctrl:
131      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
132    o model/src/load_fields_driver.F :
133      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
134        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
135    o OpenAD verification experiments:
136      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
137        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
138        for now, only in pkgs used in OpenAD verification experiments.
139      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
140        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
141        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
142        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
143    o OpenAD verification tests:
144      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
145      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
146        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
147      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
148        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
149    o model/src & generic_advdiff:
150      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
151        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
152        dynamics requires valid tracer forcing only over tile interior but, for
153        some diagnostics, may need to extend it over 1 point in tile halo region.
154      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
155        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
156        setting in temp/salt/ptracer_integrate.F
157    o pkg/dic:
158      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
159        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
160        in gchem_forcing_sep.F
161    o pkg/autodiff & obcs:
162      - add storage of current OB values for U & V (was already done for T & S).
163    
164    checkpoint65c (2014/08/30)
165    o pkg/dic:
166      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
167        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
168        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
169    o verification:
170      - new experiment testing OBCS and DIC pkgs, using params & output from
171        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
172        passage: take OBCS from the last year of a 2 yrs simulation and initial
173        conditions from t=1.yr while keeping the same forcing.
174    o model/src:
175      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
176        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
177    o pkg/diagnostics (Stats-Diags):
178      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
179        a) refine region where stats are computed, excluding where arrhFac=0 ;
180        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
181        c) extend regional stats over the region edges (for U or V pt location).
182    o pkg/gchem:
183      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
184        pkg/dic is currently changing/updating ptracers values beyond the OB).
185    o verification (hs94):
186      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
187        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
188        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
189        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
190    o pkg/ptracers:
191      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
192        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
193      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
194        with AB-2 code (so that it get tested).
195    o model/src:
196      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
197        with AB-2 code (previously only available with AB-3 code).
198        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
199        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
200        there, by calling CYCLE_AB_TRACER).
201    o pkg/generic_advdiff:
202      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
203        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
204        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
205        S/R temp/salt/ptracers_integrate.F
206    o model/src & pkg/ptracers:
207      - remove common block variables gT,gS (in DYNVARS.h), except when
208         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
209      - remove common block variable gPtr.
210    o model/src & pkgs:
211      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
212         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
213         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
214         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
215      + change accordingly all calling S/R.
216      - use local temperature/salinity/ptracer tendency array (without bi,bj)
217        in S/R temp/salt/ptracers_integrate.F
218    o pkg/seaice:
219      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
220        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
221      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
222        in seaice_lsr
223      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
224        in s/r seaice_lsr_calc_coeffs
225    o pkg/mdsio:
226      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
227        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
228        too long (e.g., > MAX_LEN_FNAM/2 )
229    
230    checkpoint65b (2014/08/12)
231    o pkg/matrix:
232      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
233    o model/src:
234      - fix initialisation of geothermalFile; compile geothermal-flux code in
235        natl_box verification experiment.
236    o model/src & pkg/down_slope:
237      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
238      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
239        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
240        results at machine truncation level: update output of experiments
241        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
242    o pkg/diagnostics (Stats-Diags):
243      - do not cumulate the full volume when DIAGNOSTICS_FILL is
244        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
245        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
246        times (but Min,Max and StD are still wrong).
247    o model/src:
248      - add geothermal flux forcing: read in ini_forcing.F as time-constant
249        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
250    o model/src:
251      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
252        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
253        arrays are already updated while adjustments (filters, conv.adjustment) are
254        still applied later, in S/R TRACERS_CORRECTION_STEP.
255    o model/src:
256      - store in common bloc array "rhoInSitu" the virtual potential temperature
257        anomaly that is used to compute geopotential: this make the atmos code
258        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
259    o pkg/seaice/seaice_lsr.F
260      - rename integer variable ilcall to ipass (that's what it is called
261        in the residual diagnostics
262      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
263        default) for improved non-linear convergence of the first few steps
264      - adjust a few comments and add new ones to explain some of the store
265        directives
266    o pkg/generic_advdiff (& ptracers):
267      - re-work the code to check for valid advection scheme and for minimum
268        size of overlap (now stored in local common bloc in gad_advscheme.F)
269    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
270      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
271      - add an auxilliary variable "bet" and fix store directives and keys in
272        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
273        less exact gradients in my tests); but there are still
274        recomputation warning (although gradients are sort of OK), when
275        SEAICE_LSR_VECTORIZE is not defined, so this flag and
276        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
277      - update verification experiments lab_sea.
278      - change some comments in S/R seaice_calc_viscosities
279    o model/src:
280      - if staggerTimeStep=T, always apply exchange to velocity field in
281        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
282        (independent of using multi-dim advection or not); no effect on FWD run
283        but affects AD results (at machine truncation level): update output of
284        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
285        and isomip (oad: 12.d).
