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revision 1.2002 by jmc, Wed May 28 23:14:38 2014 UTC revision 1.2160 by jmc, Mon Jun 15 15:22:24 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 coupler (atm & ocn _compon_interf):
8      - avoid using Exch2 IO mapping if not suitable.
9    
10    checkpoint65m (2015/06/15)
11    o pkg/layers:
12      - clean-up old parameters setting (from Sep 2012):
13        + remove old parameters setting from common block (declared locally);
14        + stop if any old parameter is mixed with new parameters;
15        + check for valid or consistent parameter setting (e.g., layers_name)
16      - check that layers_bounds for Pot.Density are in the right range;
17        this is supposed to catch un-updated setting after recently shifting
18        potential density field "prho" by -1000 (now in "sigma" scale).
19    o pkg/layers:
20      - Added missing call to layers_fill for keeping track of tottend in
21        pkg/diagnostics/diagnostics_fill_state.F
22    o pkg/layers:
23      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
24        of diapycnal fluxes
25    o pkg/layers:
26      - reverted changes to interpolation to previous treatment; there
27        was never actually a problem
28    o pkg/layers:
29      - fix interpolation of layers tracers in the presence of partial cells
30      - add lots of new functionality to compute water mass transformation
31        (enabled by CPP flag LAYERS_THERMODYNAMICS)
32      - add new calls from main code (diags_oceanic_surf_flux.F,
33        thermodynamics.F, impldiff.F) and gad to save the necessary fields
34        for layers_thermodynamics calculations
35    o pkg/ptracers:
36      - add capability of stepping a passive tracer forward without advection
37        by setting PTRACERS_advScheme to 0.
38    o pkg/diagnostics:
39      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
40    o pkg/layers:
41      - shift potential density field "prho" by -1000 for density layer averaging so
42        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
43        Note that density bin boundaries (layers_bounds in data.layers) have
44        to be set accordingly (i.e., shifted, in sigma scale).
45    o pkg/layers:
46      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
47      - fix calculation of layer non-weighted velocity and layer probability
48      - add diagnostics for pot.density used for layer averaging
49    o pkg/seaice:
50      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
51        positiveness, modify a few comments and improve variable names,
52      - the changed computation of deltaC affects most seaice-related
53        experiments at the truncation level.
54        seaice_itd.thermo is affected by far the most, with
55        only 7 digits of agreement remaining; update experiments.
56    
57    checkpoint65l (2015/05/04)
58    o pkg/shelfice:
59      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
60        factor drKp1 to zero where it is negative (ie. do not use
61        SHELFICEBoundaryLayer if hFacC>1)
62      - the same for factor drLoc in shelfice_forcing.F
63    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
64        with modules in ptracers, when using testreport option "-small_f"
65    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
66      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
67    o verification/testreport
68      - add new option -small_f
69        with this option testreport first makes the target small_f (*.f files)
70        before running make (all). This is useful for explicit inlining when
71        all sources need to be full available.
72    o pkg/exf/exf_interp.F:
73        remove previous changes related to reverse (decreasing) input grids latitude
74    
75    checkpoint65k (2015/04/01)
76    o pkg/ecco:
77        fix missing cosphi initialization; use eccoiter in place of optimcycle;
78        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
79        instead of active read/write
80    o pkg/ctrl:
81        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
82        instead of active read/write.
83    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
84        return if .NOT.useAUTODIFF
85    o pkg/seaice: add CPP brackets (cost function related).
86    o model/src:
87        add useAUTODIFF run time switch.
88    o pkg/exf/exf_interp.F:
89        add code to allow input grids with latitude starting in the north (i.e. when
90        j=1 corresponds to northern edge of field); modify global_with_exf to test
91        this feature.
92    o verification/testreport:
93      - replace "grep -A3" with POSIX conformal sed command, because there are
94        implementations of grep that cannot do contextual searches
95      - replace "cat -n" by "nl" (two occurrences), because not all implementations
96        of "cat" have the option "-n"
97    o model/src:
98        add new file gsw_teos10.F that contains 3 functions, more or less a copy
99        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
100        convert from conservative to potential temperature. For now they are not
101        called anywhere.
