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revision 1.2057 by jmc, Thu Sep 4 20:11:53 2014 UTC revision 1.2250 by jmc, Sun May 8 19:15:17 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 verification/global_ocean.cs32x15:
8      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
9        with "selectNHfreeSurf=1".
10    o model/src (non-hydrostatic free-surface):
11      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
12        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
13      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
14        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
15        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
16        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
17      - Update output (changes at machine truncation level) of verification exp:
18        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
19        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
20    o pkg/seaice: ITD code
21      - fix picking up from a single category model by initialising
22        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
23      - split a long warning message in seaice_check_pickup.F into two lines,
24        because NEC SX-ACE cannot deal with the long line.
25    o model/src:
26      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
27    o pkg/seaice:
28      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
29    o pkg/seaice:
30      - add basal stress as parameterisation for grounding ice
31        following Lemieux et al. (2015)
32      - turn on by setting new parameter SEAICEbasalDragK2 to a value
33        larger than 0. Lemieux et al. (2015) recommend 15.
34      - The adjoint complains with extra recomputations so there is also a
35        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
36        order to postpone the problem
37      - compile the new code in lab_sea
38    o verification/halfpipe_streamice:
39      - update both TAF and OpenAD adm output (machine truncation differences)
40    
41    checkpoint65v (2016/04/08)
42    o verification/advect_xz:
43      - increase overlap size from 3 to 4 and add new secondary test for PQM
44        advection scheme (with mono & wino limiter).
45      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
46    o model/src:
47      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
48        added phi0Ref) to set vertical axis origin and phiRef origin;
49        keep Ro_SeaLevel for backward compatibility (with a warning).
50       According to coordinate and fluid type:
51        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
52        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
53        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
54        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
55      - remove Ro_SeaLevel from ATM experiment parameter files;
56      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
57        complement; update output.txt (changes at machine truncation level).
58    o pkg/seaice/seaice_evp.F
59      - simplify computation of deltaZ and zetaZ to simple averaging following
60        Bouillon et al. (2013). This removes a lot of code, but also changes
61        verification experiment lab_sea.hb87 -> updated
62    
63    checkpoint65u (2016/03/14)
64    o pkg/generic_advdiff:
65      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
66        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
67        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
68        testing and not for actual use.
69    o model/src:
70      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
71        origin r = rF(1);
72      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
73        in EOS for height coordinate: enable to include NH Pressure or to use
74        more accurate pressure vertical profile; options not linked to EOS type
75        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
76      - start to implement variable gravity (along vertical): for now, only with
77        z-coords (not even z*).
78      - add Ideal Gas equation of state for height coordinate.
79      - update OpenAD output (affected at machine truncation level) of exp:
80        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
81    o pkg/exf:
82      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
83        of exf interpolation (before any rescaling, rotation or interpolation
84        to velocity point) for each field that gets loaded from file. This option
85        identically mimics the input file organization (e.g. record numbers in year
86        by year input files) besides the change in horizontal grid.
87      - add rotateStressOnAgrid run-time switch so that wind stress fields
88        can be provided on the A-grid in zonal/meridional direction and
89        rotated on the fly. This only applies to the case when the exf
90        interpolation is off and rotateStressOnAgrid is false by default.
91    o model/src:
92      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
93        it's also used with pkg/atm_phys) and add few more parameters (but still
94        inactive, src code yet to come)
95    
96    checkpoint65t (2016/02/10)
97    o pkg/atm_phys:
98      - from Ruth Geen: add optical depth dependence on CO2 concentration.
99    o model/src:
100      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
101        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
102        Update output of exp. deep_anelastic (changes at truncation level).
103    o tools:
104      - add a hack in "remove_comments_sed" (used only with TAF) for recent
105        version of OpenMPI (shipped with FC.23): comment out the new header
106        file "mpif-sizeof.h" which causes problems to TAF.
107    o pkg/seaice:
108      - change the termination criterion so that maxits (SEAICElinearIterMax)
109        has an effect
110      - unify iteration parameters for implicit solvers (JFNK and Picard)
111        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
112        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
113        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
114        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
115        SEAICEnonLinTol     replaces JFNKgamma_nonlin
116      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
117      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
118        use with SEAICEuseKrylov
119    o pkg/seaice/seaice_lsr.F
120        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
121        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
122        an effect.
123    o pkg/seaice: add two new parameters
124      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
125        parameter is not in any namelist)
126      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
127        a preconditioner for the non-linear Newton iteration of the JFNK
128        solver
129    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
130      affects some experiments at truncation level:
131      - global_ocean.cs32x15.icedyn (11 digits),
132      - global_ocean.cs32x15.seaice (11 digits),
133      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
134      - also update global_ocean.cs32x15 adjoint and tangent-linear results
135    o pkg/salt_plume & pkg/thsice:
136      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
137        connect salt_plume flux to ATM-OCN coupling pkgs interface:
138       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
139         export to coupler interface) even without compiling pkg/salt_plume ;
140       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
141         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
142    o pkg/dic:
143      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
144        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
145        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
146      - move also update with values from ATM-OCN Coupler in the same new S/R
147        (previously done in ocn_apply_import.F).
