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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2169 by heimbach, Fri Jul 3 21:36:38 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 OpenAD
8     - Adding preliminary ggl90 test to OpenAD verification.
9       Config. with ggl90 currently diverges after 64 time steps
10       so will need more work to become more stable
11     - Merge and update from Krishna Narayanan's contrib area:
12       * Add one variable for preliminary OpenAD DIVA
13       * Add replacement time-stepping for OpenAD DIVA
14       * genmake2 flag -diva (but only for OpenAD; preliminary)
15       * required modifs for OAD_support
16       successful preliminary test for tutorial_global_oce_biogeo/
17    o pkg/seaice:
18     - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
19     - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
20       delta with a smooth function in s/r seaice_calc_viscosity
21       (no effect on EVP)
22     - rename local suffix "sqr" into "sq" for more consistent variable names
23    o pkg/seaice: add new parameter SEAICE_deltaMin that is used ***only***
24      for regularizing Delta (and nothing else, like the parameter
25      which is also used for all sorts of things SEAICE_EPS). Defaults to
26      SEAICE_EPS for backward compatibility only.
27    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
28      the wrong key by inialising it before use -> fixes a recomputation
29      problem but does not fix the gradient
30    o pkg/layers:
31      - move resetting of flux arrays to outside the iLa loop
32        (this caused layers_diapycnal to not work with more than one layer coord.)
33      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
34    o pkg/layers:
35      - remove from common block 3D layers fields (used to diagnose transport
36        in tracer coords) and declare them as local arrays in layers_calc.F
37    o pkg/seaice:
38      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
39        in lab_sea forward experiment (changes results -> updated)
40      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
41    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
42      computations; for SEAICE_VECTORIZE_LSR
43      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
44        sweep to the outside,
45      - remove store directives and add "CADJ loop sequential" directives
46        in analogy to model/src/solve_tridiagonal.F
47      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
48        boundaries to yield more readable code. This has also the charming side
49        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
50        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
51        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
52        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
53        an additional option)
54       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
55       but the adjoint gradients (which are affected by this change) still explode.
56    o coupler (atm & ocn _compon_interf):
57      - avoid using Exch2 IO mapping if not suitable.
58    
59    checkpoint65m (2015/06/15)
60    o pkg/layers:
61      - clean-up old parameters setting (from Sep 2012):
62        + remove old parameters setting from common block (declared locally);
63        + stop if any old parameter is mixed with new parameters;
64        + check for valid or consistent parameter setting (e.g., layers_name)
65      - check that layers_bounds for Pot.Density are in the right range;
66        this is supposed to catch un-updated setting after recently shifting
67        potential density field "prho" by -1000 (now in "sigma" scale).
68    o pkg/layers:
69      - Added missing call to layers_fill for keeping track of tottend in
70        pkg/diagnostics/diagnostics_fill_state.F
71    o pkg/layers:
72      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
73        of diapycnal fluxes
74    o pkg/layers:
75      - reverted changes to interpolation to previous treatment; there
76        was never actually a problem
77    o pkg/layers:
78      - fix interpolation of layers tracers in the presence of partial cells
79      - add lots of new functionality to compute water mass transformation
80        (enabled by CPP flag LAYERS_THERMODYNAMICS)
81      - add new calls from main code (diags_oceanic_surf_flux.F,
82        thermodynamics.F, impldiff.F) and gad to save the necessary fields
83        for layers_thermodynamics calculations
84    o pkg/ptracers:
85      - add capability of stepping a passive tracer forward without advection
86        by setting PTRACERS_advScheme to 0.
87    o pkg/diagnostics:
88      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
89    o pkg/layers:
90      - shift potential density field "prho" by -1000 for density layer averaging so
91        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
92        Note that density bin boundaries (layers_bounds in data.layers) have
93        to be set accordingly (i.e., shifted, in sigma scale).
94    o pkg/layers:
95      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
96      - fix calculation of layer non-weighted velocity and layer probability
97      - add diagnostics for pot.density used for layer averaging
98    o pkg/seaice:
99      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
100        positiveness, modify a few comments and improve variable names,
101      - the changed computation of deltaC affects most seaice-related
102        experiments at the truncation level.
103        seaice_itd.thermo is affected by far the most, with
104        only 7 digits of agreement remaining; update experiments.
105    
106    checkpoint65l (2015/05/04)
107    o pkg/shelfice:
108      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
109        factor drKp1 to zero where it is negative (ie. do not use
110        SHELFICEBoundaryLayer if hFacC>1)
111      - the same for factor drLoc in shelfice_forcing.F
112    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
113        with modules in ptracers, when using testreport option "-small_f"
114    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
115      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
116    o verification/testreport
117      - add new option -small_f
118        with this option testreport first makes the target small_f (*.f files)
119        before running make (all). This is useful for explicit inlining when
120        all sources need to be full available.
121    o pkg/exf/exf_interp.F:
122        remove previous changes related to reverse (decreasing) input grids latitude
123    
124    checkpoint65k (2015/04/01)
125    o pkg/ecco:
126        fix missing cosphi initialization; use eccoiter in place of optimcycle;
127        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
128        instead of active read/write
129    o pkg/ctrl:
130        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
131        instead of active read/write.
