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revision 1.2040 by jmc, Wed Aug 6 23:19:25 2014 UTC revision 1.2140 by mlosch, Fri Mar 13 14:25:55 2015 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/exf/exf_interp.F: add code to allow input grids with latitude
8      starting in the north (i.e. when j=1 corresponds to northern edge of
9      field); modify global_with_exf to test this feature
10    o verification/testreport:
11      - replace "grep -A3" with POSIX conformal sed command, because there are
12        implementations of grep that cannot do contextual searches
13      - replace "cat -n" by "nl" (two occurrences), because not all implementations
14        of "cat" have the option "-n"
15    o model/src: add new file gsw_teos10.F that contains
16        3 functions, more or less a copy of the gsw_toolbox.f90 of the TEOS-10
17        fortran interface, that are used to convert from conservative to
18        potential temperature. For now they are not called anywhere.
19    o pkg/ggl90: make "useIDEMIX" useful
20      - re-organize code in s/r ggl90_calc a little to move computations that
21        are different for idemix into separate loops (changes verification
22        experiment idemix at truncation level, 12 digits remain -> updated)
23      - requires 2 new 2D fields KappaM, verticalShear
24      - make hFacI and recip_hFacI local 3D variables that are passed to
25        s/r ggl90_idemix
26      - fix and improve some comments
27    
28    checkpoint65j (2015/02/25)
29    o pkg/openad
30      - synchronize seawater.F with version in model/src: replace routine
31        body of sw_temp by calling sw_ptmp and fix/add a few comments.
32    o pkg/mnc:
33      - change default value of pickup_read/write_mnc params to FALSE
34        (since few features are missing in reading MNC pickup files).
35    o model/src:
36      - change default (background) vertical diffusivity for salt to be the
37        temperature (background) vertical diffusivity.
38      - change background vertical diffusivity in vertical mixing pkgs ggl90,
39        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
40        This makes ptracers default diffusivity (that uses salt diffKr) more
41        consistent with vertical mixing schemes.
42    o verification/testreport:
43      - fix typo in "-pcls" option ;
44      - put temp files in /tmp (instead of in local dir)
45      - add option "-ncad" to use genmake2 new option "-nocat4ad"
46      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
47    o pkg/ggl90 (idemix code):
48      - apply few fixes ; add some missing "_d 0" ; update output of exp.
49        global_ocean.90x40x15.idemix
50    o OpenAD
51      - enable active file I/O and begin removal of work-around code
52        for OpenAD for handling control variables (memory vs. active files)
53      - new CPP options file OPENAD_OPTIONS.h
54      - revert to genarr2d gradient check for hs94.1x64x5
55      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
56      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
57    o tools/genmake2:
58      - add option for an alternative Makefile (from Martin) where multiple
59        source files are sent to TAF (instead of all in one file).
60    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
61      - code provided by Carsten Eden as an extension of ggl90
62      - so far the code is turned on within ggl90 by setting a CPP-flag at
63        compile time; a runtime flag implementation is not yet complete
64      - tested in new verification experiment global_ocean.90x40x15.idemix
65    o verification:
66      - reduce length of the AD test run by half for experiments
67        global_ocean.cs32x15 (std + thsice) and isomip
68      - enable active file I/O for OpenAD, adjust verifications accordingly
69      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
70    o verification/testreport:
71      - fix two non-POSIX sed statements so that there are no error messages
72        on Mac OS X
73      - replace hostname -s with hostname | sed 's/\..*$//'
74    o model/src/seawater.F:
75      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
76        (following the matlab code), which would have avoided the bug caught
77        by Matt (see below) in the first place
78    o pkg/shelfice:
79      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
80        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
81      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
82        ice-shelf case (i.e., within surface level).
83      - add config summary in shelfice_check.F
84      - remove global variable recip_SHELFICElatentHeat and replace by a local
85        variable recip_latentHeat
86      - introduce diagnostics for friction velocity uStar (in case of
87        SHELFICEuseGammaFrict)
88      - change verification experiment isomip.htd:
89        + start from pickup (as input_ad at nIter0=8640)
90        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
91        + test SHELFICEuseGammaFrict = .TRUE.
92        + test SHELFICEadvDiffHeatFlux = .TRUE.
93    o model/src:
94      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
95        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
96        update output of experiments global_with_exf.yearly and isomip (all 6).
97    o pkg/shelfice:
98      - change setting of kTopC to also be zero where there is no ice-shelf.
99      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
100        ice-shelf is.