286    o pkg/generic_advdiff:
287      - stop if doAB_onGtGs is set to FALSE but ignored
288      - refine warning related to stability of tracer time-stepping
289        regarding internal wave dynamics.
290      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
291        on staggerTimeStep & implicitIntGravWave (will now get a warning
292        if potentially unstable).
293    o pkg/kl10:
294      - add new pkg "kl10" for mixing due to internal wave breaking, from
295        http://www.sciencedirect.com/science/article/pii/S1463500310000144
296        (contribution from Jody Klymak), tested in verification experiment
297        verification/internal_wave/input.kl10/
298    o isomip experiment:
299      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
300        (input.htd) and update the output.
301    o cd_code experiments:
302      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
303        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
304        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
305        update the corresponding output.
306    o pkg/seaice:
307      - reduce the number of include files and store directives in
308        S/R seaice_lsr_tridiagu/v
309      - change the order of loops in one case in S/R seaice_lsr_tridiagv
310        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
311        get rid off one store directive (a TAF bug?)
312      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
313        S/R seaice_lsr_tridiagv to change the loop range for consistency
314      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
315      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
316        S/R seaice_lsr_tridiagu/v (requires update of
317        offline_exf_seaice/input.dyn_jfnk)
318    
319    checkpoint65a (2014/07/27)
320    o model/src:
321      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
322        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
323        (topo in p-coords, ice-shelf in z-coords); update output of experiments
324        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
325    o model/src:
326      - collect momentum forcing tendency into local 2-D array (passed as argument
327        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
328        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
329        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
330      - collect T & S forcing tendency into local 2-D array (passed as argument to
331        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
332        affects results at machine truncation level (e.g., ocean: if using
333        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
334        correction due to vertical advection).
335      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
336        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
337        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
338        obcs_ctrl (ad & fwd grd @ 12 & 7).
339    o pkg/ptracers & diagnostics:
340      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
341        title (to avoid some unexpected truncation); sort out ptracers diags units.
342      - collect ptracer forcing tendency into local 2-D array (passed as argument
343        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
344    
345    checkpoint65 (2014/07/18)
346    o pkg/fizhi:
347      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
348        affects results at machine truncation level. Update output of experiments
349        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
350    o pkg/seaice: more clean up
351      - rename TAF common block tapes to be more consistent and remove
352        unnecessary duplicates
353      - add store directives to remove more recomputations, but use smaller
354        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
355        The idea behind this flag is to reduce the memory footprint when the
356        adjoint of the LSR is not required. As of now, defining the flag
357        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
358        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
359        For experiment offline_exf_seaice, this means on a linux box with gfortran
360        nearly a factor of 10 (but keep in mind there is mostly seaice code in
361        this experiment):
362        > size mitgcmuv_ad
363        text    data        bss     dec        hex  
364        5100659 1216  220458952  225560827  d71c8fb
365        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
366        but only a moderate increase of 36% for global_ocean.cs32x15:
367        text    data        bss     dec        hex
368        6695027 1648 1014578664 1021275339 3cdf6ccb
369        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
370      - note: there are still recomputations in global_ocean.cs32x15 and
371        offline_exf_seaice and the gradient agreement changes (gets a
372        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
373      - in general, the AD gradients still are wrong
374    o OpenAD
375      - clean up code_oad/ directories somewhat by moving files
376        dontCompile, dontTransform, keepOriginal to OAD_support/
377    o model/src:
378      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
379        (not currently tested): add dissipation terms before NLFS rescaling of
380        tendencies (previously done after).
381    o pkg/diagnostics:
382      - write stats-diags in ascii file with more digits (same as in monitor).
383    o pkg/down_slope:
384      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
385        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
386    o model/src:
387      - new file "apply_forcing.F" containing all the code previously in
388        external_forcing.F, but with new argument list: pass, as new argument,
389        the current level tendency array to update (instead of a direct update
390        of the common bloc array). Change the corresponding calls.
391      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
392        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
393    o pkg/seaice/seaice_lsr, a little bit of clean up
394      - rearrange some code blocks, so that now all calculations for
395        setting up the right-hand-sides done within one single block
396        (I find that easier to read and understand)
397      - rearrange freedrift-code to reduce the number of ifdefs
398      - adjust some indentations and comments
399    
400    checkpoint64z (2014/07/10)
401    o model/src and several pkgs:
402      - change argument list of all S/R called from external_forcing.F and
403        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
404        to pass, as argument, the current level tendency array to update
405        (instead of a direct update of the common bloc array).