102    o pkg/ggl90: make "useIDEMIX" useful
103      - re-organize code in s/r ggl90_calc a little to move computations that
104        are different for idemix into separate loops (changes verification
105        experiment idemix at truncation level, 12 digits remain -> updated)
106      - requires 2 new 2D fields KappaM, verticalShear
107      - make hFacI and recip_hFacI local 3D variables that are passed to
108        s/r ggl90_idemix
109      - fix and improve some comments
110    
111    checkpoint65j (2015/02/25)
112    o pkg/openad
113      - synchronize seawater.F with version in model/src: replace routine
114        body of sw_temp by calling sw_ptmp and fix/add a few comments.
115    o pkg/mnc:
116      - change default value of pickup_read/write_mnc params to FALSE
117        (since few features are missing in reading MNC pickup files).
118    o model/src:
119      - change default (background) vertical diffusivity for salt to be the
120        temperature (background) vertical diffusivity.
121      - change background vertical diffusivity in vertical mixing pkgs ggl90,
122        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
123        This makes ptracers default diffusivity (that uses salt diffKr) more
124        consistent with vertical mixing schemes.
125    o verification/testreport:
126      - fix typo in "-pcls" option ;
127      - put temp files in /tmp (instead of in local dir)
128      - add option "-ncad" to use genmake2 new option "-nocat4ad"
129      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
130    o pkg/ggl90 (idemix code):
131      - apply few fixes ; add some missing "_d 0" ; update output of exp.
132        global_ocean.90x40x15.idemix
133    o OpenAD
134      - enable active file I/O and begin removal of work-around code
135        for OpenAD for handling control variables (memory vs. active files)
136      - new CPP options file OPENAD_OPTIONS.h
137      - revert to genarr2d gradient check for hs94.1x64x5
138      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
139      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
140    o tools/genmake2:
141      - add option for an alternative Makefile (from Martin) where multiple
142        source files are sent to TAF (instead of all in one file).
143    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
144      - code provided by Carsten Eden as an extension of ggl90
145      - so far the code is turned on within ggl90 by setting a CPP-flag at
146        compile time; a runtime flag implementation is not yet complete
147      - tested in new verification experiment global_ocean.90x40x15.idemix
148    o verification:
149      - reduce length of the AD test run by half for experiments
150        global_ocean.cs32x15 (std + thsice) and isomip
151      - enable active file I/O for OpenAD, adjust verifications accordingly
152      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
153    o verification/testreport:
154      - fix two non-POSIX sed statements so that there are no error messages
155        on Mac OS X
156      - replace hostname -s with hostname | sed 's/\..*$//'
157    o model/src/seawater.F:
158      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
159        (following the matlab code), which would have avoided the bug caught
160        by Matt (see below) in the first place
161    o pkg/shelfice:
162      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
163        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
164      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
165        ice-shelf case (i.e., within surface level).
166      - add config summary in shelfice_check.F
167      - remove global variable recip_SHELFICElatentHeat and replace by a local
168        variable recip_latentHeat
169      - introduce diagnostics for friction velocity uStar (in case of
170        SHELFICEuseGammaFrict)
171      - change verification experiment isomip.htd:
172        + start from pickup (as input_ad at nIter0=8640)
173        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
174        + test SHELFICEuseGammaFrict = .TRUE.
175        + test SHELFICEadvDiffHeatFlux = .TRUE.
176    o model/src:
177      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
178        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
179        update output of experiments global_with_exf.yearly and isomip (all 6).
180    o pkg/shelfice:
181      - change setting of kTopC to also be zero where there is no ice-shelf.
182      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
183        ice-shelf is.
184      - first attempt to get RealFreshWaterFlux effects: for now, only without
185        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
186    o pkg/seaice: add the option to prescribe a fixed thickness PDF
187      for thermodynamic calculations
188      - because of divisions of the type 7/7 not exactly equal to 1, this change
189        affects results of some verification experiments by up to 4 digits:
190        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
191        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
192        adjoint: lab_sea, lab_sea.noseaicedyn
193        -> updated
194    
195    checkpoint65i (2015/01/23)
196    o model/src:
197      - change units of frictionHeating field from W to W/m^2
198      - fix bug in frictional heating from stratospheric drag in
199        S/R ATM_PHYS_TENDENCY_APPLY_V
200      - with synchronous time-stepping: move resetting to zero of frictionHeating
201        field from load_fields_driver.F to thermodynamics.F ;
202      - add diagnostics for frictional heating.
203    o model/src & gmredi K3D:
204      - add frictionHeating field to pickup-files (for synchronous time-stepping)
205      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
206      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
207        and name in pickup file).
