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revision 1.2074 by jmc, Sun Sep 28 13:47:43 2014 UTC revision 1.2244 by jmc, Tue Apr 12 16:59:43 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/halfpipe_streamice:
8      - update both TAF and OpenAD adm output (machine truncation differences)
9    
10    checkpoint65v (2016/04/08)
11    o verification/advect_xz:
12      - increase overlap size from 3 to 4 and add new secondary test for PQM
13        advection scheme (with mono & wino limiter).
14      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
15    o model/src:
16      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
17        added phi0Ref) to set vertical axis origin and phiRef origin;
18        keep Ro_SeaLevel for backward compatibility (with a warning).
19       According to coordinate and fluid type:
20        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
21        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
22        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
23        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
24      - remove Ro_SeaLevel from ATM experiment parameter files;
25      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
26        complement; update output.txt (changes at machine truncation level).
27    o pkg/seaice/seaice_evp.F
28      - simplify computation of deltaZ and zetaZ to simple averaging following
29        Bouillon et al. (2013). This removes a lot of code, but also changes
30        verification experiment lab_sea.hb87 -> updated
31    
32    checkpoint65u (2016/03/14)
33    o pkg/generic_advdiff:
34      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
35        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
36        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
37        testing and not for actual use.
38    o model/src:
39      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
40        origin r = rF(1);
41      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
42        in EOS for height coordinate: enable to include NH Pressure or to use
43        more accurate pressure vertical profile; options not linked to EOS type
44        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
45      - start to implement variable gravity (along vertical): for now, only with
46        z-coords (not even z*).
47      - add Ideal Gas equation of state for height coordinate.
48      - update OpenAD output (affected at machine truncation level) of exp:
49        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
50    o pkg/exf:
51      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
52        of exf interpolation (before any rescaling, rotation or interpolation
53        to velocity point) for each field that gets loaded from file. This option
54        identically mimics the input file organization (e.g. record numbers in year
55        by year input files) besides the change in horizontal grid.
56      - add rotateStressOnAgrid run-time switch so that wind stress fields
57        can be provided on the A-grid in zonal/meridional direction and
58        rotated on the fly. This only applies to the case when the exf
59        interpolation is off and rotateStressOnAgrid is false by default.
60    o model/src:
61      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
62        it's also used with pkg/atm_phys) and add few more parameters (but still
63        inactive, src code yet to come)
64    
65    checkpoint65t (2016/02/10)
66    o pkg/atm_phys:
67      - from Ruth Geen: add optical depth dependence on CO2 concentration.
68    o model/src:
69      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
70        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
71        Update output of exp. deep_anelastic (changes at truncation level).
72    o tools:
73      - add a hack in "remove_comments_sed" (used only with TAF) for recent
74        version of OpenMPI (shipped with FC.23): comment out the new header
75        file "mpif-sizeof.h" which causes problems to TAF.
76    o pkg/seaice:
77      - change the termination criterion so that maxits (SEAICElinearIterMax)
78        has an effect
79      - unify iteration parameters for implicit solvers (JFNK and Picard)
80        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
81        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
82        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
83        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
84        SEAICEnonLinTol     replaces JFNKgamma_nonlin
85      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
86      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
87        use with SEAICEuseKrylov
88    o pkg/seaice/seaice_lsr.F
89        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
90        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
91        an effect.
92    o pkg/seaice: add two new parameters
93      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
94        parameter is not in any namelist)
95      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
96        a preconditioner for the non-linear Newton iteration of the JFNK
97        solver
98    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
99      affects some experiments at truncation level:
100      - global_ocean.cs32x15.icedyn (11 digits),
101      - global_ocean.cs32x15.seaice (11 digits),
102      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
103      - also update global_ocean.cs32x15 adjoint and tangent-linear results
104    o pkg/salt_plume & pkg/thsice:
105      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
106        connect salt_plume flux to ATM-OCN coupling pkgs interface:
107       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
108         export to coupler interface) even without compiling pkg/salt_plume ;
109       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
110         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
111    o pkg/dic:
112      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
113        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
114        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
115      - move also update with values from ATM-OCN Coupler in the same new S/R
116        (previously done in ocn_apply_import.F).
117    o tools/adjoint_options:
118      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
119        has been changed on Jan 14, 2016.
120    o pkg/ggl90:
121      - add alternative discretisation of vertical shear (off by default), to
122        compute the mean (@ grid-cell center) of vertical shear compon instead of
123        vertical shear of mean flow (@ grid-cell center).
124      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
125        results on adjacent faces of cubed-sphere grids; this fix the restart.
