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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.2076 by gforget, Fri Oct 3 15:29:37 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: extend generic cost capabilities
8      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
9        capabilities via gencost_preproc, gencost_posproc, gencost_nrecperiod,
10        gencost_outputlevel, gencost_scalefile arguments to cost_generic
11      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
12        and active_read, making room for gencost_preproc to take effect.
13        Added preproc code ('climmon ') to replace GENERIC_BAR_MONTH.
14      - pkg/ecco/cost_generic.F :
15        compute and store misfit maks*(model-data) in localdif that is
16        then used in cost and for output, output misfit if outlev.GT.0
17      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
18        rather gencost_barfile for deciding whether to write barfile
19      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
20      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
21        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
22      - pkg/ecco/ecco_summary.F : report gencost variables
23    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
24    o pkg/ecco: internal re-organization
25      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
26        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
27        mv relevant variables definition from ecco_cost.h to ecco.h,
28        make sure gencost routines only include ecco.h)
29      - throughout : add missing CCP switches, rm unused variables,
30        and rm un-necessary CPP switches
31      - throughout gencost routines : replace modelstartdate with
32        gencost_startdate when needed
33      - cost_bp_read.F : use arguments, instead of common blocs
34        so that it can be used also by (new) cost_gencost_bpv4.F
35      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
36      - ecco_phys.F : compute etanFull
37      - ecco_readparms.F : rename using_topex as using_tpj, add
38        bpv4-grace to gencost list, initialize added parameters
39      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
40    
41    checkpoint65e (2014/09/28)
42    o pkg/obcs:
43      - replaced the just-added CPP options with run-time variables
44        (see pkg/obcs/OBCS_PARAMS.h for details)
45    o pkg/obcs:
46      - add additional CPP options for sponge boundary layers
47        (see pkg/obcs/OBCS_OPTIONS.h for details)
48    o pkg/atm_phys:
49      - implement simple (obliquity only, assuming circular planet orbit)
50        seasonal cycle for incoming insolation ; used when run-time parameter
51        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
52    o pkg/exf, pkg/ecco, pkg/ctrl:
53      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
54      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
55      - implement gentim2d for xx_tauu, xx_tauv
56    o pkg/ctrl, pkg/ecco :
57      - fix and complement the generic controls implementation
58    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
59        pkg/shelfice/shelfice_thermodynamics.F,
60        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
61        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
62      - add weight in CTRL_GET_GEN calls
63    o pkg/ctrl :
64      - ctrl_get_gen.F : add weight as input parameter, and apply
65        it directly rather than using smooth_correl2Dw (to be retired).
66      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
67    o pkg/ctrl :
68      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
69        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
70      - re-activate ctrl_summary (call in ctrl_init.F)
71    o pkg/ctrl/ctrl_cost_gen.F :
72      - fix CCP brackets, remove un-necessary myiter, mytime
73    o pkg/ecco, pkg/ctrl :
74      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
75      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
76      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
77      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
78    
79    checkpoint65d (2014/09/15)
80    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
81      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
82        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
83    o pkg/ctrl/ctrl_map_ini_genarr.F :
84      - remove compilation failure
85      - replace hard coded example
86      - use ctrl_map_ini_gen2D, 3D
87    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
88      - on/off switch based upon xx_genarr2d_weight,3d
89    o src/packages_init_variables.F :
90      - regroup pkg/estimation calls
91      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
92        (moved to ctrl_init_variables)
93    o cost/cost_init_varia.F :
94      - remove ecco_cost_init_varia
95        (moved to ecco_init_varia)
96    o ctrl/ctrl_init_variables.F :
97      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
98      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
99    o ctrl/ctrl_map_ini.F :
100      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
101        (moved to ctrl_init_variables)
102    o ctrl/ctrl_map_ini_ecco.F :
103      - remove ECCO_PHYS (mv to ecco_init_varia)
104      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
105    o ecco/ecco_ad_diff.list :
106      - add ecco_init_varia.f
107    o ecco/ecco_init_varia.F
108      - new routine
109    o pkg/streamice:
110      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
111        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
112      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
113    o pkg/generic_advdiff:
114      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
115    o pkg/exf:
116      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
117         xxg_precip capability
118      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
119    o pkg/ctrl:
120      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
121    o model/src/load_fields_driver.F :
122      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
123        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
124    o OpenAD verification experiments:
125      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
126        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
127        for now, only in pkgs used in OpenAD verification experiments.
128      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
129        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
130        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
131        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
132    o OpenAD verification tests:
133      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
134      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
135        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
136      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
137        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
138    o model/src & generic_advdiff:
139      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
140        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
141        dynamics requires valid tracer forcing only over tile interior but, for
142        some diagnostics, may need to extend it over 1 point in tile halo region.
143      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
144        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
145        setting in temp/salt/ptracer_integrate.F
146    o pkg/dic:
147      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
148        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
149        in gchem_forcing_sep.F
150    o pkg/autodiff & obcs:
151      - add storage of current OB values for U & V (was already done for T & S).
152    
153    checkpoint65c (2014/08/30)
154    o pkg/dic:
155      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
156        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
157        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
158    o verification:
159      - new experiment testing OBCS and DIC pkgs, using params & output from
160        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
161        passage: take OBCS from the last year of a 2 yrs simulation and initial
162        conditions from t=1.yr while keeping the same forcing.