101      - first attempt to get RealFreshWaterFlux effects: for now, only without
102        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
103    o pkg/seaice: add the option to prescribe a fixed thickness PDF
104      for thermodynamic calculations
105      - because of divisions of the type 7/7 not exactly equal to 1, this change
106        affects results of some verification experiments by up to 4 digits:
107        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
108        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
109        adjoint: lab_sea, lab_sea.noseaicedyn
110        -> updated
111    
112    checkpoint65i (2015/01/23)
113    o model/src:
114      - change units of frictionHeating field from W to W/m^2
115      - fix bug in frictional heating from stratospheric drag in
116        S/R ATM_PHYS_TENDENCY_APPLY_V
117      - with synchronous time-stepping: move resetting to zero of frictionHeating
118        field from load_fields_driver.F to thermodynamics.F ;
119      - add diagnostics for frictional heating.
120    o model/src & gmredi K3D:
121      - add frictionHeating field to pickup-files (for synchronous time-stepping)
122      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
123      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
124        and name in pickup file).
125      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
126    o model/src:
127      - move (from ini_forcing.F) initialisation of all arrays in header file
128        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
129        (since Nov 2012) with option selectAddFluid=1.
130    o pkg/shelfice:
131      - change units (+ document) of newly added field "shelfIceMassDynTendency"
132      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
133    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
134    o pkg/seaice: two new runtime parameters:
135      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
136        long overdue
137      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
138        parameterization of tensil stress for fast ice (does not do anything yet)
139    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
140        for LSR: move checking overlaps out of JFNK-if-block
141    o pkg/atm_phys:
142      - move copy of grid and dynamical fields out of atm_phys_driver.F into
143        new S/R ATM_PHYS_DYN2PHYS.
144      - fix level height for Linear Free-Surf case (to be consistent with
145        fixed-in-time pressure levels).
146    o pkg/mom_common (bottomdrag):
147      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
148        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
149        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
150    o pkg/shelfice (u/v_drag):
151      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
152      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
153        (now similar to shelfice_u_drag.F)
154      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
155        from mom_vecinv.F (similar to mom_fluxform calls).
156    o pkg/mom_common (bottomdrag):
157      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
158      - add options for alternative discretisation of velocity norm in quadratic
159        bottom drag: averaging of grid-cell-center KE to U.point and V.point
160        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
161        improves when averaging only the other component (e.g. vVel for U bottom
162        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
163      - add options (bottomVisc_pCell) to account for partial-cell in bottom
164        friction (no-slip BC) thus getting the true distance from the bottom;
165        off by default since this also reduces model stability (explicit bottom
166        friction). Changes produce different machine truncation with linear-drag
167        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
168        front_relax (bvp & mxl, 10 & 11 digits).
169    o model/src & mom pkgs:
170      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
171        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
172      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
173        just copy level Nr value to level Nr+1.
174    o doc:
175      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
176    o pkg/streamice:
177      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
178        SHELFICE.h: move array shelficemass to init_varia, initialise
179        from array shelficemassinit, which is set in init_fixed and
180        has option to be set from file; introduce array
181        shelficeMassDynTend array, set thru file in init_fixed
182      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
183        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
184        pkg/streamice
185      - shelfice_thermodynamics.F: call shelfice_step_icemass if
186        SHELFICEMassStepping = .true.
187      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
188    
189    checkpoint65h (2014/12/17)
190    o verification/global_ocean.90x40x15, global_ocean_ebm:
191      - update to generic controls.
192    o pkg/ctrl:
193      - ctrl_map_ini_genarr.F: test for igen>0
194      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
195      - move gentim2d part of ctrl_map_ini_genarr.F to
196        new separate routine : ctrl_map_ini_gentim2d.F
197      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
198        add time variable weights and cyclic controls (time mean,
199        seasonal cycle, etc) capabilities to gentim2d
200    o pkg/ecco:
201      - move reading of error, conversion to weights from
202        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
203    o global_oce_llc90, cs32:
204      - activte sbo.
205      - CTRL_SIZE.h : add maxCtrlProc.
206      - activate the new genctrl capabilities.
207      - update following reorganization of global_oce_input_fields.tar.gz  
208    o pkg/ctrl/ctrl_ad_diff.list:
209      - add missing ctrl_init_rec.f
210    o tools/OAD_support/keepOriginal:
211      - add ctrl_init_rec.F
212    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
213      - avoid recomputations of xx_gentim2d_dummy.
214    o momentum diagnostics:
215      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
216        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
217    o pkg/seaice/seaice_lsr.F:
218      - fix computation of BU/BV, make sure they are non-zero, only necessary
219        for cubed sphere exchanges and SEAICE_OLx/y>0.