132    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
133        return if .NOT.useAUTODIFF
134    o pkg/seaice: add CPP brackets (cost function related).
135    o model/src:
136        add useAUTODIFF run time switch.
137    o pkg/exf/exf_interp.F:
138        add code to allow input grids with latitude starting in the north (i.e. when
139        j=1 corresponds to northern edge of field); modify global_with_exf to test
140        this feature.
141    o verification/testreport:
142      - replace "grep -A3" with POSIX conformal sed command, because there are
143        implementations of grep that cannot do contextual searches
144      - replace "cat -n" by "nl" (two occurrences), because not all implementations
145        of "cat" have the option "-n"
146    o model/src:
147        add new file gsw_teos10.F that contains 3 functions, more or less a copy
148        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
149        convert from conservative to potential temperature. For now they are not
150        called anywhere.
151    o pkg/ggl90: make "useIDEMIX" useful
152      - re-organize code in s/r ggl90_calc a little to move computations that
153        are different for idemix into separate loops (changes verification
154        experiment idemix at truncation level, 12 digits remain -> updated)
155      - requires 2 new 2D fields KappaM, verticalShear
156      - make hFacI and recip_hFacI local 3D variables that are passed to
157        s/r ggl90_idemix
158      - fix and improve some comments
159    
160    checkpoint65j (2015/02/25)
161    o pkg/openad
162      - synchronize seawater.F with version in model/src: replace routine
163        body of sw_temp by calling sw_ptmp and fix/add a few comments.
164    o pkg/mnc:
165      - change default value of pickup_read/write_mnc params to FALSE
166        (since few features are missing in reading MNC pickup files).
167    o model/src:
168      - change default (background) vertical diffusivity for salt to be the
169        temperature (background) vertical diffusivity.
170      - change background vertical diffusivity in vertical mixing pkgs ggl90,
171        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
172        This makes ptracers default diffusivity (that uses salt diffKr) more
173        consistent with vertical mixing schemes.
174    o verification/testreport:
175      - fix typo in "-pcls" option ;
176      - put temp files in /tmp (instead of in local dir)
177      - add option "-ncad" to use genmake2 new option "-nocat4ad"
178      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
179    o pkg/ggl90 (idemix code):
180      - apply few fixes ; add some missing "_d 0" ; update output of exp.
181        global_ocean.90x40x15.idemix
182    o OpenAD
183      - enable active file I/O and begin removal of work-around code
184        for OpenAD for handling control variables (memory vs. active files)
185      - new CPP options file OPENAD_OPTIONS.h
186      - revert to genarr2d gradient check for hs94.1x64x5
187      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
188      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
189    o tools/genmake2:
190      - add option for an alternative Makefile (from Martin) where multiple
191        source files are sent to TAF (instead of all in one file).
192    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
193      - code provided by Carsten Eden as an extension of ggl90
194      - so far the code is turned on within ggl90 by setting a CPP-flag at
195        compile time; a runtime flag implementation is not yet complete
196      - tested in new verification experiment global_ocean.90x40x15.idemix
197    o verification:
198      - reduce length of the AD test run by half for experiments
199        global_ocean.cs32x15 (std + thsice) and isomip
200      - enable active file I/O for OpenAD, adjust verifications accordingly
201      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
202    o verification/testreport:
203      - fix two non-POSIX sed statements so that there are no error messages
204        on Mac OS X
205      - replace hostname -s with hostname | sed 's/\..*$//'
206    o model/src/seawater.F:
207      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
208        (following the matlab code), which would have avoided the bug caught
209        by Matt (see below) in the first place
210    o pkg/shelfice:
211      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
212        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
213      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
214        ice-shelf case (i.e., within surface level).
215      - add config summary in shelfice_check.F
216      - remove global variable recip_SHELFICElatentHeat and replace by a local
217        variable recip_latentHeat
218      - introduce diagnostics for friction velocity uStar (in case of
219        SHELFICEuseGammaFrict)
220      - change verification experiment isomip.htd:
221        + start from pickup (as input_ad at nIter0=8640)
222        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
223        + test SHELFICEuseGammaFrict = .TRUE.
224        + test SHELFICEadvDiffHeatFlux = .TRUE.
225    o model/src:
226      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
227        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
228        update output of experiments global_with_exf.yearly and isomip (all 6).
229    o pkg/shelfice:
230      - change setting of kTopC to also be zero where there is no ice-shelf.
231      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
232        ice-shelf is.
233      - first attempt to get RealFreshWaterFlux effects: for now, only without
234        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
235    o pkg/seaice: add the option to prescribe a fixed thickness PDF
236      for thermodynamic calculations
237      - because of divisions of the type 7/7 not exactly equal to 1, this change
238        affects results of some verification experiments by up to 4 digits:
239        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
240        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
241        adjoint: lab_sea, lab_sea.noseaicedyn
242        -> updated
243    
244    checkpoint65i (2015/01/23)
245    o model/src:
246      - change units of frictionHeating field from W to W/m^2
247      - fix bug in frictional heating from stratospheric drag in
248        S/R ATM_PHYS_TENDENCY_APPLY_V
249      - with synchronous time-stepping: move resetting to zero of frictionHeating
250        field from load_fields_driver.F to thermodynamics.F ;
251      - add diagnostics for frictional heating.
