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revision 1.66 by jmc, Tue Mar 5 15:36:06 2002 UTC revision 1.2275 by jmc, Fri Oct 7 04:14:35 2016 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  checkpoint44g_post  o model/src & generic_advdiff:
8      - add parenthesis in main diagonal calculation of implicit vertical
9        diffusion matrix (impldiff.F & gad_implicit_r.F).
10        This affects results at machine truncation level; update output of many
11        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
12    o pkg/mom_commom & generic_advdiff:
13      - add deep atmosphere and anelastic scaling factor in implicit vertical
14        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
15    o model/src:
16      - remove few unnecessary temp array copies in solve_tridiagonal.F
17        & solve_pentadiagonal.F
18    
19    checkpoint65z (2016/09/28)
20    o pkg/seaice: fix multithreading for seaice_fgmres.F
21      - remove unecessary variables from common blocks
22      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
23        basis, that are stored in commom blocks (including integer variable i1)
24      - clean up code a little by removing commented lines that refer to
25        original code
26      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
27    o MITgcm manual:
28      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
29        preliminary documentation for generic controls (8.3; ctrl.tex),
30        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
31        ecco_costfunction.tex
32    o pkg/ecco:
33      - update and cleanup list of CCP options
34      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
35        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
36      - add checks that retired run-time options are not used, and in relation
37        to gencost_mask and gencost_errfile
38      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
39        gencost_nrecperiod
40      - fix m_eta computation for virtual salt flux case
41      - add m_horflux_vol case (selected via gencost_barfile) that computes
42        transports via cost_gencost_boxmean (gencost_flag=-3)
43      - use gencost_flag more systematically (i.e., avoid using gencost_name)
44        for code switches (aside from physical variable selection)
45    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
46      attempt appears to be a bit of a hack and my need some repair down the road
47    o pkg/exf:
48      - interpolation near South Pole: fix criteria on input field latitude.
49    o pkg/icefront & pkg/exf:
50      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
51        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
52    o pkg/exf:
53      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
54        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
55        (add suffix "_out" instead of a prefix); keep same record number as in
56        input file but always write record 1 first (to avoid a STOP in I/O S/R).
57        Change output file content by writing interpolated field before applying
58        land-sea mask (helpful for debug).
59      - 2 compon. vector interpolation with rotation: apply scaling factor on
60        each compon. (Eastward and Northward) just before rotation.
61    o pkg/bling:
62      - Cleaned package. Removed not needed code and comments.
63      - adjoint example now works
64        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
65    o pkg/ptracers:
66      - add Bruno Deremble's code to complete the linear surface correction
67        for tracer conservation;
68      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
69    
70    checkpoint65y (2016/07/29)
71    o pkg/debug (stats):
72      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
73        proc/thread mapping);
74      - fix Min & Max for case where 1 thread has only empty tiles;
75      - use RL variable to count number of wet grid points (with big domain,
76        can be too large to fit into integer*4).
77    o pkg/monitor:
78      - use RL variable to count number of wet grid points (but used only for del2)
79      - add new routine to compute Advective CFL within tracer time-stepping with
80        writing delayed until next monitor output.
81    o pkg/obcs:
82      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
83    o pkg/cal:
84      - calandar-dump: treat case myTime < timePhase in the same way as in
85        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
86    o pkg/dic & seaice:
87      - fix compilation of ocean component for coupled atm+ocn model with
88        seaice dynamics & dic.
89    
90    checkpoint65x (2016/06/11)
91    o add a license text file in main MITgcm tree.
92    o added pkg/bling:
93      - intermediate complexity biogeochemical model
94      - see bling_description.txt for details
95      - verification experiment is global_oce_biogeo_bling (for now, in
96        Contrib/verification_other/); tested daily on baudelaire with gfortran.
97      - add entry point in pkg/gchem for new pkg "bling".
98    o pkg/seaice: fix tensile stength computation
99      - replace global field tensileStrength by tensileStrFac
100      - tensileStrFac can be computed once in S/R seaice_init_varia
101      - fortunately that does not affect any verification results
102    
103    checkpoint65w (2016/05/12)
104    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
105         with ECCO_CTRL_DEPRECATED defined
106    o verification/global_ocean.cs32x15:
107      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
108        with "selectNHfreeSurf=1".
109    o model/src (non-hydrostatic free-surface):
110      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
111        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
112      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
113        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
114        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
115        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
116      - Update output (changes at machine truncation level) of verification exp:
117        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
118        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
119    o pkg/seaice: ITD code
120      - fix picking up from a single category model by initialising
121        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
122      - split a long warning message in seaice_check_pickup.F into two lines,
123        because NEC SX-ACE cannot deal with the long line.
124    o model/src:
125      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
126    o pkg/seaice:
127      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
128    o pkg/seaice:
129      - add basal stress as parameterisation for grounding ice
130        following Lemieux et al. (2015)
131      - turn on by setting new parameter SEAICEbasalDragK2 to a value
132        larger than 0. Lemieux et al. (2015) recommend 15.
133      - The adjoint complains with extra recomputations so there is also a
134        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
135        order to postpone the problem
136      - compile the new code in lab_sea
137    o verification/halfpipe_streamice:
138      - update both TAF and OpenAD adm output (machine truncation differences)
139    
140    checkpoint65v (2016/04/08)
141    o verification/advect_xz:
142      - increase overlap size from 3 to 4 and add new secondary test for PQM
143        advection scheme (with mono & wino limiter).
144      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
145    o model/src:
146      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
147        added phi0Ref) to set vertical axis origin and phiRef origin;
148        keep Ro_SeaLevel for backward compatibility (with a warning).
149       According to coordinate and fluid type:
150        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
151        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
152        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
153        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
154      - remove Ro_SeaLevel from ATM experiment parameter files;
155      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
156        complement; update output.txt (changes at machine truncation level).
157    o pkg/seaice/seaice_evp.F
158      - simplify computation of deltaZ and zetaZ to simple averaging following
159        Bouillon et al. (2013). This removes a lot of code, but also changes
160        verification experiment lab_sea.hb87 -> updated
161    
162    checkpoint65u (2016/03/14)
163    o pkg/generic_advdiff:
164      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
165        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
166        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
167        testing and not for actual use.
168    o model/src:
169      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
170        origin r = rF(1);
171      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
172        in EOS for height coordinate: enable to include NH Pressure or to use
173        more accurate pressure vertical profile; options not linked to EOS type
174        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
175      - start to implement variable gravity (along vertical): for now, only with
176        z-coords (not even z*).
177      - add Ideal Gas equation of state for height coordinate.
178      - update OpenAD output (affected at machine truncation level) of exp:
179        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
180    o pkg/exf:
181      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
182        of exf interpolation (before any rescaling, rotation or interpolation
183        to velocity point) for each field that gets loaded from file. This option
184        identically mimics the input file organization (e.g. record numbers in year
185        by year input files) besides the change in horizontal grid.
186      - add rotateStressOnAgrid run-time switch so that wind stress fields
187        can be provided on the A-grid in zonal/meridional direction and
188        rotated on the fly. This only applies to the case when the exf
189        interpolation is off and rotateStressOnAgrid is false by default.
190    o model/src:
191      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
192        it's also used with pkg/atm_phys) and add few more parameters (but still
193        inactive, src code yet to come)
194    
195    checkpoint65t (2016/02/10)
196    o pkg/atm_phys:
197      - from Ruth Geen: add optical depth dependence on CO2 concentration.
198    o model/src:
199      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
200        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
201        Update output of exp. deep_anelastic (changes at truncation level).
202    o tools:
203      - add a hack in "remove_comments_sed" (used only with TAF) for recent
204        version of OpenMPI (shipped with FC.23): comment out the new header
205        file "mpif-sizeof.h" which causes problems to TAF.
206    o pkg/seaice:
207      - change the termination criterion so that maxits (SEAICElinearIterMax)
208        has an effect
209      - unify iteration parameters for implicit solvers (JFNK and Picard)
210        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
211        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
212        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
213        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
214        SEAICEnonLinTol     replaces JFNKgamma_nonlin
215      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
216      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
217        use with SEAICEuseKrylov
218    o pkg/seaice/seaice_lsr.F
219        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
220        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
221        an effect.
222    o pkg/seaice: add two new parameters
223      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
224        parameter is not in any namelist)
225      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
226        a preconditioner for the non-linear Newton iteration of the JFNK
227        solver
228    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
229      affects some experiments at truncation level:
230      - global_ocean.cs32x15.icedyn (11 digits),
231      - global_ocean.cs32x15.seaice (11 digits),
232      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
233      - also update global_ocean.cs32x15 adjoint and tangent-linear results
234    o pkg/salt_plume & pkg/thsice:
235      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
236        connect salt_plume flux to ATM-OCN coupling pkgs interface:
237       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
238         export to coupler interface) even without compiling pkg/salt_plume ;
239       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
240         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
241    o pkg/dic:
242      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
243        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
244        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
245      - move also update with values from ATM-OCN Coupler in the same new S/R
246        (previously done in ocn_apply_import.F).
247    o tools/adjoint_options:
248      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
249        has been changed on Jan 14, 2016.
250    o pkg/ggl90:
251      - add alternative discretisation of vertical shear (off by default), to
252        compute the mean (@ grid-cell center) of vertical shear compon instead of
253        vertical shear of mean flow (@ grid-cell center).
254      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
255        results on adjacent faces of cubed-sphere grids; this fix the restart.
256    o pkg/atm_compon_interf:
257      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
258        pass last value, stored directly before export to CPL ;
259        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
260      - remove atmSLPr from pickup files (no longer needed for restart)
261    
262    checkpoint65s (2016/01/13)
263    o eesupp & genmake2:
264       - first check for Function ETIME and, if it fails, then check for subroutine
265         ETIME and consistent output; use the appropriate version in timers.F
266    o model/src:
267      - to check restart test, add option to apply EXCH to U,V earlier, just before
268        integr_continuity; turned off by default.
269    o pkg/dic:
270      - remove CPP option USE_ATMOSCO2 (not needed)
271    o tools/tst_2+2:
272      - try to ignore difference between +0 and -0 in binary file, causing test
273        to fail for no good reason.
274    o eesupp & genmake2:
275      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
276        but also check (in genmake2) that test runs and returns meaningful results.
277    o coupler pkgs:
278      Finish implementation of optionally-exchanged variable switches (started on
279       Nov 12) with addition of few more exchanged fields, including 2-way exchange
280       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
281       advection in OCN component; this requires sequential coupling.
282      coupler (pkg/atm_ocn_coupler):
283      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
284        routines (useful for debug).
285      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
286         flux, DIC fields) if corresponding switch is ON.
287      - add option to export RunOff to OCN (to use for DIC river input)
288      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
289      components (pkg/atm_ & ocn_compon_interf):
290      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
291        optionally exchanged fields; add a check & stop in cpl_readparms.F.
292        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
293        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
294      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
295        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
296      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
297      - hold in common block coupler optionally-exchanged variable switch
298        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
299      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
300        this is intended to replace the OCN cplFldtave.* output files (not updated
301        to contain new additional exchanged fields).
302    o pkg/dic:
303      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
304    o pkg/thsice:
305      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
306        and writing of thsice pickup files.
307    o pkg/atm_compon_interf:
308      - move all field individual export-call out of cpl_export_import_data.F
309        into new S/R ATM_EXPORT_FIELDS
310    o pkg/atm_compon_interf:
311      - store state variables (for now, only thSIce fields) just before beeing
312        exported (in cpl_export_import_data.F, like on ocean side) instead of from
313        atm_store_my_data.F like all exported fluxes.
314      - new version of pickup_cpl: write field names into meta file and read meta
315        file to find field postion in pickup. Also only write/read fields meeded for
316        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
317    o pkg/dic:
318      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
319    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
320        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
321        value can be from domain [0,1] to average between the two methods
322    o pkg/atm_phys:
323      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
324        hold fixed in time).
325    
326    checkpoint65r (2015/12/21)
327    o pkg/seaice:
328        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
329        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
330    o pkg/seaice:
331      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
332        when SEAICEscaleSurfStress=.TRUE.,
333      - apply areaW and areaS in S/R seaice_calc_lhs
334    o pkg/atm_phys:
335      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
336        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
337        for individual contribution (convection, LSC cond, radiation)
338      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
339        information); activated with: solar_exponent=0. and wv_exponent=-1.
340    o pkg/ggl90:
341      - within IDEMIX add upper limit for horizontal group velocity to
342        avoid instability problems in the explicit horizontal diffusion term for
343        long time steps or high resolution
344    o pkg/diagnostics:
345      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
346        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
347    o testreport:
348      - remove "-v" (verbose option) in default mpirun command.
349    o pkg/seaice/seaice_growth:
350      - catch potential division by zero in ITD code, does not change
351        verification results
352    o pkg/ecco:
353      - retire old codes to the Attic. The calls to retired functions are
354        left in a commented form in case they ever need to be re-activated.
355      - ecco_check.F: issue warning if any old CPP option is
356        defined that corresponds to retired codes -- then stop.
357    o pkg/atm_compon_interf:
358      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
359        coupler: use last time-step value instead of average over cplSendFrq_iter
360        time-step, similar to what is done for seaIceMass.
361        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
362    o eesupp & genmake2:
363      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
364        <= remove until a fix is found for some ifort version on ia32 machine.
365    o pkg/seaice/seaice_evp:
366      - refine residual computation
367    
368    checkpoint65q (2015/11/18)
369    o pkg/seaice/seaice_evp:
370      - fix residual computations so that they no longer affect the actual
371        simulation code
372      - fix seaice_readparams to be able to actually set new parameters
373        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
374    o model/src:
375      - fix wrong truncation (single prec) from "FLOAT" function in expressions
376        like: deltaT*FLOAT(myIter) when myIter is large:
377         a) replaced by DFLOAT (if not seen by TAF);
378         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
379    o pkg/aim_v23:
380      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
381        when pickupSuff is set ; do write rolling pickups + at the end of the run.
382    o pkg/atm_ocn_coupler + ocn_compon_interf:
383      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
384        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
385        add corresponding call in DO_OCEANIC_PHYS.
386    o coupler pkgs:
387      Start a new way to set-up optionally-exchanged variables (previously, only
388       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
389       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
390       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
391       compononent param default can be set accordingly).
392      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
393       but rather applies to a group a fields (going both ways like for DIC)
394       and corresponds to an option of coupling config.
395      coupler (pkg/atm_ocn_coupler):
396      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
397        and read namelist directly (without eessup S/R calls) instead of
398        in the very un-flexible old way, 1 param per line, in fixed order;
399      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
400        cleanly in CPL_CHECK_CPLCONFIG
401      - add new coupling-exchange selectors (some not yet active) including
402        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
403                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
404      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
405        component ; called directly from coupler.F, after comp. registrations;
406      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
407         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
408          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
409      components (pkg/atm_ & ocn_compon_interf):
410      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
411        CPP header file in all pkg source files.
412      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
413        ATM/OCN_CHECK_CPLCONFIG;
414      - add error-counter to track errors (e.g., in "data.cpl") and to stop
415        cleanly in ATM/OCN_CHECK_CPLCONFIG;
416      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
417        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
418        before PACKAGES_READPARMS;
419      verification/cpl_aim+ocn/:
420      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
421        "data.cpl" for coupler (in input_cpl).
422    o eesupp/inc:
423      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
424        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
425        to always cumulate tile local-sum in the same order (still uses
426        MPI_Allreduce like standard code).
427      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
428        that are now identical to standard version (in eesupp/inc).
429    o pkg/shelfice:
430      - add SHELFICETransCoeffTFile for initializing spatially varying
431        heat and salt transfer coefficients
432    o pkg/atm_compon_interf & ocn_compon_interf:
433      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
434        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
435      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
436    o pkg/atm_ocn_coupler:
437      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
438    o pkg/rbcs:
439      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
440        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
441      - add a short report (to STDOUT) about RBCS-mask settings.
442    
443    checkpoint65p (2015/10/23)
444    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
445        there is no adjoint test for EVP, we don't know what it does to the adjoint
446        solution, but at least there are no more recomputation warnings left
447    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
448        a chance of giving the same results as a fully converged VP (JFNK) solver
449    o tools/adjoint_options/adjoint_diva:
450      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
451    o pkg/streamice:
452      - spotted bug in streamice_driving_stress using dyG where should have been dxG
453    o pkg/exf:
454      - remove STOP statement that prevented to use wind or (wind-)stress
455        interpolation for constant-in-time forcing fields (wind/stress period = 0).
456    o pkg/seaice:
457      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
458        5 additionals 2D fields and 6 new store directives
459      - change logic in seaice_readparms.F: EVP code can now be turned on in
460        various ways, setting SEAICE_deltaTev is no longer required,
461        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
462        or SEAICEaEVPcoeff
463    o pkg/shelfice/shelfice_thermodynamics.F
464      - redefining uLoc/vLoc to u/v, instead of 2u/v
465    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
466      - this is an intermediate state of a truely converging EVP that has
467        the potential of outperforming implicit VP methods, I do not recommend
468        using it yet.
469      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
470        and all parameters are hardwired
471      - for convergence it still requires very smooth regularisations, that means,
472        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
473        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
474        specific averaging appears to be required, still subject to tuning
475      - still needs cleaning and I need to turn parameter into runtime parameters
476      - add code to compute and print residuals of iteration, compile with
477        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
478    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
479      that entered with r1.54 on Sep04, 2015, -> update results
480    
481    checkpoint65o (2015/09/14)
482    o pkg/mom_vecinv & mom_common:
483      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
484        called from there.
485      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
486        allows to use Vector-Invariant form in deep atmos and anelastic formulation
487    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
488      and Koenig-Beatty+Holland (2012)
489      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
490      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
491      - requires an extra input argument for S/R seaice_calc_viscosities
492      - tensileStrength's depth dependence is different from Itkin et al. (2015)
493        (to be changed and played with, for now exponential)
494    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
495      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
496        by AREA according to Connelly et al. (2004), JPO.
497      - For EVP and the LSR solver, the implicit part of the drag term is
498        the only non-zero term in the denominator when there is no ice (which
499        prevented running the model with zero ice-ocean drag). If
500        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
501        (or zero main diagonals BU/BV) which need to be caught. A practical
502        consequence is that for open water, the momentum equation reduce
503        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
504        they happen to be zero, often leading to a non-zero solution over
505        open water.
506    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
507        efficient EVP method.
508      - introduce area-weighted averages for e12 (analogously to
509        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
510        remain, but also changing the order of terms in the previous average
511        changed the results as much) -> update experiment
512      - add SEAICE_DELTA_SMOOTHREG code
513      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
514        TEM-code
515      - adjust loop bounds so that only required fields are computed
516      - add new averaging code for zetaZ/deltaZ (again similar to
517        seaice_calc_viscosities.F), inactive by default for now (will change
518        results again), but will replace old code eventually
519    o eesupp/src:
520      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
521        to always cumulate tile local-sum in the same order
522        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
523        Still uses MPI_Allreduce (like standard code) but on array of tiles
524        and should be faster than GLOBAL_SUM_SEND_RECV code.
525      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
526        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
527      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
528         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
529         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
530         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
531         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
532    
533    checkpoint65n (2015/07/29)
534    o pkg/thsice:
535      - add a warning when used with pkg/aim but without updating SST
536        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
537    o pkg/offline:
538      - change where Offline-Fields are loaded, from load_fields_driver.F to
539        directly within FORWARD_STEP, just after updating iter number and time;
540      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
541        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
542       These changes allow:
543        a) to recover exactly on-line results using deltaToffline=deltaTClock,
544        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
545        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
546        time-step, both with GM & KPP files and with recomputing these fields;
547        b) no needs to switch on staggerTimeStep anymore;
548        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
549      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
550    o pkg/offline:
551      - change (rarely used) offset-iteration parameter to an offset time (in s):
552        can easily recover previous offset-iter effect by setting offset-time
553        (offlineTimeOffset) to offset-iter x deltaToffline;
554      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
555        in KPP as part of surface buoyancy forcing) in offline run.
556      - fix ptracers KPP non-local term in the case where KPP is re-computed.
557    o OpenAD
558      - Adding preliminary ggl90 test to OpenAD verification.
559        Config. with ggl90 currently diverges after 64 time steps
560        so will need more work to become more stable
561      - Adding preliminary kpp test to OpenAD verification.
562        required small tweakes in kpp_routines.F
563      - Merge and update from Krishna Narayanan's contrib area:
564        * Add one variable for preliminary OpenAD DIVA
565        * Add replacement time-stepping for OpenAD DIVA
566        * genmake2 flag -diva (but only for OpenAD; preliminary)
567        * required modifs for OAD_support
568        successful preliminary test for tutorial_global_oce_biogeo/
569    o pkg/seaice:
570      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
571      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
572        delta with a smooth function in s/r seaice_calc_viscosity
573        (no effect on EVP)
574      - rename local suffix "sqr" into "sq" for more consistent variable names
575    o pkg/seaice:
576        add new parameter SEAICE_deltaMin that is used ***only***
577        for regularizing Delta (and nothing else, like the parameter
578        which is also used for all sorts of things SEAICE_EPS).
579        Defaults to SEAICE_EPS for backward compatibility only.
580    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
581        the wrong key by inialising it before use -> fixes a recomputation
582        problem but does not fix the gradient
583    o pkg/layers:
584      - move resetting of flux arrays to outside the iLa loop
585        (this caused layers_diapycnal to not work with more than one layer coord.)
586      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
587    o pkg/layers:
588      - remove from common block 3D layers fields (used to diagnose transport
589        in tracer coords) and declare them as local arrays in layers_calc.F
590    o pkg/seaice:
591      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
592        in lab_sea forward experiment (changes results -> updated)
593      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
594    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
595       computations; for SEAICE_VECTORIZE_LSR
596      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
597        sweep to the outside,
598      - remove store directives and add "CADJ loop sequential" directives
599        in analogy to model/src/solve_tridiagonal.F
600      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
601        boundaries to yield more readable code. This has also the charming side
602        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
603        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
604        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
605        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
606        an additional option)
607       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
608       but the adjoint gradients (which are affected by this change) still explode.
609    o coupler (atm & ocn _compon_interf):
610      - avoid using Exch2 IO mapping if not suitable.
611    
612    checkpoint65m (2015/06/15)
613    o pkg/layers:
614      - clean-up old parameters setting (from Sep 2012):
615        + remove old parameters setting from common block (declared locally);
616        + stop if any old parameter is mixed with new parameters;
617        + check for valid or consistent parameter setting (e.g., layers_name)
618      - check that layers_bounds for Pot.Density are in the right range;
619        this is supposed to catch un-updated setting after recently shifting
620        potential density field "prho" by -1000 (now in "sigma" scale).
621    o pkg/layers:
622      - Added missing call to layers_fill for keeping track of tottend in
623        pkg/diagnostics/diagnostics_fill_state.F
624    o pkg/layers:
625      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
626        of diapycnal fluxes
627    o pkg/layers:
628      - reverted changes to interpolation to previous treatment; there
629        was never actually a problem
630    o pkg/layers:
631      - fix interpolation of layers tracers in the presence of partial cells
632      - add lots of new functionality to compute water mass transformation
633        (enabled by CPP flag LAYERS_THERMODYNAMICS)
634      - add new calls from main code (diags_oceanic_surf_flux.F,
635        thermodynamics.F, impldiff.F) and gad to save the necessary fields
636        for layers_thermodynamics calculations
637    o pkg/ptracers:
638      - add capability of stepping a passive tracer forward without advection
639        by setting PTRACERS_advScheme to 0.
640    o pkg/diagnostics:
641      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
642    o pkg/layers:
643      - shift potential density field "prho" by -1000 for density layer averaging so
644        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
645        Note that density bin boundaries (layers_bounds in data.layers) have
646        to be set accordingly (i.e., shifted, in sigma scale).
647    o pkg/layers:
648      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
649      - fix calculation of layer non-weighted velocity and layer probability
650      - add diagnostics for pot.density used for layer averaging
651    o pkg/seaice:
652      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
653        positiveness, modify a few comments and improve variable names,
654      - the changed computation of deltaC affects most seaice-related
655        experiments at the truncation level.
656        seaice_itd.thermo is affected by far the most, with
657        only 7 digits of agreement remaining; update experiments.
658    
659    checkpoint65l (2015/05/04)
660    o pkg/shelfice:
661      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
662        factor drKp1 to zero where it is negative (ie. do not use
663        SHELFICEBoundaryLayer if hFacC>1)
664      - the same for factor drLoc in shelfice_forcing.F
665    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
666        with modules in ptracers, when using testreport option "-small_f"
667    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
668      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
669    o verification/testreport
670      - add new option -small_f
671        with this option testreport first makes the target small_f (*.f files)
672        before running make (all). This is useful for explicit inlining when
673        all sources need to be full available.
674    o pkg/exf/exf_interp.F:
675        remove previous changes related to reverse (decreasing) input grids latitude
676    
677    checkpoint65k (2015/04/01)
678    o pkg/ecco:
679        fix missing cosphi initialization; use eccoiter in place of optimcycle;
680        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
681        instead of active read/write
682    o pkg/ctrl:
683        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
684        instead of active read/write.
685    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
686        return if .NOT.useAUTODIFF
687    o pkg/seaice: add CPP brackets (cost function related).
688    o model/src:
689        add useAUTODIFF run time switch.
690    o pkg/exf/exf_interp.F:
691        add code to allow input grids with latitude starting in the north (i.e. when
692        j=1 corresponds to northern edge of field); modify global_with_exf to test
693        this feature.
694    o verification/testreport:
695      - replace "grep -A3" with POSIX conformal sed command, because there are
696        implementations of grep that cannot do contextual searches
697      - replace "cat -n" by "nl" (two occurrences), because not all implementations
698        of "cat" have the option "-n"
699    o model/src:
700        add new file gsw_teos10.F that contains 3 functions, more or less a copy
701        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
702        convert from conservative to potential temperature. For now they are not
703        called anywhere.
704    o pkg/ggl90: make "useIDEMIX" useful
705      - re-organize code in s/r ggl90_calc a little to move computations that
706        are different for idemix into separate loops (changes verification
707        experiment idemix at truncation level, 12 digits remain -> updated)
708      - requires 2 new 2D fields KappaM, verticalShear
709      - make hFacI and recip_hFacI local 3D variables that are passed to
710        s/r ggl90_idemix
711      - fix and improve some comments
712    
713    checkpoint65j (2015/02/25)
714    o pkg/openad
715      - synchronize seawater.F with version in model/src: replace routine
716        body of sw_temp by calling sw_ptmp and fix/add a few comments.
717    o pkg/mnc:
718      - change default value of pickup_read/write_mnc params to FALSE
719        (since few features are missing in reading MNC pickup files).
720    o model/src:
721      - change default (background) vertical diffusivity for salt to be the
722        temperature (background) vertical diffusivity.
723      - change background vertical diffusivity in vertical mixing pkgs ggl90,
724        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
725        This makes ptracers default diffusivity (that uses salt diffKr) more
726        consistent with vertical mixing schemes.
727    o verification/testreport:
728      - fix typo in "-pcls" option ;
729      - put temp files in /tmp (instead of in local dir)
730      - add option "-ncad" to use genmake2 new option "-nocat4ad"
731      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
732    o pkg/ggl90 (idemix code):
733      - apply few fixes ; add some missing "_d 0" ; update output of exp.
734        global_ocean.90x40x15.idemix
735    o OpenAD
736      - enable active file I/O and begin removal of work-around code
737        for OpenAD for handling control variables (memory vs. active files)
738      - new CPP options file OPENAD_OPTIONS.h
739      - revert to genarr2d gradient check for hs94.1x64x5
740      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
741      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
742    o tools/genmake2:
743      - add option for an alternative Makefile (from Martin) where multiple
744        source files are sent to TAF (instead of all in one file).
745    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
746      - code provided by Carsten Eden as an extension of ggl90
747      - so far the code is turned on within ggl90 by setting a CPP-flag at
748        compile time; a runtime flag implementation is not yet complete
749      - tested in new verification experiment global_ocean.90x40x15.idemix
750    o verification:
751      - reduce length of the AD test run by half for experiments
752        global_ocean.cs32x15 (std + thsice) and isomip
753      - enable active file I/O for OpenAD, adjust verifications accordingly
754      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
755    o verification/testreport:
756      - fix two non-POSIX sed statements so that there are no error messages
757        on Mac OS X
758      - replace hostname -s with hostname | sed 's/\..*$//'
759    o model/src/seawater.F:
760      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
761        (following the matlab code), which would have avoided the bug caught
762        by Matt (see below) in the first place
763    o pkg/shelfice:
764      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
765        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
766      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
767        ice-shelf case (i.e., within surface level).
768      - add config summary in shelfice_check.F
769      - remove global variable recip_SHELFICElatentHeat and replace by a local
770        variable recip_latentHeat
771      - introduce diagnostics for friction velocity uStar (in case of
772        SHELFICEuseGammaFrict)
773      - change verification experiment isomip.htd:
774        + start from pickup (as input_ad at nIter0=8640)
775        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
776        + test SHELFICEuseGammaFrict = .TRUE.
777        + test SHELFICEadvDiffHeatFlux = .TRUE.
778    o model/src:
779      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
780        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
781        update output of experiments global_with_exf.yearly and isomip (all 6).
782    o pkg/shelfice:
783      - change setting of kTopC to also be zero where there is no ice-shelf.
784      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
785        ice-shelf is.
786      - first attempt to get RealFreshWaterFlux effects: for now, only without
787        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
788    o pkg/seaice: add the option to prescribe a fixed thickness PDF
789      for thermodynamic calculations
790      - because of divisions of the type 7/7 not exactly equal to 1, this change
791        affects results of some verification experiments by up to 4 digits:
792        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
793        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
794        adjoint: lab_sea, lab_sea.noseaicedyn
795        -> updated
796    
797    checkpoint65i (2015/01/23)
798    o model/src:
799      - change units of frictionHeating field from W to W/m^2
800      - fix bug in frictional heating from stratospheric drag in
801        S/R ATM_PHYS_TENDENCY_APPLY_V
802      - with synchronous time-stepping: move resetting to zero of frictionHeating
803        field from load_fields_driver.F to thermodynamics.F ;
804      - add diagnostics for frictional heating.
805    o model/src & gmredi K3D:
806      - add frictionHeating field to pickup-files (for synchronous time-stepping)
807      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
808      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
809        and name in pickup file).
810      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
811    o model/src:
812      - move (from ini_forcing.F) initialisation of all arrays in header file
813        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
814        (since Nov 2012) with option selectAddFluid=1.
815    o pkg/shelfice:
816      - change units (+ document) of newly added field "shelfIceMassDynTendency"
817      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
818    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
819    o pkg/seaice: two new runtime parameters:
820      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
821        long overdue
822      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
823        parameterization of tensil stress for fast ice (does not do anything yet)
824    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
825        for LSR: move checking overlaps out of JFNK-if-block
826    o pkg/atm_phys:
827      - move copy of grid and dynamical fields out of atm_phys_driver.F into
828        new S/R ATM_PHYS_DYN2PHYS.
829      - fix level height for Linear Free-Surf case (to be consistent with
830        fixed-in-time pressure levels).
831    o pkg/mom_common (bottomdrag):
832      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
833        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
834        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
835    o pkg/shelfice (u/v_drag):
836      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
837      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
838        (now similar to shelfice_u_drag.F)
839      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
840        from mom_vecinv.F (similar to mom_fluxform calls).
841    o pkg/mom_common (bottomdrag):
842      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
843      - add options for alternative discretisation of velocity norm in quadratic
844        bottom drag: averaging of grid-cell-center KE to U.point and V.point
845        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
846        improves when averaging only the other component (e.g. vVel for U bottom
847        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
848      - add options (bottomVisc_pCell) to account for partial-cell in bottom
849        friction (no-slip BC) thus getting the true distance from the bottom;
850        off by default since this also reduces model stability (explicit bottom
851        friction). Changes produce different machine truncation with linear-drag
852        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
853        front_relax (bvp & mxl, 10 & 11 digits).
854    o model/src & mom pkgs:
855      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
856        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
857      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
858        just copy level Nr value to level Nr+1.
859    o doc:
860      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
861    o pkg/shelfice:
862      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
863        SHELFICE.h: move array shelficemass to init_varia, initialise
864        from array shelficemassinit, which is set in init_fixed and
865        has option to be set from file; introduce array
866        shelficeMassDynTend array, set thru file in init_fixed
867      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
868        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
869        pkg/streamice
870      - shelfice_thermodynamics.F: call shelfice_step_icemass if
871        SHELFICEMassStepping = .true.
872      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
873    
874    checkpoint65h (2014/12/17)
875    o verification/global_ocean.90x40x15, global_ocean_ebm:
876      - update to generic controls.
877    o pkg/ctrl:
878      - ctrl_map_ini_genarr.F: test for igen>0
879      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
880      - move gentim2d part of ctrl_map_ini_genarr.F to
881        new separate routine : ctrl_map_ini_gentim2d.F
882      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
883        add time variable weights and cyclic controls (time mean,
884        seasonal cycle, etc) capabilities to gentim2d
885    o pkg/ecco:
886      - move reading of error, conversion to weights from
887        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
888    o global_oce_llc90, cs32:
889      - activte sbo.
890      - CTRL_SIZE.h : add maxCtrlProc.
891      - activate the new genctrl capabilities.
892      - update following reorganization of global_oce_input_fields.tar.gz  
893    o pkg/ctrl/ctrl_ad_diff.list:
894      - add missing ctrl_init_rec.f
895    o tools/OAD_support/keepOriginal:
896      - add ctrl_init_rec.F
897    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
898      - avoid recomputations of xx_gentim2d_dummy.
899    o momentum diagnostics:
900      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
901        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
902    o pkg/seaice/seaice_lsr.F:
903      - fix computation of BU/BV, make sure they are non-zero, only necessary
904        for cubed sphere exchanges and SEAICE_OLx/y>0.
905        This makes calling s/r fill_cs_corner_rl obsolete (removed).
906    o verification/global_ocean.cs32x15/input.seaice
907      - add test for strong implicit coupling and restricted addtive Schwarz
908        methods for LSR
909      - update results/output.seaice.txt
910    o verification/tutorial_global_oce_biogeo:
911      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
912        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
913        update output_adm,_oadm,_tlm.txt
914    o pkg/dic:
915      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
916      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
917        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
918    o verification/tutorial_global_oce_biogeo:
919      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
920        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
921        update output_adm,_oadm,_tlm.txt
922    o eesupp/src:
923      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
924        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
925    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
926      LSR (following Hutchings et al. 2004)
927      - introduce zetaZ as a global variable (requires adjustments in
928        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
929        in seaice_calc_viscosities.F
930      - new flag SEAICEuseStrImpCpl (default off)
931      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
932        momentum equations
933      - JFNK-solver (preconditioner) adjusted to allow using this method
934        (where it does not have any positive effect)
935    o pkg/seaice
936      - add overlap for restrictive additive Schwartz method also to LSR, but
937        turn it off by default (because it only seems to work for non-cubed
938        sphere/llc topologies)
939    o pkg/autodiff
940      - add extra exchanges in addummy_in_steppging also for mnc output
941    o pkg/seaice:
942      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
943        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
944    o pkg/obcs:
945      - add option to specify domain-connected piece Id along OB though files
946        (for now, only used to diagnose PhiVel; default =1 -> global correction)
947      - modify obcs_diag_balance.F to process each connected-part separately;
948        exclude OB where Id = 0 but keep the full divergence there (-> constant
949        Psi along this portion of OB and all inflow derived from grad(Phi))
950      - add example of OB-conect files in verification/so_box_biogeo/input.
951    o pkg/diagnostics:
952      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
953      a) use non zero matrix element across OB and solve for Phi 1 grid point
954         outside OB (i.e, where tracer OBCS are applied).
955      b) global imbalance of inFlow/outFlow across OB: instead of modifying
956         velocity across OB, spread it uniformly along the OB in the RHS.
957    
958    checkpoint65g (2014/11/19)
959    o pkg/diagnostcis:
960      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
961    o pkg/my82,pp81,kl10:
962      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
963        field diffKr as background diffusivity to set minimum diffusivity value.
964    o pkg/seaice:
965      - add new parameter SEAICEuseEVPrev (for revisited EVP by
966        Bouillon et al 2013)
967      - add SEAICE_evpAlpha/Beta to namelist
968      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
969        involve trivial re-ordering of divisions/multiplications that should not
970        have any effects, but ... they do change the results of lab_sea.hb87 so
971        that only 2 digits of agreement remain, in line with the general
972        instability/fragility of the evp-code. For now, I do not care and just
973        update the verification experiment
974    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
975      - remove xx_genarr2d_numsmooth etc
976      - use xx_genarr2d_preproc etc instead
977      - carry out smooth_correl2D at initialization stage rather than during
978        time stepping.
