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revision 1.2032 by jmc, Sun Jul 27 18:04:14 2014 UTC revision 1.2194 by jmc, Tue Oct 27 23:59:53 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/atm_compon_interf & ocn_compon_interf:
8      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
9        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
10      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
11    o pkg/atm_ocn_coupler:
12      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
13    o pkg/rbcs:
14      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
15        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
16      - add a short report (to STDOUT) about RBCS-mask settings.
17    
18    checkpoint65p (2015/10/23)
19    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
20        there is no adjoint test for EVP, we don't know what it does to the adjoint
21        solution, but at least there are no more recomputation warnings left
22    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
23        a chance of giving the same results as a fully converged VP (JFNK) solver
24    o tools/adjoint_options/adjoint_diva:
25      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
26    o pkg/streamice:
27      - spotted bug in streamice_driving_stress using dyG where should have been dxG
28    o pkg/exf:
29      - remove STOP statement that prevented to use wind or (wind-)stress
30        interpolation for constant-in-time forcing fields (wind/stress period = 0).
31    o pkg/seaice:
32      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
33        5 additionals 2D fields and 6 new store directives
34      - change logic in seaice_readparms.F: EVP code can now be turned on in
35        various ways, setting SEAICE_deltaTev is no longer required,
36        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
37        or SEAICEaEVPcoeff
38    o pkg/shelfice/shelfice_thermodynamics.F
39      - redefining uLoc/vLoc to u/v, instead of 2u/v
40    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
41      - this is an intermediate state of a truely converging EVP that has
42        the potential of outperforming implicit VP methods, I do not recommend
43        using it yet.
44      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
45        and all parameters are hardwired
46      - for convergence it still requires very smooth regularisations, that means,
47        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
48        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
49        specific averaging appears to be required, still subject to tuning
50      - still needs cleaning and I need to turn parameter into runtime parameters
51      - add code to compute and print residuals of iteration, compile with
52        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
53    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
54      that entered with r1.54 on Sep04, 2015, -> update results
55    
56    checkpoint65o (2015/09/14)
57    o pkg/mom_vecinv & mom_common:
58      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
59        called from there.
60      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
61        allows to use Vector-Invariant form in deep atmos and anelastic formulation
62    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
63      and Koenig-Beatty+Holland (2012)
64      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
65      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
66      - requires an extra input argument for S/R seaice_calc_viscosities
67      - tensileStrength's depth dependence is different from Itkin et al. (2015)
68        (to be changed and played with, for now exponential)
69    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
70      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
71        by AREA according to Connelly et al. (2004), JPO.
72      - For EVP and the LSR solver, the implicit part of the drag term is
73        the only non-zero term in the denominator when there is no ice (which
74        prevented running the model with zero ice-ocean drag). If
75        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
76        (or zero main diagonals BU/BV) which need to be caught. A practical
77        consequence is that for open water, the momentum equation reduce
78        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
79        they happen to be zero, often leading to a non-zero solution over
80        open water.
81    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
82        efficient EVP method.
83      - introduce area-weighted averages for e12 (analogously to
84        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
85        remain, but also changing the order of terms in the previous average
86        changed the results as much) -> update experiment
87      - add SEAICE_DELTA_SMOOTHREG code
88      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
89        TEM-code
90      - adjust loop bounds so that only required fields are computed
91      - add new averaging code for zetaZ/deltaZ (again similar to
92        seaice_calc_viscosities.F), inactive by default for now (will change
93        results again), but will replace old code eventually
94    o eesupp/src:
95      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
96        to always cumulate tile local-sum in the same order
97        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
98        Still uses MPI_Allreduce (like standard code) but on array of tiles
99        and should be faster than GLOBAL_SUM_SEND_RECV code.
100      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
101        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
102      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
103         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
104         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
105         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
106         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
107    
108    checkpoint65n (2015/07/29)
109    o pkg/thsice:
110      - add a warning when used with pkg/aim but without updating SST
111        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
112    o pkg/offline:
113      - change where Offline-Fields are loaded, from load_fields_driver.F to
114        directly within FORWARD_STEP, just after updating iter number and time;
115      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
116        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
117       These changes allow:
118        a) to recover exactly on-line results using deltaToffline=deltaTClock,
119        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
120        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
121        time-step, both with GM & KPP files and with recomputing these fields;
122        b) no needs to switch on staggerTimeStep anymore;
123        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
124      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
125    o pkg/offline:
126      - change (rarely used) offset-iteration parameter to an offset time (in s):
127        can easily recover previous offset-iter effect by setting offset-time
128        (offlineTimeOffset) to offset-iter x deltaToffline;
129      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
130        in KPP as part of surface buoyancy forcing) in offline run.