208      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
209    o model/src:
210      - move (from ini_forcing.F) initialisation of all arrays in header file
211        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
212        (since Nov 2012) with option selectAddFluid=1.
213    o pkg/shelfice:
214      - change units (+ document) of newly added field "shelfIceMassDynTendency"
215      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
216    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
217    o pkg/seaice: two new runtime parameters:
218      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
219        long overdue
220      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
221        parameterization of tensil stress for fast ice (does not do anything yet)
222    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
223        for LSR: move checking overlaps out of JFNK-if-block
224    o pkg/atm_phys:
225      - move copy of grid and dynamical fields out of atm_phys_driver.F into
226        new S/R ATM_PHYS_DYN2PHYS.
227      - fix level height for Linear Free-Surf case (to be consistent with
228        fixed-in-time pressure levels).
229    o pkg/mom_common (bottomdrag):
230      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
231        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
232        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
233    o pkg/shelfice (u/v_drag):
234      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
235      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
236        (now similar to shelfice_u_drag.F)
237      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
238        from mom_vecinv.F (similar to mom_fluxform calls).
239    o pkg/mom_common (bottomdrag):
240      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
241      - add options for alternative discretisation of velocity norm in quadratic
242        bottom drag: averaging of grid-cell-center KE to U.point and V.point
243        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
244        improves when averaging only the other component (e.g. vVel for U bottom
245        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
246      - add options (bottomVisc_pCell) to account for partial-cell in bottom
247        friction (no-slip BC) thus getting the true distance from the bottom;
248        off by default since this also reduces model stability (explicit bottom
249        friction). Changes produce different machine truncation with linear-drag
250        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
251        front_relax (bvp & mxl, 10 & 11 digits).
252    o model/src & mom pkgs:
253      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
254        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
255      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
256        just copy level Nr value to level Nr+1.
257    o doc:
258      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
259    o pkg/streamice:
260      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
261        SHELFICE.h: move array shelficemass to init_varia, initialise
262        from array shelficemassinit, which is set in init_fixed and
263        has option to be set from file; introduce array
264        shelficeMassDynTend array, set thru file in init_fixed
265      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
266        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
267        pkg/streamice
268      - shelfice_thermodynamics.F: call shelfice_step_icemass if
269        SHELFICEMassStepping = .true.
270      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
271    
272    checkpoint65h (2014/12/17)
273    o verification/global_ocean.90x40x15, global_ocean_ebm:
274      - update to generic controls.
275    o pkg/ctrl:
276      - ctrl_map_ini_genarr.F: test for igen>0
277      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
278      - move gentim2d part of ctrl_map_ini_genarr.F to
279        new separate routine : ctrl_map_ini_gentim2d.F
280      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
281        add time variable weights and cyclic controls (time mean,
282        seasonal cycle, etc) capabilities to gentim2d
283    o pkg/ecco:
284      - move reading of error, conversion to weights from
285        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
286    o global_oce_llc90, cs32:
287      - activte sbo.
288      - CTRL_SIZE.h : add maxCtrlProc.
289      - activate the new genctrl capabilities.
290      - update following reorganization of global_oce_input_fields.tar.gz  
291    o pkg/ctrl/ctrl_ad_diff.list:
292      - add missing ctrl_init_rec.f
293    o tools/OAD_support/keepOriginal:
294      - add ctrl_init_rec.F
295    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
296      - avoid recomputations of xx_gentim2d_dummy.
297    o momentum diagnostics:
298      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
299        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
300    o pkg/seaice/seaice_lsr.F:
301      - fix computation of BU/BV, make sure they are non-zero, only necessary
302        for cubed sphere exchanges and SEAICE_OLx/y>0.
