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revision 1.2078 by gforget, Mon Oct 6 14:12:28 2014 UTC revision 1.2247 by jmc, Wed Apr 27 22:12:20 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 model/src:
8      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
9    o pkg/seaice:
10      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
11    o pkg/seaice:
12      - add basal stress as parameterisation for grounding ice
13        following Lemieux et al. (2015)
14      - turn on by setting new parameter SEAICEbasalDragK2 to a value
15        larger than 0. Lemieux et al. (2015) recommend 15.
16      - The adjoint complains with extra recomputations so there is also a
17        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
18        order to postpone the problem
19      - compile the new code in lab_sea
20    o verification/halfpipe_streamice:
21      - update both TAF and OpenAD adm output (machine truncation differences)
22    
23    checkpoint65v (2016/04/08)
24    o verification/advect_xz:
25      - increase overlap size from 3 to 4 and add new secondary test for PQM
26        advection scheme (with mono & wino limiter).
27      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
28    o model/src:
29      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
30        added phi0Ref) to set vertical axis origin and phiRef origin;
31        keep Ro_SeaLevel for backward compatibility (with a warning).
32       According to coordinate and fluid type:
33        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
34        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
35        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
36        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
37      - remove Ro_SeaLevel from ATM experiment parameter files;
38      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
39        complement; update output.txt (changes at machine truncation level).
40    o pkg/seaice/seaice_evp.F
41      - simplify computation of deltaZ and zetaZ to simple averaging following
42        Bouillon et al. (2013). This removes a lot of code, but also changes
43        verification experiment lab_sea.hb87 -> updated
44    
45    checkpoint65u (2016/03/14)
46    o pkg/generic_advdiff:
47      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
48        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
49        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
50        testing and not for actual use.
51    o model/src:
52      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
53        origin r = rF(1);
54      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
55        in EOS for height coordinate: enable to include NH Pressure or to use
56        more accurate pressure vertical profile; options not linked to EOS type
57        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
58      - start to implement variable gravity (along vertical): for now, only with
59        z-coords (not even z*).
60      - add Ideal Gas equation of state for height coordinate.
61      - update OpenAD output (affected at machine truncation level) of exp:
62        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
63    o pkg/exf:
64      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
65        of exf interpolation (before any rescaling, rotation or interpolation
66        to velocity point) for each field that gets loaded from file. This option
67        identically mimics the input file organization (e.g. record numbers in year
68        by year input files) besides the change in horizontal grid.
69      - add rotateStressOnAgrid run-time switch so that wind stress fields
70        can be provided on the A-grid in zonal/meridional direction and
71        rotated on the fly. This only applies to the case when the exf
72        interpolation is off and rotateStressOnAgrid is false by default.
73    o model/src:
74      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
75        it's also used with pkg/atm_phys) and add few more parameters (but still
76        inactive, src code yet to come)
77    
78    checkpoint65t (2016/02/10)
79    o pkg/atm_phys:
80      - from Ruth Geen: add optical depth dependence on CO2 concentration.
81    o model/src:
82      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
83        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
84        Update output of exp. deep_anelastic (changes at truncation level).
85    o tools:
86      - add a hack in "remove_comments_sed" (used only with TAF) for recent
87        version of OpenMPI (shipped with FC.23): comment out the new header
88        file "mpif-sizeof.h" which causes problems to TAF.
89    o pkg/seaice:
90      - change the termination criterion so that maxits (SEAICElinearIterMax)
91        has an effect
92      - unify iteration parameters for implicit solvers (JFNK and Picard)
93        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
94        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
95        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
96        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
97        SEAICEnonLinTol     replaces JFNKgamma_nonlin
98      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
99      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
100        use with SEAICEuseKrylov
101    o pkg/seaice/seaice_lsr.F
102        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
103        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
104        an effect.
105    o pkg/seaice: add two new parameters
106      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
107        parameter is not in any namelist)
108      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
109        a preconditioner for the non-linear Newton iteration of the JFNK
110        solver
111    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
112      affects some experiments at truncation level:
113      - global_ocean.cs32x15.icedyn (11 digits),
114      - global_ocean.cs32x15.seaice (11 digits),
115      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
116      - also update global_ocean.cs32x15 adjoint and tangent-linear results
117    o pkg/salt_plume & pkg/thsice:
118      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
119        connect salt_plume flux to ATM-OCN coupling pkgs interface:
120       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
121         export to coupler interface) even without compiling pkg/salt_plume ;
122       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
123         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
124    o pkg/dic:
125      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
126        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
127        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
128      - move also update with values from ATM-OCN Coupler in the same new S/R
129        (previously done in ocn_apply_import.F).
130    o tools/adjoint_options:
131      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
132        has been changed on Jan 14, 2016.