148    o tools/adjoint_options:
149      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
150        has been changed on Jan 14, 2016.
151    o pkg/ggl90:
152      - add alternative discretisation of vertical shear (off by default), to
153        compute the mean (@ grid-cell center) of vertical shear compon instead of
154        vertical shear of mean flow (@ grid-cell center).
155      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
156        results on adjacent faces of cubed-sphere grids; this fix the restart.
157    o pkg/atm_compon_interf:
158      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
159        pass last value, stored directly before export to CPL ;
160        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
161      - remove atmSLPr from pickup files (no longer needed for restart)
162    
163    checkpoint65s (2016/01/13)
164    o eesupp & genmake2:
165       - first check for Function ETIME and, if it fails, then check for subroutine
166         ETIME and consistent output; use the appropriate version in timers.F
167    o model/src:
168      - to check restart test, add option to apply EXCH to U,V earlier, just before
169        integr_continuity; turned off by default.
170    o pkg/dic:
171      - remove CPP option USE_ATMOSCO2 (not needed)
172    o tools/tst_2+2:
173      - try to ignore difference between +0 and -0 in binary file, causing test
174        to fail for no good reason.
175    o eesupp & genmake2:
176      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
177        but also check (in genmake2) that test runs and returns meaningful results.
178    o coupler pkgs:
179      Finish implementation of optionally-exchanged variable switches (started on
180       Nov 12) with addition of few more exchanged fields, including 2-way exchange
181       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
182       advection in OCN component; this requires sequential coupling.
183      coupler (pkg/atm_ocn_coupler):
184      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
185        routines (useful for debug).
186      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
187         flux, DIC fields) if corresponding switch is ON.
188      - add option to export RunOff to OCN (to use for DIC river input)
189      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
190      components (pkg/atm_ & ocn_compon_interf):
191      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
192        optionally exchanged fields; add a check & stop in cpl_readparms.F.
193        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
194        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
195      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
196        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
197      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
198      - hold in common block coupler optionally-exchanged variable switch
199        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
200      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
201        this is intended to replace the OCN cplFldtave.* output files (not updated
202        to contain new additional exchanged fields).
203    o pkg/dic:
204      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
205    o pkg/thsice:
206      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
207        and writing of thsice pickup files.
208    o pkg/atm_compon_interf:
209      - move all field individual export-call out of cpl_export_import_data.F
210        into new S/R ATM_EXPORT_FIELDS
211    o pkg/atm_compon_interf:
212      - store state variables (for now, only thSIce fields) just before beeing
213        exported (in cpl_export_import_data.F, like on ocean side) instead of from
214        atm_store_my_data.F like all exported fluxes.
215      - new version of pickup_cpl: write field names into meta file and read meta
216        file to find field postion in pickup. Also only write/read fields meeded for
217        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
218    o pkg/dic:
219      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
220    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
221        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
222        value can be from domain [0,1] to average between the two methods
223    o pkg/atm_phys:
224      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
225        hold fixed in time).
226    
227    checkpoint65r (2015/12/21)
228    o pkg/seaice:
229        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
230        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
231    o pkg/seaice:
232      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
233        when SEAICEscaleSurfStress=.TRUE.,
234      - apply areaW and areaS in S/R seaice_calc_lhs
235    o pkg/atm_phys:
236      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
237        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
238        for individual contribution (convection, LSC cond, radiation)
239      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
240        information); activated with: solar_exponent=0. and wv_exponent=-1.
241    o pkg/ggl90:
242      - within IDEMIX add upper limit for horizontal group velocity to
243        avoid instability problems in the explicit horizontal diffusion term for
244        long time steps or high resolution
245    o pkg/diagnostics:
246      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
247        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
248    o testreport:
249      - remove "-v" (verbose option) in default mpirun command.
250    o pkg/seaice/seaice_growth:
251      - catch potential division by zero in ITD code, does not change
252        verification results
253    o pkg/ecco:
254      - retire old codes to the Attic. The calls to retired functions are
255        left in a commented form in case they ever need to be re-activated.
256      - ecco_check.F: issue warning if any old CPP option is
257        defined that corresponds to retired codes -- then stop.
258    o pkg/atm_compon_interf:
259      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
260        coupler: use last time-step value instead of average over cplSendFrq_iter
261        time-step, similar to what is done for seaIceMass.
262        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
263    o eesupp & genmake2:
264      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
265        <= remove until a fix is found for some ifort version on ia32 machine.
266    o pkg/seaice/seaice_evp:
267      - refine residual computation
268    
269    checkpoint65q (2015/11/18)
270    o pkg/seaice/seaice_evp:
271      - fix residual computations so that they no longer affect the actual
272        simulation code
273      - fix seaice_readparams to be able to actually set new parameters
274        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
275    o model/src:
276      - fix wrong truncation (single prec) from "FLOAT" function in expressions
277        like: deltaT*FLOAT(myIter) when myIter is large:
278         a) replaced by DFLOAT (if not seen by TAF);
279         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
280    o pkg/aim_v23:
281      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
282        when pickupSuff is set ; do write rolling pickups + at the end of the run.
283    o pkg/atm_ocn_coupler + ocn_compon_interf:
284      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
285        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
286        add corresponding call in DO_OCEANIC_PHYS.