979      - get smoothOpNb from xx_gentim2d_preproc
980    o global_oce_cs32 :
981      - add test of generic ecco capabilities.
982    o pkg/exf/exf_getsurfacefluxes.F :
983      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
984    o pkg/ctrl,ecco :
985      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
986        is defined.
987    o pkg/seaice: add diagnostics for Delta (deformation parameter)
988    o model/src:
989      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
990        diffusivity (background) is specified but ignored.
991    o verification:
992      - in testreport, convert hostname to lower case for default output dir name
993    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
994    o pkg/dic: add modifications from Hajoon:
995      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
996      - light attenuation: add self-shading effect by climatological Chlorophyll
997        (read from file).
998    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
999        compiles when SEAICE_ALLOW_DYNAMICS is undefined
1000    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
1001        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
1002        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
1003        approach where CPP_OPTIONS.h includes an omnipotent
1004        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
1005    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
1006        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
1007    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
1008        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
1009        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
1010    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
1011      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
1012      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
1013      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
1014      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
1015    o pkg/ctrl,ecco,exf :
1016      - remove variables associated with NON-generic costs,
1017        unless ECCO_CTRL_DEPRECATED is defined.
1018      - remove NON-generic NON-obcs controls,
1019        unless ECCO_CTRL_DEPRECATED is defined.
1020    o pkg/ctrl : added ctrl_local_params.h
1021    o pkg/ecco : added ecco_local_params.h
1022    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
1023        experiments, which will progressively be removed once the
1024        experiments are revised to use only generic controls/costs.
1025    
1026    checkpoint65f (2014/10/13)
1027    o pkg/ctrl, ecco, seaice : minor changes in headers
1028    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
1029        cost function and control capabilities added since checkpoint65c.
1030    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
1031    o pkg/ecco: increase modularity and improve logic
1032      - ecco_toolbox.F (new) : basic operations that are often used,
1033        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
1034        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
1035      - cost_gencal.F (new) : determine filnames and records.
1036      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
1037      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
1038        and exploit the above functions leading to more compact code.
1039      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
1040      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
1041        using_ers, using_gfo, using_mdt is now only defined within gencost)
1042    o pkg/ecco: extend generic cost capabilities
1043      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
1044        capabilities via gencost_preproc (+ _c,_i,_r related params),
1045        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
1046        gencost_outputlevel arguments to cost_generic
1047      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
1048        and active_read, making room for gencost_preproc to take effect.
1049        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
1050      - pkg/ecco/cost_generic.F :
1051        compute and store misfit maks*(model-data) in localdif that is
1052        then used in cost and for output, output misfit if outlev.GT.0
1053      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
1054        rather gencost_barfile for deciding whether to write barfile
1055      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
1056      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
1057        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
1058      - pkg/ecco/ecco_summary.F : report gencost variables
1059      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
1060    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
1061    o pkg/ecco: internal re-organization
1062      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
1063        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
1064        mv relevant variables definition from ecco_cost.h to ecco.h,
1065        make sure gencost routines only include ecco.h)
1066      - throughout : add missing CCP switches, rm unused variables,
1067        and rm un-necessary CPP switches
1068      - throughout gencost routines : replace modelstartdate with
1069        gencost_startdate when needed
1070      - cost_bp_read.F : use arguments, instead of common blocs
1071        so that it can be used also by (new) cost_gencost_bpv4.F
1072      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
1073      - ecco_phys.F : compute etanFull
1074      - ecco_readparms.F : rename using_topex as using_tpj, add
1075        bpv4-grace to gencost list, initialize added parameters
1076      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
1077    
1078    checkpoint65e (2014/09/28)
1079    o pkg/obcs:
1080      - replaced the just-added CPP options with run-time variables
1081        (see pkg/obcs/OBCS_PARAMS.h for details)
1082    o pkg/obcs:
1083      - add additional CPP options for sponge boundary layers
1084        (see pkg/obcs/OBCS_OPTIONS.h for details)
1085    o pkg/atm_phys:
1086      - implement simple (obliquity only, assuming circular planet orbit)
1087        seasonal cycle for incoming insolation ; used when run-time parameter
1088        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
1089    o pkg/exf, pkg/ecco, pkg/ctrl:
1090      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
1091      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
1092      - implement gentim2d for xx_tauu, xx_tauv
1093    o pkg/ctrl, pkg/ecco :
1094      - fix and complement the generic controls implementation
1095    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
1096        pkg/shelfice/shelfice_thermodynamics.F,
1097        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
1098        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
1099      - add weight in CTRL_GET_GEN calls
1100    o pkg/ctrl :
1101      - ctrl_get_gen.F : add weight as input parameter, and apply
1102        it directly rather than using smooth_correl2Dw (to be retired).
1103      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
1104    o pkg/ctrl :
1105      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
1106        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
1107      - re-activate ctrl_summary (call in ctrl_init.F)
1108    o pkg/ctrl/ctrl_cost_gen.F :
1109      - fix CCP brackets, remove un-necessary myiter, mytime
1110    o pkg/ecco, pkg/ctrl :
1111      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
1112      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
1113      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
1114      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
1115    
1116    checkpoint65d (2014/09/15)
1117    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
1118      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
1119        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
1120    o pkg/ctrl/ctrl_map_ini_genarr.F :
1121      - remove compilation failure
1122      - replace hard coded example
1123      - use ctrl_map_ini_gen2D, 3D
1124    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
1125      - on/off switch based upon xx_genarr2d_weight,3d
1126    o src/packages_init_variables.F :
1127      - regroup pkg/estimation calls
1128      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1129        (moved to ctrl_init_variables)
1130    o cost/cost_init_varia.F :
1131      - remove ecco_cost_init_varia
1132        (moved to ecco_init_varia)
1133    o ctrl/ctrl_init_variables.F :
1134      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1135      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
1136    o ctrl/ctrl_map_ini.F :
1137      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
1138        (moved to ctrl_init_variables)
1139    o ctrl/ctrl_map_ini_ecco.F :
1140      - remove ECCO_PHYS (mv to ecco_init_varia)
1141      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
1142    o ecco/ecco_ad_diff.list :
1143      - add ecco_init_varia.f
1144    o ecco/ecco_init_varia.F
1145      - new routine
1146    o pkg/streamice:
1147      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
1148        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
1149      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
1150    o pkg/generic_advdiff:
1151      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
1152    o pkg/exf:
1153      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
1154         xxg_precip capability
1155      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
1156    o pkg/ctrl:
1157      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
1158    o model/src/load_fields_driver.F :
1159      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
1160        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
1161    o OpenAD verification experiments:
1162      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
1163        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
1164        for now, only in pkgs used in OpenAD verification experiments.
1165      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
1166        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
1167        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
1168        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
1169    o OpenAD verification tests:
1170      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
1171      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
1172        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
1173      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
1174        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
1175    o model/src & generic_advdiff:
1176      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
1177        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
1178        dynamics requires valid tracer forcing only over tile interior but, for
1179        some diagnostics, may need to extend it over 1 point in tile halo region.
1180      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
1181        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
1182        setting in temp/salt/ptracer_integrate.F
1183    o pkg/dic:
1184      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
1185        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
1186        in gchem_forcing_sep.F
1187    o pkg/autodiff & obcs:
1188      - add storage of current OB values for U & V (was already done for T & S).
1189    
1190    checkpoint65c (2014/08/30)
1191    o pkg/dic:
1192      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
1193        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
1194        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
1195    o verification:
1196      - new experiment testing OBCS and DIC pkgs, using params & output from
1197        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
1198        passage: take OBCS from the last year of a 2 yrs simulation and initial
1199        conditions from t=1.yr while keeping the same forcing.
1200    o model/src:
1201      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
1202        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
1203    o pkg/diagnostics (Stats-Diags):
1204      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
1205        a) refine region where stats are computed, excluding where arrhFac=0 ;
1206        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
1207        c) extend regional stats over the region edges (for U or V pt location).
1208    o pkg/gchem:
1209      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
1210        pkg/dic is currently changing/updating ptracers values beyond the OB).
1211    o verification (hs94):
1212      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
1213        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
1214        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
1215        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1216    o pkg/ptracers:
1217      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
1218        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
1219      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
1220        with AB-2 code (so that it get tested).
1221    o model/src:
1222      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
1223        with AB-2 code (previously only available with AB-3 code).
1224        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
1225        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
1226        there, by calling CYCLE_AB_TRACER).
1227    o pkg/generic_advdiff:
1228      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
1229        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
1230        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
1231        S/R temp/salt/ptracers_integrate.F
1232    o model/src & pkg/ptracers:
1233      - remove common block variables gT,gS (in DYNVARS.h), except when
1234         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
1235      - remove common block variable gPtr.
1236    o model/src & pkgs:
1237      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
1238         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
1239         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
1240         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
1241      + change accordingly all calling S/R.
1242      - use local temperature/salinity/ptracer tendency array (without bi,bj)
1243        in S/R temp/salt/ptracers_integrate.F
1244    o pkg/seaice:
1245      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
1246        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
1247      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
1248        in seaice_lsr
1249      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
1250        in s/r seaice_lsr_calc_coeffs
1251    o pkg/mdsio:
1252      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
1253        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
1254        too long (e.g., > MAX_LEN_FNAM/2 )
1255    
1256    checkpoint65b (2014/08/12)
1257    o pkg/matrix:
1258      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1259    o model/src:
1260      - fix initialisation of geothermalFile; compile geothermal-flux code in
1261        natl_box verification experiment.
1262    o model/src & pkg/down_slope:
1263      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1264      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1265        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1266        results at machine truncation level: update output of experiments
1267        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1268    o pkg/diagnostics (Stats-Diags):
1269      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1270        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1271        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1272        times (but Min,Max and StD are still wrong).
1273    o model/src:
1274      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1275        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1276    o model/src:
1277      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1278        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1279        arrays are already updated while adjustments (filters, conv.adjustment) are
1280        still applied later, in S/R TRACERS_CORRECTION_STEP.
1281    o model/src:
1282      - store in common bloc array "rhoInSitu" the virtual potential temperature
1283        anomaly that is used to compute geopotential: this make the atmos code
1284        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1285    o pkg/seaice/seaice_lsr.F
1286      - rename integer variable ilcall to ipass (that's what it is called
1287        in the residual diagnostics
1288      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1289        default) for improved non-linear convergence of the first few steps
1290      - adjust a few comments and add new ones to explain some of the store
1291        directives
1292    o pkg/generic_advdiff (& ptracers):
1293      - re-work the code to check for valid advection scheme and for minimum
1294        size of overlap (now stored in local common bloc in gad_advscheme.F)
1295    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1296      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1297      - add an auxilliary variable "bet" and fix store directives and keys in
1298        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1299        less exact gradients in my tests); but there are still
1300        recomputation warning (although gradients are sort of OK), when
1301        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1302        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1303      - update verification experiments lab_sea.
1304      - change some comments in S/R seaice_calc_viscosities
1305    o model/src:
1306      - if staggerTimeStep=T, always apply exchange to velocity field in
1307        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1308        (independent of using multi-dim advection or not); no effect on FWD run
1309        but affects AD results (at machine truncation level): update output of
1310        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1311        and isomip (oad: 12.d).
1312    o pkg/generic_advdiff:
1313      - stop if doAB_onGtGs is set to FALSE but ignored
1314      - refine warning related to stability of tracer time-stepping
1315        regarding internal wave dynamics.
1316      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1317        on staggerTimeStep & implicitIntGravWave (will now get a warning
1318        if potentially unstable).
1319    o pkg/kl10:
1320      - add new pkg "kl10" for mixing due to internal wave breaking, from
1321        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1322        (contribution from Jody Klymak), tested in verification experiment
1323        verification/internal_wave/input.kl10/
1324    o isomip experiment:
1325      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1326        (input.htd) and update the output.
1327    o cd_code experiments:
1328      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1329        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1330        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1331        update the corresponding output.
1332    o pkg/seaice:
1333      - reduce the number of include files and store directives in
1334        S/R seaice_lsr_tridiagu/v
1335      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1336        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1337        get rid off one store directive (a TAF bug?)
1338      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1339        S/R seaice_lsr_tridiagv to change the loop range for consistency
1340      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1341      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1342        S/R seaice_lsr_tridiagu/v (requires update of
1343        offline_exf_seaice/input.dyn_jfnk)
1344    
1345    checkpoint65a (2014/07/27)
1346    o model/src:
1347      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1348        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1349        (topo in p-coords, ice-shelf in z-coords); update output of experiments
1350        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1351    o model/src:
1352      - collect momentum forcing tendency into local 2-D array (passed as argument
1353        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1354        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1355        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1356      - collect T & S forcing tendency into local 2-D array (passed as argument to
1357        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1358        affects results at machine truncation level (e.g., ocean: if using
1359        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1360        correction due to vertical advection).
1361      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1362        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1363        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1364        obcs_ctrl (ad & fwd grd @ 12 & 7).
1365    o pkg/ptracers & diagnostics:
1366      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1367        title (to avoid some unexpected truncation); sort out ptracers diags units.
1368      - collect ptracer forcing tendency into local 2-D array (passed as argument
1369        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1370    
1371    checkpoint65 (2014/07/18)
1372    o pkg/fizhi:
1373      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1374        affects results at machine truncation level. Update output of experiments
1375        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1376    o pkg/seaice: more clean up
1377      - rename TAF common block tapes to be more consistent and remove
1378        unnecessary duplicates
1379      - add store directives to remove more recomputations, but use smaller
1380        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1381        The idea behind this flag is to reduce the memory footprint when the
1382        adjoint of the LSR is not required. As of now, defining the flag
1383        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1384        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1385        For experiment offline_exf_seaice, this means on a linux box with gfortran
1386        nearly a factor of 10 (but keep in mind there is mostly seaice code in
1387        this experiment):
1388        > size mitgcmuv_ad
1389        text    data        bss     dec        hex
1390        5100659 1216  220458952  225560827  d71c8fb
1391        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1392        but only a moderate increase of 36% for global_ocean.cs32x15:
1393        text    data        bss     dec        hex
1394        6695027 1648 1014578664 1021275339 3cdf6ccb
1395        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1396      - note: there are still recomputations in global_ocean.cs32x15 and
1397        offline_exf_seaice and the gradient agreement changes (gets a
1398        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1399      - in general, the AD gradients still are wrong
1400    o OpenAD
1401      - clean up code_oad/ directories somewhat by moving files
1402        dontCompile, dontTransform, keepOriginal to OAD_support/
1403    o model/src:
1404      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1405        (not currently tested): add dissipation terms before NLFS rescaling of
1406        tendencies (previously done after).
1407    o pkg/diagnostics:
1408      - write stats-diags in ascii file with more digits (same as in monitor).
1409    o pkg/down_slope:
1410      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1411        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1412    o model/src:
1413      - new file "apply_forcing.F" containing all the code previously in
1414        external_forcing.F, but with new argument list: pass, as new argument,
1415        the current level tendency array to update (instead of a direct update
1416        of the common bloc array). Change the corresponding calls.
1417      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1418        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1419    o pkg/seaice/seaice_lsr, a little bit of clean up
1420      - rearrange some code blocks, so that now all calculations for
1421        setting up the right-hand-sides done within one single block
1422        (I find that easier to read and understand)
1423      - rearrange freedrift-code to reduce the number of ifdefs
1424      - adjust some indentations and comments
1425    
1426    checkpoint64z (2014/07/10)
1427    o model/src and several pkgs:
1428      - change argument list of all S/R called from external_forcing.F and
1429        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1430        to pass, as argument, the current level tendency array to update
1431        (instead of a direct update of the common bloc array).
1432      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1433      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1434    o pkg/seaice/seaice_lsr.F
1435      - always initialize local arrays in seaice_lsr_tridiagu/v
1436      - add more local tapes to seaice_lsr_tridiagu/v
1437      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1438        keep it in bi/bj loop; this seems to be essential
1439      - gradients are still wrong but only by 4-7 orders of magnitude
1440        instead of 15 orders of magnitude, lab_sea improves a little
1441    o pkg/seaice
1442      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1443        generates unnecessary code in seaice_lsr_ad
1444      - add more store directives in seaice_lsr to avoid unnecessary code
1445        in seaice_lsr_ad
1446      - exclude some residual computations in seaice_lsr when
1447        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1448        in seaice_lsr_ad
1449      - add more storing, a new tape (model/src/the_main_loop.F) and
1450        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1451        and klockey should be checked by a specialist)
1452      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1453        and update lab_sea after previous changes in pkg/seaice below
1454    o pkg/autodiff:
1455      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1456        viscFacInAd : run time parameters allowing for adjoint switches
1457        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1458    o pkg/ecco:
1459      - introduce cost_gencost_boxmean.F that computes a box mean
1460        temperature (for use in adjoint sensitivity studies).
1461    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1462    o pkg/mom_common/mom_calc_visc.F:
1463      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1464    o pkg/seaice/seaice_summary.F:
1465      - statement for SEAICEadjMODE now in autodiff_readparms.F
1466    o pkg/seaice:
1467      - remove some store directives and add new ones in an effort to get
1468        finally rid off the recomputation warnings. This is successful
1469        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1470        defined (i.e. no extensive recomputation warnings left), but there
1471        are still too many recomputations on the solver iteration level
1472      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1473      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1474        SEAICE_SIZE.h
1475      - add a store directive in S/R seaice_calc_viscosities
1476    o pkg/seaice (ITD code):
1477      - fix definition of Hlimit for multi-threaded case
1478      - use double precision arithmetic to compute Hlimit: this affects results;
1479        update output of experiment seaice_itd.
1480    o replace content of verification/seaice_itd
1481      - instead of a 1D column use the configuration of offline_exf_seaice
1482        to test the ice thickness distribution code with ridging
1483      - this is a first shot at this experiment
1484      - change of some defaults of ridging parameters SEAICEhStar (from
1485        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1486        and lot of new comments.
1487    
1488    checkpoint64y (2014/06/20)
1489    o pkg/seaice/seaice_reg_ridge.F:
1490      - modify the regularization of very small volumes of ice; only check
1491        total volume HEFF, and do not apply correction to individual ice
1492        classes because that leads to funny patterns in the heat and fw-fluxes
1493        into the ocean. Adjust seaice_itd/results/output.txt
1494      - replace nITD by SEAICE_multDim in loop-ranges
1495    o pkg/exf:
1496      - add code to process the case field period = -12. with UV interpolation.
1497      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1498        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1499    o verification/global_with_exf:
1500      - switch all fields period to -12. (was previously untested) in input/data.exf
1501        (but keep secondary test ".yearly" unchanged); update the reference output.
1502    o pkg/cal:
1503      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1504    o pkg/exf:
1505      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1506        to replace logical switch "exf_verbose"
1507      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1508    o pkg/sbo:
1509      - update from Katherine Quinn: evaluate mass directly from density and SSH
1510        (budget using Finite Volume method) instead of from bottom pressure.
1511      - allow testreport to collect few selected SBO output ; tested in exp.
1512        global_ocean.90x40x15 (after updating the results, to include SBO output).
1513      - fix some multi-threading issues (in output part).
1514    o model/src & most packages:
1515      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1516      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1517        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1518        "data.{pkg}" exist ; and leave the S/R (return) just after.
1519      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1520        + call LAND_READPARMS from packages_readparms.F
1521    o pkg/seaice:
1522      - remove code that resets useThSice in S/R seaice_readparms and
1523        replace it by a warning in S/R seaice_check
1524      - remove parameter MULTDIM, replace with nITD and runtime
1525        parameter SEAICE_multDim (still hard-wired to nITD if
1526        SEAICE_ITD is defined)
1527    
1528    checkpoint64x (2014/05/24)
1529    o verification/lab_sea:
1530      - update adjoint and TLM output following changes to pkg/salt_plume
1531      - un-do the update after putting back local recip_Cp in few places.
1532    o pkg/salt_plume: modifications by An Nguyen:
1533      - add capability to do brine rejection (salt-plume) as function of
1534        volume+tracers (instead of only salinity tracer).
1535      - conserve volume by exchanging volume from each kLev to above to
1536        accommodate in-coming brine volume
1537      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1538      - switch KPP surf buoyancy due to brine forcing to 3-d
1539        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1540      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1541      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1542        in East/West Arctic.
1543    o pkg/sbo:
1544      - incorporate modifications from Katherine Quinn to enable the use of sbo
1545        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1546        output for future testreport verification (unfinished).
1547    o pkg/atm_phys:
1548      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1549        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1550        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1551    o pkg/seaice
1552      seaice_calc_ice_strength.F: modify expression to avoid divisions
1553        (affects truncation)
1554      seaice_do_ridging.F: clean up the insectarium
1555      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1556      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1557      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1558      - add some debugging information and error messages (warnings)
1559    o model/src: modifications relatd to atmosphere p*:
1560      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1561      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1562        of vertical profile tRef in geopotential background and anomaly.
1563      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1564        and pkg/atm_phys.
1565      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1566        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1567    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1568    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1569        not used right now, but can be used in BGC packages to fix conservation.
1570    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1571        other packages too.
1572    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1573        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1574    o model/src:
1575      - since we have several heat capacity (even in model/src), define "recip_Cp"
1576        as local variable (no longer in common block) to avoid any confusion.
1577      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1578    o pkg/exf:
1579      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1580        air density as function of air Temp, Humidity and atm pressure.
1581    
1582    checkpoint64w (2014/05/02)
1583    o verification:
1584      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1585        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1586        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1587        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1588        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1589    o model/src: for atmosphere in p* coords:
1590      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1591      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1592        but not yet activated.
1593    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1594      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1595      - this changes the results (but not for any verification experiment, because
1596        none tests this), but avoids having an extra field in the restart files
1597    o pkg/seaice: remove global variable TICE (not needed)
1598      - replace by TICES or local variable where necessary (cost_seaice_test,
1599        seaice_diagnostics_state)
1600      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1601      - use specific read/write routines for reading and writing individual leves
1602        of a multilevel field
1603    o pkg/ctrl & model/inc:
1604      - move additional anomaly fields of control vars (related to options:
1605         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1606        from DYNVARS.h into new header file: CTRL_FIELDS.h
1607    o pkg/seaice: some small modifications to the ridging code
1608      - make fw2ObyRidge a global variable and add the freshwater flux to
1609        seaice_growth
1610      - pass actual thickness from seaice_prepare_ridging, so that it is
1611        computed only in one place and compute it in the same way as in
1612        seaice_growth
1613      - initialise more fields in seaice_do_ridging that where cause floating
1614        point exceptions over land
1615    o pkg/seaice: preparations for ridging code and first real ridging code
1616      - move most of "PART 1" of S/R seaice_growth into a new and separate
1617        S/R seaice_reg_ridge that will both regularize the state variable after
1618        advection call the actual ridging routine;
1619      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1620        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1621      - remove ridging code from seaice_advdiff
1622      - clean up remaining part 1 of seaice_growth in an attempt to make it
1623        more readable (this is probably subjective)
1624      - call seaice_itd_redist once in the initialisation phase to have the initial
1625        conditions in the correct category
1626      - finally: add new ridging routine for ITD code
1627    
1628    checkpoint64v (2014/04/11)
1629    o pkg/ecco:
1630      - add runtime parameters mdt[start,end]date[1,2]
1631      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
1632    o pkg/seaice:
1633      - make deltaC a global variable, so that it can be used in ridging code
1634      - first step towards ridging: introduce new routines that compute
1635        ice strength based on ridging parameters
1636      - add diagnostic for HSNOWITD
1637      - add opnWtrFrac as a global variable (required for ridging scheme)
1638    o pkg/salt_plume + pkg/seaice/seaice_growth.F
1639      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
1640        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
1641    o verification/hs94.1x64x5:
1642      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
1643      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
1644    o autodiff:
1645      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
1646        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
1647        For now, only in pkgs used in verification/hs94.1x64x5.
1648      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
1649        which are specific to TAF/TAMC).
1650      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
1651        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
1652        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
1653      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
1654        building mitgcmuv_ad (make adAll).
1655    o pkg/ecco:
1656      - cost_gencost_seaicev4.F:
1657         reformulate proxy cost as function of sst and local param SEAICE_freeze
1658         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
1659      - add stop statement if old names siv4-[sst,vol] are used
1660      - add snapshots + cost reports for atmospheric longwave
1661      - remove factor 0.1 in front of wtau[u,v]
1662      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
1663         ALLOW_TMI_SST_COST_CONTRIBUTION
1664    o pkg/atm_phys:
1665      - add some diagnostics for Short-wave and for convection S/R.
1666    o pkg/seaice/seaice_growth:
1667      - fix a bug in the lateral melt parameterization for SEAICE_ITD
1668        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
1669      - rearrange loop order for better vector code in the same code block
1670      - rewrite the floeDiameter formula to have fewer divisions
1671      -  (miraculously) none of this changes the results of seaice_itd
1672    o pkg/smooth:
1673      - move param smooth2Ddiffnbt to pkg/ecco
1674    o pkg/salt_plume:
1675      - salt_plume_frac.F:
1676         clean up local param names
1677         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
1678    o pkg/rw:
1679      - add RS version of S/R READ_MFLDS_LEV.
1680    o pkg/streamice:
1681      - fix the restart test by writing/reading pickup_streamice files.
1682    o pkg/seaice:
1683      - refine checks for jfnk-related parameters
1684      - comment out if statement with SEAICEuseIMEX parameter as long as there
1685        is no IMEX code to avoid confusion and surprises
1686    
1687    checkpoint64u (2014/03/07)
1688    o verification/MLAdjust:
1689      - rename secondary test suffix:
1690         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
1691         0.leithD -> AhFlxF  + switch to flux-form
1692         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
1693         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
1694    o pkg/mom_vecinv:
1695      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
1696        to be before mom_calc_visc.F)
1697      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
1698      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
1699        this is simpler for the adjoint and for diagnostics.
1700    o model/src + pkg/momentum:
1701      - add input files for  2-D additional Western and Southern cell-edge wall
1702         (e.g., to add "thin-wall" where it is =1).
1703      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
1704        using 2nd hFacZ that is computed from initial (fix domain) hFac
1705      - known limitations of thin wall implementation: not yet coded for sigma
1706        coords; not working with CD-scheme neither.
1707    o pkg/seaice:
1708      - rename recently introduced parameters from (wrong name) AB to
1709        BDF (backward difference time discretisation)
1710      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
1711    o tools/adjoint_options:
1712      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
1713    
1714    checkpoint64t (2014/02/01)
1715    o pkg/ecco
1716      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
1717        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
1718      - replace hard-coded record number and period which only work for monthly
1719        with read-in runtime param that works for other periods (month,day,year)
1720    o pkg/thsice
1721      - corrected store directive fixes thsice adjoint gradient checks
1722    o genmake2 & testreport:
1723      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
1724        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
1725        Update testreport accordingly. No need to set "export OPENAD=true"
1726        in adjoint_options/adjoint_oad anymore (will be removed later).
1727    o pkg/shelfice:
1728      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
1729        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
1730        so that surface forcing applies to k=kSurf if using pkg/shelfice.
1731    o pkg/ctrl, pkg/grdchk, pkg/ecco:
1732      - Changes to make GENARR more modular (i.e. invisible if not used)
1733    o model/src/temp_integrate.F and salt_integrate.F
1734      - re-include store directives that were removed on Dec 27th.
1735    o model/src/external_forcing_surf.F
1736      - add storage directives for EmPmR and PmEpR to avoid recomputation of
1737        seaice_model in the adjoint that is problematic when seaice_model is
1738        turned off in the adjoint. The resolved issue dated back to July when
1739        EXTERNAL_FORCING_SURF call was moved.
1740        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
1741    o pkg/exf/exf_check.F
1742      - fix a small bug again (originally found by Wentao Liu, now found again)
1743      - streamline error output
1744    o pkg/streamice and aim_v23:
1745      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
1746        Apple's /usr/bin/cpp knows what to do:
1747        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
1748        Target: x86_64-apple-darwin13.0.0
1749    
1750    checkpoint64s (2014/01/05)
1751    o tools/adjoint_options:
1752      - switch to fastopt.net TAF server (instead of default fastopt.de) for
1753        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
1754    o model/src:
1755      - remove some unnecessary TAF storage directives in forward_step.F and
1756        in dynamics.F (note: not always removed by TAF, e.g., double storage
1757        of kappaRU,kappaRV in former version of dynamics.F).
1758    o model/src & pkg/ptracers:
1759      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
1760        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
1761        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
1762      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
1763      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
1764      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
1765    o useSingleCpuInput separates single-CPU input from single-CPU output;
1766        for now only implemented for in exf_interp_read.F
1767    o verification/advect_xy:
1768      - fix missing EXCH call in local version of ini_salt.F and update output.
1769    o momentum diagnostics:
1770      - fix which deltaT is used in Total-Tendency diagnostics.
1771      - fix typo in diagnostics for momentum tendency from AB.
1772    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
1773        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
1774    
1775    checkpoint64r (2013/12/08)
1776    o verification/*/results:
1777      - Update reference output of experiments that were passing with just 13 digits
1778         (make it easier to detect future changes in results)
1779    o model/src & pkg/ptracers:
1780      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
1781        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
1782        to inside ptracers_integrate.F ; remove ptracers_advection.F
1783    o coupling interface pkgs:
1784        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
1785      - change the config check to test the agreement of Ocean Depth
1786        with ATM land/sea mask (instead of ATM orography);
1787      - send to coupler the number of coupler time-steps to do for this run:
1788        this allows to check for consistency and don't need anymore to be
1789        specified in parameter file "data";
1790      in coupler:
1791      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
1792      - improve report to log-file of config setting (pass log-file unit to few S/R)
1793    o pkg/compon_communic:
1794      - add coupling send/receive for non-tiled integer vector;
1795      - add S/R to check and stop if any proc has an error (similar to
1796        eesupp/src/stop_if_error.F but single thread and across Comm_World).
1797    o pkg/exch2:
1798      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
1799        through list of all tiles my proc owns.
1800    o model/src:
1801      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
1802        from rTrans) to simplify dependencies (no need to store rTrans anymore in
1803        calling S/R); this affects AD results at machine truncation level:
1804        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
1805        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
1806    o tools/build_options:
1807      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
1808    o coupling interface pkgs:
1809        [compon_communic, atm_compon_interf & ocn_compon_interf]
1810      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
1811        to each S/R that needs it; remove un-used variables.
1812      - change component tile registration (cpl_register.F in both compon_interf
1813        and mitcomponent_tile_register.F) to pass the full list of tiles
1814        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
1815      - with pkg/exch2: adopt the same convention used for I/O to define mapping
1816        towards coupler global array (unless W2_useE2ioLayOut=F):
1817         a) can now use different tiling between atm & ocn comp.
1818         b) no needs to modify the run-Off map when changing tiling (was needed
1819            even if using the same tiling between atm & ocn).
1820         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
1821            full land tiles); not yet tested.
1822      - check for valid mapping from comp. tile to coupler global array
1823      - improve report of tile registration results to log file.
1824    o pkg/exch2:
1825      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
1826        tile-registration (CPL_REGISTER);
1827      - activate (un-comment) definition and setting of "W2_tileIndex" list to
1828        store the local bi,bj indices of each tile;
1829      - also print bi,bj in local report to log file;
1830      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
1831        Jun 2009 modif of pkg/exch2).
1832    o testing on baudelaire:
1833      - run 2 tests at a time: no significant slow down (since enough cpu) and
1834        get the full set of test done earlier
1835      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
1836    o model/src/thermodynamics.F and routines called from it:
1837      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
1838        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
1839        velocity (outp) by adding bolus velocity.
1840      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
1841        mass transport from velocity + lateral grid cell area
1842      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
1843      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
1844     in thermodynamics.F
1845      - remove k from thermodynamics.F and move it to temp_integrate.F
1846        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
1847        loop).
1848      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
1849        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
1850        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
1851        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
1852      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
1853        global_ocean.90x40x15, tutorial_global_oce_biogeo and
1854        tutorial_tracer_adjsens (+ TLM output).
1855    o tools/OAD_support and (verification/*/) code_oad:
1856      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
1857        module conversion ; remove unneeded CPP_EEOPTIONS.h.
1858      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
1859        version (closer to model/inc/CPP_OPTIONS.h).
1860    o model/src:
1861      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
1862        retired list of parameters (routine FREEZE has been replace by surface
1863        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
1864    o pkg/gmredi:
1865      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
1866        velocity (same scheme but affects machine truncation) for GM_AdvForm.
1867      - update output of FWD experiments: front_relax.bvp,
1868        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
1869    
1870    checkpoint64q (2013/11/17)
1871    o verification:
1872      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
1873        tutorial_global_oce_biogeo and global_ocean.90x40x15.
1874      - generate new output (growth & melt) for seaice_itd experiment after
1875        updating the input pickup_seaice files (previously wrong).
1876    o pkg/cost:
1877      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
1878        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
1879        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
1880          cannot be applied to var in common block).
1881        o allows to get results independent of tile-per-proc setting (if using
1882          slower GLOBAL_SUM_SEND_RECV option).
1883      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
1884        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
1885        forward gradients: update output).
1886      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
1887        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
1888    o pkg/mom_common:
1889      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
1890        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
1891        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
1892        ensure that all field value that are used are set.
1893    o tutorial_deep_convection (smag3d):
1894      - add missing scaling in mom_calc_smag_3d.F;
1895      - set smag3D_coeff in input.smag3d such that results do not change.
1896    o pkg/dic:
1897      - change dic_cost.F to compute cost on each tile first and then apply
1898        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
1899        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
1900      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
1901    o eesupp/src & pkg/mdsio:
1902      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
1903        (from pkg/mdsio) since they are no longer used for tape IO.
1904      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
1905        (+ keep a copy in pkg/atm_ocn_coupler).
1906    o verification/isomip:
1907      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
1908    o tools/build_options:
1909      - optfile linux_amd64_ifort11, fast (no ieee) case:
1910        to get a working restart for all experiments, add "-fp-model source"
1911        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
1912    
1913    checkpoint64p (2013/10/20)
1914    o pkg/autodiff:
1915      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
1916        criteria, return to simple (default) tape IO format.
1917    o pkg/mdsio (+ eesupp/src):
1918      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
1919        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
1920      - fix globalFile and singleCpuIO options using simpler global mapping.
1921      - new pairs of scatter/gather vector S/R (one for each type, generated from
1922        template) corresponding to simpler global mapping.
1923      - adread_write.F: switch to new S/R (but leave old calls commented) and write
1924        to globalFile when parameter globalFiles is set to True.
1925      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
1926    o pkg/autodiff:
1927      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
1928        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
1929        missing, just add a STOP if array type do not match.
1930    o pkg/exf:
1931      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
1932         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
1933         and rename array obsSIce to exf_iceFraction.
1934    o tutorial_deep_convection:
1935      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
1936        for now all in this exp. code dir.
1937      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
1938        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
1939    o eesupp/src:
1940      - added SINGLE_DISK_IO option because reading of parameter files on
1941        very large number of processors did not work with existing set-up
1942    
1943    checkpoint64o (2013/09/25)
1944    o pkg/atm_phys & atm_compon_interf:
1945      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
1946    o tools/build_options:
1947      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
1948        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
1949        remove CPP setting (was identical to genmake2 default).
1950    o pkg/gmredi & model/src: Some updating and work done on the residual model.
1951      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
1952      - fixed up the calculation of the eddy stress and how it is added to the
1953        external forcing via taueddy_external_forcing.F
1954      - at the moment, it is very experimental and only works with the variable eddy
1955        diffusivity calculated in gmredi_k3d.F
1956    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
1957        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
1958    o testreport (& tools/do_tst_2+2):
1959      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
1960    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
1961      - remove CPP='cpp -traditional -P' (this is genmake2 default)
1962      - add switch (for big setups) to use 'medium' memory-model (but leave it
1963        commented out for now). Note: needed with FC 19 to compile big setups.
1964    o pkg/atm_compon_interf:
1965      - regroup per field origin (model & pkgs) the coupling storage routines
1966         (which accumalate in time each coupling field)
1967      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
1968        update accordingly + simplify aim_do_physics.F
1969    
1970    checkpoint64n (2013/08/26)
1971    o pkg/bbl:
1972      - update formulation to reduce dispersion of tracer properties in bbl
1973      - replaced horizontal and vertical transport parameters with velocities
1974      - changes results for verification/global_with_exf.yearly
1975    o verification/halfpipe_streamice:
1976      - change to matrix construction; update both Fwd & AD output.
1977    o verification/tutorial_tracer_adjsens:
1978      - OpenAD test: switch to vector-invariant momentum since fluxform with
1979        rStar causes problems with OpenAD; update output.
1980    o tools:
1981      - genmake2: define a common prefix for all temp-file names ; move them
1982        to local /tmp disk (but would be easy to move them back);
1983      - xmakedepend: apply the same switch for temp-files.
