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revision 1.2000 by mlosch, Tue May 27 15:27:14 2014 UTC revision 1.2186 by jmc, Tue Oct 13 22:11:12 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o pkg/seaice:  o pkg/exf:
8      - remove STOP statement that prevented to use wind or (wind-)stress
9        interpolation for constant-in-time forcing fields (wind/stress period = 0).
10    o pkg/seaice:
11      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
12        5 additionals 2D fields and 6 new store directives
13      - change logic in seaice_readparms.F: EVP code can now be turned on in
14        various ways, setting SEAICE_deltaTev is no longer required,
15        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
16        or SEAICEaEVPcoeff
17    o pkg/shelfice/shelfice_thermodynamics.F
18      - redefining uLoc/vLoc to u/v, instead of 2u/v
19    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
20      - this is an intermediate state of a truely converging EVP that has
21        the potential of outperforming implicit VP methods, I do not recommend
22        using it yet.
23      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
24        and all parameters are hardwired
25      - for convergence it still requires very smooth regularisations, that means,
26        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
27        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
28        specific averaging appears to be required, still subject to tuning
29      - still needs cleaning and I need to turn parameter into runtime parameters
30      - add code to compute and print residuals of iteration, compile with
31        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
32    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
33      that entered with r1.54 on Sep04, 2015, -> update results
34    
35    checkpoint65o (2015/09/14)
36    o pkg/mom_vecinv & mom_common:
37      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
38        called from there.
39      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
40        allows to use Vector-Invariant form in deep atmos and anelastic formulation
41    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
42      and Koenig-Beatty+Holland (2012)
43      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
44      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
45      - requires an extra input argument for S/R seaice_calc_viscosities
46      - tensileStrength's depth dependence is different from Itkin et al. (2015)
47        (to be changed and played with, for now exponential)
48    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
49      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
50        by AREA according to Connelly et al. (2004), JPO.
51      - For EVP and the LSR solver, the implicit part of the drag term is
52        the only non-zero term in the denominator when there is no ice (which
53        prevented running the model with zero ice-ocean drag). If
54        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
55        (or zero main diagonals BU/BV) which need to be caught. A practical
56        consequence is that for open water, the momentum equation reduce
57        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
58        they happen to be zero, often leading to a non-zero solution over
59        open water.
60    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
61        efficient EVP method.
62      - introduce area-weighted averages for e12 (analogously to
63        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
64        remain, but also changing the order of terms in the previous average
65        changed the results as much) -> update experiment
66      - add SEAICE_DELTA_SMOOTHREG code
67      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
68        TEM-code
69      - adjust loop bounds so that only required fields are computed
70      - add new averaging code for zetaZ/deltaZ (again similar to
71        seaice_calc_viscosities.F), inactive by default for now (will change
72        results again), but will replace old code eventually
73    o eesupp/src:
74      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
75        to always cumulate tile local-sum in the same order
76        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
77        Still uses MPI_Allreduce (like standard code) but on array of tiles
78        and should be faster than GLOBAL_SUM_SEND_RECV code.
79      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
80        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
81      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
82         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
83         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
84         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
85         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
86    
87    checkpoint65n (2015/07/29)
88    o pkg/thsice:
89      - add a warning when used with pkg/aim but without updating SST
90        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
91    o pkg/offline:
92      - change where Offline-Fields are loaded, from load_fields_driver.F to
93        directly within FORWARD_STEP, just after updating iter number and time;
94      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
95        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
96       These changes allow:
97        a) to recover exactly on-line results using deltaToffline=deltaTClock,
98        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
99        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
100        time-step, both with GM & KPP files and with recomputing these fields;
101        b) no needs to switch on staggerTimeStep anymore;
102        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
103      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
104    o pkg/offline:
105      - change (rarely used) offset-iteration parameter to an offset time (in s):
106        can easily recover previous offset-iter effect by setting offset-time
107        (offlineTimeOffset) to offset-iter x deltaToffline;
108      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
109        in KPP as part of surface buoyancy forcing) in offline run.
110      - fix ptracers KPP non-local term in the case where KPP is re-computed.
111    o OpenAD
112      - Adding preliminary ggl90 test to OpenAD verification.
113        Config. with ggl90 currently diverges after 64 time steps
114        so will need more work to become more stable
115      - Adding preliminary kpp test to OpenAD verification.
116        required small tweakes in kpp_routines.F
117      - Merge and update from Krishna Narayanan's contrib area:
118        * Add one variable for preliminary OpenAD DIVA
119        * Add replacement time-stepping for OpenAD DIVA
120        * genmake2 flag -diva (but only for OpenAD; preliminary)
121        * required modifs for OAD_support
122        successful preliminary test for tutorial_global_oce_biogeo/
123    o pkg/seaice:
124      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
125      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
126        delta with a smooth function in s/r seaice_calc_viscosity
127        (no effect on EVP)
128      - rename local suffix "sqr" into "sq" for more consistent variable names
129    o pkg/seaice:
130        add new parameter SEAICE_deltaMin that is used ***only***
131        for regularizing Delta (and nothing else, like the parameter
132        which is also used for all sorts of things SEAICE_EPS).