287    o coupler pkgs:
288      Start a new way to set-up optionally-exchanged variables (previously, only
289       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
290       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
291       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
292       compononent param default can be set accordingly).
293      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
294       but rather applies to a group a fields (going both ways like for DIC)
295       and corresponds to an option of coupling config.
296      coupler (pkg/atm_ocn_coupler):
297      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
298        and read namelist directly (without eessup S/R calls) instead of
299        in the very un-flexible old way, 1 param per line, in fixed order;
300      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
301        cleanly in CPL_CHECK_CPLCONFIG
302      - add new coupling-exchange selectors (some not yet active) including
303        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
304                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
305      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
306        component ; called directly from coupler.F, after comp. registrations;
307      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
308         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
309          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
310      components (pkg/atm_ & ocn_compon_interf):
311      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
312        CPP header file in all pkg source files.
313      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
314        ATM/OCN_CHECK_CPLCONFIG;
315      - add error-counter to track errors (e.g., in "data.cpl") and to stop
316        cleanly in ATM/OCN_CHECK_CPLCONFIG;
317      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
318        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
319        before PACKAGES_READPARMS;
320      verification/cpl_aim+ocn/:
321      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
322        "data.cpl" for coupler (in input_cpl).
323    o eesupp/inc:
324      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
325        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
326        to always cumulate tile local-sum in the same order (still uses
327        MPI_Allreduce like standard code).
328      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
329        that are now identical to standard version (in eesupp/inc).
330    o pkg/shelfice:
331      - add SHELFICETransCoeffTFile for initializing spatially varying
332        heat and salt transfer coefficients
333    o pkg/atm_compon_interf & ocn_compon_interf:
334      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
335        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
336      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
337    o pkg/atm_ocn_coupler:
338      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
339    o pkg/rbcs:
340      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
341        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
342      - add a short report (to STDOUT) about RBCS-mask settings.
343    
344    checkpoint65p (2015/10/23)
345    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
346        there is no adjoint test for EVP, we don't know what it does to the adjoint
347        solution, but at least there are no more recomputation warnings left
348    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
349        a chance of giving the same results as a fully converged VP (JFNK) solver
350    o tools/adjoint_options/adjoint_diva:
351      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
352    o pkg/streamice:
353      - spotted bug in streamice_driving_stress using dyG where should have been dxG
354    o pkg/exf:
355      - remove STOP statement that prevented to use wind or (wind-)stress
356        interpolation for constant-in-time forcing fields (wind/stress period = 0).
357    o pkg/seaice:
358      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
359        5 additionals 2D fields and 6 new store directives
360      - change logic in seaice_readparms.F: EVP code can now be turned on in
361        various ways, setting SEAICE_deltaTev is no longer required,
362        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
363        or SEAICEaEVPcoeff
364    o pkg/shelfice/shelfice_thermodynamics.F
365      - redefining uLoc/vLoc to u/v, instead of 2u/v
366    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
367      - this is an intermediate state of a truely converging EVP that has
368        the potential of outperforming implicit VP methods, I do not recommend
369        using it yet.
370      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
371        and all parameters are hardwired
372      - for convergence it still requires very smooth regularisations, that means,
373        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
374        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
375        specific averaging appears to be required, still subject to tuning
376      - still needs cleaning and I need to turn parameter into runtime parameters
377      - add code to compute and print residuals of iteration, compile with
378        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
379    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
380      that entered with r1.54 on Sep04, 2015, -> update results
381    
382    checkpoint65o (2015/09/14)
383    o pkg/mom_vecinv & mom_common:
384      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
385        called from there.
386      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
387        allows to use Vector-Invariant form in deep atmos and anelastic formulation
388    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
389      and Koenig-Beatty+Holland (2012)
390      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
391      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
392      - requires an extra input argument for S/R seaice_calc_viscosities
393      - tensileStrength's depth dependence is different from Itkin et al. (2015)
394        (to be changed and played with, for now exponential)
395    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
396      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
397        by AREA according to Connelly et al. (2004), JPO.
398      - For EVP and the LSR solver, the implicit part of the drag term is
399        the only non-zero term in the denominator when there is no ice (which
400        prevented running the model with zero ice-ocean drag). If
401        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
402        (or zero main diagonals BU/BV) which need to be caught. A practical
403        consequence is that for open water, the momentum equation reduce
404        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
405        they happen to be zero, often leading to a non-zero solution over
406        open water.
407    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
408        efficient EVP method.
409      - introduce area-weighted averages for e12 (analogously to
410        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
411        remain, but also changing the order of terms in the previous average
412        changed the results as much) -> update experiment
413      - add SEAICE_DELTA_SMOOTHREG code
414      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
415        TEM-code
416      - adjust loop bounds so that only required fields are computed
417      - add new averaging code for zetaZ/deltaZ (again similar to
418        seaice_calc_viscosities.F), inactive by default for now (will change
419        results again), but will replace old code eventually
420    o eesupp/src:
421      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
422        to always cumulate tile local-sum in the same order
423        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
424        Still uses MPI_Allreduce (like standard code) but on array of tiles
425        and should be faster than GLOBAL_SUM_SEND_RECV code.
