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revision 1.2078 by gforget, Mon Oct 6 14:12:28 2014 UTC revision 1.2260 by jmc, Tue Jul 26 16:25:01 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 pkg/debug (stats):
8      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
9        proc/thread mapping);
10      - fix Min & Max for case where 1 thread has only empty tiles;
11      - use RL variable to count number of wet grid points (with big domain,
12        can be too large to fit into integer*4).
13    o pkg/monitor:
14      - use RL variable to count number of wet grid points (but used only for del2)
15      - add new routine to compute Advective CFL within tracer time-stepping with
16        writing delayed until next monitor output.
17    o pkg/obcs:
18      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
19    o pkg/dic & seaice:
20      - fix compilation of ocean component for coupled atm+ocn model with
21        seaice dynamics & dic.
22    
23    checkpoint65x (2016/06/11)
24    o add a license text file in main MITgcm tree.
25    o added pkg/bling:
26      - intermediate complexity biogeochemical model
27      - see bling_description.txt for details
28      - verification experiment is global_oce_biogeo_bling (for now, in
29        Contrib/verification_other/); tested daily on baudelaire with gfortran.
30      - add entry point in pkg/gchem for new pkg "bling".
31    o pkg/seaice: fix tensile stength computation
32      - replace global field tensileStrength by tensileStrFac
33      - tensileStrFac can be computed once in S/R seaice_init_varia
34      - fortunately that does not affect any verification results
35    
36    checkpoint65w (2016/05/12)
37    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
38         with ECCO_CTRL_DEPRECATED defined
39    o verification/global_ocean.cs32x15:
40      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
41        with "selectNHfreeSurf=1".
42    o model/src (non-hydrostatic free-surface):
43      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
44        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
45      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
46        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
47        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
48        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
49      - Update output (changes at machine truncation level) of verification exp:
50        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
51        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
52    o pkg/seaice: ITD code
53      - fix picking up from a single category model by initialising
54        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
55      - split a long warning message in seaice_check_pickup.F into two lines,
56        because NEC SX-ACE cannot deal with the long line.
57    o model/src:
58      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
59    o pkg/seaice:
60      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
61    o pkg/seaice:
62      - add basal stress as parameterisation for grounding ice
63        following Lemieux et al. (2015)
64      - turn on by setting new parameter SEAICEbasalDragK2 to a value
65        larger than 0. Lemieux et al. (2015) recommend 15.
66      - The adjoint complains with extra recomputations so there is also a
67        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
68        order to postpone the problem
69      - compile the new code in lab_sea
70    o verification/halfpipe_streamice:
71      - update both TAF and OpenAD adm output (machine truncation differences)
72    
73    checkpoint65v (2016/04/08)
74    o verification/advect_xz:
75      - increase overlap size from 3 to 4 and add new secondary test for PQM
76        advection scheme (with mono & wino limiter).
77      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
78    o model/src:
79      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
80        added phi0Ref) to set vertical axis origin and phiRef origin;
81        keep Ro_SeaLevel for backward compatibility (with a warning).
82       According to coordinate and fluid type:
83        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
84        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
85        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
86        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
87      - remove Ro_SeaLevel from ATM experiment parameter files;
88      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
89        complement; update output.txt (changes at machine truncation level).
90    o pkg/seaice/seaice_evp.F
91      - simplify computation of deltaZ and zetaZ to simple averaging following
92        Bouillon et al. (2013). This removes a lot of code, but also changes
93        verification experiment lab_sea.hb87 -> updated
94    
95    checkpoint65u (2016/03/14)
96    o pkg/generic_advdiff:
97      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
98        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
99        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
100        testing and not for actual use.
101    o model/src:
102      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
103        origin r = rF(1);
104      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
105        in EOS for height coordinate: enable to include NH Pressure or to use
106        more accurate pressure vertical profile; options not linked to EOS type
107        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
108      - start to implement variable gravity (along vertical): for now, only with
109        z-coords (not even z*).
110      - add Ideal Gas equation of state for height coordinate.
111      - update OpenAD output (affected at machine truncation level) of exp:
112        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
113    o pkg/exf:
114      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
115        of exf interpolation (before any rescaling, rotation or interpolation
116        to velocity point) for each field that gets loaded from file. This option
117        identically mimics the input file organization (e.g. record numbers in year
118        by year input files) besides the change in horizontal grid.
119      - add rotateStressOnAgrid run-time switch so that wind stress fields
120        can be provided on the A-grid in zonal/meridional direction and
121        rotated on the fly. This only applies to the case when the exf
122        interpolation is off and rotateStressOnAgrid is false by default.
123    o model/src:
124      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
125        it's also used with pkg/atm_phys) and add few more parameters (but still
126        inactive, src code yet to come)
127    
128    checkpoint65t (2016/02/10)
129    o pkg/atm_phys:
130      - from Ruth Geen: add optical depth dependence on CO2 concentration.
