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revision 1.2085 by gforget, Tue Oct 21 14:22:26 2014 UTC revision 1.2249 by jmc, Wed May 4 23:20:38 2016 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate  o model/src (non-hydrostatic free-surface):
8    AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than    - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
9    ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,      was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
10    approach where CPP_OPTIONS.h includes an omnipotent    - Calculate surface vertical velocity after 2-D solver adjustment (accounts
11    ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').      for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
12  o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where      and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
13    ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.      This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
14      - Update output (changes at machine truncation level) of verification exp:
15        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
16        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
17    o pkg/seaice: ITD code
18      - fix picking up from a single category model by initialising
19        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
20      - split a long warning message in seaice_check_pickup.F into two lines,
21        because NEC SX-ACE cannot deal with the long line.
22    o model/src:
23      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
24    o pkg/seaice:
25      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
26    o pkg/seaice:
27      - add basal stress as parameterisation for grounding ice
28        following Lemieux et al. (2015)
29      - turn on by setting new parameter SEAICEbasalDragK2 to a value
30        larger than 0. Lemieux et al. (2015) recommend 15.
31      - The adjoint complains with extra recomputations so there is also a
32        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
33        order to postpone the problem
34      - compile the new code in lab_sea
35    o verification/halfpipe_streamice:
36      - update both TAF and OpenAD adm output (machine truncation differences)
37    
38    checkpoint65v (2016/04/08)
39    o verification/advect_xz:
40      - increase overlap size from 3 to 4 and add new secondary test for PQM
41        advection scheme (with mono & wino limiter).
42      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
43    o model/src:
44      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
45        added phi0Ref) to set vertical axis origin and phiRef origin;
46        keep Ro_SeaLevel for backward compatibility (with a warning).
47       According to coordinate and fluid type:
48        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
49        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
50        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
51        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
52      - remove Ro_SeaLevel from ATM experiment parameter files;
53      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
54        complement; update output.txt (changes at machine truncation level).
55    o pkg/seaice/seaice_evp.F
56      - simplify computation of deltaZ and zetaZ to simple averaging following
57        Bouillon et al. (2013). This removes a lot of code, but also changes
58        verification experiment lab_sea.hb87 -> updated
59    
60    checkpoint65u (2016/03/14)
61    o pkg/generic_advdiff:
62      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
63        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
64        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
65        testing and not for actual use.
66    o model/src:
67      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
68        origin r = rF(1);
69      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
70        in EOS for height coordinate: enable to include NH Pressure or to use
71        more accurate pressure vertical profile; options not linked to EOS type
72        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
73      - start to implement variable gravity (along vertical): for now, only with
74        z-coords (not even z*).
75      - add Ideal Gas equation of state for height coordinate.
76      - update OpenAD output (affected at machine truncation level) of exp:
77        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
78    o pkg/exf:
79      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
80        of exf interpolation (before any rescaling, rotation or interpolation
81        to velocity point) for each field that gets loaded from file. This option
82        identically mimics the input file organization (e.g. record numbers in year
83        by year input files) besides the change in horizontal grid.
84      - add rotateStressOnAgrid run-time switch so that wind stress fields
85        can be provided on the A-grid in zonal/meridional direction and
86        rotated on the fly. This only applies to the case when the exf
87        interpolation is off and rotateStressOnAgrid is false by default.
88    o model/src:
89      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
90        it's also used with pkg/atm_phys) and add few more parameters (but still
91        inactive, src code yet to come)
92    
93    checkpoint65t (2016/02/10)
94    o pkg/atm_phys:
95      - from Ruth Geen: add optical depth dependence on CO2 concentration.
96    o model/src:
97      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
98        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
99        Update output of exp. deep_anelastic (changes at truncation level).
100    o tools:
101      - add a hack in "remove_comments_sed" (used only with TAF) for recent
102        version of OpenMPI (shipped with FC.23): comment out the new header
103        file "mpif-sizeof.h" which causes problems to TAF.
104    o pkg/seaice:
105      - change the termination criterion so that maxits (SEAICElinearIterMax)
106        has an effect
107      - unify iteration parameters for implicit solvers (JFNK and Picard)
108        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
109        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
110        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
111        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
112        SEAICEnonLinTol     replaces JFNKgamma_nonlin
113      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
114      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
115        use with SEAICEuseKrylov
116    o pkg/seaice/seaice_lsr.F
117        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
118        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
119        an effect.