1984    o pkg/offline:
1985      - changes for use with rStar (NLFS): assume that we continue to provide
1986        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
1987        output files) and apply r* scaling at each time-step (function of the time
1988        varying Eta field); use normal pickup files (needed for restart with NLFS).
1989    o adjoint with OpenAD:
1990      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
1991        package openad.  This package has to be compiled for all runs with OpenAD
1992        instead of specifying code_oad_all as a modification directory.
1993      - link the fortran templates from tools/OAD_support to the build directory
1994        for preprocessing to avoid conflicts between different setups compiled
1995        simultaneously and simplify cleanup.
1996    o pkg/exf:
1997      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
1998        main model or other pkgs are exchanged in EXF_MAPFIELDS).
1999    o model/src:
2000      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
2001        (similar to do_fields_blocking_exchanges.F).
2002    o tools/genmake2:
2003      - remove TAF output src code just before calling staf (when not doing a fresh
2004        built, will stop if things go wrong with staf).
2005      - fix target "adobj" (left from TAF version-2 transition)
2006    o pkg/diagnostics:
2007      - add a parameter to track the status of pkg/diagnostics activation;
2008        this replace/extend the use of logical param "settingDiags" (to check
2009        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
2010        New S/R to print error message and stop when pkgStatus is not right.
2011      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
2012    
2013    checkpoint64m (2013/08/13)
2014    o model/inc:
2015      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
2016        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
2017    o pkg/kpp & aim_v23:
2018      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2019    o pkg/seaice:
2020      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
2021        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
2022      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2023    o eesupp/src:
2024      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
2025        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
2026    o switch to TAF version-2:
2027      - add flow directives to "freeze" naming convention for ad-routines that
2028        are used in I/O routines of adjoint state and associated common blocks
2029        that are used in adcommon.h (backward compatible with version-1)
2030      - update all ad-optfiles (in tools/adjoint_options + few local to some
2031        verification exp) to switch to latest TAF version (currently 2.5.5);
2032        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
2033        out except for diva).
2034      - the major change with TAF version-2 is that both the differentiated
2035        routines and the forward routines (new) are returned as part of the TAF
2036        output source code. Update genmake2 accordingly.
2037      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
2038        with version-2 when compared to TLM or FWD gradient); other experiments
2039        output show minor changes (machine truncation level); update the few AD &
2040        TLM output with 12 matching digits only (some prior to version-2 switch).
2041    
2042    checkpoint64l (2013/08/05)
2043    o model/src:
2044      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
2045      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
2046        when using TAF but only if using OpenAD.
2047    o pkg/mom_common+fluxform+vecinv:
2048      - always set horiz. viscosity arrays to background value before calling
2049        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
2050        only when using variable horiz. viscosity (useVariableVisc=T);
2051      - simplify mom_vecinv.F (only 1 block for momViscosity).
2052    o pkg/mom_common: variable horiz. viscosity in NH code
2053      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
2054        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
2055      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
2056        useBiharmonicVisc & useVariableVisc.
2057      - fix old bug (already in 1rst implementation of variable horizontal viscosity
2058        in calc_gw.F, version 1.27, 2006/06/20):
2059        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
2060        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
2061      - change background horiz viscosity in vertical momentum (gW) to always be
2062        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
2063        any type of variable viscosity, e.g., viscAh/4Grid)
2064      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
2065        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
2066        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
2067        default viscAh,viscA4 is zero).
2068    o model/src:
2069      - extend length of drC & recip_drC from Nr to Nr+1.
2070    o Divided Adjoint (DIVA) with MPI:
2071      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
2072      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
2073        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
2074    
2075    checkpoint64k (2013/07/23)
2076    o tools/OAD_support:
2077      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
2078        and remove it from genmake2.
2079    o tools/build_options:
2080      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
2081        MPI_HEADER_FILES list (let genmake2 find the missing headers)
2082    o verification/halfpipe_streamice:
2083      - change to driving stress formulation; update both Fwd & AD output.
2084    o tools/genmake2 and Divided Adjoint with MPI:
2085      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
2086      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
2087      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
2088        Makefile, which is set by genmake2, and check which mpi-headers are needed.
2089        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
2090      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
2091    o testreport:
2092      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
2093        perform additional runs (number of additional runs is "add_DIVA_runs" taken
2094        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
2095    o verification/lab_sea (AD test):
2096      - change to test Divided Adjoint Run in this set-up (both standard AD test
2097        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
2098    o pkg atm_ & ocn_compon_interf:
2099      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
2100        staggerTimeStep implementation) and disable (retired) corresponding
2101        parameter.
2102    o pkg/offline:
2103      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
2104      - add S/R OFFLINE_CHECK to print offline parameter summary
2105        and stop if loading a file that is not used;
2106      - enable to calculate GMRedi tensor, KPP mixing and convective index
2107        when the corresponding file(s) is/are not specified (but pkg is used).
2108      - comment out resetting of monitorFreq (to endTime) since it still useful
2109        for monitoring CFL numbers and checking offline fields.
2110    o OpenAD:
2111      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
2112        smaller standard output) and generate new (smaller) output (on baudelaire
2113        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
2114    o model/src:
2115      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
2116        (where external_forcing_adjust was called) and change list of arguments;
2117      - merge external_forcing_adjust.F into external_forcing_surf.F
2118      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
2119        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
2120        previously in file "balance_relax.F", now removed); remove corresponding
2121        arrays in FFIELDS.h.
2122      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
2123        a hack for getting back surfaceForcingS (loaded from file) when using
2124        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
2125      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
2126        (was getting only 11 digits for AD-grad, due to different truncation
2127         error in AD code).
2128    
2129    checkpoint64j (2013/07/04)
2130    o pkg/offline:
2131      - to enable the use of other features with pkg offline (e.g., obcs),
2132        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
2133      - comment out "allowFreezing" (now active) in 2 offline testing exp.
2134    o pkg/exf ALLOW_RUNOFTEMP
2135      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
2136      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
2137      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
2138    o pkg/atm_phys:
2139      - allows to add some damping on uVel,vVel (strength only function of k).
2140    o verification, ad-tests:
2141      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
2142        global_ocean_ebm and offline_exf_seaice.thsice.
2143    o verification/halfpipe_streamice:
2144      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
2145        flux input boundary conditions to be ignored; a fix for this bug changed
2146        verification results for forward test.
2147      - add adjoint test.
2148    o pkg/ptracers:
2149      - allow to restart without SOM pickup (resetting SOM to zero).
2150    o pkg/gmredi:
2151      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
2152      - It uses mixing length theory and suppression by steering level effects to
2153        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
2154        to JPO, for more details).
2155      - It also uses the diffusivity to calculate an eddy induced streamfunction
2156        based on a PV closure (rather than a buoyancy closure as in GM).
2157      - New files added to pkg/gmredi:
2158        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
2159          induced overturning streamfunction (called from gmredi_calc_tensor)
2160        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
2161          for use in gmredi_k3d
2162        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
2163          the eddy diffusivity
2164    
2165    checkpoint64i (2013/06/18)
2166    o pkg/cheapaml:
2167      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
2168        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
2169        with pkg/cheapaml.
2170    o utils/python: add subpackage for cubed sphere function, first example is
2171        simple cs.pcol to plot 2D fields on a map
2172    o pkg/streamice:
2173      - This is a new package in MITgcm, which solves dynamic equations for ice
2174         sheets and ice streams
2175      - At the moment it is independent of atmosphere/ocean dynamics, or any
2176        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
2177        ed that this will change)
2178      - There is a new verification exercise that tests it, halfpipe_streamice,
2179        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
2180        rectangular embayment
2181      - halfpipe_streamice is forward-only for now, will have TAF test soon
2182      - for questions, email dgoldber@mit.edu
2183    o pkg/thsice:
2184      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
2185        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
2186      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
2187         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
2188      - allow precip from pkg/cheapaml to make snow over seaice.
2189    o pkg/cfc:
2190      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
2191      - remove atmos CFC 2-D arrays from common bloc (now local variables)
2192      - change some hard-coded constant to run time parameter for reading and
2193        and interpolating atmospheric CFC ; keep same default as previously.
2194      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
2195      - put arguments in standard order: myTime, myIter, myThid
2196      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
2197        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
2198      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
2199      - new routine to print summary of CFC params and check for consistency.
2200    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
2201      similar to thsice_advdiff.
2202      Note that for the B-grid case the routine parameters uc/vc are overwritten.
2203    o pkg/cfc:
2204      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
2205        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
2206      - fix interpolation of atmphspheric CFC between Sorthern and Northern
2207        hemisphere value.
2208    o pkg/seaice:
2209      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
2210    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
2211                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
2212      - requires an additional time level that is stored in the pickup
2213      - you can start with AB2 from a pickup without this time level with
2214        pickupStrictlyMatch = .false.
2215    
2216    checkpoint64h (2013/05/26)
2217    o pkg/cheapaml:
2218      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
2219        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
2220      - consistent treatment of uWind,vWind location: assume everywhere in
2221        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
2222        (Note: was already the case for Tair,Qair advection);
2223        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
2224      - compute diabatic forcing only in the interior (excluding overlap regions)
2225      - fill in array "Qsw" (for short-wave heating);
2226      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
2227        before any update (consistent with MITgcm state var diagnostics);
2228      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
2229        non periodic ; + adjusted for uWind,vWind (C-grid).
2230    o pkg/seaice:
2231      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
2232        add explicitly pkg/exf in experiments that currently use pkg/seaice.
2233      - allows to compile pkg/seaice without pkg/exf.
2234    o tools/OAD_support:
2235      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
2236        of array "ourStepOf" in function rvNextAction (revolve.F90).
2237    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
2238      - change pkg name (to be used with other atmospheric physics pkg)
2239        but by-pass CVS when making the new pkg so that we keep the CVS history.
2240    o pkg/offline:
2241      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
2242        (previously called from pkg/dic_surfforcing_init.F)
2243    o model/src:
2244      - re-order sequence of calls within packages_init_variables.F, using
2245        standard order, except for:
2246         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
2247         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
2248    o new pkg: atm_phys
2249      - add entry point and source code (previously in contrib
2250          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
2251        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
2252      - re-order sequence of calls within packages_readparms.F,
2253         packages_init_fixed.F and packages_write_pickup.F
2254        (but skip packages_init_variables.F because of TAF issues).
2255      - update contrib/*/atm_gray/ experiment.
2256    o pkg/seaice (ITD code):
2257      - simplify and fix the writing of pickup-files for ITD case
2258    o pkg/seaice (ITD code):
2259      - introduce floe size dependent lateral melt for ITD case;
2260      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
2261      - update seaice_itd experiment main output.
2262    o pkg/thsice:
2263      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
2264        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
2265        changed accordingly pkg/atm2d.
2266    
2267    checkpoint64g (2013/05/01)
2268    o pkg/exf ALLOW_RUNOFTEMP
2269      - if defined,  river and glacier runoff temperature can be read-in from
2270        runoftempfile; runoftempfile needs to have same format as runofffile
2271    o pkg/thsice (& pkg/bulk_force):
2272      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2273        for energy content of Precip + RunOff & Evap (like with pkg/exf).
2274      - change computation domain to always be the interior (without overlap).
2275      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
2276    o verification/tutorial_global_oce_biogeo:
2277      - add preliminary OpenAD setup (still has problems)
2278    o pkg/seaice:
2279      - turn some parameters for choosing the convergence criterion of
2280        the inexact Newton method (JFNK) into runtime parameters for convenience
2281      - clean up seaice_calc_viscosities.F: remove/retire two options for
2282        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
2283        the results of lab_sea/input because a division has been replaced by
2284        a multiplication with the reciprocal (sumNorm)
2285      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
2286        convergence of solver (changes results, of course), and to test some
2287        new features
2288    o model/src:
2289      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
2290      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
2291      - move forcing adjustment (balancing surface forcing) in specific S/R
2292        where might also be applied exchanges (if needed) to forcing arrays.
2293    o pkg/shelfice:
2294      - allow to specify the Ice-Shelf mass per unit area (instead of
2295        shelficeLoadAnomaly) and do the conversion from one to the other
2296      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
2297        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
2298        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
2299        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
2300      - update isomip experiment forward output (get machine truncation error
2301        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
2302    o verification/offline_exf_seaice:
2303      revise data.seaice in input.thermo and input_ad and update results accordingly
2304        HO = 0.2, SEAICE_areaLossFormula = 2,
2305        SEAICE_growMeltByConv = .TRUE.,
2306        SEAICE_doOpenWaterMelt = .TRUE.,
2307      Improve consistency with input.thsice and fix the spurious 500m ice corners
2308    o verification/global_ocean.cs32x15:
2309      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
2310        in icedyn (thsice+seaice-dyn) test and update output.
2311    o verification/offline_exf_seaice:
2312      - adjust list of tested variables (with testreport) and update
2313        standard test output with better slection of monitored fields.
2314    o pkg/cd_code:
2315      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
2316        experiment lab_sea.hb87
2317    o tools/genmake2:
2318      - change default makedepend from the system default to tools/xmakedepend:
2319        When no makedepend is specified, select tools/xmakedepend it the test pass,
2320        otherwise select the system default (if exist and pass the test) or
2321        try to build cyrus-makedepend ; stop if none of the 3 works.
2322    o pkg/exf & pkg/thsice:
2323      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2324        for energy content of Precip + RunOff & Evap. Assumes:
2325       1) Rain has same temp as Air.
2326       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
2327       3) Run-Off comes at the temp of surface water (with same Cp)
2328       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
2329        put directly into Latent Heat flux & should use water-vapor heat capacity.
2330       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
2331        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
2332    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
2333        (compile when SEAICE_ALLOW_JFNK is defined)
2334    o pkg/thsice:
2335      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
2336        implementation): move THSICE_AVE call after the advection (called directly
2337        from thsice_do_advect.F).
2338    o verification/global_ocean.90x40x15 and OpenAD:
2339      New experiment for OpenAD is identical to the one in input_ad except that
2340        multiDimAdvection=.FALSE.,
2341      There is still an issue with this.
2342    o pkg/thsice:
2343      - account for ice velocity (ocean relative velocity) in turbulent heat flux
2344        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
2345        and offline_exf_seaice (main test).
2346    
2347    checkpoint64f (2013/03/31)
2348    o verification/OpenAD:
2349      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
2350    o verification/isomip, pkg/shelfice and OpenAD:
2351      - add OpenAD setup to this exp and make shelfice package work with OpenAD
2352    o verification/tutorial_global_oce_biogeo:
2353      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
2354    o verification/offline_exf_seaice:
2355      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
2356    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
2357      - add OpenAD setup to this exp and make ptracers package work with OpenAD
2358    o pkg/seaice/seaice_evp.F:
2359       mask the asymmetric contribution of the ice-ocean stress (when
2360       the turningAngle is non-zero) over open water to avoid stripes
2361       in the EVP-solutions after many EVP-substeps. This does not change
2362       the verification experiment (because turningAngle=0 in that experiment),
2363       but will affect other EVP solutions with turningAngle.ne.0
2364    o verification, AD & TLM output:
2365      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
2366        additions and multiplications which affect results at machine truncation
2367        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
2368        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
2369        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
2370        digits of matching.
2371    o pkg/seaice:
2372       modify lsr-algorithm so that it vectorizes AND converges by using a
2373       "zebra" method: split vector loop into two with step size 2; this
2374       solves a general convergence problem for the JFNK solver on a vector
2375       computer. It has the potential to even improve convergence for
2376       non-vector machines, but it does change the results so it is turned
2377       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
2378       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
2379    
2380    checkpoint64e (2013/03/05)
2381    o pkg/ecco and several verification experiments:
2382       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
2383       from ecco package, and revert to unified routine in model/src/
2384       Adjust verification experiments accordingly, especially gloal_oce_llc90
2385       Should conclude long-standing work by Gael to reconsile the_main_loop with
2386       ECCO and will enable OpenAD's revolve loop in ECCO setup.
2387    o pkg/generic_advdiff:
2388      - implement compressible flow method for multi-dim advection (similar to
2389        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
2390        TAF generates many recomputations) to use it; no yet coded with implicit
2391        vertical advection.
2392      - change experiment advect_cs (new output) and advect_xy (same output)
2393        to test compressible flow multi-dim advection.
2394    o pkg/generic_advdiff:
2395      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
2396        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
2397    o pkg/seaice:
2398      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
2399        bug affects two verification experiments (lab_sea and lab_sea.hb87),
2400        recover old (wrong) results by setting noSlipFac = 2. in
2401        seaice_calc_strainrates.F;
2402      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
2403      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
2404        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
2405      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
2406    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
2407      - new subroutines seaice_lsr_tridiagu/v
2408      - introduce loop bounds i/jmin/max to be able to use a restricted
2409        additive Schwarz method, but not used for now.
2410      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
2411      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
2412    o OpenAD support
2413       Reorganize S/R call for overall time-stepping loop to facilitate
2414       OpenAD revolve loop replacement
2415       (new S/R main_do_loop.F)
2416    o model/src:
2417      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
2418      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
2419        ADAMS_BASHFORTH2.
2420    o pkg/cheapaml:
2421      - add new parameter (default=F, same as before) to disable full domain
2422        (including land) periodicity in X & Y dir.
2423      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
2424        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
2425        into single S/R CHEAPAML_TIMESTEP.
2426    
2427    checkpoint64d (2013/02/17)
2428    o pkg/monitor (angular momentum):
2429      - do not add Eta contribution to the total AM if using rigid-lid;
2430      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
2431      - horizontal discretisation: compute Zonal wind contribution separately for
2432        each component (instead of from cell centered averaged) and use the 4
2433        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
2434      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
2435        FreeSurf) if using vectorInvariant momentum.
2436    o model/src (horizontal grid):
2437      - move initialisation of all horizontal grid arrays to null value
2438        from specific horizontal grid S/R to main S/R INI_GRID;
2439      - add 2 new arrays to project model C-grid velocity on to zonal direction
2440        (similar to AngleCosC & -AngleSinC but at U and V point location) and
2441        compute them in S/R CALC_GRID_ANGLES.
2442    o pkg/seaice: replace a hard coded parameter by a runtime parameter
2443        SEAICE_JFNK_tolIter
2444    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
2445        preconditioner for JFNK (run LSR into the overlaps as far as possible,
2446        i.e OLx/y-2, but overwrite the solution in the overlaps)
2447      - extend loop range in seaice_calc_viscosity
2448      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
2449      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
2450      - slightly modify loops in tridiagonal solver lsr-preconditioner
2451      - by default remove the extra exchange in seaice_preconditioner with a
2452        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
2453      - modify offline_exf_seaice so that old results without RAS are reproduced
2454        for output.dyn_jfnk.txt
2455      in seaice_fgmres.F (unrelated to RAS)
2456      - add a cpp-flag option for a re-ordered mapping (potentially more
2457        efficient), but because this changes the results, turn it off by
2458        default
2459      - replace the save statement by local common blocks
2460    o utils/matlab:
2461      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
2462      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
2463        instead of local script "load_cs.m".
2464    o pkg/seaice:
2465      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
2466        to the scalarProductMetric and the unrolling. By chance this does not
2467        change the verification experiment, because of the particular domain
2468        decomposition
2469    o pkg/diagnostics:
2470      - change default missing_value from UNSET_RL to -999.
2471    o pkg/layers: improve vectorization of layers_fluxcalc.F
2472      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
2473        time spent in this routine by more than a factor of 3 on an NEC-SX8
2474      - step 2: replace search algorithm by a bisection algorithm found in
2475        Press et al. Numerical Recipes in Fortran. This algorithm can be
2476        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
2477        For now, use this algorithm only for TARGET_NEC_SX defined.
2478      - moved the search algorithm into a separate subroutine, that is kept
2479        within the same file for automatic inlining.
2480      - modified catching potential errors
2481    o pkg/ecco:
2482      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
2483    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
2484      - modifications for ALLOW_GENTIM2D_CONTROL
2485      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
2486      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
2487      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
2488      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
2489    o model/src:
2490      - account for moist thermodynamics in (dry) potential temperature equation;
2491        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
2492        and cpl_aim+ocn.
2493      - also switch to standard compiler (gfortran, was using ifort previously)
2494        for fizhi-cs experiments reference output.
2495    o pkg/ctrl:
2496      - 1st step toward generic time-varying control variable (2D) via CPP option
2497        ALLOW_GENTIM2D_CONTROL
2498      - note new namelist ctrl_nml_genarr in data.ctrl
2499    o verification/global_ocean.cs32x15:
2500      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
2501        thsice calling sequence and update "output.icedyn.txt" output file.
2502    o pkg/ptracers:
2503      - from Ryan A.: code to allow to restart a tracer at regular time interval
2504        specifying a reset frequency and a reset-phase (for each tracers).
2505    o pkg/thsice:
2506      - implement new sequence of calls for thsice+seaice:
2507          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
2508          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
2509      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
2510        in CPP_OPTIONS.h) to recover old sequence;
2511      - update diagnostics for Intermediate State thsice diagnostics: now filled
2512        just before advection (instead of just after advection in old sequence);
2513      - update output of experiment offline_exf_seaice (standard test);
2514      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
2515        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
2516    o pkg/aim_v23:
2517      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
2518      - use standard pkg/mdsio routines to read & write CO2 pickup file;
2519      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
2520      - Implement new sequence of calls for seaice advection (with thsice and
2521        seaice diffusion): do ice advection after ice-Thermodynamic (previously
2522        was done before); change aim_do_physics.F (split the bi,bj loops block);
2523      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
2524    o pkg/thsice:
2525      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
2526        where just seaice diffusion is used without seaice-dynamics.
2527    
2528    checkpoint64c (2013/01/18)
2529    o pkg/seaice:
2530      - add a parameter JFNKres_tFac that can replace JFNKres_t
2531        (= JFNKres_tFac*JFNKresidual before JFNK solver)
2532      - add a line search option to the JFNK solver
2533      - move update of u/vIce and computation of initial residual into a separate
2534        routine (same file); makes the code a little easier to read (?)
2535      - the line search requires computation of the residual and for some reason
2536        I cannot do the update of u/vIce at the beginning of the Newton loop
2537        without changing the results, so we move computation of the new residual
2538        also to the end of the Newton loop, even without the line search
2539    o pkg/mdsio:
2540      - write missing value (corresponding to undefined array value) to meta files;
2541        skip this if missing value is one (UNSET_RL would be a better value for the
2542        case of undefined missing value but it's current the default missing-value);
2543        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
2544    o pkg/exf & thsice:
2545      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
2546        diagnostics) even when SHORTWAVE_HEATING is #undef;
2547    o verification/cfc_example:
2548      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
2549        illustrate how to use it).
2550    o verification/offline_exf_seaice:
2551      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
2552        files to only one time-record.
2553      in input.thermo: narrow the 2 bands of low initial ice-concentration near
2554        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
2555        snapshot output; same mcPheePiston value as in thsice with
2556        surf-current=0.2m/s.
2557      in input.thsice: similar set-up as in input.thermo (channel with same seaice
2558        initial conditions).
2559    o verification/cfc_example:
2560      - update file "data" with more standard choice (default rotationPeriod,
2561        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
2562        set deltaTFreeSurf to deltaTtracer) and update the output.
2563    o pkg/layers:
2564      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
2565      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
2566    o verification/offline_exf_seaice:
2567      - set all {field}period to zero for constant-in-time forcing (not tested
2568        anywhere else).
2569    o verification/offline_exf_seaice:
2570      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
2571      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
2572    o model/src:
2573      - implement Finite-Volume method for (hydrostatic) presure gradient
2574        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
2575    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
2576      - In order to be compatible with the default EVP code, this requires changing
2577        the EVP code around a little; and because any small change immediately
2578        breaks the lab_sea.hb87 verification experiment, the reference output is
2579        updated two times (each time the remaining aggrement was only 2 digits):
2580        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
2581        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
2582        The adjoint test lab_sea.evp also needed to be updated.
2583      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
2584        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
2585        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
2586        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
2587        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
2588        kept obscure, because I need to test it a little more.
2589    o pkg/cheapaml:
2590      - fix few incorrect type (_RL/_RS) in subroutine calls.
2591    o pkg/seaice:
2592      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
2593        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
2594    o model/src:
2595      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
2596        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
2597        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
2598    o pkg/cheapaml:
2599      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
2600        update output of experiment cheapAML_box.
2601      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
2602        and set them only in one place (cheapaml_readparms.F).
2603      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
2604      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
2605        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
2606    o model/src/the_main_loop.F:
2607      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
2608    o pkg/seaice:
2609      - remove legacy branch code.
2610      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
2611    o verification/*/code*/SEAICE_OPTIONS.h:
2612      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
2613        SEAICE_CAP_HEFF).
2614    o pkg/cheapaml:
2615      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
2616        to load new forcing fields.
2617      - add missing "_d 0" where it's needed; + some editing (improve indentation).
2618      - remove switch to "-r8" compiler option (no longer needed) in verification
2619        cheapAML_box, keep same output (small trucation error differences).
2620    o verification/offline_exf_seaice:
2621      - add thermodynamics only test.
2622    o verification/cheapAML_box:
2623      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
2624        keep same output (same 14 digits for cg2d).
2625      - switch on "-r8" compiler option (some numerical values are missing
2626        the "_d 0") and update output (only 6 digits for cg2d were preserved).
2627    
2628    checkpoint64b (2012/12/24)
2629    o pkg/cheapaml:
2630      - remove un-used variables (Qnet,EmPmR) from pickup files.
2631      - store tendency of advected variables into cheapaml pickup file
2632        and fix the AB-2 restart.
2633    o verification/offline_exf_seaice and lab_sea adjoint:
2634      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
2635      - switch to 4 time steps in offline, consistent with lab_sea.
2636      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
2637      - update results after change of experiment seaice.
2638    o pkg/seaice:
2639      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
2640        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
2641        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
2642        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
2643    o model/src:
2644      - add run-time parameter to select CG2D solver minimum-residual solution
2645        (in case of a poor convergence).
2646    o pkg/seaice/seaice_lsr.F
2647      - move calculation of matrix coefficients into new
2648        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
2649        file; the main purpose of this change is to be able to reuse the code
2650        in S/R SEAICE_PRECONDITIONER
2651      - modify the computation of the residual so that the mass of sea-ice
2652        is not used twice; this simplifies the calculations, but since
2653        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
2654        not tested in testreport---this does not affect the testreport results.
2655    o verification/seaice_obcs:
2656      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
2657        verification/lab_sea/input.salt_plume; changes results/output.txt*
2658    o model/src:
2659      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
2660    o pkg/seaice:
2661      - improve description of parameters in seaice_fgmres.F and start
2662        cleaning up the code
2663      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
2664        second argument
2665      - add a metric based on grid cell area to SEAICE_SCALPROD; update
2666        results of offline_exf_seaice.dyn_jfnk
2667      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
2668    o pkg/aim_v23:
2669      - fix an other bug in dissipation heating (grid-cell area was missing).
2670    o model/src + pkg/seaice:
2671      - add global (multi-tile) linear solver for pair of tri-diagonal system
2672        along X and Y lines, respectively for U and V component.
2673        Note: 1) MPI and cube-exchange not yet coded.
2674            2) probably not accurate for poorly conditioned / large size problem.
2675      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
2676        default: not compiled and not used.
2677    o pkg/seaice:
2678      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
2679        introduce bi/bj loops and use global_sum_tile_rl instead of
2680        mpi_allreduce in seaice_fgmres.F
2681      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
2682      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
2683      - add a verification experiment for JFNK in offline_exf_seaice
2684    o verification:
2685      - change (for now, only fwd test) offline_exf_seaice experiment:
2686        use a re-entrant channel with idealized coastline (trapezoidal shape)
2687        at southern boundary to explore seaice dynamics and thermodynamics
2688        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
2689        secondary test (input.thsice) use thermodynamics only with SST relaxation.
2690      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
2691    o pkg/exf:
2692      - disable "sstExtrapol" when Nr=1
2693    o verification:
2694      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
2695        to test pkg/cheapaml.
2696    o pkg/aim_v23 & pkg/shap_filt:
2697      - fix dissipation heating (erroneous gravity multiplication factor).
2698    o pkg/seaice:
2699      - remove unused field pressPre from jfnk solver
2700      - rename two subroutines in seaice_preconditioner.F
2701    o eesupp/src:
2702       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
2703    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
2704       - remove wrong parts of the rhs and the lhs (were in there
2705         because I did not understand the concept of this preconditioner)
2706       - add an exchange between u- and v-sweep. This increases communication
2707         by a factor of two but improves the convergence of jfnk. Ideally,
2708         one would like the u- and v-sweep to be independent. So far within
2709         undocumented ifdefs
2710       - reorganize the extra computations for printing the residuals
2711    o tools/genmake2:
2712      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
2713        since it's not necessary (and was preventing to use MNC in some cases).
2714    
2715    checkpoint64a (2012/11/16)
2716    o pkg/autodiff:
2717      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
2718        autodiff_readparms.F no longer depends on calling order (within
2719        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
2720        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
2721        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
2722    o pkg/obcs:
2723      - adding tidal velocity forcing capability to obcs
2724        for usage example, see verification/seaice_obcs/input.tides
2725    o pkg/seaice:
2726      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
2727        SEAICE_LSRrelaxU/V
2728      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
2729    o pkg/aim_v23:
2730      - implement heating from friction (bottom friction and stratospheric drag).
2731    o pkg/shap_filt:
2732      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
2733        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
2734    o model/src:
2735      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
2736        time-constant addMass field from file (addMassFile);
2737      - support for heating due to friction (and Kinetic Energy dissipation):
2738        add option, run-time switch and 3-D field array + support code ; each pkg
2739        or S/R can add heating contribution (if there is a sink of KE); the sum is
2740        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
2741    o pkg/seaice:
2742      - complete merge of ITD code into seaice_growth.F
2743        from MITgcm_contrib/torge/itd/code/
2744        no verification so far, but Torge Martin tested
2745        "1-D test case and Beaufort set up;
2746        deliver okay results after 1 model year."
2747      - complete merge of SEAICE_SIZE.h into all relevant routines
2748      - move computation of eta at Z-points into calc_viscosities
2749        + introduce global field etaZ
2750        + add different methods for computing etaZ, for now the old
2751          method (simple averages of eta to Z-points) is hardwired
2752        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
2753          seaice_preconditioner
2754      - simplify computations for SEAICE_ZETA_SMOOTHREG
2755      - seaice_preconditioner:
2756        + replace one remaining press by pressLoc (mistake)
2757        + adjust printing of residuals
2758      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
2759        + add (SEAICE.h) and rename some counters (initiliased in
2760          seaice_init_fixed.F)
2761        + add _BEGIN/END_MASTER (myThid)  around print statements
2762        + print total number of iterations and failures over SEAICE_monFreq
2763          interval to STDOUT
2764      - move control over output-messages by fgmres to seaice_jfnk to save
2765        some operations
2766      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
2767        in order to make restarts with sol .ne. zero (fgmres with restarts)
2768        (seaice_jfnk.F, seaice_fgmres.F)
2769      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
2770        a serious convergence problem when open boundaries are involved
2771    o pkg/ggl90: fix computation of control volumes for the case of
2772      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
2773      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
2774    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
2775    o pkg/autodiff
2776      - Add inAdMode switch for SEAICEuseDYNAMICS:
2777        SEAICEuseDYNAMICSinAdMode
2778        (extend logic in ADAUTODIFF_INADMODE_SET)
2779    o pkg/seaice
2780      - Step 1 of merging ice-thickness distribution (ITD) code from
2781        MITgcm_contrib/torge/itd/ (author: Torge Martin)
2782        The code implements concept laid out in Thorndike et al. (1975);
2783        code is enabled via CPP flag SEAICE_ITD
2784        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
2785        code is not complete yet!!
2786      - SEAICE_SIZE.h now included in almost all seaice routines
2787    o verification (using seaice):
2788      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
2789        global_ocean.cs32x15.seaice ; update results.
2790      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
2791      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
2792        offline_exf_seaice (previously compiling B-grid).
2793    o pkg/exf:
2794      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
2795        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
2796        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
2797    o pkg/layers (adjust changes from Sept 19):
2798      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
2799        this allows to remove "layers_maxNum" dimension from all layers arrays.
2800    o pkg/layers (adjust changes from Sept 19):
2801      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
2802      - snap-shot extended to all type of layers (not just the 1rst type);
2803      - remove layers variables when corresponding CPP option is undef.
2804    o pkg/layers:
2805      - rename pkg/layers variable and add new output (layer exist & un-weighted
2806        velocity in layer)
2807    o pkg/seaice:
2808      - simplify (?) ocean-drag coefficent computations by using
2809        the same routine in all three solvers (saves some code lines)
2810      - remove global fields DRAGA and DRAGS from C-grid code and
2811        declare them locally in lsr.F (the only place where they are
2812        still used)
2813      - update AD output of lab_sea.evp (very sensitive anyway).
2814    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
2815      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
2816      and SEAICEuseJFNK=.true. A few things to note:
2817      - involves a FGMRES, that is parallel but very inefficient,
2818        because of many scalar products (global sums) in the Gram-Schmidt
2819        orthogonalization method. Needs to be replaced. Original code
2820        from J.-F. Lemieux
2821      - preconditioner for FGMRES is a stripped down version of LSOR
2822      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
2823        preconditioner. For the preconditioner, the default is set to 10.
2824      - Jacobian times vector is computed with finite differences
2825      - marginally related to JFNK-solver: add a smooth regularization for
2826        zeta with tanh that will improve convergence (Lemieux and Tremblay,
2827        2009) for any implicit solver (not implemented for EVP because EVP
2828        does not need this regularization in the first place). Define
2829        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
2830    o eesupp/src:
2831      - check in genmake2 that intrinsic S/R flush is available.
2832      - add S/R to flush IO unit (if intrinsic S/R flush is available)
2833      - flush standard & error msg unit before MPI termination
2834      - if debugMode, flush IO unit after printing msg
2835    o pkg/ctrl:
2836      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
2837        to ctrl_set_unpack_xyz.
2838    
2839    checkpoint64 (2012/10/09)
2840    o pkg/shelfice
2841      - in mom_fluxform.F, mom_vecinv.F:
2842        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
2843        Bug fix KappaRU -> KappaRV
2844        does not change verification/isomip but may change other setups
2845        (presumably constant KappaRU=KappaRV)
2846      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
2847    o pkg/obcs:
2848      - fixed some indexing bugs in obcs_seaice_sponge.F
2849      - added obcs relaxation subroutines for HSALT and HSNOW
2850      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
2851    o pkg/seaice:
2852      - add "multicategory" parameterization for snow in analogy to ice,
2853        default is off for now.
2854    o pkg/obcs:
2855      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
2856        see verification/seaice_obcs/input.seaiceSponge for example application.
2857      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
2858        index setting by master-thread. This fix multi-threads Pb in previous modifs.
2859    o pkg/layers :
2860      - add diagnostics to pkg/layers
2861      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
2862        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
2863    o pkg/generic_advdiff/gad_implicit_r.F :
2864      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
2865    o pkg/seaice/seaice_growth.F:
2866      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
2867    o pkg/obcs:
2868      - change default setting of OBCS_UVICE_OLD from defined to undef;
2869      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
2870        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
2871      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
2872      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
2873        with Southern & Western OB at a tile edge (at least in a simple set-up).
2874    o pkg/obcs:
2875      - change settings of OB index in case OB coincides with tile edge (shared by
2876        2 tiles), so that common OB location is registered by both tiles (instead of
2877        only 1). However, for Southern and Western OB, index value = 0 is not
2878        recognized as valid OB index (=default null value) and needs to be fixed.
2879      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
2880      - new parameter "OB_indexNone" for null index value (for now, still zero)
2881        to replace hard-coded null index value of zero.
2882    o pkg/exch2:
2883      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
2884        always check buffer-size (but outside the loop); move checking for valid
2885        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
2886        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
2887    o pkg/ctrl (pack & unpack):
2888      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
2889        (locally defined) for different variables (+ remove the variable-specific
2890        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
2891        (to be extended to other local file names in ctrl.h).
2892    o pkg/flt:
2893      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
2894    o pkg/mdsio:
2895      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
2896    o tools/genmake2:
2897      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
2898        (added by Alistair in version 1.51 for building without make depend);
2899      - remove Header files list (H_SRC_FILES) from the dependence of targets
2900         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
2901        place in version 1.23): this save going through staf when unrelated header
2902        file has been modified.
2903       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
2904        "make depend" step, still need to do "make links" before "make adtaf".
2905    o eesupp/src (+ few pkg src files) & genmake2:
2906      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
2907      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
2908      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
2909         upper/lower case ; account for space between "#" and undef/define)
2910    o pkg/flt (with exch2):
2911      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
2912      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
2913    
2914    checkpoint63s (2012/09/05)
2915    o pkg/ecco:
2916      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
2917      - add more relevant #ifdef ALLOW_SMOOTH ones.