133        Defaults to SEAICE_EPS for backward compatibility only.
134    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
135        the wrong key by inialising it before use -> fixes a recomputation
136        problem but does not fix the gradient
137    o pkg/layers:
138      - move resetting of flux arrays to outside the iLa loop
139        (this caused layers_diapycnal to not work with more than one layer coord.)
140      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
141    o pkg/layers:
142      - remove from common block 3D layers fields (used to diagnose transport
143        in tracer coords) and declare them as local arrays in layers_calc.F
144    o pkg/seaice:
145      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
146        in lab_sea forward experiment (changes results -> updated)
147      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
148    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
149       computations; for SEAICE_VECTORIZE_LSR
150      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
151        sweep to the outside,
152      - remove store directives and add "CADJ loop sequential" directives
153        in analogy to model/src/solve_tridiagonal.F
154      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
155        boundaries to yield more readable code. This has also the charming side
156        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
157        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
158        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
159        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
160        an additional option)
161       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
162       but the adjoint gradients (which are affected by this change) still explode.
163    o coupler (atm & ocn _compon_interf):
164      - avoid using Exch2 IO mapping if not suitable.
165    
166    checkpoint65m (2015/06/15)
167    o pkg/layers:
168      - clean-up old parameters setting (from Sep 2012):
169        + remove old parameters setting from common block (declared locally);
170        + stop if any old parameter is mixed with new parameters;
171        + check for valid or consistent parameter setting (e.g., layers_name)
172      - check that layers_bounds for Pot.Density are in the right range;
173        this is supposed to catch un-updated setting after recently shifting
174        potential density field "prho" by -1000 (now in "sigma" scale).
175    o pkg/layers:
176      - Added missing call to layers_fill for keeping track of tottend in
177        pkg/diagnostics/diagnostics_fill_state.F
178    o pkg/layers:
179      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
180        of diapycnal fluxes
181    o pkg/layers:
182      - reverted changes to interpolation to previous treatment; there
183        was never actually a problem
184    o pkg/layers:
185      - fix interpolation of layers tracers in the presence of partial cells
186      - add lots of new functionality to compute water mass transformation
187        (enabled by CPP flag LAYERS_THERMODYNAMICS)
188      - add new calls from main code (diags_oceanic_surf_flux.F,
189        thermodynamics.F, impldiff.F) and gad to save the necessary fields
190        for layers_thermodynamics calculations
191    o pkg/ptracers:
192      - add capability of stepping a passive tracer forward without advection
193        by setting PTRACERS_advScheme to 0.
194    o pkg/diagnostics:
195      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
196    o pkg/layers:
197      - shift potential density field "prho" by -1000 for density layer averaging so
198        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
199        Note that density bin boundaries (layers_bounds in data.layers) have
200        to be set accordingly (i.e., shifted, in sigma scale).
201    o pkg/layers:
202      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
203      - fix calculation of layer non-weighted velocity and layer probability
204      - add diagnostics for pot.density used for layer averaging
205    o pkg/seaice:
206      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
207        positiveness, modify a few comments and improve variable names,
208      - the changed computation of deltaC affects most seaice-related
209        experiments at the truncation level.
210        seaice_itd.thermo is affected by far the most, with
211        only 7 digits of agreement remaining; update experiments.
212    
213    checkpoint65l (2015/05/04)
214    o pkg/shelfice:
215      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
216        factor drKp1 to zero where it is negative (ie. do not use
217        SHELFICEBoundaryLayer if hFacC>1)
218      - the same for factor drLoc in shelfice_forcing.F
219    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
220        with modules in ptracers, when using testreport option "-small_f"
221    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
222      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
223    o verification/testreport
224      - add new option -small_f
225        with this option testreport first makes the target small_f (*.f files)
226        before running make (all). This is useful for explicit inlining when
227        all sources need to be full available.
228    o pkg/exf/exf_interp.F:
229        remove previous changes related to reverse (decreasing) input grids latitude
230    
231    checkpoint65k (2015/04/01)
232    o pkg/ecco:
233        fix missing cosphi initialization; use eccoiter in place of optimcycle;
234        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
235        instead of active read/write
236    o pkg/ctrl:
237        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
238        instead of active read/write.
239    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
240        return if .NOT.useAUTODIFF
241    o pkg/seaice: add CPP brackets (cost function related).
242    o model/src:
243        add useAUTODIFF run time switch.
244    o pkg/exf/exf_interp.F:
245        add code to allow input grids with latitude starting in the north (i.e. when
246        j=1 corresponds to northern edge of field); modify global_with_exf to test
247        this feature.
248    o verification/testreport:
249      - replace "grep -A3" with POSIX conformal sed command, because there are
250        implementations of grep that cannot do contextual searches
251      - replace "cat -n" by "nl" (two occurrences), because not all implementations
252        of "cat" have the option "-n"
253    o model/src:
254        add new file gsw_teos10.F that contains 3 functions, more or less a copy
255        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
256        convert from conservative to potential temperature. For now they are not
257        called anywhere.