120    o pkg/seaice: add two new parameters
121      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
122        parameter is not in any namelist)
123      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
124        a preconditioner for the non-linear Newton iteration of the JFNK
125        solver
126    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
127      affects some experiments at truncation level:
128      - global_ocean.cs32x15.icedyn (11 digits),
129      - global_ocean.cs32x15.seaice (11 digits),
130      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
131      - also update global_ocean.cs32x15 adjoint and tangent-linear results
132    o pkg/salt_plume & pkg/thsice:
133      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
134        connect salt_plume flux to ATM-OCN coupling pkgs interface:
135       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
136         export to coupler interface) even without compiling pkg/salt_plume ;
137       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
138         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
139    o pkg/dic:
140      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
141        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
142        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
143      - move also update with values from ATM-OCN Coupler in the same new S/R
144        (previously done in ocn_apply_import.F).
145    o tools/adjoint_options:
146      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
147        has been changed on Jan 14, 2016.
148    o pkg/ggl90:
149      - add alternative discretisation of vertical shear (off by default), to
150        compute the mean (@ grid-cell center) of vertical shear compon instead of
151        vertical shear of mean flow (@ grid-cell center).
152      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
153        results on adjacent faces of cubed-sphere grids; this fix the restart.
154    o pkg/atm_compon_interf:
155      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
156        pass last value, stored directly before export to CPL ;
157        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
158      - remove atmSLPr from pickup files (no longer needed for restart)
159    
160    checkpoint65s (2016/01/13)
161    o eesupp & genmake2:
162       - first check for Function ETIME and, if it fails, then check for subroutine
163         ETIME and consistent output; use the appropriate version in timers.F
164    o model/src:
165      - to check restart test, add option to apply EXCH to U,V earlier, just before
166        integr_continuity; turned off by default.
167    o pkg/dic:
168      - remove CPP option USE_ATMOSCO2 (not needed)
169    o tools/tst_2+2:
170      - try to ignore difference between +0 and -0 in binary file, causing test
171        to fail for no good reason.
172    o eesupp & genmake2:
173      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
174        but also check (in genmake2) that test runs and returns meaningful results.
175    o coupler pkgs:
176      Finish implementation of optionally-exchanged variable switches (started on
177       Nov 12) with addition of few more exchanged fields, including 2-way exchange
178       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
179       advection in OCN component; this requires sequential coupling.
180      coupler (pkg/atm_ocn_coupler):
181      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
182        routines (useful for debug).
183      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
184         flux, DIC fields) if corresponding switch is ON.
185      - add option to export RunOff to OCN (to use for DIC river input)
186      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
187      components (pkg/atm_ & ocn_compon_interf):
188      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
189        optionally exchanged fields; add a check & stop in cpl_readparms.F.
190        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
191        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
192      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
193        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
194      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
195      - hold in common block coupler optionally-exchanged variable switch
196        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
197      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
198        this is intended to replace the OCN cplFldtave.* output files (not updated
199        to contain new additional exchanged fields).
200    o pkg/dic:
201      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
202    o pkg/thsice:
203      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
204        and writing of thsice pickup files.
205    o pkg/atm_compon_interf:
206      - move all field individual export-call out of cpl_export_import_data.F
207        into new S/R ATM_EXPORT_FIELDS
208    o pkg/atm_compon_interf:
209      - store state variables (for now, only thSIce fields) just before beeing
210        exported (in cpl_export_import_data.F, like on ocean side) instead of from
211        atm_store_my_data.F like all exported fluxes.
212      - new version of pickup_cpl: write field names into meta file and read meta
213        file to find field postion in pickup. Also only write/read fields meeded for
214        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
215    o pkg/dic:
216      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
217    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
218        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
219        value can be from domain [0,1] to average between the two methods
220    o pkg/atm_phys:
221      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
222        hold fixed in time).
223    
224    checkpoint65r (2015/12/21)
225    o pkg/seaice:
226        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
227        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
228    o pkg/seaice:
229      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
230        when SEAICEscaleSurfStress=.TRUE.,
231      - apply areaW and areaS in S/R seaice_calc_lhs
232    o pkg/atm_phys:
233      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
234        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
235        for individual contribution (convection, LSC cond, radiation)
236      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
237        information); activated with: solar_exponent=0. and wv_exponent=-1.
238    o pkg/ggl90:
239      - within IDEMIX add upper limit for horizontal group velocity to
240        avoid instability problems in the explicit horizontal diffusion term for
241        long time steps or high resolution
242    o pkg/diagnostics:
243      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
244        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
245    o testreport:
246      - remove "-v" (verbose option) in default mpirun command.
247    o pkg/seaice/seaice_growth:
248      - catch potential division by zero in ITD code, does not change
249        verification results
250    o pkg/ecco:
251      - retire old codes to the Attic. The calls to retired functions are
252        left in a commented form in case they ever need to be re-activated.