303        This makes calling s/r fill_cs_corner_rl obsolete (removed).
304    o verification/global_ocean.cs32x15/input.seaice
305      - add test for strong implicit coupling and restricted addtive Schwarz
306        methods for LSR
307      - update results/output.seaice.txt
308    o verification/tutorial_global_oce_biogeo:
309      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
310        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
311        update output_adm,_oadm,_tlm.txt
312    o pkg/dic:
313      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
314      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
315        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
316    o verification/tutorial_global_oce_biogeo:
317      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
318        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
319        update output_adm,_oadm,_tlm.txt
320    o eesupp/src:
321      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
322        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
323    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
324      LSR (following Hutchings et al. 2004)
325      - introduce zetaZ as a global variable (requires adjustments in
326        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
327        in seaice_calc_viscosities.F
328      - new flag SEAICEuseStrImpCpl (default off)
329      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
330        momentum equations
331      - JFNK-solver (preconditioner) adjusted to allow using this method
332        (where it does not have any positive effect)
333    o pkg/seaice
334      - add overlap for restrictive additive Schwartz method also to LSR, but
335        turn it off by default (because it only seems to work for non-cubed
336        sphere/llc topologies)
337    o pkg/autodiff
338      - add extra exchanges in addummy_in_steppging also for mnc output
339    o pkg/seaice:
340      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
341        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
342    o pkg/obcs:
343      - add option to specify domain-connected piece Id along OB though files
344        (for now, only used to diagnose PhiVel; default =1 -> global correction)
345      - modify obcs_diag_balance.F to process each connected-part separately;
346        exclude OB where Id = 0 but keep the full divergence there (-> constant
347        Psi along this portion of OB and all inflow derived from grad(Phi))
348      - add example of OB-conect files in verification/so_box_biogeo/input.
349    o pkg/diagnostics:
350      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
351      a) use non zero matrix element across OB and solve for Phi 1 grid point
352         outside OB (i.e, where tracer OBCS are applied).
353      b) global imbalance of inFlow/outFlow across OB: instead of modifying
354         velocity across OB, spread it uniformly along the OB in the RHS.
355    
356    checkpoint65g (2014/11/19)
357    o pkg/diagnostcis:
358      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
359    o pkg/my82,pp81,kl10:
360      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
361        field diffKr as background diffusivity to set minimum diffusivity value.
362    o pkg/seaice:
363      - add new parameter SEAICEuseEVPrev (for revisited EVP by
364        Bouillon et al 2013)
365      - add SEAICE_evpAlpha/Beta to namelist
366      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
367        involve trivial re-ordering of divisions/multiplications that should not
368        have any effects, but ... they do change the results of lab_sea.hb87 so
369        that only 2 digits of agreement remain, in line with the general
370        instability/fragility of the evp-code. For now, I do not care and just
371        update the verification experiment
372    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
373      - remove xx_genarr2d_numsmooth etc
374      - use xx_genarr2d_preproc etc instead
375      - carry out smooth_correl2D at initialization stage rather than during
376        time stepping.
377      - get smoothOpNb from xx_gentim2d_preproc
378    o global_oce_cs32 :
379      - add test of generic ecco capabilities.
380    o pkg/exf/exf_getsurfacefluxes.F :
381      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
382    o pkg/ctrl,ecco :
383      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
384        is defined.
385    o pkg/seaice: add diagnostics for Delta (deformation parameter)
386    o model/src:
387      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
388        diffusivity (background) is specified but ignored.
389    o verification:
390      - in testreport, convert hostname to lower case for default output dir name
391    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
392    o pkg/dic: add modifications from Hajoon:
393      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
394      - light attenuation: add self-shading effect by climatological Chlorophyll
395        (read from file).
396    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
397        compiles when SEAICE_ALLOW_DYNAMICS is undefined
398    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
399        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
400        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
401        approach where CPP_OPTIONS.h includes an omnipotent
402        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
403    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
404        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
405    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
406        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
407        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
408    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
409      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
410      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
411      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
412      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
413    o pkg/ctrl,ecco,exf :
414      - remove variables associated with NON-generic costs,
415        unless ECCO_CTRL_DEPRECATED is defined.
416      - remove NON-generic NON-obcs controls,
417        unless ECCO_CTRL_DEPRECATED is defined.
418    o pkg/ctrl : added ctrl_local_params.h
419    o pkg/ecco : added ecco_local_params.h
420    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
421        experiments, which will progressively be removed once the
422        experiments are revised to use only generic controls/costs.
423    
424    checkpoint65f (2014/10/13)
425    o pkg/ctrl, ecco, seaice : minor changes in headers
426    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
427        cost function and control capabilities added since checkpoint65c.
428    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
429    o pkg/ecco: increase modularity and improve logic
430      - ecco_toolbox.F (new) : basic operations that are often used,
431        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
432        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
433      - cost_gencal.F (new) : determine filnames and records.
434      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
435      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
436        and exploit the above functions leading to more compact code.
437      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
438      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
439        using_ers, using_gfo, using_mdt is now only defined within gencost)
440    o pkg/ecco: extend generic cost capabilities
441      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
442        capabilities via gencost_preproc (+ _c,_i,_r related params),
443        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
444        gencost_outputlevel arguments to cost_generic
445      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
446        and active_read, making room for gencost_preproc to take effect.