163    o model/src:
164      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
165        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
166    o pkg/diagnostics (Stats-Diags):
167      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
168        a) refine region where stats are computed, excluding where arrhFac=0 ;
169        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
170        c) extend regional stats over the region edges (for U or V pt location).
171    o pkg/gchem:
172      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
173        pkg/dic is currently changing/updating ptracers values beyond the OB).
174    o verification (hs94):
175      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
176        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
177        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
178        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
179    o pkg/ptracers:
180      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
181        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
182      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
183        with AB-2 code (so that it get tested).
184    o model/src:
185      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
186        with AB-2 code (previously only available with AB-3 code).
187        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
188        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
189        there, by calling CYCLE_AB_TRACER).
190    o pkg/generic_advdiff:
191      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
192        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
193        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
194        S/R temp/salt/ptracers_integrate.F
195    o model/src & pkg/ptracers:
196      - remove common block variables gT,gS (in DYNVARS.h), except when
197         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
198      - remove common block variable gPtr.
199    o model/src & pkgs:
200      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
201         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
202         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
203         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
204      + change accordingly all calling S/R.
205      - use local temperature/salinity/ptracer tendency array (without bi,bj)
206        in S/R temp/salt/ptracers_integrate.F
207    o pkg/seaice:
208      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
209        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
210      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
211        in seaice_lsr
212      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
213        in s/r seaice_lsr_calc_coeffs
214    o pkg/mdsio:
215      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
216        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
217        too long (e.g., > MAX_LEN_FNAM/2 )
218    
219    checkpoint65b (2014/08/12)
220    o pkg/matrix:
221      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
222    o model/src:
223      - fix initialisation of geothermalFile; compile geothermal-flux code in
224        natl_box verification experiment.
225    o model/src & pkg/down_slope:
226      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
227      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
228        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
229        results at machine truncation level: update output of experiments
230        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
231    o pkg/diagnostics (Stats-Diags):
232      - do not cumulate the full volume when DIAGNOSTICS_FILL is
233        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
234        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
235        times (but Min,Max and StD are still wrong).
236    o model/src:
237      - add geothermal flux forcing: read in ini_forcing.F as time-constant
238        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
239    o model/src:
240      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
241        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
242        arrays are already updated while adjustments (filters, conv.adjustment) are
243        still applied later, in S/R TRACERS_CORRECTION_STEP.
244    o model/src:
245      - store in common bloc array "rhoInSitu" the virtual potential temperature
246        anomaly that is used to compute geopotential: this make the atmos code
247        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
248    o pkg/seaice/seaice_lsr.F
249      - rename integer variable ilcall to ipass (that's what it is called
250        in the residual diagnostics
251      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
252        default) for improved non-linear convergence of the first few steps
253      - adjust a few comments and add new ones to explain some of the store
254        directives
255    o pkg/generic_advdiff (& ptracers):
256      - re-work the code to check for valid advection scheme and for minimum
257        size of overlap (now stored in local common bloc in gad_advscheme.F)
258    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
259      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
260      - add an auxilliary variable "bet" and fix store directives and keys in
261        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
262        less exact gradients in my tests); but there are still
263        recomputation warning (although gradients are sort of OK), when
264        SEAICE_LSR_VECTORIZE is not defined, so this flag and
265        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
266      - update verification experiments lab_sea.
267      - change some comments in S/R seaice_calc_viscosities
268    o model/src:
269      - if staggerTimeStep=T, always apply exchange to velocity field in
270        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
271        (independent of using multi-dim advection or not); no effect on FWD run
272        but affects AD results (at machine truncation level): update output of
273        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
274        and isomip (oad: 12.d).
275    o pkg/generic_advdiff:
276      - stop if doAB_onGtGs is set to FALSE but ignored
277      - refine warning related to stability of tracer time-stepping
278        regarding internal wave dynamics.
279      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
280        on staggerTimeStep & implicitIntGravWave (will now get a warning
281        if potentially unstable).
282    o pkg/kl10:
283      - add new pkg "kl10" for mixing due to internal wave breaking, from
284        http://www.sciencedirect.com/science/article/pii/S1463500310000144
285        (contribution from Jody Klymak), tested in verification experiment
286        verification/internal_wave/input.kl10/
287    o isomip experiment:
288      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
289        (input.htd) and update the output.
290    o cd_code experiments:
291      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
292        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
293        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
294        update the corresponding output.
295    o pkg/seaice:
296      - reduce the number of include files and store directives in
297        S/R seaice_lsr_tridiagu/v
298      - change the order of loops in one case in S/R seaice_lsr_tridiagv
299        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
300        get rid off one store directive (a TAF bug?)
301      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
302        S/R seaice_lsr_tridiagv to change the loop range for consistency
303      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
304      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
305        S/R seaice_lsr_tridiagu/v (requires update of
306        offline_exf_seaice/input.dyn_jfnk)
307    
308    checkpoint65a (2014/07/27)
309    o model/src:
310      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
311        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
312        (topo in p-coords, ice-shelf in z-coords); update output of experiments
313        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
314    o model/src:
315      - collect momentum forcing tendency into local 2-D array (passed as argument
316        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
317        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
318        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
319      - collect T & S forcing tendency into local 2-D array (passed as argument to
320        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
321        affects results at machine truncation level (e.g., ocean: if using
322        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
323        correction due to vertical advection).