220        This makes calling s/r fill_cs_corner_rl obsolete (removed).
221    o verification/global_ocean.cs32x15/input.seaice
222      - add test for strong implicit coupling and restricted addtive Schwarz
223        methods for LSR
224      - update results/output.seaice.txt
225    o verification/tutorial_global_oce_biogeo:
226      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
227        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
228        update output_adm,_oadm,_tlm.txt
229    o pkg/dic:
230      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
231      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
232        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
233    o verification/tutorial_global_oce_biogeo:
234      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
235        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
236        update output_adm,_oadm,_tlm.txt
237    o eesupp/src:
238      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
239        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
240    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
241      LSR (following Hutchings et al. 2004)
242      - introduce zetaZ as a global variable (requires adjustments in
243        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
244        in seaice_calc_viscosities.F
245      - new flag SEAICEuseStrImpCpl (default off)
246      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
247        momentum equations
248      - JFNK-solver (preconditioner) adjusted to allow using this method
249        (where it does not have any positive effect)
250    o pkg/seaice
251      - add overlap for restrictive additive Schwartz method also to LSR, but
252        turn it off by default (because it only seems to work for non-cubed
253        sphere/llc topologies)
254    o pkg/autodiff
255      - add extra exchanges in addummy_in_steppging also for mnc output
256    o pkg/seaice:
257      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
258        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
259    o pkg/obcs:
260      - add option to specify domain-connected piece Id along OB though files
261        (for now, only used to diagnose PhiVel; default =1 -> global correction)
262      - modify obcs_diag_balance.F to process each connected-part separately;
263        exclude OB where Id = 0 but keep the full divergence there (-> constant
264        Psi along this portion of OB and all inflow derived from grad(Phi))
265      - add example of OB-conect files in verification/so_box_biogeo/input.
266    o pkg/diagnostics:
267      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
268      a) use non zero matrix element across OB and solve for Phi 1 grid point
269         outside OB (i.e, where tracer OBCS are applied).
270      b) global imbalance of inFlow/outFlow across OB: instead of modifying
271         velocity across OB, spread it uniformly along the OB in the RHS.
272    
273    checkpoint65g (2014/11/19)
274    o pkg/diagnostcis:
275      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
276    o pkg/my82,pp81,kl10:
277      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
278        field diffKr as background diffusivity to set minimum diffusivity value.
279    o pkg/seaice:
280      - add new parameter SEAICEuseEVPrev (for revisited EVP by
281        Bouillon et al 2013)
282      - add SEAICE_evpAlpha/Beta to namelist
283      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
284        involve trivial re-ordering of divisions/multiplications that should not
285        have any effects, but ... they do change the results of lab_sea.hb87 so
286        that only 2 digits of agreement remain, in line with the general
287        instability/fragility of the evp-code. For now, I do not care and just
288        update the verification experiment
289    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
290      - remove xx_genarr2d_numsmooth etc
291      - use xx_genarr2d_preproc etc instead
292      - carry out smooth_correl2D at initialization stage rather than during
293        time stepping.
294      - get smoothOpNb from xx_gentim2d_preproc
295    o global_oce_cs32 :
296      - add test of generic ecco capabilities.
297    o pkg/exf/exf_getsurfacefluxes.F :
298      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
299    o pkg/ctrl,ecco :
300      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
301        is defined.
302    o pkg/seaice: add diagnostics for Delta (deformation parameter)
303    o model/src:
304      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
305        diffusivity (background) is specified but ignored.
306    o verification:
307      - in testreport, convert hostname to lower case for default output dir name
308    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
309    o pkg/dic: add modifications from Hajoon:
310      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
311      - light attenuation: add self-shading effect by climatological Chlorophyll
312        (read from file).
313    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
314        compiles when SEAICE_ALLOW_DYNAMICS is undefined
315    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
316        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
317        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
318        approach where CPP_OPTIONS.h includes an omnipotent
319        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
320    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
321        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
322    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
323        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
324        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
325    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
326      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
327      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
328      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
329      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
330    o pkg/ctrl,ecco,exf :
331      - remove variables associated with NON-generic costs,
332        unless ECCO_CTRL_DEPRECATED is defined.
333      - remove NON-generic NON-obcs controls,
334        unless ECCO_CTRL_DEPRECATED is defined.
335    o pkg/ctrl : added ctrl_local_params.h
336    o pkg/ecco : added ecco_local_params.h
337    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
338        experiments, which will progressively be removed once the
339        experiments are revised to use only generic controls/costs.
