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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2189 by jmc, Tue Oct 20 13:43:32 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 tools/adjoint_options/adjoint_diva:
8      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
9    o pkg/streamice:
10      - spotted bug in streamice_driving_stress using dyG where should have been dxG
11    o pkg/exf:
12      - remove STOP statement that prevented to use wind or (wind-)stress
13        interpolation for constant-in-time forcing fields (wind/stress period = 0).
14    o pkg/seaice:
15      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
16        5 additionals 2D fields and 6 new store directives
17      - change logic in seaice_readparms.F: EVP code can now be turned on in
18        various ways, setting SEAICE_deltaTev is no longer required,
19        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
20        or SEAICEaEVPcoeff
21    o pkg/shelfice/shelfice_thermodynamics.F
22      - redefining uLoc/vLoc to u/v, instead of 2u/v
23    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
24      - this is an intermediate state of a truely converging EVP that has
25        the potential of outperforming implicit VP methods, I do not recommend
26        using it yet.
27      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
28        and all parameters are hardwired
29      - for convergence it still requires very smooth regularisations, that means,
30        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
31        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
32        specific averaging appears to be required, still subject to tuning
33      - still needs cleaning and I need to turn parameter into runtime parameters
34      - add code to compute and print residuals of iteration, compile with
35        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
36    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
37      that entered with r1.54 on Sep04, 2015, -> update results
38    
39    checkpoint65o (2015/09/14)
40    o pkg/mom_vecinv & mom_common:
41      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
42        called from there.
43      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
44        allows to use Vector-Invariant form in deep atmos and anelastic formulation
45    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
46      and Koenig-Beatty+Holland (2012)
47      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
48      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
49      - requires an extra input argument for S/R seaice_calc_viscosities
50      - tensileStrength's depth dependence is different from Itkin et al. (2015)
51        (to be changed and played with, for now exponential)
52    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
53      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
54        by AREA according to Connelly et al. (2004), JPO.
55      - For EVP and the LSR solver, the implicit part of the drag term is
56        the only non-zero term in the denominator when there is no ice (which
57        prevented running the model with zero ice-ocean drag). If
58        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
59        (or zero main diagonals BU/BV) which need to be caught. A practical
60        consequence is that for open water, the momentum equation reduce
61        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
62        they happen to be zero, often leading to a non-zero solution over
63        open water.
64    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
65        efficient EVP method.
66      - introduce area-weighted averages for e12 (analogously to
67        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
68        remain, but also changing the order of terms in the previous average
69        changed the results as much) -> update experiment
70      - add SEAICE_DELTA_SMOOTHREG code
71      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
72        TEM-code
73      - adjust loop bounds so that only required fields are computed
74      - add new averaging code for zetaZ/deltaZ (again similar to
75        seaice_calc_viscosities.F), inactive by default for now (will change
76        results again), but will replace old code eventually
77    o eesupp/src:
78      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
79        to always cumulate tile local-sum in the same order
80        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
81        Still uses MPI_Allreduce (like standard code) but on array of tiles
82        and should be faster than GLOBAL_SUM_SEND_RECV code.
83      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
84        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
85      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
86         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
87         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
88         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
89         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
90    
91    checkpoint65n (2015/07/29)
92    o pkg/thsice:
93      - add a warning when used with pkg/aim but without updating SST
94        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
95    o pkg/offline:
96      - change where Offline-Fields are loaded, from load_fields_driver.F to
97        directly within FORWARD_STEP, just after updating iter number and time;
98      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
99        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
100       These changes allow:
101        a) to recover exactly on-line results using deltaToffline=deltaTClock,
102        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
103        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
104        time-step, both with GM & KPP files and with recomputing these fields;
105        b) no needs to switch on staggerTimeStep anymore;
106        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
107      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
108    o pkg/offline:
109      - change (rarely used) offset-iteration parameter to an offset time (in s):
110        can easily recover previous offset-iter effect by setting offset-time
111        (offlineTimeOffset) to offset-iter x deltaToffline;
112      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
113        in KPP as part of surface buoyancy forcing) in offline run.
114      - fix ptracers KPP non-local term in the case where KPP is re-computed.
115    o OpenAD
116      - Adding preliminary ggl90 test to OpenAD verification.
117        Config. with ggl90 currently diverges after 64 time steps
118        so will need more work to become more stable
119      - Adding preliminary kpp test to OpenAD verification.
120        required small tweakes in kpp_routines.F
121      - Merge and update from Krishna Narayanan's contrib area:
122        * Add one variable for preliminary OpenAD DIVA
123        * Add replacement time-stepping for OpenAD DIVA
124        * genmake2 flag -diva (but only for OpenAD; preliminary)
125        * required modifs for OAD_support
126        successful preliminary test for tutorial_global_oce_biogeo/
127    o pkg/seaice:
128      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
129      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
130        delta with a smooth function in s/r seaice_calc_viscosity
131        (no effect on EVP)
132      - rename local suffix "sqr" into "sq" for more consistent variable names
133    o pkg/seaice:
134        add new parameter SEAICE_deltaMin that is used ***only***
135        for regularizing Delta (and nothing else, like the parameter
136        which is also used for all sorts of things SEAICE_EPS).
137        Defaults to SEAICE_EPS for backward compatibility only.
138    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
139        the wrong key by inialising it before use -> fixes a recomputation
140        problem but does not fix the gradient
141    o pkg/layers:
142      - move resetting of flux arrays to outside the iLa loop
143        (this caused layers_diapycnal to not work with more than one layer coord.)