253      - ecco_check.F: issue warning if any old CPP option is
254        defined that corresponds to retired codes -- then stop.
255    o pkg/atm_compon_interf:
256      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
257        coupler: use last time-step value instead of average over cplSendFrq_iter
258        time-step, similar to what is done for seaIceMass.
259        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
260    o eesupp & genmake2:
261      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
262        <= remove until a fix is found for some ifort version on ia32 machine.
263    o pkg/seaice/seaice_evp:
264      - refine residual computation
265    
266    checkpoint65q (2015/11/18)
267    o pkg/seaice/seaice_evp:
268      - fix residual computations so that they no longer affect the actual
269        simulation code
270      - fix seaice_readparams to be able to actually set new parameters
271        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
272    o model/src:
273      - fix wrong truncation (single prec) from "FLOAT" function in expressions
274        like: deltaT*FLOAT(myIter) when myIter is large:
275         a) replaced by DFLOAT (if not seen by TAF);
276         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
277    o pkg/aim_v23:
278      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
279        when pickupSuff is set ; do write rolling pickups + at the end of the run.
280    o pkg/atm_ocn_coupler + ocn_compon_interf:
281      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
282        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
283        add corresponding call in DO_OCEANIC_PHYS.
284    o coupler pkgs:
285      Start a new way to set-up optionally-exchanged variables (previously, only
286       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
287       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
288       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
289       compononent param default can be set accordingly).
290      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
291       but rather applies to a group a fields (going both ways like for DIC)
292       and corresponds to an option of coupling config.
293      coupler (pkg/atm_ocn_coupler):
294      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
295        and read namelist directly (without eessup S/R calls) instead of
296        in the very un-flexible old way, 1 param per line, in fixed order;
297      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
298        cleanly in CPL_CHECK_CPLCONFIG
299      - add new coupling-exchange selectors (some not yet active) including
300        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
301                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
302      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
303        component ; called directly from coupler.F, after comp. registrations;
304      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
305         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
306          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
307      components (pkg/atm_ & ocn_compon_interf):
308      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
309        CPP header file in all pkg source files.
310      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
311        ATM/OCN_CHECK_CPLCONFIG;
312      - add error-counter to track errors (e.g., in "data.cpl") and to stop
313        cleanly in ATM/OCN_CHECK_CPLCONFIG;
314      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
315        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
316        before PACKAGES_READPARMS;
317      verification/cpl_aim+ocn/:
318      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
319        "data.cpl" for coupler (in input_cpl).
320    o eesupp/inc:
321      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
322        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
323        to always cumulate tile local-sum in the same order (still uses
324        MPI_Allreduce like standard code).
325      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
326        that are now identical to standard version (in eesupp/inc).
327    o pkg/shelfice:
328      - add SHELFICETransCoeffTFile for initializing spatially varying
329        heat and salt transfer coefficients
330    o pkg/atm_compon_interf & ocn_compon_interf:
331      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
332        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
333      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
334    o pkg/atm_ocn_coupler:
335      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
336    o pkg/rbcs:
337      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
338        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
339      - add a short report (to STDOUT) about RBCS-mask settings.
340    
341    checkpoint65p (2015/10/23)
342    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
343        there is no adjoint test for EVP, we don't know what it does to the adjoint
344        solution, but at least there are no more recomputation warnings left
345    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
346        a chance of giving the same results as a fully converged VP (JFNK) solver
347    o tools/adjoint_options/adjoint_diva:
348      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
349    o pkg/streamice:
350      - spotted bug in streamice_driving_stress using dyG where should have been dxG
351    o pkg/exf:
352      - remove STOP statement that prevented to use wind or (wind-)stress
353        interpolation for constant-in-time forcing fields (wind/stress period = 0).
354    o pkg/seaice:
355      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
356        5 additionals 2D fields and 6 new store directives
357      - change logic in seaice_readparms.F: EVP code can now be turned on in
358        various ways, setting SEAICE_deltaTev is no longer required,
359        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
360        or SEAICEaEVPcoeff
361    o pkg/shelfice/shelfice_thermodynamics.F
362      - redefining uLoc/vLoc to u/v, instead of 2u/v
363    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
364      - this is an intermediate state of a truely converging EVP that has
365        the potential of outperforming implicit VP methods, I do not recommend
366        using it yet.
367      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
368        and all parameters are hardwired
369      - for convergence it still requires very smooth regularisations, that means,
370        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
371        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
372        specific averaging appears to be required, still subject to tuning
373      - still needs cleaning and I need to turn parameter into runtime parameters
374      - add code to compute and print residuals of iteration, compile with
375        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
376    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
377      that entered with r1.54 on Sep04, 2015, -> update results
378    
379    checkpoint65o (2015/09/14)
380    o pkg/mom_vecinv & mom_common:
381      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
382        called from there.