133    o pkg/ggl90:
134      - add alternative discretisation of vertical shear (off by default), to
135        compute the mean (@ grid-cell center) of vertical shear compon instead of
136        vertical shear of mean flow (@ grid-cell center).
137      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
138        results on adjacent faces of cubed-sphere grids; this fix the restart.
139    o pkg/atm_compon_interf:
140      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
141        pass last value, stored directly before export to CPL ;
142        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
143      - remove atmSLPr from pickup files (no longer needed for restart)
144    
145    checkpoint65s (2016/01/13)
146    o eesupp & genmake2:
147       - first check for Function ETIME and, if it fails, then check for subroutine
148         ETIME and consistent output; use the appropriate version in timers.F
149    o model/src:
150      - to check restart test, add option to apply EXCH to U,V earlier, just before
151        integr_continuity; turned off by default.
152    o pkg/dic:
153      - remove CPP option USE_ATMOSCO2 (not needed)
154    o tools/tst_2+2:
155      - try to ignore difference between +0 and -0 in binary file, causing test
156        to fail for no good reason.
157    o eesupp & genmake2:
158      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
159        but also check (in genmake2) that test runs and returns meaningful results.
160    o coupler pkgs:
161      Finish implementation of optionally-exchanged variable switches (started on
162       Nov 12) with addition of few more exchanged fields, including 2-way exchange
163       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
164       advection in OCN component; this requires sequential coupling.
165      coupler (pkg/atm_ocn_coupler):
166      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
167        routines (useful for debug).
168      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
169         flux, DIC fields) if corresponding switch is ON.
170      - add option to export RunOff to OCN (to use for DIC river input)
171      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
172      components (pkg/atm_ & ocn_compon_interf):
173      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
174        optionally exchanged fields; add a check & stop in cpl_readparms.F.
175        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
176        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
177      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
178        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
179      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
180      - hold in common block coupler optionally-exchanged variable switch
181        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
182      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
183        this is intended to replace the OCN cplFldtave.* output files (not updated
184        to contain new additional exchanged fields).
185    o pkg/dic:
186      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
187    o pkg/thsice:
188      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
189        and writing of thsice pickup files.
190    o pkg/atm_compon_interf:
191      - move all field individual export-call out of cpl_export_import_data.F
192        into new S/R ATM_EXPORT_FIELDS
193    o pkg/atm_compon_interf:
194      - store state variables (for now, only thSIce fields) just before beeing
195        exported (in cpl_export_import_data.F, like on ocean side) instead of from
196        atm_store_my_data.F like all exported fluxes.
197      - new version of pickup_cpl: write field names into meta file and read meta
198        file to find field postion in pickup. Also only write/read fields meeded for
199        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
200    o pkg/dic:
201      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
202    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
203        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
204        value can be from domain [0,1] to average between the two methods
205    o pkg/atm_phys:
206      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
207        hold fixed in time).
208    
209    checkpoint65r (2015/12/21)
210    o pkg/seaice:
211        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
212        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
213    o pkg/seaice:
214      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
215        when SEAICEscaleSurfStress=.TRUE.,
216      - apply areaW and areaS in S/R seaice_calc_lhs
217    o pkg/atm_phys:
218      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
219        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
220        for individual contribution (convection, LSC cond, radiation)
221      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
222        information); activated with: solar_exponent=0. and wv_exponent=-1.
223    o pkg/ggl90:
224      - within IDEMIX add upper limit for horizontal group velocity to
225        avoid instability problems in the explicit horizontal diffusion term for
226        long time steps or high resolution
227    o pkg/diagnostics:
228      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
229        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
230    o testreport:
231      - remove "-v" (verbose option) in default mpirun command.
232    o pkg/seaice/seaice_growth:
233      - catch potential division by zero in ITD code, does not change
234        verification results
235    o pkg/ecco:
236      - retire old codes to the Attic. The calls to retired functions are
237        left in a commented form in case they ever need to be re-activated.
238      - ecco_check.F: issue warning if any old CPP option is
239        defined that corresponds to retired codes -- then stop.
240    o pkg/atm_compon_interf:
241      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
242        coupler: use last time-step value instead of average over cplSendFrq_iter
243        time-step, similar to what is done for seaIceMass.
244        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
245    o eesupp & genmake2:
246      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
247        <= remove until a fix is found for some ifort version on ia32 machine.
248    o pkg/seaice/seaice_evp:
249      - refine residual computation
250    
251    checkpoint65q (2015/11/18)
252    o pkg/seaice/seaice_evp:
253      - fix residual computations so that they no longer affect the actual
254        simulation code
255      - fix seaice_readparams to be able to actually set new parameters
256        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
257    o model/src:
258      - fix wrong truncation (single prec) from "FLOAT" function in expressions
259        like: deltaT*FLOAT(myIter) when myIter is large:
260         a) replaced by DFLOAT (if not seen by TAF);
261         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
262    o pkg/aim_v23:
263      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
264        when pickupSuff is set ; do write rolling pickups + at the end of the run.