126    o pkg/atm_compon_interf:
127      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
128        pass last value, stored directly before export to CPL ;
129        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
130      - remove atmSLPr from pickup files (no longer needed for restart)
131    
132    checkpoint65s (2016/01/13)
133    o eesupp & genmake2:
134       - first check for Function ETIME and, if it fails, then check for subroutine
135         ETIME and consistent output; use the appropriate version in timers.F
136    o model/src:
137      - to check restart test, add option to apply EXCH to U,V earlier, just before
138        integr_continuity; turned off by default.
139    o pkg/dic:
140      - remove CPP option USE_ATMOSCO2 (not needed)
141    o tools/tst_2+2:
142      - try to ignore difference between +0 and -0 in binary file, causing test
143        to fail for no good reason.
144    o eesupp & genmake2:
145      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
146        but also check (in genmake2) that test runs and returns meaningful results.
147    o coupler pkgs:
148      Finish implementation of optionally-exchanged variable switches (started on
149       Nov 12) with addition of few more exchanged fields, including 2-way exchange
150       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
151       advection in OCN component; this requires sequential coupling.
152      coupler (pkg/atm_ocn_coupler):
153      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
154        routines (useful for debug).
155      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
156         flux, DIC fields) if corresponding switch is ON.
157      - add option to export RunOff to OCN (to use for DIC river input)
158      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
159      components (pkg/atm_ & ocn_compon_interf):
160      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
161        optionally exchanged fields; add a check & stop in cpl_readparms.F.
162        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
163        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
164      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
165        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
166      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
167      - hold in common block coupler optionally-exchanged variable switch
168        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
169      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
170        this is intended to replace the OCN cplFldtave.* output files (not updated
171        to contain new additional exchanged fields).
172    o pkg/dic:
173      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
174    o pkg/thsice:
175      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
176        and writing of thsice pickup files.
177    o pkg/atm_compon_interf:
178      - move all field individual export-call out of cpl_export_import_data.F
179        into new S/R ATM_EXPORT_FIELDS
180    o pkg/atm_compon_interf:
181      - store state variables (for now, only thSIce fields) just before beeing
182        exported (in cpl_export_import_data.F, like on ocean side) instead of from
183        atm_store_my_data.F like all exported fluxes.
184      - new version of pickup_cpl: write field names into meta file and read meta
185        file to find field postion in pickup. Also only write/read fields meeded for
186        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
187    o pkg/dic:
188      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
189    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
190        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
191        value can be from domain [0,1] to average between the two methods
192    o pkg/atm_phys:
193      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
194        hold fixed in time).
195    
196    checkpoint65r (2015/12/21)
197    o pkg/seaice:
198        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
199        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
200    o pkg/seaice:
201      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
202        when SEAICEscaleSurfStress=.TRUE.,
203      - apply areaW and areaS in S/R seaice_calc_lhs
204    o pkg/atm_phys:
205      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
206        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
207        for individual contribution (convection, LSC cond, radiation)
208      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
209        information); activated with: solar_exponent=0. and wv_exponent=-1.
210    o pkg/ggl90:
211      - within IDEMIX add upper limit for horizontal group velocity to
212        avoid instability problems in the explicit horizontal diffusion term for
213        long time steps or high resolution
214    o pkg/diagnostics:
215      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
216        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
217    o testreport:
218      - remove "-v" (verbose option) in default mpirun command.
219    o pkg/seaice/seaice_growth:
220      - catch potential division by zero in ITD code, does not change
221        verification results
222    o pkg/ecco:
223      - retire old codes to the Attic. The calls to retired functions are
224        left in a commented form in case they ever need to be re-activated.
225      - ecco_check.F: issue warning if any old CPP option is
226        defined that corresponds to retired codes -- then stop.
227    o pkg/atm_compon_interf:
228      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
229        coupler: use last time-step value instead of average over cplSendFrq_iter
230        time-step, similar to what is done for seaIceMass.
231        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
232    o eesupp & genmake2:
233      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
234        <= remove until a fix is found for some ifort version on ia32 machine.
235    o pkg/seaice/seaice_evp:
236      - refine residual computation
237    
238    checkpoint65q (2015/11/18)
239    o pkg/seaice/seaice_evp:
240      - fix residual computations so that they no longer affect the actual
241        simulation code
242      - fix seaice_readparams to be able to actually set new parameters
243        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
244    o model/src:
245      - fix wrong truncation (single prec) from "FLOAT" function in expressions
246        like: deltaT*FLOAT(myIter) when myIter is large:
247         a) replaced by DFLOAT (if not seen by TAF);
248         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
249    o pkg/aim_v23:
250      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
251        when pickupSuff is set ; do write rolling pickups + at the end of the run.