131    o model/src:
132      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
133        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
134        Update output of exp. deep_anelastic (changes at truncation level).
135    o tools:
136      - add a hack in "remove_comments_sed" (used only with TAF) for recent
137        version of OpenMPI (shipped with FC.23): comment out the new header
138        file "mpif-sizeof.h" which causes problems to TAF.
139    o pkg/seaice:
140      - change the termination criterion so that maxits (SEAICElinearIterMax)
141        has an effect
142      - unify iteration parameters for implicit solvers (JFNK and Picard)
143        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
144        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
145        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
146        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
147        SEAICEnonLinTol     replaces JFNKgamma_nonlin
148      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
149      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
150        use with SEAICEuseKrylov
151    o pkg/seaice/seaice_lsr.F
152        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
153        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
154        an effect.
155    o pkg/seaice: add two new parameters
156      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
157        parameter is not in any namelist)
158      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
159        a preconditioner for the non-linear Newton iteration of the JFNK
160        solver
161    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
162      affects some experiments at truncation level:
163      - global_ocean.cs32x15.icedyn (11 digits),
164      - global_ocean.cs32x15.seaice (11 digits),
165      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
166      - also update global_ocean.cs32x15 adjoint and tangent-linear results
167    o pkg/salt_plume & pkg/thsice:
168      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
169        connect salt_plume flux to ATM-OCN coupling pkgs interface:
170       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
171         export to coupler interface) even without compiling pkg/salt_plume ;
172       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
173         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
174    o pkg/dic:
175      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
176        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
177        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
178      - move also update with values from ATM-OCN Coupler in the same new S/R
179        (previously done in ocn_apply_import.F).
180    o tools/adjoint_options:
181      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
182        has been changed on Jan 14, 2016.
183    o pkg/ggl90:
184      - add alternative discretisation of vertical shear (off by default), to
185        compute the mean (@ grid-cell center) of vertical shear compon instead of
186        vertical shear of mean flow (@ grid-cell center).
187      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
188        results on adjacent faces of cubed-sphere grids; this fix the restart.
189    o pkg/atm_compon_interf:
190      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
191        pass last value, stored directly before export to CPL ;
192        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
193      - remove atmSLPr from pickup files (no longer needed for restart)
194    
195    checkpoint65s (2016/01/13)
196    o eesupp & genmake2:
197       - first check for Function ETIME and, if it fails, then check for subroutine
198         ETIME and consistent output; use the appropriate version in timers.F
199    o model/src:
200      - to check restart test, add option to apply EXCH to U,V earlier, just before
201        integr_continuity; turned off by default.
202    o pkg/dic:
203      - remove CPP option USE_ATMOSCO2 (not needed)
204    o tools/tst_2+2:
205      - try to ignore difference between +0 and -0 in binary file, causing test
206        to fail for no good reason.
207    o eesupp & genmake2:
208      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
209        but also check (in genmake2) that test runs and returns meaningful results.
210    o coupler pkgs:
211      Finish implementation of optionally-exchanged variable switches (started on
212       Nov 12) with addition of few more exchanged fields, including 2-way exchange
213       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
214       advection in OCN component; this requires sequential coupling.
215      coupler (pkg/atm_ocn_coupler):
216      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
217        routines (useful for debug).
218      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
219         flux, DIC fields) if corresponding switch is ON.
220      - add option to export RunOff to OCN (to use for DIC river input)
221      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
222      components (pkg/atm_ & ocn_compon_interf):
223      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
224        optionally exchanged fields; add a check & stop in cpl_readparms.F.
225        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
226        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
227      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
228        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
229      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
230      - hold in common block coupler optionally-exchanged variable switch
231        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
232      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
233        this is intended to replace the OCN cplFldtave.* output files (not updated
234        to contain new additional exchanged fields).
235    o pkg/dic:
236      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
237    o pkg/thsice:
238      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
239        and writing of thsice pickup files.
240    o pkg/atm_compon_interf:
241      - move all field individual export-call out of cpl_export_import_data.F
242        into new S/R ATM_EXPORT_FIELDS
243    o pkg/atm_compon_interf:
244      - store state variables (for now, only thSIce fields) just before beeing
245        exported (in cpl_export_import_data.F, like on ocean side) instead of from
246        atm_store_my_data.F like all exported fluxes.
247      - new version of pickup_cpl: write field names into meta file and read meta
248        file to find field postion in pickup. Also only write/read fields meeded for
249        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
250    o pkg/dic:
251      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
252    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
253        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
254        value can be from domain [0,1] to average between the two methods
255    o pkg/atm_phys:
256      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
257        hold fixed in time).
258    
259    checkpoint65r (2015/12/21)
260    o pkg/seaice:
261        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
262        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
263    o pkg/seaice:
264      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
265        when SEAICEscaleSurfStress=.TRUE.,
266      - apply areaW and areaS in S/R seaice_calc_lhs
267    o pkg/atm_phys:
268      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
269        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
270        for individual contribution (convection, LSC cond, radiation)
271      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
272        information); activated with: solar_exponent=0. and wv_exponent=-1.