258    o pkg/ggl90: make "useIDEMIX" useful
259      - re-organize code in s/r ggl90_calc a little to move computations that
260        are different for idemix into separate loops (changes verification
261        experiment idemix at truncation level, 12 digits remain -> updated)
262      - requires 2 new 2D fields KappaM, verticalShear
263      - make hFacI and recip_hFacI local 3D variables that are passed to
264        s/r ggl90_idemix
265      - fix and improve some comments
266    
267    checkpoint65j (2015/02/25)
268    o pkg/openad
269      - synchronize seawater.F with version in model/src: replace routine
270        body of sw_temp by calling sw_ptmp and fix/add a few comments.
271    o pkg/mnc:
272      - change default value of pickup_read/write_mnc params to FALSE
273        (since few features are missing in reading MNC pickup files).
274    o model/src:
275      - change default (background) vertical diffusivity for salt to be the
276        temperature (background) vertical diffusivity.
277      - change background vertical diffusivity in vertical mixing pkgs ggl90,
278        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
279        This makes ptracers default diffusivity (that uses salt diffKr) more
280        consistent with vertical mixing schemes.
281    o verification/testreport:
282      - fix typo in "-pcls" option ;
283      - put temp files in /tmp (instead of in local dir)
284      - add option "-ncad" to use genmake2 new option "-nocat4ad"
285      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
286    o pkg/ggl90 (idemix code):
287      - apply few fixes ; add some missing "_d 0" ; update output of exp.
288        global_ocean.90x40x15.idemix
289    o OpenAD
290      - enable active file I/O and begin removal of work-around code
291        for OpenAD for handling control variables (memory vs. active files)
292      - new CPP options file OPENAD_OPTIONS.h
293      - revert to genarr2d gradient check for hs94.1x64x5
294      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
295      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
296    o tools/genmake2:
297      - add option for an alternative Makefile (from Martin) where multiple
298        source files are sent to TAF (instead of all in one file).
299    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
300      - code provided by Carsten Eden as an extension of ggl90
301      - so far the code is turned on within ggl90 by setting a CPP-flag at
302        compile time; a runtime flag implementation is not yet complete
303      - tested in new verification experiment global_ocean.90x40x15.idemix
304    o verification:
305      - reduce length of the AD test run by half for experiments
306        global_ocean.cs32x15 (std + thsice) and isomip
307      - enable active file I/O for OpenAD, adjust verifications accordingly
308      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
309    o verification/testreport:
310      - fix two non-POSIX sed statements so that there are no error messages
311        on Mac OS X
312      - replace hostname -s with hostname | sed 's/\..*$//'
313    o model/src/seawater.F:
314      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
315        (following the matlab code), which would have avoided the bug caught
316        by Matt (see below) in the first place
317    o pkg/shelfice:
318      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
319        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
320      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
321        ice-shelf case (i.e., within surface level).
322      - add config summary in shelfice_check.F
323      - remove global variable recip_SHELFICElatentHeat and replace by a local
324        variable recip_latentHeat
325      - introduce diagnostics for friction velocity uStar (in case of
326        SHELFICEuseGammaFrict)
327      - change verification experiment isomip.htd:
328        + start from pickup (as input_ad at nIter0=8640)
329        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
330        + test SHELFICEuseGammaFrict = .TRUE.
331        + test SHELFICEadvDiffHeatFlux = .TRUE.
332    o model/src:
333      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
334        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
335        update output of experiments global_with_exf.yearly and isomip (all 6).
336    o pkg/shelfice:
337      - change setting of kTopC to also be zero where there is no ice-shelf.
338      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
339        ice-shelf is.
340      - first attempt to get RealFreshWaterFlux effects: for now, only without
341        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
342    o pkg/seaice: add the option to prescribe a fixed thickness PDF
343      for thermodynamic calculations
344      - because of divisions of the type 7/7 not exactly equal to 1, this change
345        affects results of some verification experiments by up to 4 digits:
346        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
347        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
348        adjoint: lab_sea, lab_sea.noseaicedyn
349        -> updated
350    
351    checkpoint65i (2015/01/23)
352    o model/src:
353      - change units of frictionHeating field from W to W/m^2
354      - fix bug in frictional heating from stratospheric drag in
355        S/R ATM_PHYS_TENDENCY_APPLY_V
356      - with synchronous time-stepping: move resetting to zero of frictionHeating
357        field from load_fields_driver.F to thermodynamics.F ;
358      - add diagnostics for frictional heating.
359    o model/src & gmredi K3D:
360      - add frictionHeating field to pickup-files (for synchronous time-stepping)
361      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
362      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
363        and name in pickup file).
364      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
365    o model/src:
366      - move (from ini_forcing.F) initialisation of all arrays in header file
367        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
368        (since Nov 2012) with option selectAddFluid=1.
369    o pkg/shelfice:
370      - change units (+ document) of newly added field "shelfIceMassDynTendency"
371      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
372    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
373    o pkg/seaice: two new runtime parameters:
374      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
375        long overdue
376      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
377        parameterization of tensil stress for fast ice (does not do anything yet)
378    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
379        for LSR: move checking overlaps out of JFNK-if-block
380    o pkg/atm_phys:
381      - move copy of grid and dynamical fields out of atm_phys_driver.F into
382        new S/R ATM_PHYS_DYN2PHYS.