447        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
448      - pkg/ecco/cost_generic.F :
449        compute and store misfit maks*(model-data) in localdif that is
450        then used in cost and for output, output misfit if outlev.GT.0
451      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
452        rather gencost_barfile for deciding whether to write barfile
453      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
454      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
455        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
456      - pkg/ecco/ecco_summary.F : report gencost variables
457      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
458    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
459    o pkg/ecco: internal re-organization
460      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
461        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
462        mv relevant variables definition from ecco_cost.h to ecco.h,
463        make sure gencost routines only include ecco.h)
464      - throughout : add missing CCP switches, rm unused variables,
465        and rm un-necessary CPP switches
466      - throughout gencost routines : replace modelstartdate with
467        gencost_startdate when needed
468      - cost_bp_read.F : use arguments, instead of common blocs
469        so that it can be used also by (new) cost_gencost_bpv4.F
470      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
471      - ecco_phys.F : compute etanFull
472      - ecco_readparms.F : rename using_topex as using_tpj, add
473        bpv4-grace to gencost list, initialize added parameters
474      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
475    
476    checkpoint65e (2014/09/28)
477    o pkg/obcs:
478      - replaced the just-added CPP options with run-time variables
479        (see pkg/obcs/OBCS_PARAMS.h for details)
480    o pkg/obcs:
481      - add additional CPP options for sponge boundary layers
482        (see pkg/obcs/OBCS_OPTIONS.h for details)
483    o pkg/atm_phys:
484      - implement simple (obliquity only, assuming circular planet orbit)
485        seasonal cycle for incoming insolation ; used when run-time parameter
486        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
487    o pkg/exf, pkg/ecco, pkg/ctrl:
488      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
489      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
490      - implement gentim2d for xx_tauu, xx_tauv
491    o pkg/ctrl, pkg/ecco :
492      - fix and complement the generic controls implementation
493    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
494        pkg/shelfice/shelfice_thermodynamics.F,
495        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
496        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
497      - add weight in CTRL_GET_GEN calls
498    o pkg/ctrl :
499      - ctrl_get_gen.F : add weight as input parameter, and apply
500        it directly rather than using smooth_correl2Dw (to be retired).
501      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
502    o pkg/ctrl :
503      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
504        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
505      - re-activate ctrl_summary (call in ctrl_init.F)
506    o pkg/ctrl/ctrl_cost_gen.F :
507      - fix CCP brackets, remove un-necessary myiter, mytime
508    o pkg/ecco, pkg/ctrl :
509      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
510      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
511      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
512      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
513    
514    checkpoint65d (2014/09/15)
515    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
516      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
517        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
518    o pkg/ctrl/ctrl_map_ini_genarr.F :
519      - remove compilation failure
520      - replace hard coded example
521      - use ctrl_map_ini_gen2D, 3D
522    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
523      - on/off switch based upon xx_genarr2d_weight,3d
524    o src/packages_init_variables.F :
525      - regroup pkg/estimation calls
526      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
527        (moved to ctrl_init_variables)
528    o cost/cost_init_varia.F :
529      - remove ecco_cost_init_varia
530        (moved to ecco_init_varia)
531    o ctrl/ctrl_init_variables.F :
532      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
533      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
534    o ctrl/ctrl_map_ini.F :
535      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
536        (moved to ctrl_init_variables)
537    o ctrl/ctrl_map_ini_ecco.F :
538      - remove ECCO_PHYS (mv to ecco_init_varia)
539      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
540    o ecco/ecco_ad_diff.list :
541      - add ecco_init_varia.f
542    o ecco/ecco_init_varia.F
543      - new routine
544    o pkg/streamice:
545      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
546        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
547      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
548    o pkg/generic_advdiff:
549      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
550    o pkg/exf:
551      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
552         xxg_precip capability
553      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
554    o pkg/ctrl:
555      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
556    o model/src/load_fields_driver.F :
557      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
558        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
559    o OpenAD verification experiments:
560      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
561        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
562        for now, only in pkgs used in OpenAD verification experiments.
563      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
564        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
565        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
566        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
567    o OpenAD verification tests:
568      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
569      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
570        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
571      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
572        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
573    o model/src & generic_advdiff:
574      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
575        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
576        dynamics requires valid tracer forcing only over tile interior but, for
577        some diagnostics, may need to extend it over 1 point in tile halo region.