383      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
384        allows to use Vector-Invariant form in deep atmos and anelastic formulation
385    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
386      and Koenig-Beatty+Holland (2012)
387      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
388      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
389      - requires an extra input argument for S/R seaice_calc_viscosities
390      - tensileStrength's depth dependence is different from Itkin et al. (2015)
391        (to be changed and played with, for now exponential)
392    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
393      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
394        by AREA according to Connelly et al. (2004), JPO.
395      - For EVP and the LSR solver, the implicit part of the drag term is
396        the only non-zero term in the denominator when there is no ice (which
397        prevented running the model with zero ice-ocean drag). If
398        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
399        (or zero main diagonals BU/BV) which need to be caught. A practical
400        consequence is that for open water, the momentum equation reduce
401        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
402        they happen to be zero, often leading to a non-zero solution over
403        open water.
404    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
405        efficient EVP method.
406      - introduce area-weighted averages for e12 (analogously to
407        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
408        remain, but also changing the order of terms in the previous average
409        changed the results as much) -> update experiment
410      - add SEAICE_DELTA_SMOOTHREG code
411      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
412        TEM-code
413      - adjust loop bounds so that only required fields are computed
414      - add new averaging code for zetaZ/deltaZ (again similar to
415        seaice_calc_viscosities.F), inactive by default for now (will change
416        results again), but will replace old code eventually
417    o eesupp/src:
418      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
419        to always cumulate tile local-sum in the same order
420        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
421        Still uses MPI_Allreduce (like standard code) but on array of tiles
422        and should be faster than GLOBAL_SUM_SEND_RECV code.
423      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
424        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
425      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
426         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
427         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
428         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
429         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
430    
431    checkpoint65n (2015/07/29)
432    o pkg/thsice:
433      - add a warning when used with pkg/aim but without updating SST
434        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
435    o pkg/offline:
436      - change where Offline-Fields are loaded, from load_fields_driver.F to
437        directly within FORWARD_STEP, just after updating iter number and time;
438      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
439        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
440       These changes allow:
441        a) to recover exactly on-line results using deltaToffline=deltaTClock,
442        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
443        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
444        time-step, both with GM & KPP files and with recomputing these fields;
445        b) no needs to switch on staggerTimeStep anymore;
446        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
447      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
448    o pkg/offline:
449      - change (rarely used) offset-iteration parameter to an offset time (in s):
450        can easily recover previous offset-iter effect by setting offset-time
451        (offlineTimeOffset) to offset-iter x deltaToffline;
452      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
453        in KPP as part of surface buoyancy forcing) in offline run.
454      - fix ptracers KPP non-local term in the case where KPP is re-computed.
455    o OpenAD
456      - Adding preliminary ggl90 test to OpenAD verification.
457        Config. with ggl90 currently diverges after 64 time steps
458        so will need more work to become more stable
459      - Adding preliminary kpp test to OpenAD verification.
460        required small tweakes in kpp_routines.F
461      - Merge and update from Krishna Narayanan's contrib area:
462        * Add one variable for preliminary OpenAD DIVA
463        * Add replacement time-stepping for OpenAD DIVA
464        * genmake2 flag -diva (but only for OpenAD; preliminary)
465        * required modifs for OAD_support
466        successful preliminary test for tutorial_global_oce_biogeo/
467    o pkg/seaice:
468      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
469      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
470        delta with a smooth function in s/r seaice_calc_viscosity
471        (no effect on EVP)
472      - rename local suffix "sqr" into "sq" for more consistent variable names
473    o pkg/seaice:
474        add new parameter SEAICE_deltaMin that is used ***only***
475        for regularizing Delta (and nothing else, like the parameter
476        which is also used for all sorts of things SEAICE_EPS).
477        Defaults to SEAICE_EPS for backward compatibility only.
478    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
479        the wrong key by inialising it before use -> fixes a recomputation
480        problem but does not fix the gradient
481    o pkg/layers:
482      - move resetting of flux arrays to outside the iLa loop
483        (this caused layers_diapycnal to not work with more than one layer coord.)
484      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
485    o pkg/layers:
486      - remove from common block 3D layers fields (used to diagnose transport
487        in tracer coords) and declare them as local arrays in layers_calc.F
488    o pkg/seaice:
489      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
490        in lab_sea forward experiment (changes results -> updated)
491      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
492    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
493       computations; for SEAICE_VECTORIZE_LSR
494      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
495        sweep to the outside,
496      - remove store directives and add "CADJ loop sequential" directives
497        in analogy to model/src/solve_tridiagonal.F
498      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
499        boundaries to yield more readable code. This has also the charming side
500        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
501        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
502        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
503        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
504        an additional option)
505       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
506       but the adjoint gradients (which are affected by this change) still explode.