144      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
145    o pkg/layers:
146      - remove from common block 3D layers fields (used to diagnose transport
147        in tracer coords) and declare them as local arrays in layers_calc.F
148    o pkg/seaice:
149      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
150        in lab_sea forward experiment (changes results -> updated)
151      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
152    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
153       computations; for SEAICE_VECTORIZE_LSR
154      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
155        sweep to the outside,
156      - remove store directives and add "CADJ loop sequential" directives
157        in analogy to model/src/solve_tridiagonal.F
158      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
159        boundaries to yield more readable code. This has also the charming side
160        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
161        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
162        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
163        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
164        an additional option)
165       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
166       but the adjoint gradients (which are affected by this change) still explode.
167    o coupler (atm & ocn _compon_interf):
168      - avoid using Exch2 IO mapping if not suitable.
169    
170    checkpoint65m (2015/06/15)
171    o pkg/layers:
172      - clean-up old parameters setting (from Sep 2012):
173        + remove old parameters setting from common block (declared locally);
174        + stop if any old parameter is mixed with new parameters;
175        + check for valid or consistent parameter setting (e.g., layers_name)
176      - check that layers_bounds for Pot.Density are in the right range;
177        this is supposed to catch un-updated setting after recently shifting
178        potential density field "prho" by -1000 (now in "sigma" scale).
179    o pkg/layers:
180      - Added missing call to layers_fill for keeping track of tottend in
181        pkg/diagnostics/diagnostics_fill_state.F
182    o pkg/layers:
183      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
184        of diapycnal fluxes
185    o pkg/layers:
186      - reverted changes to interpolation to previous treatment; there
187        was never actually a problem
188    o pkg/layers:
189      - fix interpolation of layers tracers in the presence of partial cells
190      - add lots of new functionality to compute water mass transformation
191        (enabled by CPP flag LAYERS_THERMODYNAMICS)
192      - add new calls from main code (diags_oceanic_surf_flux.F,
193        thermodynamics.F, impldiff.F) and gad to save the necessary fields
194        for layers_thermodynamics calculations
195    o pkg/ptracers:
196      - add capability of stepping a passive tracer forward without advection
197        by setting PTRACERS_advScheme to 0.
198    o pkg/diagnostics:
199      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
200    o pkg/layers:
201      - shift potential density field "prho" by -1000 for density layer averaging so
202        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
203        Note that density bin boundaries (layers_bounds in data.layers) have
204        to be set accordingly (i.e., shifted, in sigma scale).
205    o pkg/layers:
206      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
207      - fix calculation of layer non-weighted velocity and layer probability
208      - add diagnostics for pot.density used for layer averaging
209    o pkg/seaice:
210      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
211        positiveness, modify a few comments and improve variable names,
212      - the changed computation of deltaC affects most seaice-related
213        experiments at the truncation level.
214        seaice_itd.thermo is affected by far the most, with
215        only 7 digits of agreement remaining; update experiments.
216    
217    checkpoint65l (2015/05/04)
218    o pkg/shelfice:
219      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
220        factor drKp1 to zero where it is negative (ie. do not use
221        SHELFICEBoundaryLayer if hFacC>1)
222      - the same for factor drLoc in shelfice_forcing.F
223    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
224        with modules in ptracers, when using testreport option "-small_f"
225    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
226      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
227    o verification/testreport
228      - add new option -small_f
229        with this option testreport first makes the target small_f (*.f files)
230        before running make (all). This is useful for explicit inlining when
231        all sources need to be full available.
232    o pkg/exf/exf_interp.F:
233        remove previous changes related to reverse (decreasing) input grids latitude
234    
235    checkpoint65k (2015/04/01)
236    o pkg/ecco:
237        fix missing cosphi initialization; use eccoiter in place of optimcycle;
238        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
239        instead of active read/write
240    o pkg/ctrl:
241        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
242        instead of active read/write.
243    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
244        return if .NOT.useAUTODIFF
245    o pkg/seaice: add CPP brackets (cost function related).
246    o model/src:
247        add useAUTODIFF run time switch.
248    o pkg/exf/exf_interp.F:
249        add code to allow input grids with latitude starting in the north (i.e. when
250        j=1 corresponds to northern edge of field); modify global_with_exf to test
251        this feature.
252    o verification/testreport:
253      - replace "grep -A3" with POSIX conformal sed command, because there are
254        implementations of grep that cannot do contextual searches
255      - replace "cat -n" by "nl" (two occurrences), because not all implementations
256        of "cat" have the option "-n"
257    o model/src:
258        add new file gsw_teos10.F that contains 3 functions, more or less a copy
259        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
260        convert from conservative to potential temperature. For now they are not
261        called anywhere.
262    o pkg/ggl90: make "useIDEMIX" useful
263      - re-organize code in s/r ggl90_calc a little to move computations that
264        are different for idemix into separate loops (changes verification
265        experiment idemix at truncation level, 12 digits remain -> updated)
266      - requires 2 new 2D fields KappaM, verticalShear
267      - make hFacI and recip_hFacI local 3D variables that are passed to
268        s/r ggl90_idemix
269      - fix and improve some comments
270    
271    checkpoint65j (2015/02/25)
272    o pkg/openad
273      - synchronize seawater.F with version in model/src: replace routine
274        body of sw_temp by calling sw_ptmp and fix/add a few comments.
275    o pkg/mnc:
276      - change default value of pickup_read/write_mnc params to FALSE
277        (since few features are missing in reading MNC pickup files).
278    o model/src:
279      - change default (background) vertical diffusivity for salt to be the
280        temperature (background) vertical diffusivity.