324      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
325        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
326        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
327        obcs_ctrl (ad & fwd grd @ 12 & 7).
328    o pkg/ptracers & diagnostics:
329      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
330        title (to avoid some unexpected truncation); sort out ptracers diags units.
331      - collect ptracer forcing tendency into local 2-D array (passed as argument
332        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
333    
334    checkpoint65 (2014/07/18)
335    o pkg/fizhi:
336      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
337        affects results at machine truncation level. Update output of experiments
338        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
339    o pkg/seaice: more clean up
340      - rename TAF common block tapes to be more consistent and remove
341        unnecessary duplicates
342      - add store directives to remove more recomputations, but use smaller
343        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
344        The idea behind this flag is to reduce the memory footprint when the
345        adjoint of the LSR is not required. As of now, defining the flag
346        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
347        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
348        For experiment offline_exf_seaice, this means on a linux box with gfortran
349        nearly a factor of 10 (but keep in mind there is mostly seaice code in
350        this experiment):
351        > size mitgcmuv_ad
352        text    data        bss     dec        hex  
353        5100659 1216  220458952  225560827  d71c8fb
354        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
355        but only a moderate increase of 36% for global_ocean.cs32x15:
356        text    data        bss     dec        hex
357        6695027 1648 1014578664 1021275339 3cdf6ccb
358        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
359      - note: there are still recomputations in global_ocean.cs32x15 and
360        offline_exf_seaice and the gradient agreement changes (gets a
361        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
362      - in general, the AD gradients still are wrong
363    o OpenAD
364      - clean up code_oad/ directories somewhat by moving files
365        dontCompile, dontTransform, keepOriginal to OAD_support/
366    o model/src:
367      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
368        (not currently tested): add dissipation terms before NLFS rescaling of
369        tendencies (previously done after).
370    o pkg/diagnostics:
371      - write stats-diags in ascii file with more digits (same as in monitor).
372    o pkg/down_slope:
373      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
374        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
375    o model/src:
376      - new file "apply_forcing.F" containing all the code previously in
377        external_forcing.F, but with new argument list: pass, as new argument,
378        the current level tendency array to update (instead of a direct update
379        of the common bloc array). Change the corresponding calls.
380      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
381        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
382    o pkg/seaice/seaice_lsr, a little bit of clean up
383      - rearrange some code blocks, so that now all calculations for
384        setting up the right-hand-sides done within one single block
385        (I find that easier to read and understand)
386      - rearrange freedrift-code to reduce the number of ifdefs
387      - adjust some indentations and comments
388    
389    checkpoint64z (2014/07/10)
390    o model/src and several pkgs:
391      - change argument list of all S/R called from external_forcing.F and
392        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
393        to pass, as argument, the current level tendency array to update
394        (instead of a direct update of the common bloc array).
395      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
396      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
397    o pkg/seaice/seaice_lsr.F
398      - always initialize local arrays in seaice_lsr_tridiagu/v
399      - add more local tapes to seaice_lsr_tridiagu/v
400      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
401        keep it in bi/bj loop; this seems to be essential
402      - gradients are still wrong but only by 4-7 orders of magnitude
403        instead of 15 orders of magnitude, lab_sea improves a little
404    o pkg/seaice
405      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
406        generates unnecessary code in seaice_lsr_ad
407      - add more store directives in seaice_lsr to avoid unnecessary code
408        in seaice_lsr_ad
409      - exclude some residual computations in seaice_lsr when
410        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
411        in seaice_lsr_ad
412      - add more storing, a new tape (model/src/the_main_loop.F) and
413        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
414        and klockey should be checked by a specialist)
415      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
416        and update lab_sea after previous changes in pkg/seaice below
417    o pkg/autodiff:
418      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
419        viscFacInAd : run time parameters allowing for adjoint switches
420        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
421    o pkg/ecco:
422      - introduce cost_gencost_boxmean.F that computes a box mean
423        temperature (for use in adjoint sensitivity studies).
424    o model/src/set_defaults.F : initialize viscFacAdj to 1.
425    o pkg/mom_common/mom_calc_visc.F:
426      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
427    o pkg/seaice/seaice_summary.F:
428      - statement for SEAICEadjMODE now in autodiff_readparms.F
429    o pkg/seaice:
430      - remove some store directives and add new ones in an effort to get
431        finally rid off the recomputation warnings. This is successful
432        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
433        defined (i.e. no extensive recomputation warnings left), but there
434        are still too many recomputations on the solver iteration level
435      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
436      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
437        SEAICE_SIZE.h
438      - add a store directive in S/R seaice_calc_viscosities
439    o pkg/seaice (ITD code):
440      - fix definition of Hlimit for multi-threaded case
441      - use double precision arithmetic to compute Hlimit: this affects results;
442        update output of experiment seaice_itd.