273    o pkg/ggl90:
274      - within IDEMIX add upper limit for horizontal group velocity to
275        avoid instability problems in the explicit horizontal diffusion term for
276        long time steps or high resolution
277    o pkg/diagnostics:
278      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
279        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
280    o testreport:
281      - remove "-v" (verbose option) in default mpirun command.
282    o pkg/seaice/seaice_growth:
283      - catch potential division by zero in ITD code, does not change
284        verification results
285    o pkg/ecco:
286      - retire old codes to the Attic. The calls to retired functions are
287        left in a commented form in case they ever need to be re-activated.
288      - ecco_check.F: issue warning if any old CPP option is
289        defined that corresponds to retired codes -- then stop.
290    o pkg/atm_compon_interf:
291      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
292        coupler: use last time-step value instead of average over cplSendFrq_iter
293        time-step, similar to what is done for seaIceMass.
294        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
295    o eesupp & genmake2:
296      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
297        <= remove until a fix is found for some ifort version on ia32 machine.
298    o pkg/seaice/seaice_evp:
299      - refine residual computation
300    
301    checkpoint65q (2015/11/18)
302    o pkg/seaice/seaice_evp:
303      - fix residual computations so that they no longer affect the actual
304        simulation code
305      - fix seaice_readparams to be able to actually set new parameters
306        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
307    o model/src:
308      - fix wrong truncation (single prec) from "FLOAT" function in expressions
309        like: deltaT*FLOAT(myIter) when myIter is large:
310         a) replaced by DFLOAT (if not seen by TAF);
311         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
312    o pkg/aim_v23:
313      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
314        when pickupSuff is set ; do write rolling pickups + at the end of the run.
315    o pkg/atm_ocn_coupler + ocn_compon_interf:
316      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
317        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
318        add corresponding call in DO_OCEANIC_PHYS.
319    o coupler pkgs:
320      Start a new way to set-up optionally-exchanged variables (previously, only
321       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
322       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
323       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
324       compononent param default can be set accordingly).
325      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
326       but rather applies to a group a fields (going both ways like for DIC)
327       and corresponds to an option of coupling config.
328      coupler (pkg/atm_ocn_coupler):
329      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
330        and read namelist directly (without eessup S/R calls) instead of
331        in the very un-flexible old way, 1 param per line, in fixed order;
332      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
333        cleanly in CPL_CHECK_CPLCONFIG
334      - add new coupling-exchange selectors (some not yet active) including
335        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
336                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
337      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
338        component ; called directly from coupler.F, after comp. registrations;
339      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
340         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
341          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
342      components (pkg/atm_ & ocn_compon_interf):
343      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
344        CPP header file in all pkg source files.
345      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
346        ATM/OCN_CHECK_CPLCONFIG;
347      - add error-counter to track errors (e.g., in "data.cpl") and to stop
348        cleanly in ATM/OCN_CHECK_CPLCONFIG;
349      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
350        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
351        before PACKAGES_READPARMS;
352      verification/cpl_aim+ocn/:
353      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
354        "data.cpl" for coupler (in input_cpl).
355    o eesupp/inc:
356      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
357        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
358        to always cumulate tile local-sum in the same order (still uses
359        MPI_Allreduce like standard code).
360      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
361        that are now identical to standard version (in eesupp/inc).
362    o pkg/shelfice:
363      - add SHELFICETransCoeffTFile for initializing spatially varying
364        heat and salt transfer coefficients
365    o pkg/atm_compon_interf & ocn_compon_interf:
366      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
367        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
368      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
369    o pkg/atm_ocn_coupler:
370      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
371    o pkg/rbcs:
372      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
373        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
374      - add a short report (to STDOUT) about RBCS-mask settings.
375    
376    checkpoint65p (2015/10/23)
377    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
378        there is no adjoint test for EVP, we don't know what it does to the adjoint
379        solution, but at least there are no more recomputation warnings left
380    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
381        a chance of giving the same results as a fully converged VP (JFNK) solver
382    o tools/adjoint_options/adjoint_diva:
383      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
384    o pkg/streamice:
385      - spotted bug in streamice_driving_stress using dyG where should have been dxG
386    o pkg/exf:
387      - remove STOP statement that prevented to use wind or (wind-)stress
388        interpolation for constant-in-time forcing fields (wind/stress period = 0).
389    o pkg/seaice:
390      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
391        5 additionals 2D fields and 6 new store directives
392      - change logic in seaice_readparms.F: EVP code can now be turned on in
393        various ways, setting SEAICE_deltaTev is no longer required,
394        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
395        or SEAICEaEVPcoeff
396    o pkg/shelfice/shelfice_thermodynamics.F
397      - redefining uLoc/vLoc to u/v, instead of 2u/v
398    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
399      - this is an intermediate state of a truely converging EVP that has
400        the potential of outperforming implicit VP methods, I do not recommend
401        using it yet.