281      - change background vertical diffusivity in vertical mixing pkgs ggl90,
282        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
283        This makes ptracers default diffusivity (that uses salt diffKr) more
284        consistent with vertical mixing schemes.
285    o verification/testreport:
286      - fix typo in "-pcls" option ;
287      - put temp files in /tmp (instead of in local dir)
288      - add option "-ncad" to use genmake2 new option "-nocat4ad"
289      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
290    o pkg/ggl90 (idemix code):
291      - apply few fixes ; add some missing "_d 0" ; update output of exp.
292        global_ocean.90x40x15.idemix
293    o OpenAD
294      - enable active file I/O and begin removal of work-around code
295        for OpenAD for handling control variables (memory vs. active files)
296      - new CPP options file OPENAD_OPTIONS.h
297      - revert to genarr2d gradient check for hs94.1x64x5
298      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
299      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
300    o tools/genmake2:
301      - add option for an alternative Makefile (from Martin) where multiple
302        source files are sent to TAF (instead of all in one file).
303    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
304      - code provided by Carsten Eden as an extension of ggl90
305      - so far the code is turned on within ggl90 by setting a CPP-flag at
306        compile time; a runtime flag implementation is not yet complete
307      - tested in new verification experiment global_ocean.90x40x15.idemix
308    o verification:
309      - reduce length of the AD test run by half for experiments
310        global_ocean.cs32x15 (std + thsice) and isomip
311      - enable active file I/O for OpenAD, adjust verifications accordingly
312      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
313    o verification/testreport:
314      - fix two non-POSIX sed statements so that there are no error messages
315        on Mac OS X
316      - replace hostname -s with hostname | sed 's/\..*$//'
317    o model/src/seawater.F:
318      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
319        (following the matlab code), which would have avoided the bug caught
320        by Matt (see below) in the first place
321    o pkg/shelfice:
322      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
323        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
324      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
325        ice-shelf case (i.e., within surface level).
326      - add config summary in shelfice_check.F
327      - remove global variable recip_SHELFICElatentHeat and replace by a local
328        variable recip_latentHeat
329      - introduce diagnostics for friction velocity uStar (in case of
330        SHELFICEuseGammaFrict)
331      - change verification experiment isomip.htd:
332        + start from pickup (as input_ad at nIter0=8640)
333        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
334        + test SHELFICEuseGammaFrict = .TRUE.
335        + test SHELFICEadvDiffHeatFlux = .TRUE.
336    o model/src:
337      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
338        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
339        update output of experiments global_with_exf.yearly and isomip (all 6).
340    o pkg/shelfice:
341      - change setting of kTopC to also be zero where there is no ice-shelf.
342      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
343        ice-shelf is.
344      - first attempt to get RealFreshWaterFlux effects: for now, only without
345        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
346    o pkg/seaice: add the option to prescribe a fixed thickness PDF
347      for thermodynamic calculations
348      - because of divisions of the type 7/7 not exactly equal to 1, this change
349        affects results of some verification experiments by up to 4 digits:
350        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
351        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
352        adjoint: lab_sea, lab_sea.noseaicedyn
353        -> updated
354    
355    checkpoint65i (2015/01/23)
356    o model/src:
357      - change units of frictionHeating field from W to W/m^2
358      - fix bug in frictional heating from stratospheric drag in
359        S/R ATM_PHYS_TENDENCY_APPLY_V
360      - with synchronous time-stepping: move resetting to zero of frictionHeating
361        field from load_fields_driver.F to thermodynamics.F ;
362      - add diagnostics for frictional heating.
363    o model/src & gmredi K3D:
364      - add frictionHeating field to pickup-files (for synchronous time-stepping)
365      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
366      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
367        and name in pickup file).
368      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
369    o model/src:
370      - move (from ini_forcing.F) initialisation of all arrays in header file
371        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
372        (since Nov 2012) with option selectAddFluid=1.
373    o pkg/shelfice:
374      - change units (+ document) of newly added field "shelfIceMassDynTendency"
375      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
376    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
377    o pkg/seaice: two new runtime parameters:
378      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
379        long overdue
380      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
381        parameterization of tensil stress for fast ice (does not do anything yet)
382    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
383        for LSR: move checking overlaps out of JFNK-if-block
384    o pkg/atm_phys:
385      - move copy of grid and dynamical fields out of atm_phys_driver.F into
386        new S/R ATM_PHYS_DYN2PHYS.
387      - fix level height for Linear Free-Surf case (to be consistent with
388        fixed-in-time pressure levels).
389    o pkg/mom_common (bottomdrag):
390      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
391        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
392        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
393    o pkg/shelfice (u/v_drag):
394      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
395      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
396        (now similar to shelfice_u_drag.F)
397      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
398        from mom_vecinv.F (similar to mom_fluxform calls).
399    o pkg/mom_common (bottomdrag):
400      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
401      - add options for alternative discretisation of velocity norm in quadratic
402        bottom drag: averaging of grid-cell-center KE to U.point and V.point
403        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
404        improves when averaging only the other component (e.g. vVel for U bottom
405        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
406      - add options (bottomVisc_pCell) to account for partial-cell in bottom
407        friction (no-slip BC) thus getting the true distance from the bottom;
408        off by default since this also reduces model stability (explicit bottom
409        friction). Changes produce different machine truncation with linear-drag
410        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
411        front_relax (bvp & mxl, 10 & 11 digits).
412    o model/src & mom pkgs:
413      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
414        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
415      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
416        just copy level Nr value to level Nr+1.