131      - fix ptracers KPP non-local term in the case where KPP is re-computed.
132    o OpenAD
133      - Adding preliminary ggl90 test to OpenAD verification.
134        Config. with ggl90 currently diverges after 64 time steps
135        so will need more work to become more stable
136      - Adding preliminary kpp test to OpenAD verification.
137        required small tweakes in kpp_routines.F
138      - Merge and update from Krishna Narayanan's contrib area:
139        * Add one variable for preliminary OpenAD DIVA
140        * Add replacement time-stepping for OpenAD DIVA
141        * genmake2 flag -diva (but only for OpenAD; preliminary)
142        * required modifs for OAD_support
143        successful preliminary test for tutorial_global_oce_biogeo/
144    o pkg/seaice:
145      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
146      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
147        delta with a smooth function in s/r seaice_calc_viscosity
148        (no effect on EVP)
149      - rename local suffix "sqr" into "sq" for more consistent variable names
150    o pkg/seaice:
151        add new parameter SEAICE_deltaMin that is used ***only***
152        for regularizing Delta (and nothing else, like the parameter
153        which is also used for all sorts of things SEAICE_EPS).
154        Defaults to SEAICE_EPS for backward compatibility only.
155    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
156        the wrong key by inialising it before use -> fixes a recomputation
157        problem but does not fix the gradient
158    o pkg/layers:
159      - move resetting of flux arrays to outside the iLa loop
160        (this caused layers_diapycnal to not work with more than one layer coord.)
161      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
162    o pkg/layers:
163      - remove from common block 3D layers fields (used to diagnose transport
164        in tracer coords) and declare them as local arrays in layers_calc.F
165    o pkg/seaice:
166      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
167        in lab_sea forward experiment (changes results -> updated)
168      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
169    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
170       computations; for SEAICE_VECTORIZE_LSR
171      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
172        sweep to the outside,
173      - remove store directives and add "CADJ loop sequential" directives
174        in analogy to model/src/solve_tridiagonal.F
175      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
176        boundaries to yield more readable code. This has also the charming side
177        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
178        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
179        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
180        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
181        an additional option)
182       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
183       but the adjoint gradients (which are affected by this change) still explode.
184    o coupler (atm & ocn _compon_interf):
185      - avoid using Exch2 IO mapping if not suitable.
186    
187    checkpoint65m (2015/06/15)
188    o pkg/layers:
189      - clean-up old parameters setting (from Sep 2012):
190        + remove old parameters setting from common block (declared locally);
191        + stop if any old parameter is mixed with new parameters;
192        + check for valid or consistent parameter setting (e.g., layers_name)
193      - check that layers_bounds for Pot.Density are in the right range;
194        this is supposed to catch un-updated setting after recently shifting
195        potential density field "prho" by -1000 (now in "sigma" scale).
196    o pkg/layers:
197      - Added missing call to layers_fill for keeping track of tottend in
198        pkg/diagnostics/diagnostics_fill_state.F
199    o pkg/layers:
200      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
201        of diapycnal fluxes
202    o pkg/layers:
203      - reverted changes to interpolation to previous treatment; there
204        was never actually a problem
205    o pkg/layers:
206      - fix interpolation of layers tracers in the presence of partial cells
207      - add lots of new functionality to compute water mass transformation
208        (enabled by CPP flag LAYERS_THERMODYNAMICS)
209      - add new calls from main code (diags_oceanic_surf_flux.F,
210        thermodynamics.F, impldiff.F) and gad to save the necessary fields
211        for layers_thermodynamics calculations
212    o pkg/ptracers:
213      - add capability of stepping a passive tracer forward without advection
214        by setting PTRACERS_advScheme to 0.
215    o pkg/diagnostics:
216      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
217    o pkg/layers:
218      - shift potential density field "prho" by -1000 for density layer averaging so
219        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
220        Note that density bin boundaries (layers_bounds in data.layers) have
221        to be set accordingly (i.e., shifted, in sigma scale).