265    o pkg/atm_ocn_coupler + ocn_compon_interf:
266      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
267        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
268        add corresponding call in DO_OCEANIC_PHYS.
269    o coupler pkgs:
270      Start a new way to set-up optionally-exchanged variables (previously, only
271       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
272       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
273       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
274       compononent param default can be set accordingly).
275      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
276       but rather applies to a group a fields (going both ways like for DIC)
277       and corresponds to an option of coupling config.
278      coupler (pkg/atm_ocn_coupler):
279      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
280        and read namelist directly (without eessup S/R calls) instead of
281        in the very un-flexible old way, 1 param per line, in fixed order;
282      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
283        cleanly in CPL_CHECK_CPLCONFIG
284      - add new coupling-exchange selectors (some not yet active) including
285        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
286                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
287      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
288        component ; called directly from coupler.F, after comp. registrations;
289      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
290         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
291          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
292      components (pkg/atm_ & ocn_compon_interf):
293      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
294        CPP header file in all pkg source files.
295      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
296        ATM/OCN_CHECK_CPLCONFIG;
297      - add error-counter to track errors (e.g., in "data.cpl") and to stop
298        cleanly in ATM/OCN_CHECK_CPLCONFIG;
299      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
300        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
301        before PACKAGES_READPARMS;
302      verification/cpl_aim+ocn/:
303      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
304        "data.cpl" for coupler (in input_cpl).
305    o eesupp/inc:
306      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
307        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
308        to always cumulate tile local-sum in the same order (still uses
309        MPI_Allreduce like standard code).
310      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
311        that are now identical to standard version (in eesupp/inc).
312    o pkg/shelfice:
313      - add SHELFICETransCoeffTFile for initializing spatially varying
314        heat and salt transfer coefficients
315    o pkg/atm_compon_interf & ocn_compon_interf:
316      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
317        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
318      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
319    o pkg/atm_ocn_coupler:
320      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
321    o pkg/rbcs:
322      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
323        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
324      - add a short report (to STDOUT) about RBCS-mask settings.
325    
326    checkpoint65p (2015/10/23)
327    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
328        there is no adjoint test for EVP, we don't know what it does to the adjoint
329        solution, but at least there are no more recomputation warnings left
330    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
331        a chance of giving the same results as a fully converged VP (JFNK) solver
332    o tools/adjoint_options/adjoint_diva:
333      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
334    o pkg/streamice:
335      - spotted bug in streamice_driving_stress using dyG where should have been dxG
336    o pkg/exf:
337      - remove STOP statement that prevented to use wind or (wind-)stress
338        interpolation for constant-in-time forcing fields (wind/stress period = 0).
339    o pkg/seaice:
340      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
341        5 additionals 2D fields and 6 new store directives
342      - change logic in seaice_readparms.F: EVP code can now be turned on in
343        various ways, setting SEAICE_deltaTev is no longer required,
344        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
345        or SEAICEaEVPcoeff
346    o pkg/shelfice/shelfice_thermodynamics.F
347      - redefining uLoc/vLoc to u/v, instead of 2u/v
348    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
349      - this is an intermediate state of a truely converging EVP that has
350        the potential of outperforming implicit VP methods, I do not recommend
351        using it yet.
352      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
353        and all parameters are hardwired
354      - for convergence it still requires very smooth regularisations, that means,
355        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
356        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
357        specific averaging appears to be required, still subject to tuning
358      - still needs cleaning and I need to turn parameter into runtime parameters
359      - add code to compute and print residuals of iteration, compile with
360        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
361    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
362      that entered with r1.54 on Sep04, 2015, -> update results
363    
364    checkpoint65o (2015/09/14)
365    o pkg/mom_vecinv & mom_common:
366      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
367        called from there.
368      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
369        allows to use Vector-Invariant form in deep atmos and anelastic formulation
370    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
371      and Koenig-Beatty+Holland (2012)
372      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
373      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
374      - requires an extra input argument for S/R seaice_calc_viscosities
375      - tensileStrength's depth dependence is different from Itkin et al. (2015)
376        (to be changed and played with, for now exponential)
377    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
378      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
379        by AREA according to Connelly et al. (2004), JPO.
380      - For EVP and the LSR solver, the implicit part of the drag term is
381        the only non-zero term in the denominator when there is no ice (which
382        prevented running the model with zero ice-ocean drag). If
383        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
384        (or zero main diagonals BU/BV) which need to be caught. A practical
385        consequence is that for open water, the momentum equation reduce
386        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
387        they happen to be zero, often leading to a non-zero solution over
388        open water.
389    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
390        efficient EVP method.