406      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
407      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
408    o pkg/seaice/seaice_lsr.F
409      - always initialize local arrays in seaice_lsr_tridiagu/v
410      - add more local tapes to seaice_lsr_tridiagu/v
411      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
412        keep it in bi/bj loop; this seems to be essential
413      - gradients are still wrong but only by 4-7 orders of magnitude
414        instead of 15 orders of magnitude, lab_sea improves a little
415    o pkg/seaice
416      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
417        generates unnecessary code in seaice_lsr_ad
418      - add more store directives in seaice_lsr to avoid unnecessary code
419        in seaice_lsr_ad
420      - exclude some residual computations in seaice_lsr when
421        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
422        in seaice_lsr_ad
423      - add more storing, a new tape (model/src/the_main_loop.F) and
424        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
425        and klockey should be checked by a specialist)
426      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
427        and update lab_sea after previous changes in pkg/seaice below
428    o pkg/autodiff:
429      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
430        viscFacInAd : run time parameters allowing for adjoint switches
431        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
432    o pkg/ecco:
433      - introduce cost_gencost_boxmean.F that computes a box mean
434        temperature (for use in adjoint sensitivity studies).
435    o model/src/set_defaults.F : initialize viscFacAdj to 1.
436    o pkg/mom_common/mom_calc_visc.F:
437      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
438    o pkg/seaice/seaice_summary.F:
439      - statement for SEAICEadjMODE now in autodiff_readparms.F
440    o pkg/seaice:
441      - remove some store directives and add new ones in an effort to get
442        finally rid off the recomputation warnings. This is successful
443        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
444        defined (i.e. no extensive recomputation warnings left), but there
445        are still too many recomputations on the solver iteration level
446      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
447      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
448        SEAICE_SIZE.h
449      - add a store directive in S/R seaice_calc_viscosities
450    o pkg/seaice (ITD code):
451      - fix definition of Hlimit for multi-threaded case
452      - use double precision arithmetic to compute Hlimit: this affects results;
453        update output of experiment seaice_itd.
454    o replace content of verification/seaice_itd
455      - instead of a 1D column use the configuration of offline_exf_seaice
456        to test the ice thickness distribution code with ridging
457      - this is a first shot at this experiment
458      - change of some defaults of ridging parameters SEAICEhStar (from
459        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
460        and lot of new comments.
461    
462    checkpoint64y (2014/06/20)
463    o pkg/seaice/seaice_reg_ridge.F:
464      - modify the regularization of very small volumes of ice; only check
465        total volume HEFF, and do not apply correction to individual ice
466        classes because that leads to funny patterns in the heat and fw-fluxes
467        into the ocean. Adjust seaice_itd/results/output.txt
468      - replace nITD by SEAICE_multDim in loop-ranges
469    o pkg/exf:
470      - add code to process the case field period = -12. with UV interpolation.
471      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
472        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
473    o verification/global_with_exf:
474      - switch all fields period to -12. (was previously untested) in input/data.exf
475        (but keep secondary test ".yearly" unchanged); update the reference output.
476    o pkg/cal:
477      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
478    o pkg/exf:
479      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
480        to replace logical switch "exf_verbose"
481      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
482    o pkg/sbo:
483      - update from Katherine Quinn: evaluate mass directly from density and SSH
484        (budget using Finite Volume method) instead of from bottom pressure.
485      - allow testreport to collect few selected SBO output ; tested in exp.
486        global_ocean.90x40x15 (after updating the results, to include SBO output).
487      - fix some multi-threading issues (in output part).
488    o model/src & most packages:
489      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
490      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
491        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
492        "data.{pkg}" exist ; and leave the S/R (return) just after.
493      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
494        + call LAND_READPARMS from packages_readparms.F
495    o pkg/seaice:
496      - remove code that resets useThSice in S/R seaice_readparms and
497        replace it by a warning in S/R seaice_check
498      - remove parameter MULTDIM, replace with nITD and runtime
499        parameter SEAICE_multDim (still hard-wired to nITD if
500        SEAICE_ITD is defined)
501    
502    checkpoint64x (2014/05/24)
503    o verification/lab_sea:
504      - update adjoint and TLM output following changes to pkg/salt_plume
505      - un-do the update after putting back local recip_Cp in few places.
506    o pkg/salt_plume: modifications by An Nguyen:
507      - add capability to do brine rejection (salt-plume) as function of
508        volume+tracers (instead of only salinity tracer).
509      - conserve volume by exchanging volume from each kLev to above to
510        accommodate in-coming brine volume
511      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
512      - switch KPP surf buoyancy due to brine forcing to 3-d
513        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
514      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
515      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
516        in East/West Arctic.
517    o pkg/sbo:
518      - incorporate modifications from Katherine Quinn to enable the use of sbo
519        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
520        output for future testreport verification (unfinished).