383      - fix level height for Linear Free-Surf case (to be consistent with
384        fixed-in-time pressure levels).
385    o pkg/mom_common (bottomdrag):
386      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
387        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
388        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
389    o pkg/shelfice (u/v_drag):
390      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
391      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
392        (now similar to shelfice_u_drag.F)
393      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
394        from mom_vecinv.F (similar to mom_fluxform calls).
395    o pkg/mom_common (bottomdrag):
396      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
397      - add options for alternative discretisation of velocity norm in quadratic
398        bottom drag: averaging of grid-cell-center KE to U.point and V.point
399        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
400        improves when averaging only the other component (e.g. vVel for U bottom
401        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
402      - add options (bottomVisc_pCell) to account for partial-cell in bottom
403        friction (no-slip BC) thus getting the true distance from the bottom;
404        off by default since this also reduces model stability (explicit bottom
405        friction). Changes produce different machine truncation with linear-drag
406        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
407        front_relax (bvp & mxl, 10 & 11 digits).
408    o model/src & mom pkgs:
409      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
410        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
411      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
412        just copy level Nr value to level Nr+1.
413    o doc:
414      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
415    o pkg/streamice:
416      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
417        SHELFICE.h: move array shelficemass to init_varia, initialise
418        from array shelficemassinit, which is set in init_fixed and
419        has option to be set from file; introduce array
420        shelficeMassDynTend array, set thru file in init_fixed
421      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
422        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
423        pkg/streamice
424      - shelfice_thermodynamics.F: call shelfice_step_icemass if
425        SHELFICEMassStepping = .true.
426      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
427    
428    checkpoint65h (2014/12/17)
429    o verification/global_ocean.90x40x15, global_ocean_ebm:
430      - update to generic controls.
431    o pkg/ctrl:
432      - ctrl_map_ini_genarr.F: test for igen>0
433      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
434      - move gentim2d part of ctrl_map_ini_genarr.F to
435        new separate routine : ctrl_map_ini_gentim2d.F
436      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
437        add time variable weights and cyclic controls (time mean,
438        seasonal cycle, etc) capabilities to gentim2d
439    o pkg/ecco:
440      - move reading of error, conversion to weights from
441        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
442    o global_oce_llc90, cs32:
443      - activte sbo.
444      - CTRL_SIZE.h : add maxCtrlProc.
445      - activate the new genctrl capabilities.
446      - update following reorganization of global_oce_input_fields.tar.gz  
447    o pkg/ctrl/ctrl_ad_diff.list:
448      - add missing ctrl_init_rec.f
449    o tools/OAD_support/keepOriginal:
450      - add ctrl_init_rec.F
451    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
452      - avoid recomputations of xx_gentim2d_dummy.
453    o momentum diagnostics:
454      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
455        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
456    o pkg/seaice/seaice_lsr.F:
457      - fix computation of BU/BV, make sure they are non-zero, only necessary
458        for cubed sphere exchanges and SEAICE_OLx/y>0.
459        This makes calling s/r fill_cs_corner_rl obsolete (removed).
460    o verification/global_ocean.cs32x15/input.seaice
461      - add test for strong implicit coupling and restricted addtive Schwarz
462        methods for LSR
463      - update results/output.seaice.txt
464    o verification/tutorial_global_oce_biogeo:
465      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
466        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
467        update output_adm,_oadm,_tlm.txt
468    o pkg/dic:
469      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
470      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
471        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
472    o verification/tutorial_global_oce_biogeo:
473      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
474        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
475        update output_adm,_oadm,_tlm.txt
476    o eesupp/src:
477      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
478        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
479    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
480      LSR (following Hutchings et al. 2004)
481      - introduce zetaZ as a global variable (requires adjustments in
482        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
483        in seaice_calc_viscosities.F
484      - new flag SEAICEuseStrImpCpl (default off)
485      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
486        momentum equations
487      - JFNK-solver (preconditioner) adjusted to allow using this method
488        (where it does not have any positive effect)
489    o pkg/seaice
490      - add overlap for restrictive additive Schwartz method also to LSR, but
491        turn it off by default (because it only seems to work for non-cubed
492        sphere/llc topologies)
493    o pkg/autodiff
494      - add extra exchanges in addummy_in_steppging also for mnc output
495    o pkg/seaice:
496      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
497        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
498    o pkg/obcs:
499      - add option to specify domain-connected piece Id along OB though files
500        (for now, only used to diagnose PhiVel; default =1 -> global correction)
501      - modify obcs_diag_balance.F to process each connected-part separately;
502        exclude OB where Id = 0 but keep the full divergence there (-> constant
503        Psi along this portion of OB and all inflow derived from grad(Phi))
504      - add example of OB-conect files in verification/so_box_biogeo/input.
505    o pkg/diagnostics:
506      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
507      a) use non zero matrix element across OB and solve for Phi 1 grid point
508         outside OB (i.e, where tracer OBCS are applied).
509      b) global imbalance of inFlow/outFlow across OB: instead of modifying
510         velocity across OB, spread it uniformly along the OB in the RHS.