507    o coupler (atm & ocn _compon_interf):
508      - avoid using Exch2 IO mapping if not suitable.
509    
510    checkpoint65m (2015/06/15)
511    o pkg/layers:
512      - clean-up old parameters setting (from Sep 2012):
513        + remove old parameters setting from common block (declared locally);
514        + stop if any old parameter is mixed with new parameters;
515        + check for valid or consistent parameter setting (e.g., layers_name)
516      - check that layers_bounds for Pot.Density are in the right range;
517        this is supposed to catch un-updated setting after recently shifting
518        potential density field "prho" by -1000 (now in "sigma" scale).
519    o pkg/layers:
520      - Added missing call to layers_fill for keeping track of tottend in
521        pkg/diagnostics/diagnostics_fill_state.F
522    o pkg/layers:
523      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
524        of diapycnal fluxes
525    o pkg/layers:
526      - reverted changes to interpolation to previous treatment; there
527        was never actually a problem
528    o pkg/layers:
529      - fix interpolation of layers tracers in the presence of partial cells
530      - add lots of new functionality to compute water mass transformation
531        (enabled by CPP flag LAYERS_THERMODYNAMICS)
532      - add new calls from main code (diags_oceanic_surf_flux.F,
533        thermodynamics.F, impldiff.F) and gad to save the necessary fields
534        for layers_thermodynamics calculations
535    o pkg/ptracers:
536      - add capability of stepping a passive tracer forward without advection
537        by setting PTRACERS_advScheme to 0.
538    o pkg/diagnostics:
539      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
540    o pkg/layers:
541      - shift potential density field "prho" by -1000 for density layer averaging so
542        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
543        Note that density bin boundaries (layers_bounds in data.layers) have
544        to be set accordingly (i.e., shifted, in sigma scale).
545    o pkg/layers:
546      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
547      - fix calculation of layer non-weighted velocity and layer probability
548      - add diagnostics for pot.density used for layer averaging
549    o pkg/seaice:
550      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
551        positiveness, modify a few comments and improve variable names,
552      - the changed computation of deltaC affects most seaice-related
553        experiments at the truncation level.
554        seaice_itd.thermo is affected by far the most, with
555        only 7 digits of agreement remaining; update experiments.
556    
557    checkpoint65l (2015/05/04)
558    o pkg/shelfice:
559      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
560        factor drKp1 to zero where it is negative (ie. do not use
561        SHELFICEBoundaryLayer if hFacC>1)
562      - the same for factor drLoc in shelfice_forcing.F
563    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
564        with modules in ptracers, when using testreport option "-small_f"
565    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
566      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
567    o verification/testreport
568      - add new option -small_f
569        with this option testreport first makes the target small_f (*.f files)
570        before running make (all). This is useful for explicit inlining when
571        all sources need to be full available.
572    o pkg/exf/exf_interp.F:
573        remove previous changes related to reverse (decreasing) input grids latitude
574    
575    checkpoint65k (2015/04/01)
576    o pkg/ecco:
577        fix missing cosphi initialization; use eccoiter in place of optimcycle;
578        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
579        instead of active read/write
580    o pkg/ctrl:
581        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
582        instead of active read/write.
583    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
584        return if .NOT.useAUTODIFF
585    o pkg/seaice: add CPP brackets (cost function related).
586    o model/src:
587        add useAUTODIFF run time switch.
588    o pkg/exf/exf_interp.F:
589        add code to allow input grids with latitude starting in the north (i.e. when
590        j=1 corresponds to northern edge of field); modify global_with_exf to test
591        this feature.
592    o verification/testreport:
593      - replace "grep -A3" with POSIX conformal sed command, because there are
594        implementations of grep that cannot do contextual searches
595      - replace "cat -n" by "nl" (two occurrences), because not all implementations
596        of "cat" have the option "-n"
597    o model/src:
598        add new file gsw_teos10.F that contains 3 functions, more or less a copy
599        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
600        convert from conservative to potential temperature. For now they are not
601        called anywhere.
602    o pkg/ggl90: make "useIDEMIX" useful
603      - re-organize code in s/r ggl90_calc a little to move computations that
604        are different for idemix into separate loops (changes verification
605        experiment idemix at truncation level, 12 digits remain -> updated)
606      - requires 2 new 2D fields KappaM, verticalShear
607      - make hFacI and recip_hFacI local 3D variables that are passed to
608        s/r ggl90_idemix
609      - fix and improve some comments
610    
611    checkpoint65j (2015/02/25)
612    o pkg/openad
613      - synchronize seawater.F with version in model/src: replace routine
614        body of sw_temp by calling sw_ptmp and fix/add a few comments.