521    o pkg/atm_phys:
522      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
523        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
524        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
525    o pkg/seaice
526      seaice_calc_ice_strength.F: modify expression to avoid divisions
527        (affects truncation)
528      seaice_do_ridging.F: clean up the insectarium
529      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
530      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
531      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
532      - add some debugging information and error messages (warnings)
533    o model/src: modifications relatd to atmosphere p*:
534      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
535      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
536        of vertical profile tRef in geopotential background and anomaly.
537      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
538        and pkg/atm_phys.
539      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
540        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
541    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
542    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
543        not used right now, but can be used in BGC packages to fix conservation.
544    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
545        other packages too.
546    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
547        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
548    o model/src:
549      - since we have several heat capacity (even in model/src), define "recip_Cp"
550        as local variable (no longer in common block) to avoid any confusion.
551      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
552    o pkg/exf:
553      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
554        air density as function of air Temp, Humidity and atm pressure.
555    
556    checkpoint64w (2014/05/02)
557    o verification:
558      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
559        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
560        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
561        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
562        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
563    o model/src: for atmosphere in p* coords:
564      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
565      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
566        but not yet activated.
567    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
568      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
569      - this changes the results (but not for any verification experiment, because
570        none tests this), but avoids having an extra field in the restart files
571    o pkg/seaice: remove global variable TICE (not needed)
572      - replace by TICES or local variable where necessary (cost_seaice_test,
573        seaice_diagnostics_state)
574      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
575      - use specific read/write routines for reading and writing individual leves
576        of a multilevel field
577    o pkg/ctrl & model/inc:
578      - move additional anomaly fields of control vars (related to options:
579         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
580        from DYNVARS.h into new header file: CTRL_FIELDS.h
581    o pkg/seaice: some small modifications to the ridging code
582      - make fw2ObyRidge a global variable and add the freshwater flux to
583        seaice_growth
584      - pass actual thickness from seaice_prepare_ridging, so that it is
585        computed only in one place and compute it in the same way as in
586        seaice_growth
587      - initialise more fields in seaice_do_ridging that where cause floating
588        point exceptions over land
589    o pkg/seaice: preparations for ridging code and first real ridging code
590      - move most of "PART 1" of S/R seaice_growth into a new and separate
591        S/R seaice_reg_ridge that will both regularize the state variable after
592        advection call the actual ridging routine;
593      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
594        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
595      - remove ridging code from seaice_advdiff
596      - clean up remaining part 1 of seaice_growth in an attempt to make it
597        more readable (this is probably subjective)
598      - call seaice_itd_redist once in the initialisation phase to have the initial
599        conditions in the correct category
600      - finally: add new ridging routine for ITD code
601    
602    checkpoint64v (2014/04/11)
603    o pkg/ecco:
604      - add runtime parameters mdt[start,end]date[1,2]
605      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
606    o pkg/seaice:
607      - make deltaC a global variable, so that it can be used in ridging code
608      - first step towards ridging: introduce new routines that compute
609        ice strength based on ridging parameters
610      - add diagnostic for HSNOWITD
611      - add opnWtrFrac as a global variable (required for ridging scheme)
612    o pkg/salt_plume + pkg/seaice/seaice_growth.F
613      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
614        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
615    o verification/hs94.1x64x5:
616      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
617      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
618    o autodiff:
619      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
620        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
621        For now, only in pkgs used in verification/hs94.1x64x5.
622      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
623        which are specific to TAF/TAMC).
624      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
625        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
626        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
627      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
628        building mitgcmuv_ad (make adAll).
629    o pkg/ecco:
630      - cost_gencost_seaicev4.F:
631         reformulate proxy cost as function of sst and local param SEAICE_freeze
632         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
633      - add stop statement if old names siv4-[sst,vol] are used
634      - add snapshots + cost reports for atmospheric longwave
635      - remove factor 0.1 in front of wtau[u,v]
636      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
637         ALLOW_TMI_SST_COST_CONTRIBUTION
638    o pkg/atm_phys:
639      - add some diagnostics for Short-wave and for convection S/R.
640    o pkg/seaice/seaice_growth:
641      - fix a bug in the lateral melt parameterization for SEAICE_ITD
642        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
643      - rearrange loop order for better vector code in the same code block
644      - rewrite the floeDiameter formula to have fewer divisions
645      -  (miraculously) none of this changes the results of seaice_itd
646    o pkg/smooth:
647      - move param smooth2Ddiffnbt to pkg/ecco
648    o pkg/salt_plume:
649      - salt_plume_frac.F:
650         clean up local param names
651         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
652    o pkg/rw:
653      - add RS version of S/R READ_MFLDS_LEV.