252    o model/src & gmredi K3D:
253      - add frictionHeating field to pickup-files (for synchronous time-stepping)
254      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
255      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
256        and name in pickup file).
257      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
258    o model/src:
259      - move (from ini_forcing.F) initialisation of all arrays in header file
260        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
261        (since Nov 2012) with option selectAddFluid=1.
262    o pkg/shelfice:
263      - change units (+ document) of newly added field "shelfIceMassDynTendency"
264      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
265    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
266    o pkg/seaice: two new runtime parameters:
267      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
268        long overdue
269      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
270        parameterization of tensil stress for fast ice (does not do anything yet)
271    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
272        for LSR: move checking overlaps out of JFNK-if-block
273    o pkg/atm_phys:
274      - move copy of grid and dynamical fields out of atm_phys_driver.F into
275        new S/R ATM_PHYS_DYN2PHYS.
276      - fix level height for Linear Free-Surf case (to be consistent with
277        fixed-in-time pressure levels).
278    o pkg/mom_common (bottomdrag):
279      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
280        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
281        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
282    o pkg/shelfice (u/v_drag):
283      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
284      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
285        (now similar to shelfice_u_drag.F)
286      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
287        from mom_vecinv.F (similar to mom_fluxform calls).
288    o pkg/mom_common (bottomdrag):
289      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
290      - add options for alternative discretisation of velocity norm in quadratic
291        bottom drag: averaging of grid-cell-center KE to U.point and V.point
292        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
293        improves when averaging only the other component (e.g. vVel for U bottom
294        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
295      - add options (bottomVisc_pCell) to account for partial-cell in bottom
296        friction (no-slip BC) thus getting the true distance from the bottom;
297        off by default since this also reduces model stability (explicit bottom
298        friction). Changes produce different machine truncation with linear-drag
299        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
300        front_relax (bvp & mxl, 10 & 11 digits).
301    o model/src & mom pkgs:
302      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
303        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
304      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
305        just copy level Nr value to level Nr+1.
306    o doc:
307      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
308    o pkg/streamice:
309      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
310        SHELFICE.h: move array shelficemass to init_varia, initialise
311        from array shelficemassinit, which is set in init_fixed and
312        has option to be set from file; introduce array
313        shelficeMassDynTend array, set thru file in init_fixed
314      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
315        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
316        pkg/streamice
317      - shelfice_thermodynamics.F: call shelfice_step_icemass if
318        SHELFICEMassStepping = .true.
319      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
320    
321    checkpoint65h (2014/12/17)
322    o verification/global_ocean.90x40x15, global_ocean_ebm:
323      - update to generic controls.
324    o pkg/ctrl:
325      - ctrl_map_ini_genarr.F: test for igen>0
326      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
327      - move gentim2d part of ctrl_map_ini_genarr.F to
328        new separate routine : ctrl_map_ini_gentim2d.F
329      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
330        add time variable weights and cyclic controls (time mean,
331        seasonal cycle, etc) capabilities to gentim2d
332    o pkg/ecco:
333      - move reading of error, conversion to weights from
334        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
335    o global_oce_llc90, cs32:
336      - activte sbo.
337      - CTRL_SIZE.h : add maxCtrlProc.
338      - activate the new genctrl capabilities.
339      - update following reorganization of global_oce_input_fields.tar.gz  
340    o pkg/ctrl/ctrl_ad_diff.list:
341      - add missing ctrl_init_rec.f
342    o tools/OAD_support/keepOriginal:
343      - add ctrl_init_rec.F
344    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
345      - avoid recomputations of xx_gentim2d_dummy.
346    o momentum diagnostics:
347      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
348        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
349    o pkg/seaice/seaice_lsr.F:
350      - fix computation of BU/BV, make sure they are non-zero, only necessary
351        for cubed sphere exchanges and SEAICE_OLx/y>0.