222    o pkg/layers:
223      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
224      - fix calculation of layer non-weighted velocity and layer probability
225      - add diagnostics for pot.density used for layer averaging
226    o pkg/seaice:
227      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
228        positiveness, modify a few comments and improve variable names,
229      - the changed computation of deltaC affects most seaice-related
230        experiments at the truncation level.
231        seaice_itd.thermo is affected by far the most, with
232        only 7 digits of agreement remaining; update experiments.
233    
234    checkpoint65l (2015/05/04)
235    o pkg/shelfice:
236      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
237        factor drKp1 to zero where it is negative (ie. do not use
238        SHELFICEBoundaryLayer if hFacC>1)
239      - the same for factor drLoc in shelfice_forcing.F
240    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
241        with modules in ptracers, when using testreport option "-small_f"
242    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
243      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
244    o verification/testreport
245      - add new option -small_f
246        with this option testreport first makes the target small_f (*.f files)
247        before running make (all). This is useful for explicit inlining when
248        all sources need to be full available.
249    o pkg/exf/exf_interp.F:
250        remove previous changes related to reverse (decreasing) input grids latitude
251    
252    checkpoint65k (2015/04/01)
253    o pkg/ecco:
254        fix missing cosphi initialization; use eccoiter in place of optimcycle;
255        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
256        instead of active read/write
257    o pkg/ctrl:
258        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
259        instead of active read/write.
260    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
261        return if .NOT.useAUTODIFF
262    o pkg/seaice: add CPP brackets (cost function related).
263    o model/src:
264        add useAUTODIFF run time switch.
265    o pkg/exf/exf_interp.F:
266        add code to allow input grids with latitude starting in the north (i.e. when
267        j=1 corresponds to northern edge of field); modify global_with_exf to test
268        this feature.
269    o verification/testreport:
270      - replace "grep -A3" with POSIX conformal sed command, because there are
271        implementations of grep that cannot do contextual searches
272      - replace "cat -n" by "nl" (two occurrences), because not all implementations
273        of "cat" have the option "-n"
274    o model/src:
275        add new file gsw_teos10.F that contains 3 functions, more or less a copy
276        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
277        convert from conservative to potential temperature. For now they are not
278        called anywhere.
279    o pkg/ggl90: make "useIDEMIX" useful
280      - re-organize code in s/r ggl90_calc a little to move computations that
281        are different for idemix into separate loops (changes verification
282        experiment idemix at truncation level, 12 digits remain -> updated)
283      - requires 2 new 2D fields KappaM, verticalShear
284      - make hFacI and recip_hFacI local 3D variables that are passed to
285        s/r ggl90_idemix
286      - fix and improve some comments
287    
288    checkpoint65j (2015/02/25)
289    o pkg/openad
290      - synchronize seawater.F with version in model/src: replace routine
291        body of sw_temp by calling sw_ptmp and fix/add a few comments.
292    o pkg/mnc:
293      - change default value of pickup_read/write_mnc params to FALSE
294        (since few features are missing in reading MNC pickup files).
295    o model/src:
296      - change default (background) vertical diffusivity for salt to be the
297        temperature (background) vertical diffusivity.
298      - change background vertical diffusivity in vertical mixing pkgs ggl90,
299        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
300        This makes ptracers default diffusivity (that uses salt diffKr) more
301        consistent with vertical mixing schemes.
302    o verification/testreport:
303      - fix typo in "-pcls" option ;
304      - put temp files in /tmp (instead of in local dir)
305      - add option "-ncad" to use genmake2 new option "-nocat4ad"
306      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
307    o pkg/ggl90 (idemix code):
308      - apply few fixes ; add some missing "_d 0" ; update output of exp.
309        global_ocean.90x40x15.idemix
310    o OpenAD
311      - enable active file I/O and begin removal of work-around code
312        for OpenAD for handling control variables (memory vs. active files)
313      - new CPP options file OPENAD_OPTIONS.h
314      - revert to genarr2d gradient check for hs94.1x64x5
315      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
316      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
317    o tools/genmake2:
318      - add option for an alternative Makefile (from Martin) where multiple
319        source files are sent to TAF (instead of all in one file).