654    o pkg/streamice:
655      - fix the restart test by writing/reading pickup_streamice files.
656    o pkg/seaice:
657      - refine checks for jfnk-related parameters
658      - comment out if statement with SEAICEuseIMEX parameter as long as there
659        is no IMEX code to avoid confusion and surprises
660    
661    checkpoint64u (2014/03/07)
662    o verification/MLAdjust:
663      - rename secondary test suffix:
664         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
665         0.leithD -> AhFlxF  + switch to flux-form
666         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
667         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
668    o pkg/mom_vecinv:
669      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
670        to be before mom_calc_visc.F)
671      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
672      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
673        this is simpler for the adjoint and for diagnostics.
674    o model/src + pkg/momentum:
675      - add input files for  2-D additional Western and Southern cell-edge wall
676         (e.g., to add "thin-wall" where it is =1).
677      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
678        using 2nd hFacZ that is computed from initial (fix domain) hFac
679      - known limitations of thin wall implementation: not yet coded for sigma
680        coords; not working with CD-scheme neither.
681    o pkg/seaice:
682      - rename recently introduced parameters from (wrong name) AB to
683        BDF (backward difference time discretisation)
684      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
685    o tools/adjoint_options:
686      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
687    
688    checkpoint64t (2014/02/01)
689    o pkg/ecco
690      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
691        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
692      - replace hard-coded record number and period which only work for monthly
693        with read-in runtime param that works for other periods (month,day,year)
694    o pkg/thsice
695      - corrected store directive fixes thsice adjoint gradient checks
696    o genmake2 & testreport:
697      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
698        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
699        Update testreport accordingly. No need to set "export OPENAD=true"
700        in adjoint_options/adjoint_oad anymore (will be removed later).
701    o pkg/shelfice:
702      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
703        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
704        so that surface forcing applies to k=kSurf if using pkg/shelfice.
705    o pkg/ctrl, pkg/grdchk, pkg/ecco:
706      - Changes to make GENARR more modular (i.e. invisible if not used)
707    o model/src/temp_integrate.F and salt_integrate.F
708      - re-include store directives that were removed on Dec 27th.
709    o model/src/external_forcing_surf.F
710      - add storage directives for EmPmR and PmEpR to avoid recomputation of
711        seaice_model in the adjoint that is problematic when seaice_model is
712        turned off in the adjoint. The resolved issue dated back to July when
713        EXTERNAL_FORCING_SURF call was moved.
714        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
715    o pkg/exf/exf_check.F
716      - fix a small bug again (originally found by Wentao Liu, now found again)
717      - streamline error output
718    o pkg/streamice and aim_v23:
719      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
720        Apple's /usr/bin/cpp knows what to do:
721        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
722        Target: x86_64-apple-darwin13.0.0
723    
724    checkpoint64s (2014/01/05)
725    o tools/adjoint_options:
726      - switch to fastopt.net TAF server (instead of default fastopt.de) for
727        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
728    o model/src:
729      - remove some unnecessary TAF storage directives in forward_step.F and
730        in dynamics.F (note: not always removed by TAF, e.g., double storage
731        of kappaRU,kappaRV in former version of dynamics.F).
732    o model/src & pkg/ptracers:
733      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
734        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
735        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
736      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
737      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
738      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
739    o useSingleCpuInput separates single-CPU input from single-CPU output;
740        for now only implemented for in exf_interp_read.F
741    o verification/advect_xy:
742      - fix missing EXCH call in local version of ini_salt.F and update output.
743    o momentum diagnostics:
744      - fix which deltaT is used in Total-Tendency diagnostics.
745      - fix typo in diagnostics for momentum tendency from AB.
746    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
747        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
748    
749    checkpoint64r (2013/12/08)
750    o verification/*/results:
751      - Update reference output of experiments that were passing with just 13 digits
752         (make it easier to detect future changes in results)
753    o model/src & pkg/ptracers:
754      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
755        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
756        to inside ptracers_integrate.F ; remove ptracers_advection.F
757    o coupling interface pkgs:
758        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
759      - change the config check to test the agreement of Ocean Depth
760        with ATM land/sea mask (instead of ATM orography);
761      - send to coupler the number of coupler time-steps to do for this run:
762        this allows to check for consistency and don't need anymore to be
763        specified in parameter file "data";
764      in coupler:
765      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
766      - improve report to log-file of config setting (pass log-file unit to few S/R)
767    o pkg/compon_communic:
768      - add coupling send/receive for non-tiled integer vector;
769      - add S/R to check and stop if any proc has an error (similar to
770        eesupp/src/stop_if_error.F but single thread and across Comm_World).
