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revision 1.1901 by jmc, Thu Jul 25 01:12:45 2013 UTC revision 1.2070 by jmc, Wed Sep 24 00:17:35 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/atm_phys:
8      - implement simple (obliquity only, assuming circular planet orbit)
9        seasonal cycle for incoming insolation ; used when run-time parameter
10        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
11    o pkg/exf/exf_getffields.F :
12        add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
13        and activate gentim2d for xx_atemp, xx_aqh, xx_swdown, xx_lwdown, xx_precip
14    o pkg/exf/exf_getsurfacefluxes.F :
15        implement gentim2d for xx_tauu, xx_tauv
16        and add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets.
17    o pkg/ecco/cost_forcing.F, cost_hyd.F, cost_internal_params.F :
18        add .NOT.ctrlUseGen exclusive brackets -- ctrl_cost_driver
19        is used instead when ctrlUseGen is .TRUE.
20    o pkg/ecco/ecco_cost_final.F : print f_genarr3d to stdout
21    o pkg/ctrl/ctrl_cost_driver.F : add ctrl_cost_gen3d loop
22    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
23        pkg/shelfice/shelfice_thermodynamics.F,
24        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
25        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
26      - add weight in CTRL_GET_GEN calls
27    o pkg/ctrl :
28      - ctrl_get_gen.F : add weight as input parameter, and apply
29        it directly rather than using smooth_correl2Dw (to be retired).
30      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
31    o pkg/ctrl :
32      - CTRL_GENARR.h : add xx_gentim2d_numsmooth
33      - ctrl_cost_driver.F : bug fix (iarr, not 1)
34      - ctrl_init.F : bug fix (missing iarr)
35      - ctrl_readparms.F : add xx_gentim2d_numsmooth, improve numsmooth defaults
36      - ctrl_summary.F : improved report of controls settings
37    o pkg/ecco/ecco_cost_final.F : add genarr2d, genarr3d cost contributions
38    o pkg/ctrl :
39      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
40        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
41      - re-activate ctrl_summary (call in ctrl_init.F)
42    o pkg/ctrl/ctrl_cost_gen.F :
43      - rename ctrl_cost_gen2d input parameters {wmean_gen,wgen,genmask}
44        as {xx_gen_wmean,xx_gen_weight,xx_gen_mask}
45      - add ctrl_cost_gen3d for ARR3D (ctrl_cost_gen2d is for ARR2D,TIM2D)
46    o pkg/ctrl/CTRL_GENARR.h :
47      - add objf_genarr2d,  num_genarr2d, mult_genarr2d
48      - add objf_genarr3d,  num_genarr3d, mult_genarr3d
49      - add wgenarr2d, wgenarr3d
50    o pkg/ctrl/ctrl_readparms.F :
51      - add mult_genarr2d,mult_genarr3d in namelist
52    o pkg/ctrl_map_ini_genarr.F :
53      - bug fixes
54    o pkg/ctrl/ctrl_cost_driver.F :
55      - remove un-necessary cal.h, fix CCP brackets, remove un-necessary
56        myiter, mytime, add return
57    o pkg/ctrl/ctrl_cost_gen.F :
58      - fix CCP brackets, remove un-necessary myiter, mytime
59    o pkg/ecco :
60      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
61      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
62      - update cost_forcing_gen calls in cost_forcing.F
63      - update cost_genctrl call in ecco_cost_driver.F
64      - update ecco_ad_diff.list accordingly
65    o pkg/ctrl :
66      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
67      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
68      - update ctrl_ad_diff.list accordingly
69    
70    checkpoint65d (2014/09/15)
71    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
72      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
73        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
74    o pkg/ctrl/ctrl_map_ini_genarr.F :
75      - remove compilation failure
76      - replace hard coded example
77      - use ctrl_map_ini_gen2D, 3D
78    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
79      - on/off switch based upon xx_genarr2d_weight,3d
80    o src/packages_init_variables.F :
81      - regroup pkg/estimation calls
82      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
83        (moved to ctrl_init_variables)
84    o cost/cost_init_varia.F :
85      - remove ecco_cost_init_varia
86        (moved to ecco_init_varia)
87    o ctrl/ctrl_init_variables.F :
88      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
89      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
90    o ctrl/ctrl_map_ini.F :
91      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
92        (moved to ctrl_init_variables)
93    o ctrl/ctrl_map_ini_ecco.F :
94      - remove ECCO_PHYS (mv to ecco_init_varia)
95      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
96    o ecco/ecco_ad_diff.list :
97      - add ecco_init_varia.f
98    o ecco/ecco_init_varia.F
99      - new routine
100    o pkg/streamice:
101      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
102        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
103      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
104    o pkg/generic_advdiff:
105      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
106    o pkg/exf:
107      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
108         xxg_precip capability
109      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
110    o pkg/ctrl:
111      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
112    o model/src/load_fields_driver.F :
113      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
114        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
115    o OpenAD verification experiments:
116      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
117        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
118        for now, only in pkgs used in OpenAD verification experiments.