511    
512    checkpoint65g (2014/11/19)
513    o pkg/diagnostcis:
514      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
515    o pkg/my82,pp81,kl10:
516      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
517        field diffKr as background diffusivity to set minimum diffusivity value.
518    o pkg/seaice:
519      - add new parameter SEAICEuseEVPrev (for revisited EVP by
520        Bouillon et al 2013)
521      - add SEAICE_evpAlpha/Beta to namelist
522      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
523        involve trivial re-ordering of divisions/multiplications that should not
524        have any effects, but ... they do change the results of lab_sea.hb87 so
525        that only 2 digits of agreement remain, in line with the general
526        instability/fragility of the evp-code. For now, I do not care and just
527        update the verification experiment
528    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
529      - remove xx_genarr2d_numsmooth etc
530      - use xx_genarr2d_preproc etc instead
531      - carry out smooth_correl2D at initialization stage rather than during
532        time stepping.
533      - get smoothOpNb from xx_gentim2d_preproc
534    o global_oce_cs32 :
535      - add test of generic ecco capabilities.
536    o pkg/exf/exf_getsurfacefluxes.F :
537      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
538    o pkg/ctrl,ecco :
539      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
540        is defined.
541    o pkg/seaice: add diagnostics for Delta (deformation parameter)
542    o model/src:
543      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
544        diffusivity (background) is specified but ignored.
545    o verification:
546      - in testreport, convert hostname to lower case for default output dir name
547    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
548    o pkg/dic: add modifications from Hajoon:
549      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
550      - light attenuation: add self-shading effect by climatological Chlorophyll
551        (read from file).
552    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
553        compiles when SEAICE_ALLOW_DYNAMICS is undefined
554    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
555        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
556        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
557        approach where CPP_OPTIONS.h includes an omnipotent
558        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
559    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
560        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
561    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
562        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
563        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
564    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
565      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
566      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
567      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
568      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
569    o pkg/ctrl,ecco,exf :
570      - remove variables associated with NON-generic costs,
571        unless ECCO_CTRL_DEPRECATED is defined.
572      - remove NON-generic NON-obcs controls,
573        unless ECCO_CTRL_DEPRECATED is defined.
574    o pkg/ctrl : added ctrl_local_params.h
575    o pkg/ecco : added ecco_local_params.h
576    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
577        experiments, which will progressively be removed once the
578        experiments are revised to use only generic controls/costs.
579    
580    checkpoint65f (2014/10/13)
581    o pkg/ctrl, ecco, seaice : minor changes in headers
582    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
583        cost function and control capabilities added since checkpoint65c.
584    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
585    o pkg/ecco: increase modularity and improve logic
586      - ecco_toolbox.F (new) : basic operations that are often used,
587        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
588        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
589      - cost_gencal.F (new) : determine filnames and records.
590      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
591      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
592        and exploit the above functions leading to more compact code.
593      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
594      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
595        using_ers, using_gfo, using_mdt is now only defined within gencost)
596    o pkg/ecco: extend generic cost capabilities
597      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
598        capabilities via gencost_preproc (+ _c,_i,_r related params),
599        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
600        gencost_outputlevel arguments to cost_generic
601      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
602        and active_read, making room for gencost_preproc to take effect.
603        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
604      - pkg/ecco/cost_generic.F :
605        compute and store misfit maks*(model-data) in localdif that is
606        then used in cost and for output, output misfit if outlev.GT.0
607      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
608        rather gencost_barfile for deciding whether to write barfile
609      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
610      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
611        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
612      - pkg/ecco/ecco_summary.F : report gencost variables
613      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
614    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
615    o pkg/ecco: internal re-organization
616      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
617        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
618        mv relevant variables definition from ecco_cost.h to ecco.h,
619        make sure gencost routines only include ecco.h)
620      - throughout : add missing CCP switches, rm unused variables,
621        and rm un-necessary CPP switches
622      - throughout gencost routines : replace modelstartdate with
623        gencost_startdate when needed
624      - cost_bp_read.F : use arguments, instead of common blocs
625        so that it can be used also by (new) cost_gencost_bpv4.F
626      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
627      - ecco_phys.F : compute etanFull
628      - ecco_readparms.F : rename using_topex as using_tpj, add
629        bpv4-grace to gencost list, initialize added parameters
630      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
631    
632    checkpoint65e (2014/09/28)
633    o pkg/obcs:
634      - replaced the just-added CPP options with run-time variables
635        (see pkg/obcs/OBCS_PARAMS.h for details)
636    o pkg/obcs:
637      - add additional CPP options for sponge boundary layers
638        (see pkg/obcs/OBCS_OPTIONS.h for details)
639    o pkg/atm_phys:
640      - implement simple (obliquity only, assuming circular planet orbit)
641        seasonal cycle for incoming insolation ; used when run-time parameter
642        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
643    o pkg/exf, pkg/ecco, pkg/ctrl:
644      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
645      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
646      - implement gentim2d for xx_tauu, xx_tauv
647    o pkg/ctrl, pkg/ecco :
648      - fix and complement the generic controls implementation
649    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
650        pkg/shelfice/shelfice_thermodynamics.F,
651        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
652        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
653      - add weight in CTRL_GET_GEN calls
654    o pkg/ctrl :
655      - ctrl_get_gen.F : add weight as input parameter, and apply
656        it directly rather than using smooth_correl2Dw (to be retired).