578      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
579        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
580        setting in temp/salt/ptracer_integrate.F
581    o pkg/dic:
582      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
583        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
584        in gchem_forcing_sep.F
585    o pkg/autodiff & obcs:
586      - add storage of current OB values for U & V (was already done for T & S).
587    
588    checkpoint65c (2014/08/30)
589    o pkg/dic:
590      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
591        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
592        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
593    o verification:
594      - new experiment testing OBCS and DIC pkgs, using params & output from
595        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
596        passage: take OBCS from the last year of a 2 yrs simulation and initial
597        conditions from t=1.yr while keeping the same forcing.
598    o model/src:
599      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
600        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
601    o pkg/diagnostics (Stats-Diags):
602      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
603        a) refine region where stats are computed, excluding where arrhFac=0 ;
604        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
605        c) extend regional stats over the region edges (for U or V pt location).
606    o pkg/gchem:
607      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
608        pkg/dic is currently changing/updating ptracers values beyond the OB).
609    o verification (hs94):
610      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
611        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
612        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
613        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
614    o pkg/ptracers:
615      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
616        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
617      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
618        with AB-2 code (so that it get tested).
619    o model/src:
620      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
621        with AB-2 code (previously only available with AB-3 code).
622        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
623        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
624        there, by calling CYCLE_AB_TRACER).
625    o pkg/generic_advdiff:
626      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
627        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
628        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
629        S/R temp/salt/ptracers_integrate.F
630    o model/src & pkg/ptracers:
631      - remove common block variables gT,gS (in DYNVARS.h), except when
632         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
633      - remove common block variable gPtr.
634    o model/src & pkgs:
635      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
636         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
637         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
638         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
639      + change accordingly all calling S/R.
640      - use local temperature/salinity/ptracer tendency array (without bi,bj)
641        in S/R temp/salt/ptracers_integrate.F
642    o pkg/seaice:
643      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
644        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
645      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
646        in seaice_lsr
647      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
648        in s/r seaice_lsr_calc_coeffs
649    o pkg/mdsio:
650      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
651        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
652        too long (e.g., > MAX_LEN_FNAM/2 )
653    
654    checkpoint65b (2014/08/12)
655    o pkg/matrix:
656      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
657    o model/src:
658      - fix initialisation of geothermalFile; compile geothermal-flux code in
659        natl_box verification experiment.
660    o model/src & pkg/down_slope:
661      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
662      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
663        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
664        results at machine truncation level: update output of experiments
665        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
666    o pkg/diagnostics (Stats-Diags):
667      - do not cumulate the full volume when DIAGNOSTICS_FILL is
668        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
669        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
670        times (but Min,Max and StD are still wrong).
671    o model/src:
672      - add geothermal flux forcing: read in ini_forcing.F as time-constant
673        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
674    o model/src:
675      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
676        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
677        arrays are already updated while adjustments (filters, conv.adjustment) are
678        still applied later, in S/R TRACERS_CORRECTION_STEP.
679    o model/src:
680      - store in common bloc array "rhoInSitu" the virtual potential temperature
681        anomaly that is used to compute geopotential: this make the atmos code
682        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
683    o pkg/seaice/seaice_lsr.F
684      - rename integer variable ilcall to ipass (that's what it is called
685        in the residual diagnostics
686      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
687        default) for improved non-linear convergence of the first few steps
688      - adjust a few comments and add new ones to explain some of the store
689        directives
690    o pkg/generic_advdiff (& ptracers):
691      - re-work the code to check for valid advection scheme and for minimum
692        size of overlap (now stored in local common bloc in gad_advscheme.F)
693    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
694      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
695      - add an auxilliary variable "bet" and fix store directives and keys in
696        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
697        less exact gradients in my tests); but there are still
698        recomputation warning (although gradients are sort of OK), when
699        SEAICE_LSR_VECTORIZE is not defined, so this flag and
700        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
701      - update verification experiments lab_sea.
702      - change some comments in S/R seaice_calc_viscosities
703    o model/src:
704      - if staggerTimeStep=T, always apply exchange to velocity field in
705        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
706        (independent of using multi-dim advection or not); no effect on FWD run
707        but affects AD results (at machine truncation level): update output of
708        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
709        and isomip (oad: 12.d).
710    o pkg/generic_advdiff:
711      - stop if doAB_onGtGs is set to FALSE but ignored
712      - refine warning related to stability of tracer time-stepping
713        regarding internal wave dynamics.