443    o replace content of verification/seaice_itd
444      - instead of a 1D column use the configuration of offline_exf_seaice
445        to test the ice thickness distribution code with ridging
446      - this is a first shot at this experiment
447      - change of some defaults of ridging parameters SEAICEhStar (from
448        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
449        and lot of new comments.
450    
451    checkpoint64y (2014/06/20)
452    o pkg/seaice/seaice_reg_ridge.F:
453      - modify the regularization of very small volumes of ice; only check
454        total volume HEFF, and do not apply correction to individual ice
455        classes because that leads to funny patterns in the heat and fw-fluxes
456        into the ocean. Adjust seaice_itd/results/output.txt
457      - replace nITD by SEAICE_multDim in loop-ranges
458    o pkg/exf:
459      - add code to process the case field period = -12. with UV interpolation.
460      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
461        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
462    o verification/global_with_exf:
463      - switch all fields period to -12. (was previously untested) in input/data.exf
464        (but keep secondary test ".yearly" unchanged); update the reference output.
465    o pkg/cal:
466      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
467    o pkg/exf:
468      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
469        to replace logical switch "exf_verbose"
470      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
471    o pkg/sbo:
472      - update from Katherine Quinn: evaluate mass directly from density and SSH
473        (budget using Finite Volume method) instead of from bottom pressure.
474      - allow testreport to collect few selected SBO output ; tested in exp.
475        global_ocean.90x40x15 (after updating the results, to include SBO output).
476      - fix some multi-threading issues (in output part).
477    o model/src & most packages:
478      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
479      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
480        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
481        "data.{pkg}" exist ; and leave the S/R (return) just after.
482      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
483        + call LAND_READPARMS from packages_readparms.F
484    o pkg/seaice:
485      - remove code that resets useThSice in S/R seaice_readparms and
486        replace it by a warning in S/R seaice_check
487      - remove parameter MULTDIM, replace with nITD and runtime
488        parameter SEAICE_multDim (still hard-wired to nITD if
489        SEAICE_ITD is defined)
490    
491    checkpoint64x (2014/05/24)
492    o verification/lab_sea:
493      - update adjoint and TLM output following changes to pkg/salt_plume
494      - un-do the update after putting back local recip_Cp in few places.
495    o pkg/salt_plume: modifications by An Nguyen:
496      - add capability to do brine rejection (salt-plume) as function of
497        volume+tracers (instead of only salinity tracer).
498      - conserve volume by exchanging volume from each kLev to above to
499        accommodate in-coming brine volume
500      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
501      - switch KPP surf buoyancy due to brine forcing to 3-d
502        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
503      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
504      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
505        in East/West Arctic.
506    o pkg/sbo:
507      - incorporate modifications from Katherine Quinn to enable the use of sbo
508        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
509        output for future testreport verification (unfinished).
510    o pkg/atm_phys:
511      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
512        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
513        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
514    o pkg/seaice
515      seaice_calc_ice_strength.F: modify expression to avoid divisions
516        (affects truncation)
517      seaice_do_ridging.F: clean up the insectarium
518      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
519      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
520      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
521      - add some debugging information and error messages (warnings)
522    o model/src: modifications relatd to atmosphere p*:
523      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
524      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
525        of vertical profile tRef in geopotential background and anomaly.
526      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
527        and pkg/atm_phys.
528      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
529        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
530    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
531    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
532        not used right now, but can be used in BGC packages to fix conservation.
533    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
534        other packages too.
535    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
536        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
537    o model/src:
538      - since we have several heat capacity (even in model/src), define "recip_Cp"
539        as local variable (no longer in common block) to avoid any confusion.
540      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
541    o pkg/exf:
542      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
543        air density as function of air Temp, Humidity and atm pressure.
544    
545    checkpoint64w (2014/05/02)
546    o verification:
547      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
548        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
549        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
550        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
551        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
552    o model/src: for atmosphere in p* coords:
553      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
554      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
555        but not yet activated.
556    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
557      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
558      - this changes the results (but not for any verification experiment, because
559        none tests this), but avoids having an extra field in the restart files
560    o pkg/seaice: remove global variable TICE (not needed)
561      - replace by TICES or local variable where necessary (cost_seaice_test,
562        seaice_diagnostics_state)
563      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
564      - use specific read/write routines for reading and writing individual leves
565        of a multilevel field
566    o pkg/ctrl & model/inc:
567      - move additional anomaly fields of control vars (related to options:
568         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
569        from DYNVARS.h into new header file: CTRL_FIELDS.h
570    o pkg/seaice: some small modifications to the ridging code
571      - make fw2ObyRidge a global variable and add the freshwater flux to
572        seaice_growth
573      - pass actual thickness from seaice_prepare_ridging, so that it is
574        computed only in one place and compute it in the same way as in
575        seaice_growth
576      - initialise more fields in seaice_do_ridging that where cause floating
577        point exceptions over land
578    o pkg/seaice: preparations for ridging code and first real ridging code
579      - move most of "PART 1" of S/R seaice_growth into a new and separate
580        S/R seaice_reg_ridge that will both regularize the state variable after
581        advection call the actual ridging routine;
582      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
583        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
584      - remove ridging code from seaice_advdiff
585      - clean up remaining part 1 of seaice_growth in an attempt to make it
586        more readable (this is probably subjective)
587      - call seaice_itd_redist once in the initialisation phase to have the initial
588        conditions in the correct category
589      - finally: add new ridging routine for ITD code
590    
591    checkpoint64v (2014/04/11)
592    o pkg/ecco:
593      - add runtime parameters mdt[start,end]date[1,2]
594      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
595    o pkg/seaice:
596      - make deltaC a global variable, so that it can be used in ridging code
597      - first step towards ridging: introduce new routines that compute
598        ice strength based on ridging parameters
599      - add diagnostic for HSNOWITD
600      - add opnWtrFrac as a global variable (required for ridging scheme)
601    o pkg/salt_plume + pkg/seaice/seaice_growth.F
602      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
603        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
604    o verification/hs94.1x64x5:
605      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
606      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
607    o autodiff:
608      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
609        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
610        For now, only in pkgs used in verification/hs94.1x64x5.
611      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
612        which are specific to TAF/TAMC).
613      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
614        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
615        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
616      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
617        building mitgcmuv_ad (make adAll).
618    o pkg/ecco:
619      - cost_gencost_seaicev4.F:
620         reformulate proxy cost as function of sst and local param SEAICE_freeze
621         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
622      - add stop statement if old names siv4-[sst,vol] are used
623      - add snapshots + cost reports for atmospheric longwave
624      - remove factor 0.1 in front of wtau[u,v]
625      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
626         ALLOW_TMI_SST_COST_CONTRIBUTION
627    o pkg/atm_phys:
628      - add some diagnostics for Short-wave and for convection S/R.
629    o pkg/seaice/seaice_growth:
630      - fix a bug in the lateral melt parameterization for SEAICE_ITD
631        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
632      - rearrange loop order for better vector code in the same code block
633      - rewrite the floeDiameter formula to have fewer divisions
634      -  (miraculously) none of this changes the results of seaice_itd
635    o pkg/smooth:
636      - move param smooth2Ddiffnbt to pkg/ecco
637    o pkg/salt_plume:
638      - salt_plume_frac.F:
639         clean up local param names
640         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
641    o pkg/rw:
642      - add RS version of S/R READ_MFLDS_LEV.
643    o pkg/streamice:
644      - fix the restart test by writing/reading pickup_streamice files.
645    o pkg/seaice:
646      - refine checks for jfnk-related parameters
647      - comment out if statement with SEAICEuseIMEX parameter as long as there
648        is no IMEX code to avoid confusion and surprises
649    
650    checkpoint64u (2014/03/07)
651    o verification/MLAdjust:
652      - rename secondary test suffix:
653         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
654         0.leithD -> AhFlxF  + switch to flux-form
655         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
656         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
657    o pkg/mom_vecinv:
658      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
659        to be before mom_calc_visc.F)
660      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
661      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
662        this is simpler for the adjoint and for diagnostics.
663    o model/src + pkg/momentum:
664      - add input files for  2-D additional Western and Southern cell-edge wall
665         (e.g., to add "thin-wall" where it is =1).
666      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
667        using 2nd hFacZ that is computed from initial (fix domain) hFac
668      - known limitations of thin wall implementation: not yet coded for sigma
669        coords; not working with CD-scheme neither.
670    o pkg/seaice:
671      - rename recently introduced parameters from (wrong name) AB to
672        BDF (backward difference time discretisation)
673      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
674    o tools/adjoint_options:
675      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
676    
677    checkpoint64t (2014/02/01)
678    o pkg/ecco
679      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
680        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
681      - replace hard-coded record number and period which only work for monthly
682        with read-in runtime param that works for other periods (month,day,year)
683    o pkg/thsice
684      - corrected store directive fixes thsice adjoint gradient checks
685    o genmake2 & testreport:
686      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
687        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
688        Update testreport accordingly. No need to set "export OPENAD=true"
689        in adjoint_options/adjoint_oad anymore (will be removed later).
690    o pkg/shelfice:
691      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
692        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
693        so that surface forcing applies to k=kSurf if using pkg/shelfice.
694    o pkg/ctrl, pkg/grdchk, pkg/ecco:
695      - Changes to make GENARR more modular (i.e. invisible if not used)
696    o model/src/temp_integrate.F and salt_integrate.F
697      - re-include store directives that were removed on Dec 27th.
698    o model/src/external_forcing_surf.F
699      - add storage directives for EmPmR and PmEpR to avoid recomputation of
700        seaice_model in the adjoint that is problematic when seaice_model is
701        turned off in the adjoint. The resolved issue dated back to July when
702        EXTERNAL_FORCING_SURF call was moved.
703        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
704    o pkg/exf/exf_check.F
705      - fix a small bug again (originally found by Wentao Liu, now found again)
706      - streamline error output
707    o pkg/streamice and aim_v23:
708      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
709        Apple's /usr/bin/cpp knows what to do:
710        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
711        Target: x86_64-apple-darwin13.0.0
712    
713    checkpoint64s (2014/01/05)
714    o tools/adjoint_options:
715      - switch to fastopt.net TAF server (instead of default fastopt.de) for
716        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
717    o model/src:
718      - remove some unnecessary TAF storage directives in forward_step.F and
719        in dynamics.F (note: not always removed by TAF, e.g., double storage
720        of kappaRU,kappaRV in former version of dynamics.F).