657      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
658    o pkg/ctrl :
659      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
660        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
661      - re-activate ctrl_summary (call in ctrl_init.F)
662    o pkg/ctrl/ctrl_cost_gen.F :
663      - fix CCP brackets, remove un-necessary myiter, mytime
664    o pkg/ecco, pkg/ctrl :
665      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
666      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
667      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
668      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
669    
670    checkpoint65d (2014/09/15)
671    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
672      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
673        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
674    o pkg/ctrl/ctrl_map_ini_genarr.F :
675      - remove compilation failure
676      - replace hard coded example
677      - use ctrl_map_ini_gen2D, 3D
678    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
679      - on/off switch based upon xx_genarr2d_weight,3d
680    o src/packages_init_variables.F :
681      - regroup pkg/estimation calls
682      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
683        (moved to ctrl_init_variables)
684    o cost/cost_init_varia.F :
685      - remove ecco_cost_init_varia
686        (moved to ecco_init_varia)
687    o ctrl/ctrl_init_variables.F :
688      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
689      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
690    o ctrl/ctrl_map_ini.F :
691      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
692        (moved to ctrl_init_variables)
693    o ctrl/ctrl_map_ini_ecco.F :
694      - remove ECCO_PHYS (mv to ecco_init_varia)
695      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
696    o ecco/ecco_ad_diff.list :
697      - add ecco_init_varia.f
698    o ecco/ecco_init_varia.F
699      - new routine
700    o pkg/streamice:
701      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
702        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
703      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
704    o pkg/generic_advdiff:
705      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
706    o pkg/exf:
707      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
708         xxg_precip capability
709      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
710    o pkg/ctrl:
711      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
712    o model/src/load_fields_driver.F :
713      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
714        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
715    o OpenAD verification experiments:
716      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
717        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
718        for now, only in pkgs used in OpenAD verification experiments.
719      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
720        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
721        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
722        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
723    o OpenAD verification tests:
724      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
725      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
726        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
727      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
728        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
729    o model/src & generic_advdiff:
730      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
731        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
732        dynamics requires valid tracer forcing only over tile interior but, for
733        some diagnostics, may need to extend it over 1 point in tile halo region.
734      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
735        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
736        setting in temp/salt/ptracer_integrate.F
737    o pkg/dic:
738      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
739        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
740        in gchem_forcing_sep.F
741    o pkg/autodiff & obcs:
742      - add storage of current OB values for U & V (was already done for T & S).
743    
744    checkpoint65c (2014/08/30)
745    o pkg/dic:
746      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
747        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
748        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
749    o verification:
750      - new experiment testing OBCS and DIC pkgs, using params & output from
751        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
752        passage: take OBCS from the last year of a 2 yrs simulation and initial
753        conditions from t=1.yr while keeping the same forcing.
754    o model/src:
755      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
756        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
757    o pkg/diagnostics (Stats-Diags):
758      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
759        a) refine region where stats are computed, excluding where arrhFac=0 ;
760        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
761        c) extend regional stats over the region edges (for U or V pt location).
762    o pkg/gchem:
763      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
764        pkg/dic is currently changing/updating ptracers values beyond the OB).
765    o verification (hs94):
766      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
767        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
768        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
769        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
770    o pkg/ptracers:
771      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
772        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
773      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
774        with AB-2 code (so that it get tested).
775    o model/src:
776      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
777        with AB-2 code (previously only available with AB-3 code).
778        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
779        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
780        there, by calling CYCLE_AB_TRACER).
781    o pkg/generic_advdiff:
782      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
783        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
784        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
785        S/R temp/salt/ptracers_integrate.F
786    o model/src & pkg/ptracers:
787      - remove common block variables gT,gS (in DYNVARS.h), except when
788         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
789      - remove common block variable gPtr.
790    o model/src & pkgs:
791      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
792         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
793         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
794         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
795      + change accordingly all calling S/R.
796      - use local temperature/salinity/ptracer tendency array (without bi,bj)
797        in S/R temp/salt/ptracers_integrate.F
798    o pkg/seaice:
799      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
800        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
801      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
802        in seaice_lsr
803      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
804        in s/r seaice_lsr_calc_coeffs
805    o pkg/mdsio:
806      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
807        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
808        too long (e.g., > MAX_LEN_FNAM/2 )
809    
810    checkpoint65b (2014/08/12)
811    o pkg/matrix:
812      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
813    o model/src:
814      - fix initialisation of geothermalFile; compile geothermal-flux code in
815        natl_box verification experiment.
816    o model/src & pkg/down_slope:
817      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
818      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
819        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
820        results at machine truncation level: update output of experiments
821        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
822    o pkg/diagnostics (Stats-Diags):
823      - do not cumulate the full volume when DIAGNOSTICS_FILL is
824        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
825        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
826        times (but Min,Max and StD are still wrong).