252    o pkg/atm_ocn_coupler + ocn_compon_interf:
253      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
254        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
255        add corresponding call in DO_OCEANIC_PHYS.
256    o coupler pkgs:
257      Start a new way to set-up optionally-exchanged variables (previously, only
258       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
259       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
260       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
261       compononent param default can be set accordingly).
262      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
263       but rather applies to a group a fields (going both ways like for DIC)
264       and corresponds to an option of coupling config.
265      coupler (pkg/atm_ocn_coupler):
266      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
267        and read namelist directly (without eessup S/R calls) instead of
268        in the very un-flexible old way, 1 param per line, in fixed order;
269      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
270        cleanly in CPL_CHECK_CPLCONFIG
271      - add new coupling-exchange selectors (some not yet active) including
272        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
273                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
274      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
275        component ; called directly from coupler.F, after comp. registrations;
276      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
277         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
278          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
279      components (pkg/atm_ & ocn_compon_interf):
280      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
281        CPP header file in all pkg source files.
282      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
283        ATM/OCN_CHECK_CPLCONFIG;
284      - add error-counter to track errors (e.g., in "data.cpl") and to stop
285        cleanly in ATM/OCN_CHECK_CPLCONFIG;
286      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
287        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
288        before PACKAGES_READPARMS;
289      verification/cpl_aim+ocn/:
290      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
291        "data.cpl" for coupler (in input_cpl).
292    o eesupp/inc:
293      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
294        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
295        to always cumulate tile local-sum in the same order (still uses
296        MPI_Allreduce like standard code).
297      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
298        that are now identical to standard version (in eesupp/inc).
299    o pkg/shelfice:
300      - add SHELFICETransCoeffTFile for initializing spatially varying
301        heat and salt transfer coefficients
302    o pkg/atm_compon_interf & ocn_compon_interf:
303      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
304        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
305      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
306    o pkg/atm_ocn_coupler:
307      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
308    o pkg/rbcs:
309      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
310        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
311      - add a short report (to STDOUT) about RBCS-mask settings.
312    
313    checkpoint65p (2015/10/23)
314    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
315        there is no adjoint test for EVP, we don't know what it does to the adjoint
316        solution, but at least there are no more recomputation warnings left
317    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
318        a chance of giving the same results as a fully converged VP (JFNK) solver
319    o tools/adjoint_options/adjoint_diva:
320      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
321    o pkg/streamice:
322      - spotted bug in streamice_driving_stress using dyG where should have been dxG
323    o pkg/exf:
324      - remove STOP statement that prevented to use wind or (wind-)stress
325        interpolation for constant-in-time forcing fields (wind/stress period = 0).
326    o pkg/seaice:
327      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
328        5 additionals 2D fields and 6 new store directives
329      - change logic in seaice_readparms.F: EVP code can now be turned on in
330        various ways, setting SEAICE_deltaTev is no longer required,
331        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
332        or SEAICEaEVPcoeff
333    o pkg/shelfice/shelfice_thermodynamics.F
334      - redefining uLoc/vLoc to u/v, instead of 2u/v
335    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
336      - this is an intermediate state of a truely converging EVP that has
337        the potential of outperforming implicit VP methods, I do not recommend
338        using it yet.
339      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
340        and all parameters are hardwired
341      - for convergence it still requires very smooth regularisations, that means,
342        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
343        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
344        specific averaging appears to be required, still subject to tuning
345      - still needs cleaning and I need to turn parameter into runtime parameters
346      - add code to compute and print residuals of iteration, compile with
347        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
348    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
349      that entered with r1.54 on Sep04, 2015, -> update results
350    
351    checkpoint65o (2015/09/14)
352    o pkg/mom_vecinv & mom_common:
353      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
354        called from there.
355      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
356        allows to use Vector-Invariant form in deep atmos and anelastic formulation
357    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
358      and Koenig-Beatty+Holland (2012)
359      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
360      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
361      - requires an extra input argument for S/R seaice_calc_viscosities
362      - tensileStrength's depth dependence is different from Itkin et al. (2015)
363        (to be changed and played with, for now exponential)
364    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
365      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
366        by AREA according to Connelly et al. (2004), JPO.
367      - For EVP and the LSR solver, the implicit part of the drag term is
368        the only non-zero term in the denominator when there is no ice (which
369        prevented running the model with zero ice-ocean drag). If
370        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
371        (or zero main diagonals BU/BV) which need to be caught. A practical
372        consequence is that for open water, the momentum equation reduce
373        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
374        they happen to be zero, often leading to a non-zero solution over
375        open water.
376    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
377        efficient EVP method.