417    o doc:
418      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
419    o pkg/streamice:
420      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
421        SHELFICE.h: move array shelficemass to init_varia, initialise
422        from array shelficemassinit, which is set in init_fixed and
423        has option to be set from file; introduce array
424        shelficeMassDynTend array, set thru file in init_fixed
425      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
426        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
427        pkg/streamice
428      - shelfice_thermodynamics.F: call shelfice_step_icemass if
429        SHELFICEMassStepping = .true.
430      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
431    
432    checkpoint65h (2014/12/17)
433    o verification/global_ocean.90x40x15, global_ocean_ebm:
434      - update to generic controls.
435    o pkg/ctrl:
436      - ctrl_map_ini_genarr.F: test for igen>0
437      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
438      - move gentim2d part of ctrl_map_ini_genarr.F to
439        new separate routine : ctrl_map_ini_gentim2d.F
440      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
441        add time variable weights and cyclic controls (time mean,
442        seasonal cycle, etc) capabilities to gentim2d
443    o pkg/ecco:
444      - move reading of error, conversion to weights from
445        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
446    o global_oce_llc90, cs32:
447      - activte sbo.
448      - CTRL_SIZE.h : add maxCtrlProc.
449      - activate the new genctrl capabilities.
450      - update following reorganization of global_oce_input_fields.tar.gz  
451    o pkg/ctrl/ctrl_ad_diff.list:
452      - add missing ctrl_init_rec.f
453    o tools/OAD_support/keepOriginal:
454      - add ctrl_init_rec.F
455    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
456      - avoid recomputations of xx_gentim2d_dummy.
457    o momentum diagnostics:
458      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
459        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
460    o pkg/seaice/seaice_lsr.F:
461      - fix computation of BU/BV, make sure they are non-zero, only necessary
462        for cubed sphere exchanges and SEAICE_OLx/y>0.
463        This makes calling s/r fill_cs_corner_rl obsolete (removed).
464    o verification/global_ocean.cs32x15/input.seaice
465      - add test for strong implicit coupling and restricted addtive Schwarz
466        methods for LSR
467      - update results/output.seaice.txt
468    o verification/tutorial_global_oce_biogeo:
469      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
470        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
471        update output_adm,_oadm,_tlm.txt
472    o pkg/dic:
473      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
474      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
475        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
476    o verification/tutorial_global_oce_biogeo:
477      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
478        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
479        update output_adm,_oadm,_tlm.txt
480    o eesupp/src:
481      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
482        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
483    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
484      LSR (following Hutchings et al. 2004)
485      - introduce zetaZ as a global variable (requires adjustments in
486        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
487        in seaice_calc_viscosities.F
488      - new flag SEAICEuseStrImpCpl (default off)
489      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
490        momentum equations
491      - JFNK-solver (preconditioner) adjusted to allow using this method
492        (where it does not have any positive effect)
493    o pkg/seaice
494      - add overlap for restrictive additive Schwartz method also to LSR, but
495        turn it off by default (because it only seems to work for non-cubed
496        sphere/llc topologies)
497    o pkg/autodiff
498      - add extra exchanges in addummy_in_steppging also for mnc output
499    o pkg/seaice:
500      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
501        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
502    o pkg/obcs:
503      - add option to specify domain-connected piece Id along OB though files
504        (for now, only used to diagnose PhiVel; default =1 -> global correction)
505      - modify obcs_diag_balance.F to process each connected-part separately;
506        exclude OB where Id = 0 but keep the full divergence there (-> constant
507        Psi along this portion of OB and all inflow derived from grad(Phi))
508      - add example of OB-conect files in verification/so_box_biogeo/input.
509    o pkg/diagnostics:
510      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
511      a) use non zero matrix element across OB and solve for Phi 1 grid point
512         outside OB (i.e, where tracer OBCS are applied).
513      b) global imbalance of inFlow/outFlow across OB: instead of modifying
514         velocity across OB, spread it uniformly along the OB in the RHS.
515    
516    checkpoint65g (2014/11/19)
517    o pkg/diagnostcis:
518      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
519    o pkg/my82,pp81,kl10:
520      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
521        field diffKr as background diffusivity to set minimum diffusivity value.
522    o pkg/seaice:
523      - add new parameter SEAICEuseEVPrev (for revisited EVP by
524        Bouillon et al 2013)
525      - add SEAICE_evpAlpha/Beta to namelist
526      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
527        involve trivial re-ordering of divisions/multiplications that should not
528        have any effects, but ... they do change the results of lab_sea.hb87 so
529        that only 2 digits of agreement remain, in line with the general
530        instability/fragility of the evp-code. For now, I do not care and just
531        update the verification experiment
532    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
533      - remove xx_genarr2d_numsmooth etc
534      - use xx_genarr2d_preproc etc instead
535      - carry out smooth_correl2D at initialization stage rather than during
536        time stepping.
537      - get smoothOpNb from xx_gentim2d_preproc
538    o global_oce_cs32 :
539      - add test of generic ecco capabilities.
540    o pkg/exf/exf_getsurfacefluxes.F :
541      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
542    o pkg/ctrl,ecco :
543      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
544        is defined.
545    o pkg/seaice: add diagnostics for Delta (deformation parameter)
546    o model/src:
547      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
548        diffusivity (background) is specified but ignored.
549    o verification:
550      - in testreport, convert hostname to lower case for default output dir name
551    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
552    o pkg/dic: add modifications from Hajoon:
553      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
554      - light attenuation: add self-shading effect by climatological Chlorophyll
555        (read from file).