352        This makes calling s/r fill_cs_corner_rl obsolete (removed).
353    o verification/global_ocean.cs32x15/input.seaice
354      - add test for strong implicit coupling and restricted addtive Schwarz
355        methods for LSR
356      - update results/output.seaice.txt
357    o verification/tutorial_global_oce_biogeo:
358      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
359        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
360        update output_adm,_oadm,_tlm.txt
361    o pkg/dic:
362      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
363      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
364        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
365    o verification/tutorial_global_oce_biogeo:
366      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
367        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
368        update output_adm,_oadm,_tlm.txt
369    o eesupp/src:
370      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
371        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
372    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
373      LSR (following Hutchings et al. 2004)
374      - introduce zetaZ as a global variable (requires adjustments in
375        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
376        in seaice_calc_viscosities.F
377      - new flag SEAICEuseStrImpCpl (default off)
378      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
379        momentum equations
380      - JFNK-solver (preconditioner) adjusted to allow using this method
381        (where it does not have any positive effect)
382    o pkg/seaice
383      - add overlap for restrictive additive Schwartz method also to LSR, but
384        turn it off by default (because it only seems to work for non-cubed
385        sphere/llc topologies)
386    o pkg/autodiff
387      - add extra exchanges in addummy_in_steppging also for mnc output
388    o pkg/seaice:
389      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
390        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
391    o pkg/obcs:
392      - add option to specify domain-connected piece Id along OB though files
393        (for now, only used to diagnose PhiVel; default =1 -> global correction)
394      - modify obcs_diag_balance.F to process each connected-part separately;
395        exclude OB where Id = 0 but keep the full divergence there (-> constant
396        Psi along this portion of OB and all inflow derived from grad(Phi))
397      - add example of OB-conect files in verification/so_box_biogeo/input.
398    o pkg/diagnostics:
399      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
400      a) use non zero matrix element across OB and solve for Phi 1 grid point
401         outside OB (i.e, where tracer OBCS are applied).
402      b) global imbalance of inFlow/outFlow across OB: instead of modifying
403         velocity across OB, spread it uniformly along the OB in the RHS.
404    
405    checkpoint65g (2014/11/19)
406    o pkg/diagnostcis:
407      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
408    o pkg/my82,pp81,kl10:
409      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
410        field diffKr as background diffusivity to set minimum diffusivity value.
411    o pkg/seaice:
412      - add new parameter SEAICEuseEVPrev (for revisited EVP by
413        Bouillon et al 2013)
414      - add SEAICE_evpAlpha/Beta to namelist
415      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
416        involve trivial re-ordering of divisions/multiplications that should not
417        have any effects, but ... they do change the results of lab_sea.hb87 so
418        that only 2 digits of agreement remain, in line with the general
419        instability/fragility of the evp-code. For now, I do not care and just
420        update the verification experiment
421    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
422      - remove xx_genarr2d_numsmooth etc
423      - use xx_genarr2d_preproc etc instead
424      - carry out smooth_correl2D at initialization stage rather than during
425        time stepping.
426      - get smoothOpNb from xx_gentim2d_preproc
427    o global_oce_cs32 :
428      - add test of generic ecco capabilities.
429    o pkg/exf/exf_getsurfacefluxes.F :
430      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
431    o pkg/ctrl,ecco :
432      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
433        is defined.
434    o pkg/seaice: add diagnostics for Delta (deformation parameter)
435    o model/src:
436      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
437        diffusivity (background) is specified but ignored.
438    o verification:
439      - in testreport, convert hostname to lower case for default output dir name
440    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
441    o pkg/dic: add modifications from Hajoon:
442      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
443      - light attenuation: add self-shading effect by climatological Chlorophyll
444        (read from file).
445    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
446        compiles when SEAICE_ALLOW_DYNAMICS is undefined
447    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
448        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
449        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
450        approach where CPP_OPTIONS.h includes an omnipotent
451        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
452    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
453        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
454    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
455        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
456        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
457    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
458      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
459      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
460      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
461      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
462    o pkg/ctrl,ecco,exf :
463      - remove variables associated with NON-generic costs,
464        unless ECCO_CTRL_DEPRECATED is defined.
465      - remove NON-generic NON-obcs controls,
466        unless ECCO_CTRL_DEPRECATED is defined.
467    o pkg/ctrl : added ctrl_local_params.h
468    o pkg/ecco : added ecco_local_params.h
469    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
470        experiments, which will progressively be removed once the
471        experiments are revised to use only generic controls/costs.
472    
473    checkpoint65f (2014/10/13)
474    o pkg/ctrl, ecco, seaice : minor changes in headers
475    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
476        cost function and control capabilities added since checkpoint65c.
477    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
478    o pkg/ecco: increase modularity and improve logic
479      - ecco_toolbox.F (new) : basic operations that are often used,
480        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
481        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
482      - cost_gencal.F (new) : determine filnames and records.
483      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
484      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
485        and exploit the above functions leading to more compact code.
486      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
487      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
488        using_ers, using_gfo, using_mdt is now only defined within gencost)
489    o pkg/ecco: extend generic cost capabilities
490      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
491        capabilities via gencost_preproc (+ _c,_i,_r related params),
492        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
493        gencost_outputlevel arguments to cost_generic
494      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
495        and active_read, making room for gencost_preproc to take effect.