827    o model/src:
828      - add geothermal flux forcing: read in ini_forcing.F as time-constant
829        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
830    o model/src:
831      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
832        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
833        arrays are already updated while adjustments (filters, conv.adjustment) are
834        still applied later, in S/R TRACERS_CORRECTION_STEP.
835    o model/src:
836      - store in common bloc array "rhoInSitu" the virtual potential temperature
837        anomaly that is used to compute geopotential: this make the atmos code
838        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
839    o pkg/seaice/seaice_lsr.F
840      - rename integer variable ilcall to ipass (that's what it is called
841        in the residual diagnostics
842      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
843        default) for improved non-linear convergence of the first few steps
844      - adjust a few comments and add new ones to explain some of the store
845        directives
846    o pkg/generic_advdiff (& ptracers):
847      - re-work the code to check for valid advection scheme and for minimum
848        size of overlap (now stored in local common bloc in gad_advscheme.F)
849    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
850      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
851      - add an auxilliary variable "bet" and fix store directives and keys in
852        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
853        less exact gradients in my tests); but there are still
854        recomputation warning (although gradients are sort of OK), when
855        SEAICE_LSR_VECTORIZE is not defined, so this flag and
856        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
857      - update verification experiments lab_sea.
858      - change some comments in S/R seaice_calc_viscosities
859    o model/src:
860      - if staggerTimeStep=T, always apply exchange to velocity field in
861        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
862        (independent of using multi-dim advection or not); no effect on FWD run
863        but affects AD results (at machine truncation level): update output of
864        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
865        and isomip (oad: 12.d).
866    o pkg/generic_advdiff:
867      - stop if doAB_onGtGs is set to FALSE but ignored
868      - refine warning related to stability of tracer time-stepping
869        regarding internal wave dynamics.
870      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
871        on staggerTimeStep & implicitIntGravWave (will now get a warning
872        if potentially unstable).
873    o pkg/kl10:
874      - add new pkg "kl10" for mixing due to internal wave breaking, from
875        http://www.sciencedirect.com/science/article/pii/S1463500310000144
876        (contribution from Jody Klymak), tested in verification experiment
877        verification/internal_wave/input.kl10/
878    o isomip experiment:
879      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
880        (input.htd) and update the output.
881    o cd_code experiments:
882      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
883        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
884        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
885        update the corresponding output.
886    o pkg/seaice:
887      - reduce the number of include files and store directives in
888        S/R seaice_lsr_tridiagu/v
889      - change the order of loops in one case in S/R seaice_lsr_tridiagv
890        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
891        get rid off one store directive (a TAF bug?)
892      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
893        S/R seaice_lsr_tridiagv to change the loop range for consistency
894      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
895      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
896        S/R seaice_lsr_tridiagu/v (requires update of
897        offline_exf_seaice/input.dyn_jfnk)
898    
899    checkpoint65a (2014/07/27)
900    o model/src:
901      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
902        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
903        (topo in p-coords, ice-shelf in z-coords); update output of experiments
904        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
905    o model/src:
906      - collect momentum forcing tendency into local 2-D array (passed as argument
907        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
908        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
909        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
910      - collect T & S forcing tendency into local 2-D array (passed as argument to
911        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
912        affects results at machine truncation level (e.g., ocean: if using
913        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
914        correction due to vertical advection).
915      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
916        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
917        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
918        obcs_ctrl (ad & fwd grd @ 12 & 7).
919    o pkg/ptracers & diagnostics:
920      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
921        title (to avoid some unexpected truncation); sort out ptracers diags units.
922      - collect ptracer forcing tendency into local 2-D array (passed as argument
923        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
924    
925    checkpoint65 (2014/07/18)
926    o pkg/fizhi:
927      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
928        affects results at machine truncation level. Update output of experiments
929        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
930    o pkg/seaice: more clean up
931      - rename TAF common block tapes to be more consistent and remove
932        unnecessary duplicates
933      - add store directives to remove more recomputations, but use smaller
934        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
935        The idea behind this flag is to reduce the memory footprint when the
936        adjoint of the LSR is not required. As of now, defining the flag
937        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
938        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
939        For experiment offline_exf_seaice, this means on a linux box with gfortran
940        nearly a factor of 10 (but keep in mind there is mostly seaice code in
941        this experiment):
942        > size mitgcmuv_ad
943        text    data        bss     dec        hex
944        5100659 1216  220458952  225560827  d71c8fb
945        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
946        but only a moderate increase of 36% for global_ocean.cs32x15:
947        text    data        bss     dec        hex
948        6695027 1648 1014578664 1021275339 3cdf6ccb
949        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
950      - note: there are still recomputations in global_ocean.cs32x15 and
951        offline_exf_seaice and the gradient agreement changes (gets a
952        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
953      - in general, the AD gradients still are wrong
954    o OpenAD
955      - clean up code_oad/ directories somewhat by moving files
956        dontCompile, dontTransform, keepOriginal to OAD_support/
957    o model/src:
958      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
959        (not currently tested): add dissipation terms before NLFS rescaling of
960        tendencies (previously done after).
961    o pkg/diagnostics:
962      - write stats-diags in ascii file with more digits (same as in monitor).