119      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
120        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
121        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
122        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
123    o OpenAD verification tests:
124      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
125      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
126        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
127      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
128        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
129    o model/src & generic_advdiff:
130      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
131        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
132        dynamics requires valid tracer forcing only over tile interior but, for
133        some diagnostics, may need to extend it over 1 point in tile halo region.
134      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
135        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
136        setting in temp/salt/ptracer_integrate.F
137    o pkg/dic:
138      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
139        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
140        in gchem_forcing_sep.F
141    o pkg/autodiff & obcs:
142      - add storage of current OB values for U & V (was already done for T & S).
143    
144    checkpoint65c (2014/08/30)
145    o pkg/dic:
146      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
147        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
148        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
149    o verification:
150      - new experiment testing OBCS and DIC pkgs, using params & output from
151        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
152        passage: take OBCS from the last year of a 2 yrs simulation and initial
153        conditions from t=1.yr while keeping the same forcing.
154    o model/src:
155      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
156        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
157    o pkg/diagnostics (Stats-Diags):
158      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
159        a) refine region where stats are computed, excluding where arrhFac=0 ;
160        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
161        c) extend regional stats over the region edges (for U or V pt location).
162    o pkg/gchem:
163      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
164        pkg/dic is currently changing/updating ptracers values beyond the OB).
165    o verification (hs94):
166      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
167        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
168        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
169        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
170    o pkg/ptracers:
171      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
172        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
173      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
174        with AB-2 code (so that it get tested).
175    o model/src:
176      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
177        with AB-2 code (previously only available with AB-3 code).
178        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
179        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
180        there, by calling CYCLE_AB_TRACER).
181    o pkg/generic_advdiff:
182      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
183        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
184        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
185        S/R temp/salt/ptracers_integrate.F
186    o model/src & pkg/ptracers:
187      - remove common block variables gT,gS (in DYNVARS.h), except when
188         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
189      - remove common block variable gPtr.
190    o model/src & pkgs:
191      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
192         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
193         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
194         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
195      + change accordingly all calling S/R.
196      - use local temperature/salinity/ptracer tendency array (without bi,bj)
197        in S/R temp/salt/ptracers_integrate.F
198    o pkg/seaice:
199      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
200        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
201      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
202        in seaice_lsr
203      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
204        in s/r seaice_lsr_calc_coeffs
205    o pkg/mdsio:
206      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
207        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
208        too long (e.g., > MAX_LEN_FNAM/2 )
209    
210    checkpoint65b (2014/08/12)
211    o pkg/matrix:
212      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
213    o model/src:
214      - fix initialisation of geothermalFile; compile geothermal-flux code in
215        natl_box verification experiment.
216    o model/src & pkg/down_slope:
217      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
218      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
219        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
220        results at machine truncation level: update output of experiments
221        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
222    o pkg/diagnostics (Stats-Diags):
223      - do not cumulate the full volume when DIAGNOSTICS_FILL is
224        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
225        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
226        times (but Min,Max and StD are still wrong).
227    o model/src:
228      - add geothermal flux forcing: read in ini_forcing.F as time-constant
229        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
230    o model/src:
231      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
232        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
233        arrays are already updated while adjustments (filters, conv.adjustment) are
234        still applied later, in S/R TRACERS_CORRECTION_STEP.
235    o model/src:
236      - store in common bloc array "rhoInSitu" the virtual potential temperature
237        anomaly that is used to compute geopotential: this make the atmos code
238        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
239    o pkg/seaice/seaice_lsr.F
240      - rename integer variable ilcall to ipass (that's what it is called
241        in the residual diagnostics
242      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
243        default) for improved non-linear convergence of the first few steps
244      - adjust a few comments and add new ones to explain some of the store
245        directives
246    o pkg/generic_advdiff (& ptracers):
247      - re-work the code to check for valid advection scheme and for minimum
248        size of overlap (now stored in local common bloc in gad_advscheme.F)
249    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
250      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
251      - add an auxilliary variable "bet" and fix store directives and keys in
252        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
253        less exact gradients in my tests); but there are still
254        recomputation warning (although gradients are sort of OK), when
255        SEAICE_LSR_VECTORIZE is not defined, so this flag and
256        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
257      - update verification experiments lab_sea.
258      - change some comments in S/R seaice_calc_viscosities
259    o model/src:
260      - if staggerTimeStep=T, always apply exchange to velocity field in
261        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
262        (independent of using multi-dim advection or not); no effect on FWD run
263        but affects AD results (at machine truncation level): update output of
264        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
265        and isomip (oad: 12.d).