496        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
497      - pkg/ecco/cost_generic.F :
498        compute and store misfit maks*(model-data) in localdif that is
499        then used in cost and for output, output misfit if outlev.GT.0
500      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
501        rather gencost_barfile for deciding whether to write barfile
502      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
503      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
504        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
505      - pkg/ecco/ecco_summary.F : report gencost variables
506      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
507    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
508    o pkg/ecco: internal re-organization
509      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
510        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
511        mv relevant variables definition from ecco_cost.h to ecco.h,
512        make sure gencost routines only include ecco.h)
513      - throughout : add missing CCP switches, rm unused variables,
514        and rm un-necessary CPP switches
515      - throughout gencost routines : replace modelstartdate with
516        gencost_startdate when needed
517      - cost_bp_read.F : use arguments, instead of common blocs
518        so that it can be used also by (new) cost_gencost_bpv4.F
519      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
520      - ecco_phys.F : compute etanFull
521      - ecco_readparms.F : rename using_topex as using_tpj, add
522        bpv4-grace to gencost list, initialize added parameters
523      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
524    
525    checkpoint65e (2014/09/28)
526    o pkg/obcs:
527      - replaced the just-added CPP options with run-time variables
528        (see pkg/obcs/OBCS_PARAMS.h for details)
529    o pkg/obcs:
530      - add additional CPP options for sponge boundary layers
531        (see pkg/obcs/OBCS_OPTIONS.h for details)
532    o pkg/atm_phys:
533      - implement simple (obliquity only, assuming circular planet orbit)
534        seasonal cycle for incoming insolation ; used when run-time parameter
535        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
536    o pkg/exf, pkg/ecco, pkg/ctrl:
537      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
538      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
539      - implement gentim2d for xx_tauu, xx_tauv
540    o pkg/ctrl, pkg/ecco :
541      - fix and complement the generic controls implementation
542    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
543        pkg/shelfice/shelfice_thermodynamics.F,
544        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
545        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
546      - add weight in CTRL_GET_GEN calls
547    o pkg/ctrl :
548      - ctrl_get_gen.F : add weight as input parameter, and apply
549        it directly rather than using smooth_correl2Dw (to be retired).
550      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
551    o pkg/ctrl :
552      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
553        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
554      - re-activate ctrl_summary (call in ctrl_init.F)
555    o pkg/ctrl/ctrl_cost_gen.F :
556      - fix CCP brackets, remove un-necessary myiter, mytime
557    o pkg/ecco, pkg/ctrl :
558      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
559      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
560      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
561      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
562    
563    checkpoint65d (2014/09/15)
564    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
565      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
566        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
567    o pkg/ctrl/ctrl_map_ini_genarr.F :
568      - remove compilation failure
569      - replace hard coded example
570      - use ctrl_map_ini_gen2D, 3D
571    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
572      - on/off switch based upon xx_genarr2d_weight,3d
573    o src/packages_init_variables.F :
574      - regroup pkg/estimation calls
575      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
576        (moved to ctrl_init_variables)
577    o cost/cost_init_varia.F :
578      - remove ecco_cost_init_varia
579        (moved to ecco_init_varia)
580    o ctrl/ctrl_init_variables.F :
581      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
582      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
583    o ctrl/ctrl_map_ini.F :
584      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
585        (moved to ctrl_init_variables)
586    o ctrl/ctrl_map_ini_ecco.F :
587      - remove ECCO_PHYS (mv to ecco_init_varia)
588      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
589    o ecco/ecco_ad_diff.list :
590      - add ecco_init_varia.f
591    o ecco/ecco_init_varia.F
592      - new routine
593    o pkg/streamice:
594      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
595        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
596      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
597    o pkg/generic_advdiff:
598      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
599    o pkg/exf:
600      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
601         xxg_precip capability
602      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
603    o pkg/ctrl:
604      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
605    o model/src/load_fields_driver.F :
606      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
607        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
608    o OpenAD verification experiments:
609      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
610        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
611        for now, only in pkgs used in OpenAD verification experiments.
612      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
613        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
614        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
615        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
616    o OpenAD verification tests:
617      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
618      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
619        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
620      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
621        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
622    o model/src & generic_advdiff:
623      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
624        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
625        dynamics requires valid tracer forcing only over tile interior but, for
626        some diagnostics, may need to extend it over 1 point in tile halo region.
627      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
628        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
629        setting in temp/salt/ptracer_integrate.F
630    o pkg/dic:
631      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
632        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
633        in gchem_forcing_sep.F
634    o pkg/autodiff & obcs:
635      - add storage of current OB values for U & V (was already done for T & S).
636    
637    checkpoint65c (2014/08/30)
638    o pkg/dic:
639      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
640        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
641        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
642    o verification:
643      - new experiment testing OBCS and DIC pkgs, using params & output from
644        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
645        passage: take OBCS from the last year of a 2 yrs simulation and initial
646        conditions from t=1.yr while keeping the same forcing.
647    o model/src:
648      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
649        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
650    o pkg/diagnostics (Stats-Diags):
651      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
652        a) refine region where stats are computed, excluding where arrhFac=0 ;
653        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
654        c) extend regional stats over the region edges (for U or V pt location).
655    o pkg/gchem:
656      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
657        pkg/dic is currently changing/updating ptracers values beyond the OB).
658    o verification (hs94):
659      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
660        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
661        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
662        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
663    o pkg/ptracers:
664      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
665        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
666      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
667        with AB-2 code (so that it get tested).
668    o model/src:
669      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
670        with AB-2 code (previously only available with AB-3 code).
671        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
672        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
673        there, by calling CYCLE_AB_TRACER).