426      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
427        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
428      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
429         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
430         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
431         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
432         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
433    
434    checkpoint65n (2015/07/29)
435    o pkg/thsice:
436      - add a warning when used with pkg/aim but without updating SST
437        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
438    o pkg/offline:
439      - change where Offline-Fields are loaded, from load_fields_driver.F to
440        directly within FORWARD_STEP, just after updating iter number and time;
441      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
442        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
443       These changes allow:
444        a) to recover exactly on-line results using deltaToffline=deltaTClock,
445        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
446        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
447        time-step, both with GM & KPP files and with recomputing these fields;
448        b) no needs to switch on staggerTimeStep anymore;
449        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
450      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
451    o pkg/offline:
452      - change (rarely used) offset-iteration parameter to an offset time (in s):
453        can easily recover previous offset-iter effect by setting offset-time
454        (offlineTimeOffset) to offset-iter x deltaToffline;
455      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
456        in KPP as part of surface buoyancy forcing) in offline run.
457      - fix ptracers KPP non-local term in the case where KPP is re-computed.
458    o OpenAD
459      - Adding preliminary ggl90 test to OpenAD verification.
460        Config. with ggl90 currently diverges after 64 time steps
461        so will need more work to become more stable
462      - Adding preliminary kpp test to OpenAD verification.
463        required small tweakes in kpp_routines.F
464      - Merge and update from Krishna Narayanan's contrib area:
465        * Add one variable for preliminary OpenAD DIVA
466        * Add replacement time-stepping for OpenAD DIVA
467        * genmake2 flag -diva (but only for OpenAD; preliminary)
468        * required modifs for OAD_support
469        successful preliminary test for tutorial_global_oce_biogeo/
470    o pkg/seaice:
471      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
472      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
473        delta with a smooth function in s/r seaice_calc_viscosity
474        (no effect on EVP)
475      - rename local suffix "sqr" into "sq" for more consistent variable names
476    o pkg/seaice:
477        add new parameter SEAICE_deltaMin that is used ***only***
478        for regularizing Delta (and nothing else, like the parameter
479        which is also used for all sorts of things SEAICE_EPS).
480        Defaults to SEAICE_EPS for backward compatibility only.
481    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
482        the wrong key by inialising it before use -> fixes a recomputation
483        problem but does not fix the gradient
484    o pkg/layers:
485      - move resetting of flux arrays to outside the iLa loop
486        (this caused layers_diapycnal to not work with more than one layer coord.)
487      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
488    o pkg/layers:
489      - remove from common block 3D layers fields (used to diagnose transport
490        in tracer coords) and declare them as local arrays in layers_calc.F
491    o pkg/seaice:
492      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
493        in lab_sea forward experiment (changes results -> updated)
494      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
495    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
496       computations; for SEAICE_VECTORIZE_LSR
497      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
498        sweep to the outside,
499      - remove store directives and add "CADJ loop sequential" directives
500        in analogy to model/src/solve_tridiagonal.F
501      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
502        boundaries to yield more readable code. This has also the charming side
503        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
504        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
505        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
506        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
507        an additional option)
508       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
509       but the adjoint gradients (which are affected by this change) still explode.
510    o coupler (atm & ocn _compon_interf):
511      - avoid using Exch2 IO mapping if not suitable.
512    
513    checkpoint65m (2015/06/15)
514    o pkg/layers:
515      - clean-up old parameters setting (from Sep 2012):
516        + remove old parameters setting from common block (declared locally);
517        + stop if any old parameter is mixed with new parameters;
518        + check for valid or consistent parameter setting (e.g., layers_name)
519      - check that layers_bounds for Pot.Density are in the right range;
520        this is supposed to catch un-updated setting after recently shifting
521        potential density field "prho" by -1000 (now in "sigma" scale).
522    o pkg/layers:
523      - Added missing call to layers_fill for keeping track of tottend in
524        pkg/diagnostics/diagnostics_fill_state.F
525    o pkg/layers:
526      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
527        of diapycnal fluxes
528    o pkg/layers:
529      - reverted changes to interpolation to previous treatment; there
530        was never actually a problem
531    o pkg/layers:
532      - fix interpolation of layers tracers in the presence of partial cells
533      - add lots of new functionality to compute water mass transformation
534        (enabled by CPP flag LAYERS_THERMODYNAMICS)
535      - add new calls from main code (diags_oceanic_surf_flux.F,
536        thermodynamics.F, impldiff.F) and gad to save the necessary fields
537        for layers_thermodynamics calculations
538    o pkg/ptracers:
539      - add capability of stepping a passive tracer forward without advection
540        by setting PTRACERS_advScheme to 0.
541    o pkg/diagnostics:
542      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
543    o pkg/layers:
544      - shift potential density field "prho" by -1000 for density layer averaging so
545        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
546        Note that density bin boundaries (layers_bounds in data.layers) have
547        to be set accordingly (i.e., shifted, in sigma scale).
548    o pkg/layers:
549      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
550      - fix calculation of layer non-weighted velocity and layer probability
551      - add diagnostics for pot.density used for layer averaging
552    o pkg/seaice:
553      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
554        positiveness, modify a few comments and improve variable names,
555      - the changed computation of deltaC affects most seaice-related
556        experiments at the truncation level.