721    o model/src & pkg/ptracers:
722      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
723        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
724        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
725      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
726      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
727      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
728    o useSingleCpuInput separates single-CPU input from single-CPU output;
729        for now only implemented for in exf_interp_read.F
730    o verification/advect_xy:
731      - fix missing EXCH call in local version of ini_salt.F and update output.
732    o momentum diagnostics:
733      - fix which deltaT is used in Total-Tendency diagnostics.
734      - fix typo in diagnostics for momentum tendency from AB.
735    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
736        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
737    
738    checkpoint64r (2013/12/08)
739    o verification/*/results:
740      - Update reference output of experiments that were passing with just 13 digits
741         (make it easier to detect future changes in results)
742    o model/src & pkg/ptracers:
743      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
744        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
745        to inside ptracers_integrate.F ; remove ptracers_advection.F
746    o coupling interface pkgs:
747        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
748      - change the config check to test the agreement of Ocean Depth
749        with ATM land/sea mask (instead of ATM orography);
750      - send to coupler the number of coupler time-steps to do for this run:
751        this allows to check for consistency and don't need anymore to be
752        specified in parameter file "data";
753      in coupler:
754      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
755      - improve report to log-file of config setting (pass log-file unit to few S/R)
756    o pkg/compon_communic:
757      - add coupling send/receive for non-tiled integer vector;
758      - add S/R to check and stop if any proc has an error (similar to
759        eesupp/src/stop_if_error.F but single thread and across Comm_World).
760    o pkg/exch2:
761      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
762        through list of all tiles my proc owns.
763    o model/src:
764      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
765        from rTrans) to simplify dependencies (no need to store rTrans anymore in
766        calling S/R); this affects AD results at machine truncation level:
767        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
768        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
769    o tools/build_options:
770      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
771    o coupling interface pkgs:
772        [compon_communic, atm_compon_interf & ocn_compon_interf]
773      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
774        to each S/R that needs it; remove un-used variables.
775      - change component tile registration (cpl_register.F in both compon_interf
776        and mitcomponent_tile_register.F) to pass the full list of tiles
777        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
778      - with pkg/exch2: adopt the same convention used for I/O to define mapping
779        towards coupler global array (unless W2_useE2ioLayOut=F):
780         a) can now use different tiling between atm & ocn comp.
781         b) no needs to modify the run-Off map when changing tiling (was needed
782            even if using the same tiling between atm & ocn).
783         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
784            full land tiles); not yet tested.
785      - check for valid mapping from comp. tile to coupler global array
786      - improve report of tile registration results to log file.
787    o pkg/exch2:
788      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
789        tile-registration (CPL_REGISTER);
790      - activate (un-comment) definition and setting of "W2_tileIndex" list to
791        store the local bi,bj indices of each tile;
792      - also print bi,bj in local report to log file;
793      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
794        Jun 2009 modif of pkg/exch2).
795    o testing on baudelaire:
796      - run 2 tests at a time: no significant slow down (since enough cpu) and
797        get the full set of test done earlier
798      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
799    o model/src/thermodynamics.F and routines called from it:
800      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
801        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
802        velocity (outp) by adding bolus velocity.
803      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
804        mass transport from velocity + lateral grid cell area
805      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
806      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
807     in thermodynamics.F
808      - remove k from thermodynamics.F and move it to temp_integrate.F
809        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
810        loop).
811      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
812        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
813        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
814        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
815      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
816        global_ocean.90x40x15, tutorial_global_oce_biogeo and
817        tutorial_tracer_adjsens (+ TLM output).
818    o tools/OAD_support and (verification/*/) code_oad:
819      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
820        module conversion ; remove unneeded CPP_EEOPTIONS.h.
821      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
822        version (closer to model/inc/CPP_OPTIONS.h).
823    o model/src:
824      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
825        retired list of parameters (routine FREEZE has been replace by surface
826        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
827    o pkg/gmredi:
828      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
829        velocity (same scheme but affects machine truncation) for GM_AdvForm.
830      - update output of FWD experiments: front_relax.bvp,
831        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
832    
833    checkpoint64q (2013/11/17)
834    o verification:
835      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
836        tutorial_global_oce_biogeo and global_ocean.90x40x15.
837      - generate new output (growth & melt) for seaice_itd experiment after
838        updating the input pickup_seaice files (previously wrong).
839    o pkg/cost:
840      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
841        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
842        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
843          cannot be applied to var in common block).
844        o allows to get results independent of tile-per-proc setting (if using
845          slower GLOBAL_SUM_SEND_RECV option).
846      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
847        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
848        forward gradients: update output).
849      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
850        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
851    o pkg/mom_common:
852      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
853        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
854        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
855        ensure that all field value that are used are set.
856    o tutorial_deep_convection (smag3d):
857      - add missing scaling in mom_calc_smag_3d.F;
858      - set smag3D_coeff in input.smag3d such that results do not change.
859    o pkg/dic:
860      - change dic_cost.F to compute cost on each tile first and then apply
861        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
862        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
863      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
864    o eesupp/src & pkg/mdsio:
865      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
866        (from pkg/mdsio) since they are no longer used for tape IO.