391      - introduce area-weighted averages for e12 (analogously to
392        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
393        remain, but also changing the order of terms in the previous average
394        changed the results as much) -> update experiment
395      - add SEAICE_DELTA_SMOOTHREG code
396      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
397        TEM-code
398      - adjust loop bounds so that only required fields are computed
399      - add new averaging code for zetaZ/deltaZ (again similar to
400        seaice_calc_viscosities.F), inactive by default for now (will change
401        results again), but will replace old code eventually
402    o eesupp/src:
403      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
404        to always cumulate tile local-sum in the same order
405        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
406        Still uses MPI_Allreduce (like standard code) but on array of tiles
407        and should be faster than GLOBAL_SUM_SEND_RECV code.
408      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
409        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
410      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
411         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
412         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
413         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
414         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
415    
416    checkpoint65n (2015/07/29)
417    o pkg/thsice:
418      - add a warning when used with pkg/aim but without updating SST
419        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
420    o pkg/offline:
421      - change where Offline-Fields are loaded, from load_fields_driver.F to
422        directly within FORWARD_STEP, just after updating iter number and time;
423      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
424        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
425       These changes allow:
426        a) to recover exactly on-line results using deltaToffline=deltaTClock,
427        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
428        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
429        time-step, both with GM & KPP files and with recomputing these fields;
430        b) no needs to switch on staggerTimeStep anymore;
431        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
432      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
433    o pkg/offline:
434      - change (rarely used) offset-iteration parameter to an offset time (in s):
435        can easily recover previous offset-iter effect by setting offset-time
436        (offlineTimeOffset) to offset-iter x deltaToffline;
437      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
438        in KPP as part of surface buoyancy forcing) in offline run.
439      - fix ptracers KPP non-local term in the case where KPP is re-computed.
440    o OpenAD
441      - Adding preliminary ggl90 test to OpenAD verification.
442        Config. with ggl90 currently diverges after 64 time steps
443        so will need more work to become more stable
444      - Adding preliminary kpp test to OpenAD verification.
445        required small tweakes in kpp_routines.F
446      - Merge and update from Krishna Narayanan's contrib area:
447        * Add one variable for preliminary OpenAD DIVA
448        * Add replacement time-stepping for OpenAD DIVA
449        * genmake2 flag -diva (but only for OpenAD; preliminary)
450        * required modifs for OAD_support
451        successful preliminary test for tutorial_global_oce_biogeo/
452    o pkg/seaice:
453      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
454      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
455        delta with a smooth function in s/r seaice_calc_viscosity
456        (no effect on EVP)
457      - rename local suffix "sqr" into "sq" for more consistent variable names
458    o pkg/seaice:
459        add new parameter SEAICE_deltaMin that is used ***only***
460        for regularizing Delta (and nothing else, like the parameter
461        which is also used for all sorts of things SEAICE_EPS).
462        Defaults to SEAICE_EPS for backward compatibility only.
463    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
464        the wrong key by inialising it before use -> fixes a recomputation
465        problem but does not fix the gradient
466    o pkg/layers:
467      - move resetting of flux arrays to outside the iLa loop
468        (this caused layers_diapycnal to not work with more than one layer coord.)
469      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
470    o pkg/layers:
471      - remove from common block 3D layers fields (used to diagnose transport
472        in tracer coords) and declare them as local arrays in layers_calc.F
473    o pkg/seaice:
474      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
475        in lab_sea forward experiment (changes results -> updated)
476      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
477    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
478       computations; for SEAICE_VECTORIZE_LSR
479      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
480        sweep to the outside,
481      - remove store directives and add "CADJ loop sequential" directives
482        in analogy to model/src/solve_tridiagonal.F
483      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
484        boundaries to yield more readable code. This has also the charming side
485        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
486        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
487        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
488        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
489        an additional option)
490       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
491       but the adjoint gradients (which are affected by this change) still explode.
492    o coupler (atm & ocn _compon_interf):
493      - avoid using Exch2 IO mapping if not suitable.
494    
495    checkpoint65m (2015/06/15)
496    o pkg/layers:
497      - clean-up old parameters setting (from Sep 2012):
498        + remove old parameters setting from common block (declared locally);
499        + stop if any old parameter is mixed with new parameters;
500        + check for valid or consistent parameter setting (e.g., layers_name)
501      - check that layers_bounds for Pot.Density are in the right range;
502        this is supposed to catch un-updated setting after recently shifting
503        potential density field "prho" by -1000 (now in "sigma" scale).