320    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
321      - code provided by Carsten Eden as an extension of ggl90
322      - so far the code is turned on within ggl90 by setting a CPP-flag at
323        compile time; a runtime flag implementation is not yet complete
324      - tested in new verification experiment global_ocean.90x40x15.idemix
325    o verification:
326      - reduce length of the AD test run by half for experiments
327        global_ocean.cs32x15 (std + thsice) and isomip
328      - enable active file I/O for OpenAD, adjust verifications accordingly
329      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
330    o verification/testreport:
331      - fix two non-POSIX sed statements so that there are no error messages
332        on Mac OS X
333      - replace hostname -s with hostname | sed 's/\..*$//'
334    o model/src/seawater.F:
335      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
336        (following the matlab code), which would have avoided the bug caught
337        by Matt (see below) in the first place
338    o pkg/shelfice:
339      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
340        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
341      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
342        ice-shelf case (i.e., within surface level).
343      - add config summary in shelfice_check.F
344      - remove global variable recip_SHELFICElatentHeat and replace by a local
345        variable recip_latentHeat
346      - introduce diagnostics for friction velocity uStar (in case of
347        SHELFICEuseGammaFrict)
348      - change verification experiment isomip.htd:
349        + start from pickup (as input_ad at nIter0=8640)
350        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
351        + test SHELFICEuseGammaFrict = .TRUE.
352        + test SHELFICEadvDiffHeatFlux = .TRUE.
353    o model/src:
354      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
355        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
356        update output of experiments global_with_exf.yearly and isomip (all 6).
357    o pkg/shelfice:
358      - change setting of kTopC to also be zero where there is no ice-shelf.
359      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
360        ice-shelf is.
361      - first attempt to get RealFreshWaterFlux effects: for now, only without
362        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
363    o pkg/seaice: add the option to prescribe a fixed thickness PDF
364      for thermodynamic calculations
365      - because of divisions of the type 7/7 not exactly equal to 1, this change
366        affects results of some verification experiments by up to 4 digits:
367        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
368        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
369        adjoint: lab_sea, lab_sea.noseaicedyn
370        -> updated
371    
372    checkpoint65i (2015/01/23)
373    o model/src:
374      - change units of frictionHeating field from W to W/m^2
375      - fix bug in frictional heating from stratospheric drag in
376        S/R ATM_PHYS_TENDENCY_APPLY_V
377      - with synchronous time-stepping: move resetting to zero of frictionHeating
378        field from load_fields_driver.F to thermodynamics.F ;
379      - add diagnostics for frictional heating.
380    o model/src & gmredi K3D:
381      - add frictionHeating field to pickup-files (for synchronous time-stepping)
382      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
383      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
384        and name in pickup file).
385      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
386    o model/src:
387      - move (from ini_forcing.F) initialisation of all arrays in header file
388        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
389        (since Nov 2012) with option selectAddFluid=1.
390    o pkg/shelfice:
391      - change units (+ document) of newly added field "shelfIceMassDynTendency"
392      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
393    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
394    o pkg/seaice: two new runtime parameters:
395      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
396        long overdue
397      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
398        parameterization of tensil stress for fast ice (does not do anything yet)
399    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
400        for LSR: move checking overlaps out of JFNK-if-block
401    o pkg/atm_phys:
402      - move copy of grid and dynamical fields out of atm_phys_driver.F into
403        new S/R ATM_PHYS_DYN2PHYS.
404      - fix level height for Linear Free-Surf case (to be consistent with
405        fixed-in-time pressure levels).
406    o pkg/mom_common (bottomdrag):
407      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
408        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
409        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
410    o pkg/shelfice (u/v_drag):
411      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
412      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
413        (now similar to shelfice_u_drag.F)
414      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
415        from mom_vecinv.F (similar to mom_fluxform calls).
416    o pkg/mom_common (bottomdrag):
417      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
418      - add options for alternative discretisation of velocity norm in quadratic
419        bottom drag: averaging of grid-cell-center KE to U.point and V.point
420        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
421        improves when averaging only the other component (e.g. vVel for U bottom
422        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
423      - add options (bottomVisc_pCell) to account for partial-cell in bottom
424        friction (no-slip BC) thus getting the true distance from the bottom;
425        off by default since this also reduces model stability (explicit bottom
426        friction). Changes produce different machine truncation with linear-drag
427        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
428        front_relax (bvp & mxl, 10 & 11 digits).
429    o model/src & mom pkgs:
430      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
431        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
432      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
433        just copy level Nr value to level Nr+1.