615    o pkg/mnc:
616      - change default value of pickup_read/write_mnc params to FALSE
617        (since few features are missing in reading MNC pickup files).
618    o model/src:
619      - change default (background) vertical diffusivity for salt to be the
620        temperature (background) vertical diffusivity.
621      - change background vertical diffusivity in vertical mixing pkgs ggl90,
622        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
623        This makes ptracers default diffusivity (that uses salt diffKr) more
624        consistent with vertical mixing schemes.
625    o verification/testreport:
626      - fix typo in "-pcls" option ;
627      - put temp files in /tmp (instead of in local dir)
628      - add option "-ncad" to use genmake2 new option "-nocat4ad"
629      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
630    o pkg/ggl90 (idemix code):
631      - apply few fixes ; add some missing "_d 0" ; update output of exp.
632        global_ocean.90x40x15.idemix
633    o OpenAD
634      - enable active file I/O and begin removal of work-around code
635        for OpenAD for handling control variables (memory vs. active files)
636      - new CPP options file OPENAD_OPTIONS.h
637      - revert to genarr2d gradient check for hs94.1x64x5
638      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
639      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
640    o tools/genmake2:
641      - add option for an alternative Makefile (from Martin) where multiple
642        source files are sent to TAF (instead of all in one file).
643    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
644      - code provided by Carsten Eden as an extension of ggl90
645      - so far the code is turned on within ggl90 by setting a CPP-flag at
646        compile time; a runtime flag implementation is not yet complete
647      - tested in new verification experiment global_ocean.90x40x15.idemix
648    o verification:
649      - reduce length of the AD test run by half for experiments
650        global_ocean.cs32x15 (std + thsice) and isomip
651      - enable active file I/O for OpenAD, adjust verifications accordingly
652      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
653    o verification/testreport:
654      - fix two non-POSIX sed statements so that there are no error messages
655        on Mac OS X
656      - replace hostname -s with hostname | sed 's/\..*$//'
657    o model/src/seawater.F:
658      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
659        (following the matlab code), which would have avoided the bug caught
660        by Matt (see below) in the first place
661    o pkg/shelfice:
662      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
663        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
664      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
665        ice-shelf case (i.e., within surface level).
666      - add config summary in shelfice_check.F
667      - remove global variable recip_SHELFICElatentHeat and replace by a local
668        variable recip_latentHeat
669      - introduce diagnostics for friction velocity uStar (in case of
670        SHELFICEuseGammaFrict)
671      - change verification experiment isomip.htd:
672        + start from pickup (as input_ad at nIter0=8640)
673        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
674        + test SHELFICEuseGammaFrict = .TRUE.
675        + test SHELFICEadvDiffHeatFlux = .TRUE.
676    o model/src:
677      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
678        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
679        update output of experiments global_with_exf.yearly and isomip (all 6).
680    o pkg/shelfice:
681      - change setting of kTopC to also be zero where there is no ice-shelf.
682      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
683        ice-shelf is.
684      - first attempt to get RealFreshWaterFlux effects: for now, only without
685        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
686    o pkg/seaice: add the option to prescribe a fixed thickness PDF
687      for thermodynamic calculations
688      - because of divisions of the type 7/7 not exactly equal to 1, this change
689        affects results of some verification experiments by up to 4 digits:
690        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
691        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
692        adjoint: lab_sea, lab_sea.noseaicedyn
693        -> updated
694    
695    checkpoint65i (2015/01/23)
696    o model/src:
697      - change units of frictionHeating field from W to W/m^2
698      - fix bug in frictional heating from stratospheric drag in
699        S/R ATM_PHYS_TENDENCY_APPLY_V
700      - with synchronous time-stepping: move resetting to zero of frictionHeating
701        field from load_fields_driver.F to thermodynamics.F ;
702      - add diagnostics for frictional heating.
703    o model/src & gmredi K3D:
704      - add frictionHeating field to pickup-files (for synchronous time-stepping)
705      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
706      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
707        and name in pickup file).
708      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
709    o model/src:
710      - move (from ini_forcing.F) initialisation of all arrays in header file
711        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
712        (since Nov 2012) with option selectAddFluid=1.
713    o pkg/shelfice:
714      - change units (+ document) of newly added field "shelfIceMassDynTendency"
715      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
716    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
717    o pkg/seaice: two new runtime parameters:
718      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
719        long overdue
720      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
721        parameterization of tensil stress for fast ice (does not do anything yet)
722    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
723        for LSR: move checking overlaps out of JFNK-if-block
724    o pkg/atm_phys:
725      - move copy of grid and dynamical fields out of atm_phys_driver.F into
726        new S/R ATM_PHYS_DYN2PHYS.