378      - introduce area-weighted averages for e12 (analogously to
379        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
380        remain, but also changing the order of terms in the previous average
381        changed the results as much) -> update experiment
382      - add SEAICE_DELTA_SMOOTHREG code
383      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
384        TEM-code
385      - adjust loop bounds so that only required fields are computed
386      - add new averaging code for zetaZ/deltaZ (again similar to
387        seaice_calc_viscosities.F), inactive by default for now (will change
388        results again), but will replace old code eventually
389    o eesupp/src:
390      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
391        to always cumulate tile local-sum in the same order
392        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
393        Still uses MPI_Allreduce (like standard code) but on array of tiles
394        and should be faster than GLOBAL_SUM_SEND_RECV code.
395      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
396        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
397      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
398         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
399         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
400         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
401         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
402    
403    checkpoint65n (2015/07/29)
404    o pkg/thsice:
405      - add a warning when used with pkg/aim but without updating SST
406        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
407    o pkg/offline:
408      - change where Offline-Fields are loaded, from load_fields_driver.F to
409        directly within FORWARD_STEP, just after updating iter number and time;
410      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
411        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
412       These changes allow:
413        a) to recover exactly on-line results using deltaToffline=deltaTClock,
414        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
415        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
416        time-step, both with GM & KPP files and with recomputing these fields;
417        b) no needs to switch on staggerTimeStep anymore;
418        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
419      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
420    o pkg/offline:
421      - change (rarely used) offset-iteration parameter to an offset time (in s):
422        can easily recover previous offset-iter effect by setting offset-time
423        (offlineTimeOffset) to offset-iter x deltaToffline;
424      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
425        in KPP as part of surface buoyancy forcing) in offline run.
426      - fix ptracers KPP non-local term in the case where KPP is re-computed.
427    o OpenAD
428      - Adding preliminary ggl90 test to OpenAD verification.
429        Config. with ggl90 currently diverges after 64 time steps
430        so will need more work to become more stable
431      - Adding preliminary kpp test to OpenAD verification.
432        required small tweakes in kpp_routines.F
433      - Merge and update from Krishna Narayanan's contrib area:
434        * Add one variable for preliminary OpenAD DIVA
435        * Add replacement time-stepping for OpenAD DIVA
436        * genmake2 flag -diva (but only for OpenAD; preliminary)
437        * required modifs for OAD_support
438        successful preliminary test for tutorial_global_oce_biogeo/
439    o pkg/seaice:
440      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
441      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
442        delta with a smooth function in s/r seaice_calc_viscosity
443        (no effect on EVP)
444      - rename local suffix "sqr" into "sq" for more consistent variable names
445    o pkg/seaice:
446        add new parameter SEAICE_deltaMin that is used ***only***
447        for regularizing Delta (and nothing else, like the parameter
448        which is also used for all sorts of things SEAICE_EPS).
449        Defaults to SEAICE_EPS for backward compatibility only.
450    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
451        the wrong key by inialising it before use -> fixes a recomputation
452        problem but does not fix the gradient
453    o pkg/layers:
454      - move resetting of flux arrays to outside the iLa loop
455        (this caused layers_diapycnal to not work with more than one layer coord.)
456      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
457    o pkg/layers:
458      - remove from common block 3D layers fields (used to diagnose transport
459        in tracer coords) and declare them as local arrays in layers_calc.F
460    o pkg/seaice:
461      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
462        in lab_sea forward experiment (changes results -> updated)
463      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
464    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
465       computations; for SEAICE_VECTORIZE_LSR
466      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
467        sweep to the outside,
468      - remove store directives and add "CADJ loop sequential" directives
469        in analogy to model/src/solve_tridiagonal.F
470      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
471        boundaries to yield more readable code. This has also the charming side
472        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
473        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
474        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
475        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
476        an additional option)
477       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
478       but the adjoint gradients (which are affected by this change) still explode.
479    o coupler (atm & ocn _compon_interf):
480      - avoid using Exch2 IO mapping if not suitable.
481    
482    checkpoint65m (2015/06/15)
483    o pkg/layers:
484      - clean-up old parameters setting (from Sep 2012):
485        + remove old parameters setting from common block (declared locally);
486        + stop if any old parameter is mixed with new parameters;
487        + check for valid or consistent parameter setting (e.g., layers_name)
488      - check that layers_bounds for Pot.Density are in the right range;
489        this is supposed to catch un-updated setting after recently shifting
490        potential density field "prho" by -1000 (now in "sigma" scale).