434    o doc:
435      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
436    o pkg/streamice:
437      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
438        SHELFICE.h: move array shelficemass to init_varia, initialise
439        from array shelficemassinit, which is set in init_fixed and
440        has option to be set from file; introduce array
441        shelficeMassDynTend array, set thru file in init_fixed
442      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
443        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
444        pkg/streamice
445      - shelfice_thermodynamics.F: call shelfice_step_icemass if
446        SHELFICEMassStepping = .true.
447      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
448    
449    checkpoint65h (2014/12/17)
450    o verification/global_ocean.90x40x15, global_ocean_ebm:
451      - update to generic controls.
452    o pkg/ctrl:
453      - ctrl_map_ini_genarr.F: test for igen>0
454      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
455      - move gentim2d part of ctrl_map_ini_genarr.F to
456        new separate routine : ctrl_map_ini_gentim2d.F
457      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
458        add time variable weights and cyclic controls (time mean,
459        seasonal cycle, etc) capabilities to gentim2d
460    o pkg/ecco:
461      - move reading of error, conversion to weights from
462        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
463    o global_oce_llc90, cs32:
464      - activte sbo.
465      - CTRL_SIZE.h : add maxCtrlProc.
466      - activate the new genctrl capabilities.
467      - update following reorganization of global_oce_input_fields.tar.gz  
468    o pkg/ctrl/ctrl_ad_diff.list:
469      - add missing ctrl_init_rec.f
470    o tools/OAD_support/keepOriginal:
471      - add ctrl_init_rec.F
472    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
473      - avoid recomputations of xx_gentim2d_dummy.
474    o momentum diagnostics:
475      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
476        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
477    o pkg/seaice/seaice_lsr.F:
478      - fix computation of BU/BV, make sure they are non-zero, only necessary
479        for cubed sphere exchanges and SEAICE_OLx/y>0.
480        This makes calling s/r fill_cs_corner_rl obsolete (removed).
481    o verification/global_ocean.cs32x15/input.seaice
482      - add test for strong implicit coupling and restricted addtive Schwarz
483        methods for LSR
484      - update results/output.seaice.txt
485    o verification/tutorial_global_oce_biogeo:
486      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
487        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
488        update output_adm,_oadm,_tlm.txt
489    o pkg/dic:
490      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
491      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
492        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
493    o verification/tutorial_global_oce_biogeo:
494      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
495        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
496        update output_adm,_oadm,_tlm.txt
497    o eesupp/src:
498      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
499        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
500    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
501      LSR (following Hutchings et al. 2004)
502      - introduce zetaZ as a global variable (requires adjustments in
503        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
504        in seaice_calc_viscosities.F
505      - new flag SEAICEuseStrImpCpl (default off)
506      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
507        momentum equations
508      - JFNK-solver (preconditioner) adjusted to allow using this method
509        (where it does not have any positive effect)
510    o pkg/seaice
511      - add overlap for restrictive additive Schwartz method also to LSR, but
512        turn it off by default (because it only seems to work for non-cubed
513        sphere/llc topologies)
514    o pkg/autodiff
515      - add extra exchanges in addummy_in_steppging also for mnc output
516    o pkg/seaice:
517      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
518        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
519    o pkg/obcs:
520      - add option to specify domain-connected piece Id along OB though files
521        (for now, only used to diagnose PhiVel; default =1 -> global correction)
522      - modify obcs_diag_balance.F to process each connected-part separately;
523        exclude OB where Id = 0 but keep the full divergence there (-> constant
524        Psi along this portion of OB and all inflow derived from grad(Phi))
525      - add example of OB-conect files in verification/so_box_biogeo/input.
526    o pkg/diagnostics:
527      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
528      a) use non zero matrix element across OB and solve for Phi 1 grid point
529         outside OB (i.e, where tracer OBCS are applied).
530      b) global imbalance of inFlow/outFlow across OB: instead of modifying
531         velocity across OB, spread it uniformly along the OB in the RHS.
532    
533    checkpoint65g (2014/11/19)
534    o pkg/diagnostcis:
535      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
536    o pkg/my82,pp81,kl10:
537      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
538        field diffKr as background diffusivity to set minimum diffusivity value.
539    o pkg/seaice:
540      - add new parameter SEAICEuseEVPrev (for revisited EVP by
541        Bouillon et al 2013)
542      - add SEAICE_evpAlpha/Beta to namelist
543      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
544        involve trivial re-ordering of divisions/multiplications that should not
545        have any effects, but ... they do change the results of lab_sea.hb87 so
546        that only 2 digits of agreement remain, in line with the general
547        instability/fragility of the evp-code. For now, I do not care and just
548        update the verification experiment
549    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
550      - remove xx_genarr2d_numsmooth etc
551      - use xx_genarr2d_preproc etc instead
552      - carry out smooth_correl2D at initialization stage rather than during
553        time stepping.