727      - fix level height for Linear Free-Surf case (to be consistent with
728        fixed-in-time pressure levels).
729    o pkg/mom_common (bottomdrag):
730      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
731        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
732        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
733    o pkg/shelfice (u/v_drag):
734      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
735      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
736        (now similar to shelfice_u_drag.F)
737      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
738        from mom_vecinv.F (similar to mom_fluxform calls).
739    o pkg/mom_common (bottomdrag):
740      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
741      - add options for alternative discretisation of velocity norm in quadratic
742        bottom drag: averaging of grid-cell-center KE to U.point and V.point
743        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
744        improves when averaging only the other component (e.g. vVel for U bottom
745        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
746      - add options (bottomVisc_pCell) to account for partial-cell in bottom
747        friction (no-slip BC) thus getting the true distance from the bottom;
748        off by default since this also reduces model stability (explicit bottom
749        friction). Changes produce different machine truncation with linear-drag
750        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
751        front_relax (bvp & mxl, 10 & 11 digits).
752    o model/src & mom pkgs:
753      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
754        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
755      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
756        just copy level Nr value to level Nr+1.
757    o doc:
758      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
759    o pkg/streamice:
760      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
761        SHELFICE.h: move array shelficemass to init_varia, initialise
762        from array shelficemassinit, which is set in init_fixed and
763        has option to be set from file; introduce array
764        shelficeMassDynTend array, set thru file in init_fixed
765      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
766        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
767        pkg/streamice
768      - shelfice_thermodynamics.F: call shelfice_step_icemass if
769        SHELFICEMassStepping = .true.
770      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
771    
772    checkpoint65h (2014/12/17)
773    o verification/global_ocean.90x40x15, global_ocean_ebm:
774      - update to generic controls.
775    o pkg/ctrl:
776      - ctrl_map_ini_genarr.F: test for igen>0
777      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
778      - move gentim2d part of ctrl_map_ini_genarr.F to
779        new separate routine : ctrl_map_ini_gentim2d.F
780      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
781        add time variable weights and cyclic controls (time mean,
782        seasonal cycle, etc) capabilities to gentim2d
783    o pkg/ecco:
784      - move reading of error, conversion to weights from
785        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
786    o global_oce_llc90, cs32:
787      - activte sbo.
788      - CTRL_SIZE.h : add maxCtrlProc.
789      - activate the new genctrl capabilities.
790      - update following reorganization of global_oce_input_fields.tar.gz  
791    o pkg/ctrl/ctrl_ad_diff.list:
792      - add missing ctrl_init_rec.f
793    o tools/OAD_support/keepOriginal:
794      - add ctrl_init_rec.F
795    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
796      - avoid recomputations of xx_gentim2d_dummy.
797    o momentum diagnostics:
798      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
799        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
800    o pkg/seaice/seaice_lsr.F:
801      - fix computation of BU/BV, make sure they are non-zero, only necessary
802        for cubed sphere exchanges and SEAICE_OLx/y>0.
803        This makes calling s/r fill_cs_corner_rl obsolete (removed).
804    o verification/global_ocean.cs32x15/input.seaice
805      - add test for strong implicit coupling and restricted addtive Schwarz
806        methods for LSR
807      - update results/output.seaice.txt
808    o verification/tutorial_global_oce_biogeo:
809      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
810        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
811        update output_adm,_oadm,_tlm.txt
812    o pkg/dic:
813      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
814      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
815        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
816    o verification/tutorial_global_oce_biogeo:
817      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
818        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
819        update output_adm,_oadm,_tlm.txt
820    o eesupp/src:
821      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
822        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
823    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
824      LSR (following Hutchings et al. 2004)
825      - introduce zetaZ as a global variable (requires adjustments in
826        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
827        in seaice_calc_viscosities.F
828      - new flag SEAICEuseStrImpCpl (default off)
829      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
830        momentum equations
831      - JFNK-solver (preconditioner) adjusted to allow using this method
832        (where it does not have any positive effect)
833    o pkg/seaice
834      - add overlap for restrictive additive Schwartz method also to LSR, but
835        turn it off by default (because it only seems to work for non-cubed
836        sphere/llc topologies)
837    o pkg/autodiff
838      - add extra exchanges in addummy_in_steppging also for mnc output
839    o pkg/seaice:
840      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
841        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
842    o pkg/obcs:
843      - add option to specify domain-connected piece Id along OB though files
844        (for now, only used to diagnose PhiVel; default =1 -> global correction)
845      - modify obcs_diag_balance.F to process each connected-part separately;
846        exclude OB where Id = 0 but keep the full divergence there (-> constant
847        Psi along this portion of OB and all inflow derived from grad(Phi))
848      - add example of OB-conect files in verification/so_box_biogeo/input.