867      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
868        (+ keep a copy in pkg/atm_ocn_coupler).
869    o verification/isomip:
870      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
871    o tools/build_options:
872      - optfile linux_amd64_ifort11, fast (no ieee) case:
873        to get a working restart for all experiments, add "-fp-model source"
874        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
875    
876    checkpoint64p (2013/10/20)
877    o pkg/autodiff:
878      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
879        criteria, return to simple (default) tape IO format.
880    o pkg/mdsio (+ eesupp/src):
881      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
882        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
883      - fix globalFile and singleCpuIO options using simpler global mapping.
884      - new pairs of scatter/gather vector S/R (one for each type, generated from
885        template) corresponding to simpler global mapping.
886      - adread_write.F: switch to new S/R (but leave old calls commented) and write
887        to globalFile when parameter globalFiles is set to True.
888      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
889    o pkg/autodiff:
890      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
891        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
892        missing, just add a STOP if array type do not match.
893    o pkg/exf:
894      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
895         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
896         and rename array obsSIce to exf_iceFraction.
897    o tutorial_deep_convection:
898      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
899        for now all in this exp. code dir.
900      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
901        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
902    o eesupp/src:
903      - added SINGLE_DISK_IO option because reading of parameter files on
904        very large number of processors did not work with existing set-up
905    
906    checkpoint64o (2013/09/25)
907    o pkg/atm_phys & atm_compon_interf:
908      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
909    o tools/build_options:
910      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
911        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
912        remove CPP setting (was identical to genmake2 default).
913    o pkg/gmredi & model/src: Some updating and work done on the residual model.
914      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
915      - fixed up the calculation of the eddy stress and how it is added to the
916        external forcing via taueddy_external_forcing.F
917      - at the moment, it is very experimental and only works with the variable eddy
918        diffusivity calculated in gmredi_k3d.F
919    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
920        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
921    o testreport (& tools/do_tst_2+2):
922      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
923    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
924      - remove CPP='cpp -traditional -P' (this is genmake2 default)
925      - add switch (for big setups) to use 'medium' memory-model (but leave it
926        commented out for now). Note: needed with FC 19 to compile big setups.
927    o pkg/atm_compon_interf:
928      - regroup per field origin (model & pkgs) the coupling storage routines
929         (which accumalate in time each coupling field)
930      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
931        update accordingly + simplify aim_do_physics.F
932    
933    checkpoint64n (2013/08/26)
934    o pkg/bbl:
935      - update formulation to reduce dispersion of tracer properties in bbl
936      - replaced horizontal and vertical transport parameters with velocities
937      - changes results for verification/global_with_exf.yearly
938    o verification/halfpipe_streamice:
939      - change to matrix construction; update both Fwd & AD output.
940    o verification/tutorial_tracer_adjsens:
941      - OpenAD test: switch to vector-invariant momentum since fluxform with
942        rStar causes problems with OpenAD; update output.
943    o tools:
944      - genmake2: define a common prefix for all temp-file names ; move them
945        to local /tmp disk (but would be easy to move them back);
946      - xmakedepend: apply the same switch for temp-files.
947    o pkg/offline:
948      - changes for use with rStar (NLFS): assume that we continue to provide
949        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
950        output files) and apply r* scaling at each time-step (function of the time
951        varying Eta field); use normal pickup files (needed for restart with NLFS).
952    o adjoint with OpenAD:
953      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
954        package openad.  This package has to be compiled for all runs with OpenAD
955        instead of specifying code_oad_all as a modification directory.
956      - link the fortran templates from tools/OAD_support to the build directory
957        for preprocessing to avoid conflicts between different setups compiled
958        simultaneously and simplify cleanup.
959    o pkg/exf:
960      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
961        main model or other pkgs are exchanged in EXF_MAPFIELDS).
962    o model/src:
963      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
964        (similar to do_fields_blocking_exchanges.F).
965    o tools/genmake2:
966      - remove TAF output src code just before calling staf (when not doing a fresh
967        built, will stop if things go wrong with staf).
968      - fix target "adobj" (left from TAF version-2 transition)
969    o pkg/diagnostics:
970      - add a parameter to track the status of pkg/diagnostics activation;
971        this replace/extend the use of logical param "settingDiags" (to check
972        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
973        New S/R to print error message and stop when pkgStatus is not right.
974      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
975    
976    checkpoint64m (2013/08/13)
977    o model/inc:
978      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
979        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
980    o pkg/kpp & aim_v23:
981      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
982    o pkg/seaice:
983      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
984        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
985      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
986    o eesupp/src:
987      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
988        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
989    o switch to TAF version-2:
990      - add flow directives to "freeze" naming convention for ad-routines that
991        are used in I/O routines of adjoint state and associated common blocks
992        that are used in adcommon.h (backward compatible with version-1)
993      - update all ad-optfiles (in tools/adjoint_options + few local to some
994        verification exp) to switch to latest TAF version (currently 2.5.5);
995        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
996        out except for diva).
997      - the major change with TAF version-2 is that both the differentiated
998        routines and the forward routines (new) are returned as part of the TAF
999        output source code. Update genmake2 accordingly.