266    o pkg/generic_advdiff:
267      - stop if doAB_onGtGs is set to FALSE but ignored
268      - refine warning related to stability of tracer time-stepping
269        regarding internal wave dynamics.
270      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
271        on staggerTimeStep & implicitIntGravWave (will now get a warning
272        if potentially unstable).
273    o pkg/kl10:
274      - add new pkg "kl10" for mixing due to internal wave breaking, from
275        http://www.sciencedirect.com/science/article/pii/S1463500310000144
276        (contribution from Jody Klymak), tested in verification experiment
277        verification/internal_wave/input.kl10/
278    o isomip experiment:
279      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
280        (input.htd) and update the output.
281    o cd_code experiments:
282      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
283        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
284        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
285        update the corresponding output.
286    o pkg/seaice:
287      - reduce the number of include files and store directives in
288        S/R seaice_lsr_tridiagu/v
289      - change the order of loops in one case in S/R seaice_lsr_tridiagv
290        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
291        get rid off one store directive (a TAF bug?)
292      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
293        S/R seaice_lsr_tridiagv to change the loop range for consistency
294      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
295      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
296        S/R seaice_lsr_tridiagu/v (requires update of
297        offline_exf_seaice/input.dyn_jfnk)
298    
299    checkpoint65a (2014/07/27)
300    o model/src:
301      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
302        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
303        (topo in p-coords, ice-shelf in z-coords); update output of experiments
304        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
305    o model/src:
306      - collect momentum forcing tendency into local 2-D array (passed as argument
307        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
308        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
309        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
310      - collect T & S forcing tendency into local 2-D array (passed as argument to
311        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
312        affects results at machine truncation level (e.g., ocean: if using
313        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
314        correction due to vertical advection).
315      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
316        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
317        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
318        obcs_ctrl (ad & fwd grd @ 12 & 7).
319    o pkg/ptracers & diagnostics:
320      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
321        title (to avoid some unexpected truncation); sort out ptracers diags units.
322      - collect ptracer forcing tendency into local 2-D array (passed as argument
323        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
324    
325    checkpoint65 (2014/07/18)
326    o pkg/fizhi:
327      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
328        affects results at machine truncation level. Update output of experiments
329        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
330    o pkg/seaice: more clean up
331      - rename TAF common block tapes to be more consistent and remove
332        unnecessary duplicates
333      - add store directives to remove more recomputations, but use smaller
334        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
335        The idea behind this flag is to reduce the memory footprint when the
336        adjoint of the LSR is not required. As of now, defining the flag
337        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
338        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
339        For experiment offline_exf_seaice, this means on a linux box with gfortran
340        nearly a factor of 10 (but keep in mind there is mostly seaice code in
341        this experiment):
342        > size mitgcmuv_ad
343        text    data        bss     dec        hex  
344        5100659 1216  220458952  225560827  d71c8fb
345        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
346        but only a moderate increase of 36% for global_ocean.cs32x15:
347        text    data        bss     dec        hex
348        6695027 1648 1014578664 1021275339 3cdf6ccb
349        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
350      - note: there are still recomputations in global_ocean.cs32x15 and
351        offline_exf_seaice and the gradient agreement changes (gets a
352        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
353      - in general, the AD gradients still are wrong
354    o OpenAD
355      - clean up code_oad/ directories somewhat by moving files
356        dontCompile, dontTransform, keepOriginal to OAD_support/
357    o model/src:
358      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
359        (not currently tested): add dissipation terms before NLFS rescaling of
360        tendencies (previously done after).
361    o pkg/diagnostics:
362      - write stats-diags in ascii file with more digits (same as in monitor).
363    o pkg/down_slope:
364      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
365        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
366    o model/src:
367      - new file "apply_forcing.F" containing all the code previously in
368        external_forcing.F, but with new argument list: pass, as new argument,
369        the current level tendency array to update (instead of a direct update
370        of the common bloc array). Change the corresponding calls.
371      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
372        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
373    o pkg/seaice/seaice_lsr, a little bit of clean up
374      - rearrange some code blocks, so that now all calculations for
375        setting up the right-hand-sides done within one single block
376        (I find that easier to read and understand)
377      - rearrange freedrift-code to reduce the number of ifdefs
378      - adjust some indentations and comments
379    
380    checkpoint64z (2014/07/10)
381    o model/src and several pkgs:
382      - change argument list of all S/R called from external_forcing.F and
383        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
384        to pass, as argument, the current level tendency array to update
385        (instead of a direct update of the common bloc array).