556    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
557        compiles when SEAICE_ALLOW_DYNAMICS is undefined
558    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
559        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
560        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
561        approach where CPP_OPTIONS.h includes an omnipotent
562        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
563    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
564        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
565    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
566        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
567        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
568    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
569      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
570      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
571      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
572      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
573    o pkg/ctrl,ecco,exf :
574      - remove variables associated with NON-generic costs,
575        unless ECCO_CTRL_DEPRECATED is defined.
576      - remove NON-generic NON-obcs controls,
577        unless ECCO_CTRL_DEPRECATED is defined.
578    o pkg/ctrl : added ctrl_local_params.h
579    o pkg/ecco : added ecco_local_params.h
580    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
581        experiments, which will progressively be removed once the
582        experiments are revised to use only generic controls/costs.
583    
584    checkpoint65f (2014/10/13)
585    o pkg/ctrl, ecco, seaice : minor changes in headers
586    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
587        cost function and control capabilities added since checkpoint65c.
588    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
589    o pkg/ecco: increase modularity and improve logic
590      - ecco_toolbox.F (new) : basic operations that are often used,
591        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
592        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
593      - cost_gencal.F (new) : determine filnames and records.
594      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
595      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
596        and exploit the above functions leading to more compact code.
597      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
598      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
599        using_ers, using_gfo, using_mdt is now only defined within gencost)
600    o pkg/ecco: extend generic cost capabilities
601      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
602        capabilities via gencost_preproc (+ _c,_i,_r related params),
603        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
604        gencost_outputlevel arguments to cost_generic
605      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
606        and active_read, making room for gencost_preproc to take effect.
607        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
608      - pkg/ecco/cost_generic.F :
609        compute and store misfit maks*(model-data) in localdif that is
610        then used in cost and for output, output misfit if outlev.GT.0
611      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
612        rather gencost_barfile for deciding whether to write barfile
613      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
614      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
615        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
616      - pkg/ecco/ecco_summary.F : report gencost variables
617      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
618    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
619    o pkg/ecco: internal re-organization
620      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
621        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
622        mv relevant variables definition from ecco_cost.h to ecco.h,
623        make sure gencost routines only include ecco.h)
624      - throughout : add missing CCP switches, rm unused variables,
625        and rm un-necessary CPP switches
626      - throughout gencost routines : replace modelstartdate with
627        gencost_startdate when needed
628      - cost_bp_read.F : use arguments, instead of common blocs
629        so that it can be used also by (new) cost_gencost_bpv4.F
630      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
631      - ecco_phys.F : compute etanFull
632      - ecco_readparms.F : rename using_topex as using_tpj, add
633        bpv4-grace to gencost list, initialize added parameters
634      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
635    
636    checkpoint65e (2014/09/28)
637    o pkg/obcs:
638      - replaced the just-added CPP options with run-time variables
639        (see pkg/obcs/OBCS_PARAMS.h for details)
640    o pkg/obcs:
641      - add additional CPP options for sponge boundary layers
642        (see pkg/obcs/OBCS_OPTIONS.h for details)
643    o pkg/atm_phys:
644      - implement simple (obliquity only, assuming circular planet orbit)
645        seasonal cycle for incoming insolation ; used when run-time parameter
646        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
647    o pkg/exf, pkg/ecco, pkg/ctrl:
648      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
649      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
650      - implement gentim2d for xx_tauu, xx_tauv
651    o pkg/ctrl, pkg/ecco :
652      - fix and complement the generic controls implementation
653    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
654        pkg/shelfice/shelfice_thermodynamics.F,
655        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
656        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
657      - add weight in CTRL_GET_GEN calls
658    o pkg/ctrl :
659      - ctrl_get_gen.F : add weight as input parameter, and apply
660        it directly rather than using smooth_correl2Dw (to be retired).
661      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
662    o pkg/ctrl :
663      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
664        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
665      - re-activate ctrl_summary (call in ctrl_init.F)
666    o pkg/ctrl/ctrl_cost_gen.F :
667      - fix CCP brackets, remove un-necessary myiter, mytime
668    o pkg/ecco, pkg/ctrl :
669      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
670      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
671      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
672      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
673    
674    checkpoint65d (2014/09/15)
675    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
676      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
677        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
678    o pkg/ctrl/ctrl_map_ini_genarr.F :
679      - remove compilation failure
680      - replace hard coded example
681      - use ctrl_map_ini_gen2D, 3D
682    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
683      - on/off switch based upon xx_genarr2d_weight,3d
684    o src/packages_init_variables.F :
685      - regroup pkg/estimation calls
686      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
687        (moved to ctrl_init_variables)
688    o cost/cost_init_varia.F :
689      - remove ecco_cost_init_varia
690        (moved to ecco_init_varia)
691    o ctrl/ctrl_init_variables.F :
692      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
693      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
694    o ctrl/ctrl_map_ini.F :
695      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
696        (moved to ctrl_init_variables)
697    o ctrl/ctrl_map_ini_ecco.F :
698      - remove ECCO_PHYS (mv to ecco_init_varia)
699      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
700    o ecco/ecco_ad_diff.list :
701      - add ecco_init_varia.f
702    o ecco/ecco_init_varia.F
703      - new routine
704    o pkg/streamice:
705      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
706        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
707      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
708    o pkg/generic_advdiff:
709      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
710    o pkg/exf:
711      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
712         xxg_precip capability
713      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
714    o pkg/ctrl:
715      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
716    o model/src/load_fields_driver.F :
717      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
718        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
719    o OpenAD verification experiments:
720      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
721        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
722        for now, only in pkgs used in OpenAD verification experiments.