504    o pkg/layers:
505      - Added missing call to layers_fill for keeping track of tottend in
506        pkg/diagnostics/diagnostics_fill_state.F
507    o pkg/layers:
508      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
509        of diapycnal fluxes
510    o pkg/layers:
511      - reverted changes to interpolation to previous treatment; there
512        was never actually a problem
513    o pkg/layers:
514      - fix interpolation of layers tracers in the presence of partial cells
515      - add lots of new functionality to compute water mass transformation
516        (enabled by CPP flag LAYERS_THERMODYNAMICS)
517      - add new calls from main code (diags_oceanic_surf_flux.F,
518        thermodynamics.F, impldiff.F) and gad to save the necessary fields
519        for layers_thermodynamics calculations
520    o pkg/ptracers:
521      - add capability of stepping a passive tracer forward without advection
522        by setting PTRACERS_advScheme to 0.
523    o pkg/diagnostics:
524      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
525    o pkg/layers:
526      - shift potential density field "prho" by -1000 for density layer averaging so
527        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
528        Note that density bin boundaries (layers_bounds in data.layers) have
529        to be set accordingly (i.e., shifted, in sigma scale).
530    o pkg/layers:
531      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
532      - fix calculation of layer non-weighted velocity and layer probability
533      - add diagnostics for pot.density used for layer averaging
534    o pkg/seaice:
535      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
536        positiveness, modify a few comments and improve variable names,
537      - the changed computation of deltaC affects most seaice-related
538        experiments at the truncation level.
539        seaice_itd.thermo is affected by far the most, with
540        only 7 digits of agreement remaining; update experiments.
541    
542    checkpoint65l (2015/05/04)
543    o pkg/shelfice:
544      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
545        factor drKp1 to zero where it is negative (ie. do not use
546        SHELFICEBoundaryLayer if hFacC>1)
547      - the same for factor drLoc in shelfice_forcing.F
548    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
549        with modules in ptracers, when using testreport option "-small_f"
550    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
551      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
552    o verification/testreport
553      - add new option -small_f
554        with this option testreport first makes the target small_f (*.f files)
555        before running make (all). This is useful for explicit inlining when
556        all sources need to be full available.
557    o pkg/exf/exf_interp.F:
558        remove previous changes related to reverse (decreasing) input grids latitude
559    
560    checkpoint65k (2015/04/01)
561    o pkg/ecco:
562        fix missing cosphi initialization; use eccoiter in place of optimcycle;
563        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
564        instead of active read/write
565    o pkg/ctrl:
566        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
567        instead of active read/write.
568    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
569        return if .NOT.useAUTODIFF
570    o pkg/seaice: add CPP brackets (cost function related).
571    o model/src:
572        add useAUTODIFF run time switch.
573    o pkg/exf/exf_interp.F:
574        add code to allow input grids with latitude starting in the north (i.e. when
575        j=1 corresponds to northern edge of field); modify global_with_exf to test
576        this feature.
577    o verification/testreport:
578      - replace "grep -A3" with POSIX conformal sed command, because there are
579        implementations of grep that cannot do contextual searches
580      - replace "cat -n" by "nl" (two occurrences), because not all implementations
581        of "cat" have the option "-n"
582    o model/src:
583        add new file gsw_teos10.F that contains 3 functions, more or less a copy
584        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
585        convert from conservative to potential temperature. For now they are not
586        called anywhere.
587    o pkg/ggl90: make "useIDEMIX" useful
588      - re-organize code in s/r ggl90_calc a little to move computations that
589        are different for idemix into separate loops (changes verification
590        experiment idemix at truncation level, 12 digits remain -> updated)
591      - requires 2 new 2D fields KappaM, verticalShear
592      - make hFacI and recip_hFacI local 3D variables that are passed to
593        s/r ggl90_idemix
594      - fix and improve some comments
595    
596    checkpoint65j (2015/02/25)
597    o pkg/openad
598      - synchronize seawater.F with version in model/src: replace routine
599        body of sw_temp by calling sw_ptmp and fix/add a few comments.
600    o pkg/mnc:
601      - change default value of pickup_read/write_mnc params to FALSE
602        (since few features are missing in reading MNC pickup files).
603    o model/src:
604      - change default (background) vertical diffusivity for salt to be the
605        temperature (background) vertical diffusivity.
606      - change background vertical diffusivity in vertical mixing pkgs ggl90,
607        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
608        This makes ptracers default diffusivity (that uses salt diffKr) more
609        consistent with vertical mixing schemes.
610    o verification/testreport:
611      - fix typo in "-pcls" option ;
612      - put temp files in /tmp (instead of in local dir)
613      - add option "-ncad" to use genmake2 new option "-nocat4ad"
614      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
615    o pkg/ggl90 (idemix code):
616      - apply few fixes ; add some missing "_d 0" ; update output of exp.
617        global_ocean.90x40x15.idemix
618    o OpenAD
619      - enable active file I/O and begin removal of work-around code
620        for OpenAD for handling control variables (memory vs. active files)
621      - new CPP options file OPENAD_OPTIONS.h
622      - revert to genarr2d gradient check for hs94.1x64x5
623      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
624      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
625    o tools/genmake2:
626      - add option for an alternative Makefile (from Martin) where multiple
627        source files are sent to TAF (instead of all in one file).