674    o pkg/generic_advdiff:
675      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
676        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
677        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
678        S/R temp/salt/ptracers_integrate.F
679    o model/src & pkg/ptracers:
680      - remove common block variables gT,gS (in DYNVARS.h), except when
681         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
682      - remove common block variable gPtr.
683    o model/src & pkgs:
684      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
685         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
686         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
687         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
688      + change accordingly all calling S/R.
689      - use local temperature/salinity/ptracer tendency array (without bi,bj)
690        in S/R temp/salt/ptracers_integrate.F
691    o pkg/seaice:
692      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
693        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
694      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
695        in seaice_lsr
696      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
697        in s/r seaice_lsr_calc_coeffs
698    o pkg/mdsio:
699      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
700        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
701        too long (e.g., > MAX_LEN_FNAM/2 )
702    
703    checkpoint65b (2014/08/12)
704    o pkg/matrix:
705      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
706    o model/src:
707      - fix initialisation of geothermalFile; compile geothermal-flux code in
708        natl_box verification experiment.
709    o model/src & pkg/down_slope:
710      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
711      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
712        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
713        results at machine truncation level: update output of experiments
714        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
715    o pkg/diagnostics (Stats-Diags):
716      - do not cumulate the full volume when DIAGNOSTICS_FILL is
717        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
718        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
719        times (but Min,Max and StD are still wrong).
720    o model/src:
721      - add geothermal flux forcing: read in ini_forcing.F as time-constant
722        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
723    o model/src:
724      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
725        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
726        arrays are already updated while adjustments (filters, conv.adjustment) are
727        still applied later, in S/R TRACERS_CORRECTION_STEP.
728    o model/src:
729      - store in common bloc array "rhoInSitu" the virtual potential temperature
730        anomaly that is used to compute geopotential: this make the atmos code
731        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
732    o pkg/seaice/seaice_lsr.F
733      - rename integer variable ilcall to ipass (that's what it is called
734        in the residual diagnostics
735      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
736        default) for improved non-linear convergence of the first few steps
737      - adjust a few comments and add new ones to explain some of the store
738        directives
739    o pkg/generic_advdiff (& ptracers):
740      - re-work the code to check for valid advection scheme and for minimum
741        size of overlap (now stored in local common bloc in gad_advscheme.F)
742    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
743      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
744      - add an auxilliary variable "bet" and fix store directives and keys in
745        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
746        less exact gradients in my tests); but there are still
747        recomputation warning (although gradients are sort of OK), when
748        SEAICE_LSR_VECTORIZE is not defined, so this flag and
749        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
750      - update verification experiments lab_sea.
751      - change some comments in S/R seaice_calc_viscosities
752    o model/src:
753      - if staggerTimeStep=T, always apply exchange to velocity field in
754        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
755        (independent of using multi-dim advection or not); no effect on FWD run
756        but affects AD results (at machine truncation level): update output of
757        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
758        and isomip (oad: 12.d).
759    o pkg/generic_advdiff:
760      - stop if doAB_onGtGs is set to FALSE but ignored
761      - refine warning related to stability of tracer time-stepping
762        regarding internal wave dynamics.
763      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
764        on staggerTimeStep & implicitIntGravWave (will now get a warning
765        if potentially unstable).
766    o pkg/kl10:
767      - add new pkg "kl10" for mixing due to internal wave breaking, from
768        http://www.sciencedirect.com/science/article/pii/S1463500310000144
769        (contribution from Jody Klymak), tested in verification experiment
770        verification/internal_wave/input.kl10/
771    o isomip experiment:
772      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
773        (input.htd) and update the output.
774    o cd_code experiments:
775      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
776        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
777        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
778        update the corresponding output.
779    o pkg/seaice:
780      - reduce the number of include files and store directives in
781        S/R seaice_lsr_tridiagu/v
782      - change the order of loops in one case in S/R seaice_lsr_tridiagv
783        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
784        get rid off one store directive (a TAF bug?)
785      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
786        S/R seaice_lsr_tridiagv to change the loop range for consistency
787      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
788      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
789        S/R seaice_lsr_tridiagu/v (requires update of
790        offline_exf_seaice/input.dyn_jfnk)
791    
792    checkpoint65a (2014/07/27)
793    o model/src:
794      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
795        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
796        (topo in p-coords, ice-shelf in z-coords); update output of experiments
797        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
798    o model/src:
799      - collect momentum forcing tendency into local 2-D array (passed as argument
800        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
801        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
802        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
803      - collect T & S forcing tendency into local 2-D array (passed as argument to
804        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
805        affects results at machine truncation level (e.g., ocean: if using
806        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
807        correction due to vertical advection).
808      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
809        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
810        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
811        obcs_ctrl (ad & fwd grd @ 12 & 7).
812    o pkg/ptracers & diagnostics:
813      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
814        title (to avoid some unexpected truncation); sort out ptracers diags units.