402      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
403        and all parameters are hardwired
404      - for convergence it still requires very smooth regularisations, that means,
405        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
406        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
407        specific averaging appears to be required, still subject to tuning
408      - still needs cleaning and I need to turn parameter into runtime parameters
409      - add code to compute and print residuals of iteration, compile with
410        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
411    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
412      that entered with r1.54 on Sep04, 2015, -> update results
413    
414    checkpoint65o (2015/09/14)
415    o pkg/mom_vecinv & mom_common:
416      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
417        called from there.
418      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
419        allows to use Vector-Invariant form in deep atmos and anelastic formulation
420    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
421      and Koenig-Beatty+Holland (2012)
422      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
423      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
424      - requires an extra input argument for S/R seaice_calc_viscosities
425      - tensileStrength's depth dependence is different from Itkin et al. (2015)
426        (to be changed and played with, for now exponential)
427    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
428      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
429        by AREA according to Connelly et al. (2004), JPO.
430      - For EVP and the LSR solver, the implicit part of the drag term is
431        the only non-zero term in the denominator when there is no ice (which
432        prevented running the model with zero ice-ocean drag). If
433        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
434        (or zero main diagonals BU/BV) which need to be caught. A practical
435        consequence is that for open water, the momentum equation reduce
436        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
437        they happen to be zero, often leading to a non-zero solution over
438        open water.
439    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
440        efficient EVP method.
441      - introduce area-weighted averages for e12 (analogously to
442        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
443        remain, but also changing the order of terms in the previous average
444        changed the results as much) -> update experiment
445      - add SEAICE_DELTA_SMOOTHREG code
446      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
447        TEM-code
448      - adjust loop bounds so that only required fields are computed
449      - add new averaging code for zetaZ/deltaZ (again similar to
450        seaice_calc_viscosities.F), inactive by default for now (will change
451        results again), but will replace old code eventually
452    o eesupp/src:
453      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
454        to always cumulate tile local-sum in the same order
455        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
456        Still uses MPI_Allreduce (like standard code) but on array of tiles
457        and should be faster than GLOBAL_SUM_SEND_RECV code.
458      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
459        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
460      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
461         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
462         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
463         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
464         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
465    
466    checkpoint65n (2015/07/29)
467    o pkg/thsice:
468      - add a warning when used with pkg/aim but without updating SST
469        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
470    o pkg/offline:
471      - change where Offline-Fields are loaded, from load_fields_driver.F to
472        directly within FORWARD_STEP, just after updating iter number and time;
473      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
474        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
475       These changes allow:
476        a) to recover exactly on-line results using deltaToffline=deltaTClock,
477        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
478        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
479        time-step, both with GM & KPP files and with recomputing these fields;
480        b) no needs to switch on staggerTimeStep anymore;
481        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
482      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
483    o pkg/offline:
484      - change (rarely used) offset-iteration parameter to an offset time (in s):
485        can easily recover previous offset-iter effect by setting offset-time
486        (offlineTimeOffset) to offset-iter x deltaToffline;
487      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
488        in KPP as part of surface buoyancy forcing) in offline run.
489      - fix ptracers KPP non-local term in the case where KPP is re-computed.
490    o OpenAD
491      - Adding preliminary ggl90 test to OpenAD verification.
492        Config. with ggl90 currently diverges after 64 time steps
493        so will need more work to become more stable
494      - Adding preliminary kpp test to OpenAD verification.
495        required small tweakes in kpp_routines.F
496      - Merge and update from Krishna Narayanan's contrib area:
497        * Add one variable for preliminary OpenAD DIVA
498        * Add replacement time-stepping for OpenAD DIVA
499        * genmake2 flag -diva (but only for OpenAD; preliminary)
500        * required modifs for OAD_support
501        successful preliminary test for tutorial_global_oce_biogeo/
502    o pkg/seaice:
503      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
504      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
505        delta with a smooth function in s/r seaice_calc_viscosity
506        (no effect on EVP)
507      - rename local suffix "sqr" into "sq" for more consistent variable names
508    o pkg/seaice:
509        add new parameter SEAICE_deltaMin that is used ***only***
510        for regularizing Delta (and nothing else, like the parameter
511        which is also used for all sorts of things SEAICE_EPS).
512        Defaults to SEAICE_EPS for backward compatibility only.
513    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
514        the wrong key by inialising it before use -> fixes a recomputation
515        problem but does not fix the gradient
516    o pkg/layers:
517      - move resetting of flux arrays to outside the iLa loop
518        (this caused layers_diapycnal to not work with more than one layer coord.)
519      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
520    o pkg/layers:
521      - remove from common block 3D layers fields (used to diagnose transport
522        in tracer coords) and declare them as local arrays in layers_calc.F
523    o pkg/seaice:
524      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
525        in lab_sea forward experiment (changes results -> updated)
526      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
527    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
528       computations; for SEAICE_VECTORIZE_LSR
529      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
530        sweep to the outside,
531      - remove store directives and add "CADJ loop sequential" directives
532        in analogy to model/src/solve_tridiagonal.F
533      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
534        boundaries to yield more readable code. This has also the charming side
535        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
536        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
537        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
538        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
539        an additional option)
540       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
541       but the adjoint gradients (which are affected by this change) still explode.