628    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
629      - code provided by Carsten Eden as an extension of ggl90
630      - so far the code is turned on within ggl90 by setting a CPP-flag at
631        compile time; a runtime flag implementation is not yet complete
632      - tested in new verification experiment global_ocean.90x40x15.idemix
633    o verification:
634      - reduce length of the AD test run by half for experiments
635        global_ocean.cs32x15 (std + thsice) and isomip
636      - enable active file I/O for OpenAD, adjust verifications accordingly
637      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
638    o verification/testreport:
639      - fix two non-POSIX sed statements so that there are no error messages
640        on Mac OS X
641      - replace hostname -s with hostname | sed 's/\..*$//'
642    o model/src/seawater.F:
643      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
644        (following the matlab code), which would have avoided the bug caught
645        by Matt (see below) in the first place
646    o pkg/shelfice:
647      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
648        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
649      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
650        ice-shelf case (i.e., within surface level).
651      - add config summary in shelfice_check.F
652      - remove global variable recip_SHELFICElatentHeat and replace by a local
653        variable recip_latentHeat
654      - introduce diagnostics for friction velocity uStar (in case of
655        SHELFICEuseGammaFrict)
656      - change verification experiment isomip.htd:
657        + start from pickup (as input_ad at nIter0=8640)
658        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
659        + test SHELFICEuseGammaFrict = .TRUE.
660        + test SHELFICEadvDiffHeatFlux = .TRUE.
661    o model/src:
662      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
663        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
664        update output of experiments global_with_exf.yearly and isomip (all 6).
665    o pkg/shelfice:
666      - change setting of kTopC to also be zero where there is no ice-shelf.
667      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
668        ice-shelf is.
669      - first attempt to get RealFreshWaterFlux effects: for now, only without
670        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
671    o pkg/seaice: add the option to prescribe a fixed thickness PDF
672      for thermodynamic calculations
673      - because of divisions of the type 7/7 not exactly equal to 1, this change
674        affects results of some verification experiments by up to 4 digits:
675        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
676        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
677        adjoint: lab_sea, lab_sea.noseaicedyn
678        -> updated
679    
680    checkpoint65i (2015/01/23)
681    o model/src:
682      - change units of frictionHeating field from W to W/m^2
683      - fix bug in frictional heating from stratospheric drag in
684        S/R ATM_PHYS_TENDENCY_APPLY_V
685      - with synchronous time-stepping: move resetting to zero of frictionHeating
686        field from load_fields_driver.F to thermodynamics.F ;
687      - add diagnostics for frictional heating.
688    o model/src & gmredi K3D:
689      - add frictionHeating field to pickup-files (for synchronous time-stepping)
690      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
691      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
692        and name in pickup file).
693      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
694    o model/src:
695      - move (from ini_forcing.F) initialisation of all arrays in header file
696        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
697        (since Nov 2012) with option selectAddFluid=1.
698    o pkg/shelfice:
699      - change units (+ document) of newly added field "shelfIceMassDynTendency"
700      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
701    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
702    o pkg/seaice: two new runtime parameters:
703      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
704        long overdue
705      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
706        parameterization of tensil stress for fast ice (does not do anything yet)
707    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
708        for LSR: move checking overlaps out of JFNK-if-block
709    o pkg/atm_phys:
710      - move copy of grid and dynamical fields out of atm_phys_driver.F into
711        new S/R ATM_PHYS_DYN2PHYS.
712      - fix level height for Linear Free-Surf case (to be consistent with
713        fixed-in-time pressure levels).
714    o pkg/mom_common (bottomdrag):
715      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
716        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
717        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
718    o pkg/shelfice (u/v_drag):
719      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
720      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
721        (now similar to shelfice_u_drag.F)
722      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
723        from mom_vecinv.F (similar to mom_fluxform calls).
724    o pkg/mom_common (bottomdrag):
725      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
726      - add options for alternative discretisation of velocity norm in quadratic
727        bottom drag: averaging of grid-cell-center KE to U.point and V.point
728        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
729        improves when averaging only the other component (e.g. vVel for U bottom
730        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
731      - add options (bottomVisc_pCell) to account for partial-cell in bottom
732        friction (no-slip BC) thus getting the true distance from the bottom;
733        off by default since this also reduces model stability (explicit bottom
734        friction). Changes produce different machine truncation with linear-drag
735        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
736        front_relax (bvp & mxl, 10 & 11 digits).
737    o model/src & mom pkgs:
738      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
739        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
740      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
741        just copy level Nr value to level Nr+1.