2918      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
2919    o pkg/ctrl:
2920      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
2921        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
2922      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
2923        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
2924        ctrlSmoothCorrel3D (new).
2925        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
2926      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
2927      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
2928        controls when useAtmWind, and vice versa.
2929      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
2930      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
2931          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
2932      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
2933          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
2934      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
2935        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
2936    o pkg/smooth:
2937      - remove un-necessary includes.
2938      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
2939        Those CPP options were never defined, and not necessary.
2940    o model/src:
2941      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
2942      - standard treatment of useSMOOTH.
2943    o pkg/autodiff:
2944      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
2945        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
2946    o pkg/exch2:
2947      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
2948        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
2949      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
2950        and tiles to process mapping.
2951      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
2952        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
2953        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
2954        from w2_eeboot.F to w2_readparms.F.
2955    o eesupp/src:
2956      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
2957        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
2958        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
2959      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
2960        is defined (remove condition on usingMPI) to match cases where MPI_INIT
2961        has been called.
2962      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
2963      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
2964        (so that on 1 proc, get same myPid independently of usingMPI)
2965      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
2966        useCubedSphereExchange with EXCH-1 (safer).
2967      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
2968    o pkg/ggl90:
2969      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
2970        used in ALLOW_GGL90_SMOOTH code.
2971    o pkg/flt:
2972      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
2973        floats at the Southern end of the domain).
2974    o eesupp/inc:
2975      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
2976        but not used (and not to be used) anywhere, just for documentation.
2977    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
2978      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
2979        a) can damage previously written records in any other multi-record files.
2980        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
2981    o tools/genmake2:
2982      - define variable MAKE within Makefile and use it in place of 'make';
2983      - update AD_CONFIG.h (if needed) before building any of the executable
2984        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
2985        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
2986      - always print usual warning comment 'this file is automatically generated'
2987        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
2988    o pkg/cheapaml:
2989      - updated to correspond to the code used in accepted paper (Nico Wienders).
2990    o pkg/exf:
2991        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
2992        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
2993        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
2994    o pkg/exf, autodiff, ctrl, ecco and seaice:
2995        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
2996    o pkg/ctrl, ecco:
2997        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
2998        Depending on useAtmWind, one is inactive, and the other is active (see
2999        exf_getffields.F/exf_getsurfacefluxes.F).
3000    o tools/genmake2:
3001      - improve error msg when failing in 2nd test of check_for_broken_Ff
3002      - fix option '-makefile' short-name (-mf according to genmake2 -help)
3003      - source local config file "genmake_local" just after processing the genmake2
3004        command arguments (previously done before processing arg).
3005    o pkg/grdchk:
3006      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
3007        to this routine from cost_final has been dropped in g_cost_final)
3008      - improve printed information (more explicit msg, no longer using "print *,"
3009         fix fcpertminus printed value).
3010    o model/src:
3011      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
3012        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
3013        this prevents getting cost-funct reset in adinitialise_varia recomputations.
3014    o pkg/dic:
3015      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
3016        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
3017    o pkg/grdchk:
3018      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
3019      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
3020    o pkg/autodiff/ctrl/grdchk :
3021      - attempt to sort out what works and what does not,
3022        with regard to I/O, and to warn/stop accordingly.
3023    o pkg/grdchk:
3024      - attempt to fix grdchk in the case of useSingleCpuIO.
3025      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
3026       statements were moved from grdchk_main.F and into
3027       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
3028      - a global sum is applied to record numbers icvrec/layer
3029       out of grdchk_loc so that they be passed to I/O routines.
3030    o pkg/smooth:
3031      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
3032        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
3033    o verification/testreport:
3034      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
3035      - can also use compressed (gzip) reference output file;
3036      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
3037        to be easier to collect by testreport.
3038      - update existing TLM output (half out-of-date by more than 3 yrs).
3039      - report NETCDF & LAPACK settings (from genmake2) in output dir.
3040      - report run-time in each individual summary (previously only for AD test);
3041        for TLM test, add also TAF version.
3042      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
3043    
3044    checkpoint63r (2012/08/15)
3045    o tools/genmake2:
3046      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
3047    o pkg/ecco/ecco_cost_final.F :
3048      - fix fc print statements (to stdout and costfunction0000) so
3049        that the printed value is always after the global sum.
3050    o pkg/seaice/seaice_dynsolver.F :
3051      - fix ice strength assymptote at SEAICE_area_max<1
3052        (no change for the standard case of SEAICE_area_max=1)
3053    o some cleaning:
3054      - pkg source files: ensure that all *.F files from each pkg included the
3055        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
3056        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
3057        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
3058        includes;
3059      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
3060      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
3061        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
3062        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
3063      - update option-file CPP_OPTIONS.h of all AD experiments:
3064        * no longer include PACKAGES_CONFIG.h ;
3065        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
3066        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
3067          including ECCO_CPPOPTIONS.h).
3068    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
3069      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
3070        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
3071        not necessary accurate).
3072      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
3073        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
3074        deliberately break compilation (a remainder that it needs to be customized)
3075      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
3076      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
3077      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
3078    o tools/genamke2:
3079      - check for lapack.
3080    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
3081      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
3082        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
3083        from both packages.
3084      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
3085      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
3086      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
3087        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
3088    o pkg/cost : add comments to explain special and/or untested setups.
3089    o pkg/exf:
3090      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
3091        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
3092    o verification/*/code_ad:
3093      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
3094      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
3095      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
3096        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
3097    o pkg/seaice :
3098      - added possibility to change ice strength/PRESS0 relationship to
3099        HEFF, according to the following run time parameters
3100        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
3101        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
3102        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
3103    o pkg/ggl90 :
3104      - added run time flag mxlSurfFlag to include the code that ensure
3105        mixing between first and second level (previously included as a comment)
3106    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
3107      - add test of newly added dumpAdByRec=T option where
3108        we write all records to one file per variable.
3109    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
3110      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
3111        to check that this code is ok with taf and compiles in adjoint.
3112    o pkg/autodiff :
3113      - added run time param dumpAdByRec : ad dump format switch.
3114        If true then write all records to one file per variable.
3115        Else write one file per record (remains the default).
3116      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
3117    o pkg/seaice:
3118     - Added SEAICEuseTILT run time switch : if set to
3119       false then omit the tilt term in seaice dynamics.
3120     - Fix free drift calculation.
3121    o pkg/shelfice:
3122      When initializing SHELFICEDragQuadratic, set default to be
3123      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
3124      but retain option to set it independently
3125      (inconsistenty spotted by Veronique Dansereau)
3126    o eesupp/inc:
3127      - in EEPARAMS.h, add real-type constant for some frequently used simple number
3128         (0,1,2,1/2), with name explicitly referring to RS/RL type.
3129    o model/src:
3130      - move balancing of relaxation terms to new S/R balance_relax.F.
3131    o pkg/autodiff:
3132      re-write active I/O high-level (control) S/R:
3133      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
3134      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
3135      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
3136        MDS_READ/WRITE_FIELD); change loops to multi-threads.
3137      - update and merge active_file_control_slice.flow into active_file_control.flow
3138      - update the calls in lower level S/R (active_file.F, active_file_g.F and
3139        active_file_ad.F) keeping the argument list and function unchanged.
3140      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
3141        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
3142      - new low-level active I/O routines, one for each type (RL/RS), for active var
3143        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
3144        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
3145        right type.
3146    o autodiff and RS=real*4:
3147      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
3148        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
3149      - change argument type of 3-D mask argument to _RS to match type in the call
3150        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
3151    o pkg/thsice:
3152      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
3153      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
3154        fresh-water flux: uniform correction or proportional to local precip.
3155    o pkg/ctrl:
3156      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
3157      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
3158                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
3159      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
3160    
3161    checkpoint63q (2012/07/30)
3162    o pkg/autodiff:
3163      note about monitor and snap-shot of ad-variables:
3164      a) need to apply ADEXCH before monitor or output of ad-vars to include
3165       overlap contributions (was done for adjDump but missing for monitor).
3166      b) since ADEXCH implies adding overlap values to interior array, machine
3167       truncation error is expected when adding an ADEXCH call in the middle of
3168       the time-stepping (although mathematically identical).
3169      modifs:
3170      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
3171        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
3172      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
3173        apply ADEXCH before monitor or snap-shot of ad-variables:
3174           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
3175      - implement new method (copy+adexch) for snap-shot and monitor of main model
3176        ad-vars (initially not used by default -> output unchanged).
3177      - change default (set to 2) to use new method and update few output_adm.txt
3178        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
3179        and both tutorial_tracer_adjsens tests).
3180      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
3181        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
3182    o pkg/ctrl:
3183      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
3184      generic control variables via
3185      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
3186      Only required customization should be S/R ctrl_map_ini_genarr.F
3187      (routine in repository contains example)
3188    o pkg/exf:
3189      - fix and refine checking of surface-relaxation setting when using EXF
3190    o verification (adjoint exp):
3191      - reduce length of simulation by half for experiment global_ocean.cs32x15
3192        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
3193    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
3194      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
3195        of KE that can occur with aggressive optimization
3196      + put quadratic bottom drag calculation in separated loops (only done if
3197        using bottomDragQuadratic)
3198    o model/src: CG2D_NSA
3199      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
3200         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
3201      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
3202         change cg2d residual target to be expressed in Wunits (=> do not normalise
3203         RHS ; this fix global_max Pb with TAF); update output.
3204    o verification/tutorial_tracer_adjsens:
3205       improve parameter consistency (and get rid of warnings):
3206       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
3207       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
3208       - use staggerTimeStep (for stability) in som81; use default rotation period.
3209    o pkg/exch2:
3210      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
3211        reset to 0 = 1 long line in X)
3212    o pkg/mdsio:
3213      - fix reading of dimensions from meta file for large-size domain
3214    o model/src:
3215      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
3216      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
3217        Cubed-Sphere Exch with CS-corners inside the domain;
3218        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
3219        globalArea and to set hasWetCSCorners.
3220      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
3221        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
3222      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
3223        useCDscheme and useCubedSphereExchange).
3224    o pkg/seaice/seaice_growth.F :
3225      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
3226        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
3227        when the previous code was not correct.
3228      - in all cases diagnoze the boundary condition mismatch to SIaaflux
3229      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
3230        that term to QNET (essentially to set the melt/freeze water to 0degC).
3231        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
3232    o verification/global_ocean.cs32x15/input.seaice :
3233      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
3234      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
3235      - update results (output.seaice.txt) accordingly.
3236    o verification/lab_sea/input/data.seaice :
3237      - remove SEAICEheatConsFix, which is now be tested
3238        in global_ocean.cs32x15. The presently coded fix
3239        is only consistent with real fresh water + nlfs.
3240      - update results (output.txt) accordingly.
3241    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
3242    o AD_CONFIG.h file:
3243      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
3244      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
3245        add it explicitly in each fortran src file where it is needed.
3246        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
3247        thus introducing potentially wrong dependency; therefore, better to include
3248        it only where it's really needed, and after any other included OPTIONS file
3249        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
3250        or ALLOW_TANGENTLINEAR_RUN).
3251    
3252    checkpoint63p (2012/07/06)
3253    o pkg/autodiff:
3254      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
3255      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
3256        which are now read from new parameter file "data.autodiff" (inAdExact
3257        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
3258      - add file "data.autodiff" in all verification/*/input_ad/ directories.
3259      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
3260        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
3261    o verification/tutorial_tracer_adjsens/
3262      - add extra sub-verification which uses "SOM" advection scheme
3263        (2nd Order-Moment Advection Scheme, Prather Limiter) with
3264          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
3265        and in data:
3266          multiDimAdvection=.TRUE.,
3267          tempAdvScheme=81,
3268          saltAdvScheme=81,
3269    o model/src:
3270      - introduce ALLOW_BALANCE_RELAX which allow the removal
3271       of the global mean of relaxation terms by setting
3272       balanceThetaClimRelax and balanceSaltClimRelax
3273      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
3274       This case is now treated appropriately in seaice_growth.F
3275    o pkg/seaice:
3276      - do balanceEmPmR and balanceQnet based on the net fluxes
3277        (SItflux) that enter the ocean+ice system rather than QNET
3278        and EMPMR. Works best in real fresh water.
3279      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
3280        out of the diagnotics bloc, and stored in global arrays.
3281    
3282    checkpoint63o (2012/06/29)
3283    o vertical mixing schemes:
3284      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
3285      - replace computation of density (in Function STATE1, opps_calc.F) by a call
3286        to S/R FIND_RHO_SCALAR
3287      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
3288        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
3289        affects output (vermix.ggl90) at truncation level.
3290    o testreport:
3291      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
3292        (nSx,nSy) for the number of threads (from eedata.mth)
3293    o model/src:
3294      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
3295        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
3296    o verification/tutorial_tracer_adjsens/
3297      - compile with ALLOW_CG2D_NSA
3298      - run with nonlinFreeSurf=3
3299      - update reference output_adm.txt
3300    o tools/genmake2:
3301      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
3302        refine usePROFILES switching off (only when NetCDF is not available).
3303    o verification (atmospheric set-up):
3304      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
3305    o pkg/profiles : refine profiles and files handling.
3306    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
3307    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
3308      - changes to use model/src/the_main_loop.F rather than the ecco version
3309        in ecco type adjoint runs.
3310    o model/src:
3311      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
3312      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
3313      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
3314    o model/src:
3315      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
3316        update output of test experiment bottom_ctrl_5x5.
3317    o pkg/generic_advdiff:
3318      - implement vertical bi-harmonic diffusion (for now, only for T & S and
3319        only explicitly).
3320    o verification/bottom_ctrl_5x5/
3321      update reference output (results changed quite some time ago,
3322      not sure when; but new reference results look ok in terms of grdchk)
3323    o verification/1D_ocean_ice_column/
3324      For verification purposes, the exact adjoint rather than an approx.
3325      should be used (e.g., to comare against F.D. or TLM).
3326      removed autodiff_inadmode*_ad.F routines in code_ad/
3327      Update results/ accordingly.
3328    o pkg/cal:
3329      - change cal_getdate.F so that output date is function of input time only
3330        (less ambiguous, not mixed up with input iteration number).
3331      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
3332    o pkg/diagnostics:
3333      - implement calendarDumps also for stats-diags
3334      - implement calendarDumps also for snap-shot output (negative freq)
3335      - for now, ignores calendarDumps if non-zero phase-lag.
3336    
3337    checkpoint63n (2012/06/04)
3338    o model/src:
3339      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
3340        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
3341      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
3342        similar to calc_r_star.F); update results of experiment internal_wave and
3343        tutorial_global_oce_in_p (affected @ truncation level).
3344    o pkg/shelfice:
3345      - add parameterisation of advective-diffusive flux into the ice shelf
3346        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
3347      - simply eps3/3a computation
3348    o eesupp:
3349     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
3350       between tiles, just fill-in edges assuming locally periodic subdomain) and
3351       add corresponding exchange subroutines (EXCH0);
3352     - new CG-solver version (_EX0) for disconnected-tiles special case.
3353    o model/src (CG-solvers):
3354     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
3355       (similar final residual output and max-Iter number as with standard version);
3356     - allows to store and use lowest-residual solution (standard & _SR versions);
3357     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
3358     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
3359    o eesup/src:
3360     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
3361       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
3362    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
3363    
3364    checkpoint63m (2012/04/27)
3365    o pkg/shelfice:
3366     - account for partical cells in surface level below ice-shelf for hydrostatic
3367       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
3368    o ad test experiments:
3369     - update and rename to "ad_optfile.local" local AD-optfile specific to a
3370       particular adjoint verification experiment (in verification/*/code_ad/)
3371    o pkg/seaice & pkg/exf:
3372     - Part two of ECCO-CLIVAR code merges.
3373       Completes merge of seaice area relax. code.
3374       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
3375       to be set in EXF_OPTIONS.h since this pkg controls its I/O
3376       (and avoids second CPP option in SEAICE_OPTIONS.h)
3377     - change default value of costIceStart & costIceEnd to a valid date.
3378     - add snowPrecip to HSNOW in seaice_growth
3379    o pkg/ptracers:
3380     - move ptracers summary and setup check into separated S/R ; add a check for
3381       valid PTRACERS_Iter0 value (error+stop or just warning).
3382    o pkg/cal (+ pkg/ecco):
3383     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
3384       as input; and for AD, unless both are not differentiable (e.g., k index)).
3385    o model/src:
3386     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
3387       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
3388       temporary set to usingZCoords value (to be changed to F when using shelfice).
3389     - hydrostatic pressure: implement partial cell near the surface also for
3390       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
3391       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
3392    o pkg/ctrl/ctrl_init.F:
3393     - add a formal parameter to s/r ctrl_init_rec to print
3394       xx_$(ctrl_valiable)_file for easier debugging
3395     - move call of cal_* routines into the if-block where they are really
3396       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
3397       to specify a startdate
3398    o pkg/seaice:
3399     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
3400       global_ocean.cs32x15/code versions).
3401     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
3402       verification experiment global_ocean.cs32x15.seaice and update results.
3403    o pkg/exf:
3404     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
3405       (according to useExfYearlyFields).
3406    o pkg/cal:
3407     - move calendar setting & summary (previously in cal_readparams.F) into new
3408       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
3409       length of the simulation is set (after SET_PARMS call); This is an attempt
3410       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
3411     - For safety: keep a record of pkg/cal parameter settings status
3412               to allow to STOP if one pkg/cal S/R is called too early.
3413     - add a stop in all basic pkg/cal subroutines if called before setting is done.
3414     - modify cal_getdate.F: stop when nothing was returned;
3415       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
3416       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
3417    
3418    checkpoint63l (2012/04/04)
3419    o pkg/bbl:
3420      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
3421        update global_with_exf output.yearly.txt file.
3422    o pkg/cal:
3423      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
3424      - remove 2 unsused and very short (1 line only) functions ;
3425      - remove unsused subroutines from AD-Diff list.
3426    o model/src:
3427      - start to implement clean wait to stop in initialization S/R (config_check.F,
3428         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
3429    o folowing PRINT_MESSAGE changes:
3430      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
3431    o pkg/bbl:
3432      - modification so it can work with z*
3433      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
3434      - global_with_exf/input.yearly verification; changes output.yearly.txt
3435    o eesupp/src:
3436      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
3437        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
3438      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
3439        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
3440      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
3441      - when using MPI, always set usingMPI=T ; set default accordingly and stop
3442        if not consistent.
3443      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
3444        argument is zero (in case called within single-thread section).
3445    o pkg/fizhi:
3446        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
3447        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
3448    o pkg/exch2:
3449      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
3450        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
3451      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
3452        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
3453        with bad ones coming from a not-yet-updated halo.
3454        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
3455    o pkg/frazil:
3456        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
3457        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
3458    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
3459    o verification/lab_sea
3460      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
3461      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
3462      * nTimeSteps 3 -> 4
3463      * changed reference output accordingly
3464    o pkg/ctrl:
3465      * fix ctrl_get_gen for xx_sst, xx_sss
3466    o pkg/fizhi:
3467      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
3468        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
3469      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
3470        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
3471        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
3472    o pkg/gmredi:
3473      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
3474    o pkg/fizhi:
3475      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
3476        (old)aces open64 tuv test.
3477    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
3478    o pkg/mom_vecinv:
3479      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
3480        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
3481        with non-lin free-surf).
3482    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
3483      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
3484      some compilers (gfortran 4.6.0 on MacOS)
3485    o momentum:
3486      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
3487        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
3488        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
3489    
3490    checkpoint63k (2012/03/17)
3491    o model/src:
3492       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
3493         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
3494       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
3495         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
3496    o model/src: solve_*diagonal.F
3497       - replace division with multiplication by inverse (similar to original version)
3498         update output of AD exp. global_ocean.90x40x15.
3499       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
3500         to enable the use of the vectorized & differentiable solve_tridiagonal.F
3501       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
3502         vertical advection (to get solve_tridiagonal tested in AD mode).
3503    o pkg/seaice: ECCO-CLIVAR merge:
3504      1. seaice AREA relaxation
3505         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
3506         * runtime flag: SEAICE_tauAreaObsRelax
3507      2. modified global mean cost imbalance code: CPP option
3508          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
3509    o another iteration on solve_*diagonal.F
3510       Make choices independent of AUTODIFF
3511       Default will be the adjoinable vectorized version.
3512       Alternative choices are:
3513       * non-adjoinable original version with low memory footprint:
3514         #define SOLVE_DIAGONAL_LOWMEMORY
3515       * still adjoinable but does not vectorize (k as inner-most loop):
3516         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
3517    o testreport
3518     - add option to use a home made wrapper around "make"
3519     - remove MITGCM_IEEE env. variable (no longer active)
3520    o pkg/shelfice
3521     - improve computation of friction velocity for velocity dependent
3522       exchange coefficients: include velocities into SHELFICEBoundaryLayer
3523       block to average velocities vertically
3524     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
3525    o Modify diagonal solvers, now three versions (upon request):
3526      #ifndef SOLVE_DIAGONAL_AUTODIFF
3527        1. default version (dating back a while ago)
3528      #else /* def SOLVE_DIAGONAL_AUTODIFF */
3529      # ifdef SOLVE_DIAGONAL_KINNER
3530        2. adjoinable version with k-innermost loop (G. Forget)
3531      # else
3532        3. adjoinable vectorized version of 2.
3533      # endif
3534      #endif /* SOLVE_DIAGONAL_AUTODIFF */
3535      All flags are currently set within routines, but could/should be moved to CPP-options.
3536      Array bounds for 1. are as before, for 2.,3. cover the entire domain
3537      (could be changed for 1. too).
3538    o verification/lab_sea (fwd):
3539      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
3540        use 7 categories (except hb87), new solve4temp params (except salt_plume),
3541        constant salinity (=4) or variable salinity (salt_plume) done through
3542        SItracer.
3543    o pkg/seaice:
3544      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
3545      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
3546         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
3547        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
3548        SEAICE_freeze got retired) but already better than previously with
3549        SEAICE_freeze=123456.7 deg.C;
3550      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
3551        (safer multi-threaded setting); always set SEAICEuseEVP;
3552      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
3553        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
3554        stop if multiple specifications for the same coeff; make sure default
3555        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
3556    o pkg/obcs:
3557      - allow to switch to upwind 1rst order advection scheme for the advective
3558        flux computation at the open-boundary; disabled for adjoint built.
3559    o pkg/ptracers:
3560      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
3561      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
3562      - add parameter to decide when to start a tracer; use internal flag to
3563        know which tracer to step-forward; switch this internal flag at the top
3564        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
3565        for adjoint built.
3566    o pkg/seaice:
3567      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
3568      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
3569      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
3570    o pkg/ecco:
3571      - fix writing of output file DiagnosCost_ClimSalt/Theta
3572        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
3573    o pkg/seaice:
3574      - add missing initialisation of COR_ICE array in dynsolver.F
3575      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
3576        compiled either way, and is tested in all exps (multidim was only tested
3577        in lab_sea ad before).
3578      - cosmetic change to prepare for future addition of ITD. no change to results.
3579        no defaults change.
3580      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
3581      - by lack of adequate verification experiments, I further used custom versions
3582        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
3583        should be correct.
3584      - avoid recomputations in ad.
3585    o array initialisation in adjoint mode:
3586      1) pkg/mom_common/mom_calc_ke.F:
3587        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
3588        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
3589        part this initialisation is gone, resulting in Floating Point Exception
3590        (caught by open64 compiler with debug option).
3591      2) model/src/convective_weights.F
3592        set output convectCount over the full array range (instead of doing
3593        an update): this fix a similar issue when called within recomputation (adjoint)
3594        which could by-pass the initialisation (normally done in the caller S/R).
3595    o pkg/seaice:
3596      - final version of turbulent flux params, as agreed at MIT ice meet:
3597           SEAICE_mcPheePiston (default is ~ 0.000875)
3598           SEAICE_mcPheeTaper (default is 0.)
3599           SEAICE_frazilFrac (defualt is 1.)
3600           SEAICE_mcPheeStepFunc (default is false)
3601      - changes results at trunction error level
3602      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
3603    o added pkg/frazil:
3604      - see frazil_description.tex for details
3605      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
3606    o pkg/shelfice/shelfice_thermodynamics.F
3607      - fix exponents for velocity dependent exchange coefficients: change
3608        from 2/3(=0) to 0.66666666666666667
3609      - move computation of velocity dependent exchange coefficients into
3610        separate loop, so that it applies to both thermodynamics
3611      - move some divisions by constants out of loops
3612    
3613    checkpoint63j (2012/02/16)
3614    o pkg/seaice:
3615      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
3616      - SItracer:  added run time params, and allow coupling to ocn salinity.
3617    o pkg/seaice: remove (almost) all divisions by constants within loops
3618      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
3619      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
3620      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
3621      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
3622    o pkg/seaice :
3623      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
3624        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
3625      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
3626      - add permanent SItflux diag that corresponds to TFLUX but includes
3627        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
3628      - allow activation/testing of a fix for suspected missing term in
3629        ocn-ice heat budget (to be confirmed). To test this, you want to
3630        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
3631        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
3632      - no change in results, fwd or ad.
3633    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
3634      - switch to variable freezing point.
3635           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
3636      - bug fix : the sublimation term that was missing is now activated.
3637           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
3638      - bug fix : flooding sign term for SIsal0.NE.0.
3639           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
3640    o pkg/seaice:
3641      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
3642        is now the default, and the old default constant freezing point is recovered
3643        with SEAICE_tempFrz0    = -1.96,
3644             SEAICE_dTempFrz_dS = 0.,
3645      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
3646      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
3647      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
3648        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
3649      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
3650        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
3651      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
3652        seaice_growth r149 for legacy branch (no results change).
3653      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
3654        from I. Fenty).
3655      - results did not change except for global_ocean.cs32x15, mostly due to the
3656        switch to variable freezing point (see above item for detail).
3657    o pkg/thsice:
3658      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
3659        seawater freezing in thsice_calc_thickn (not used).
3660    o pkg/seaice: turbulent flux term specification via run time params.
3661      - replace CPP switches with run time switches to facilitate testing
3662      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
3663                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
3664      - added runtime parameter : SEAICEturbFluxFormula
3665      - move Mcphee constants to SEAICE_PARAMS.h
3666      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
3667                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
3668                 remove seaice_summary call (moved to seaice_init_fixed)
3669      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
3670        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
3671      - seaice_summary.F : add missing report of read turbulent flux term set up
3672                           and SITRACER.
3673      - seaice_check.F : check range; inform and stop if retired CPPs are used
3674                         (incl. SEAICE_AGE).
3675      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
3676             CPP switch, same computation as before for the different options.
3677      - change results at the truncation level.
3678    o pkg/seaice:
3679      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
3680        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
3681        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
3682      - update verification/*/input*/data.seaice:
3683        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
3684        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
3685        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
3686        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
3687    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
3688      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
3689        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
3690        difference in results only due to machine truncation.
3691      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
3692        MaykutPolySatVap; keep MIN_LWDOWN.
3693      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
3694      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
3695        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
3696    o pkg/salt_plume:
3697      - isolate saltPlumeFlux array exch into a specific S/R called from
3698        do_oceanic_phys.F
3699      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
3700    o verification:
3701      - move untested set-up to MITgcm_contrib/verification_other.
3702    o pkg/seaice:
3703      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
3704    o pkg/seaice:
3705      - seaice_solve4temp.F (keeping results unchanged):
3706        * add 2 future run-time params to select which saturation vapor pressure
3707          formula is used and how post-iteration fluxes are set.
3708          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
3709        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
3710          the linearized expression to stay consistent with tsurf finding.
3711      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
3712        can be < 0.
3713    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
3714      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
3715        conductive heat flux F_c , and add it explicitly when updating tsurf as
3716        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
3717        so that now F_ia has a consistent meaning through the entire routine.
3718        This causes differences at truncation level: update output of fwd exp.
3719        global_ocean.cs32x15.seaice.
3720    o pkg/seaice:
3721      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
3722        of arrays, sign/direction of fluxes; no effect on results.
3723      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
3724        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
3725        note: this should have been done before changing celsius2K default.
3726      - to keep results unchanged, add back old value of celsius2K in verification
3727        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
3728      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
3729        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
3730        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
3731        freezing temp is consistent with value in seaice_growth.F ; this causes
3732        differences at machine truncation level: update lab_sea AD output (3/4).
3733    o pkg/seaice:
3734      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
3735        and climsst/sss even when using seaice (to prevent calculation that might
3736        use SST on land); does not affect any verification exp.
3737      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
3738        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
3739    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
3740      over land (non-legacy code)
3741    o vectorize salt_plume package:
3742      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
3743      - this code computes plumebk everywhere (also over land), thus requires
3744        code to avoid divisions by zero and catch the case of kLev=Nr.
3745      - efficiency of salt_plume_frac is still sub-optimal
3746    o tools (genmake2):
3747      - fix makefile NAME specification (option: -makefile NAME) by adding
3748        "-f $MAKEFILE" in few places where it was missing including makedepend
3749        command (contribution from Paul).
3750    
3751    checkpoint63i (2012/01/24)
3752    o model/src:
3753      - add factorized versions of some EOS code to find_rho.F,
3754        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
3755    o model/src:
3756      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
3757      - change default celsius2K from 273.16 to 273.15
3758      - to keep results unchanged, add back old value of celsius2K in verification
3759        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
3760         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
3761    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
3762      to make TAF generate vectorizable code
3763    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
3764       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
3765       have flags that do this more efficiently.
3766    o pkg/diagnostics/diagstats_calc.F
3767      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
3768    o pkg/obcs (with exch2):
3769      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
3770        and remove code (in obcs_readparms.F) which was based on EXCH of indices
3771        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
3772    o pkg/exf and seaice exp:
3773      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
3774        so that switching off area & heff advection flags does not affect results.
3775      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
3776      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
3777        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
3778        results of verification experiments: 1D_ocean_ice_column(fwd),
3779        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
3780        and offline_exf_seaice (all 4).
3781    o pkg/seaice:
3782      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
3783        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
3784      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
3785        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
3786        not multi-dim advection;
3787      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
3788        SHORTWAVE_HEATING #undef.
3789    o optim: make Makefile more robust (?)
3790    o pkg/obcs:
3791      * fix treatment of obcs_read_pickup for TAF
3792    o pkg/shelfice:
3793      * add missing initialisation of num_shifwflx
3794      * new adjoint verification exp. for isomip
3795      * change Prandtl and Schmidt numbers from generic formulations
3796        (in terms of model diffus. and visc.) to separate runtime
3797        parameters, with Holland and Jenkins (1999) default values.
3798    o pkg/exf (interpolation):
3799      - extended input field (2 rows) near the N & S poles:
3800        * fill in with the symetric value (when even Nb of data in longitude)
3801        * add average value at the poles only for scalar quantities ; for vector
3802          component interpolation, skip the averaging and keep duplicated values,
3803          unless the 2 components have same location (uvInterp=T) in which case
3804          interpolate the 2 components together using S/R EXF_INTERP_UV.
3805      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
3806        together: this allows to account properly for local orientation when
3807        averaging at N & S pole.
3808      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
3809        exf-interpolation near N & S poles. Undef by default.
3810      - add debug check/print on 1rst iter if debugLevel >=2.
3811    o pkg/exf:
3812      - change masking flags definition (no longer "parameter"), put them in
3813        common block and set them in S/R EXF_INIT_FIXED.
3814      - change recognized masking flag from s,u,v to c,w,s since the mask
3815        to use (maskC,W,S) depends on position on model grid and has little to
3816        do with scalar/vector difference; fix masking if using P-coordinates.
3817      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
3818        and update results of exp. global_with_exf (x2).
3819      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
3820    o pkg/obcs
3821      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
3822    o pkg/exf (interpolation):
3823      - assume periodicity in X only if input field cover full longitude range.
3824      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
3825        and should vectorise).
3826      - fix input lat of the 2 added row (in case we provide N.pole data).
3827    
3828    checkpoint63h (2011/12/30)
3829    o pkg/seaice:
3830      - change declaration of UVM from _RL to _RS in order to get B-grid
3831        uIce,vIce monitor when _RS = real*4
3832    o pkg/offline:
3833      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
3834      - compute vertical velocity if not read from file (switch on exactConserv
3835        & staggerTimeStep);
3836      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
3837    o verification:
3838      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
3839        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
3840        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
3841      - update output of exp. global_ocean.cs32x15.viscA4 after changing
3842        grid-file angles (used here for coriolis-3d);
3843      - remove (or gzip) few files not needed to run fizhi-cs experiments.
3844    o pkg/exf (vector interpolation):
3845      - rotate vector component toward local grid-axis orientation using grid-angles
3846        (stored in GRID.h) instead of locally computed rotation angle; keep old code
3847        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
3848    o pkg/seaice:
3849      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
3850        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
3851    o pkg/PKG_OPTIONS.h files:
3852      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
3853        outside of the #ifdef ALLOW_THISPKG / #endif block.
3854      - update verification/*/code/PKG_OPTIONS.h files.
3855    o add a verification experiment (offline_exf_seaice/input.seaice) that test
3856      the B-grid LSOR solver
3857    o pkg/seaice: sort out emissivity and long wave radiation step 2:
3858      - add emissivity for snow and ice as new run-time parameters
3859        (unfortunately) that default to the corresponding exf values; this
3860        changes results in most verification experiments so that for backward
3861        compatibility these parameter have to be set explicitly to inconsistent
3862        values (ugly);
3863      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
3864        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
3865        until we agree how to handle this bug properly
3866    o pkg/exf (interpolation):
3867      - add a set of run-time param ({inputfield}_interpMethod), one for
3868        each interpolated input field, to select the interpolation method
3869        with a value of zero switching off the interpolation;
3870      - print interpolation parameters to standard output;
3871      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
3872        (to use instead runoff_interpMethod=0 in data.exf).
3873      - simplify default setting of interpolation parameters (for all fields,
3874        set position to match model grid cell-center position, leading to trivial
3875        interpolation in case of regular Lat-Lon grid) and fix for the case of
3876        non-uniform delY.
3877    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
3878       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
3879       this factor is absolutely required, because the lw exitance (= out-going
3880       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
3881       where the reflectivity rho = 1-emissivity for conservation reasons. Once
3882       this is established, we can remove the CPP-Flag (if we want to).
3883    o pkg/seaice:
3884      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
3885        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
3886      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
3887        what the name implies (and not emissivity*BoltzmannConstant), this means
3888        the old default value of 5.5e-8 now means
3889        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
3890        S/R exf_readparms
3891      - FV-discretization of the B-grid LSOR solver, turn on with
3892        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
3893        of the calling routine dynsolver, so that B and C-grid code look a
3894        little more alike.
3895      - fix index bugs in ostres.F (B-grid code)
3896    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
3897    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
3898      default for SEAICE_emissivity, if useEXF; requires setting a wrong
3899      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
3900      backward compatiblity
3901    o model/src: use sigmaR in calc_ivdc
3902    
3903    checkpoint63g (2011/12/16)
3904    o pkg/seaice/seaice_growth.F:
3905      fix heat conservation of the coupled ocean-seaice system.
3906      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
3907      solid vs liquid water treatment is resolved via QNET.
3908    o pkg/seaice/seaice_growth.F:
3909      add missing term for sublimation in saltFlux, which was breaking conservation.
3910    o pkg/seaice/seaice_model.F:
3911      Remove this patholigical case treatment in evolution branch,
3912      where it is un-necessary and breaks conservation.
3913      Update global_ocean.cs32x15/results accordingly for
3914      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
3915    o model/src:
3916      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
3917      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
3918    o pkg/obcs:
3919      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
3920      tendency for temperature and salinity that is then applied to update
3921      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
3922      horizontal advection and diffusion contributions on the boundary (in
3923      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
3924      removing the mask in S/R timestep_tracer. The advantage of this approach is
3925      that the updated tracer values include contributions from the surface
3926      forcing and vertical diffusion.
3927      This modification changes exp4.stevens because of vertical diffusion.
3928    o model/src:
3929      change non-curvilinear grid setting to also work with exch2 + blank tiles:
3930      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
3931        face dimensions.
3932      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
3933        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
3934        and INI_SPHERICAL_POLAR_GRID.
3935      change test-experiment global_ocean.90x40x15:
3936      - split the domain in many more tiles (9x4 tiles of 10x10 each);
3937      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
3938      - update results of both test (std & dwnslp).
3939    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
3940       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
3941    o model/src:
3942      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
3943        and fix initialisation when using sigma-coords.