815      - collect ptracer forcing tendency into local 2-D array (passed as argument
816        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
817    
818    checkpoint65 (2014/07/18)
819    o pkg/fizhi:
820      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
821        affects results at machine truncation level. Update output of experiments
822        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
823    o pkg/seaice: more clean up
824      - rename TAF common block tapes to be more consistent and remove
825        unnecessary duplicates
826      - add store directives to remove more recomputations, but use smaller
827        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
828        The idea behind this flag is to reduce the memory footprint when the
829        adjoint of the LSR is not required. As of now, defining the flag
830        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
831        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
832        For experiment offline_exf_seaice, this means on a linux box with gfortran
833        nearly a factor of 10 (but keep in mind there is mostly seaice code in
834        this experiment):
835        > size mitgcmuv_ad
836        text    data        bss     dec        hex
837        5100659 1216  220458952  225560827  d71c8fb
838        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
839        but only a moderate increase of 36% for global_ocean.cs32x15:
840        text    data        bss     dec        hex
841        6695027 1648 1014578664 1021275339 3cdf6ccb
842        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
843      - note: there are still recomputations in global_ocean.cs32x15 and
844        offline_exf_seaice and the gradient agreement changes (gets a
845        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
846      - in general, the AD gradients still are wrong
847    o OpenAD
848      - clean up code_oad/ directories somewhat by moving files
849        dontCompile, dontTransform, keepOriginal to OAD_support/
850    o model/src:
851      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
852        (not currently tested): add dissipation terms before NLFS rescaling of
853        tendencies (previously done after).
854    o pkg/diagnostics:
855      - write stats-diags in ascii file with more digits (same as in monitor).
856    o pkg/down_slope:
857      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
858        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
859    o model/src:
860      - new file "apply_forcing.F" containing all the code previously in
861        external_forcing.F, but with new argument list: pass, as new argument,
862        the current level tendency array to update (instead of a direct update
863        of the common bloc array). Change the corresponding calls.
864      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
865        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
866    o pkg/seaice/seaice_lsr, a little bit of clean up
867      - rearrange some code blocks, so that now all calculations for
868        setting up the right-hand-sides done within one single block
869        (I find that easier to read and understand)
870      - rearrange freedrift-code to reduce the number of ifdefs
871      - adjust some indentations and comments
872    
873    checkpoint64z (2014/07/10)
874    o model/src and several pkgs:
875      - change argument list of all S/R called from external_forcing.F and
876        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
877        to pass, as argument, the current level tendency array to update
878        (instead of a direct update of the common bloc array).
879      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
880      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
881    o pkg/seaice/seaice_lsr.F
882      - always initialize local arrays in seaice_lsr_tridiagu/v
883      - add more local tapes to seaice_lsr_tridiagu/v
884      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
885        keep it in bi/bj loop; this seems to be essential
886      - gradients are still wrong but only by 4-7 orders of magnitude
887        instead of 15 orders of magnitude, lab_sea improves a little
888    o pkg/seaice
889      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
890        generates unnecessary code in seaice_lsr_ad
891      - add more store directives in seaice_lsr to avoid unnecessary code
892        in seaice_lsr_ad
893      - exclude some residual computations in seaice_lsr when
894        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
895        in seaice_lsr_ad
896      - add more storing, a new tape (model/src/the_main_loop.F) and
897        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
898        and klockey should be checked by a specialist)
899      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
900        and update lab_sea after previous changes in pkg/seaice below
901    o pkg/autodiff:
902      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
903        viscFacInAd : run time parameters allowing for adjoint switches
904        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
905    o pkg/ecco:
906      - introduce cost_gencost_boxmean.F that computes a box mean
907        temperature (for use in adjoint sensitivity studies).
908    o model/src/set_defaults.F : initialize viscFacAdj to 1.
909    o pkg/mom_common/mom_calc_visc.F:
910      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
911    o pkg/seaice/seaice_summary.F:
912      - statement for SEAICEadjMODE now in autodiff_readparms.F
913    o pkg/seaice:
914      - remove some store directives and add new ones in an effort to get
915        finally rid off the recomputation warnings. This is successful
916        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
917        defined (i.e. no extensive recomputation warnings left), but there
918        are still too many recomputations on the solver iteration level
919      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
920      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
921        SEAICE_SIZE.h
922      - add a store directive in S/R seaice_calc_viscosities
923    o pkg/seaice (ITD code):
924      - fix definition of Hlimit for multi-threaded case
925      - use double precision arithmetic to compute Hlimit: this affects results;
926        update output of experiment seaice_itd.
927    o replace content of verification/seaice_itd
928      - instead of a 1D column use the configuration of offline_exf_seaice
929        to test the ice thickness distribution code with ridging
930      - this is a first shot at this experiment
931      - change of some defaults of ridging parameters SEAICEhStar (from
932        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
933        and lot of new comments.
934    
935    checkpoint64y (2014/06/20)
936    o pkg/seaice/seaice_reg_ridge.F:
937      - modify the regularization of very small volumes of ice; only check
938        total volume HEFF, and do not apply correction to individual ice
939        classes because that leads to funny patterns in the heat and fw-fluxes
940        into the ocean. Adjust seaice_itd/results/output.txt
941      - replace nITD by SEAICE_multDim in loop-ranges
942    o pkg/exf:
943      - add code to process the case field period = -12. with UV interpolation.