386      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
387      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
388    o pkg/seaice/seaice_lsr.F
389      - always initialize local arrays in seaice_lsr_tridiagu/v
390      - add more local tapes to seaice_lsr_tridiagu/v
391      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
392        keep it in bi/bj loop; this seems to be essential
393      - gradients are still wrong but only by 4-7 orders of magnitude
394        instead of 15 orders of magnitude, lab_sea improves a little
395    o pkg/seaice
396      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
397        generates unnecessary code in seaice_lsr_ad
398      - add more store directives in seaice_lsr to avoid unnecessary code
399        in seaice_lsr_ad
400      - exclude some residual computations in seaice_lsr when
401        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
402        in seaice_lsr_ad
403      - add more storing, a new tape (model/src/the_main_loop.F) and
404        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
405        and klockey should be checked by a specialist)
406      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
407        and update lab_sea after previous changes in pkg/seaice below
408    o pkg/autodiff:
409      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
410        viscFacInAd : run time parameters allowing for adjoint switches
411        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
412    o pkg/ecco:
413      - introduce cost_gencost_boxmean.F that computes a box mean
414        temperature (for use in adjoint sensitivity studies).
415    o model/src/set_defaults.F : initialize viscFacAdj to 1.
416    o pkg/mom_common/mom_calc_visc.F:
417      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
418    o pkg/seaice/seaice_summary.F:
419      - statement for SEAICEadjMODE now in autodiff_readparms.F
420    o pkg/seaice:
421      - remove some store directives and add new ones in an effort to get
422        finally rid off the recomputation warnings. This is successful
423        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
424        defined (i.e. no extensive recomputation warnings left), but there
425        are still too many recomputations on the solver iteration level
426      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
427      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
428        SEAICE_SIZE.h
429      - add a store directive in S/R seaice_calc_viscosities
430    o pkg/seaice (ITD code):
431      - fix definition of Hlimit for multi-threaded case
432      - use double precision arithmetic to compute Hlimit: this affects results;
433        update output of experiment seaice_itd.
434    o replace content of verification/seaice_itd
435      - instead of a 1D column use the configuration of offline_exf_seaice
436        to test the ice thickness distribution code with ridging
437      - this is a first shot at this experiment
438      - change of some defaults of ridging parameters SEAICEhStar (from
439        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
440        and lot of new comments.
441    
442    checkpoint64y (2014/06/20)
443    o pkg/seaice/seaice_reg_ridge.F:
444      - modify the regularization of very small volumes of ice; only check
445        total volume HEFF, and do not apply correction to individual ice
446        classes because that leads to funny patterns in the heat and fw-fluxes
447        into the ocean. Adjust seaice_itd/results/output.txt
448      - replace nITD by SEAICE_multDim in loop-ranges
449    o pkg/exf:
450      - add code to process the case field period = -12. with UV interpolation.
451      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
452        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
453    o verification/global_with_exf:
454      - switch all fields period to -12. (was previously untested) in input/data.exf
455        (but keep secondary test ".yearly" unchanged); update the reference output.
456    o pkg/cal:
457      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
458    o pkg/exf:
459      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
460        to replace logical switch "exf_verbose"
461      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
462    o pkg/sbo:
463      - update from Katherine Quinn: evaluate mass directly from density and SSH
464        (budget using Finite Volume method) instead of from bottom pressure.
465      - allow testreport to collect few selected SBO output ; tested in exp.
466        global_ocean.90x40x15 (after updating the results, to include SBO output).
467      - fix some multi-threading issues (in output part).
468    o model/src & most packages:
469      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
470      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
471        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
472        "data.{pkg}" exist ; and leave the S/R (return) just after.
473      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
474        + call LAND_READPARMS from packages_readparms.F
475    o pkg/seaice:
476      - remove code that resets useThSice in S/R seaice_readparms and
477        replace it by a warning in S/R seaice_check
478      - remove parameter MULTDIM, replace with nITD and runtime
479        parameter SEAICE_multDim (still hard-wired to nITD if
480        SEAICE_ITD is defined)
481    
482    checkpoint64x (2014/05/24)
483    o verification/lab_sea:
484      - update adjoint and TLM output following changes to pkg/salt_plume
485      - un-do the update after putting back local recip_Cp in few places.
486    o pkg/salt_plume: modifications by An Nguyen:
487      - add capability to do brine rejection (salt-plume) as function of
488        volume+tracers (instead of only salinity tracer).
489      - conserve volume by exchanging volume from each kLev to above to
490        accommodate in-coming brine volume
491      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
492      - switch KPP surf buoyancy due to brine forcing to 3-d
493        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
494      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
495      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
496        in East/West Arctic.
497    o pkg/sbo:
498      - incorporate modifications from Katherine Quinn to enable the use of sbo
499        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
500        output for future testreport verification (unfinished).
501    o pkg/atm_phys:
502      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
503        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
504        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
505    o pkg/seaice
506      seaice_calc_ice_strength.F: modify expression to avoid divisions
507        (affects truncation)
508      seaice_do_ridging.F: clean up the insectarium
509      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
510      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
511      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
512      - add some debugging information and error messages (warnings)
513    o model/src: modifications relatd to atmosphere p*:
514      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
515      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
516        of vertical profile tRef in geopotential background and anomaly.