3944    o model/src:
3945     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
3946       to their current value at the beginning of forward_step.F": add a new run-time
3947       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
3948     - set doResetHFactors=T in the following test exp:
3949        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
3950        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
3951        and tutorial_global_oce_in_p (nonLinFS in p)
3952    o pkg/ecco
3953      - added IES cost term
3954    o verification/advect_xz
3955      - scale down the depth by 1/100 (from 200 km to just 2.km)
3956      - add secondary test using divergent flow, r-star and implicit vertical advection.
3957      - add note (check_conserve_TS.txt) and matlab script to check global
3958        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
3959    o pkg/rbcs:
3960      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
3961    o pkg/obcs (Stevens BCs):
3962      - fix various problems in the phase speed computations of the Stevens
3963        boundary conditions:
3964        - sign error for western and southern boundaries,
3965        - time tendencies were underestimated by factor of dTracerLev and some just
3966          zero (for multidim advection schemes) -> now estimate time tendencies
3967          from difference between previous (n) time level and the one before (n-1);
3968          this requires storing a field per tracer per boundary, also in the pickup
3969          files.
3970        - replace deltaTmom in cflMer/Zon computation with dTracerLev
3971        - set default phase velocity to cflMer/Zon
3972      - update verification experiment exp4.stevens
3973    o pkg/generic_advdiff (implicit_r):
3974      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
3975        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
3976      - fix implicit vertical diffusion or advection with NonLin FreeSurf
3977        (was using current recip_hFacC instead of future recip_hFacC): set future
3978        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
3979        solver S/R ;
3980      - fill diagnostics of vertical advective fluxes (computed from tendency)
3981        when using implicit vert. advection;
3982      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
3983         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
3984         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
3985         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
3986    o pkg/diagnostics:
3987      - add diags for T & S tendency which goes through Adams-Bashforth.
3988    
3989    checkpoint63f (2011/11/30)
3990    o pkg/obcs/obcs_calc_stevens.F:
3991      - join some loops to reduce number of if-statements
3992      - fix a bug in code for northern and southern boundaries.
3993    o pkg/seaice/seaice_init_varia.F
3994      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
3995        caused zero ice-velocities for the B-grid code
3996    o pkg/seaice/seaice_init_fixed.F
3997      - fix a bug in the initialisation of the second metric terms
3998        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
3999      - this affects all seaice configurations with useCurviLinearGrid = .true.
4000        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
4001        = .true. (default)
4002      - the only verification experiment affected is global_ocean.cs32x15:
4003        icedyn, seaice, and seaice_dynmix (AD)
4004    o pkg/thsice/thsice_diagnostics_state.F
4005      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
4006        not contain garbage that can lead to surprises in diagstats_calc.F
4007    o model/src:
4008      - move bi,bj loops inside INTEGR_CONTINUITY ;
4009      - call INTEGR_CONTINUITY directly from forward_step.F
4010        (previously called from momentum_correction_step.F)
4011      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
4012        forward_step.F and pkg/ecco/the_main_loop.F
4013    o model/src/do_oceanic_phys.F:
4014      - reset addMass to zero only if useICEFRONT ;
4015      - separated k-loop for rhoInSitu calculation ;
4016      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
4017        and at constant T,S (= WdRHOdP);
4018      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
4019        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
4020        transport of locally-referenced potential density);
4021        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
4022    o gluemnc:
4023      - replace ncrcat with ncks when adding variables to *.glob.nc
4024      - change the way variables without record dimensions are handled so that
4025        files that have variables with and without record variables can be glued:
4026        add a record dimension with a new unique name to be able to differentiate
4027        between variable with and without a-prior record dimensions. Remove
4028        this record dimension before adding the variable to the *.glob.nc file.
4029        This procedure automatically works also for grid.*.nc files that do not
4030        have any record dimension.
4031    o verification/cpl_aim+ocn:
4032      - generate new reference output on baudelaire (gfortran, mpich2) (previously
4033        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
4034    o pkg/obcs/obcs_calc_stevens.F:
4035      - add code for northern and southern boundaries.
4036      - reorder some loops to save some operations and so that drFBar can be scalar
4037    o model/src:
4038      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
4039        truncation) and add diagnostics for Adams-Bashforth tendency increment.
4040      - update test-exp. AD output:
4041        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
4042      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
4043        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
4044        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
4045        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
4046        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
4047        tutorial_plume_on_slope.
4048    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
4049      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
4050      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
4051      does not even come with an F77 compiler anymore, this should not be
4052      a limitation
4053    
4054    checkpoint63e (2011/11/06)
4055    o pkg/seaice adjoint of LSR:
4056      - substantially rework STORE dirs.
4057      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
4058        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
4059        and only perform SOLV_MAX_FIXED adjoint iters.
4060        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
4061        always goes to same record, meaning that the last forward field will be
4062        the one used in the adjoint - an approximation.
4063      - now produces non-zero LSR-related gradients, and acceptable gradients for
4064        An's zonal (x-z) test case (to be checked in)
4065      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
4066        (but these are screwed up by the thermodynamics in the first place);
4067        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
4068        output_adm.txt also reflects changes to seaice_lsr
4069      - global_ocean.cs32x15:
4070        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
4071          (output_adm.seaice.txt was updated)
4072        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
4073          (output_adm.seaice_dynmix.txt)
4074    o test-exp. exp4+stevens:
4075      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
4076    o pkg/seaice (lsr solver):
4077      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
4078        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
4079      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
4080      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
4081        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
4082      - compute (with new S/R) and print initial (+ free-driff sol. if available)
4083        and final residual of linearised system.
4084    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
4085      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
4086    o pkg/obcs: Stevens BCs (still only for east and west)
4087      - fix Stevens BCs by using intermediate velocities of previous
4088        time step as "baroclinic" contribution rather velocity of one grid cell
4089        inside the boundaries; more consistent but makes the entire treatment
4090        more complicated, requires new pickup files and two new S/Rs:
4091        obcs_copy_uv_n and obcs_save_uv_n
4092        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
4093        (undefined by default)
4094      - silently move computation of some grid factors into separate loops to
4095        save some recomputations
4096      - add a hack for non-linear free surface
4097      - add a verification experiment to exp4 that tests this code
4098    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
4099    
4100    checkpoint63d (2011/10/25)
4101    o pkg/obcs + seaice-dynamics:
4102      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
4103        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
4104        values (consistent with an implicit method).
4105      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
4106        return to older implementation (same results as before); note that none of
4107        the "experimental" OBCS_SEAICE options are implemented in the new version.
4108      - switch test exp. seaice_obcs to use new version (update output).
4109    o pkg/seaice:
4110      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
4111      - add parenthesis in Water-Ice drag calculations (evp & lsr);
4112      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
4113        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
4114      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
4115        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
4116    o pkg/layers:
4117      - Include potential density as new coordinate (Thanks to David Munday)
4118    o pkg/dic:
4119      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
4120        carbonate computation/output to CALC_PCO2_APPROX
4121    o pkg/generic_advdiff
4122      - make TAF generate code that vectorizes:
4123        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
4124    o model/src:
4125      - improve vectorization also for adjoint code of
4126        solve_tridiagonal and solve_pentadiagonal. As this requires up to
4127        5 new 3D-fields, this code is only turned on for the combination of
4128        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
4129        for singular matrix check (only for TARGET_NEC_SX).
4130      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
4131        ALLOW_AUTODIFF. This flag now needs to be set outside of
4132        solve_tri/pentadiagonal.F
4133    o pkg/exf:
4134      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
4135        optional namelist EXF_NML_OBCS).
4136      - add many debug-print (to trace down where pkg/cal error msg comes from)
4137    o pkg/mom_vecinv/mom_vi_hdissip.F
4138      - rearrange loops so that vectorization is improved and in particular
4139        the adjoint routine vectorizes. The code is a little longer now, but I
4140        think easier to read.
4141        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
4142    o pkg/seaice:
4143      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
4144    o pkg/exch2:
4145      - alternative code (without tile x tile matrix) for cumulated (global) sum;
4146        used as default; keep using matrix version in adjustment.cs-32x32x1.
4147    o tools/build_options:
4148      - after merging some MPI and/or multi-threads specific optfiles so that
4149        the modified default optfile support both built (using genmake2 -mpi
4150        for the MPI built, using genmake2 -omp for OpenMP built),
4151        move now obsolete optfiles to tools/build_options/unsupported/
4152       (add copy of email sent to support list in doc/optfiles_changes.txt)
4153    
4154    checkpoint63c (2011/09/28)
4155    o pkg/ebm:
4156      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
4157        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
4158    o pkg/seaice (SItracer pickup)
4159    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
4160      To be done:
4161      - thorough testing of missing fields in S/R seaice_read_pickup
4162      - thorough matching between generic tracers and specific fields used
4163        (e.g. volume-weighted age, area-weighted age, salinity, ...)
4164    o pkg/grdchk:
4165      - all procs calculate and print finite-difference gradient (for testreport)
4166      - change description output used by testreport;
4167      - AD testing: also compare and report Finite-difference gradient;
4168        => update all output_adm*.txt
4169    o test exp. global_ocean_ebm:
4170      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
4171        and turn on exactConserve; update (fwd) output.
4172    o pkg/seaice (LSR):
4173      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
4174      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
4175        * identical results with non-CS topology (but save up to half of EXCH calls)
4176        * no much changes in cs-32 verification tests since no ice at face edges
4177         (differences due to convergence criteria, since nb of iterations changed)
4178        * expect some differences on lat-lon-cap grid.
4179        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
4180    o pkg/exch2:
4181      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
4182        many tiles); until alternative coding is added, just add a stop.
4183    o pkg/kpp:
4184      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
4185        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
4186    o optfiles:
4187      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
4188        into corresponding standard one, which now support different build:
4189        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
4190      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
4191    o pkg/obcs (seaice):
4192      - add missing EXCH for uIce,vIce after applying OBCS;
4193      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
4194        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
4195        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
4196      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
4197      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
4198        and eedata.mth for MPI and mutlti-threaded testing.
4199    o pkg/flt:
4200      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
4201      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
4202      - fix pickup and trajectories + profiles output with multi-threads;
4203      - add parameter to select group of fields to write along trajectory and
4204        profile (default unchanged);
4205      - only call PORT_RAND* function when flt_noise <> 0;
4206      - add multi-threaded test for verification exp. flt_example.
4207    o eesupp/src:
4208      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
4209      - USE_OMP_THREADING: check that number of threads (from eedata) matches
4210        actual number (from env.var. setting).
4211    o pkg/ebm:
4212      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
4213      - add multi-threaded test for verification exp. global_ocean_ebm
4214    
4215    checkpoint63b (2011/08/29)
4216    o pkg/ebm:
4217      - fix sign of runoff;
4218      - update directly forcing fields (Qnet,EmPmR) to use standard
4219        external_forcing_surf.F (remove ebm_forcing_surf.F);
4220      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
4221      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
4222        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
4223      - update global_ocean_ebm parameters file data and update output (fwd+ad).
4224    o verification/matrix_example:
4225      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
4226        MPI and mutlti-threaded testing.
4227    o pkg/matrix:
4228      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
4229      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
4230      - fix for multi-threaded (remove DATA statement);
4231      - use standard DIFFERENT_MULTIPLE function;
4232      - add MATRIX_OPTIONS.h
4233    o verification/matrix_example:
4234       To allow to split the domain in several tiles, change the domain size
4235        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
4236        Western side) of land points.
4237    o (*_)write_pickup:
4238      - fix few bugs in mypackage_read/write_pickup.F
4239      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
4240        array of length 1 (was caught by compiler syntax-check).
4241    o pkg/diagnostics (velocity potential solver):
4242      - fix initialisation of main diagonal matrix (for overlap values)
4243    o tools/build_options:
4244      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
4245        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
4246      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
4247        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
4248        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
4249        and use "-devel" testreport option for standard testing on baudelaire.
4250    o pkg/grdchk:
4251      - Assume that all gradient-check position are within the same tile
4252        corresponding to global indices (iGloTile,jGloTile) and that
4253        positions (i,j indices or nbeg) are local to this tile;
4254      - set tile local-indices and proc. number according to tile global-indices;
4255      - remove grdchkwhichproc from namelist (retired param);
4256      - send adjoint gradient to all procs so that all procs print it to STDOUT;
4257      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
4258    o adding package bbl (Bottom Boundary Layer)
4259      description in MITgcm/pkg/bbl/bbl_description.tex
4260      example/test experiment in MITgcm_contrib/bbl
4261    o adjoint verifications
4262      - changed 5 experiments to multi-tiles
4263        * global_ocean.90x40x15
4264        * obcs_ctrl
4265        * offline_exf_seaice
4266        * tutorial_dic_adjoffline
4267        * tutorial_tracer_adjsens
4268        changed reference output for those that crossed tile boundaries
4269        (changed choices of gradient check positions)
4270      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
4271      - temporary bug fix in grdchk_loc.F for obcs
4272    o genmake2 & testreport
4273      - add target "obj" (just for OBJFILES files) to Makefile;
4274      - add option to specify FEXTRAFLAGS on command line.
4275    o pkg/mypackage:
4276      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
4277    
4278    checkpoint63a (2011/08/02)
4279    o pkg/diagnostics (velocity potential):
4280      - fix velocity-potential calculation when using OBCS: balance net inflow
4281        at each level (new S/R OBCS_DIAG_BALANCE).
4282      - fix some of the problems with OBCS in stream-function calculation.
4283    o pkg/exf/exf_readparms.F
4284      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
4285        EXF_NML_OBCS) more consistent, so that you need not have these lists
4286        in data.exf when they are not used.
4287    o optim/optim_readdata.F:
4288      - add some output about obcs variables that might help debugging
4289      - add a check about nvarlength
4290    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
4291    o pkg/diagnostics (velocity potential):
4292      - fix mask for OBCS (still problems in stream-function with OBCS);
4293      - add specific parameter (default = main code CG2D params) for solver;
4294      - in case of poor convergence, use solution corresponding to lowest residual.
4295    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
4296      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
4297      and should be avoided where possible.
4298    o model/src (rStar):
4299      - include r* effect on reference-state (PhiRef) in totPhiHyd
4300        (so that it's really the potential anomaly at the cell center);
4301        affect solution only if z* with full pressure in EOS.
4302      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
4303        update output (because of z* in totPhiHyd and viscA4 changes);
4304      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
4305        @ constant r) until interpolation at constant r is implemented.
4306    o pkg/diagnostics
4307      - fix RCENTER diagnostics in case cell center is not at interface middle
4308    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
4309      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
4310      that THETA and SALT are "conservative temperature" and "absolute
4311      salinity"
4312    o pkg/ctrl
4313      - fix computation of endrec in s/r ctrl_init_rec
4314      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
4315    o pkg/seaice/seaice_growth.F
4316      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
4317        remove then obsolete STORE directives
4318      - fix STORE directives for tice and tices, so that only the
4319        appropriate part of the fields are stored (and not the entire
4320        field); update global_ocean.cs32x15.seaice AD output.
4321      - cosmetic changes: adjust CPP flags and indentation for better
4322        legibilty
4323    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
4324      Chris Wilson)
4325    o pkg/gmredi:
4326       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
4327       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
4328    
4329    checkpoint63  (2011/07/11)
4330    o pkg/exch2:
4331     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
4332     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
4333       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
4334       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
4335    o pkg/diagnostics:
4336     - deal with pairs of post-processed diags which are computed together; in
4337       particular, re-order list of diags within 1 file to save 2nd computation.
4338     - add S/R to compute velocity stream-function (called after velocity-potential
4339       calculation) from divergence free transport -> new diagnostics "PsiVEL".
4340     - add parameter to select grid-point location where PsiVEL == 0.
4341    o eesupp/src:
4342       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
4343       (specific S/R needed with exch2 topology - for now, just print an error msg)
4344    o pkg/shelfice
4345     - Implement friction velocity-dependent transfer coefficients following
4346       Holland and Jenkins, JPO, 1999
4347       Original code by M. Losch with small modifs.
4348       Enable with CPP option SHI_ALLOW_GAMMAFRICT
4349       and runtime flag SHELFICEuseGammaFrict
4350    o verification lab_sea & global_ocean.cs32x15:
4351     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
4352       does not miss some dependencies (but is slower) and also works with many files
4353       (default makedepend limitation for AD built).
4354     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
4355    o pkg/diagnostics:
4356     - add run-time parameter "useMissingValue" (def=False) to fill land-point
4357        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
4358       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
4359     - Extend the use of "missing_value" setting from data.diagnostics for the case
4360       of counter-diagnostics (where fraction-weight is zero). This applies both to
4361       MNC and MDS output files.
4362    o pkg/seaice/seaice_growth.F:
4363      - add 'a priori' cap of latent heat flux based on actual mass considerations
4364        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
4365        non-legacy seaice_solve4temp.
4366      - add diagnostic of the residual sublimation freshwater flux (the freshwater
4367        flux taken from the ocean if the total actual latent heat fluxes exceed
4368        the maximum)
4369      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
4370       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
4371      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
4372       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
4373      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
4374      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
4375    o verification 1D_ocean_ice_column:
4376       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
4377       update results
4378    o pkg/diagnostics:
4379     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
4380       which are not filled-up but computed from other diags ; In this case, the mate
4381       diag points to the primary (filled-up) diag to used for post processing.
4382     - Update Velocity-potential computation using post-processed diag framework.
4383     ==> Change the ordering of fields and time-periods in MDS output file
4384       when using periodic averaging: now writes one time record with the full set
4385       of fields for this time period, then the next time reccord (it used to be
4386       one field with the full set of time records then the next field).
4387         Note: this is now similar to NetCDF (MNC) output file. <==
4388    
4389    checkpoint62z (2011/06/21)
4390    o adjoint monitor:
4391     - Add adjoint monitor output for packages exf, seaice
4392       and update relevant testreport output
4393    o pkg/seaice:
4394     - re-order diags inits so that they appear in order in available_diagnostics.log
4395     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
4396       area/heff/hsnow preceeding thermodynamic growth/melt.
4397     - modified diag: SIdA; output actual effect, as the description states.
4398     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
4399     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
4400       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
4401        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
4402     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
4403     - added diagnostics for seaice generic tracers (SItr*).
4404     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
4405     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
4406     I. Fenty: 18-Jun-2011:
4407     Minor changes to seaice package:
4408     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
4409        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
4410       - Differentiated "regularization variables" from "floor variables"
4411        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
4412        * hiceMin became SEAICE_hice_reg (old hiceMin)
4413          (with _reg meaning regularization variable)
4414       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
4415        so as to ensure energy conservation when going between phases
4416      - A22 was not used anywhere
4417     2) Changed regularization procedure for heffActual and hsnowActual to ensure
4418        well-boundedness and smooth adjoint in seaice_growth.F
4419     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
4420        because the old regularization always set heffActual >= 0.05 cm
4421     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
4422        on AREA when HEFF > 0.
4423      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
4424        requiring that DISABLE_AREA_FLOOR *not* be defined
4425     Affected verifications:
4426      - 1D_ocean_ice_column (output.txt output_adm.txt)
4427      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
4428    o pkg/diagnostics:
4429      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
4430      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
4431        (was _RL, now integer) with option = 0 to retrieve all levels.
4432      - add pieces of code to compute velocity potential at each level (new diagnostics
4433        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
4434        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
4435      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
4436        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
4437        and in diagnostics_fract_fill.F (do not need a valid pointer for the
4438        diagnostics counter-mate); check that definition of counter-diagnostic
4439        includes a valid counter-mate (in diagnostics_set_levels.F).
4440    o model/src (rStar):
4441      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
4442        affect solution only if z* with full pressure in EOS;
4443        update output of test-exp global_ocean.90x40x15.
4444    o pkg/seaice:
4445      - introduce siEps=1e-5 parameter
4446      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
4447      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
4448      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
4449        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
4450        as well as ice cover age and ridging index (attached to AREA).
4451        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
4452        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
4453        Up to SItrMaxNum=3 tracers can be used simultaneously.
4454    o pkg/salt_plume:
4455      -introduce SPsalFRAC run time parameter that sets the fraction of the
4456       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
4457       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
4458    o model debug options:
4459      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
4460        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
4461      - Refine debug-msg printing selection (3 new levels):
4462        debugMode  : controls printing of debug messages (sequence of S/R calls).
4463        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
4464         debLevZero =  0 ; /* level of disabled aux. msg printing */
4465         debLevA =  1 ; /* level of minimum  aux. msg printing */
4466         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
4467         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
4468         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
4469         debLevE =  5 ; /* level of extensive debug printing */
4470        New debugLevel default: with default debugMode value (=F),
4471          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
4472          and if debugMode=T, default debugLevel = 4 (debLevD).
4473        Relation with previous settings:
4474         debLevB (=2) corresponds to former debLevA (=1)
4475         debLevD (=4) corresponds to former debLevB (=2)
4476        Note:
4477         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
4478         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
4479            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
4480      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
4481        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
4482    o pkg/obcs:
4483      - change OBCSfixTopo default from True to False (should not change the results);
4484        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
4485    o pkg/thsice:
4486      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
4487        2nd layer seaice sublimation (unlikely to happen)
4488      - use Interior mask for OBCS in thsice_advection.F (similar to what is
4489        done in gad_advection & seaice_advection).
4490    o adjoint:
4491      bug fix spotted by Gael Forget:
4492      seaice_advection and thsice_advection still had
4493      legacy CPP options to avoid CS corner updates for adjoint
4494    o pkg/seaice:
4495      => Change some of the defaults (2011/05/29):
4496         - change SEAICEuseFluxForm default (from False to True)
4497         - change DIFF1 default (from 0.004 m/s to 0. m/s)
4498         And print warnings if DIFF1 is not set in data.seaice and centered
4499          avection scheme is used without any diffusion.
4500      also:
4501      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
4502      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
4503      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
4504        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
4505        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
4506      update results of test exp.:
4507         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
4508             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
4509             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
4510         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
4511         seaice_obcs: output (SEAICEuseFluxForm=T)
4512      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
4513          for standard fwd & AD lab_sea tests (to keep the same output).
4514    o pkg/seaice/seaice_growth.F:
4515      - use Ian Fenty's capping formulas for actual ice
4516      thickness thoughout EVOLUTION branch.
4517      - put treatment pathological case #2) in CPP brackets
4518      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
4519      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
4520    o pkg/seaice:
4521      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
4522      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
4523      also pass fac as a param, which can be 1. (to update the tendency
4524      field) or the time step (to update the field itself).
4525      - seaice_advdiff.F: for multidim, call seaice_diffusion with
4526      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
4527      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
4528      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
4529      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
4530    o pkg/seaice:
4531      diffusion with centered advection scheme (diffus.F & advect.F):
4532      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
4533        to just compute the laplacian of input-field.
4534      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
4535      - fix flux-form version in diffus.F to conserve tracer.
4536      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
4537       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
4538    
4539    checkpoint62y (2011/05/26)
4540    o pkg/seaice:
4541     - seaice_growth.F : in EVOLUTION branch, always include
4542       a_QSWbyATM_cover in qnet (as it should be).
4543     - verification/global_ocean.cs32x15 : update results accordingly
4544       (output.seaice.txt output_adm.seaice.txt).
4545    o pkg/seaice + obcs:
4546     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
4547       equivalent of assuming no tracer gradient outside the OB region.
4548       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
4549     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
4550       after changes above);
4551     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
4552       only at OB location (instead of over a band of OLx width).
4553    o pkg/seaice:
4554     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
4555       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
4556    o pkg/obcs:
4557      - split header file "OBCS.h" into 4 separated files:
4558        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
4559       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
4560         (contain no conditional statement which depends on OBCS options).
4561      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
4562        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
4563    o ctrl, cost, grdchk & autodiff pkgs:
4564      - make options file more standard (like other {PKG}_OPTIONS.h file but
4565        with AD_CONFIG.h); clean-up some of the included header files.
4566    o pkg/obcs:
4567      - do not mask tracer when applying OB (tracer == 0 could generate problems)
4568      - apply tracer OB values to tracer field only at OB location (instead of
4569        over a band of OLx width)
4570      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
4571      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
4572        obcs_apply_tloc.F & obcs_apply_sloc.F
4573    o obcs in model/src:
4574      - call OBCS_APPLY_W only if NonHydrostatic.
4575      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
4576      - reset dEtaHdt and wVel to zero outside OB interior region ;
4577      - leave tracer unchanged outside OB interior region: This has no effect
4578        on the solution but just to prevent unrealistic tracer value outside OB.
4579      - zero out velocity outside OB interior region: This has no effect on
4580        the solution but just to prevent unrealistic velocity outside OB.
4581    o obcs and non-lin free-surf:
4582       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
4583       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
4584       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
4585       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
4586       update results of test-exp. exp4(nlfs).
4587    o exp4 (nlfs) test-exp:
4588       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
4589       with NonLin-FreeSurf); update output.nlfs.txt
4590    o obcs and 2d/3d solver norm:
4591       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
4592       and outside OB interior region (will allow to place OB further inside the
4593       domain). Depending on the domain, can affects cg2d-Norm (previous
4594       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
4595       and cg3d-Norm (previous Norm was computed before canceling OB terms),
4596       e.g. in tutorial_plume_on_slope.
4597      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
4598    o pkg rbcs:
4599      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
4600      - add capability to apply relaxation to horizontal velocity uVel & vVel.
4601    o pkg/grdchk: add gradient check for control variable xx_shifwflx
4602    o pkg/shelfice/shelfice_init_fixed.F
4603      fix CPP-flag combinations
4604    o pkg/seaice: Merge iceage code of Pierre Rampal
4605      * update/change/correct ice age calculations
4606      * add age updates for pathological cases
4607      Probably needs more testing...
4608    
4609    checkpoint62x (2011/05/13)
4610    o pkg/mom_vecinv:
4611       high-order vorticity scheme: use interior masks (maskInW & S)
4612       to zero-out (outside OB) gradient of vorticity.
4613    o verification exp.:
4614       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
4615       hs94.128x64x5 and seaice_obcs ; update results.
4616    o pkg/obcs:
4617      fix bug in OBeta for YZ sections in obcs_exf_load.F
4618    o pkg/ctrl, pkg/shelfice, and optim:
4619      - add new control variable xx_shifwflx (fresh water flux underneath ice
4620        shelves). This is almost as tedious as obcs-ctrl, because the
4621        variables needs its own mask.
4622      - add a cost function term that penalizes the deviation of xx_shifwflx
4623        from the first guess (zero) in analogy to other control variables
4624    o pkg/shelfice:
4625      - start basic adjoint
4626    o pkg/ctrl:
4627      - remove extra 2D field "for good measure" when initializing in
4628        ctrl_set_globfld_[xy/xz/yz].F
4629      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
4630      - improve error messages in ctrl_set_unpack_*
4631    o OBC implementation in momentum:
4632       use interior masks (maskInC,W & S) in momentum S/R:
4633       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
4634       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
4635       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
4636       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
4637       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
4638        (and also with Leith/Smagorinsky harmonic-viscosity).
4639       Update output of experiment dome and exp4 (+nlfs).
4640    o exp4 test-exp:
4641      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
4642        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
4643        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
4644        time-varying OB at Western-side for wVel (NonHyd); update output.
4645      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
4646        and biharmonic-viscosity ; also use prescribed time varying OB.
4647    o pkg/obcs:
4648      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
4649    o model/src:
4650      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
4651      - initialise startTime & nIter0 with unlikely values: allows to set one
4652        from the other without ambiguity.
4653    o seaice_obcs test-exp.:
4654      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
4655    o pkg/obcs:
4656      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
4657        no longer needed with maskInC,W,S in pkg/generic_advdiff.
4658    o pkg/seaice:
4659      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
4660        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
4661      - fixed bug in the initialization of sea ice salinity variable HSALT
4662        in seaice_init_varia.F  (removed dependence on ICE2WATR)
4663    o fizhi-cs test exp.:
4664       switch reference output convention for these 2 non-standard test-exp,
4665        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
4666          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
4667       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
4668    o model/inc:
4669      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
4670        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
4671    o pkg/seaice:
4672      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
4673    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
4674      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
4675        and initial HSALT
4676    
4677    checkpoint62w (2011/04/26)
4678    o pkg/mom_fluxform:
4679      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
4680      - use parameter "sideDragFactor" in no-slip BC side-drag part.
4681      - update output of exp. global_ocean.90x40x15
4682    o pkg/mom_vecinv:
4683      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
4684    o update seaice exp.:
4685      use more consistent parameter values (remove "backward compatability only":
4686       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
4687      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
4688       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
4689    o update test-exp global_ocean.90x40x15:
4690      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
4691      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
4692      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
4693      o turn on zStar & viscA4 in standard set-up (dir input/)
4694        and update output files: output.txt & output.dwnslp.txt
4695    o new AD-test experiment: obcs_ctrl
4696      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
4697    o pkg/dic:
4698      fix two bugs in handling water vapour pressure in carbonate chemistry
4699      and air-sea fluxes. Found by Val Bennington and Galen McKinley
4700      (add DIC Option = WATERVAP_BUG to recover old results)
4701      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
4702    o adding allowInteriorFreezing option to check for water below freezing point
4703      at depth and bring the negative heat anomaly to the surface level
4704    o pkgs _fields_load:
4705      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
4706      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
4707        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
4708        rbcs to get interpolation weights and time reccord number.
4709      - fix multi-threading in aim_fields_load.F
4710      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
4711    o external_fields_load:
4712      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
4713       interpolation weights) to use in a periodic time-series ; do not divide by
4714       time-step to convert to integer:
4715       - this fixes case where externForcingPeriod is not multiple of time-step
4716          (Thanks to Christopher L. Wolfe)
4717       - this fixes case where externForcingPeriod is an odd multiple of time-step
4718         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
4719      store index of time-record which is currently loaded:
4720       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
4721       - needed for the adjoint but not yet used because of extensive recomputations;
4722         (to be fixed soon)
4723    
4724    checkpoint62v (2011/04/02)
4725    o verification/1D_ocean_ice_column added to test Ian Fenty's
4726      pkg/seaice_growth.F modifications for improving sea ice code differentiability
4727    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
4728      (new velocity statistics after changing maskInW & maskInS definition)
4729    o pkg/generic_advdiff with OBCS:
4730      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
4731      equivalent to assumption of no tracer gradient outside the OB region.
4732      This will affect the results if using obcs+biharmonic diffusion.
4733      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
4734    o pkg/obcs:
4735      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
4736      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
4737      in Interior region. No impact on solution but affects Velocity monitor stats.
4738    o pkg/ptracers (adjoint)
4739      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
4740      tape file for each tracer
4741    o model/inc/src and pkg/autodiff: add parameters that allow to turn
4742      of parts of the adjoint code at run time. For now, there are only
4743      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
4744      parameters are set in data.pkg.
4745      This is the lazy coward's version of doing this, but still useful for
4746      debugging. In order to do it right, everything needs to be moved to
4747      pkg/autodiff.
4748    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
4749      the end; this fixes the adjoint balancing code for open boundaries.
4750    o pkg/ctrl:
4751      - change behavior of xx_${varname}period to be analogous to exf-conventions:
4752        xx_${varname}period =   0.,  means time-independent control part
4753        xx_${varname}period = -12., means one-year-periodic monthly control part
4754      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
4755        clean up ctrl_init a little, remove unused variables
4756      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
4757      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
4758    
4759    checkpoint62u (2011/03/15)
4760    o model/src:
4761      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
4762        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
4763      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
4764        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
4765    o pkg/ctrl/obcs/ecco:
4766      - remove obsolete, unused, and partially broken code:
4767        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
4768        ALLOW_CTRL_OBCS_BALANCE
4769      - put a stop statement into ecco/cost_obcsvol.F, but also add
4770        cost_obcsvol to ecco_ad_diff.list
4771    o pkg/ecco: fix counting cost function contributions for obcs (code
4772      by Matt M.) and diffkr for diagnostics
4773    o pkg/ecco, pkg/ctrl, pkg/grdchk:
4774      add cost penalty terms for initial uvel, vvel, eta controls
4775      and I/O for prior error files
4776    o pkg/mdsio:
4777       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
4778       (new argument) to check for tiled file in mdsioLocalDir : this fix the
4779       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
4780    o pkg/ctrl:
4781     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
4782       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
4783       unused and superfluous variables
4784     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
4785    o pkg/ecco
4786     - enable adjoint of Stevens OB
4787    o pkg/ctrl/ecco/grdchk:
4788      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
4789        Fortunately, we do not have any tests for the numerous cpp-flagged
4790        option of "obcs as control parameters" so we will never know
4791        if this is an improvement (but at least now things compile).
4792      - remove an obsolete initialization from ecco_cost_init_barfiles.F
4793      - fix some problems within never used ifdefs to make the code compile
4794    o pkg/obcs:
4795     - Refine Interior mask definition to work with more complex OB (e.g.
4796       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
4797       read in Interior mask from file. Check if Interior mask is consistent
4798       with OB list of indices.
4799    o pkg/seaice
4800     - beginning code for a seaice tracer package,
4801       but currently only used for seaice age: SEAICE_AGE
4802       SEAICE_num = 4
4803       iTracer = 1: area-weighted ice age
4804               = 2: volume-weighted ice age
4805               = 3, 4: template for one-year vs. multi-year ice
4806       data.seaice has new namelist SEAICE_PARM03 for arrays related to
4807       SEAICE_num
4808    
4809    checkpoint62t (2011/03/05)
4810    o pkg/obcs:
4811     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
4812       then normal component. This ensures that the normal component is set
4813       correctly even when it conficts with tangential setting from an other OB.
4814       Affects results of test-experiment seaice_obcs: update the output.txt
4815    o pkg/obcs:
4816     - add code to monitor statistics of dynamical fields at OB.
4817     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
4818       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
4819       - change default: balance the Net inflow through all OB (instead of balancing
4820         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
4821     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
4822       to match Nortern OB inflow (OBCS_balanceFacN=0).
4823    o pkg/seaice:
4824     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
4825    o pkg/seaice (seaice_growth v 1.113):
4826     - reverting seaice_growth to v 1.111 in order to have code with exact bit
4827       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
4828       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
4829       runtime flag SEAICEareaFormula is kept but is inactive
4830    o model/src:
4831     - add new param to scale curvilinear grid distance and area when using
4832       a different sphere radius from the grid-files.
4833     - test/check multi-threads EXCH applied to local variable (cg2d_x)
4834    o adjoint:
4835     - enable adjoint of Stevens OB
4836     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
4837       (a bit delicate because of potentially modified adj. common block structure;
4838       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
4839    
4840    checkpoint62s (2011/02/15)
4841    o pkg/seaice (seaice_growth v 1.112):
4842     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
4843       computing the ice cover tendency from effective thickness tendencies. Include
4844       Ian Fenty's formula.
4845     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
4846       SEAICEareaFormula.
4847     - simplify notations for the various d_HEFF/d_AREA terms.
4848    o pkg/gmredi:
4849     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
4850       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
4851       add a verification test-run (front_relax.bvp) to test GM_useBVP.
4852    o pkg/seaice (seaice_growth v 1.111):
4853     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
4854     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
4855       also melt ice.
4856    o pkg/seaice:
4857     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
4858     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
4859    o pkg/cheapaml:
4860     - from Nico Wienders: New version of this package.
4861    o pkg/flt:
4862     - add CPP options to prevent floats to re-enter the opposite side of
4863       a periodic domain (default: keep periodicity)
4864    o pkg/gmredi:
4865     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
4866       (needed for multi-dim advection).
4867     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
4868    o model/src:
4869     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
4870    o tutorial_tracer_adjsens
4871     - extend to NLFS and replace maskC by hFacC
4872       (change reference output accordingly)
4873    
4874    checkpoint62r (2011/01/24)
4875    o testreport:
4876     - add option -deloutp (-do) to remove output file after successful run
4877     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
4878       extract exact list of procs from this file ; adjust COMMAND by
4879       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
4880    o pkg/ecco: replace old ineffective way of penalizing deviations from
4881      first guess (of obcs) with code by Matt Mazloff
4882    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
4883      exf/cal
4884      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
4885        and handle case of obcs?period == 0
4886        Not affected by these changes: There is still an inconsistency in
4887        the computation of start/endrec for the obcs variables for ALLOW_CAL
4888        defined (see comment by Menemenlis, 7-Mar-2003)
4889      - make S/R ctrl_get_gen_rec return something meaningful even if
4890        ALLOW_CAL is not defined
4891      - ctrl_getobcs?: simplify code so that it does not need to use
4892                       S/R exf_swapfields
4893    o testreport:
4894       allow to test MPI with different number of processors for each experiment:
4895       create file "SIZE.h.mpi" in each build dir.
4896       Note: update of "-command" argument not yet implemented.
4897    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
4898      alleviate the need for additional 3D tapes when using
4899      the non-inear free surface in the adjoint. This is done
4900      by adding an 'update' of hfacc etc. to their current
4901      value at the beginning of forward_step.F.