714      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
715        on staggerTimeStep & implicitIntGravWave (will now get a warning
716        if potentially unstable).
717    o pkg/kl10:
718      - add new pkg "kl10" for mixing due to internal wave breaking, from
719        http://www.sciencedirect.com/science/article/pii/S1463500310000144
720        (contribution from Jody Klymak), tested in verification experiment
721        verification/internal_wave/input.kl10/
722    o isomip experiment:
723      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
724        (input.htd) and update the output.
725    o cd_code experiments:
726      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
727        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
728        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
729        update the corresponding output.
730    o pkg/seaice:
731      - reduce the number of include files and store directives in
732        S/R seaice_lsr_tridiagu/v
733      - change the order of loops in one case in S/R seaice_lsr_tridiagv
734        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
735        get rid off one store directive (a TAF bug?)
736      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
737        S/R seaice_lsr_tridiagv to change the loop range for consistency
738      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
739      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
740        S/R seaice_lsr_tridiagu/v (requires update of
741        offline_exf_seaice/input.dyn_jfnk)
742    
743    checkpoint65a (2014/07/27)
744    o model/src:
745      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
746        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
747        (topo in p-coords, ice-shelf in z-coords); update output of experiments
748        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
749    o model/src:
750      - collect momentum forcing tendency into local 2-D array (passed as argument
751        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
752        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
753        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
754      - collect T & S forcing tendency into local 2-D array (passed as argument to
755        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
756        affects results at machine truncation level (e.g., ocean: if using
757        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
758        correction due to vertical advection).
759      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
760        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
761        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
762        obcs_ctrl (ad & fwd grd @ 12 & 7).
763    o pkg/ptracers & diagnostics:
764      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
765        title (to avoid some unexpected truncation); sort out ptracers diags units.
766      - collect ptracer forcing tendency into local 2-D array (passed as argument
767        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
768    
769    checkpoint65 (2014/07/18)
770    o pkg/fizhi:
771      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
772        affects results at machine truncation level. Update output of experiments
773        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
774    o pkg/seaice: more clean up
775      - rename TAF common block tapes to be more consistent and remove
776        unnecessary duplicates
777      - add store directives to remove more recomputations, but use smaller
778        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
779        The idea behind this flag is to reduce the memory footprint when the
780        adjoint of the LSR is not required. As of now, defining the flag
781        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
782        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
783        For experiment offline_exf_seaice, this means on a linux box with gfortran
784        nearly a factor of 10 (but keep in mind there is mostly seaice code in
785        this experiment):
786        > size mitgcmuv_ad
787        text    data        bss     dec        hex
788        5100659 1216  220458952  225560827  d71c8fb
789        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
790        but only a moderate increase of 36% for global_ocean.cs32x15:
791        text    data        bss     dec        hex
792        6695027 1648 1014578664 1021275339 3cdf6ccb
793        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
794      - note: there are still recomputations in global_ocean.cs32x15 and
795        offline_exf_seaice and the gradient agreement changes (gets a
796        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
797      - in general, the AD gradients still are wrong
798    o OpenAD
799      - clean up code_oad/ directories somewhat by moving files
800        dontCompile, dontTransform, keepOriginal to OAD_support/
801    o model/src:
802      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
803        (not currently tested): add dissipation terms before NLFS rescaling of
804        tendencies (previously done after).
805    o pkg/diagnostics:
806      - write stats-diags in ascii file with more digits (same as in monitor).
807    o pkg/down_slope:
808      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
809        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
810    o model/src:
811      - new file "apply_forcing.F" containing all the code previously in
812        external_forcing.F, but with new argument list: pass, as new argument,
813        the current level tendency array to update (instead of a direct update
814        of the common bloc array). Change the corresponding calls.
815      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
816        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
817    o pkg/seaice/seaice_lsr, a little bit of clean up
818      - rearrange some code blocks, so that now all calculations for
819        setting up the right-hand-sides done within one single block
820        (I find that easier to read and understand)
821      - rearrange freedrift-code to reduce the number of ifdefs
822      - adjust some indentations and comments
823    
824    checkpoint64z (2014/07/10)
825    o model/src and several pkgs:
826      - change argument list of all S/R called from external_forcing.F and
827        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
828        to pass, as argument, the current level tendency array to update
829        (instead of a direct update of the common bloc array).