517      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
518        and pkg/atm_phys.
519      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
520        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
521    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
522    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
523        not used right now, but can be used in BGC packages to fix conservation.
524    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
525        other packages too.
526    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
527        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
528    o model/src:
529      - since we have several heat capacity (even in model/src), define "recip_Cp"
530        as local variable (no longer in common block) to avoid any confusion.
531      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
532    o pkg/exf:
533      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
534        air density as function of air Temp, Humidity and atm pressure.
535    
536    checkpoint64w (2014/05/02)
537    o verification:
538      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
539        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
540        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
541        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
542        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
543    o model/src: for atmosphere in p* coords:
544      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
545      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
546        but not yet activated.
547    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
548      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
549      - this changes the results (but not for any verification experiment, because
550        none tests this), but avoids having an extra field in the restart files
551    o pkg/seaice: remove global variable TICE (not needed)
552      - replace by TICES or local variable where necessary (cost_seaice_test,
553        seaice_diagnostics_state)
554      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
555      - use specific read/write routines for reading and writing individual leves
556        of a multilevel field
557    o pkg/ctrl & model/inc:
558      - move additional anomaly fields of control vars (related to options:
559         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
560        from DYNVARS.h into new header file: CTRL_FIELDS.h
561    o pkg/seaice: some small modifications to the ridging code
562      - make fw2ObyRidge a global variable and add the freshwater flux to
563        seaice_growth
564      - pass actual thickness from seaice_prepare_ridging, so that it is
565        computed only in one place and compute it in the same way as in
566        seaice_growth
567      - initialise more fields in seaice_do_ridging that where cause floating
568        point exceptions over land
569    o pkg/seaice: preparations for ridging code and first real ridging code
570      - move most of "PART 1" of S/R seaice_growth into a new and separate
571        S/R seaice_reg_ridge that will both regularize the state variable after
572        advection call the actual ridging routine;
573      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
574        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
575      - remove ridging code from seaice_advdiff
576      - clean up remaining part 1 of seaice_growth in an attempt to make it
577        more readable (this is probably subjective)
578      - call seaice_itd_redist once in the initialisation phase to have the initial
579        conditions in the correct category
580      - finally: add new ridging routine for ITD code
581    
582    checkpoint64v (2014/04/11)
583    o pkg/ecco:
584      - add runtime parameters mdt[start,end]date[1,2]
585      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
586    o pkg/seaice:
587      - make deltaC a global variable, so that it can be used in ridging code
588      - first step towards ridging: introduce new routines that compute
589        ice strength based on ridging parameters
590      - add diagnostic for HSNOWITD
591      - add opnWtrFrac as a global variable (required for ridging scheme)
592    o pkg/salt_plume + pkg/seaice/seaice_growth.F
593      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
594        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
595    o verification/hs94.1x64x5:
596      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
597      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
598    o autodiff:
599      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
600        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
601        For now, only in pkgs used in verification/hs94.1x64x5.
602      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
603        which are specific to TAF/TAMC).
604      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
605        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
606        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
607      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
608        building mitgcmuv_ad (make adAll).
609    o pkg/ecco:
610      - cost_gencost_seaicev4.F:
611         reformulate proxy cost as function of sst and local param SEAICE_freeze
612         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
613      - add stop statement if old names siv4-[sst,vol] are used
614      - add snapshots + cost reports for atmospheric longwave
615      - remove factor 0.1 in front of wtau[u,v]
616      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
617         ALLOW_TMI_SST_COST_CONTRIBUTION
618    o pkg/atm_phys:
619      - add some diagnostics for Short-wave and for convection S/R.
620    o pkg/seaice/seaice_growth:
621      - fix a bug in the lateral melt parameterization for SEAICE_ITD
622        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
623      - rearrange loop order for better vector code in the same code block
624      - rewrite the floeDiameter formula to have fewer divisions
625      -  (miraculously) none of this changes the results of seaice_itd
626    o pkg/smooth:
627      - move param smooth2Ddiffnbt to pkg/ecco
628    o pkg/salt_plume:
629      - salt_plume_frac.F:
630         clean up local param names
631         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
632    o pkg/rw:
633      - add RS version of S/R READ_MFLDS_LEV.
634    o pkg/streamice:
635      - fix the restart test by writing/reading pickup_streamice files.
636    o pkg/seaice:
637      - refine checks for jfnk-related parameters
638      - comment out if statement with SEAICEuseIMEX parameter as long as there
639        is no IMEX code to avoid confusion and surprises
640    
641    checkpoint64u (2014/03/07)
642    o verification/MLAdjust:
643      - rename secondary test suffix:
644         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
645         0.leithD -> AhFlxF  + switch to flux-form
646         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
647         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
648    o pkg/mom_vecinv:
649      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
650        to be before mom_calc_visc.F)
651      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
652      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
653        this is simpler for the adjoint and for diagnostics.