340    
341    checkpoint65f (2014/10/13)
342    o pkg/ctrl, ecco, seaice : minor changes in headers
343    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
344        cost function and control capabilities added since checkpoint65c.
345    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
346    o pkg/ecco: increase modularity and improve logic
347      - ecco_toolbox.F (new) : basic operations that are often used,
348        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
349        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
350      - cost_gencal.F (new) : determine filnames and records.
351      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
352      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
353        and exploit the above functions leading to more compact code.
354      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
355      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
356        using_ers, using_gfo, using_mdt is now only defined within gencost)
357    o pkg/ecco: extend generic cost capabilities
358      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
359        capabilities via gencost_preproc (+ _c,_i,_r related params),
360        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
361        gencost_outputlevel arguments to cost_generic
362      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
363        and active_read, making room for gencost_preproc to take effect.
364        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
365      - pkg/ecco/cost_generic.F :
366        compute and store misfit maks*(model-data) in localdif that is
367        then used in cost and for output, output misfit if outlev.GT.0
368      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
369        rather gencost_barfile for deciding whether to write barfile
370      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
371      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
372        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
373      - pkg/ecco/ecco_summary.F : report gencost variables
374      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
375    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
376    o pkg/ecco: internal re-organization
377      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
378        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
379        mv relevant variables definition from ecco_cost.h to ecco.h,
380        make sure gencost routines only include ecco.h)
381      - throughout : add missing CCP switches, rm unused variables,
382        and rm un-necessary CPP switches
383      - throughout gencost routines : replace modelstartdate with
384        gencost_startdate when needed
385      - cost_bp_read.F : use arguments, instead of common blocs
386        so that it can be used also by (new) cost_gencost_bpv4.F
387      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
388      - ecco_phys.F : compute etanFull
389      - ecco_readparms.F : rename using_topex as using_tpj, add
390        bpv4-grace to gencost list, initialize added parameters
391      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
392    
393    checkpoint65e (2014/09/28)
394    o pkg/obcs:
395      - replaced the just-added CPP options with run-time variables
396        (see pkg/obcs/OBCS_PARAMS.h for details)
397    o pkg/obcs:
398      - add additional CPP options for sponge boundary layers
399        (see pkg/obcs/OBCS_OPTIONS.h for details)
400    o pkg/atm_phys:
401      - implement simple (obliquity only, assuming circular planet orbit)
402        seasonal cycle for incoming insolation ; used when run-time parameter
403        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
404    o pkg/exf, pkg/ecco, pkg/ctrl:
405      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
406      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
407      - implement gentim2d for xx_tauu, xx_tauv
408    o pkg/ctrl, pkg/ecco :
409      - fix and complement the generic controls implementation
410    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
411        pkg/shelfice/shelfice_thermodynamics.F,
412        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
413        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
414      - add weight in CTRL_GET_GEN calls
415    o pkg/ctrl :
416      - ctrl_get_gen.F : add weight as input parameter, and apply
417        it directly rather than using smooth_correl2Dw (to be retired).
418      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
419    o pkg/ctrl :
420      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
421        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
422      - re-activate ctrl_summary (call in ctrl_init.F)
423    o pkg/ctrl/ctrl_cost_gen.F :
424      - fix CCP brackets, remove un-necessary myiter, mytime
425    o pkg/ecco, pkg/ctrl :
426      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
427      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
428      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
429      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
430    
431    checkpoint65d (2014/09/15)
432    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
433      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
434        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
435    o pkg/ctrl/ctrl_map_ini_genarr.F :
436      - remove compilation failure
437      - replace hard coded example
438      - use ctrl_map_ini_gen2D, 3D
439    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
440      - on/off switch based upon xx_genarr2d_weight,3d
441    o src/packages_init_variables.F :
442      - regroup pkg/estimation calls
443      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
444        (moved to ctrl_init_variables)
445    o cost/cost_init_varia.F :
446      - remove ecco_cost_init_varia
447        (moved to ecco_init_varia)
448    o ctrl/ctrl_init_variables.F :
449      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
450      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
451    o ctrl/ctrl_map_ini.F :
452      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
453        (moved to ctrl_init_variables)
454    o ctrl/ctrl_map_ini_ecco.F :
455      - remove ECCO_PHYS (mv to ecco_init_varia)
456      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
457    o ecco/ecco_ad_diff.list :
458      - add ecco_init_varia.f
459    o ecco/ecco_init_varia.F
460      - new routine
461    o pkg/streamice:
462      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
463        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
464      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
465    o pkg/generic_advdiff:
466      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
467    o pkg/exf:
468      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
469         xxg_precip capability
470      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
471    o pkg/ctrl:
472      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
473    o model/src/load_fields_driver.F :
474      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
475        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
476    o OpenAD verification experiments:
477      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
478        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
479        for now, only in pkgs used in OpenAD verification experiments.