771    o pkg/exch2:
772      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
773        through list of all tiles my proc owns.
774    o model/src:
775      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
776        from rTrans) to simplify dependencies (no need to store rTrans anymore in
777        calling S/R); this affects AD results at machine truncation level:
778        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
779        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
780    o tools/build_options:
781      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
782    o coupling interface pkgs:
783        [compon_communic, atm_compon_interf & ocn_compon_interf]
784      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
785        to each S/R that needs it; remove un-used variables.
786      - change component tile registration (cpl_register.F in both compon_interf
787        and mitcomponent_tile_register.F) to pass the full list of tiles
788        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
789      - with pkg/exch2: adopt the same convention used for I/O to define mapping
790        towards coupler global array (unless W2_useE2ioLayOut=F):
791         a) can now use different tiling between atm & ocn comp.
792         b) no needs to modify the run-Off map when changing tiling (was needed
793            even if using the same tiling between atm & ocn).
794         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
795            full land tiles); not yet tested.
796      - check for valid mapping from comp. tile to coupler global array
797      - improve report of tile registration results to log file.
798    o pkg/exch2:
799      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
800        tile-registration (CPL_REGISTER);
801      - activate (un-comment) definition and setting of "W2_tileIndex" list to
802        store the local bi,bj indices of each tile;
803      - also print bi,bj in local report to log file;
804      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
805        Jun 2009 modif of pkg/exch2).
806    o testing on baudelaire:
807      - run 2 tests at a time: no significant slow down (since enough cpu) and
808        get the full set of test done earlier
809      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
810    o model/src/thermodynamics.F and routines called from it:
811      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
812        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
813        velocity (outp) by adding bolus velocity.
814      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
815        mass transport from velocity + lateral grid cell area
816      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
817      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
818     in thermodynamics.F
819      - remove k from thermodynamics.F and move it to temp_integrate.F
820        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
821        loop).
822      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
823        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
824        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
825        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
826      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
827        global_ocean.90x40x15, tutorial_global_oce_biogeo and
828        tutorial_tracer_adjsens (+ TLM output).
829    o tools/OAD_support and (verification/*/) code_oad:
830      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
831        module conversion ; remove unneeded CPP_EEOPTIONS.h.
832      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
833        version (closer to model/inc/CPP_OPTIONS.h).
834    o model/src:
835      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
836        retired list of parameters (routine FREEZE has been replace by surface
837        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
838    o pkg/gmredi:
839      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
840        velocity (same scheme but affects machine truncation) for GM_AdvForm.
841      - update output of FWD experiments: front_relax.bvp,
842        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
843    
844    checkpoint64q (2013/11/17)
845    o verification:
846      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
847        tutorial_global_oce_biogeo and global_ocean.90x40x15.
848      - generate new output (growth & melt) for seaice_itd experiment after
849        updating the input pickup_seaice files (previously wrong).
850    o pkg/cost:
851      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
852        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
853        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
854          cannot be applied to var in common block).
855        o allows to get results independent of tile-per-proc setting (if using
856          slower GLOBAL_SUM_SEND_RECV option).
857      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
858        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
859        forward gradients: update output).
860      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
861        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
862    o pkg/mom_common:
863      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
864        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
865        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
866        ensure that all field value that are used are set.
867    o tutorial_deep_convection (smag3d):
868      - add missing scaling in mom_calc_smag_3d.F;
869      - set smag3D_coeff in input.smag3d such that results do not change.
870    o pkg/dic:
871      - change dic_cost.F to compute cost on each tile first and then apply
872        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
873        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
874      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
875    o eesupp/src & pkg/mdsio:
876      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
877        (from pkg/mdsio) since they are no longer used for tape IO.
878      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
879        (+ keep a copy in pkg/atm_ocn_coupler).
880    o verification/isomip:
881      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
882    o tools/build_options:
883      - optfile linux_amd64_ifort11, fast (no ieee) case:
884        to get a working restart for all experiments, add "-fp-model source"
885        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
886    
887    checkpoint64p (2013/10/20)
888    o pkg/autodiff:
889      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
890        criteria, return to simple (default) tape IO format.
891    o pkg/mdsio (+ eesupp/src):
892      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
893        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
894      - fix globalFile and singleCpuIO options using simpler global mapping.
895      - new pairs of scatter/gather vector S/R (one for each type, generated from
896        template) corresponding to simpler global mapping.
897      - adread_write.F: switch to new S/R (but leave old calls commented) and write
898        to globalFile when parameter globalFiles is set to True.
899      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
900    o pkg/autodiff:
901      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
902        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
903        missing, just add a STOP if array type do not match.