4902    o pkg/seaice
4903      seaice_lsr: move stress-divergence computations out of outer pseudo-
4904      timestepping loop
4905    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
4906      up, so that the calls of the ctrl_* subroutines are really at the end
4907      of the routine.
4908    o pkg/gmredi:
4909      allow to specify a 2-D horizontal map and a 1-D vertical profil
4910      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
4911    o pkg/seaice:
4912      move lsr iterations from seaice_dynsolver to seaice_lsr.
4913    o pkg/seaice:
4914      reduce memory footprint of seaice mutldim advection tapes,
4915      by using a 2D tape independent of the generic_advdiff ones,
4916      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
4917    
4918    checkpoint62q (2010/12/29)
4919    o model/src:
4920      - check horizontal grid-spacing for unset or zero/negative values.
4921      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
4922    o pkg/flt:
4923      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
4924      - precision of input and output files set according to readBinaryPrec
4925        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
4926      - initial float position from tiled file was not converted to index space
4927        (looks like a bug): fixed to make it similar to initial pos. global file.
4928    o global_ocean.cs32x15:
4929       change SIZE.h of AD set-up to get same tiling as with MPI.
4930       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
4931    o model/src:
4932       add flag to control printing of domain fields (bathymetry, hFac ...) in
4933       ini_mask_etc (call to plot_fieds_xy*).
4934    o pkg/thsice:
4935       if useEXF, some forcing fields are not valid in overlap: fixed by computing
4936       over the interior only + apply EXCH at the end (like with SEAICE advection).
4937    o pkg/mdsio:
4938      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
4939        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
4940      - change barrier call for safe multi-threads access to 3-D shared buffer.
4941      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
4942      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
4943        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
4944    o pkg/flt:
4945      - add fourth-order Runge-Kutta integration
4946      - add basic exch2 support (only 1 facet supported so far!)
4947    o pkg/mdsio+rw:
4948      new S/R to read local (or tile independent) vector (read counterpart of
4949       mds_writevec_loc, and front-end write_glvec_rl/rs).
4950    o global_ocean.cs32x15: additional input_ad.seaice experiment
4951        that uses pkg/seaice rather than pkg/thsice.
4952        (using multidim advection for seaice)
4953    o towards more F95 syntax for array specification in namelist:
4954      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
4955        of all verification experiments.
4956           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
4957          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
4958      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
4959    o global_ocean.cs32x15: additional input.seaice experiment
4960        that uses pkg/seaice rather than pkg/thsice.
4961    
4962    checkpoint62p (2010/12/17)
4963    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
4964        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
4965    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
4966        allow for use of multim. advection in seaice adjoint.
4967    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
4968      - first attempt to close budgets by taking into account the freshwater
4969        flux implied by the sublimation of snow and ice. So far only the
4970        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
4971        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
4972    o eesupp/src:
4973      new S/R with new option (NML_EXTENDED_F77) to change array specification
4974      from F95 standard to commonly accepted extended F77 form.
4975      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
4976      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
4977      for less tolerant f77 compiler (e.g., pgf77, g77).
4978    o globalFiles:
4979      commented out in parameter file "data" since it's not safe with MPI
4980      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
4981      in this case); no longer commented out in restart test (tst_2+2).
4982    o add adTapeDir to specify a special directory where adjoint tapes are
4983      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
4984      and cannot be used together with mdsioLocalDir.
4985    o nesting pkgs:
4986      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
4987      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
4988      - add parameter files + utils dir + output from short run on beagle.
4989    o pkg/seaice:
4990        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
4991    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
4992      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
4993    
4994    checkpoint62o (2010/11/25)
4995    o pkg/exf:
4996      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
4997    o pkg/seaice:
4998      - seaice_ocean_stress: split a loop for better vectorization of the
4999        adjoint code
5000      - seaice_growth.F: fix bug in conservation of freshwater connected to
5001        capping of heff, put contribution into d_HEFFbyNEG
5002      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
5003        by something more sensible (parameters that are what their name implies)
5004      - change some defaults, so that by default exf-parameters are used for
5005        things like rhoAir, cpAir,latent/sensible heat parameters, in order
5006        to reproduce the old results, many data.seaice now contain funny values
5007        for cpAir and latent heat of sublimation
5008    o packages_readparms.F: move exf_readparms up in line so that
5009        exf-parameters are visible for other packages (e.g. seaice)
5010    o debugMode & debugLevel=2:
5011      - differentiate between debugMode & debugLevel=2:
5012        debugMode: controls printing of debug messages (sequence of S/R calls).
5013        debugLevel: controls printing of algorithm intermediate results and stats.
5014      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
5015        => allows to print debug-stats without all sequence of call messages.
5016      - switch control of debug print from debugLevel to debugMode in many S/R.
5017    o pkg/obcs (obcs-sponge):
5018        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
5019        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
5020    o pkg/generic_advdiff:
5021      - record overlap minimum size for each advection scheme;
5022      - refine criteria on overlap minimum size;
5023      - check and stop (in gad_check) if overlap size is too small.
5024    o pkg/obcs:
5025      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
5026        once, in ptracers_implicit.F)
5027      - with seaice: remove test on empty file name in obcs_apply_seaice (always
5028        apply OB values when tile has OB)
5029    o model/src, coriolis setting:
5030      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
5031        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
5032        files (selectCoriMap=3) with any grid.
5033      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
5034    o pkg/seaice/seaice_growth.F:
5035        a few cosmetic changes that reduce the number of lines of code
5036    o pkg/obcs: add boundary conditions following Stevens (1990)
5037      - the code follows old MOM/NAOSIM code
5038      - so far it is only implemented for the eastern and western boundaries
5039        and NOT for pTracers
5040    o pkg/rbcs:
5041      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
5042        beginning of the first rbcs forcing period.
5043      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
5044        offline package, i.e., one file per time, labeled by iteration number;
5045        deltaTrbcs sets the timestep with which the data was generated;
5046        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
5047      - rbcsForcingCycle=0 makes forcing non-cyclic.
5048      - make arithmetic safe for negative times and odd forcing periods.
5049    
5050    checkpoint62n (2010/11/09)
5051    o pkg/seaice:
5052        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
5053    o pkg/obcs:
5054       New S/R to copy tracer value from the OB location to narrow band region
5055        (width = same as overlap) beyond the OB: preserve OB value (needed for
5056        high-order scheme) which were overwritten by EXCH call if in overlap
5057        region. Applied to theta, salt, ptracer and advected seaice variables.
5058       With seaice: use maskInC in similar way as in gad_advection.F,
5059        in seaice_advection.F and advect.F.
5060       Update output of experiment seaice_obcs and change exp4 to test OBCS with
5061        4th order Adv.Scheme. for pasive salt and ptracer.
5062    o tools/genmake2:
5063      - when looking for an optfile (not specified), only search for Fortran compiler
5064        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
5065      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
5066        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
5067      - set default for CPP to "cpp -traditional -P" (was the case without specifying
5068        an optfile, but otherwise default was just "cpp".
5069      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
5070      - when "CC" is not set in the optfile, look for possible C compiler
5071        (instead of just setting CC=cc)
5072      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
5073        => add a ".F" to ".o" rule for source files with no "#include" (such as
5074           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
5075      - move gfortran before g77 in list of possible Fortran compiler (consistent
5076        with reference compiler switch from g77 to gfortran)
5077    o pkg/seaice:
5078      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
5079        seaice_check that stops the model, when the CPP flag is used.
5080      o seaice_growth.F: make capping of ice volume conserving by returning the
5081        capped ice as freshwater to EmPmR. This does not change the verification
5082        experiments but will change runs where the capping is acutally active
5083    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
5084      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
5085         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
5086         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
5087    o tools/genmake2:
5088      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
5089      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
5090      - clean previous genmake log files before anything else.
5091      - change Makefile to remove testreport log files (*.tr_log) and genmake log
5092        files only with "CLEAN" target (instead of "Clean");
5093    o pkg/generic_advdiff:
5094      Change OBCS in multiDim advection (gad_advection.F):
5095       Use maskInC to prevent intermediate update of tracer-field in OB regions,
5096       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
5097       which were applying future time-step OB values.
5098      This way, all explicit calculations use current-time-step OB values
5099       (simpler and more consistent).
5100      Affects results when set-up uses time-varying OBC and multi-dim advection;
5101       update output of experiment seaice_obcs.
5102    o pkg/seaice:
5103      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
5104       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
5105         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
5106      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
5107       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
5108       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
5109    o pkg aim (2010/10/26):
5110      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
5111        formulation with obliquity, eccentricity, ... as run-time parameters,
5112      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
5113        upward shortwave radition at the surface (all-sky and clear-sky).
5114    o pkg/obcs:
5115      - writing sections with globalFiles=T does not work: switch to tiled-files
5116        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
5117      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
5118      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
5119    
5120    checkpoint62m (2010/10/21)
5121    o pkg/seaice: vectorize seaice_solve4temp.F
5122      - move iterations loops outside of i/j-loops
5123      - requires 2D arrays for TB and effConduct
5124      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
5125        modified in this routine
5126      - a little bit of clean up, adjusting indentation, etc.
5127      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
5128        performance and '**TWO' by '**2' (because TWO is a float),
5129        replaced ONE, ZERO
5130    o eesupp/src:
5131       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
5132    o pkg/seaice/seaice_growth.F
5133      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
5134      merging process. The merged routine has two branches, and one activates the 'evolution'
5135      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
5136      In summary, here is what the '10/10 revision' did consist of
5137        part 1: seaice_growth.F revisions 1.71 to 1.75
5138          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
5139            The emphasis here was on improving readability (e.g. by trying to use meaningful
5140            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
5141        part 1.5:
5142          - revising the lab_sea experiment to make it a more useful (i.e. stable
5143            and representative of an actual model run). This was done by generating a
5144            (winter) pickup to start from, switching back the main experiment dynamic
5145            solver from evp to lsr, having one of the experiments use the free drift solution.
5146        part 2: seaice_growth.F revisions 1.76 to 1.85
5147          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
5148          - Sorting out the various fields units and sign (set early on and reset at the end)
5149            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
5150            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
5151          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
5152            and simplifying logical expressions to further improve readibility.
5153        part 3: seaice_growth.F revisions 1.86 to 1.89
5154          - Re-organize the blocks of code more logically.
5155          - Merging the '_if.F' pieces that add something new.
5156    o pkg/thsice:
5157      - vectorize thsice_solve4temp and thsice_get_exf.
5158        Problem: thsice_solve4temp has an unvectorizable statement that
5159        might also be problematic for TAF
5160      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
5161        does not change the verifcation experiment, but will change all
5162        experiments that have this flag undefined (not tested in verification);
5163        a little reorganization to save a few 2D fields and recomputations
5164      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
5165      - 2nd step:  fix some store dirs
5166        o seems to work somewhat, i.e. using ifort but not g77
5167        o likely cause are incomplete init. or recomputation
5168        o start verification/global_ocean.cs32x15/input_ad.thsice
5169    o pkg/obcs: add support for exch2
5170      - the position of the boundary and prescribed values are specified using
5171        a global domain with exch2 facets stacked
5172        - in x for N,S boundaries (like W2_mapIO=-1)
5173        - in y for E,W boundaries (so E,W boundaries do not overlap)
5174    o pkg/mdsio: add support for writing global sections with exch2
5175        file layout is as for obcs described above:
5176        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
5177        - for y-z sections, facets are stacked in y
5178    o pkg/thsice:
5179       - change a few routines for better vectorization: thsice_albedo.F,
5180         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
5181         not affected, but in particular the latter routine has changed
5182         dramatically (not necessarily easier to read now).
5183       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
5184       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
5185    o verification/lab_sea:
5186      - overhaul of the forward model experiments. The main motivation
5187        for this revision is that lab_sea has proven quite fragile (when
5188        changing the sea-ice code, and switching platforms) to a point
5189        when failures were very hard to attribute to specific code problems.
5190      - the suspected reason for this fragility is noise amplification by evp so,
5191        to start with, we decided to replace evp with lsr in the main experiment.
5192      - the input.lsr experiment thus became obsolete and was removed.
5193      - it was replaced with the input.fd experiment that uses an
5194        analytical "free drift" solution as the ice velocity field.
5195      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
5196        will hopefully allow us to discriminate problems due to dynamic solvers
5197        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
5198        us to test additional options, along with the salt plume package.
5199      - Finally a pickup was generated (at the end of a one year run) to
5200        make the tests more representative of an actual model run. Previously
5201        the tests starting point was a 1m thickness of ice everywhere.
5202    o pkg/seaice:
5203      - introducing S\R seaice_freedrift.F that compute the
5204        analytical solution to an approximate ice momentum
5205        equation (i.e. the simple stress/coriolis balance).
5206      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
5207        of the free drift velocity field, and enable its use.
5208        To actually use the free drift solution as the model ice
5209        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
5210    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
5211    
5212    checkpoint62l (2010/10/04)
5213    o pkg/seaice:
5214      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
5215      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
5216       version (with USE_ORIGINAL_SBI undef);
5217    o add hooks for new packages OASIS, the package will follow
5218      (hooks exclude the seaice pkg for now)
5219    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
5220      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
5221      rather than mdsio_readvector.F/mdsio_writevector.F, within
5222      adread_adwrite.F to read/write adjoint-related tapes to disk.
5223    o eesupp and pkg/mdsio: ALLOW_WHIO
5224      Option to write/read 2D fields to files including tiles halos.
5225      The main purpose is for adjoint related "tape I/O".
5226      The secondary purpose is for debugging phases.
5227      A word on those rather specifically intended purposes.
5228      The code was meant to be stripped down to the bare minimum.
5229      Typically, there is a unique and basic mapping to the global
5230      buffer (tile by tile, then proc by proc, then level by level), and
5231      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
5232      meant to generate user friendly outputs of various shapes and forms.
5233      Rather it is intended, for the knowledgeabale developers,
5234      to be largely independent of the many mdsio options, to allow
5235      outputs of tiles+halos in debugging phases and in adjoint runs,
5236      and to allow some flexibility in tuning (adoint) I/O depending on each
5237      file system behavior. With regard to tuning, most of the potential knobs
5238      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
5239      to specify directories, to specify the typical size of I/O calls, etc.)
5240      are not yet included, and will be added if they prove useful.
5241    o pkg/seaice:
5242       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
5243    o pkg/seaice:
5244       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
5245       code (seaice_budget_ice_if.F) which enable to recover old standard
5246       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
5247       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
5248    o model/src (rStar):
5249       use simple average (not area weighted) of rStarFac at U,V point when using
5250       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
5251       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
5252    
5253    checkpoint62k (2010/09/17)
5254    o adjoint
5255       * changed verification/global_ocean.cs32x15 ; adjoint now tests
5256         Adams-Bashforth 3 + NLFS + RSTAR
5257       * some more modifs required for ECCO-GODAE v4
5258    o pkg/seaice
5259       add SEAICE_AGE_VOL option to use volume instead of area for
5260       integrating SEAICE_AGE
5261    o model/src:
5262       first check-in of sigma & hybrid-sigma coordinate code ; also includes
5263       non-linear free-surface parts ; but pressure-gradient not yet coded.
5264    o pkg/ptracers:
5265       option for ptracer to convert Salt Relax into additional EmP.
5266        tested in exp. global_ocean.90x40x15.dwnslp (update output)
5267    
5268    checkpoint62j (2010/08/25)
5269    o pkg/ggl90:
5270       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
5271    o pkg/dic: car_flux.F, phos_flux.F
5272      - reduce number of exp-calls in order to improve performance
5273      - clean up a little (replace fields by their macros, etc., fix
5274        typo in CPP-flag)
5275    o pkg/ggl90: minor changes
5276      - GGL90diffKrS was removed --> always use GGL90diffKr
5277      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
5278      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
5279        (commented out for now)
5280      - change in max/min operations to ensure that smoothing is ok
5281      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
5282      - always use diffKrNrT as background profile (i.e. never use diffKr field)
5283    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
5284    o pkg/dic:
5285      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
5286        vectorization
5287      - small bug fix in insol for the unlikely case of a cartesian grid
5288      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
5289        + now vectorize, which also removes adjoint recomputations;
5290        + replace integer maksp1 by _RL maskp1
5291        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
5292    
5293    checkpoint62i (2010/07/21)
5294    o pkg/flt:
5295      - with OBCS: stop floats which enter the OB region
5296    o model/src:
5297      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
5298        for implicit vertical advection.
5299    o pkg/seaice:
5300     - account for melting in seaice age evolution.
5301     - remove double counting of seaice ridging effect on seaice age.
5302    
5303    checkpoint62h (2010/06/18)
5304    o pkg/exch2:
5305     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
5306    o tools/genmake2
5307      - remove "-pdefault" option: redundant with the use of "packages.conf";
5308      - remove file pkg/pkg_default : set the default as a pkg group
5309        ("default_pkg_list") defined in pkg/pkg_groups;
5310      - fix for case pkg/pkg_depend is missing (was hanging before);
5311      - add option "-pgroups" to specify a different pkg_groups than the default.
5312    o verification/adjustment.cs-32x32x1:
5313       add a "minimal" set-up test (code_min & input_min) which only compiles
5314       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
5315    o tools/genmake2
5316      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
5317      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
5318    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
5319      files are nearly the same anyway.
5320      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
5321       - redefinition of tau(i,i) (by a factor of ustar)
5322       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
5323       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
5324       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
5325       - replace
5326         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
5327         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
5328         by
5329         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
5330         (changes results)
5331       -> exf_bulkformulae v1.22,
5332          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
5333          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
5334                    output.txt 1.63
5335           offline_exf_seaice: output.seaicetd.txt 1.7
5336           seaice_obcs: output.txt 1.10)
5337      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
5338       -> exf_bulkformulae v1.23,
5339          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
5340          and global_ocean.cs32x15.icedyn (only 11 matching digits)
5341      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
5342    o adjoint of exch-1:
5343     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
5344       (note: was already like this when using EXCH-2) and remove flow dir
5345       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
5346     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
5347     - update pkg/exch2 diff list.
5348    
5349    checkpoint62g (2010/05/19)
5350    o eesupp/src (exch-1):
5351     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
5352       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
5353       (renamed to exch1_*rx_cube.F).
5354     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
5355       to call new exch1 S/R ; update Makefile and .cvsignore.
5356     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
5357       exch2_xy_rx later)
5358      Note: after updating your code, need to run "make clean" in eesupp/src
5359    o test experiment bottom_ctrl_5x5:
5360       new output_adm.txt with fewer grdchk & less monitor output.
5361    o model/src:
5362      remove the call to ini_cori in initialise_varia.F (just keep the usual one
5363       in initialise_fixed.F). More consistent with coriolis & horizontal grid
5364       beeing treated in the same way (ini_grid is not called a 2nd time).
5365    o pkg/exf:
5366      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
5367      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
5368      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
5369      - cosmetic changes to exf_bulkformulae.F to make it look more like
5370        exf_bulk_largeyeager04.F
5371    o eesupp/src (exch-1):
5372      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
5373      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
5374        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
5375        (even without using MPI).
5376      - Message mode: move RecvAck setting (indicator of buffer being ready)
5377        from send_put to recv_get S/R (was useless before, but not sure if
5378        it's much more useful now);
5379      - Switch the order of sync: MPI-proc 1rst and then threads;
5380      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
5381      - fix AD code for communication mode ='get' (but not used).
5382    o model/src:
5383      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
5384      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
5385    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
5386    o pkg/ctrl: require a specific set of control variables and exf-flags for
5387      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
5388    o model/src:
5389     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
5390       1rst forward sweep, to avoid over-writing output files during recomputations
5391       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
5392     b) 2nd version:
5393      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
5394      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
5395         writePickupAtEnd) + seaice & ptracers output;
5396      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
5397    o model/src:
5398      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
5399    o pkg/exch2:
5400      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
5401      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
5402    o pkg/autodiff & exch2:
5403      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
5404      (for now, only if ALLOW_EXCH2 is defined).
5405    o pkg/autodiff:
5406      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
5407        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
5408       + clean-up comments (_RS is not always real*4)
5409      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
5410      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
5411        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
5412    o testreport (AD-tests):
5413      no longer link files from dir "../input" (1rst link files from
5414      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
5415    
5416    checkpoint62f (2010/04/29)
5417    o model/src/the_main_loop.F:
5418      adjust store directives for seaice evp and multicategory according to
5419      pkg/ecco/the_main_loop.F
5420    o adjoint:
5421      global_sum_ad was incomplete (noted many times by many people ;)
5422      nice description by Jean U. as follows:
5423      * allreduce(var) in global_sum.F can be interpreted as
5424        reduce(sum) followed by broadcast of sum.
5425      * The adjoint of that is
5426        sum(adjoint) followed by broadcast(summed adjoint value)
5427        or in other words, allreduce(sum, adjoint vars)
5428      We were missing the sum(adjoint)!
5429      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
5430      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
5431      The fix should produce 16-digit accuracy between
5432      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
5433      multi-CPU single-tile (e.g. nSx=1, nPx-2)
5434      We'll probably change this yet again shortly
5435    o eesupp/src:
5436      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
5437    o pkg/icefront
5438      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
5439        specification of addmass array based on a 2D field, which is added
5440        at bottommost wet level at each horizontal location.
5441    o model/src:
5442     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
5443     layout; (not always compatible with delX,delY setting; commented out for now).
5444    o pkg/exch2:
5445     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
5446     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
5447    
5448    checkpoint62e (2010/04/15)
5449    o pkg/obcs:
5450      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
5451    o pkg/dic:
5452      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
5453        (note: not presently tested in any forward verification exp.)
5454       update tutorial_global_oce_biogeo AD output file.
5455    o pkg/exf:
5456      - account for the variation of albedo as a function of zenith angle
5457        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
5458    o build_options:
5459     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
5460    o pkg/dic:
5461      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
5462      - use binary pickup file for restart;
5463      - initialise atmos-CO2 box from dic_pCO2 parameter;
5464      - fix multi-threaded.
5465    o pkg/rbcs:
5466     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
5467       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
5468     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
5469       and update output.txt
5470    o pkg/kpp:
5471     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
5472     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
5473       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
5474       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
5475     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
5476       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
5477    o pkg/offline:
5478      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
5479      (bug was added in version 1.10 on 2007-08-23).
5480    o pkg/offline:
5481      - no need to specify periodicExternalForcing, etc ... to use offline pack
5482      - offline input files no longer just single prec --> parameter offlineLoadPrec
5483    o verification/lab_sea:
5484      change AD test to multi-tile setup and update all 4 AD output.
5485      NOTE: while cost function values remain very similar,
5486      gradients are very different, although gradient checks are self-consistent
5487      Should try to get to the bottom of this (cost function summation order?)
5488    o pkg/dic:
5489      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
5490      a weakness of TAF that drops part of double precision in log10 derivative.
5491      <= changes removed since problem has been fixed in current TAF version 1.9.71
5492      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
5493    o pkg/ecco:
5494      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
5495      update all 4 lab_sea AD output.
5496    
5497    checkpoint62d (2010/03/22)
5498    o build_options:
5499      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
5500    o remove unbalanced quote (single or double) in commented line of source code
5501      (may cause some warning with some preprocessor/makedepend versions).
5502    o pkg/seaice:
5503      fix seaice_model.F for adjoint (gael) and update AD results of experiments
5504       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
5505    o testreport:
5506      add option '-runonly' (short: '-ro') to just do the run part (without make).
5507    o eesupp: remove JAM communication code (obsolete).
5508    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
5509      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
5510      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
5511      (update also the output).
5512    
5513    checkpoint62c (2010/03/02)
5514    o tools/build_options :
5515       move (some) old optfiles from build_options/ to build_options/unsupported/
5516    o model/src and pkg/exf
5517       surface relaxation -- separating data and data.exf options
5518       The point is to ensure that we specify the surface relaxation
5519       either in data or in data.exf (but not half and half) and to
5520       avoid an accidental relaxation to 0 (which happened if a time
5521       scale was specified but the file name was left empty)
5522    o model/src model/inc and pkg/mom_common
5523       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
5524       => addition to the viscosity field as computed by others schemes
5525    o tools/build_options:
5526      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
5527        but keep the former optfile for few weeks for smooth transition
5528    o pkg/ecco
5529      - allow user defined cost function contributions
5530         CPP: ALLOW_USERCOST_CONTRIBUTION
5531         USAGE: compute contributions in cost_usercost_all.F
5532      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
5533          the two options are complementary.
5534    o pkg/smooth
5535      - migration from contrib to the main repository
5536    
5537    checkpoint62b (2010/01/26)
5538    o pkg/monitor:
5539      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
5540        (in case someone forgot to update customized pieces of code)
5541    o nonHydrostatic:
5542      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
5543      - add a simple 2-D experiment (short_surf_wave) to test it.
5544    o pkg/icefront:
5545       adding the shell of, and the hooks to, a new package that
5546       will model melting and freezing of vertical glacier ice fronts
5547    o momentum:
5548      add diagnostics of momentum tendency from Hydrostatic pressure gradient
5549       (without surf.pressure term: would need a 2nd filling since implicit term).
5550    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
5551      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
5552      cannot deal with the former
5553    o cleaning:
5554      - remove all (except OpenAD) old TLM output from results_ad dirs.
5555      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
5556      - comment out maskH definition (replaced by maskInC)
5557    o pkg/monitor:
5558      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
5559        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
5560    
5561    checkpoint62a (2010/01/15)
5562    o model/src:
5563      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
5564    o pkg/diagnostics:
5565      - add optional level number diagnostics (i.e., level number to be define
5566        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
5567      - strictly check for valid parser-code(10) ;
5568      - check if adding diag to the list from the right place.
5569    o pkg/longstep:
5570      - change parameters and fix tracer conservation with rstar/nonlinear free surface
5571    o diagnostics:
5572     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
5573       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
5574    o pkg/diagnostics:
5575     - Add option for writing vertical integral (sum of selected levels) of an output
5576        field instead of writing output field levels. Activate this option on a per
5577        output-file basis, by setting the 2nd character of fileflag to 'I'.
5578     - Add field-specific information relative to level integral in 3rd postion
5579        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
5580        vertically (x level-thickness x hFac), "r"=same but without hFac.
5581    o do_the_model_io:
5582      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
5583        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
5584        writing pickups and stopping.
5585    o pkg/diagnostics (for now, only with mdsio):
5586      - write time information to meta file (and modify accordingly rdmds.m) :
5587        time-averaged diagnostics output: write starting and ending time of the
5588        time-averaging interval ; snap-shot diagnostics output remains unchanged;
5589    o pkg/timeave:
5590      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
5591        always Nr), now assumed to be equal to number of levels of averaged field;
5592        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
5593    o pkg/sbo:
5594      - fix ocean bottom pressure global-average & 2-D time-ave output (was
5595        neither initialised nor filled).
5596      - add starting iteration in suffix of global-average output file
5597        (to avoid over-writing the file after a restart)
5598      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
5599    o time-average:
5600      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
5601        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
5602         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
5603        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
5604      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
5605      - fix missing accumulation for pkg/opps.
5606      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
5607         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
5608      - fix initialisation of time-ave vars and do only full time-step increment
5609        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
5610    o pkg/layers:
5611      - use standard RW pkg S/R to write the output
5612        and remove local write_fld version (which had a problem).
5613      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
5614      - fix LAYERS_CALC argument list.
5615    o pkg/timeave:
5616      - store cumulative-time in a simple tiled array (drop the level index)
5617      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
5618    o pkg/ocn,aim_compon_interf
5619      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
5620    
5621    checkpoint62  (2009/12/23)
5622    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
5623        (was not previously tested in any other exp.)
5624    o pkg/monitor:
5625      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
5626        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
5627        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
5628      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
5629      - change del2 calculation.
5630      - use interior masks (instead of maskH, <- to be remove).
5631      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
5632    o mask & obcs:
5633      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
5634      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
5635        (called after packages_init_fixed)
5636    o pkg/obcs:
5637      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
5638        Fixes bug in obcs+exf with nSx*nSy.GT.1
5639      - fix multi-tile handling in obcs balance code
5640    o nonHydrostatic:
5641      - Implement AB-3 for non-hydrostatic vertical momentum ;
5642        (change ordering of var. stored in pickup file when using NH)
5643      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
5644      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
5645        (in prep. for new NH free surface form).
5646    o pkg/obcs:
5647      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
5648    o model/src:
5649      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
5650    
5651    checkpoint61z (2009/12/01)
5652    o nonHydrostatic:
5653      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
5654        a spurious source of energy in simple baroclinic adjusment test case.
5655      Update all non-hydrostatic exp output.
5656    o model/src (3-d solver):
5657      Change again 3-D solver free-surface RHS term when exactConserv=T:
5658        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
5659        (which was not the case with previous formulation).
5660      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
5661      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
5662    o nonHydrostatic:
5663      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
5664        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
5665      - change 3-D solver to work with r* (for now, only with linear free-surf.)
5666      - add few debug diagnostics (cg3d_x, residual)
5667    o model/src:
5668      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
5669        update output of exp. global_ocean.cs32x15.viscA4
5670    o update output of exp. global_ocean.cs32x15.icedyn after removing
5671      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
5672    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
5673    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
5674      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
5675    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
5676      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
5677      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
5678      to test this code
5679    o pkg/cd_code:
5680      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
5681       C-grid momentum. D-grid velocity used to be stepped forward in time with
5682       Adams-Bashforth only on surface pressure term. Tests show that using AB on
5683       D-grid coriolis term improves stability (as expected from CD-scheme paper).
5684      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
5685      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
5686       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
5687       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
5688      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
5689           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
5690    o pkg/obcs:
5691     - fix bug in initialisation (broken since Oct 1rst modification)
5692       for useOBCSprescribe without useEXF.
5693    
5694    checkpoint61y (2009/11/15)
5695    o pkg/seaice
5696     - change (once again) the discretization for the evp solver: rather than
5697       squaring the averages of strain rates, average the squares to give
5698       a better approximation to VP behavior (in simple test); this breaks
5699       verification experiments that use EVP (lab_sea and lab_sea.hb87)
5700        --> update outputs
5701    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
5702      to improve vectorization of adjoint code on TARGET_NEC_SX
5703    o verification/vermix:
5704      - change vermix to a more "classical" 1d column with high vertical
5705        resolution, seasonal heat flux forcing and constant wind forcing
5706        --> update outputs
5707    o pkg/seaice
5708     - fix diagnostics of principal stress components for EVP
5709     - add optional diagnostics of non-linear convergence for LSOR solver
5710     - make maximum zeta a runtime parameter
5711    o model/src (3-d solver):
5712      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
5713       which consisted in removing the Surf. Non-Hydrostatic pressure from the
5714       whole column and adding it to Eta (inspired from Casualli, 1999):
5715       Only affects 3-D solver initial guess and only if using ExactConserv,
5716       but tests did show a degradation of solver convergence. For this reason,
5717       decide to disable this piece of code.
5718       to recover previous version, just set zeroPsNH = exactConserv (line 78).
5719      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
5720    o pkg/ggl90:
5721     - fix previous modif (unfortunatly has not been documented here).
5722    o pkg/seaice/autodiff:
5723     - add CPP flag to include clipping of zeta in EVP code;
5724       although clipping of zeta is not necessary for EVP and not recommended
5725       it was done by default, now clipping is disabled by default
5726     - modify computation and store zetaC/Z in seaice_evp for TAF
5727     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
5728     - change seaice_calc_viscosities/strainrates for better
5729       vectorization after AD by TAF
5730     - rearrange common blocks in SEAICE.h once again for easier dumps of
5731       adjoint output, adjust adcommon.h and g_common.h
5732     - change flux form of default advection scheme for better vectorization
5733       of adjoint code
5734     - modify lab_sea/input.lsr to test the flux form of default advection
5735       scheme
5736    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
5737      transition in checkpoint61r)
5738    
5739    checkpoint61x (2009/10/19)
5740    o adjoint: adding two new verification experiments
5741      * tutorial_global_biogeo: an online dic sensitivity experiment
5742        (work with G. Forget)
5743      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
5744        (an update of the Dutkiewicz et al., 2006 paper)
5745      Both use the same CO2FLUX cost function, but different controls
5746      Gradient checks look good, but some recomp. could still be traightened out
5747      Should add xx_dic control variable to test at some point
5748    o model/src:
5749      add run-time parameters to check and/or mask initial Temp & Salt
5750    o pkg/ptracers:
5751      apply zonal filter (if used) to all passive tracers
5752    
5753    checkpoint61w (2009/10/12)
5754    o adjoint:
5755      * update and finish work on adjoint of dic package (G. Forget)
5756      * start adjoint of offline package
5757      * bug fix for cube-sphere TLM code (active_file_g.F)
5758    o tutorial_global_oce_optim:
5759      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
5760      and add SIZE.h_mpi for MPI testing
5761    o pkg autodiff
5762     - fix bug in autodiff_restore
5763     - make genmake2 remove comments and empty lines from ad_input_code.f in
5764       order to reduce file size (new script file remove_comments_sed)
5765    o allows to specify vertical profile of vertical viscosity (viscArNr)
5766    o pkg autodiff
5767      autodiff_ini_model_io: comment out writing of grid information to netcdf
5768      files, because at this time the grid fields are a bunch of zeros
5769      (this is analogous to ini_mnc_vars.F)
5770    o pkg seaice/autodiff:
5771     left-over from removing the 3-time-level fields:
5772     - small rearrangement of common blocks (SEAICE.h)
5773     - fix field declaration in order to get meaningful output in
5774       adseaice.*.nc (adcommon.h)
5775    o pkg obcs:
5776     - go through NH code only if nonHydrostatic=T
5777     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
5778     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
5779       => Update output of experiment seaice_obcs
5780     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
5781     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
5782     - fix restart for useOBCSprescribe + useEXF
5783    o pkg ctrl
5784     - make obcs as control parameter work also with useSingleCPUio
5785     - replace a few sny and snx by Ny and Nx to be consistent with
5786       ctrl_set_globfld_x/yz.F
5787    o pkg seaice
5788     - re-introduce global field frWtrAtm for the case of
5789       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
5790     - catch the case of an empty filename in seaice_cost_init_fixed.F
5791    o pkg ecco:
5792     - small bug fixes in the_main_loop
5793      . fix order of monitor arguments
5794      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
5795      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
5796        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
5797     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
5798       imbalance diagnostics for wmean_h/sflux = 0
5799     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
5800     - catch the case of empty filenames in ecco_cost_init_fixed.F
5801       and ecco_readparms.F
5802     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
5803       to make this statement meaningfull in ecco_cost_weights.F
5804    o pkg zonal_filt:
5805      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
5806      - when using rStar, filter uVel*hFacW instead of uVel
5807       (tested without topography: fix a Pb of growing instability with NLFS)
5808    o pkg/aim/thsice:
5809     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
5810      (works as SST restoring)
5811    o pkg/thsice:
5812     -add specific parameter for salt restoring in slab mixed-layer
5813       (by default equal to the temperature restoring)
5814    
5815    checkpoint61v (2009/09/21)
5816    o pkg/kpp:
5817     -add double diffusive contributions as a hack, turned off by default
5818      for now, and the code can be excluded with a CPP-flag
5819      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
5820     -add a verification experiments to "vermix" to test this code
5821    o pkg/mom_common:
5822      Move computation of length scales to mom_init_fixed.F (avoid recomputation
5823      at each time-steps*levels).
5824    o pkg/layers:
5825      Created a new package for computing volume fluxes in temperature or
5826      [not yet implemented] density layers, e.g. for calculating residual
5827      overturning circulations.
5828    o pkg/diagnostics:
5829      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
5830    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
5831    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
5832      To avoid mixing type (RS/RL) of input/output array argument,
5833      replace single mixed-type array with a pair from each type (RS/RL).
5834    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
5835      is now implemented for all pkgs (previously only done for the main pickup)
5836    
5837    checkpoint61u (2009/08/25)
5838    o pkg/obcs:
5839      - change OB?eta from _RS to _RL and put them into a separate commen block
5840      - add code to read OB?eta from a file via obcs_prescribe_read: the code
5841        compiles and does not destroy any other experiments, the data is read
5842        properly, but the code is not tested in actual applications
5843    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
5844      create a meaningful unit attribute for the time coordinate variable
5845    o pkg/ebm: add plenty of missing "_d 0" ;
5846       update results of experiment global_ocean_ebm (fwd + adjoint tests)
5847      Notes: several pieces of code only works for (very) specific set up
5848       (domain size, lat range, etc ...); should be documented & stop if one
5849       of those assumptions is not meet.
5850    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
5851       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
5852          and offline_exf_seaice (seaicetd + adjoint).
5853    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
5854       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
5855        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
5856    o few changes to pass when compiling with strick checking of arguments
5857       across S/R (allow to find few bugs in S/R calls).