830      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
831      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
832    o pkg/seaice/seaice_lsr.F
833      - always initialize local arrays in seaice_lsr_tridiagu/v
834      - add more local tapes to seaice_lsr_tridiagu/v
835      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
836        keep it in bi/bj loop; this seems to be essential
837      - gradients are still wrong but only by 4-7 orders of magnitude
838        instead of 15 orders of magnitude, lab_sea improves a little
839    o pkg/seaice
840      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
841        generates unnecessary code in seaice_lsr_ad
842      - add more store directives in seaice_lsr to avoid unnecessary code
843        in seaice_lsr_ad
844      - exclude some residual computations in seaice_lsr when
845        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
846        in seaice_lsr_ad
847      - add more storing, a new tape (model/src/the_main_loop.F) and
848        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
849        and klockey should be checked by a specialist)
850      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
851        and update lab_sea after previous changes in pkg/seaice below
852    o pkg/autodiff:
853      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
854        viscFacInAd : run time parameters allowing for adjoint switches
855        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
856    o pkg/ecco:
857      - introduce cost_gencost_boxmean.F that computes a box mean
858        temperature (for use in adjoint sensitivity studies).
859    o model/src/set_defaults.F : initialize viscFacAdj to 1.
860    o pkg/mom_common/mom_calc_visc.F:
861      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
862    o pkg/seaice/seaice_summary.F:
863      - statement for SEAICEadjMODE now in autodiff_readparms.F
864    o pkg/seaice:
865      - remove some store directives and add new ones in an effort to get
866        finally rid off the recomputation warnings. This is successful
867        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
868        defined (i.e. no extensive recomputation warnings left), but there
869        are still too many recomputations on the solver iteration level
870      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
871      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
872        SEAICE_SIZE.h
873      - add a store directive in S/R seaice_calc_viscosities
874    o pkg/seaice (ITD code):
875      - fix definition of Hlimit for multi-threaded case
876      - use double precision arithmetic to compute Hlimit: this affects results;
877        update output of experiment seaice_itd.
878    o replace content of verification/seaice_itd
879      - instead of a 1D column use the configuration of offline_exf_seaice
880        to test the ice thickness distribution code with ridging
881      - this is a first shot at this experiment
882      - change of some defaults of ridging parameters SEAICEhStar (from
883        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
884        and lot of new comments.
885    
886    checkpoint64y (2014/06/20)
887    o pkg/seaice/seaice_reg_ridge.F:
888      - modify the regularization of very small volumes of ice; only check
889        total volume HEFF, and do not apply correction to individual ice
890        classes because that leads to funny patterns in the heat and fw-fluxes
891        into the ocean. Adjust seaice_itd/results/output.txt
892      - replace nITD by SEAICE_multDim in loop-ranges
893    o pkg/exf:
894      - add code to process the case field period = -12. with UV interpolation.
895      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
896        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
897    o verification/global_with_exf:
898      - switch all fields period to -12. (was previously untested) in input/data.exf
899        (but keep secondary test ".yearly" unchanged); update the reference output.
900    o pkg/cal:
901      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
902    o pkg/exf:
903      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
904        to replace logical switch "exf_verbose"
905      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
906    o pkg/sbo:
907      - update from Katherine Quinn: evaluate mass directly from density and SSH
908        (budget using Finite Volume method) instead of from bottom pressure.
909      - allow testreport to collect few selected SBO output ; tested in exp.
910        global_ocean.90x40x15 (after updating the results, to include SBO output).
911      - fix some multi-threading issues (in output part).
912  o model/src & most packages:  o model/src & most packages:
913    - always call {PKG}_READPARMS even if corresponding use{PKG}=F;    - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
914    - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R    - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
# Line 13  o model/src & most packages: Line 918  o model/src & most packages:
918      + call LAND_READPARMS from packages_readparms.F      + call LAND_READPARMS from packages_readparms.F
919  o pkg/seaice:  o pkg/seaice:
920    - remove code that resets useThSice in S/R seaice_readparms and    - remove code that resets useThSice in S/R seaice_readparms and
921      replace by a warning in S/R seaice_check      replace it by a warning in S/R seaice_check
922    - remove parameter MULTDIM, replace with nITD and runtime    - remove parameter MULTDIM, replace with nITD and runtime
923      parameter SEAICE_multDim (still hard-wired to nITD if      parameter SEAICE_multDim (still hard-wired to nITD if
924      SEAICE_ITD is defined)      SEAICE_ITD is defined)
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