554      - get smoothOpNb from xx_gentim2d_preproc
555    o global_oce_cs32 :
556      - add test of generic ecco capabilities.
557    o pkg/exf/exf_getsurfacefluxes.F :
558      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
559    o pkg/ctrl,ecco :
560      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
561        is defined.
562    o pkg/seaice: add diagnostics for Delta (deformation parameter)
563    o model/src:
564      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
565        diffusivity (background) is specified but ignored.
566    o verification:
567      - in testreport, convert hostname to lower case for default output dir name
568    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
569    o pkg/dic: add modifications from Hajoon:
570      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
571      - light attenuation: add self-shading effect by climatological Chlorophyll
572        (read from file).
573    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
574        compiles when SEAICE_ALLOW_DYNAMICS is undefined
575    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
576        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
577        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
578        approach where CPP_OPTIONS.h includes an omnipotent
579        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
580    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
581        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
582    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
583        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
584        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
585    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
586      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
587      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
588      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
589      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
590    o pkg/ctrl,ecco,exf :
591      - remove variables associated with NON-generic costs,
592        unless ECCO_CTRL_DEPRECATED is defined.
593      - remove NON-generic NON-obcs controls,
594        unless ECCO_CTRL_DEPRECATED is defined.
595    o pkg/ctrl : added ctrl_local_params.h
596    o pkg/ecco : added ecco_local_params.h
597    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
598        experiments, which will progressively be removed once the
599        experiments are revised to use only generic controls/costs.
600    
601    checkpoint65f (2014/10/13)
602    o pkg/ctrl, ecco, seaice : minor changes in headers
603    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
604        cost function and control capabilities added since checkpoint65c.
605    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
606    o pkg/ecco: increase modularity and improve logic
607      - ecco_toolbox.F (new) : basic operations that are often used,
608        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
609        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
610      - cost_gencal.F (new) : determine filnames and records.
611      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
612      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
613        and exploit the above functions leading to more compact code.
614      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
615      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
616        using_ers, using_gfo, using_mdt is now only defined within gencost)
617    o pkg/ecco: extend generic cost capabilities
618      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
619        capabilities via gencost_preproc (+ _c,_i,_r related params),
620        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
621        gencost_outputlevel arguments to cost_generic
622      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
623        and active_read, making room for gencost_preproc to take effect.
624        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
625      - pkg/ecco/cost_generic.F :
626        compute and store misfit maks*(model-data) in localdif that is
627        then used in cost and for output, output misfit if outlev.GT.0
628      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
629        rather gencost_barfile for deciding whether to write barfile
630      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
631      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
632        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
633      - pkg/ecco/ecco_summary.F : report gencost variables
634      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
635    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
636    o pkg/ecco: internal re-organization
637      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
638        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
639        mv relevant variables definition from ecco_cost.h to ecco.h,
640        make sure gencost routines only include ecco.h)
641      - throughout : add missing CCP switches, rm unused variables,
642        and rm un-necessary CPP switches
643      - throughout gencost routines : replace modelstartdate with
644        gencost_startdate when needed
645      - cost_bp_read.F : use arguments, instead of common blocs
646        so that it can be used also by (new) cost_gencost_bpv4.F
647      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
648      - ecco_phys.F : compute etanFull
649      - ecco_readparms.F : rename using_topex as using_tpj, add
650        bpv4-grace to gencost list, initialize added parameters
651      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
652    
653    checkpoint65e (2014/09/28)
654    o pkg/obcs:
655      - replaced the just-added CPP options with run-time variables
656        (see pkg/obcs/OBCS_PARAMS.h for details)
657    o pkg/obcs:
658      - add additional CPP options for sponge boundary layers
659        (see pkg/obcs/OBCS_OPTIONS.h for details)
660    o pkg/atm_phys:
661      - implement simple (obliquity only, assuming circular planet orbit)
662        seasonal cycle for incoming insolation ; used when run-time parameter
663        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
664    o pkg/exf, pkg/ecco, pkg/ctrl:
665      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
666      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
667      - implement gentim2d for xx_tauu, xx_tauv
668    o pkg/ctrl, pkg/ecco :
669      - fix and complement the generic controls implementation
670    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
671        pkg/shelfice/shelfice_thermodynamics.F,
672        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
673        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
674      - add weight in CTRL_GET_GEN calls
675    o pkg/ctrl :
676      - ctrl_get_gen.F : add weight as input parameter, and apply
677        it directly rather than using smooth_correl2Dw (to be retired).