742    o doc:
743      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
744    o pkg/streamice:
745      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
746        SHELFICE.h: move array shelficemass to init_varia, initialise
747        from array shelficemassinit, which is set in init_fixed and
748        has option to be set from file; introduce array
749        shelficeMassDynTend array, set thru file in init_fixed
750      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
751        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
752        pkg/streamice
753      - shelfice_thermodynamics.F: call shelfice_step_icemass if
754        SHELFICEMassStepping = .true.
755      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
756    
757    checkpoint65h (2014/12/17)
758    o verification/global_ocean.90x40x15, global_ocean_ebm:
759      - update to generic controls.
760    o pkg/ctrl:
761      - ctrl_map_ini_genarr.F: test for igen>0
762      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
763      - move gentim2d part of ctrl_map_ini_genarr.F to
764        new separate routine : ctrl_map_ini_gentim2d.F
765      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
766        add time variable weights and cyclic controls (time mean,
767        seasonal cycle, etc) capabilities to gentim2d
768    o pkg/ecco:
769      - move reading of error, conversion to weights from
770        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
771    o global_oce_llc90, cs32:
772      - activte sbo.
773      - CTRL_SIZE.h : add maxCtrlProc.
774      - activate the new genctrl capabilities.
775      - update following reorganization of global_oce_input_fields.tar.gz  
776    o pkg/ctrl/ctrl_ad_diff.list:
777      - add missing ctrl_init_rec.f
778    o tools/OAD_support/keepOriginal:
779      - add ctrl_init_rec.F
780    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
781      - avoid recomputations of xx_gentim2d_dummy.
782    o momentum diagnostics:
783      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
784        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
785    o pkg/seaice/seaice_lsr.F:
786      - fix computation of BU/BV, make sure they are non-zero, only necessary
787        for cubed sphere exchanges and SEAICE_OLx/y>0.
788        This makes calling s/r fill_cs_corner_rl obsolete (removed).
789    o verification/global_ocean.cs32x15/input.seaice
790      - add test for strong implicit coupling and restricted addtive Schwarz
791        methods for LSR
792      - update results/output.seaice.txt
793    o verification/tutorial_global_oce_biogeo:
794      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
795        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
796        update output_adm,_oadm,_tlm.txt
797    o pkg/dic:
798      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
799      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
800        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
801    o verification/tutorial_global_oce_biogeo:
802      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
803        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
804        update output_adm,_oadm,_tlm.txt
805    o eesupp/src:
806      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
807        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
808    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
809      LSR (following Hutchings et al. 2004)
810      - introduce zetaZ as a global variable (requires adjustments in
811        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
812        in seaice_calc_viscosities.F
813      - new flag SEAICEuseStrImpCpl (default off)
814      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
815        momentum equations
816      - JFNK-solver (preconditioner) adjusted to allow using this method
817        (where it does not have any positive effect)
818    o pkg/seaice
819      - add overlap for restrictive additive Schwartz method also to LSR, but
820        turn it off by default (because it only seems to work for non-cubed
821        sphere/llc topologies)
822    o pkg/autodiff
823      - add extra exchanges in addummy_in_steppging also for mnc output
824    o pkg/seaice:
825      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
826        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
827    o pkg/obcs:
828      - add option to specify domain-connected piece Id along OB though files
829        (for now, only used to diagnose PhiVel; default =1 -> global correction)
830      - modify obcs_diag_balance.F to process each connected-part separately;
831        exclude OB where Id = 0 but keep the full divergence there (-> constant
832        Psi along this portion of OB and all inflow derived from grad(Phi))
833      - add example of OB-conect files in verification/so_box_biogeo/input.
834    o pkg/diagnostics:
835      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
836      a) use non zero matrix element across OB and solve for Phi 1 grid point
837         outside OB (i.e, where tracer OBCS are applied).
838      b) global imbalance of inFlow/outFlow across OB: instead of modifying
839         velocity across OB, spread it uniformly along the OB in the RHS.
840    
841    checkpoint65g (2014/11/19)
842    o pkg/diagnostcis:
843      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
844    o pkg/my82,pp81,kl10:
845      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
846        field diffKr as background diffusivity to set minimum diffusivity value.
847    o pkg/seaice:
848      - add new parameter SEAICEuseEVPrev (for revisited EVP by
849        Bouillon et al 2013)
850      - add SEAICE_evpAlpha/Beta to namelist
851      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
852        involve trivial re-ordering of divisions/multiplications that should not
853        have any effects, but ... they do change the results of lab_sea.hb87 so
854        that only 2 digits of agreement remain, in line with the general
855        instability/fragility of the evp-code. For now, I do not care and just
856        update the verification experiment
857    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
858      - remove xx_genarr2d_numsmooth etc
859      - use xx_genarr2d_preproc etc instead
860      - carry out smooth_correl2D at initialization stage rather than during
861        time stepping.