944      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
945        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
946    o verification/global_with_exf:
947      - switch all fields period to -12. (was previously untested) in input/data.exf
948        (but keep secondary test ".yearly" unchanged); update the reference output.
949    o pkg/cal:
950      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
951    o pkg/exf:
952      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
953        to replace logical switch "exf_verbose"
954      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
955    o pkg/sbo:
956      - update from Katherine Quinn: evaluate mass directly from density and SSH
957        (budget using Finite Volume method) instead of from bottom pressure.
958      - allow testreport to collect few selected SBO output ; tested in exp.
959        global_ocean.90x40x15 (after updating the results, to include SBO output).
960      - fix some multi-threading issues (in output part).
961    o model/src & most packages:
962      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
963      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
964        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
965        "data.{pkg}" exist ; and leave the S/R (return) just after.
966      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
967        + call LAND_READPARMS from packages_readparms.F
968    o pkg/seaice:
969      - remove code that resets useThSice in S/R seaice_readparms and
970        replace it by a warning in S/R seaice_check
971      - remove parameter MULTDIM, replace with nITD and runtime
972        parameter SEAICE_multDim (still hard-wired to nITD if
973        SEAICE_ITD is defined)
974    
975    checkpoint64x (2014/05/24)
976    o verification/lab_sea:
977      - update adjoint and TLM output following changes to pkg/salt_plume
978      - un-do the update after putting back local recip_Cp in few places.
979    o pkg/salt_plume: modifications by An Nguyen:
980      - add capability to do brine rejection (salt-plume) as function of
981        volume+tracers (instead of only salinity tracer).
982      - conserve volume by exchanging volume from each kLev to above to
983        accommodate in-coming brine volume
984      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
985      - switch KPP surf buoyancy due to brine forcing to 3-d
986        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
987      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
988      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
989        in East/West Arctic.
990    o pkg/sbo:
991      - incorporate modifications from Katherine Quinn to enable the use of sbo
992        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
993        output for future testreport verification (unfinished).
994    o pkg/atm_phys:
995      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
996        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
997        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
998    o pkg/seaice
999      seaice_calc_ice_strength.F: modify expression to avoid divisions
1000        (affects truncation)
1001      seaice_do_ridging.F: clean up the insectarium
1002      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1003      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1004      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1005      - add some debugging information and error messages (warnings)
1006    o model/src: modifications relatd to atmosphere p*:
1007      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1008      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1009        of vertical profile tRef in geopotential background and anomaly.
1010      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1011        and pkg/atm_phys.
1012      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1013        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1014    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1015    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1016        not used right now, but can be used in BGC packages to fix conservation.
1017    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1018        other packages too.
1019    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1020        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1021    o model/src:
1022      - since we have several heat capacity (even in model/src), define "recip_Cp"
1023        as local variable (no longer in common block) to avoid any confusion.
1024      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1025    o pkg/exf:
1026      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1027        air density as function of air Temp, Humidity and atm pressure.
1028    
1029    checkpoint64w (2014/05/02)
1030    o verification:
1031      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1032        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1033        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1034        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1035        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1036    o model/src: for atmosphere in p* coords:
1037      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1038      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1039        but not yet activated.
1040    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1041      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1042      - this changes the results (but not for any verification experiment, because
1043        none tests this), but avoids having an extra field in the restart files
1044    o pkg/seaice: remove global variable TICE (not needed)
1045      - replace by TICES or local variable where necessary (cost_seaice_test,
1046        seaice_diagnostics_state)
1047      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1048      - use specific read/write routines for reading and writing individual leves
1049        of a multilevel field
1050    o pkg/ctrl & model/inc:
1051      - move additional anomaly fields of control vars (related to options:
1052         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1053        from DYNVARS.h into new header file: CTRL_FIELDS.h
1054    o pkg/seaice: some small modifications to the ridging code
1055      - make fw2ObyRidge a global variable and add the freshwater flux to
1056        seaice_growth
1057      - pass actual thickness from seaice_prepare_ridging, so that it is
1058        computed only in one place and compute it in the same way as in
1059        seaice_growth
1060      - initialise more fields in seaice_do_ridging that where cause floating
1061        point exceptions over land
1062  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1063    - move most of "PART 1" of S/R seaice_growth into a new and separate    - move most of "PART 1" of S/R seaice_growth into a new and separate
1064      S/R seaice_reg_ridge that will both regularize the state variable after      S/R seaice_reg_ridge that will both regularize the state variable after
1065      advection call the actual ridging routine;      advection call the actual ridging routine;
1066    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1067      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1068    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1069    - clean up remaining part 1 of seaice_growth in an attempt to make it    - clean up remaining part 1 of seaice_growth in an attempt to make it
1070      more readable (this is probably subjective)      more readable (this is probably subjective)
1071    - call seaice_itd_redist once in the initialisation phase to have the initial    - call seaice_itd_redist once in the initialisation phase to have the initial
1072      conditions in the correct category      conditions in the correct category
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