491    o pkg/layers:
492      - Added missing call to layers_fill for keeping track of tottend in
493        pkg/diagnostics/diagnostics_fill_state.F
494    o pkg/layers:
495      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
496        of diapycnal fluxes
497    o pkg/layers:
498      - reverted changes to interpolation to previous treatment; there
499        was never actually a problem
500    o pkg/layers:
501      - fix interpolation of layers tracers in the presence of partial cells
502      - add lots of new functionality to compute water mass transformation
503        (enabled by CPP flag LAYERS_THERMODYNAMICS)
504      - add new calls from main code (diags_oceanic_surf_flux.F,
505        thermodynamics.F, impldiff.F) and gad to save the necessary fields
506        for layers_thermodynamics calculations
507    o pkg/ptracers:
508      - add capability of stepping a passive tracer forward without advection
509        by setting PTRACERS_advScheme to 0.
510    o pkg/diagnostics:
511      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
512    o pkg/layers:
513      - shift potential density field "prho" by -1000 for density layer averaging so
514        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
515        Note that density bin boundaries (layers_bounds in data.layers) have
516        to be set accordingly (i.e., shifted, in sigma scale).
517    o pkg/layers:
518      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
519      - fix calculation of layer non-weighted velocity and layer probability
520      - add diagnostics for pot.density used for layer averaging
521    o pkg/seaice:
522      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
523        positiveness, modify a few comments and improve variable names,
524      - the changed computation of deltaC affects most seaice-related
525        experiments at the truncation level.
526        seaice_itd.thermo is affected by far the most, with
527        only 7 digits of agreement remaining; update experiments.
528    
529    checkpoint65l (2015/05/04)
530    o pkg/shelfice:
531      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
532        factor drKp1 to zero where it is negative (ie. do not use
533        SHELFICEBoundaryLayer if hFacC>1)
534      - the same for factor drLoc in shelfice_forcing.F
535    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
536        with modules in ptracers, when using testreport option "-small_f"
537    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
538      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
539    o verification/testreport
540      - add new option -small_f
541        with this option testreport first makes the target small_f (*.f files)
542        before running make (all). This is useful for explicit inlining when
543        all sources need to be full available.
544    o pkg/exf/exf_interp.F:
545        remove previous changes related to reverse (decreasing) input grids latitude
546    
547    checkpoint65k (2015/04/01)
548    o pkg/ecco:
549        fix missing cosphi initialization; use eccoiter in place of optimcycle;
550        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
551        instead of active read/write
552    o pkg/ctrl:
553        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
554        instead of active read/write.
555    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
556        return if .NOT.useAUTODIFF
557    o pkg/seaice: add CPP brackets (cost function related).
558    o model/src:
559        add useAUTODIFF run time switch.
560    o pkg/exf/exf_interp.F:
561        add code to allow input grids with latitude starting in the north (i.e. when
562        j=1 corresponds to northern edge of field); modify global_with_exf to test
563        this feature.
564    o verification/testreport:
565      - replace "grep -A3" with POSIX conformal sed command, because there are
566        implementations of grep that cannot do contextual searches
567      - replace "cat -n" by "nl" (two occurrences), because not all implementations
568        of "cat" have the option "-n"
569    o model/src:
570        add new file gsw_teos10.F that contains 3 functions, more or less a copy
571        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
572        convert from conservative to potential temperature. For now they are not
573        called anywhere.
574    o pkg/ggl90: make "useIDEMIX" useful
575      - re-organize code in s/r ggl90_calc a little to move computations that
576        are different for idemix into separate loops (changes verification
577        experiment idemix at truncation level, 12 digits remain -> updated)
578      - requires 2 new 2D fields KappaM, verticalShear
579      - make hFacI and recip_hFacI local 3D variables that are passed to
580        s/r ggl90_idemix
581      - fix and improve some comments
582    
583    checkpoint65j (2015/02/25)
584    o pkg/openad
585      - synchronize seawater.F with version in model/src: replace routine
586        body of sw_temp by calling sw_ptmp and fix/add a few comments.
587    o pkg/mnc:
588      - change default value of pickup_read/write_mnc params to FALSE
589        (since few features are missing in reading MNC pickup files).
590    o model/src:
591      - change default (background) vertical diffusivity for salt to be the
592        temperature (background) vertical diffusivity.
593      - change background vertical diffusivity in vertical mixing pkgs ggl90,
594        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
595        This makes ptracers default diffusivity (that uses salt diffKr) more
596        consistent with vertical mixing schemes.
597    o verification/testreport:
598      - fix typo in "-pcls" option ;
599      - put temp files in /tmp (instead of in local dir)
600      - add option "-ncad" to use genmake2 new option "-nocat4ad"
601      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
602    o pkg/ggl90 (idemix code):
603      - apply few fixes ; add some missing "_d 0" ; update output of exp.