557        seaice_itd.thermo is affected by far the most, with
558        only 7 digits of agreement remaining; update experiments.
559    
560    checkpoint65l (2015/05/04)
561    o pkg/shelfice:
562      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
563        factor drKp1 to zero where it is negative (ie. do not use
564        SHELFICEBoundaryLayer if hFacC>1)
565      - the same for factor drLoc in shelfice_forcing.F
566    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
567        with modules in ptracers, when using testreport option "-small_f"
568    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
569      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
570    o verification/testreport
571      - add new option -small_f
572        with this option testreport first makes the target small_f (*.f files)
573        before running make (all). This is useful for explicit inlining when
574        all sources need to be full available.
575    o pkg/exf/exf_interp.F:
576        remove previous changes related to reverse (decreasing) input grids latitude
577    
578    checkpoint65k (2015/04/01)
579    o pkg/ecco:
580        fix missing cosphi initialization; use eccoiter in place of optimcycle;
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/ctrl:
584        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
585        instead of active read/write.
586    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
587        return if .NOT.useAUTODIFF
588    o pkg/seaice: add CPP brackets (cost function related).
589    o model/src:
590        add useAUTODIFF run time switch.
591    o pkg/exf/exf_interp.F:
592        add code to allow input grids with latitude starting in the north (i.e. when
593        j=1 corresponds to northern edge of field); modify global_with_exf to test
594        this feature.
595    o verification/testreport:
596      - replace "grep -A3" with POSIX conformal sed command, because there are
597        implementations of grep that cannot do contextual searches
598      - replace "cat -n" by "nl" (two occurrences), because not all implementations
599        of "cat" have the option "-n"
600    o model/src:
601        add new file gsw_teos10.F that contains 3 functions, more or less a copy
602        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
603        convert from conservative to potential temperature. For now they are not
604        called anywhere.
605    o pkg/ggl90: make "useIDEMIX" useful
606      - re-organize code in s/r ggl90_calc a little to move computations that
607        are different for idemix into separate loops (changes verification
608        experiment idemix at truncation level, 12 digits remain -> updated)
609      - requires 2 new 2D fields KappaM, verticalShear
610      - make hFacI and recip_hFacI local 3D variables that are passed to
611        s/r ggl90_idemix
612      - fix and improve some comments
613    
614    checkpoint65j (2015/02/25)
615    o pkg/openad
616      - synchronize seawater.F with version in model/src: replace routine
617        body of sw_temp by calling sw_ptmp and fix/add a few comments.
618    o pkg/mnc:
619      - change default value of pickup_read/write_mnc params to FALSE
620        (since few features are missing in reading MNC pickup files).
621    o model/src:
622      - change default (background) vertical diffusivity for salt to be the
623        temperature (background) vertical diffusivity.
624      - change background vertical diffusivity in vertical mixing pkgs ggl90,
625        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
626        This makes ptracers default diffusivity (that uses salt diffKr) more
627        consistent with vertical mixing schemes.
628    o verification/testreport:
629      - fix typo in "-pcls" option ;
630      - put temp files in /tmp (instead of in local dir)
631      - add option "-ncad" to use genmake2 new option "-nocat4ad"
632      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
633    o pkg/ggl90 (idemix code):
634      - apply few fixes ; add some missing "_d 0" ; update output of exp.
635        global_ocean.90x40x15.idemix
636    o OpenAD
637      - enable active file I/O and begin removal of work-around code
638        for OpenAD for handling control variables (memory vs. active files)
639      - new CPP options file OPENAD_OPTIONS.h
640      - revert to genarr2d gradient check for hs94.1x64x5
641      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
642      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
643    o tools/genmake2:
644      - add option for an alternative Makefile (from Martin) where multiple
645        source files are sent to TAF (instead of all in one file).
646    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
647      - code provided by Carsten Eden as an extension of ggl90
648      - so far the code is turned on within ggl90 by setting a CPP-flag at
649        compile time; a runtime flag implementation is not yet complete
650      - tested in new verification experiment global_ocean.90x40x15.idemix
651    o verification:
652      - reduce length of the AD test run by half for experiments
653        global_ocean.cs32x15 (std + thsice) and isomip
654      - enable active file I/O for OpenAD, adjust verifications accordingly
655      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
656    o verification/testreport:
657      - fix two non-POSIX sed statements so that there are no error messages
658        on Mac OS X
659      - replace hostname -s with hostname | sed 's/\..*$//'
660    o model/src/seawater.F:
661      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
662        (following the matlab code), which would have avoided the bug caught
663        by Matt (see below) in the first place
664    o pkg/shelfice:
665      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
666        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
667      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
668        ice-shelf case (i.e., within surface level).
669      - add config summary in shelfice_check.F
670      - remove global variable recip_SHELFICElatentHeat and replace by a local
671        variable recip_latentHeat
672      - introduce diagnostics for friction velocity uStar (in case of
673        SHELFICEuseGammaFrict)
674      - change verification experiment isomip.htd:
675        + start from pickup (as input_ad at nIter0=8640)
676        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
677        + test SHELFICEuseGammaFrict = .TRUE.