5858    o pkg/seaice:
5859     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
5860       2d-fields, for slightly better performance
5861    
5862    checkpoint61t (2009/07/22)
5863    o pkg/seaice:
5864     - remove unused variables in seaice_evp
5865     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
5866    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
5867       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
5868       each processor opens a different file (a fix from Matt).
5869    o cg2d:
5870       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
5871       this reduces number of EXCH calls by 2 when using exch2.
5872       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
5873       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
5874    o pkg/thsice:
5875       add code for Near Infra-Red albedo (from Jeff)
5876       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
5877    o ini_model_io:
5878       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
5879       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
5880       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
5881    
5882    checkpoint61s (2009/06/30)
5883    o pkg/exch2 (exch2_rxN_cube*):
5884       remove last BARRIER (no need to synchronise after getting data from shared
5885       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
5886    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
5887      and generate new output (for the 2 tests) using default rotationPeriod.
5888    o pkg/exch2:
5889      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
5890        (was already the case with AUTODIFF_EXCH2 defined)
5891      - add bj in exch2 arrays and S/R.
5892      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
5893        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
5894    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
5895      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
5896        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
5897      - verification experiment natl_box.longstep
5898    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
5899      allow different versions of ifort (8 or 9) and different versions
5900       of mpi (mpich or mpich2) to be used with the same optfile.
5901      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
5902       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
5903    o pkg/seaice:
5904      fix previous modif (3-level field removed) for old-pickup reading
5905    
5906    checkpoint61r (2009/06/25)
5907    o pkg/seaice:
5908     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
5909      1. introduce fields for time step (N-1)
5910      2. do not use levels 2 and 3 anymore (but keep them)
5911      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
5912         includes changes to pkg/thsice/thsice_get_velocity.F,
5913         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
5914         pkg/obcs/obcs_apply_uvice.F.
5915     - completely remove code for leap-frog time stepping for second order
5916       advection
5917     - adjusted adjoint accordingly;
5918       gradient checks have improved by an order of magnitude!
5919    
5920    checkpoint61q (2009/06/22)
5921    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
5922     - the boundary conditions along open boundaries are unclear, because the
5923       associated masks are set to zero and are thus treated as closed when
5924       applying the slip-boundary conditions.
5925     - move initialisation of grid variables from seaice_init_varia to _fixed
5926    o adding doc/diags_changes.txt
5927    o model/src:
5928      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
5929       to avoid "_diags" naming if no relation to pkg/diagnostics.
5930      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
5931       file and only call PLOT_FIELD_XYZ if debugMode=T.
5932      remove few PLOT_FIELD_XY calls outside initialisation.
5933      remove few unnecessary BARRIER.
5934    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
5935      of salt_plume package in Southern Ocean
5936    o pkg/thsice:
5937     - fix hOceMxL in overlap (needed for sea-ice advection);
5938       update output of experiment global_ocean.cs32x15.icedyn.
5939    o pkg/seaice:
5940     - make the (placeholder-)tracer IceAge a little more meaningful
5941      by avoiding ridging of age due to convergent ice flow
5942     - add diagnostics for surface temperature, atmospheric and oceanic
5943       heat flux, and atmospheric and oceanic ice growth
5944    
5945    checkpoint61p (2009/06/10)
5946    o eesupp (global_max & global_sum):
5947     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
5948     - remove starting & endding barrier (no longer needed)
5949    o pkg/mdsio, writelocal:
5950       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
5951       (remove the STOP): uses shared buffer IO to store data from all threads
5952       and then let master-thread write nThreads tiles.
5953    o pkg/mdsio (read/write field):
5954     - tiled IO done in 1 piece (all levels at a time);
5955     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
5956     - multi-threaded: allow to read/write local (non-shared) array
5957       (was already working with singleCpuIO ; now works also without);
5958       => no longer needs barrier call after reading a file (added inside
5959       mds_read/write field).
5960     - move barrier calls outside gather/scatter_2d to mds_read/write_field
5961    o pkg/obcs/exf
5962      - exf_getffieldrec.F: add a few ". _d 0" and
5963                            add code to catch the case fldperiod = 0.  
5964      - obcs_precribe_read.F: change if statements so that they match
5965                              the variable type (_RL)
5966      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
5967        exf_iprec) as part of namelist EXF_NML_01
5968    o pkg/mdsio:
5969      - read/write tiled (local) files: read/write 1-level tile chunk at a time
5970        (instead of segment of length sNx); expected to speed up tiled IO.
5971    o pkg/exch2:
5972      - take buffer copy from/to array out of S/R exch2_send/recv into new
5973        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
5974        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
5975      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
5976      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
5977        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
5978        including Topology header file (and common blocks).
5979      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
5980        remove 2nd exch call in exch2_s3d_rx (no longer needed).
5981      - document S/R arg. list (+ update some comments)
5982    o pkg/seaice:
5983      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
5984        temperature and humidity over sea ice based on climatological values.
5985      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
5986        of LSR (this change is expected to change the results slightly because now
5987        it uses slightly difference moduli from the second last LSR solution, but
5988        that is more consistent with the stress computations; this part of the code
5989        is not tested in the verification experiments)
5990      - fix diagnostics for flux of ice in case of B-grid
5991      - turn strain rates eij and press into global fields within global
5992        common block in SEAICE.h for more straighforward diagnostics
5993      - fix diagnostics for principal stress components, press, zeta, eta
5994        to give something meaning full
5995    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
5996      new output (all 4 tests) using default rotationPeriod.
5997    o pkg KPP:
5998      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
5999      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
6000        and normal grid from 1 to Nr)
6001    o Fix computations of L4rdt in mom_calc_visc.F
6002    o eesupp:
6003      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
6004      should be called before a "stop" if we know that all process are going
6005      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
6006    
6007    checkpoint61o (2009/05/26)
6008    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
6009    o model/src/ini_curvilinear_grid.F:
6010       compute angleSin/CosC when they are not read from a file
6011    o pkg/seaice:
6012       add pseudo time stepping for LSOR
6013    o pkg/exch2:
6014       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
6015    o pkg/seaice:
6016       Adding separate sea ice albedo, drag coefficients, and HO in Southern
6017       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
6018    o SingleCpuIO:
6019       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
6020    o pkg/seaice:
6021       put exchanged variable in (local) common block for MPI+Multi-Threads
6022       to work (necessary with exch1, and for now with exch2 too).
6023    o verification: to get more experiments tested with mpi, mth and mpi+mth,
6024      change tiling of:
6025       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
6026       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
6027      update output of exp:
6028       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
6029       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
6030      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
6031                       (note: output.txt generated on faulks using only 1 tile)
6032    o eesupp & mdsio (SingleCpuIO):
6033     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
6034       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
6035       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
6036     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
6037     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
6038       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
6039    o pkg/exch2:
6040     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
6041       read parameter file "data.exch2" if it exists; otherwise try default regular
6042       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
6043     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
6044       with new code (not to be used, just as a backup solution).
6045     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
6046       in utils/exch2/input.
6047    
6048    checkpoint61n (2009/05/12)
6049    o eesupp & mdsio (SingleCpuIO):
6050      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
6051        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
6052        receive real*4 array (instead of real*8) to read/write 32.bit files.
6053        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
6054         and remove new mapping S/R)
6055    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
6056      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
6057        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
6058        when using exch2. Add S/R to map global io-buffer to global model array.
6059      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
6060    
6061    checkpoint61m (2009/04/29)
6062    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
6063      and add 3 other S/R for other types (R4,R8,RS).
6064      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
6065    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
6066     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
6067     - reduce number of macro definitions (keep only those which are used);
6068       can always call directly the corrresponding S/R if needed.
6069     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
6070       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
6071     Fixed wrong type of arg in:
6072       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
6073       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
6074     To fix: global_sum of var in common block is wrong (multi-threaded) in:
6075       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
6076     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
6077    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
6078      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
6079    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
6080    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
6081      edges are closed (zero depth); might happen with "blank tiles";
6082      for now, disabled if using OBCS.
6083    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
6084      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
6085    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
6086      to reduce length of 1.D array print in STDOUT.
6087    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
6088      + use 48 tiles (16x8): this will allow to test "blank tiles".
6089    o start to test MPI + multi-threaded (change testreport to skip tests
6090      where number of tiles do not match).
6091    o genmake2: add option "-omp" to turn on Open-MP ;
6092      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
6093    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
6094      and keep the original tile numbering. Note: compatible with old
6095      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
6096    
6097    checkpoint61l (2009/04/07)
6098    o Overlaps had been forgotten in calculating ijk keys : fixed
6099    o fix cyrus makedepend for gcc 4.4
6100    o experiment fizhi-cs-aqualev20:
6101      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
6102      and generate new output. Note: new output is much closer to the old
6103      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
6104      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
6105    o pkg/fizhi:
6106     - change to avoid indices going deliberately over array-bounds
6107     - remove unnecessary MPI stuff
6108     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
6109     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
6110       does not go over array-bounds and therefore returns reliable output.
6111     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
6112       this S/R has 4 output arguments, which are used inside "get_alarm";
6113       when it is called with the same variable "ndum" in place of several
6114       output arguments, this produces weird side effect inside "get_alarm"
6115      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
6116       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
6117       address) and produces error.
6118    o tools/gemake2: (March 27-29 2009)
6119      with option "-mpi": link *_mpi files from "MODS" dir (this is what
6120      testreport does).
6121    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
6122    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
6123       update lab_sea.lsr & lab_sea.salt_plume results
6124    o pkg/seaice:
6125      Major overhaul of the LSOR solver: change discretization from original
6126      finite differences to finite volume. The old routine is still in the
6127      file seaice_lsr.F and can be turned on with the CPP-flag
6128      SEAICE_OLD_AND_BAD_DISCRETIZATION
6129      Along with this change, the discretization of the strain rates is changed.
6130      The same flag turns on the old discretization in seaice_calc_strainrates.F
6131      All verification experiments with seaice are affected (except for
6132      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
6133      results by setting the above flag.
6134      Further changes involve changes in defaults:
6135      - ALLOW_FLOODING is defined and turned on by default
6136      - SEAICEadvSnow = .true. is now the default
6137      - SEAICEadvSalt = .true. is now the default
6138      - SEAICEadvAge  = .true. is now the default
6139      - SEAICE_clipVelocities  = .false. is now the default
6140                                         (as per J. Zhang's recommendation)
6141      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
6142        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
6143      - seaice_growth: replace computation of UG by a simple copy from wspeed
6144    
6145    checkpoint61k (2009/03/18)
6146    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
6147      seaice_lsr: fixed a few metric terms,
6148                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
6149                  add more debugging diagnostics
6150      seaice_evp: removed superfluous many metric terms of FV discretization
6151                  of stress divergence
6152                  affects lab_sea, lab_sea.hb87
6153      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
6154                  of stress divergence for non-evp solver
6155                  (this part is not tested anywhere)
6156      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
6157                  they were effectively only half slip
6158                  affects lab_sea.hb87
6159      updated all relevant verification experiments (except lab_sea//output_adm.txt
6160        which was left over, but fails at level 7 & 6)
6161    
6162    checkpoint61j (2009/03/17)
6163    o pkg/seaice: turn a few hard wired parameters into run time parameters
6164    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
6165      time in seconds as promised by the usints in seaice_monitor and exf_monitor
6166    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
6167      that are not cubed-sphere grids
6168    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
6169    o pkg/ctrl:
6170      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
6171    o non-hydrostatic (calc_gw.F):
6172      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
6173      update output of exp. global_ocean.cs32x15.viscA4
6174    o remove backward compatibility for thetaMin,phiMin
6175      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
6176    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
6177      interpolated wind field not only for curvilineargrid=.true., but also
6178      for a rotated grid (rotateGrid=.true.)
6179    o pkg/exf: add capability to bypass interpolation for runoff
6180      by setting yet another CPP-flag
6181    o eesupp/src, B-grid exchange:
6182      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
6183    o autodiff
6184      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
6185      allows to switch to single-prec common blocks;
6186      corresponding switch occurs in tamc.h, integer isbyte
6187      TAF store directivs "byte" and "kind" seem equivalent;
6188      Most tamc.h have been updated correspondingly.
6189    
6190    checkpoint61i (2009/02/13)
6191    o autodiff:
6192      fix autodiff_sore/_restore indices for obcs
6193      (spotted by I. Hoteit, M. Mazloff)
6194    o pkg/autodiff, pkg/ctrl:
6195      Add flag to reduce all tapelev I/O to single-prec.
6196      In data.ctrl set
6197        doSinglePrecTapelev = .TRUE.
6198    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
6199      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
6200    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
6201      real fresh water flux (not yet)
6202    o pkg/mdsio & rw:
6203     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
6204     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
6205    o pkg/flt:
6206     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
6207       init_fixed & ini_varia.
6208     - clean-up & simplify linear interpolation S/R:
6209       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
6210     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
6211     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
6212     - add vert. coordinate & horiz. indices to output files.
6213     - change vertical position in initial condition, from index to depth [m].
6214     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
6215       (easier to get to a curvilinear grid) ; delX,delY no longer used.
6216    o pkg/ggl90: a few modifications:
6217     - fix bottom boundary condition, and interpolation of KappaE
6218       near top and bottom
6219     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
6220     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
6221     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
6222    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
6223      (maintain temporary backward compatibility, until next checkpoint)
6224    
6225    checkpoint61h (2009/01/27)
6226    o pkg/diagnostics with "periodic averaging diagnostics":
6227      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
6228    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
6229    o pkg/obcs: fix loop ranges for balancing code
6230    o pkg/flt:
6231     - improve criteria for finding which tile owns a float.
6232     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
6233    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
6234      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
6235      with ocean biogeo)
6236    o pkg/flt:
6237     - do some cleaning and fix the restart ;
6238     - add output.txt in flt_example/results to get this pkg tested.
6239    o genmake2: add an EXTENDED_SRC option and flag.
6240       for now, cannot be turned on on command line (only through genmake_local)
6241    o pkg/mdsio: read/write vector:
6242     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
6243     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
6244       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
6245     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
6246      (drop to 4 digits matching for grad). But this test does not look very
6247      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
6248    
6249    checkpoint61g (2008/12/29)
6250    o pkg/flt:
6251      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
6252       + make OPTIONS file more standard.
6253      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
6254      - fix _BYTESWAPIO CPP-Flag
6255      - standard reading of file-parameter "data.flt"
6256      - fix argument list of S/R FLT_RESTART
6257      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
6258    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
6259    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
6260      a still unfixed compiler/optimization bug
6261    
6262    checkpoint61f (2008/11/21)
6263    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
6264      update results of global_ocean.cs32x15.icedyn test.
6265    o move getcon.F from model/src to pkg/fizhi.
6266    o pkg/exf: add parameter for extrapolation of temp up to the surface
6267       and option to prevent negative evap (in bulk_largeyeager04 only).
6268    o Prather Advection scheme: fix tracer conservation for divergent flow
6269      (e.g., when using NonLin Free-Surface).
6270    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
6271    o gmredi (Visbeck-variable-K):
6272     - add more parameters to Visbeck-variable-K.
6273     - use a 5 points average for dSigmaR in Visbeck-K calculation
6274       (more "homogenous": same stencil and same weights as in dSigmaH)
6275     - update output of ideal_2D_oce experiment.
6276    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
6277      (#undef REAL4_IS_SLOW)
6278     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
6279       coordinate variable
6280     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
6281       (surface forcing fields), removes some of the functionality
6282     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
6283     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
6284       probably not all: copy _RS surface flux fields to RL field before
6285       calling DIAGNOSTICS_FILL
6286     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
6287       real*4 (CALL EXCH_*_RS) versions.
6288     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
6289       (generate new output).
6290    
6291    checkpoint61e (2008/10/23)
6292    o gmredi (Visbeck-variable-K):
6293      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
6294      - change computation of Visbeck-K where Slope > Smax :        
6295        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
6296        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
6297    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
6298      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
6299    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
6300    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
6301      does not become too large (to avoid precision problems in implicit-diffusion
6302      solver); update ideal_2D_oce output.
6303    o pkg ggl90:
6304      - in ggl90_cal.F: compute only one set of visc/diff, used to
6305        step forward TKE/T/S/momentum
6306      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
6307        have Prandlt =1)
6308    o gmredi (fm07):
6309      - add lower limit on Transition layer thickness + lower limit on 1/lambda
6310      - allow to set few more params from data.gmredi
6311    o pkg ggl90:
6312          - add missing sqrt(2) factor in computation of mixing length
6313            scale in ggl90_calc.F
6314            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
6315    
6316    checkpoint61d (2008/09/25)
6317    o adjoint modifs
6318      - adapt to new field rhoInSitu
6319      - allow to revert from StoreDynVars2D, StoreDynVars3D
6320        to individual fields
6321        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
6322    o store 3-D (in-situ) density in commom block (DYNVARS.h)
6323     - save 1 rho computation.
6324     - no longer modify T & S inland when using down_slope pkg.
6325    o gad_som : allow to switch to SOM advection for T & S without corresponding
6326      pickup files (using new S/R: MDS_CHECK4FILE).
6327    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
6328      (for useSingleCpuIO to work in multi-threaded)
6329    o pkg/shelfice:
6330     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
6331       with SHELFICEtopoFile in data.shelfice
6332     - move code for reading ice shelf topography and modifying hFacC into separate
6333       subroutines of the shelfice package
6334     - separate initialisation of "fixed" and "variable" variables
6335     - kTopC is not (yet) replaced by kSurfC, although this is possible
6336    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
6337    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
6338      and rename:
6339      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
6340      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
6341    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
6342    
6343    checkpoint61c (2008/08/30)
6344    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
6345      to add mass source/sink of fluid in the interior (3-D generalisation
6346      of oceanic real-fresh water flux).
6347    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
6348    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
6349    o new pkg: down_slope
6350      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
6351      - presently, modify T & S inland (dwnslp_calc_rho.F).
6352        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
6353      - implementation for ocean in P-coords not tested.
6354      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
6355    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
6356      (to facilitate conversion of oceanic pkg to p-coordinate).
6357    o change FIND_RHO to FIND_RHO_2D :
6358      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
6359    o new pkg: cheapaml
6360    
6361    checkpoint61b (2008/08/05)
6362    o exch2:
6363      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
6364      - no longer depend on the order sequence (N,S,E,W).
6365      - 3rd exchange no longer needed (tested with 24 tiles).
6366      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
6367      - exch_UV_A-grid readily available (but not yet tested).
6368      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
6369      (both are no longer needed) in exch_uv: no effect in forward run; but
6370       get truncation error differences with adjoint exch.
6371    o exch2:
6372     - change index-bounds storage (moved from target to local tile,
6373       more intuitive this way) ; rename/remove some variables.
6374     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
6375    
6376    checkpoint61a (2008/07/29)
6377    o exch2/matlab-topology-generator:
6378      fix bug in index bounds for N-S internal exchange (hard to tell if this
6379      had any effect on the solution).
6380    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
6381      is exceeded
6382    o testreport: modify syntax of awk, so that it works also with
6383      awk, and not only with nawk and gawk
6384    
6385    checkpoint61 (2008/06/24)
6386    o autodiff
6387      Change default for TAF usage by removing argument '-nonew_arg'
6388      This changes TAF subroutine argument list (ordering of active var.)
6389      Omission of this flag leads to incompatibility w.r.t. TAMC
6390      To restore TAMC-compatibility, need following modifs:
6391      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
6392      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
6393      Tested TAF version is 1.9.22
6394      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
6395    
6396    checkpoint60 (2008/06/19)
6397    --->>> This is the last checkpoint for which generating the adjoint
6398    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
6399    --->>> by default.
6400    --->>> Future checkpoints will ommit this flag by default.
6401    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
6402    o pkg/grdchk: Add gradient check to etan0 perturbations.
6403    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
6404    o pkg/autodiff: more flexibility in zeroadj.
6405      model/src: modifying do_oceanic_phys.F accordingly.
6406    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
6407    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
6408      special setup of gmredi for which the adjoint is stable
6409      enough for parameter optimization.
6410    o bridging the gap between eddy stress and GM.
6411      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
6412          along with a change in CPP option (now ALLOW_EDDYPSI).
6413      -> when using GM w/ GM_AdvForm:
6414          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
6415          is applied either in the tracer Eq. or in momentum Eq.
6416          depending on data.gmredi (intro. GM_InMomAsStress).
6417      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
6418      The key modifications are in model/src/taueddy_external_forcing.F
6419      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
6420    
6421    checkpoint59r (2008/05/29)
6422    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
6423      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
6424      fix option to read coriolis(@ cell-corner) from files with CS-grid.
6425    o pkg/mnc: add some attributes to standard 1D-coordinate variables
6426    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
6427      mass points, when using mnc for output
6428      - add runtime parameter (missing_value, missing_value_int) to override
6429        default (which is the value of getcon('UNDEF'))
6430    o pkg/mnc: prepare mnc for the actual use of missing values with the
6431      diagnostics package: small fix in mnc_cw_readwrite.template and more
6432      initialisation of never used fields
6433      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
6434      versions
6435    o pkg/thsice/thsice_ini_vars.F added default initial values so that
6436      thermodynamics sea ice solver does not blow up when some initial fields
6437      are missing.
6438    o move from external_forcing_surf.F to ini_forcing.F
6439      the p-coord. hack consisting in using pLoad to set phi0surf ;
6440      update output of tutorial_global_oce_in_p (affected @ truncation level).
6441    o Freshen up a bit hs94.1x64x5, notably:
6442      remove rotationPeriod and tRef=5*0. (adjoint only), and add
6443      exactConserv=.TRUE.
6444    o pkg/generic_advdiff:
6445      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
6446      applies to files where Temperature & Salinity 2nd Order moments are used.
6447    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
6448      this uses a dynamically allocated internal state data structure
6449      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
6450      and requires a fortran 90 compiler
6451    
6452    checkpoint59q (2008/05/06)
6453    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
6454       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
6455    o Refresh tutorial_global_oce_biogeo, notably:
6456      - change bathymetry (put back seamounts in ACC, use hFacs)
6457      - change EOS (POLY3 --> JMD95Z)
6458      - use Bryan-Lewis vertical diffusivity
6459      - use multidimensional advection
6460      - remove old virtual virtual in dic pkg, now done through ptracer pkg
6461      - change a couple of parameters in dic pkg
6462    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
6463    o pkg/obcs: change default to OBCSfixTopo = .true.,
6464      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
6465      - replace "debugMode" with "debugLevel .GE. debLevB"
6466    o implementation of TAF directives for gchem,cfc,dic
6467    o remove "exp5" (replaced by tutorial_deep_convection).
6468    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
6469      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
6470      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
6471      --> changes results in exp4, seaice_obcs
6472    o tutorial_deep_convection :
6473      update the set-up and increase resolution and domain size ; start
6474      from pseudo initial conditions = output at t=120mn in order to see
6475      something happening when running testreport.
6476    o pkg/seaice: add os7mp as an advection scheme
6477                  add check for advection schemes
6478                  add a flag for restoring T and S underneath sea ice
6479    o pkg/my82: add netcdf-support and diagnostics
6480    o thsice pkg:
6481      - Now hsMax limits snow height by turning it into ice following
6482        flooding scheme (and now conserving energy)
6483      - Slight rewriting of the formula in thsice_calc_thick.F
6484      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
6485      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
6486    
6487    checkpoint59p (2008/04/10)
6488    o gchem / dic / cfc :
6489      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
6490      - add new parameter files: "data.dic" & "data.cfc" ;
6491      - various re-arrangement in initialisation & header file ;
6492      - fix tutorial_global_oce_biogeo for multi-threaded test.
6493    o pkg/dic: test for "pickup_dic" file when restarting ;
6494      if no pickup-file, can restart with a re-initialised pH (same as it did
6495      before) providing pickupStrictlyMatch is set to False.
6496    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
6497      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
6498    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
6499      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
6500    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
6501     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
6502       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
6503    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
6504       scheme to use for vorticty-term ;
6505     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
6506       (with default selectVortScheme, return to original discretisation)
6507     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
6508    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
6509    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
6510      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
6511      also fix diagnostics VISCAHW & VISCA4W.
6512    
6513    checkpoint59o (2008/03/07)
6514    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
6515    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
6516      move a few statemens out the main loop into separate loops
6517    o pkg/shelfice:
6518      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
6519        (kg/m^2/s), does not break tests, because in verification/isomip,
6520        rhoConstFresh=rhoConst (by accident)
6521      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
6522      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
6523        new file model/src/seawater.F, so that they are available for all pkgs.
6524      - convert potential temperature into in-situ temperature. This changes the
6525        isomip tests => update tests
6526    o add a flag writePickupAtEnd (default=true) to be able to suppress
6527      writing a pickup at the last timestep
6528    o tools/mpack-1.6 :
6529      - disable automake (not working) and autoconf (not needed).
6530      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
6531        also cleaner with much less compilation warnings.
6532    o pkg/profiles:
6533      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
6534      (for "less than 32 characters name" compiler requirement)
6535    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
6536      conditions that have a different sampling frequency than S/T/U/V obcs
6537    o pkg/diagnostics (stats-diags):
6538      - fix global Min/Max in case 1 processor get only empty tiles
6539    o genmake2: replace (4 times)
6540         make genmake_tc_1.o >> genmake_warnings 2>&1
6541      with
6542         COMM="$CC $CFLAGS -c genmake_tc_1.c"
6543         echo $COMM >> genmake_warnings
6544         $COMM >> genmake_warnings 2>&1
6545      to make genmake2 always see the value of CC as specified in the optfile.
6546    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
6547      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
6548      - modify verification advect_cs test to test SOM-advection on CS-grid.
6549    o pkg/ctrl:
6550      - Rewrite of ctrl_map_ini_ecco.F,
6551        introducing a generic routine (ctrl_map_ini_gen.F).
6552      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
6553    
6554    checkpoint59n (2008/02/09)
6555    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
6556      number in dedicate array "hdiag":
6557      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
6558        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
6559      - many small changes (integer format) for large number of diagnostics
6560      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
6561        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
6562    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
6563      usingSphericalGrid, this allows to define the rotated grid coordinates
6564      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
6565      geographical coordinates according to the inverse of the rotation defined
6566      by the Euler angles, so that Coriolis parameter and online-interpolation by
6567      exf works with the geographical coordinates on XC/YC/XG/YG.
6568      Naturally, this feature does not work with all packages, so some
6569      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
6570      profiles), because there the coordinates are assumed to be regular
6571      spherical grid coordinates.
6572    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
6573      - introduce isopycnal diffusion coefficient control.
6574    o tools/adjoint_options:
6575      - additional control vector components.
6576    o pkg/mnc: have mnc create marginally meaning full coordinate variables
6577      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
6578    o pkg/mypackage:
6579      - add example of read/write pickup for state-var ;
6580      - add entry points to the main code for state-vars diags & write-pickup.
6581    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
6582      transitions for useExfYearlyFields
6583      - add new subroutine that determines the file to read from for
6584        use*YearlyFields = .TRUE. and .FALSE.
6585      - add a verification experiment to global_with_exf that tests
6586        useExfYearlyFields with USE_EXF_INTERPOLATION defined
6587    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
6588      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
6589      subroutines (which could be generated from a template, because they are
6590      almost identical), for now they are included in obcs_prescribe_read.F for
6591      simplicity
6592    o pkg/exf:
6593      - add a little more diagnostic to exf_interp_read (in analogy to
6594        mds_read_field, can be turned off with debugLevel < debugLevA=1)
6595      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
6596        ugly but fast by unrolling short inner loops, inserting a unroll=8
6597        directive in routine lagran, and splitting a loop and making do while the
6598        outermost loop (the latter requires the intoduction of index arrays)
6599    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
6600    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
6601      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
6602    o verification/seaice_obcs: updated for restart test and latest options
6603    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
6604      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
6605      for now this is only available for the C-grid code and also within
6606      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
6607    
6608    checkpoint59m (2008/01/14)
6609    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
6610      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
6611    o gad_som : fix flux output (& diagnostics) to have same units as other  
6612      advection scheme fluxes (was previously multiplied by deltaT).  
6613    o added verification/seaice_obcs both to test seaice open boundaries
6614      and to provide an example matlab scrpt for generating them
6615    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
6616    o pkg/salt_plume: clean up salt_plume_frac.F to
6617      remove redundancy in PlumeMethod 1 and 4
6618    o pkg/kpp: added saltplume diagnostics
6619    o pkg/obcs and pkg/seaice:
6620      - do not set uice and vice to zero when OB*icefile are unspecified
6621      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
6622      - moved seaice tracer obcs after call to seaice_growth
6623    o pkg/salt_plume: added various options for salt plume depth
6624      criterion and for vertical distribution of the salt
6625    
6626    checkpoint59l (2007/12/18)
6627    o pkg/ptracers: new version of ptracers pickup:
6628      read meta file and write only fields which are needed to restart.
6629      ( same logic as main pickup file ; also using pickupStrictlyMatch )
6630    o pkg/seaice:
6631      - add timescale for melting due to warm mixed layer as a means of
6632        setting SEAICE_availHeatFrac more conveniently
6633      - add a CPP-flag/runtime parameter check for flooding algorithm
6634      - reformulated availHeat in seaice_growth.F to be independent of AREA
6635    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
6636      unit changes
6637    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
6638    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
6639      SX vector computer.
6640    o pkg/seaice:
6641      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
6642        seaice forcing fields can now be read only through pkg/exf
6643      - removed some unused halos
6644    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
6645    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
6646      or U/VICE from U/VWIND before computing U/VSTRESS
6647    
6648    checkpoint59k (2007/11/30)
6649    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
6650      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
6651    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
6652      all experiments pass when compile with un-initialised var. checking option.
6653    o added pkg/salt_plume
6654    o script to test restart (for now, in MITgcm_contrib/jmc_script)
6655    o pkg/seaice: new read/write pickup version.
6656      read meta file and write only fields which are needed to restart.
6657      ( same logic as main pickup file ; also using pickupStrictlyMatch )
6658    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
6659    o lab_sea.hb87: modify the domain & update output.hb87.txt :
6660      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
6661      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
6662      process. Fixed here by closing the domain at the Northern boundary.
6663    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
6664    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
6665      a set of consecutive levels in/from a 3-D array.
6666    o pkg/ptracers:
6667      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
6668      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
6669    
6670    checkpoint59j (2007/11/09)
6671    o in pkgs: dic, obcs, offline, rbcs:
6672      standard way to compute coeff. for time interpolation between 2 time reccords
6673      which retains full precision (& make results less dependent on compiler).
6674      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
6675    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
6676      packages instead of reading ice cover and wind speed separately
6677    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
6678     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
6679      to allow to compile customized code before the update)
6680    o cleaning-up:
6681      - fix CPP instruction syntax in pkg/obcs
6682      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
6683        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
6684      - fix some threads issue in IO parts.
6685    o pkg/dic:
6686      - add tons of "_d 0" (--> much better testreports !)
6687       and then update outputs of tutorial_global_oce_biogeo
6688    o pkg/mom_fluxform:
6689      add a special version of momentum advection intended to conserve momentum
6690      next to a bathymetry step or a coastline edge. (default = off = #undef)
6691    o new read/write pickup version:
6692      - for now, only implemented for main (mdsio) pickup file.
6693      - write out only what is needed to restart; merge pickup_nh , pickup_ph
6694        and main pickup together.
6695      - read meta file; read only what is needed to restart; stop if a field
6696        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
6697        if it make sense (even if the restart is not perfect).
6698      - if no meta file, assume that pickup to read corresponds exactly to
6699        a pickup that would currently be written.
6700      - read pickup written in the old format (until checkpoint59i) if it
6701        recognizes an old meta file (no field-list).
6702      - add a meta file in exp. which starts from a pickup: 2 cases:
6703        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
6704         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
6705        b) a meta file describing the content of the associated pickup file
6706         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
6707    o pkg/mdsio & pkg/rw:
6708      - new routine to read a meta file ; new set of routine to read
6709        Multiple-fields file (with meta file).
6710    o added open boundary conditions capability for seaice
6711        HSNOW, HSALT, UICE, and VICE
6712    
6713    checkpoint59i (2007/10/21)
6714    o adjoint:
6715      * fix multiDimAdvection adjoint
6716        (partial recomputation problem by TAF for fVerT(:,:,kDown)
6717        and comlev1 size definition (maxpass vs. max. number of tracers)
6718      * verification/global_ocean.90x45x15 adjoint now tests
6719        NLFS and multiDimAdvection using DST3 (=30)
6720      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
6721    o pkg/kpp: add "_d 0" to real constant (if missing);
6722      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
6723      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
6724    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
6725      for internal parameters related to restart process (formerly from PARAMS.h)
6726      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
6727    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
6728      as argument. (only atm2d & obcs write_pickup have not yet been updated)
6729    o pkg/monitor:
6730      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
6731      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
6732      - account for deep Atmosphere factor and density factor (anelastic)
6733    o added open boundary conditions capability for seaice HEFF and AREA
6734    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
6735      thermodynamics
6736      - requires a little reorganization, which affects the testreport results
6737        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
6738        so that now the conservative form is tested
6739      - add a few comments
6740    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
6741    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
6742    o add new diagnostics to seaice: advective, diffusive fluxes (only for
6743      multidim-advection, for scheme 2 they are not filled) and transports,
6744      thermodynamic growth rates
6745    o change units of EmPmR (inside the code, + within coupling interface)
6746      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
6747      Affects results @ truncation level (cg2d match) and update output of
6748       experiments: lab_sea(6), global_ocean.90x40x15(10),
6749      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
6750      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
6751      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
6752      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
6753    
6754    checkpoint59h (2007/09/29)
6755    o pkg/exf:
6756      - improve vectorization by moving if-statement out of loops in
6757        exf_mapfields, exf_radiation
6758      - exf_bulkformulae.F: introduce 2D fields and vectorize code
6759    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
6760    o testreport:
6761      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
6762        monitor & update offline_exf_seaice exp. output.
6763      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
6764    o pkg/seaice:
6765      - bug fix in the evp solver: boundary conditions were affected be
6766        masking of zMax/zMin (changes results)
6767      - minor bug fix in boundary conditions in seaice_calc_strainrates
6768        (changes results for no_slip)
6769      - seaice_lsr.F: make interpolation of eta dependent on boundaries
6770      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
6771      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
6772        stress formulation and no-slip boundary conditions
6773    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
6774      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
6775    o pkg/seaice: a first HSALT time stepping equation has been checked in
6776    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
6777      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
6778      without requiring DO-IF statements
6779    o pkg/thsice:
6780      use continuous power-law function for partition of energy between lateral
6781      melting/freezing and thinning/thickening ; old code using step function
6782      still available with #undef THSICE_FRACEN_POWERLAW
6783      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
6784    o testreport: change AD testing : check against results/output_adm.txt
6785      using same scripts as for forward test.
6786    
6787    checkpoint59g (2007/09/17)
6788    o adjoint testing: in preparation for changing testreport:
6789      - output format: cost and grad written on separated lines
6790      - ad output results in directory "results" (instead of "results_ad")
6791    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
6792    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
6793    o pkg/ecco: allow user defined cost function contributions
6794    o testreport:
6795      Allow to choose (per experiment) the list of tested output variables
6796       and the main variable (used to issue a pass/FAIL ) ;
6797      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
6798      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
6799      Also modify printing of summary:
6800       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
6801       b) echo the list of tested variables in the individual summary.txt of
6802          each experiment.
6803    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
6804      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
6805      (but still depend on the tile decompostion of the domain).
6806    o pkg/seaice: change a discretization detail to make the B-grid code
6807      "more symmetric". This change is likely to remove all "ridges/leads" that
6808      where quasi-aligned with the grid in B-grid solutions. It may also be
6809      the solution to the stress coupling issues with the B-grid.
6810    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
6811      remove .cvsignore from input dir. (since testreport no longer run here).
6812    o pkg/thsice:
6813     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
6814     - fix reshaping of sea-ice just after advection:
6815       melt all the ice only if ice-volume is too small.
6816     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
6817       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
6818     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
6819    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
6820      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
6821    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
6822      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
6823      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
6824      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
6825      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
6826      -> update output.txt
6827    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
6828     this affects truncation error: -> update output.txt of exp:
6829      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
6830      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
6831    
6832    checkpoint59f (2007/08/21)
6833    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
6834    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
6835      a bounded range (in forward mode)
6836    o pkg/ecco, ctrl, autodiff and mom_common:
6837     internal parameter controls, completements of implementations
6838    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
6839    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
6840      (not seem any difference in testing results).
6841    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
6842       at face corners.
6843    o pkg/generic_advdiff:
6844     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
6845      loop range indices for computing vertical advection tendency
6846      and do the calculation in the interior only (no overlap) ;
6847      for now, only implemented for SOM advection (to save CPU time).