542    o coupler (atm & ocn _compon_interf):
543      - avoid using Exch2 IO mapping if not suitable.
544    
545    checkpoint65m (2015/06/15)
546    o pkg/layers:
547      - clean-up old parameters setting (from Sep 2012):
548        + remove old parameters setting from common block (declared locally);
549        + stop if any old parameter is mixed with new parameters;
550        + check for valid or consistent parameter setting (e.g., layers_name)
551      - check that layers_bounds for Pot.Density are in the right range;
552        this is supposed to catch un-updated setting after recently shifting
553        potential density field "prho" by -1000 (now in "sigma" scale).
554    o pkg/layers:
555      - Added missing call to layers_fill for keeping track of tottend in
556        pkg/diagnostics/diagnostics_fill_state.F
557    o pkg/layers:
558      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
559        of diapycnal fluxes
560    o pkg/layers:
561      - reverted changes to interpolation to previous treatment; there
562        was never actually a problem
563    o pkg/layers:
564      - fix interpolation of layers tracers in the presence of partial cells
565      - add lots of new functionality to compute water mass transformation
566        (enabled by CPP flag LAYERS_THERMODYNAMICS)
567      - add new calls from main code (diags_oceanic_surf_flux.F,
568        thermodynamics.F, impldiff.F) and gad to save the necessary fields
569        for layers_thermodynamics calculations
570    o pkg/ptracers:
571      - add capability of stepping a passive tracer forward without advection
572        by setting PTRACERS_advScheme to 0.
573    o pkg/diagnostics:
574      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
575    o pkg/layers:
576      - shift potential density field "prho" by -1000 for density layer averaging so
577        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
578        Note that density bin boundaries (layers_bounds in data.layers) have
579        to be set accordingly (i.e., shifted, in sigma scale).
580    o pkg/layers:
581      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
582      - fix calculation of layer non-weighted velocity and layer probability
583      - add diagnostics for pot.density used for layer averaging
584    o pkg/seaice:
585      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
586        positiveness, modify a few comments and improve variable names,
587      - the changed computation of deltaC affects most seaice-related
588        experiments at the truncation level.
589        seaice_itd.thermo is affected by far the most, with
590        only 7 digits of agreement remaining; update experiments.
591    
592    checkpoint65l (2015/05/04)
593    o pkg/shelfice:
594      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
595        factor drKp1 to zero where it is negative (ie. do not use
596        SHELFICEBoundaryLayer if hFacC>1)
597      - the same for factor drLoc in shelfice_forcing.F
598    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
599        with modules in ptracers, when using testreport option "-small_f"
600    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
601      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
602    o verification/testreport
603      - add new option -small_f
604        with this option testreport first makes the target small_f (*.f files)
605        before running make (all). This is useful for explicit inlining when
606        all sources need to be full available.
607    o pkg/exf/exf_interp.F:
608        remove previous changes related to reverse (decreasing) input grids latitude
609    
610    checkpoint65k (2015/04/01)
611    o pkg/ecco:
612        fix missing cosphi initialization; use eccoiter in place of optimcycle;
613        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
614        instead of active read/write
615    o pkg/ctrl:
616        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
617        instead of active read/write.
618    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
619        return if .NOT.useAUTODIFF
620    o pkg/seaice: add CPP brackets (cost function related).
621    o model/src:
622        add useAUTODIFF run time switch.
623    o pkg/exf/exf_interp.F:
624        add code to allow input grids with latitude starting in the north (i.e. when
625        j=1 corresponds to northern edge of field); modify global_with_exf to test
626        this feature.
627    o verification/testreport:
628      - replace "grep -A3" with POSIX conformal sed command, because there are
629        implementations of grep that cannot do contextual searches
630      - replace "cat -n" by "nl" (two occurrences), because not all implementations
631        of "cat" have the option "-n"
632    o model/src:
633        add new file gsw_teos10.F that contains 3 functions, more or less a copy
634        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
635        convert from conservative to potential temperature. For now they are not
636        called anywhere.
637    o pkg/ggl90: make "useIDEMIX" useful
638      - re-organize code in s/r ggl90_calc a little to move computations that
639        are different for idemix into separate loops (changes verification
640        experiment idemix at truncation level, 12 digits remain -> updated)
641      - requires 2 new 2D fields KappaM, verticalShear
642      - make hFacI and recip_hFacI local 3D variables that are passed to
643        s/r ggl90_idemix
644      - fix and improve some comments
645    
646    checkpoint65j (2015/02/25)
647    o pkg/openad
648      - synchronize seawater.F with version in model/src: replace routine
649        body of sw_temp by calling sw_ptmp and fix/add a few comments.