723      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
724        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
725        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
726        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
727    o OpenAD verification tests:
728      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
729      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
730        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
731      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
732        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
733    o model/src & generic_advdiff:
734      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
735        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
736        dynamics requires valid tracer forcing only over tile interior but, for
737        some diagnostics, may need to extend it over 1 point in tile halo region.
738      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
739        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
740        setting in temp/salt/ptracer_integrate.F
741    o pkg/dic:
742      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
743        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
744        in gchem_forcing_sep.F
745    o pkg/autodiff & obcs:
746      - add storage of current OB values for U & V (was already done for T & S).
747    
748    checkpoint65c (2014/08/30)
749    o pkg/dic:
750      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
751        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
752        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
753    o verification:
754      - new experiment testing OBCS and DIC pkgs, using params & output from
755        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
756        passage: take OBCS from the last year of a 2 yrs simulation and initial
757        conditions from t=1.yr while keeping the same forcing.
758    o model/src:
759      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
760        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
761    o pkg/diagnostics (Stats-Diags):
762      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
763        a) refine region where stats are computed, excluding where arrhFac=0 ;
764        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
765        c) extend regional stats over the region edges (for U or V pt location).
766    o pkg/gchem:
767      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
768        pkg/dic is currently changing/updating ptracers values beyond the OB).
769    o verification (hs94):
770      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
771        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
772        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
773        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
774    o pkg/ptracers:
775      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
776        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
777      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
778        with AB-2 code (so that it get tested).
779    o model/src:
780      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
781        with AB-2 code (previously only available with AB-3 code).
782        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
783        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
784        there, by calling CYCLE_AB_TRACER).
785    o pkg/generic_advdiff:
786      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
787        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
788        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
789        S/R temp/salt/ptracers_integrate.F
790    o model/src & pkg/ptracers:
791      - remove common block variables gT,gS (in DYNVARS.h), except when
792         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
793      - remove common block variable gPtr.
794    o model/src & pkgs:
795      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
796         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
797         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
798         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
799      + change accordingly all calling S/R.
800      - use local temperature/salinity/ptracer tendency array (without bi,bj)
801        in S/R temp/salt/ptracers_integrate.F
802    o pkg/seaice:
803      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
804        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
805      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
806        in seaice_lsr
807      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
808        in s/r seaice_lsr_calc_coeffs
809    o pkg/mdsio:
810      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
811        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
812        too long (e.g., > MAX_LEN_FNAM/2 )
813    
814    checkpoint65b (2014/08/12)
815    o pkg/matrix:
816      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
817    o model/src:
818      - fix initialisation of geothermalFile; compile geothermal-flux code in
819        natl_box verification experiment.
820    o model/src & pkg/down_slope:
821      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
822      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
823        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
824        results at machine truncation level: update output of experiments
825        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
826    o pkg/diagnostics (Stats-Diags):
827      - do not cumulate the full volume when DIAGNOSTICS_FILL is
828        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
829        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
830        times (but Min,Max and StD are still wrong).
831    o model/src:
832      - add geothermal flux forcing: read in ini_forcing.F as time-constant
833        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
834    o model/src:
835      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
836        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
837        arrays are already updated while adjustments (filters, conv.adjustment) are
838        still applied later, in S/R TRACERS_CORRECTION_STEP.
839    o model/src:
840      - store in common bloc array "rhoInSitu" the virtual potential temperature
841        anomaly that is used to compute geopotential: this make the atmos code
842        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
843    o pkg/seaice/seaice_lsr.F
844      - rename integer variable ilcall to ipass (that's what it is called
845        in the residual diagnostics
846      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
847        default) for improved non-linear convergence of the first few steps
848      - adjust a few comments and add new ones to explain some of the store
849        directives
850    o pkg/generic_advdiff (& ptracers):
851      - re-work the code to check for valid advection scheme and for minimum
852        size of overlap (now stored in local common bloc in gad_advscheme.F)
853    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
854      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
855      - add an auxilliary variable "bet" and fix store directives and keys in
856        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
857        less exact gradients in my tests); but there are still
858        recomputation warning (although gradients are sort of OK), when
859        SEAICE_LSR_VECTORIZE is not defined, so this flag and
860        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
861      - update verification experiments lab_sea.
862      - change some comments in S/R seaice_calc_viscosities
863    o model/src:
864      - if staggerTimeStep=T, always apply exchange to velocity field in
865        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
866        (independent of using multi-dim advection or not); no effect on FWD run
867        but affects AD results (at machine truncation level): update output of
868        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
869        and isomip (oad: 12.d).
870    o pkg/generic_advdiff:
871      - stop if doAB_onGtGs is set to FALSE but ignored
872      - refine warning related to stability of tracer time-stepping
873        regarding internal wave dynamics.
874      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
875        on staggerTimeStep & implicitIntGravWave (will now get a warning
876        if potentially unstable).
877    o pkg/kl10:
878      - add new pkg "kl10" for mixing due to internal wave breaking, from
879        http://www.sciencedirect.com/science/article/pii/S1463500310000144
880        (contribution from Jody Klymak), tested in verification experiment
881        verification/internal_wave/input.kl10/
882    o isomip experiment:
883      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
884        (input.htd) and update the output.
885    o cd_code experiments:
886      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
887        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
888        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
889        update the corresponding output.