678        + test SHELFICEadvDiffHeatFlux = .TRUE.
679    o model/src:
680      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
681        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
682        update output of experiments global_with_exf.yearly and isomip (all 6).
683    o pkg/shelfice:
684      - change setting of kTopC to also be zero where there is no ice-shelf.
685      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
686        ice-shelf is.
687      - first attempt to get RealFreshWaterFlux effects: for now, only without
688        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
689    o pkg/seaice: add the option to prescribe a fixed thickness PDF
690      for thermodynamic calculations
691      - because of divisions of the type 7/7 not exactly equal to 1, this change
692        affects results of some verification experiments by up to 4 digits:
693        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
694        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
695        adjoint: lab_sea, lab_sea.noseaicedyn
696        -> updated
697    
698    checkpoint65i (2015/01/23)
699    o model/src:
700      - change units of frictionHeating field from W to W/m^2
701      - fix bug in frictional heating from stratospheric drag in
702        S/R ATM_PHYS_TENDENCY_APPLY_V
703      - with synchronous time-stepping: move resetting to zero of frictionHeating
704        field from load_fields_driver.F to thermodynamics.F ;
705      - add diagnostics for frictional heating.
706    o model/src & gmredi K3D:
707      - add frictionHeating field to pickup-files (for synchronous time-stepping)
708      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
709      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
710        and name in pickup file).
711      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
712    o model/src:
713      - move (from ini_forcing.F) initialisation of all arrays in header file
714        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
715        (since Nov 2012) with option selectAddFluid=1.
716    o pkg/shelfice:
717      - change units (+ document) of newly added field "shelfIceMassDynTendency"
718      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
719    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
720    o pkg/seaice: two new runtime parameters:
721      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
722        long overdue
723      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
724        parameterization of tensil stress for fast ice (does not do anything yet)
725    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
726        for LSR: move checking overlaps out of JFNK-if-block
727    o pkg/atm_phys:
728      - move copy of grid and dynamical fields out of atm_phys_driver.F into
729        new S/R ATM_PHYS_DYN2PHYS.
730      - fix level height for Linear Free-Surf case (to be consistent with
731        fixed-in-time pressure levels).
732    o pkg/mom_common (bottomdrag):
733      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
734        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
735        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
736    o pkg/shelfice (u/v_drag):
737      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
738      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
739        (now similar to shelfice_u_drag.F)
740      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
741        from mom_vecinv.F (similar to mom_fluxform calls).
742    o pkg/mom_common (bottomdrag):
743      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
744      - add options for alternative discretisation of velocity norm in quadratic
745        bottom drag: averaging of grid-cell-center KE to U.point and V.point
746        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
747        improves when averaging only the other component (e.g. vVel for U bottom
748        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
749      - add options (bottomVisc_pCell) to account for partial-cell in bottom
750        friction (no-slip BC) thus getting the true distance from the bottom;
751        off by default since this also reduces model stability (explicit bottom
752        friction). Changes produce different machine truncation with linear-drag
753        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
754        front_relax (bvp & mxl, 10 & 11 digits).
755    o model/src & mom pkgs:
756      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
757        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
758      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
759        just copy level Nr value to level Nr+1.
760    o doc:
761      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
762    o pkg/streamice:
763      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
764        SHELFICE.h: move array shelficemass to init_varia, initialise
765        from array shelficemassinit, which is set in init_fixed and
766        has option to be set from file; introduce array
767        shelficeMassDynTend array, set thru file in init_fixed
768      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
769        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
770        pkg/streamice
771      - shelfice_thermodynamics.F: call shelfice_step_icemass if
772        SHELFICEMassStepping = .true.
773      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
774    
775    checkpoint65h (2014/12/17)
776    o verification/global_ocean.90x40x15, global_ocean_ebm:
777      - update to generic controls.
778    o pkg/ctrl:
779      - ctrl_map_ini_genarr.F: test for igen>0
780      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
781      - move gentim2d part of ctrl_map_ini_genarr.F to
782        new separate routine : ctrl_map_ini_gentim2d.F
783      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
784        add time variable weights and cyclic controls (time mean,
785        seasonal cycle, etc) capabilities to gentim2d
786    o pkg/ecco:
787      - move reading of error, conversion to weights from
788        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
789    o global_oce_llc90, cs32:
790      - activte sbo.
791      - CTRL_SIZE.h : add maxCtrlProc.
792      - activate the new genctrl capabilities.
793      - update following reorganization of global_oce_input_fields.tar.gz  
794    o pkg/ctrl/ctrl_ad_diff.list:
795      - add missing ctrl_init_rec.f
796    o tools/OAD_support/keepOriginal:
797      - add ctrl_init_rec.F
798    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
799      - avoid recomputations of xx_gentim2d_dummy.
800    o momentum diagnostics:
801      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
802        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
803    o pkg/seaice/seaice_lsr.F:
804      - fix computation of BU/BV, make sure they are non-zero, only necessary
805        for cubed sphere exchanges and SEAICE_OLx/y>0.