480      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
481        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
482        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
483        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
484    o OpenAD verification tests:
485      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
486      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
487        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
488      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
489        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
490    o model/src & generic_advdiff:
491      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
492        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
493        dynamics requires valid tracer forcing only over tile interior but, for
494        some diagnostics, may need to extend it over 1 point in tile halo region.
495      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
496        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
497        setting in temp/salt/ptracer_integrate.F
498    o pkg/dic:
499      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
500        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
501        in gchem_forcing_sep.F
502    o pkg/autodiff & obcs:
503      - add storage of current OB values for U & V (was already done for T & S).
504    
505    checkpoint65c (2014/08/30)
506    o pkg/dic:
507      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
508        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
509        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
510    o verification:
511      - new experiment testing OBCS and DIC pkgs, using params & output from
512        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
513        passage: take OBCS from the last year of a 2 yrs simulation and initial
514        conditions from t=1.yr while keeping the same forcing.
515    o model/src:
516      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
517        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
518    o pkg/diagnostics (Stats-Diags):
519      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
520        a) refine region where stats are computed, excluding where arrhFac=0 ;
521        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
522        c) extend regional stats over the region edges (for U or V pt location).
523    o pkg/gchem:
524      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
525        pkg/dic is currently changing/updating ptracers values beyond the OB).
526    o verification (hs94):
527      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
528        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
529        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
530        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
531    o pkg/ptracers:
532      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
533        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
534      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
535        with AB-2 code (so that it get tested).
536    o model/src:
537      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
538        with AB-2 code (previously only available with AB-3 code).
539        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
540        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
541        there, by calling CYCLE_AB_TRACER).
542    o pkg/generic_advdiff:
543      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
544        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
545        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
546        S/R temp/salt/ptracers_integrate.F
547    o model/src & pkg/ptracers:
548      - remove common block variables gT,gS (in DYNVARS.h), except when
549         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
550      - remove common block variable gPtr.
551    o model/src & pkgs:
552      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
553         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
554         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
555         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
556      + change accordingly all calling S/R.
557      - use local temperature/salinity/ptracer tendency array (without bi,bj)
558        in S/R temp/salt/ptracers_integrate.F
559    o pkg/seaice:
560      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
561        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
562      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
563        in seaice_lsr
564      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
565        in s/r seaice_lsr_calc_coeffs
566    o pkg/mdsio:
567      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
568        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
569        too long (e.g., > MAX_LEN_FNAM/2 )
570    
571    checkpoint65b (2014/08/12)
572    o pkg/matrix:
573      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
574    o model/src:
575      - fix initialisation of geothermalFile; compile geothermal-flux code in
576        natl_box verification experiment.
577    o model/src & pkg/down_slope:
578      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
579      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
580        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
581        results at machine truncation level: update output of experiments
582        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
583    o pkg/diagnostics (Stats-Diags):
584      - do not cumulate the full volume when DIAGNOSTICS_FILL is
585        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
586        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
587        times (but Min,Max and StD are still wrong).
588    o model/src:
589      - add geothermal flux forcing: read in ini_forcing.F as time-constant
590        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
591    o model/src:
592      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
593        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
594        arrays are already updated while adjustments (filters, conv.adjustment) are
595        still applied later, in S/R TRACERS_CORRECTION_STEP.
596  o model/src:  o model/src:
597    - store in common bloc array "rhoInSitu" the virtual potential temperature    - store in common bloc array "rhoInSitu" the virtual potential temperature
598      anomaly that is used to compute geopotential: this make the atmos code      anomaly that is used to compute geopotential: this make the atmos code
# Line 82  o model/src: Line 671  o model/src:
671    - collect T & S forcing tendency into local 2-D array (passed as argument to    - collect T & S forcing tendency into local 2-D array (passed as argument to
672      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
673      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
674      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
675      moist correction due to vertical advection).      correction due to vertical advection).
676    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
677      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
678      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
# Line 112  o pkg/seaice: more clean up Line 701  o pkg/seaice: more clean up
701      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
702      this experiment):      this experiment):
703      > size mitgcmuv_ad      > size mitgcmuv_ad
704      text    data        bss     dec        hex        text    data        bss     dec        hex
705      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
706      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
707      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
708      text    data        bss     dec        hex      text    data        bss     dec        hex

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