604        global_ocean.90x40x15.idemix
605    o OpenAD
606      - enable active file I/O and begin removal of work-around code
607        for OpenAD for handling control variables (memory vs. active files)
608      - new CPP options file OPENAD_OPTIONS.h
609      - revert to genarr2d gradient check for hs94.1x64x5
610      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
611      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
612    o tools/genmake2:
613      - add option for an alternative Makefile (from Martin) where multiple
614        source files are sent to TAF (instead of all in one file).
615    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
616      - code provided by Carsten Eden as an extension of ggl90
617      - so far the code is turned on within ggl90 by setting a CPP-flag at
618        compile time; a runtime flag implementation is not yet complete
619      - tested in new verification experiment global_ocean.90x40x15.idemix
620    o verification:
621      - reduce length of the AD test run by half for experiments
622        global_ocean.cs32x15 (std + thsice) and isomip
623      - enable active file I/O for OpenAD, adjust verifications accordingly
624      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
625    o verification/testreport:
626      - fix two non-POSIX sed statements so that there are no error messages
627        on Mac OS X
628      - replace hostname -s with hostname | sed 's/\..*$//'
629    o model/src/seawater.F:
630      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
631        (following the matlab code), which would have avoided the bug caught
632        by Matt (see below) in the first place
633    o pkg/shelfice:
634      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
635        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
636      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
637        ice-shelf case (i.e., within surface level).
638      - add config summary in shelfice_check.F
639      - remove global variable recip_SHELFICElatentHeat and replace by a local
640        variable recip_latentHeat
641      - introduce diagnostics for friction velocity uStar (in case of
642        SHELFICEuseGammaFrict)
643      - change verification experiment isomip.htd:
644        + start from pickup (as input_ad at nIter0=8640)
645        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
646        + test SHELFICEuseGammaFrict = .TRUE.
647        + test SHELFICEadvDiffHeatFlux = .TRUE.
648    o model/src:
649      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
650        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
651        update output of experiments global_with_exf.yearly and isomip (all 6).
652    o pkg/shelfice:
653      - change setting of kTopC to also be zero where there is no ice-shelf.
654      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
655        ice-shelf is.
656      - first attempt to get RealFreshWaterFlux effects: for now, only without
657        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
658    o pkg/seaice: add the option to prescribe a fixed thickness PDF
659      for thermodynamic calculations
660      - because of divisions of the type 7/7 not exactly equal to 1, this change
661        affects results of some verification experiments by up to 4 digits:
662        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
663        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
664        adjoint: lab_sea, lab_sea.noseaicedyn
665        -> updated
666    
667    checkpoint65i (2015/01/23)
668    o model/src:
669      - change units of frictionHeating field from W to W/m^2
670      - fix bug in frictional heating from stratospheric drag in
671        S/R ATM_PHYS_TENDENCY_APPLY_V
672      - with synchronous time-stepping: move resetting to zero of frictionHeating
673        field from load_fields_driver.F to thermodynamics.F ;
674      - add diagnostics for frictional heating.
675    o model/src & gmredi K3D:
676      - add frictionHeating field to pickup-files (for synchronous time-stepping)
677      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
678      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
679        and name in pickup file).
680      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
681    o model/src:
682      - move (from ini_forcing.F) initialisation of all arrays in header file
683        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
684        (since Nov 2012) with option selectAddFluid=1.
685    o pkg/shelfice:
686      - change units (+ document) of newly added field "shelfIceMassDynTendency"
687      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
688    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
689    o pkg/seaice: two new runtime parameters:
690      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
691        long overdue
692      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
693        parameterization of tensil stress for fast ice (does not do anything yet)
694    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
695        for LSR: move checking overlaps out of JFNK-if-block
696    o pkg/atm_phys:
697      - move copy of grid and dynamical fields out of atm_phys_driver.F into
698        new S/R ATM_PHYS_DYN2PHYS.
699      - fix level height for Linear Free-Surf case (to be consistent with
700        fixed-in-time pressure levels).
701    o pkg/mom_common (bottomdrag):
702      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
703        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
704        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
705    o pkg/shelfice (u/v_drag):
706      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
707      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
708        (now similar to shelfice_u_drag.F)
709      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
710        from mom_vecinv.F (similar to mom_fluxform calls).
711    o pkg/mom_common (bottomdrag):
712      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
713      - add options for alternative discretisation of velocity norm in quadratic
714        bottom drag: averaging of grid-cell-center KE to U.point and V.point
715        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
716        improves when averaging only the other component (e.g. vVel for U bottom
717        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
718      - add options (bottomVisc_pCell) to account for partial-cell in bottom
719        friction (no-slip BC) thus getting the true distance from the bottom;
720        off by default since this also reduces model stability (explicit bottom
721        friction). Changes produce different machine truncation with linear-drag
722        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
723        front_relax (bvp & mxl, 10 & 11 digits).