904    o pkg/exf:
905      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
906         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
907         and rename array obsSIce to exf_iceFraction.
908    o tutorial_deep_convection:
909      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
910        for now all in this exp. code dir.
911      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
912        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
913    o eesupp/src:
914      - added SINGLE_DISK_IO option because reading of parameter files on
915        very large number of processors did not work with existing set-up
916    
917    checkpoint64o (2013/09/25)
918    o pkg/atm_phys & atm_compon_interf:
919      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
920    o tools/build_options:
921      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
922        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
923        remove CPP setting (was identical to genmake2 default).
924    o pkg/gmredi & model/src: Some updating and work done on the residual model.
925      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
926      - fixed up the calculation of the eddy stress and how it is added to the
927        external forcing via taueddy_external_forcing.F
928      - at the moment, it is very experimental and only works with the variable eddy
929        diffusivity calculated in gmredi_k3d.F
930    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
931        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
932    o testreport (& tools/do_tst_2+2):
933      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
934    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
935      - remove CPP='cpp -traditional -P' (this is genmake2 default)
936      - add switch (for big setups) to use 'medium' memory-model (but leave it
937        commented out for now). Note: needed with FC 19 to compile big setups.
938    o pkg/atm_compon_interf:
939      - regroup per field origin (model & pkgs) the coupling storage routines
940         (which accumalate in time each coupling field)
941      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
942        update accordingly + simplify aim_do_physics.F
943    
944    checkpoint64n (2013/08/26)
945    o pkg/bbl:
946      - update formulation to reduce dispersion of tracer properties in bbl
947      - replaced horizontal and vertical transport parameters with velocities
948      - changes results for verification/global_with_exf.yearly
949    o verification/halfpipe_streamice:
950      - change to matrix construction; update both Fwd & AD output.
951    o verification/tutorial_tracer_adjsens:
952      - OpenAD test: switch to vector-invariant momentum since fluxform with
953        rStar causes problems with OpenAD; update output.
954    o tools:
955      - genmake2: define a common prefix for all temp-file names ; move them
956        to local /tmp disk (but would be easy to move them back);
957      - xmakedepend: apply the same switch for temp-files.
958    o pkg/offline:
959      - changes for use with rStar (NLFS): assume that we continue to provide
960        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
961        output files) and apply r* scaling at each time-step (function of the time
962        varying Eta field); use normal pickup files (needed for restart with NLFS).
963    o adjoint with OpenAD:
964      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
965        package openad.  This package has to be compiled for all runs with OpenAD
966        instead of specifying code_oad_all as a modification directory.
967      - link the fortran templates from tools/OAD_support to the build directory
968        for preprocessing to avoid conflicts between different setups compiled
969        simultaneously and simplify cleanup.
970    o pkg/exf:
971      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
972        main model or other pkgs are exchanged in EXF_MAPFIELDS).
973    o model/src:
974      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
975        (similar to do_fields_blocking_exchanges.F).
976    o tools/genmake2:
977      - remove TAF output src code just before calling staf (when not doing a fresh
978        built, will stop if things go wrong with staf).
979      - fix target "adobj" (left from TAF version-2 transition)
980    o pkg/diagnostics:
981      - add a parameter to track the status of pkg/diagnostics activation;
982        this replace/extend the use of logical param "settingDiags" (to check
983        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
984        New S/R to print error message and stop when pkgStatus is not right.
985      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
986    
987    checkpoint64m (2013/08/13)
988    o model/inc:
989      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
990        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
991    o pkg/kpp & aim_v23:
992      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
993    o pkg/seaice:
994      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
995        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
996      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
997    o eesupp/src:
998      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
999        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
1000    o switch to TAF version-2:
1001      - add flow directives to "freeze" naming convention for ad-routines that
1002        are used in I/O routines of adjoint state and associated common blocks
1003        that are used in adcommon.h (backward compatible with version-1)
1004      - update all ad-optfiles (in tools/adjoint_options + few local to some
1005        verification exp) to switch to latest TAF version (currently 2.5.5);
1006        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
1007        out except for diva).
1008      - the major change with TAF version-2 is that both the differentiated
1009        routines and the forward routines (new) are returned as part of the TAF
1010        output source code. Update genmake2 accordingly.
1011      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
1012        with version-2 when compared to TLM or FWD gradient); other experiments
1013        output show minor changes (machine truncation level); update the few AD &
1014        TLM output with 12 matching digits only (some prior to version-2 switch).
1015    
1016    checkpoint64l (2013/08/05)
1017    o model/src:
1018      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
1019      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1020        when using TAF but only if using OpenAD.