650    o pkg/mnc:
651      - change default value of pickup_read/write_mnc params to FALSE
652        (since few features are missing in reading MNC pickup files).
653    o model/src:
654      - change default (background) vertical diffusivity for salt to be the
655        temperature (background) vertical diffusivity.
656      - change background vertical diffusivity in vertical mixing pkgs ggl90,
657        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
658        This makes ptracers default diffusivity (that uses salt diffKr) more
659        consistent with vertical mixing schemes.
660    o verification/testreport:
661      - fix typo in "-pcls" option ;
662      - put temp files in /tmp (instead of in local dir)
663      - add option "-ncad" to use genmake2 new option "-nocat4ad"
664      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
665    o pkg/ggl90 (idemix code):
666      - apply few fixes ; add some missing "_d 0" ; update output of exp.
667        global_ocean.90x40x15.idemix
668    o OpenAD
669      - enable active file I/O and begin removal of work-around code
670        for OpenAD for handling control variables (memory vs. active files)
671      - new CPP options file OPENAD_OPTIONS.h
672      - revert to genarr2d gradient check for hs94.1x64x5
673      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
674      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
675    o tools/genmake2:
676      - add option for an alternative Makefile (from Martin) where multiple
677        source files are sent to TAF (instead of all in one file).
678    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
679      - code provided by Carsten Eden as an extension of ggl90
680      - so far the code is turned on within ggl90 by setting a CPP-flag at
681        compile time; a runtime flag implementation is not yet complete
682      - tested in new verification experiment global_ocean.90x40x15.idemix
683    o verification:
684      - reduce length of the AD test run by half for experiments
685        global_ocean.cs32x15 (std + thsice) and isomip
686      - enable active file I/O for OpenAD, adjust verifications accordingly
687      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
688    o verification/testreport:
689      - fix two non-POSIX sed statements so that there are no error messages
690        on Mac OS X
691      - replace hostname -s with hostname | sed 's/\..*$//'
692    o model/src/seawater.F:
693      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
694        (following the matlab code), which would have avoided the bug caught
695        by Matt (see below) in the first place
696    o pkg/shelfice:
697      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
698        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
699      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
700        ice-shelf case (i.e., within surface level).
701      - add config summary in shelfice_check.F
702      - remove global variable recip_SHELFICElatentHeat and replace by a local
703        variable recip_latentHeat
704      - introduce diagnostics for friction velocity uStar (in case of
705        SHELFICEuseGammaFrict)
706      - change verification experiment isomip.htd:
707        + start from pickup (as input_ad at nIter0=8640)
708        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
709        + test SHELFICEuseGammaFrict = .TRUE.
710        + test SHELFICEadvDiffHeatFlux = .TRUE.
711    o model/src:
712      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
713        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
714        update output of experiments global_with_exf.yearly and isomip (all 6).
715    o pkg/shelfice:
716      - change setting of kTopC to also be zero where there is no ice-shelf.
717      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
718        ice-shelf is.
719      - first attempt to get RealFreshWaterFlux effects: for now, only without
720        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
721    o pkg/seaice: add the option to prescribe a fixed thickness PDF
722      for thermodynamic calculations
723      - because of divisions of the type 7/7 not exactly equal to 1, this change
724        affects results of some verification experiments by up to 4 digits:
725        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
726        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
727        adjoint: lab_sea, lab_sea.noseaicedyn
728        -> updated
729    
730    checkpoint65i (2015/01/23)
731    o model/src:
732      - change units of frictionHeating field from W to W/m^2
733      - fix bug in frictional heating from stratospheric drag in
734        S/R ATM_PHYS_TENDENCY_APPLY_V
735      - with synchronous time-stepping: move resetting to zero of frictionHeating
736        field from load_fields_driver.F to thermodynamics.F ;
737      - add diagnostics for frictional heating.
738    o model/src & gmredi K3D:
739      - add frictionHeating field to pickup-files (for synchronous time-stepping)
740      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
741      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
742        and name in pickup file).
743      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
744    o model/src:
745      - move (from ini_forcing.F) initialisation of all arrays in header file
746        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
747        (since Nov 2012) with option selectAddFluid=1.
748    o pkg/shelfice:
749      - change units (+ document) of newly added field "shelfIceMassDynTendency"
750      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
751    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
752    o pkg/seaice: two new runtime parameters:
753      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
754        long overdue
755      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
756        parameterization of tensil stress for fast ice (does not do anything yet)
757    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
758        for LSR: move checking overlaps out of JFNK-if-block
759    o pkg/atm_phys:
760      - move copy of grid and dynamical fields out of atm_phys_driver.F into
761        new S/R ATM_PHYS_DYN2PHYS.
762      - fix level height for Linear Free-Surf case (to be consistent with
763        fixed-in-time pressure levels).
764    o pkg/mom_common (bottomdrag):
765      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
766        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
767        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
768    o pkg/shelfice (u/v_drag):
769      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
770      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
771        (now similar to shelfice_u_drag.F)
772      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
773        from mom_vecinv.F (similar to mom_fluxform calls).