849    o pkg/diagnostics:
850      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
851      a) use non zero matrix element across OB and solve for Phi 1 grid point
852         outside OB (i.e, where tracer OBCS are applied).
853      b) global imbalance of inFlow/outFlow across OB: instead of modifying
854         velocity across OB, spread it uniformly along the OB in the RHS.
855    
856    checkpoint65g (2014/11/19)
857    o pkg/diagnostcis:
858      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
859    o pkg/my82,pp81,kl10:
860      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
861        field diffKr as background diffusivity to set minimum diffusivity value.
862    o pkg/seaice:
863      - add new parameter SEAICEuseEVPrev (for revisited EVP by
864        Bouillon et al 2013)
865      - add SEAICE_evpAlpha/Beta to namelist
866      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
867        involve trivial re-ordering of divisions/multiplications that should not
868        have any effects, but ... they do change the results of lab_sea.hb87 so
869        that only 2 digits of agreement remain, in line with the general
870        instability/fragility of the evp-code. For now, I do not care and just
871        update the verification experiment
872    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
873      - remove xx_genarr2d_numsmooth etc
874      - use xx_genarr2d_preproc etc instead
875      - carry out smooth_correl2D at initialization stage rather than during
876        time stepping.
877      - get smoothOpNb from xx_gentim2d_preproc
878    o global_oce_cs32 :
879      - add test of generic ecco capabilities.
880    o pkg/exf/exf_getsurfacefluxes.F :
881      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
882    o pkg/ctrl,ecco :
883      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
884        is defined.
885    o pkg/seaice: add diagnostics for Delta (deformation parameter)
886    o model/src:
887      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
888        diffusivity (background) is specified but ignored.
889    o verification:
890      - in testreport, convert hostname to lower case for default output dir name
891    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
892    o pkg/dic: add modifications from Hajoon:
893      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
894      - light attenuation: add self-shading effect by climatological Chlorophyll
895        (read from file).
896    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
897        compiles when SEAICE_ALLOW_DYNAMICS is undefined
898    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
899        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
900        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
901        approach where CPP_OPTIONS.h includes an omnipotent
902        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
903    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
904        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
905  o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF  o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
906    to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included      to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
907    (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)      (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
908  o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :  o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
909    add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed    add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
910    - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h    - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
911    - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h    - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
912    - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc    - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
913  o pkg/ctrl,ecco,exf :  o pkg/ctrl,ecco,exf :
914    - remove variables associated with NON-generic costs,    - remove variables associated with NON-generic costs,
915      unless ECCO_CTRL_DEPRECATED is defined.      unless ECCO_CTRL_DEPRECATED is defined.
916    - remove NON-generic NON-obcs controls,    - remove NON-generic NON-obcs controls,
917      unless ECCO_CTRL_DEPRECATED is defined.      unless ECCO_CTRL_DEPRECATED is defined.
918  o pkg/ctrl : added ctrl_local_params.h  o pkg/ctrl : added ctrl_local_params.h
919  o pkg/ecco : added ecco_local_params.h  o pkg/ecco : added ecco_local_params.h
920  o verification : added ECCO_CTRL_DEPRECATED to most as and oad  o verification : added ECCO_CTRL_DEPRECATED to most as and oad
921    experiments, which will progressively be removed once the      experiments, which will progressively be removed once the
922    experiments are revised to use only generic controls/costs.      experiments are revised to use only generic controls/costs.
923    
924  checkpoint65f (2014/10/13)  checkpoint65f (2014/10/13)
925  o pkg/ctrl, ecco, seaice : minor changes in headers  o pkg/ctrl, ecco, seaice : minor changes in headers
926  o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic  o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
927    cost function and control capabilities added since checkpoint65c.      cost function and control capabilities added since checkpoint65c.
928  o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.  o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
929  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
930    - ecco_toolbox.F (new) : basic operations that are often used,    - ecco_toolbox.F (new) : basic operations that are often used,
# Line 393  o pkg/seaice: more clean up Line 1284  o pkg/seaice: more clean up
1284      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
1285      this experiment):      this experiment):
1286      > size mitgcmuv_ad      > size mitgcmuv_ad
1287      text    data        bss     dec        hex        text    data        bss     dec        hex
1288      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1289      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1290      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1291      text    data        bss     dec        hex      text    data        bss     dec        hex
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