654    o model/src + pkg/momentum:
655      - add input files for  2-D additional Western and Southern cell-edge wall
656         (e.g., to add "thin-wall" where it is =1).
657      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
658        using 2nd hFacZ that is computed from initial (fix domain) hFac
659      - known limitations of thin wall implementation: not yet coded for sigma
660        coords; not working with CD-scheme neither.
661    o pkg/seaice:
662      - rename recently introduced parameters from (wrong name) AB to
663        BDF (backward difference time discretisation)
664      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
665    o tools/adjoint_options:
666      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
667    
668    checkpoint64t (2014/02/01)
669    o pkg/ecco
670      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
671        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
672      - replace hard-coded record number and period which only work for monthly
673        with read-in runtime param that works for other periods (month,day,year)
674    o pkg/thsice
675      - corrected store directive fixes thsice adjoint gradient checks
676    o genmake2 & testreport:
677      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
678        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
679        Update testreport accordingly. No need to set "export OPENAD=true"
680        in adjoint_options/adjoint_oad anymore (will be removed later).
681    o pkg/shelfice:
682      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
683        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
684        so that surface forcing applies to k=kSurf if using pkg/shelfice.
685    o pkg/ctrl, pkg/grdchk, pkg/ecco:
686      - Changes to make GENARR more modular (i.e. invisible if not used)
687    o model/src/temp_integrate.F and salt_integrate.F
688      - re-include store directives that were removed on Dec 27th.
689    o model/src/external_forcing_surf.F
690      - add storage directives for EmPmR and PmEpR to avoid recomputation of
691        seaice_model in the adjoint that is problematic when seaice_model is
692        turned off in the adjoint. The resolved issue dated back to July when
693        EXTERNAL_FORCING_SURF call was moved.
694        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
695    o pkg/exf/exf_check.F
696      - fix a small bug again (originally found by Wentao Liu, now found again)
697      - streamline error output
698    o pkg/streamice and aim_v23:
699      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
700        Apple's /usr/bin/cpp knows what to do:
701        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
702        Target: x86_64-apple-darwin13.0.0
703    
704    checkpoint64s (2014/01/05)
705    o tools/adjoint_options:
706      - switch to fastopt.net TAF server (instead of default fastopt.de) for
707        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
708    o model/src:
709      - remove some unnecessary TAF storage directives in forward_step.F and
710        in dynamics.F (note: not always removed by TAF, e.g., double storage
711        of kappaRU,kappaRV in former version of dynamics.F).
712    o model/src & pkg/ptracers:
713      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
714        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
715        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
716      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
717      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
718      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
719    o useSingleCpuInput separates single-CPU input from single-CPU output;
720        for now only implemented for in exf_interp_read.F
721    o verification/advect_xy:
722      - fix missing EXCH call in local version of ini_salt.F and update output.
723    o momentum diagnostics:
724      - fix which deltaT is used in Total-Tendency diagnostics.
725      - fix typo in diagnostics for momentum tendency from AB.
726    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
727        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
728    
729    checkpoint64r (2013/12/08)
730    o verification/*/results:
731      - Update reference output of experiments that were passing with just 13 digits
732         (make it easier to detect future changes in results)
733    o model/src & pkg/ptracers:
734      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
735        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
736        to inside ptracers_integrate.F ; remove ptracers_advection.F
737    o coupling interface pkgs:
738        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
739      - change the config check to test the agreement of Ocean Depth
740        with ATM land/sea mask (instead of ATM orography);
741      - send to coupler the number of coupler time-steps to do for this run:
742        this allows to check for consistency and don't need anymore to be
743        specified in parameter file "data";
744      in coupler:
745      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
746      - improve report to log-file of config setting (pass log-file unit to few S/R)
747    o pkg/compon_communic:
748      - add coupling send/receive for non-tiled integer vector;
749      - add S/R to check and stop if any proc has an error (similar to
750        eesupp/src/stop_if_error.F but single thread and across Comm_World).
751    o pkg/exch2:
752      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
753        through list of all tiles my proc owns.
754    o model/src:
755      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
756        from rTrans) to simplify dependencies (no need to store rTrans anymore in
757        calling S/R); this affects AD results at machine truncation level:
758        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
759        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
760    o tools/build_options:
761      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
762    o coupling interface pkgs:
763        [compon_communic, atm_compon_interf & ocn_compon_interf]
764      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
765        to each S/R that needs it; remove un-used variables.
766      - change component tile registration (cpl_register.F in both compon_interf
767        and mitcomponent_tile_register.F) to pass the full list of tiles
768        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
769      - with pkg/exch2: adopt the same convention used for I/O to define mapping
770        towards coupler global array (unless W2_useE2ioLayOut=F):
771         a) can now use different tiling between atm & ocn comp.