724    o model/src & mom pkgs:
725      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
726        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
727      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
728        just copy level Nr value to level Nr+1.
729    o doc:
730      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
731    o pkg/streamice:
732      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
733        SHELFICE.h: move array shelficemass to init_varia, initialise
734        from array shelficemassinit, which is set in init_fixed and
735        has option to be set from file; introduce array
736        shelficeMassDynTend array, set thru file in init_fixed
737      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
738        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
739        pkg/streamice
740      - shelfice_thermodynamics.F: call shelfice_step_icemass if
741        SHELFICEMassStepping = .true.
742      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
743    
744    checkpoint65h (2014/12/17)
745    o verification/global_ocean.90x40x15, global_ocean_ebm:
746      - update to generic controls.
747    o pkg/ctrl:
748      - ctrl_map_ini_genarr.F: test for igen>0
749      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
750      - move gentim2d part of ctrl_map_ini_genarr.F to
751        new separate routine : ctrl_map_ini_gentim2d.F
752      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
753        add time variable weights and cyclic controls (time mean,
754        seasonal cycle, etc) capabilities to gentim2d
755    o pkg/ecco:
756      - move reading of error, conversion to weights from
757        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
758    o global_oce_llc90, cs32:
759      - activte sbo.
760      - CTRL_SIZE.h : add maxCtrlProc.
761      - activate the new genctrl capabilities.
762      - update following reorganization of global_oce_input_fields.tar.gz  
763    o pkg/ctrl/ctrl_ad_diff.list:
764      - add missing ctrl_init_rec.f
765    o tools/OAD_support/keepOriginal:
766      - add ctrl_init_rec.F
767    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
768      - avoid recomputations of xx_gentim2d_dummy.
769    o momentum diagnostics:
770      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
771        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
772    o pkg/seaice/seaice_lsr.F:
773      - fix computation of BU/BV, make sure they are non-zero, only necessary
774        for cubed sphere exchanges and SEAICE_OLx/y>0.
775        This makes calling s/r fill_cs_corner_rl obsolete (removed).
776    o verification/global_ocean.cs32x15/input.seaice
777      - add test for strong implicit coupling and restricted addtive Schwarz
778        methods for LSR
779      - update results/output.seaice.txt
780    o verification/tutorial_global_oce_biogeo:
781      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
782        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
783        update output_adm,_oadm,_tlm.txt
784    o pkg/dic:
785      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
786      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
787        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
788    o verification/tutorial_global_oce_biogeo:
789      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
790        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
791        update output_adm,_oadm,_tlm.txt
792    o eesupp/src:
793      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
794        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
795    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
796      LSR (following Hutchings et al. 2004)
797      - introduce zetaZ as a global variable (requires adjustments in
798        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
799        in seaice_calc_viscosities.F
800      - new flag SEAICEuseStrImpCpl (default off)
801      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
802        momentum equations
803      - JFNK-solver (preconditioner) adjusted to allow using this method
804        (where it does not have any positive effect)
805    o pkg/seaice
806      - add overlap for restrictive additive Schwartz method also to LSR, but
807        turn it off by default (because it only seems to work for non-cubed
808        sphere/llc topologies)
809    o pkg/autodiff
810      - add extra exchanges in addummy_in_steppging also for mnc output
811    o pkg/seaice:
812      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
813        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
814    o pkg/obcs:
815      - add option to specify domain-connected piece Id along OB though files
816        (for now, only used to diagnose PhiVel; default =1 -> global correction)
817      - modify obcs_diag_balance.F to process each connected-part separately;
818        exclude OB where Id = 0 but keep the full divergence there (-> constant
819        Psi along this portion of OB and all inflow derived from grad(Phi))
820      - add example of OB-conect files in verification/so_box_biogeo/input.
821    o pkg/diagnostics:
822      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
823      a) use non zero matrix element across OB and solve for Phi 1 grid point
824         outside OB (i.e, where tracer OBCS are applied).
825      b) global imbalance of inFlow/outFlow across OB: instead of modifying
826         velocity across OB, spread it uniformly along the OB in the RHS.
827    
828    checkpoint65g (2014/11/19)
829    o pkg/diagnostcis:
830      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
831    o pkg/my82,pp81,kl10:
832      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
833        field diffKr as background diffusivity to set minimum diffusivity value.