1000      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
1001        with version-2 when compared to TLM or FWD gradient); other experiments
1002        output show minor changes (machine truncation level); update the few AD &
1003        TLM output with 12 matching digits only (some prior to version-2 switch).
1004    
1005    checkpoint64l (2013/08/05)
1006    o model/src:
1007      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
1008      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1009        when using TAF but only if using OpenAD.
1010    o pkg/mom_common+fluxform+vecinv:
1011      - always set horiz. viscosity arrays to background value before calling
1012        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1013        only when using variable horiz. viscosity (useVariableVisc=T);
1014      - simplify mom_vecinv.F (only 1 block for momViscosity).
1015    o pkg/mom_common: variable horiz. viscosity in NH code
1016      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1017        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1018      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1019        useBiharmonicVisc & useVariableVisc.
1020      - fix old bug (already in 1rst implementation of variable horizontal viscosity
1021        in calc_gw.F, version 1.27, 2006/06/20):
1022        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1023        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1024      - change background horiz viscosity in vertical momentum (gW) to always be
1025        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1026        any type of variable viscosity, e.g., viscAh/4Grid)
1027      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1028        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1029        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1030        default viscAh,viscA4 is zero).
1031    o model/src:
1032      - extend length of drC & recip_drC from Nr to Nr+1.
1033    o Divided Adjoint (DIVA) with MPI:
1034      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1035      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
1036        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
1037    
1038    checkpoint64k (2013/07/23)
1039    o tools/OAD_support:
1040      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
1041        and remove it from genmake2.
1042    o tools/build_options:
1043      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
1044        MPI_HEADER_FILES list (let genmake2 find the missing headers)
1045    o verification/halfpipe_streamice:
1046      - change to driving stress formulation; update both Fwd & AD output.
1047    o tools/genmake2 and Divided Adjoint with MPI:
1048      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
1049      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
1050      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
1051        Makefile, which is set by genmake2, and check which mpi-headers are needed.
1052        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
1053      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
1054    o testreport:
1055      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
1056        perform additional runs (number of additional runs is "add_DIVA_runs" taken
1057        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
1058    o verification/lab_sea (AD test):
1059      - change to test Divided Adjoint Run in this set-up (both standard AD test
1060        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
1061    o pkg atm_ & ocn_compon_interf:
1062      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
1063        staggerTimeStep implementation) and disable (retired) corresponding
1064        parameter.
1065    o pkg/offline:
1066      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
1067      - add S/R OFFLINE_CHECK to print offline parameter summary
1068        and stop if loading a file that is not used;
1069      - enable to calculate GMRedi tensor, KPP mixing and convective index
1070        when the corresponding file(s) is/are not specified (but pkg is used).
1071      - comment out resetting of monitorFreq (to endTime) since it still useful
1072        for monitoring CFL numbers and checking offline fields.
1073    o OpenAD:
1074      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
1075        smaller standard output) and generate new (smaller) output (on baudelaire
1076        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
1077    o model/src:
1078      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
1079        (where external_forcing_adjust was called) and change list of arguments;
1080      - merge external_forcing_adjust.F into external_forcing_surf.F
1081      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
1082        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
1083        previously in file "balance_relax.F", now removed); remove corresponding
1084        arrays in FFIELDS.h.
1085      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
1086        a hack for getting back surfaceForcingS (loaded from file) when using
1087        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
1088      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
1089        (was getting only 11 digits for AD-grad, due to different truncation
1090         error in AD code).
1091    
1092    checkpoint64j (2013/07/04)
1093    o pkg/offline:
1094      - to enable the use of other features with pkg offline (e.g., obcs),
1095        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
1096      - comment out "allowFreezing" (now active) in 2 offline testing exp.
1097    o pkg/exf ALLOW_RUNOFTEMP
1098      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
1099      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
1100      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
1101    o pkg/atm_phys:
1102      - allows to add some damping on uVel,vVel (strength only function of k).
1103    o verification, ad-tests:
1104      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
1105        global_ocean_ebm and offline_exf_seaice.thsice.
1106    o verification/halfpipe_streamice:
1107      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
1108        flux input boundary conditions to be ignored; a fix for this bug changed
1109        verification results for forward test.
1110      - add adjoint test.
1111    o pkg/ptracers:
1112      - allow to restart without SOM pickup (resetting SOM to zero).
1113    o pkg/gmredi:
1114      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
1115      - It uses mixing length theory and suppression by steering level effects to
1116        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
1117        to JPO, for more details).
1118      - It also uses the diffusivity to calculate an eddy induced streamfunction
1119        based on a PV closure (rather than a buoyancy closure as in GM).
1120      - New files added to pkg/gmredi:
1121        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
1122          induced overturning streamfunction (called from gmredi_calc_tensor)
1123        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
1124          for use in gmredi_k3d
1125        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
1126          the eddy diffusivity
1127    
1128  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
1129  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 1160  o pkg/cfc:
1160      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
1161    - 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
1162    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
1163    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
1164      similar to thsice_advdiff.
1165      Note that for the B-grid case the routine parameters uc/vc are overwritten.
1166  o pkg/cfc:  o pkg/cfc:
1167    - 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);
1168      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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