678      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
679    o pkg/ctrl :
680      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
681        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
682      - re-activate ctrl_summary (call in ctrl_init.F)
683    o pkg/ctrl/ctrl_cost_gen.F :
684      - fix CCP brackets, remove un-necessary myiter, mytime
685    o pkg/ecco, pkg/ctrl :
686      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
687      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
688      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
689      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
690    
691    checkpoint65d (2014/09/15)
692    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
693      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
694        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
695    o pkg/ctrl/ctrl_map_ini_genarr.F :
696      - remove compilation failure
697      - replace hard coded example
698      - use ctrl_map_ini_gen2D, 3D
699    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
700      - on/off switch based upon xx_genarr2d_weight,3d
701    o src/packages_init_variables.F :
702      - regroup pkg/estimation calls
703      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
704        (moved to ctrl_init_variables)
705    o cost/cost_init_varia.F :
706      - remove ecco_cost_init_varia
707        (moved to ecco_init_varia)
708    o ctrl/ctrl_init_variables.F :
709      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
710      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
711    o ctrl/ctrl_map_ini.F :
712      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
713        (moved to ctrl_init_variables)
714    o ctrl/ctrl_map_ini_ecco.F :
715      - remove ECCO_PHYS (mv to ecco_init_varia)
716      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
717    o ecco/ecco_ad_diff.list :
718      - add ecco_init_varia.f
719    o ecco/ecco_init_varia.F
720      - new routine
721    o pkg/streamice:
722      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
723        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
724      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
725    o pkg/generic_advdiff:
726      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
727    o pkg/exf:
728      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
729         xxg_precip capability
730      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
731    o pkg/ctrl:
732      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
733    o model/src/load_fields_driver.F :
734      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
735        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
736    o OpenAD verification experiments:
737      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
738        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
739        for now, only in pkgs used in OpenAD verification experiments.
740      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
741        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
742        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
743        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
744    o OpenAD verification tests:
745      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
746      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
747        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
748      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
749        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
750    o model/src & generic_advdiff:
751      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
752        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
753        dynamics requires valid tracer forcing only over tile interior but, for
754        some diagnostics, may need to extend it over 1 point in tile halo region.
755      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
756        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
757        setting in temp/salt/ptracer_integrate.F
758    o pkg/dic:
759      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
760        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
761        in gchem_forcing_sep.F
762    o pkg/autodiff & obcs:
763      - add storage of current OB values for U & V (was already done for T & S).
764    
765    checkpoint65c (2014/08/30)
766    o pkg/dic:
767      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
768        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
769        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
770    o verification:
771      - new experiment testing OBCS and DIC pkgs, using params & output from
772        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
773        passage: take OBCS from the last year of a 2 yrs simulation and initial
774        conditions from t=1.yr while keeping the same forcing.
775    o model/src:
776      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
777        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
778    o pkg/diagnostics (Stats-Diags):
779      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
780        a) refine region where stats are computed, excluding where arrhFac=0 ;
781        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
782        c) extend regional stats over the region edges (for U or V pt location).
783    o pkg/gchem:
784      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
785        pkg/dic is currently changing/updating ptracers values beyond the OB).
786    o verification (hs94):
787      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
788        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
789        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
790        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
791    o pkg/ptracers:
792      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
793        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
794      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
795        with AB-2 code (so that it get tested).
796    o model/src:
797      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
798        with AB-2 code (previously only available with AB-3 code).
799        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
800        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
801        there, by calling CYCLE_AB_TRACER).
802    o pkg/generic_advdiff:
803      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
804        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
805        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
806        S/R temp/salt/ptracers_integrate.F
807    o model/src & pkg/ptracers:
808      - remove common block variables gT,gS (in DYNVARS.h), except when
809         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
810      - remove common block variable gPtr.
811    o model/src & pkgs:
812      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
813         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
814         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
815         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
816      + change accordingly all calling S/R.