772         b) no needs to modify the run-Off map when changing tiling (was needed
773            even if using the same tiling between atm & ocn).
774         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
775            full land tiles); not yet tested.
776      - check for valid mapping from comp. tile to coupler global array
777      - improve report of tile registration results to log file.
778    o pkg/exch2:
779      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
780        tile-registration (CPL_REGISTER);
781      - activate (un-comment) definition and setting of "W2_tileIndex" list to
782        store the local bi,bj indices of each tile;
783      - also print bi,bj in local report to log file;
784      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
785        Jun 2009 modif of pkg/exch2).
786    o testing on baudelaire:
787      - run 2 tests at a time: no significant slow down (since enough cpu) and
788        get the full set of test done earlier
789      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
790    o model/src/thermodynamics.F and routines called from it:
791      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
792        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
793        velocity (outp) by adding bolus velocity.
794      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
795        mass transport from velocity + lateral grid cell area
796      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
797      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
798     in thermodynamics.F
799      - remove k from thermodynamics.F and move it to temp_integrate.F
800        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
801        loop).
802      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
803        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
804        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
805        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
806      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
807        global_ocean.90x40x15, tutorial_global_oce_biogeo and
808        tutorial_tracer_adjsens (+ TLM output).
809    o tools/OAD_support and (verification/*/) code_oad:
810      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
811        module conversion ; remove unneeded CPP_EEOPTIONS.h.
812      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
813        version (closer to model/inc/CPP_OPTIONS.h).
814    o model/src:
815      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
816        retired list of parameters (routine FREEZE has been replace by surface
817        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
818    o pkg/gmredi:
819      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
820        velocity (same scheme but affects machine truncation) for GM_AdvForm.
821      - update output of FWD experiments: front_relax.bvp,
822        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
823    
824    checkpoint64q (2013/11/17)
825    o verification:
826      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
827        tutorial_global_oce_biogeo and global_ocean.90x40x15.
828      - generate new output (growth & melt) for seaice_itd experiment after
829        updating the input pickup_seaice files (previously wrong).
830    o pkg/cost:
831      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
832        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
833        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
834          cannot be applied to var in common block).
835        o allows to get results independent of tile-per-proc setting (if using
836          slower GLOBAL_SUM_SEND_RECV option).
837      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
838        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
839        forward gradients: update output).
840      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
841        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
842    o pkg/mom_common:
843      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
844        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
845        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
846        ensure that all field value that are used are set.
847    o tutorial_deep_convection (smag3d):
848      - add missing scaling in mom_calc_smag_3d.F;
849      - set smag3D_coeff in input.smag3d such that results do not change.
850    o pkg/dic:
851      - change dic_cost.F to compute cost on each tile first and then apply
852        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
853        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
854      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
855    o eesupp/src & pkg/mdsio:
856      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
857        (from pkg/mdsio) since they are no longer used for tape IO.
858      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
859        (+ keep a copy in pkg/atm_ocn_coupler).
860    o verification/isomip:
861      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
862    o tools/build_options:
863      - optfile linux_amd64_ifort11, fast (no ieee) case:
864        to get a working restart for all experiments, add "-fp-model source"
865        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
866    
867    checkpoint64p (2013/10/20)
868    o pkg/autodiff:
869      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
870        criteria, return to simple (default) tape IO format.
871    o pkg/mdsio (+ eesupp/src):
872      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
873        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
874      - fix globalFile and singleCpuIO options using simpler global mapping.
875      - new pairs of scatter/gather vector S/R (one for each type, generated from
876        template) corresponding to simpler global mapping.
877      - adread_write.F: switch to new S/R (but leave old calls commented) and write
878        to globalFile when parameter globalFiles is set to True.
879      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
880    o pkg/autodiff:
881      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
882        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
883        missing, just add a STOP if array type do not match.
884    o pkg/exf:
885      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
886         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
887         and rename array obsSIce to exf_iceFraction.
888    o tutorial_deep_convection:
889      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
890        for now all in this exp. code dir.
891      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
892        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
893    o eesupp/src:
894      - added SINGLE_DISK_IO option because reading of parameter files on
895        very large number of processors did not work with existing set-up
896    
897    checkpoint64o (2013/09/25)
898    o pkg/atm_phys & atm_compon_interf:
899      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
900    o tools/build_options:
901      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
902        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
903        remove CPP setting (was identical to genmake2 default).
904    o pkg/gmredi & model/src: Some updating and work done on the residual model.