806        This makes calling s/r fill_cs_corner_rl obsolete (removed).
807    o verification/global_ocean.cs32x15/input.seaice
808      - add test for strong implicit coupling and restricted addtive Schwarz
809        methods for LSR
810      - update results/output.seaice.txt
811    o verification/tutorial_global_oce_biogeo:
812      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
813        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
814        update output_adm,_oadm,_tlm.txt
815    o pkg/dic:
816      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
817      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
818        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
819    o verification/tutorial_global_oce_biogeo:
820      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
821        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
822        update output_adm,_oadm,_tlm.txt
823    o eesupp/src:
824      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
825        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
826    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
827      LSR (following Hutchings et al. 2004)
828      - introduce zetaZ as a global variable (requires adjustments in
829        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
830        in seaice_calc_viscosities.F
831      - new flag SEAICEuseStrImpCpl (default off)
832      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
833        momentum equations
834      - JFNK-solver (preconditioner) adjusted to allow using this method
835        (where it does not have any positive effect)
836    o pkg/seaice
837      - add overlap for restrictive additive Schwartz method also to LSR, but
838        turn it off by default (because it only seems to work for non-cubed
839        sphere/llc topologies)
840    o pkg/autodiff
841      - add extra exchanges in addummy_in_steppging also for mnc output
842    o pkg/seaice:
843      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
844        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
845    o pkg/obcs:
846      - add option to specify domain-connected piece Id along OB though files
847        (for now, only used to diagnose PhiVel; default =1 -> global correction)
848      - modify obcs_diag_balance.F to process each connected-part separately;
849        exclude OB where Id = 0 but keep the full divergence there (-> constant
850        Psi along this portion of OB and all inflow derived from grad(Phi))
851      - add example of OB-conect files in verification/so_box_biogeo/input.
852    o pkg/diagnostics:
853      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
854      a) use non zero matrix element across OB and solve for Phi 1 grid point
855         outside OB (i.e, where tracer OBCS are applied).
856      b) global imbalance of inFlow/outFlow across OB: instead of modifying
857         velocity across OB, spread it uniformly along the OB in the RHS.
858    
859    checkpoint65g (2014/11/19)
860    o pkg/diagnostcis:
861      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
862    o pkg/my82,pp81,kl10:
863      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
864        field diffKr as background diffusivity to set minimum diffusivity value.
865    o pkg/seaice:
866      - add new parameter SEAICEuseEVPrev (for revisited EVP by
867        Bouillon et al 2013)
868      - add SEAICE_evpAlpha/Beta to namelist
869      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
870        involve trivial re-ordering of divisions/multiplications that should not
871        have any effects, but ... they do change the results of lab_sea.hb87 so
872        that only 2 digits of agreement remain, in line with the general
873        instability/fragility of the evp-code. For now, I do not care and just
874        update the verification experiment
875    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
876      - remove xx_genarr2d_numsmooth etc
877      - use xx_genarr2d_preproc etc instead
878      - carry out smooth_correl2D at initialization stage rather than during
879        time stepping.
880      - get smoothOpNb from xx_gentim2d_preproc
881    o global_oce_cs32 :
882      - add test of generic ecco capabilities.
883    o pkg/exf/exf_getsurfacefluxes.F :
884      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
885    o pkg/ctrl,ecco :
886      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
887        is defined.
888    o pkg/seaice: add diagnostics for Delta (deformation parameter)
889    o model/src:
890      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
891        diffusivity (background) is specified but ignored.
892    o verification:
893      - in testreport, convert hostname to lower case for default output dir name
894    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
895    o pkg/dic: add modifications from Hajoon:
896      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
897      - light attenuation: add self-shading effect by climatological Chlorophyll
898        (read from file).
899    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
900        compiles when SEAICE_ALLOW_DYNAMICS is undefined
901    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
902        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
903        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
904        approach where CPP_OPTIONS.h includes an omnipotent
905        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
906    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
907        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
908    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
909        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
910        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
911    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
912      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
913      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
914      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
915      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
916    o pkg/ctrl,ecco,exf :
917      - remove variables associated with NON-generic costs,
918        unless ECCO_CTRL_DEPRECATED is defined.
919      - remove NON-generic NON-obcs controls,
920        unless ECCO_CTRL_DEPRECATED is defined.
921    o pkg/ctrl : added ctrl_local_params.h
922    o pkg/ecco : added ecco_local_params.h
923    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
924        experiments, which will progressively be removed once the
925        experiments are revised to use only generic controls/costs.
926    
927    checkpoint65f (2014/10/13)
928    o pkg/ctrl, ecco, seaice : minor changes in headers
929    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
930        cost function and control capabilities added since checkpoint65c.
931    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
932    o pkg/ecco: increase modularity and improve logic
933      - ecco_toolbox.F (new) : basic operations that are often used,
934        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
935        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
936      - cost_gencal.F (new) : determine filnames and records.
937      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
938      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
939        and exploit the above functions leading to more compact code.
940      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
941      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
942        using_ers, using_gfo, using_mdt is now only defined within gencost)
943    o pkg/ecco: extend generic cost capabilities
944      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
945        capabilities via gencost_preproc (+ _c,_i,_r related params),
946        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
947        gencost_outputlevel arguments to cost_generic
948      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
949        and active_read, making room for gencost_preproc to take effect.