1021    o pkg/mom_common+fluxform+vecinv:
1022      - always set horiz. viscosity arrays to background value before calling
1023        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1024        only when using variable horiz. viscosity (useVariableVisc=T);
1025      - simplify mom_vecinv.F (only 1 block for momViscosity).
1026    o pkg/mom_common: variable horiz. viscosity in NH code
1027      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1028        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1029      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1030        useBiharmonicVisc & useVariableVisc.
1031      - fix old bug (already in 1rst implementation of variable horizontal viscosity
1032        in calc_gw.F, version 1.27, 2006/06/20):
1033        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1034        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1035      - change background horiz viscosity in vertical momentum (gW) to always be
1036        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1037        any type of variable viscosity, e.g., viscAh/4Grid)
1038      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1039        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1040        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1041        default viscAh,viscA4 is zero).
1042    o model/src:
1043      - extend length of drC & recip_drC from Nr to Nr+1.
1044    o Divided Adjoint (DIVA) with MPI:
1045      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1046      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
1047        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
1048    
1049    checkpoint64k (2013/07/23)
1050    o tools/OAD_support:
1051      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
1052        and remove it from genmake2.
1053    o tools/build_options:
1054      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
1055        MPI_HEADER_FILES list (let genmake2 find the missing headers)
1056    o verification/halfpipe_streamice:
1057      - change to driving stress formulation; update both Fwd & AD output.
1058    o tools/genmake2 and Divided Adjoint with MPI:
1059      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
1060      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
1061      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
1062        Makefile, which is set by genmake2, and check which mpi-headers are needed.
1063        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
1064      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
1065    o testreport:
1066      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
1067        perform additional runs (number of additional runs is "add_DIVA_runs" taken
1068        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
1069    o verification/lab_sea (AD test):
1070      - change to test Divided Adjoint Run in this set-up (both standard AD test
1071        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
1072    o pkg atm_ & ocn_compon_interf:
1073      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
1074        staggerTimeStep implementation) and disable (retired) corresponding
1075        parameter.
1076    o pkg/offline:
1077      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
1078      - add S/R OFFLINE_CHECK to print offline parameter summary
1079        and stop if loading a file that is not used;
1080      - enable to calculate GMRedi tensor, KPP mixing and convective index
1081        when the corresponding file(s) is/are not specified (but pkg is used).
1082      - comment out resetting of monitorFreq (to endTime) since it still useful
1083        for monitoring CFL numbers and checking offline fields.
1084    o OpenAD:
1085      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
1086        smaller standard output) and generate new (smaller) output (on baudelaire
1087        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
1088    o model/src:
1089      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
1090        (where external_forcing_adjust was called) and change list of arguments;
1091      - merge external_forcing_adjust.F into external_forcing_surf.F
1092      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
1093        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
1094        previously in file "balance_relax.F", now removed); remove corresponding
1095        arrays in FFIELDS.h.
1096      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
1097        a hack for getting back surfaceForcingS (loaded from file) when using
1098        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
1099      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
1100        (was getting only 11 digits for AD-grad, due to different truncation
1101         error in AD code).
1102    
1103    checkpoint64j (2013/07/04)
1104    o pkg/offline:
1105      - to enable the use of other features with pkg offline (e.g., obcs),
1106        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
1107      - comment out "allowFreezing" (now active) in 2 offline testing exp.
1108    o pkg/exf ALLOW_RUNOFTEMP
1109      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
1110      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
1111      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
1112    o pkg/atm_phys:
1113      - allows to add some damping on uVel,vVel (strength only function of k).
1114    o verification, ad-tests:
1115      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
1116        global_ocean_ebm and offline_exf_seaice.thsice.
1117    o verification/halfpipe_streamice:
1118      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
1119        flux input boundary conditions to be ignored; a fix for this bug changed
1120        verification results for forward test.
1121      - add adjoint test.
1122    o pkg/ptracers:
1123      - allow to restart without SOM pickup (resetting SOM to zero).
1124    o pkg/gmredi:
1125      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
1126      - It uses mixing length theory and suppression by steering level effects to
1127        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
1128        to JPO, for more details).
1129      - It also uses the diffusivity to calculate an eddy induced streamfunction
1130        based on a PV closure (rather than a buoyancy closure as in GM).
1131      - New files added to pkg/gmredi:
1132        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
1133          induced overturning streamfunction (called from gmredi_calc_tensor)
1134        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
1135          for use in gmredi_k3d
1136        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
1137          the eddy diffusivity
1138    
1139  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
1140  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 1171  o pkg/cfc:
1171      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
1172    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
1173    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
1174    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
1175      similar to thsice_advdiff.
1176      Note that for the B-grid case the routine parameters uc/vc are overwritten.
1177  o pkg/cfc:  o pkg/cfc:
1178    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
1179      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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