774    o pkg/mom_common (bottomdrag):
775      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
776      - add options for alternative discretisation of velocity norm in quadratic
777        bottom drag: averaging of grid-cell-center KE to U.point and V.point
778        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
779        improves when averaging only the other component (e.g. vVel for U bottom
780        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
781      - add options (bottomVisc_pCell) to account for partial-cell in bottom
782        friction (no-slip BC) thus getting the true distance from the bottom;
783        off by default since this also reduces model stability (explicit bottom
784        friction). Changes produce different machine truncation with linear-drag
785        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
786        front_relax (bvp & mxl, 10 & 11 digits).
787    o model/src & mom pkgs:
788      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
789        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
790      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
791        just copy level Nr value to level Nr+1.
792    o doc:
793      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
794    o pkg/shelfice:
795      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
796        SHELFICE.h: move array shelficemass to init_varia, initialise
797        from array shelficemassinit, which is set in init_fixed and
798        has option to be set from file; introduce array
799        shelficeMassDynTend array, set thru file in init_fixed
800      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
801        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
802        pkg/streamice
803      - shelfice_thermodynamics.F: call shelfice_step_icemass if
804        SHELFICEMassStepping = .true.
805      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
806    
807    checkpoint65h (2014/12/17)
808    o verification/global_ocean.90x40x15, global_ocean_ebm:
809      - update to generic controls.
810    o pkg/ctrl:
811      - ctrl_map_ini_genarr.F: test for igen>0
812      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
813      - move gentim2d part of ctrl_map_ini_genarr.F to
814        new separate routine : ctrl_map_ini_gentim2d.F
815      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
816        add time variable weights and cyclic controls (time mean,
817        seasonal cycle, etc) capabilities to gentim2d
818    o pkg/ecco:
819      - move reading of error, conversion to weights from
820        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
821    o global_oce_llc90, cs32:
822      - activte sbo.
823      - CTRL_SIZE.h : add maxCtrlProc.
824      - activate the new genctrl capabilities.
825      - update following reorganization of global_oce_input_fields.tar.gz  
826    o pkg/ctrl/ctrl_ad_diff.list:
827      - add missing ctrl_init_rec.f
828    o tools/OAD_support/keepOriginal:
829      - add ctrl_init_rec.F
830    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
831      - avoid recomputations of xx_gentim2d_dummy.
832    o momentum diagnostics:
833      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
834        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
835    o pkg/seaice/seaice_lsr.F:
836      - fix computation of BU/BV, make sure they are non-zero, only necessary
837        for cubed sphere exchanges and SEAICE_OLx/y>0.
838        This makes calling s/r fill_cs_corner_rl obsolete (removed).
839    o verification/global_ocean.cs32x15/input.seaice
840      - add test for strong implicit coupling and restricted addtive Schwarz
841        methods for LSR
842      - update results/output.seaice.txt
843    o verification/tutorial_global_oce_biogeo:
844      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
845        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
846        update output_adm,_oadm,_tlm.txt
847    o pkg/dic:
848      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
849      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
850        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
851    o verification/tutorial_global_oce_biogeo:
852      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
853        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
854        update output_adm,_oadm,_tlm.txt
855    o eesupp/src:
856      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
857        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
858    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
859      LSR (following Hutchings et al. 2004)
860      - introduce zetaZ as a global variable (requires adjustments in
861        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
862        in seaice_calc_viscosities.F
863      - new flag SEAICEuseStrImpCpl (default off)
864      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
865        momentum equations
866      - JFNK-solver (preconditioner) adjusted to allow using this method
867        (where it does not have any positive effect)
868    o pkg/seaice
869      - add overlap for restrictive additive Schwartz method also to LSR, but
870        turn it off by default (because it only seems to work for non-cubed
871        sphere/llc topologies)
872    o pkg/autodiff
873      - add extra exchanges in addummy_in_steppging also for mnc output
874    o pkg/seaice:
875      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
876        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
877    o pkg/obcs:
878      - add option to specify domain-connected piece Id along OB though files
879        (for now, only used to diagnose PhiVel; default =1 -> global correction)
880      - modify obcs_diag_balance.F to process each connected-part separately;
881        exclude OB where Id = 0 but keep the full divergence there (-> constant
882        Psi along this portion of OB and all inflow derived from grad(Phi))
883      - add example of OB-conect files in verification/so_box_biogeo/input.
884    o pkg/diagnostics:
885      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
886      a) use non zero matrix element across OB and solve for Phi 1 grid point
887         outside OB (i.e, where tracer OBCS are applied).
888      b) global imbalance of inFlow/outFlow across OB: instead of modifying
889         velocity across OB, spread it uniformly along the OB in the RHS.
890    
891    checkpoint65g (2014/11/19)
892    o pkg/diagnostcis:
893      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
894    o pkg/my82,pp81,kl10:
895      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
896        field diffKr as background diffusivity to set minimum diffusivity value.