862      - get smoothOpNb from xx_gentim2d_preproc
863    o global_oce_cs32 :
864      - add test of generic ecco capabilities.
865    o pkg/exf/exf_getsurfacefluxes.F :
866      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
867    o pkg/ctrl,ecco :
868      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
869        is defined.
870    o pkg/seaice: add diagnostics for Delta (deformation parameter)
871    o model/src:
872      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
873        diffusivity (background) is specified but ignored.
874    o verification:
875      - in testreport, convert hostname to lower case for default output dir name
876    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
877    o pkg/dic: add modifications from Hajoon:
878      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
879      - light attenuation: add self-shading effect by climatological Chlorophyll
880        (read from file).
881    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
882        compiles when SEAICE_ALLOW_DYNAMICS is undefined
883    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
884        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
885        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
886        approach where CPP_OPTIONS.h includes an omnipotent
887        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
888    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
889        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
890    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
891        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
892        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
893    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
894      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
895      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
896      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
897      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
898    o pkg/ctrl,ecco,exf :
899      - remove variables associated with NON-generic costs,
900        unless ECCO_CTRL_DEPRECATED is defined.
901      - remove NON-generic NON-obcs controls,
902        unless ECCO_CTRL_DEPRECATED is defined.
903    o pkg/ctrl : added ctrl_local_params.h
904    o pkg/ecco : added ecco_local_params.h
905    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
906        experiments, which will progressively be removed once the
907        experiments are revised to use only generic controls/costs.
908    
909    checkpoint65f (2014/10/13)
910    o pkg/ctrl, ecco, seaice : minor changes in headers
911    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
912        cost function and control capabilities added since checkpoint65c.
913    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
914  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
915    - ecco_toolbox.F (new) : basic operations that are often used    - ecco_toolbox.F (new) : basic operations that are often used,
916       (for now, ecco_toolbox.F simply contains function ecco_zero).      including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
917        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
918    - cost_gencal.F (new) : determine filnames and records.    - cost_gencal.F (new) : determine filnames and records.
919    - cost_gendif.F (new) : compute masked model-data difference.    - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
   - cost_genread.F : use ecco_zero to initialize field to 0s.  
920    - cost_generic.F : use spzeroloc rather than hard-coded -9999,    - cost_generic.F : use spzeroloc rather than hard-coded -9999,
921      and exploit the above functions leading to more compact code.      and exploit the above functions leading to more compact code.
922      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
923    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
924      using_ers, using_gfo, using_mdt is now only defined within gencost)      using_ers, using_gfo, using_mdt is now only defined within gencost)
925  o pkg/ecco: extend generic cost capabilities  o pkg/ecco: extend generic cost capabilities
926    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
927      capabilities via gencost_preproc (+ _c,_i,_r related params),      capabilities via gencost_preproc (+ _c,_i,_r related params),
928      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
929      gencost_outputlevel arguments to cost_generic      gencost_outputlevel arguments to cost_generic
930    - pkg/ecco/cost_genread.F (new) : interface between cost_generic    - pkg/ecco/cost_genread.F (new) : interface between cost_generic
# Line 34  o pkg/ecco: extend generic cost capabili Line 942  o pkg/ecco: extend generic cost capabili
942    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
943  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
944  o pkg/ecco: internal re-organization  o pkg/ecco: internal re-organization
945    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
946      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
947      mv relevant variables definition from ecco_cost.h to ecco.h,      mv relevant variables definition from ecco_cost.h to ecco.h,
948      make sure gencost routines only include ecco.h)      make sure gencost routines only include ecco.h)
949    - throughout : add missing CCP switches, rm unused variables,    - throughout : add missing CCP switches, rm unused variables,
950      and rm un-necessary CPP switches      and rm un-necessary CPP switches
951    - throughout gencost routines : replace modelstartdate with    - throughout gencost routines : replace modelstartdate with
952      gencost_startdate when needed      gencost_startdate when needed
953    - cost_bp_read.F : use arguments, instead of common blocs    - cost_bp_read.F : use arguments, instead of common blocs
954      so that it can be used also by (new) cost_gencost_bpv4.F      so that it can be used also by (new) cost_gencost_bpv4.F
955    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
956    - ecco_phys.F : compute etanFull    - ecco_phys.F : compute etanFull
957    - ecco_readparms.F : rename using_topex as using_tpj, add    - ecco_readparms.F : rename using_topex as using_tpj, add
# Line 361  o pkg/seaice: more clean up Line 1269  o pkg/seaice: more clean up
1269      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
1270      this experiment):      this experiment):
1271      > size mitgcmuv_ad      > size mitgcmuv_ad
1272      text    data        bss     dec        hex        text    data        bss     dec        hex
1273      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1274      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1275      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1276      text    data        bss     dec        hex      text    data        bss     dec        hex
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