890    o pkg/seaice:
891      - reduce the number of include files and store directives in
892        S/R seaice_lsr_tridiagu/v
893      - change the order of loops in one case in S/R seaice_lsr_tridiagv
894        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
895        get rid off one store directive (a TAF bug?)
896      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
897        S/R seaice_lsr_tridiagv to change the loop range for consistency
898      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
899      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
900        S/R seaice_lsr_tridiagu/v (requires update of
901        offline_exf_seaice/input.dyn_jfnk)
902    
903    checkpoint65a (2014/07/27)
904    o model/src:
905      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
906        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
907        (topo in p-coords, ice-shelf in z-coords); update output of experiments
908        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
909    o model/src:
910      - collect momentum forcing tendency into local 2-D array (passed as argument
911        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
912        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
913        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
914      - collect T & S forcing tendency into local 2-D array (passed as argument to
915        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
916        affects results at machine truncation level (e.g., ocean: if using
917        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
918        correction due to vertical advection).
919      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
920        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
921        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
922        obcs_ctrl (ad & fwd grd @ 12 & 7).
923    o pkg/ptracers & diagnostics:
924      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
925        title (to avoid some unexpected truncation); sort out ptracers diags units.
926      - collect ptracer forcing tendency into local 2-D array (passed as argument
927        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
928    
929    checkpoint65 (2014/07/18)
930    o pkg/fizhi:
931      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
932        affects results at machine truncation level. Update output of experiments
933        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
934    o pkg/seaice: more clean up
935      - rename TAF common block tapes to be more consistent and remove
936        unnecessary duplicates
937      - add store directives to remove more recomputations, but use smaller
938        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
939        The idea behind this flag is to reduce the memory footprint when the
940        adjoint of the LSR is not required. As of now, defining the flag
941        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
942        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
943        For experiment offline_exf_seaice, this means on a linux box with gfortran
944        nearly a factor of 10 (but keep in mind there is mostly seaice code in
945        this experiment):
946        > size mitgcmuv_ad
947        text    data        bss     dec        hex
948        5100659 1216  220458952  225560827  d71c8fb
949        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
950        but only a moderate increase of 36% for global_ocean.cs32x15:
951        text    data        bss     dec        hex
952        6695027 1648 1014578664 1021275339 3cdf6ccb
953        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
954      - note: there are still recomputations in global_ocean.cs32x15 and
955        offline_exf_seaice and the gradient agreement changes (gets a
956        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
957      - in general, the AD gradients still are wrong
958    o OpenAD
959      - clean up code_oad/ directories somewhat by moving files
960        dontCompile, dontTransform, keepOriginal to OAD_support/
961    o model/src:
962      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
963        (not currently tested): add dissipation terms before NLFS rescaling of
964        tendencies (previously done after).
965    o pkg/diagnostics:
966      - write stats-diags in ascii file with more digits (same as in monitor).
967    o pkg/down_slope:
968      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
969        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
970    o model/src:
971      - new file "apply_forcing.F" containing all the code previously in
972        external_forcing.F, but with new argument list: pass, as new argument,
973        the current level tendency array to update (instead of a direct update
974        of the common bloc array). Change the corresponding calls.
975      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
976        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
977    o pkg/seaice/seaice_lsr, a little bit of clean up
978      - rearrange some code blocks, so that now all calculations for
979        setting up the right-hand-sides done within one single block
980        (I find that easier to read and understand)
981      - rearrange freedrift-code to reduce the number of ifdefs
982      - adjust some indentations and comments
983    
984    checkpoint64z (2014/07/10)
985    o model/src and several pkgs:
986      - change argument list of all S/R called from external_forcing.F and
987        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
988        to pass, as argument, the current level tendency array to update
989        (instead of a direct update of the common bloc array).
990      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
991      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
992    o pkg/seaice/seaice_lsr.F
993      - always initialize local arrays in seaice_lsr_tridiagu/v
994      - add more local tapes to seaice_lsr_tridiagu/v
995      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
996        keep it in bi/bj loop; this seems to be essential
997      - gradients are still wrong but only by 4-7 orders of magnitude
998        instead of 15 orders of magnitude, lab_sea improves a little
999    o pkg/seaice
1000      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1001        generates unnecessary code in seaice_lsr_ad
1002      - add more store directives in seaice_lsr to avoid unnecessary code
1003        in seaice_lsr_ad
1004      - exclude some residual computations in seaice_lsr when
1005        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1006        in seaice_lsr_ad
1007      - add more storing, a new tape (model/src/the_main_loop.F) and
1008        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1009        and klockey should be checked by a specialist)
1010      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1011        and update lab_sea after previous changes in pkg/seaice below
1012    o pkg/autodiff:
1013      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1014        viscFacInAd : run time parameters allowing for adjoint switches
1015        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1016    o pkg/ecco:
1017      - introduce cost_gencost_boxmean.F that computes a box mean
1018        temperature (for use in adjoint sensitivity studies).
1019    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1020    o pkg/mom_common/mom_calc_visc.F:
1021      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1022    o pkg/seaice/seaice_summary.F:
1023      - statement for SEAICEadjMODE now in autodiff_readparms.F
1024    o pkg/seaice:
1025      - remove some store directives and add new ones in an effort to get
1026        finally rid off the recomputation warnings. This is successful
1027        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1028        defined (i.e. no extensive recomputation warnings left), but there
1029        are still too many recomputations on the solver iteration level
1030      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1031      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1032        SEAICE_SIZE.h
1033      - add a store directive in S/R seaice_calc_viscosities
1034    o pkg/seaice (ITD code):
1035      - fix definition of Hlimit for multi-threaded case
1036      - use double precision arithmetic to compute Hlimit: this affects results;
1037        update output of experiment seaice_itd.