950        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
951      - pkg/ecco/cost_generic.F :
952        compute and store misfit maks*(model-data) in localdif that is
953        then used in cost and for output, output misfit if outlev.GT.0
954      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
955        rather gencost_barfile for deciding whether to write barfile
956      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
957      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
958        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
959      - pkg/ecco/ecco_summary.F : report gencost variables
960      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
961    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
962    o pkg/ecco: internal re-organization
963      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
964        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
965        mv relevant variables definition from ecco_cost.h to ecco.h,
966        make sure gencost routines only include ecco.h)
967      - throughout : add missing CCP switches, rm unused variables,
968        and rm un-necessary CPP switches
969      - throughout gencost routines : replace modelstartdate with
970        gencost_startdate when needed
971      - cost_bp_read.F : use arguments, instead of common blocs
972        so that it can be used also by (new) cost_gencost_bpv4.F
973      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
974      - ecco_phys.F : compute etanFull
975      - ecco_readparms.F : rename using_topex as using_tpj, add
976        bpv4-grace to gencost list, initialize added parameters
977      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
978    
979    checkpoint65e (2014/09/28)
980    o pkg/obcs:
981      - replaced the just-added CPP options with run-time variables
982        (see pkg/obcs/OBCS_PARAMS.h for details)
983    o pkg/obcs:
984      - add additional CPP options for sponge boundary layers
985        (see pkg/obcs/OBCS_OPTIONS.h for details)
986    o pkg/atm_phys:
987      - implement simple (obliquity only, assuming circular planet orbit)
988        seasonal cycle for incoming insolation ; used when run-time parameter
989        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
990    o pkg/exf, pkg/ecco, pkg/ctrl:
991      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
992      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
993      - implement gentim2d for xx_tauu, xx_tauv
994    o pkg/ctrl, pkg/ecco :
995      - fix and complement the generic controls implementation
996    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
997        pkg/shelfice/shelfice_thermodynamics.F,
998        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
999        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
1000      - add weight in CTRL_GET_GEN calls
1001    o pkg/ctrl :
1002      - ctrl_get_gen.F : add weight as input parameter, and apply
1003        it directly rather than using smooth_correl2Dw (to be retired).
1004      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
1005    o pkg/ctrl :
1006      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
1007        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
1008      - re-activate ctrl_summary (call in ctrl_init.F)
1009    o pkg/ctrl/ctrl_cost_gen.F :
1010      - fix CCP brackets, remove un-necessary myiter, mytime
1011    o pkg/ecco, pkg/ctrl :
1012      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
1013      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
1014      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
1015      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
1016    
1017    checkpoint65d (2014/09/15)
1018    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
1019      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
1020        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
1021    o pkg/ctrl/ctrl_map_ini_genarr.F :
1022      - remove compilation failure
1023      - replace hard coded example
1024      - use ctrl_map_ini_gen2D, 3D
1025    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
1026      - on/off switch based upon xx_genarr2d_weight,3d
1027    o src/packages_init_variables.F :
1028      - regroup pkg/estimation calls
1029      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1030        (moved to ctrl_init_variables)
1031    o cost/cost_init_varia.F :
1032      - remove ecco_cost_init_varia
1033        (moved to ecco_init_varia)
1034    o ctrl/ctrl_init_variables.F :
1035      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1036      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
1037    o ctrl/ctrl_map_ini.F :
1038      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
1039        (moved to ctrl_init_variables)
1040    o ctrl/ctrl_map_ini_ecco.F :
1041      - remove ECCO_PHYS (mv to ecco_init_varia)
1042      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
1043    o ecco/ecco_ad_diff.list :
1044      - add ecco_init_varia.f
1045    o ecco/ecco_init_varia.F
1046      - new routine
1047    o pkg/streamice:
1048      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
1049        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
1050      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
1051    o pkg/generic_advdiff:
1052      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
1053    o pkg/exf:
1054      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
1055         xxg_precip capability
1056      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
1057    o pkg/ctrl:
1058      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
1059    o model/src/load_fields_driver.F :
1060      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
1061        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
1062    o OpenAD verification experiments:
1063      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
1064        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
1065        for now, only in pkgs used in OpenAD verification experiments.
1066      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
1067        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
1068        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
1069        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
1070    o OpenAD verification tests:
1071      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
1072      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
1073        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
1074      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
1075        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
1076    o model/src & generic_advdiff:
1077      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
1078        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
1079        dynamics requires valid tracer forcing only over tile interior but, for
1080        some diagnostics, may need to extend it over 1 point in tile halo region.
1081      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
1082        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
1083        setting in temp/salt/ptracer_integrate.F
1084  o pkg/dic:  o pkg/dic:
1085    - multiply tracer tendencies by maskInC (if ussing OBCS) before updating    - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
1086      gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER      gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
# Line 210  o pkg/seaice: more clean up Line 1287  o pkg/seaice: more clean up
1287      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
1288      this experiment):      this experiment):
1289      > size mitgcmuv_ad      > size mitgcmuv_ad
1290      text    data        bss     dec        hex        text    data        bss     dec        hex
1291      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1292      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1293      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1294      text    data        bss     dec        hex      text    data        bss     dec        hex
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