817      - use local temperature/salinity/ptracer tendency array (without bi,bj)
818        in S/R temp/salt/ptracers_integrate.F
819    o pkg/seaice:
820      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
821        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
822      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
823        in seaice_lsr
824      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
825        in s/r seaice_lsr_calc_coeffs
826    o pkg/mdsio:
827      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
828        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
829        too long (e.g., > MAX_LEN_FNAM/2 )
830    
831    checkpoint65b (2014/08/12)
832    o pkg/matrix:
833      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
834    o model/src:
835      - fix initialisation of geothermalFile; compile geothermal-flux code in
836        natl_box verification experiment.
837    o model/src & pkg/down_slope:
838      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
839      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
840        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
841        results at machine truncation level: update output of experiments
842        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
843    o pkg/diagnostics (Stats-Diags):
844      - do not cumulate the full volume when DIAGNOSTICS_FILL is
845        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
846        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
847        times (but Min,Max and StD are still wrong).
848    o model/src:
849      - add geothermal flux forcing: read in ini_forcing.F as time-constant
850        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
851    o model/src:
852      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
853        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
854        arrays are already updated while adjustments (filters, conv.adjustment) are
855        still applied later, in S/R TRACERS_CORRECTION_STEP.
856    o model/src:
857      - store in common bloc array "rhoInSitu" the virtual potential temperature
858        anomaly that is used to compute geopotential: this make the atmos code
859        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
860    o pkg/seaice/seaice_lsr.F
861      - rename integer variable ilcall to ipass (that's what it is called
862        in the residual diagnostics
863      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
864        default) for improved non-linear convergence of the first few steps
865      - adjust a few comments and add new ones to explain some of the store
866        directives
867    o pkg/generic_advdiff (& ptracers):
868      - re-work the code to check for valid advection scheme and for minimum
869        size of overlap (now stored in local common bloc in gad_advscheme.F)
870    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
871      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
872      - add an auxilliary variable "bet" and fix store directives and keys in
873        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
874        less exact gradients in my tests); but there are still
875        recomputation warning (although gradients are sort of OK), when
876        SEAICE_LSR_VECTORIZE is not defined, so this flag and
877        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
878      - update verification experiments lab_sea.
879      - change some comments in S/R seaice_calc_viscosities
880    o model/src:
881      - if staggerTimeStep=T, always apply exchange to velocity field in
882        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
883        (independent of using multi-dim advection or not); no effect on FWD run
884        but affects AD results (at machine truncation level): update output of
885        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
886        and isomip (oad: 12.d).
887    o pkg/generic_advdiff:
888      - stop if doAB_onGtGs is set to FALSE but ignored
889      - refine warning related to stability of tracer time-stepping
890        regarding internal wave dynamics.
891      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
892        on staggerTimeStep & implicitIntGravWave (will now get a warning
893        if potentially unstable).
894    o pkg/kl10:
895      - add new pkg "kl10" for mixing due to internal wave breaking, from
896        http://www.sciencedirect.com/science/article/pii/S1463500310000144
897        (contribution from Jody Klymak), tested in verification experiment
898        verification/internal_wave/input.kl10/
899    o isomip experiment:
900      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
901        (input.htd) and update the output.
902    o cd_code experiments:
903      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
904        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
905        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
906        update the corresponding output.
907    o pkg/seaice:
908      - reduce the number of include files and store directives in
909        S/R seaice_lsr_tridiagu/v
910      - change the order of loops in one case in S/R seaice_lsr_tridiagv
911        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
912        get rid off one store directive (a TAF bug?)
913      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
914        S/R seaice_lsr_tridiagv to change the loop range for consistency
915      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
916      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
917        S/R seaice_lsr_tridiagu/v (requires update of
918        offline_exf_seaice/input.dyn_jfnk)
919    
920  checkpoint65a (2014/07/27)  checkpoint65a (2014/07/27)
921  o model/src:  o model/src:
922    - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than    - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
# Line 18  o model/src: Line 931  o model/src:
931    - collect T & S forcing tendency into local 2-D array (passed as argument to    - collect T & S forcing tendency into local 2-D array (passed as argument to
932      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
933      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
934      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
935      moist correction due to vertical advection).      correction due to vertical advection).
936    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
937      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
938      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
# Line 48  o pkg/seaice: more clean up Line 961  o pkg/seaice: more clean up
961      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
962      this experiment):      this experiment):
963      > size mitgcmuv_ad      > size mitgcmuv_ad
964      text    data        bss     dec        hex        text    data        bss     dec        hex
965      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
966      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
967      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
968      text    data        bss     dec        hex      text    data        bss     dec        hex
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