834    o pkg/seaice:
835      - add new parameter SEAICEuseEVPrev (for revisited EVP by
836        Bouillon et al 2013)
837      - add SEAICE_evpAlpha/Beta to namelist
838      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
839        involve trivial re-ordering of divisions/multiplications that should not
840        have any effects, but ... they do change the results of lab_sea.hb87 so
841        that only 2 digits of agreement remain, in line with the general
842        instability/fragility of the evp-code. For now, I do not care and just
843        update the verification experiment
844    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
845      - remove xx_genarr2d_numsmooth etc
846      - use xx_genarr2d_preproc etc instead
847      - carry out smooth_correl2D at initialization stage rather than during
848        time stepping.
849      - get smoothOpNb from xx_gentim2d_preproc
850    o global_oce_cs32 :
851      - add test of generic ecco capabilities.
852    o pkg/exf/exf_getsurfacefluxes.F :
853      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
854    o pkg/ctrl,ecco :
855      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
856        is defined.
857    o pkg/seaice: add diagnostics for Delta (deformation parameter)
858    o model/src:
859      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
860        diffusivity (background) is specified but ignored.
861    o verification:
862      - in testreport, convert hostname to lower case for default output dir name
863    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
864    o pkg/dic: add modifications from Hajoon:
865      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
866      - light attenuation: add self-shading effect by climatological Chlorophyll
867        (read from file).
868    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
869        compiles when SEAICE_ALLOW_DYNAMICS is undefined
870    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
871        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
872        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
873        approach where CPP_OPTIONS.h includes an omnipotent
874        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
875    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
876        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
877    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
878        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
879        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
880    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
881      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
882      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
883      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
884      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
885    o pkg/ctrl,ecco,exf :
886      - remove variables associated with NON-generic costs,
887        unless ECCO_CTRL_DEPRECATED is defined.
888      - remove NON-generic NON-obcs controls,
889        unless ECCO_CTRL_DEPRECATED is defined.
890    o pkg/ctrl : added ctrl_local_params.h
891    o pkg/ecco : added ecco_local_params.h
892    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
893        experiments, which will progressively be removed once the
894        experiments are revised to use only generic controls/costs.
895    
896    checkpoint65f (2014/10/13)
897    o pkg/ctrl, ecco, seaice : minor changes in headers
898    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
899        cost function and control capabilities added since checkpoint65c.
900    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
901    o pkg/ecco: increase modularity and improve logic
902      - ecco_toolbox.F (new) : basic operations that are often used,
903        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
904        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
905      - cost_gencal.F (new) : determine filnames and records.
906      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
907      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
908        and exploit the above functions leading to more compact code.
909      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
910      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
911        using_ers, using_gfo, using_mdt is now only defined within gencost)
912    o pkg/ecco: extend generic cost capabilities
913      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
914        capabilities via gencost_preproc (+ _c,_i,_r related params),
915        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
916        gencost_outputlevel arguments to cost_generic
917      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
918        and active_read, making room for gencost_preproc to take effect.
919        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
920      - pkg/ecco/cost_generic.F :
921        compute and store misfit maks*(model-data) in localdif that is
922        then used in cost and for output, output misfit if outlev.GT.0
923      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
924        rather gencost_barfile for deciding whether to write barfile
925      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
926      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
927        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
928      - pkg/ecco/ecco_summary.F : report gencost variables
929      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
930    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
931    o pkg/ecco: internal re-organization
932      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
933        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
934        mv relevant variables definition from ecco_cost.h to ecco.h,
935        make sure gencost routines only include ecco.h)
936      - throughout : add missing CCP switches, rm unused variables,
937        and rm un-necessary CPP switches
938      - throughout gencost routines : replace modelstartdate with
939        gencost_startdate when needed
940      - cost_bp_read.F : use arguments, instead of common blocs
941        so that it can be used also by (new) cost_gencost_bpv4.F
942      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
943      - ecco_phys.F : compute etanFull
944      - ecco_readparms.F : rename using_topex as using_tpj, add
945        bpv4-grace to gencost list, initialize added parameters
946      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
947    
948  checkpoint65e (2014/09/28)  checkpoint65e (2014/09/28)
949  o pkg/obcs:  o pkg/obcs:
950    - replaced the just-added CPP options with run-time variables    - replaced the just-added CPP options with run-time variables
# Line 315  o pkg/seaice: more clean up Line 1256  o pkg/seaice: more clean up
1256      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
1257      this experiment):      this experiment):
1258      > size mitgcmuv_ad      > size mitgcmuv_ad
1259      text    data        bss     dec        hex        text    data        bss     dec        hex
1260      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1261      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1262      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1263      text    data        bss     dec        hex      text    data        bss     dec        hex
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