963    o pkg/down_slope:
964      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
965        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
966    o model/src:
967      - new file "apply_forcing.F" containing all the code previously in
968        external_forcing.F, but with new argument list: pass, as new argument,
969        the current level tendency array to update (instead of a direct update
970        of the common bloc array). Change the corresponding calls.
971      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
972        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
973    o pkg/seaice/seaice_lsr, a little bit of clean up
974      - rearrange some code blocks, so that now all calculations for
975        setting up the right-hand-sides done within one single block
976        (I find that easier to read and understand)
977      - rearrange freedrift-code to reduce the number of ifdefs
978      - adjust some indentations and comments
979    
980    checkpoint64z (2014/07/10)
981    o model/src and several pkgs:
982      - change argument list of all S/R called from external_forcing.F and
983        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
984        to pass, as argument, the current level tendency array to update
985        (instead of a direct update of the common bloc array).
986      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
987      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
988    o pkg/seaice/seaice_lsr.F
989      - always initialize local arrays in seaice_lsr_tridiagu/v
990      - add more local tapes to seaice_lsr_tridiagu/v
991      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
992        keep it in bi/bj loop; this seems to be essential
993      - gradients are still wrong but only by 4-7 orders of magnitude
994        instead of 15 orders of magnitude, lab_sea improves a little
995    o pkg/seaice
996      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
997        generates unnecessary code in seaice_lsr_ad
998      - add more store directives in seaice_lsr to avoid unnecessary code
999        in seaice_lsr_ad
1000      - exclude some residual computations in seaice_lsr when
1001        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1002        in seaice_lsr_ad
1003      - add more storing, a new tape (model/src/the_main_loop.F) and
1004        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1005        and klockey should be checked by a specialist)
1006      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1007        and update lab_sea after previous changes in pkg/seaice below
1008    o pkg/autodiff:
1009      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1010        viscFacInAd : run time parameters allowing for adjoint switches
1011        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1012    o pkg/ecco:
1013      - introduce cost_gencost_boxmean.F that computes a box mean
1014        temperature (for use in adjoint sensitivity studies).
1015    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1016    o pkg/mom_common/mom_calc_visc.F:
1017      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1018    o pkg/seaice/seaice_summary.F:
1019      - statement for SEAICEadjMODE now in autodiff_readparms.F
1020    o pkg/seaice:
1021      - remove some store directives and add new ones in an effort to get
1022        finally rid off the recomputation warnings. This is successful
1023        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1024        defined (i.e. no extensive recomputation warnings left), but there
1025        are still too many recomputations on the solver iteration level
1026      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1027      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1028        SEAICE_SIZE.h
1029      - add a store directive in S/R seaice_calc_viscosities
1030    o pkg/seaice (ITD code):
1031      - fix definition of Hlimit for multi-threaded case
1032      - use double precision arithmetic to compute Hlimit: this affects results;
1033        update output of experiment seaice_itd.
1034    o replace content of verification/seaice_itd
1035      - instead of a 1D column use the configuration of offline_exf_seaice
1036        to test the ice thickness distribution code with ridging
1037      - this is a first shot at this experiment
1038      - change of some defaults of ridging parameters SEAICEhStar (from
1039        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1040        and lot of new comments.
1041    
1042    checkpoint64y (2014/06/20)
1043    o pkg/seaice/seaice_reg_ridge.F:
1044      - modify the regularization of very small volumes of ice; only check
1045        total volume HEFF, and do not apply correction to individual ice
1046        classes because that leads to funny patterns in the heat and fw-fluxes
1047        into the ocean. Adjust seaice_itd/results/output.txt
1048      - replace nITD by SEAICE_multDim in loop-ranges
1049    o pkg/exf:
1050      - add code to process the case field period = -12. with UV interpolation.
1051      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1052        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1053    o verification/global_with_exf:
1054      - switch all fields period to -12. (was previously untested) in input/data.exf
1055        (but keep secondary test ".yearly" unchanged); update the reference output.
1056    o pkg/cal:
1057      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1058    o pkg/exf:
1059      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1060        to replace logical switch "exf_verbose"
1061      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1062    o pkg/sbo:
1063      - update from Katherine Quinn: evaluate mass directly from density and SSH
1064        (budget using Finite Volume method) instead of from bottom pressure.
1065      - allow testreport to collect few selected SBO output ; tested in exp.
1066        global_ocean.90x40x15 (after updating the results, to include SBO output).
1067      - fix some multi-threading issues (in output part).
1068    o model/src & most packages:
1069      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1070      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1071        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1072        "data.{pkg}" exist ; and leave the S/R (return) just after.
1073      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1074        + call LAND_READPARMS from packages_readparms.F
1075    o pkg/seaice:
1076    - remove code that resets useThSice in S/R seaice_readparms and    - remove code that resets useThSice in S/R seaice_readparms and
1077      replace by a warning in S/R seaice_check      replace it by a warning in S/R seaice_check
1078    - remove parameter MULTDIM, replace with nITD and runtime    - remove parameter MULTDIM, replace with nITD and runtime
1079      parameter SEAICE_multDim (still hard-wired to nITD if      parameter SEAICE_multDim (still hard-wired to nITD if
1080      SEAICE_ITD is defined)      SEAICE_ITD is defined)
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