897    o pkg/seaice:
898      - add new parameter SEAICEuseEVPrev (for revisited EVP by
899        Bouillon et al 2013)
900      - add SEAICE_evpAlpha/Beta to namelist
901      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
902        involve trivial re-ordering of divisions/multiplications that should not
903        have any effects, but ... they do change the results of lab_sea.hb87 so
904        that only 2 digits of agreement remain, in line with the general
905        instability/fragility of the evp-code. For now, I do not care and just
906        update the verification experiment
907    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
908      - remove xx_genarr2d_numsmooth etc
909      - use xx_genarr2d_preproc etc instead
910      - carry out smooth_correl2D at initialization stage rather than during
911        time stepping.
912      - get smoothOpNb from xx_gentim2d_preproc
913    o global_oce_cs32 :
914      - add test of generic ecco capabilities.
915    o pkg/exf/exf_getsurfacefluxes.F :
916      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
917    o pkg/ctrl,ecco :
918      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
919        is defined.
920    o pkg/seaice: add diagnostics for Delta (deformation parameter)
921    o model/src:
922      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
923        diffusivity (background) is specified but ignored.
924    o verification:
925      - in testreport, convert hostname to lower case for default output dir name
926    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
927    o pkg/dic: add modifications from Hajoon:
928      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
929      - light attenuation: add self-shading effect by climatological Chlorophyll
930        (read from file).
931    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
932        compiles when SEAICE_ALLOW_DYNAMICS is undefined
933    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
934        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
935        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
936        approach where CPP_OPTIONS.h includes an omnipotent
937        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
938    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
939        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
940    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
941        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
942        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
943    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
944      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
945      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
946      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
947      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
948    o pkg/ctrl,ecco,exf :
949      - remove variables associated with NON-generic costs,
950        unless ECCO_CTRL_DEPRECATED is defined.
951      - remove NON-generic NON-obcs controls,
952        unless ECCO_CTRL_DEPRECATED is defined.
953    o pkg/ctrl : added ctrl_local_params.h
954    o pkg/ecco : added ecco_local_params.h
955    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
956        experiments, which will progressively be removed once the
957        experiments are revised to use only generic controls/costs.
958    
959    checkpoint65f (2014/10/13)
960    o pkg/ctrl, ecco, seaice : minor changes in headers
961    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
962        cost function and control capabilities added since checkpoint65c.
963    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
964  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
965    - ecco_toolbox.F (new) : basic operations that are often used    - ecco_toolbox.F (new) : basic operations that are often used,
966       (for now, ecco_toolbox.F simply contains function ecco_zero).      including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
967        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
968    - cost_gencal.F (new) : determine filnames and records.    - cost_gencal.F (new) : determine filnames and records.
969    - 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.  
970    - cost_generic.F : use spzeroloc rather than hard-coded -9999,    - cost_generic.F : use spzeroloc rather than hard-coded -9999,
971      and exploit the above functions leading to more compact code.      and exploit the above functions leading to more compact code.
972      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
973    - 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,
974      using_ers, using_gfo, using_mdt is now only defined within gencost)      using_ers, using_gfo, using_mdt is now only defined within gencost)
975  o pkg/ecco: extend generic cost capabilities  o pkg/ecco: extend generic cost capabilities
976    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
977      capabilities via gencost_preproc (+ _c,_i,_r related params),      capabilities via gencost_preproc (+ _c,_i,_r related params),
978      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
979      gencost_outputlevel arguments to cost_generic      gencost_outputlevel arguments to cost_generic
980    - 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 992  o pkg/ecco: extend generic cost capabili
992    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
993  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
994  o pkg/ecco: internal re-organization  o pkg/ecco: internal re-organization
995    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
996      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
997      mv relevant variables definition from ecco_cost.h to ecco.h,      mv relevant variables definition from ecco_cost.h to ecco.h,
998      make sure gencost routines only include ecco.h)      make sure gencost routines only include ecco.h)
999    - throughout : add missing CCP switches, rm unused variables,    - throughout : add missing CCP switches, rm unused variables,
1000      and rm un-necessary CPP switches      and rm un-necessary CPP switches
1001    - throughout gencost routines : replace modelstartdate with    - throughout gencost routines : replace modelstartdate with
1002      gencost_startdate when needed      gencost_startdate when needed
1003    - cost_bp_read.F : use arguments, instead of common blocs    - cost_bp_read.F : use arguments, instead of common blocs
1004      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
1005    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
1006    - ecco_phys.F : compute etanFull    - ecco_phys.F : compute etanFull
1007    - 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 1319  o pkg/seaice: more clean up
1319      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
1320      this experiment):      this experiment):
1321      > size mitgcmuv_ad      > size mitgcmuv_ad
1322      text    data        bss     dec        hex        text    data        bss     dec        hex
1323      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1324      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1325      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1326      text    data        bss     dec        hex      text    data        bss     dec        hex
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