1038    o replace content of verification/seaice_itd
1039      - instead of a 1D column use the configuration of offline_exf_seaice
1040        to test the ice thickness distribution code with ridging
1041      - this is a first shot at this experiment
1042      - change of some defaults of ridging parameters SEAICEhStar (from
1043        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1044        and lot of new comments.
1045    
1046    checkpoint64y (2014/06/20)
1047    o pkg/seaice/seaice_reg_ridge.F:
1048      - modify the regularization of very small volumes of ice; only check
1049        total volume HEFF, and do not apply correction to individual ice
1050        classes because that leads to funny patterns in the heat and fw-fluxes
1051        into the ocean. Adjust seaice_itd/results/output.txt
1052      - replace nITD by SEAICE_multDim in loop-ranges
1053    o pkg/exf:
1054      - add code to process the case field period = -12. with UV interpolation.
1055      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1056        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1057    o verification/global_with_exf:
1058      - switch all fields period to -12. (was previously untested) in input/data.exf
1059        (but keep secondary test ".yearly" unchanged); update the reference output.
1060    o pkg/cal:
1061      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1062    o pkg/exf:
1063      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1064        to replace logical switch "exf_verbose"
1065      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1066    o pkg/sbo:
1067      - update from Katherine Quinn: evaluate mass directly from density and SSH
1068        (budget using Finite Volume method) instead of from bottom pressure.
1069      - allow testreport to collect few selected SBO output ; tested in exp.
1070        global_ocean.90x40x15 (after updating the results, to include SBO output).
1071      - fix some multi-threading issues (in output part).
1072    o model/src & most packages:
1073      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1074      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1075        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1076        "data.{pkg}" exist ; and leave the S/R (return) just after.
1077      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1078        + call LAND_READPARMS from packages_readparms.F
1079    o pkg/seaice:
1080      - remove code that resets useThSice in S/R seaice_readparms and
1081        replace it by a warning in S/R seaice_check
1082      - remove parameter MULTDIM, replace with nITD and runtime
1083        parameter SEAICE_multDim (still hard-wired to nITD if
1084        SEAICE_ITD is defined)
1085    
1086    checkpoint64x (2014/05/24)
1087    o verification/lab_sea:
1088      - update adjoint and TLM output following changes to pkg/salt_plume
1089      - un-do the update after putting back local recip_Cp in few places.
1090    o pkg/salt_plume: modifications by An Nguyen:
1091      - add capability to do brine rejection (salt-plume) as function of
1092        volume+tracers (instead of only salinity tracer).
1093      - conserve volume by exchanging volume from each kLev to above to
1094        accommodate in-coming brine volume
1095      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1096      - switch KPP surf buoyancy due to brine forcing to 3-d
1097        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1098      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1099      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1100        in East/West Arctic.
1101    o pkg/sbo:
1102      - incorporate modifications from Katherine Quinn to enable the use of sbo
1103        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1104        output for future testreport verification (unfinished).
1105    o pkg/atm_phys:
1106      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1107        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1108        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1109    o pkg/seaice
1110      seaice_calc_ice_strength.F: modify expression to avoid divisions
1111        (affects truncation)
1112      seaice_do_ridging.F: clean up the insectarium
1113      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1114      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1115      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1116      - add some debugging information and error messages (warnings)
1117    o model/src: modifications relatd to atmosphere p*:
1118      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1119      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1120        of vertical profile tRef in geopotential background and anomaly.
1121      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1122        and pkg/atm_phys.
1123      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1124        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1125    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1126    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1127        not used right now, but can be used in BGC packages to fix conservation.
1128    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1129        other packages too.
1130    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1131        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1132    o model/src:
1133      - since we have several heat capacity (even in model/src), define "recip_Cp"
1134        as local variable (no longer in common block) to avoid any confusion.
1135      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1136    o pkg/exf:
1137      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1138        air density as function of air Temp, Humidity and atm pressure.
1139    
1140    checkpoint64w (2014/05/02)
1141    o verification:
1142      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1143        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1144        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1145        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1146        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1147    o model/src: for atmosphere in p* coords:
1148      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1149      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1150        but not yet activated.
1151    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1152      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1153      - this changes the results (but not for any verification experiment, because
1154        none tests this), but avoids having an extra field in the restart files
1155    o pkg/seaice: remove global variable TICE (not needed)
1156      - replace by TICES or local variable where necessary (cost_seaice_test,
1157        seaice_diagnostics_state)
1158      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1159      - use specific read/write routines for reading and writing individual leves
1160        of a multilevel field
1161    o pkg/ctrl & model/inc:
1162      - move additional anomaly fields of control vars (related to options:
1163         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1164        from DYNVARS.h into new header file: CTRL_FIELDS.h
1165    o pkg/seaice: some small modifications to the ridging code
1166      - make fw2ObyRidge a global variable and add the freshwater flux to
1167        seaice_growth
1168      - pass actual thickness from seaice_prepare_ridging, so that it is
1169        computed only in one place and compute it in the same way as in
1170        seaice_growth
1171      - initialise more fields in seaice_do_ridging that where cause floating
1172        point exceptions over land
1173  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1174    - 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
1175      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
1176      advection call the actual ridging routine;      advection call the actual ridging routine;
1177    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1178      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1179    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1180    - 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
1181      more readable (this is probably subjective)      more readable (this is probably subjective)
1182    - 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
1183      conditions in the correct category      conditions in the correct category
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