905      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
906      - fixed up the calculation of the eddy stress and how it is added to the
907        external forcing via taueddy_external_forcing.F
908      - at the moment, it is very experimental and only works with the variable eddy
909        diffusivity calculated in gmredi_k3d.F
910    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
911        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
912    o testreport (& tools/do_tst_2+2):
913      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
914    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
915      - remove CPP='cpp -traditional -P' (this is genmake2 default)
916      - add switch (for big setups) to use 'medium' memory-model (but leave it
917        commented out for now). Note: needed with FC 19 to compile big setups.
918    o pkg/atm_compon_interf:
919      - regroup per field origin (model & pkgs) the coupling storage routines
920         (which accumalate in time each coupling field)
921      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
922        update accordingly + simplify aim_do_physics.F
923    
924    checkpoint64n (2013/08/26)
925    o pkg/bbl:
926      - update formulation to reduce dispersion of tracer properties in bbl
927      - replaced horizontal and vertical transport parameters with velocities
928      - changes results for verification/global_with_exf.yearly
929    o verification/halfpipe_streamice:
930      - change to matrix construction; update both Fwd & AD output.
931    o verification/tutorial_tracer_adjsens:
932      - OpenAD test: switch to vector-invariant momentum since fluxform with
933        rStar causes problems with OpenAD; update output.
934    o tools:
935      - genmake2: define a common prefix for all temp-file names ; move them
936        to local /tmp disk (but would be easy to move them back);
937      - xmakedepend: apply the same switch for temp-files.
938    o pkg/offline:
939      - changes for use with rStar (NLFS): assume that we continue to provide
940        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
941        output files) and apply r* scaling at each time-step (function of the time
942        varying Eta field); use normal pickup files (needed for restart with NLFS).
943    o adjoint with OpenAD:
944      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
945        package openad.  This package has to be compiled for all runs with OpenAD
946        instead of specifying code_oad_all as a modification directory.
947      - link the fortran templates from tools/OAD_support to the build directory
948        for preprocessing to avoid conflicts between different setups compiled
949        simultaneously and simplify cleanup.
950    o pkg/exf:
951      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
952        main model or other pkgs are exchanged in EXF_MAPFIELDS).
953    o model/src:
954      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
955        (similar to do_fields_blocking_exchanges.F).
956    o tools/genmake2:
957      - remove TAF output src code just before calling staf (when not doing a fresh
958        built, will stop if things go wrong with staf).
959      - fix target "adobj" (left from TAF version-2 transition)
960    o pkg/diagnostics:
961      - add a parameter to track the status of pkg/diagnostics activation;
962        this replace/extend the use of logical param "settingDiags" (to check
963        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
964        New S/R to print error message and stop when pkgStatus is not right.
965      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
966    
967    checkpoint64m (2013/08/13)
968    o model/inc:
969      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
970        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
971    o pkg/kpp & aim_v23:
972      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
973    o pkg/seaice:
974      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
975        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
976      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
977    o eesupp/src:
978      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
979        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
980    o switch to TAF version-2:
981      - add flow directives to "freeze" naming convention for ad-routines that
982        are used in I/O routines of adjoint state and associated common blocks
983        that are used in adcommon.h (backward compatible with version-1)
984      - update all ad-optfiles (in tools/adjoint_options + few local to some
985        verification exp) to switch to latest TAF version (currently 2.5.5);
986        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
987        out except for diva).
988      - the major change with TAF version-2 is that both the differentiated
989        routines and the forward routines (new) are returned as part of the TAF
990        output source code. Update genmake2 accordingly.
991      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
992        with version-2 when compared to TLM or FWD gradient); other experiments
993        output show minor changes (machine truncation level); update the few AD &
994        TLM output with 12 matching digits only (some prior to version-2 switch).
995    
996    checkpoint64l (2013/08/05)
997    o model/src:
998      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
999      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1000        when using TAF but only if using OpenAD.
1001    o pkg/mom_common+fluxform+vecinv:
1002      - always set horiz. viscosity arrays to background value before calling
1003        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1004        only when using variable horiz. viscosity (useVariableVisc=T);
1005      - simplify mom_vecinv.F (only 1 block for momViscosity).
1006    o pkg/mom_common: variable horiz. viscosity in NH code
1007      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1008        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1009      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1010        useBiharmonicVisc & useVariableVisc.
1011      - fix old bug (already in 1rst implementation of variable horizontal viscosity
1012        in calc_gw.F, version 1.27, 2006/06/20):
1013        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1014        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1015      - change background horiz viscosity in vertical momentum (gW) to always be
1016        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1017        any type of variable viscosity, e.g., viscAh/4Grid)
1018      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1019        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1020        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1021        default viscAh,viscA4 is zero).
1022    o model/src:
1023      - extend length of drC & recip_drC from Nr to Nr+1.
1024  o Divided Adjoint (DIVA) with MPI:  o Divided Adjoint (DIVA) with MPI:
1025    - genmake2: do not create local ./mpi_headers dir when no file to copy into.    - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1026    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
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