6848     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
6849    o exch2 adjoint
6850      First set of changes:
6851      - add exch2 hand-written adjoint templates
6852      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
6853        This will require cleanup in pkg/autodiff/*.F
6854        (changed routines currently kept separate in verif. code/)
6855      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
6856        that used to hide exch2 or cubed-sphere specific code
6857        (commented via 'cph-exch2')
6858    o pkg/seaice
6859      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
6860    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
6861       output of global_ocean.cs32x15.thsice .
6862    
6863    checkpoint59e (2007/07/26)
6864    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
6865      for B-grid vector (not yet tested) and C-grid vector (<- only used
6866      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
6867    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
6868      (#ifdef ALLOW_SALT_PLUME)
6869    o gather_2d/scatter_2d: removed halo regions
6870    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
6871      scheme and the corresponding test case (under front_relax dir). For now,
6872      only available with Skew-flux form and not yet tested in realistic set-up.
6873      adjoint: store directives updated, but gradient checks deteriorated,
6874      so maybe GM/Redi adjoint is now broken.
6875    o seaice adjoint
6876      * add AREA, HEFF, HSNOW as control variable
6877        (should not change lab_sea results)
6878      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
6879    o pkg/seaice:
6880      * added computation of saltFlux in seaice_growth;
6881        For time being, sea ice salinity is assumed constant
6882        contribution of snow flooding to freshening of sea ice is neglected.
6883        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
6884        defaults to 0.0 in order to maintain backward compatibility.
6885        Typical values for SEAICE_salinity are 4 to 10 g/kg.
6886      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
6887      * added SEAICE_availHeatFrac, which specifies fraction of surface level
6888        heat content used to melt or grow ice
6889      * commented out cap of HICE: it helps keep ice thinner
6890      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
6891      * applied OBCS T/S mask to HEFFM sea ice mask
6892    
6893    checkpoint59d (2007/06/21)
6894    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
6895     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
6896     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
6897    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
6898     and change default value of parameter "GM_Small_Number";
6899     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
6900       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
6901       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
6902    o pkg/ecco: cost function when applying pkg/smooth to controls
6903    o pkg/ctrl: add forcingPrecond run time parameter
6904    o pkg/seaice:
6905     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
6906     - fix bug in metric terms of u-equation in LSR solver (implicit part),
6907       changes verification/lab_sea
6908     - rearrange implicit part of u-equation in LSR solver to make it easier to
6909       read, understand, and debug. This causes changes at the truncation level.
6910     - fix (serious) bug in the boundary conditions (sign error in the implicit
6911       part) of the LSR solver. Changes all LSR results.
6912     - fixed problem with HSNOW initialization to avoid thick snow when AREA
6913       is initilized with small values - does not change lab_sea results.
6914     - added HsnowFile initialization capability
6915    o pkg/smooth: addition to model/src and pkg/ctrl so allow
6916     initialization of pkg/smooth and application to control vector
6917    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
6918    o dependencies: pkg/profiles requires pkg/cal
6919    o pkg/profiles:
6920     - added option ALLOW_PROFILES_GENERICGRID
6921         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
6922         that interpolation information (grid points and coefficients) is provided
6923         within the netcdf input files.
6924         -> sample matlab scripts can be found in MITgcm_contrib/gael
6925         that allow you to prepare netcdf input files.
6926     - also modified: cleaner include statements, cleaner error print statements,
6927       cleaner stops when error, and more tests of the netcdf input files consistency.
6928    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
6929    o pkg/seaice:
6930     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
6931       requires a new routine: seaice_diagnostics_fill.F
6932     - make sure that seaice does not move if not forced (pressure replacement
6933       method, Hibler and Ip, 1995), changes results
6934     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
6935     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
6936       It is turned off by default (=-1.), because it changes the results.
6937     - make it possible to read AREA from a file, too.
6938    
6939    checkpoint59c (2007/06/04)
6940    o add S/R and diagnostics for oceanic mixed-layer depth
6941    o move GMRedi call after all vertical mixing schemes (including KPP)
6942    o pkg/thsice:
6943     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
6944      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
6945    o pkg/obcs:
6946     - bug fix for balance code
6947    o pkg/seaice:
6948      - allow values of SEAICE_elasticParm > 1
6949      - add new parameter SEAICE_evpTauRelax as an alternative
6950        to SEAICE_elasticParm
6951      - make lsr boundary conditions free slip (by default), changes result
6952      - add code for no slip boundary conditions for lsr
6953      - set minimum of zeta to zero (and not 4e8) (changes results)
6954      - add a cap on AREA after advecting AREA if seaice_growth is not called
6955    o change calculation of Visbeck K:
6956      - no longer depend on tapering scheme; instead, compute slope (limited
6957        by GM_maxSlope). this is equivalent to what was comuted before with
6958        clipping or linear tappering.
6959      - fix vertical averaging (wrong by 1/2 level)
6960      - leave the old version (but will not be maintained) within
6961        #ifdef OLD_VISBECK_CALC / #endif
6962      - update output of exp. ideal_2D_oce
6963    o change error catch in calc_r_star to improve vectorization
6964    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
6965      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
6966    o adjoint:
6967      Re-organized adjoint checkpointing according to Matt Mazloff
6968      (but with modifs/completions/cleanups)
6969      Storing is now bundled into large arrays to optimized I/O
6970      (and second step in cleanup of the_main_loop)
6971    
6972    checkpoint59b (2007/05/16)
6973    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
6974      - export/import (between ocean & coupler) fields needed for ocean DIC.
6975    o pkg/seaice:
6976      - get rid of three more exchanges seaice_calc_viscosities (required
6977        different loop boundaries in seaice_lsr and seaice_ocean_stress)
6978      - bug fix in seaice_ocean_stress (update of lab_sea required)
6979      - reduce loop boundaries to necessary minimum also in seaice_evp
6980      - go back to the old way of computing deltaC/Z as the adjoint likes that
6981        better
6982    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
6983      passive tracer to an Age Tracer) + update output.txt
6984    o pkg/exf:
6985      - implement A-grid / C-grid selection for wind-stress input files.
6986      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
6987      for now, in exf_bulk_largeyeager04.F only :
6988      - change implementation for case where windspeed + 2. components wind-stress
6989        are read-in. AND use rhoConstFresh to convert evap.
6990    o pkg/seaice:
6991      - use correct EXCH_UV for wind-forcing (on A-grid).
6992      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
6993        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
6994    o pkg/exf:
6995      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
6996      EXF_INTERPOLATION:
6997      - merge global_with_exf/code version of exf_interp_read.F
6998        to the main code ;
6999      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
7000        reading the file ; Important: This options needs to be defined to recover
7001        previous code.
7002        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
7003      - no longer loose real*8 precision along the way when using exf_iprec=64.
7004    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
7005      - change discretisation of evp-solver in order to avoid another exchange
7006        (changes lab_sea) and clean up a little
7007      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
7008        help the adjoint (this also changes the results slightly)
7009      - add a few "_d 0" where they had been missing in seaice_evp.F
7010      - cleaning up: remove unused seaice_calc_rhs.F
7011    o pkg/exf: some cleaning-up:
7012      - change various "constants" into runtime parameters
7013      - cleaned-up Large&Yeager04 routine which should eventually
7014        replace exf_bulkformulae.F (changed names of S/R and CPP)
7015        and merged various ALLOW_ATM_WIND options
7016     only used with thsice pkg (in thsice_get_exf.F):
7017      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
7018        which are used when useStabilityFct_overIce=TRUE (= the default)
7019      - change default values of ice & snow emissivity and scale downward LW
7020        by ice & snow emissivity.
7021    o pkg/thsice:
7022     fix few little problems, in thsice_calc_thickn.F:
7023      - growth vertically (and not laterally) if iceFrac == iceMaskMax
7024      - melt only laterally if hIce < hThinIce (as the comments say)
7025      and in thsice_extend.F:
7026      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
7027      - start to form ice as soon as the minimum ice-volume is reachable.
7028     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
7029      and cpl_aim+ocn
7030    o pkg/kpp
7031     - move computation of surface related input fields to KPP into a new
7032       subroutine kpp_forcing_surf.F
7033     - remove wrong (within bi,bj loops) EXCH calls.
7034     - little cleaning (add argument myThid in last position, cvs header ...)
7035     - for now, fix conservation problem by exchanging KPPviscAz (may not
7036       be the best fix)
7037    o pkg/seaice
7038     - check for inconsistent evp parameter/cpp-flag combination
7039     - remove leftover errIO flat for obsolete name list error handling
7040    o OpenAD
7041     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
7042    
7043    checkpoint59a (2007/05/01)
7044    o pkg/seaice: some parameter clarifications and a little bit of clean up
7045    o pkg/thsice: rename run-time parameters:
7046       himin       -> hIceMin
7047       himin0      -> hThinIce
7048       hihig       -> hThickIce
7049       i0          -> i0swFrac
7050       transCoef   -> bMeltCoef
7051       frac_energy -> fracMelting
7052      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
7053       with default values (for now) that do not change the results.
7054      remove old version of thsice vars advection in pkg/seaice.
7055    o in FFIELDS.h:
7056      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
7057      - make pLoad & sIceLoad always available (but still only used if
7058         ATMOSPHERIC_LOADING is #define).
7059    o pkg/kpp: replaced _KPP_RL with _RL
7060    o bug fixes for vertical diffusivity computations when both KPP and
7061        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
7062        are no longer updating the vertical diffusivity array
7063        (passed as argument) but are (re-) setting those arrays.
7064    o pkg/seaice: fix bug in evp solver, while doing that
7065      - change (improve?) discretization of stress computations for both
7066        cgrid-lsr and evp solver
7067      - add a new routine to compute strain rates
7068      - the above changes lab_sea results
7069      - add no slip conditions for evp solver (off by default), lsr-version
7070        may follow
7071      - fix exchange for shear at Z-points (does not change lab_sea)
7072      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
7073        (to force the user to pick a time step since there is not "safe" way
7074        of choosing it)
7075      - add principal stress diagnostics
7076      - rearrange fields for evp a little to avoid having to call a: too many
7077        exchanges and b: exchanges for stress trensor components which we do
7078        not have.
7079      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
7080        of evp, complete rewrite for lsr case (latter is does not yet work
7081        in all cases)
7082    o pkg/kpp: add code to have mixing in shelf ice caverns
7083      - add myThid to all kpp routines (long overdue)
7084    
7085    checkpoint59 (2007/04/19)
7086    o pkg/exf:
7087      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
7088        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
7089      - move exf header files from lower_case.h to UPPER_CASE.h ;
7090        add missing cvs Header & Name
7091      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
7092      - add namelist param. selectStressGridPosition, exf_monFreq
7093      - retire many _CLIM routines, and remove data.exf_clim
7094        + params moved to data.exf
7095        + climsst, climsss now handled by exf_set_gen, i.e.
7096          climss?period=0 refers to constant field,
7097          climss?period=-12 to monthly forcing
7098      - split up namelists in data.exf
7099    o pkg/seaice:
7100      - remove seaice_exch and seaice_exch_uv
7101      - remove superfluous exchange of theta
7102      - add myThid to seaice_budget_ocean/ice
7103      - add new interface for atmospheric wind forcing (C-grid only)
7104        + new routine
7105        + two new field (taux, tauy for stress over ice)
7106        + removed one global field (DAIRN) for C-grid case only
7107    o pkg/thsise
7108      - 2nd set of modifs for thsice adjoint in conjunction with exf
7109    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
7110    
7111    checkpoint58y_post (2007/04/15)
7112    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
7113      vertical diffusivity, similar to that in MOM4; turned on using
7114      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
7115      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
7116    o Added capability for 3D specification of background vertical diffusion
7117      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
7118      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
7119      "data" file that contains the 3D vertical diffusivity coefficients.
7120    o ice dynamics (pkg/seaice) with thsice thermodynamics:
7121      - add code within pkg thsice to advect & diffuse sea-ice fields
7122      similar to (and will replace) what has been added in  seaice_advdiff.F,
7123      but: - conserving Mass, Heat & Salt.
7124           - better when using non-linear advection scheme (not yet fully tested)
7125           - can also be used in atmospheric set-up (for now, only the diffusion).
7126    
7127    checkpoint58x_post (2007/04/04)
7128    o IO option for global-file compact format:
7129      - add options when generating topology (utils/exch2/matlab-topology-generator)
7130      - add I/O capability (pkg/mdsio).
7131      - adapt utils/matlab/rdmds.m to read this format.
7132      for now long-line format not yet supported by pkg/mdsio (& exch2).
7133    o shelfice: add a few diagnostics
7134    
7135    checkpoint58w_post (2007/03/13)
7136    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
7137      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
7138      (and replace horiVertRatio in NH code).
7139      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
7140                         and tutorial_plume_on_slope (sensitive to truncation)
7141    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
7142      directly to drive seaice model (C-grid only)
7143    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
7144     - reintroduce computation of wind from stress,
7145     - compute tau (in exf_bulkformulae.F) from windstress averaged to
7146       mass points to avoid tau = 0
7147     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
7148    o rdmnc.m: make it work with "global" files created with gluemnc
7149    o rdmnc.m : some improvements in dealing with singleton dimension
7150      (tested on all testreport mnc output files).
7151    o genmake2: disable pkg/profiles if netcdf test fails.
7152    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
7153    o move call to cal_readparms up to make calendar parameters/variable available
7154      to all packages
7155    
7156    checkpoint58v_post (2007/02/08)
7157    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
7158      useDynP_inEos_Zc tested.
7159    o pkg/exf: changes to properly interpolate/mask/scale initial fields
7160    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
7161      and portions thereof.  See read_cs.txt for description and examples.
7162    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
7163      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
7164      following the great-circle arc between those 2 points.
7165    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
7166      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
7167    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
7168     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
7169     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
7170     - still needs work (not working with some options ; efficiency to improve)
7171       and serious testing.
7172     - use this scheme for temperature & salinity in 2 advection test exp.:
7173       advect_xy & advect_xz, respectively.
7174    
7175    checkpoint58u_post (2007/01/12)
7176    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
7177    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
7178    o testreport: add option "-skipdir" to skip some test.
7179    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
7180      momentum calculation.
7181    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
7182    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
7183      remove checkpoint.F and the_correction_step.F (no longer used);
7184      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
7185    o add option (linFSConserveTr) to correct for tracer source/sink due to
7186      Linear Free surface
7187    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
7188    o pkg/thsice: fix reading mnc-pickups
7189    
7190    checkpoint58t_post (2006/12/30)
7191    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
7192    o pkg/mdsio:
7193     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
7194       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
7195       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
7196     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
7197     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
7198       either MDS_READ_FIELD or MDS_WRITE_FIELD )
7199     - new S/R (to replace MDSWRITEMETA), which allows to write more
7200       informations (variable names, time ...) to meta files.
7201     - modify rdmds.m to give back the meta file content.
7202    o pkg/diagnostics: change vertical interpolation to be safer, and more
7203       flexible (define p-levels to interpolate to in data.diagnostics);
7204      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
7205       diagnostic pointer.
7206    o pkg/seaice: more cleaning up of seaice_growth, added many comments
7207    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
7208    o fix multi-category seaice:
7209     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
7210       SEAICE_MULTICATEGORY
7211     - fix short wave heat flux
7212    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
7213       and allow to use EVP solver. Change forward lab_sea: test both EVP
7214       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
7215    o Initial check-in of lab_sea adjoint
7216      (very similar to natl_box_adjoint/code_seaice)
7217      * used C-grid and EVP solver
7218      * used KPP, GM/Redi
7219      * uses inAdExact=.TRUE.
7220      * gradient checks fail for both ADM and TLM
7221        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
7222        f.d. gradients actually seem more problematic than ADM, TLM gradients;
7223        issue is related to forward mismatch between g77 an ifort
7224    o pkg/seaice: overhaul of thermodynamics
7225     - growth.F and groatb.F are replaced by new routine seaice_growth.F
7226     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
7227     - move a few global fields out of SEAICE.h into seaice_growth.F and
7228       make them 2D (FICE/QNETO/ ...)
7229     - remove FO (it is the same as QNETO)
7230     - introduce a few local fields to avoid modifying external fields such
7231       as atemp, etc.
7232    
7233    checkpoint58s_post (2006/12/11)
7234    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
7235      changed exf_set_gen.F so that
7236        genperiod=0 means input file is one time-constant field and
7237        genperiod=-12 means input file contains 12 monthly means
7238    o CG2D: use pre-computed solver main-diagonal (stored in common block);
7239      this affects truncation error ; generate new output file for exp. which
7240      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
7241        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
7242        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
7243        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
7244        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
7245        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
7246    o start implementation of deep-atmosphere and anelastic formulation
7247    o verification: remove 2nd copy of input files and use script "prepare_run"
7248      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
7249    o mom_common/vecinv/fluxform: fix a few initialisation isssues
7250    o profiles: fix for multithreaded case
7251    
7252    o diagnostics: rename few diags:
7253      s/'PRESSURE'/'RCENTER '/g
7254      s/'TICE    '/'oceFreez'/g
7255      s/'TAUX    '/'oceTAUX '/g
7256      s/'TAUY    '/'oceTAUY '/g
7257      s/'SWFLUX  '/'oceQsw  '/g
7258      s/DIFx/DFxE/g
7259      s/DIFy/DFyE/g
7260      and add few ocean-forcing diagnostics:
7261      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
7262    o modifications to pkg/seaice/growth.F and budget.F, which change results of
7263      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
7264      as actual snow thickness.  It now refers everywhere to effective snow
7265      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
7266    
7267    checkpoint58r_post (2006/11/17)
7268    o modifications to pkg/seaice/growth.F, which change results of
7269      lab_sea experiment: fixes pertain to melting snow over open water, to
7270      masking EVAP under sea ice, and to using the correct AREA variable for
7271      computations of EVAP, PRECIP, HSNOW, and GHEFF
7272    o add ability to read bathy, salt, and theta using MNC (off by def)
7273    o add flooding algorithm and advection of HSNOW for pkg/seaice;
7274      both are turned off by default and do no change any results
7275    o seaice advection with pkg/thsice: a step toward the use of non-linear
7276      advection scheme, but #ifdef or commented out for now (requires more EXCH).
7277    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
7278      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
7279      in natl_box (affects results @ truncation level: update output.txt)
7280    o multi-threading and IO:
7281      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
7282      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
7283        (needed to work with SingleCpuIO): tested in all verif. exp.
7284    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
7285      affects the results (but none of the verification test uses this scheme).
7286    o Adding some pkg/diagnostics capability to pkg/seaice
7287      (will certainly be subject to changes)
7288    o ctrl: adding new control variables:
7289      lwflux, lwdown, evap, snowprecip, apressure, runoff
7290    
7291    checkpoint58q_post (2006/10/20)
7292    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
7293      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
7294      high_res_cube configuration by 4% on Columbia.
7295    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
7296      add (in global_with_exf/code) a version of EXF_INTERP_READ without
7297      dynamical allocation (seems to work in multi-threaded).
7298    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
7299      single CPU io) so that TAF does not have to see EESUPPORT.h
7300    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
7301    
7302    checkpoint58p_post (2006/09/08)
7303    o obcs: stop if obcs is used with useCDscheme = .true.
7304    o shelfice:
7305     - fix a sign error so that no slip at shelfice interface works
7306     - remove stop for combination non-hydrostatic code and shelfice. That does
7307       not mean, that the results are correct, but at least they are numerically
7308       stable
7309    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
7310    o added adjoint exch routined for all exch*3d* routines
7311      and updated flow directives
7312    
7313    checkpoint58o_post (2006/08/28)
7314    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
7315      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
7316    o change controling S/R for writing pickup file (new S/R do_write_pickup)
7317      and clean-up reading/writing of pickup files.
7318    o fix local version of read/write pickup (NH part) in rotating_tank/code
7319    o simplify EXCH interface:
7320     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
7321     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
7322    o added the regrid package
7323    o shelfice:
7324     - add a simple boundary layer scheme to reduce noise
7325     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
7326    
7327    checkpoint58n_post (2006/08/14)
7328    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
7329       local variable (not in common block).
7330    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
7331      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
7332      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
7333        to work with SingleCpuIO.
7334    o add "_d 0" to real constant of pkg/cfc subroutines ;
7335       update exp. cfc_exemple & tutorial_cfc_offline output files.
7336    o multi-threading and IO:
7337      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
7338        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
7339      - barrier before and after reading.
7340      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
7341      - avoid using MDS_WRITELOCAL for LAND pkg output.
7342      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
7343        common-block variables ; Allows multi-threading with master-thread IO.
7344    o change default MAX_NO_THREADS from 32 to 4 ;
7345      and stop cleanly when MAX_NO_THREADS is too small.
7346    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
7347    
7348    checkpoint58m_post (2006/07/17)
7349    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
7350       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
7351    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
7352       keep global_ocean.90x40x15 (for AD testing) with former secondary test
7353       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
7354    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
7355        add MITgcm_tutorials (= code + all the tutorials)
7356    o ecco, option to compute cost for total ssh (mean+anom)
7357    o consistent with addition of ptracer and ssh in pkg/profiles
7358    o profiles: adding ptracer and ssh
7359    o testreport: change multi-test output-file name
7360      (from output.txt.{name} to output.{name}.txt)
7361    o profiles: now ok for mutli-tiles case
7362    o seaice: add 4 parameters for different advection schemes for area,
7363      (effective) seaice thickness, enthalphy, and snow height. Their default
7364      is the standard parameter SEAICEadvScheme
7365    o calc_gw:
7366     - add cosFacU in zonal viscous flux (harmonic.visc.).
7367     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
7368       of tutorial_plume_on_slope.
7369    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
7370    o calc_gw: true flux-form, account for horizontal grid spacing.
7371      update rotating_tank results, but not plume_on_slope (affected at
7372      truncation level, 11 digits).
7373    
7374    checkpoint58l_post (2006/07/12)
7375    o calc_gw:
7376     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
7377     - remove side-drag for now (need to fix it); update plume_on_slope results.
7378     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
7379    o commit code to make SST/SSS weights spatially variable
7380      (based on either variable in-situ or variable initial T/S weights)
7381    o pkg/ecco:
7382      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
7383        now based on horizontally varying weights wthetaLev, wsaltLev
7384      * cost_averagesflags now returns year indices in addition to day, month
7385      * sflux balance is performed on annual basis
7386        (sflxumm, sfluxmm2, bal_sfluxmm)
7387      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
7388        including separate counting and multipliers
7389    o pkg/rbcs
7390      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
7391    
7392    checkpoint58k_post (2006/07/06)
7393    o testreport:
7394     - always build in dir. "build" (if not there, mkdir build instead of building
7395       & running in input)
7396     - run in dir run (if it exists), in build otherwise.
7397     - call prepare_run (if input/prepare_run exists)
7398     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
7399    o pkg/exf modifications to interpolation and rotation routines for more
7400       reasonable treatment of North Pole singularity: for tracers North Pole
7401       value is set to northernmost zonal-mean value, for zonal velocity it is
7402       set to zero, and for meridional velocity it is set to northernmost value.
7403    o pkg/exf/exf_check_range.F
7404     - add tile index to diagnostics and move stop statement to the very
7405       end of the routine.
7406    o pkg/diagnostics: (diagnostics_main_init.F)
7407      define title of isomorphic variables according to the current config.
7408    o pkg/thsice with pkg/seaice dynamics:
7409    - fix domain of computation (interior only, required for exf) and do exchanges
7410    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
7411    o towards a standard way of dealing with multi-threading in MONITOR
7412      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
7413    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
7414       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
7415    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
7416    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
7417    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
7418       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
7419    o tracer advection:
7420     - clean-up and simplify calc_common_factors.F
7421     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
7422       advection subroutine (but still not used within DST advection S/R)
7423    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
7424    
7425    checkpoint58j_post (2006/06/15)
7426    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
7427      from file (collects calls previously in FORWARD_STEP)
7428    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
7429    o adjoint store dir. adjusted accordingly
7430    o genmake2
7431      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
7432    
7433    checkpoint58i_post (2006/06/14)
7434    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
7435      on wind stress (SEAICEstressFactor defaults to 1.)
7436    o Total number of Timers is finite (<=40): comment out 2 non-essential one
7437      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
7438    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
7439      on CS-grid: no longer loosing mass.
7440    o exf & curvilinear-grid: no longer modify longitude xC & xG.
7441    o pkg/ggl90: fix sloppy output and fix a bug
7442    o pkg/seaice: added SEAICEuseEVPpickup parameter
7443      - Set to false in order to start EVP solver with
7444        non-EVP pickup files when using SEAICEuseEVP
7445      - fix sign error in diffusion in seaice_calc_rhs
7446    
7447    checkpoint58h_post (2006/06/07)
7448    * Modifications for bottom topography control
7449      o replace hFacC by _hFacC at various places
7450      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
7451      o add non-self-adjoint cg2d_nsa
7452      o update autodiff support routines
7453      o re-initialise hfac after ctrl_depth_ini
7454      o works for 5x5 box, doesnt work for global_ocean.90x40x15
7455    * Adding verification for 5x5 box (4-layer) bottom topography control
7456    
7457    checkpoint58g_post (2006/06/07)
7458    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
7459       used for mean seasonal cycle, mean diurnal cycle); add an example
7460       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
7461    o pkg/ggl90:
7462      - add parameter (minimum surface kinetic energy)
7463      - fix bug (avoiding division by zero)
7464    o couple pkg/thsice to pkg/seaice:
7465      - modify advection in seaice to accomodate new scalar fields to be advected
7466      - only muliDimAdection scheme work with seaice/thsice
7467      - mapping of thsice-variables to seaice-variables, back and forth
7468      - does not break the verification experiments, but does not give the
7469        desired results either
7470    o pkg/seaice
7471      - make (default) second order advection a bit less confusing?
7472    
7473    checkpoint58f_post (2006/06/05)
7474    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
7475      to pkg/seaice):
7476      - new routines thsice_map_exf and thsice_get_exf provide the interface
7477      - add an additional formal parameter to thsice_solve4temp
7478    o pkg/exf:
7479      - add new fields wspeed, snowprecip (to be able to couple to thsice)
7480      - correct Stefan-Boltzmann constant
7481      - new parameter for longwave surface emittance
7482      - separate some stuff from exf_bulkformulae into new routines  
7483        exf_radiation, exf_wind
7484      - add new parameters and constants: longwave emissivity for ocean, ice
7485        and snow, evaporation parameters over ice
7486      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
7487        either wind from stress or stress from wind
7488    o pkg/thSIce:
7489    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
7490    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
7491       and THSICE_CALC_THICKN
7492    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
7493    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
7494      to make debugging easier.
7495    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
7496    o pkg/bulk_force:
7497      - clean-up comments and parameters ;
7498      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
7499    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
7500      generate new output for test-experiment: aim.5l_cs.thSI
7501    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
7502      testreport accordingly
7503    
7504    checkpoint58e_post (2006/05/17)
7505    o SEAICE_CGRID adjoint done
7506    o R_STAR adjoint implemented.
7507      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
7508      * need to sort out init. of h0facc, etc.
7509    o Make pkg/profile fully independent of ecco,cost, etc. stuff
7510      to be able to use it in pure forward.
7511    
7512    checkpoint58d_post (2006/04/21)
7513    o upgrade simple test-experiment to tutorial example:
7514     step.1: duplicate the experiment and (step.2) will remove the old copy.
7515      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
7516      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
7517      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
7518      tutorial_global_oce_biogeo    <- copy of dic_example
7519      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
7520      tutorial_plume_on_slope       <- copy of plume_on_slope
7521      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
7522      tutorial_global_oce_optim     <- empty for now (David ?)
7523      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
7524     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
7525    o correct a sign problem in cost_scat.F
7526    o obcs and ptracers: fix boundary conditions for advections schemes
7527      with larger stencil
7528    o thsice adjoint: start
7529    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
7530      completeness
7531    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
7532      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
7533    o ptracers adjoint:
7534      * avoid extensive recomputatations
7535      * fix missing re-init. of gptr (missed by TAF)
7536    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
7537      me to turn off the excessive output to STDOUT that this package produces
7538    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
7539      and add those terms in Vector-Invariant formulation.
7540    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
7541      if the control period (xx_hfluxperiod etc) is 0
7542    o in profiles pkg, clean routines and fix details
7543    o in ecco pkg, reading ssh data:
7544      fix problem in case the model does not start at iter0=0
7545    o fix mnc-pickup/restart for ptracers
7546    o new package prifiles:
7547      code to compute profile-based cost by Gael Forget
7548      (modifs in ecco, ctrl, autodiff)
7549    o Benign bug fix in initialization (spotted by M. Mazloff) of
7550      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
7551    
7552    checkpoint58c_post (2006/03/23)
7553    o adjoint: finish NLFS adjoint and provide reference output in
7554      verification/global_ocean.90x40x15/results_ad_nlfs
7555    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
7556      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
7557      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
7558      with SEAICE_CGRID defined.
7559    o move calendarDumps from "data" to "data.cal" and clean-up the code
7560      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
7561    o add useEXF & useCAL flags (for now, set in hard-coded way)
7562    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
7563      (were missing in NH mode, and wrong in quasihydrostatic mode).
7564      waiting for Chris updated version of calc_gw to add those CALLs.
7565    o fix bug in quasihydrostatic S/R ;
7566      add a test for this option: global_ocean.90x40x15.qshyd
7567    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
7568      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
7569    o add on/off flag useOffLine for package OFFLINE
7570    o seaice:
7571      - modify advection so that it works also on the C-grid
7572      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
7573        problem in multi-tile runs with C-grid
7574      - add flags for clipping ice velocities and/or masking solver forcing
7575      - fix drag (ocean on ice) formulation and a bug that caused noise in the
7576        C-grid solver
7577      - added a few comments to seaice_diffusion.F
7578      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
7579        are now exclusive)
7580      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
7581        required re-ordering the code a little:
7582       + make DAIRN global variable (defined in SEAICE)
7583       + move computation of the viscosities eta and zeta into a new separate
7584         routine (because I need to recompute them in seaice_ocean_stress.F)
7585    
7586    checkpoint58b_post (2006/03/13)
7587    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
7588      update output.txt of exp. aim.5l_cs.thSI
7589    o various mnc cleanups and improvements:
7590      + shrink lookup tables by factor of ~4
7591      + better error reporting when running out of lookup space
7592      + able to handle longer path/file names (up to 500 chars)
7593    o adjoint:
7594      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
7595      - TBD: "hidden" mom_vecinv recomp. in dynamics
7596    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
7597     (allow to differentiate between forcing components using new integer flags:
7598      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
7599     and add new flag to put Dissipation tendency out of Adams-Bashforth.
7600    o ecco
7601      - enable trend removal from SSH anomaly obs.
7602    o adjoint
7603      - a fix for PmEpR when #undef EXACT_CONSERV
7604      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
7605      - try to fix "hidden" recomp. in forward_step for NLFS
7606        (NLFS seems broken sometimes after I checked it in)
7607    o seaice:
7608     - add c-grid version of the dynamic solver:
7609       + three new routines that are the c-grid substitute lsr, dynsolver
7610         and ostres
7611       + put a few fields that were local to dynsolver into global common
7612         blocks, so that I can move the computation of stresses etc into
7613         seaice_lsr (saves coding but may break the adjoint).
7614     - replace more hardwired parameters by runtime parameters
7615     - add ice masks that mask the rhs of the implicit solvers where there
7616       is no ice (commented out in seaice_dynsolver, because i am not sure
7617       if this works properly), eventually this should replace the clipping
7618       of ice velocities in seaice_dynsolver to +/-40cm/s.
7619    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
7620      include it only where its needed
7621    o move balancing of fluxes before the call of external_forcing_surf
7622    o seaice:
7623      - correct units of turning angles (now they are really in degrees)
7624      - move computation of GWATX/Y out of main routine into dynsolver
7625      - initialize GWATX/Y in seaice_init
7626    o Apply mask on Fresh-Water flux (needed for SSH forcing).
7627      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
7628    o seaice: add runtime flags for turning angles (default to zero)
7629    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
7630      and trend from exf forcing and ctrl control adjustments
7631    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
7632      (since checkpoint57x_post)
7633    o change the default rotation period to 86164.s = the Earth rotation
7634    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
7635      and based on a reference stratification. Tested within hs94.cs-32x32x5.
7636    o seaice advection: add code for choosing between the default (2nd order
7637      central differences) and multiDim advection schemes provided by
7638      pkg/generic_advdiff
7639    o seaice:
7640      - removed all references to SEAICE_GRID.h fields from
7641        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
7642        (cubed-sphere configuration will change a little)
7643      - grid computations in seaice_init are obsolete now.
7644      - cleaned up code a little so that is easier to read (hopefully).
7645      - added new (better?) discretizations of default advection and diffusion
7646        (turn on with SEAICEuseFluxForm)
7647      - replace 1 in 3d global fields by kSurface in growth.F
7648      
7649    checkpoint58a_post (2006/02/13)
7650    o seaice:
7651      - bug fix in advect.F
7652    o shelfice:
7653      - separate shelfice load anomaly from pload (breaks with time
7654        dependent forcing), => introduce constant field shelficeLoadAnomaly.
7655        Its default is 0., but it may be computed more cleverly from (unknown)
7656        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
7657        done offline. A good approximation of the pressure load anomaly is
7658        necessary to avoid large initial adjustment processes underneath
7659        deep-reaching shelfice.
7660      - small fix in ISOMIP shelfice_thermodynamics
7661      - add more sophisticated thermodynamics of Hellmer (1989), this is
7662        now the default
7663      - give a few constants more intuitive names
7664    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
7665      if bulk formulae are used in long integration (especially EmPmR). Turn
7666      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
7667      if balancePrintMean, the imbalance that is substracted is printed to
7668      STDOUT.
7669    o fix bug (typo) in obcs_apply_eta.F
7670    o add a new package shelfice which enables us to model the circulation
7671      underneath shelf-ice with draughts of hundreds of meters.
7672     - works
7673     - to do: + include improved thermodynamics
7674              + check whether kSurfC (from model/inc/SURFACE.h) can be used
7675                instead of new field kTopC
7676              + can we use topoFile, Ro_surf and existing code in ini_depth.F
7677                instead of new field R_shelfIce and new code in ini_depth.F
7678                and ini_mask_etc.F?
7679              + adjust vertical mixing schemes?
7680    o seaice pkg:
7681     - add a cpp-flag to include a simple formula for a salinity dependent
7682       freezing point of sea water at the surface
7683     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
7684       meridional stresses are now different (and hopefully correct)
7685    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
7686       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
7687       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
7688    o pkg/diagnostics: add options and parameters for regional-statistics
7689       diagnostics ; define regions by reading a region-mask from a file
7690       (might add other options later)
7691    o pkg/bulk_force:
7692     - add option and parameters to use AIM surface-flux formulae.
7693     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
7694       others forcing fields (defined in PARM05, parameter file "data") are loaded
7695       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
7696     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
7697     - use the right EXCH call for uwind,vwind (to work on CS-grid).
7698     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
7699       and parameters (note: calcWindStress replaces .NOT.readwindstress).
7700     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
7701    
7702    checkpoint58 (2006/01/12)
7703    o add "--embed-source" option to genmake2 which, when the supporting
7704      tools can be compiled (as determined by genmake2) will turn on the
7705      embed_files package which then embeds the entire MITgcm source code
7706      (*.[fFhc] + Makefile) used for the build within the executable
7707      - requested by CNH but off by default
7708      - adds a paltry <9MB to the mitgcmuv executable in most cases
7709      - only writes the output when useEMBEDSRC in eedata is true
7710    o clean up 3-dim. relaxation codes:
7711      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
7712      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
7713      * Thanks to Tom Haine for testing!
7714    
7715    checkpoint57z_post (2005/12/31)
7716    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
7717      affects output (@ truncation level) of exp. plume_on_slope ; updated.
7718    o fix the pickup behavior for obcs in combination with ptracers
7719    o fix a bug in ptracers_external_fields_load
7720    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
7721      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
7722    o transfered surface NH pressure to eta field (if exactConserv).
7723    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
7724         and update lab_sea output.txt file.
7725    o completing 3-dim. relaxation code: additional term
7726         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
7727      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
7728      * At compile time, in "EXF_OPTIONS.h" set
7729          #define  ALLOW_CLIMTEMP_RELAXATION
7730          #define  ALLOW_CLIMSALT_RELAXATION
7731      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
7732          tauThetaClimRelax3Dim = 15552000.0,
7733          tauSaltClimRelax3Dim  = 15552000.0,
7734      * 3 cases:
7735          1) Use a constant-in-time 3-dim. field
7736          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
7737          3) Real-time relax. to time-evolving prescribed field
7738    o Adding Laplacian-type smoothness constraint on
7739      initial and boundary (forcing) controls (ic, bc)
7740      * enable at compile-time via
7741        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
7742      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
7743      * Absolute scale somewhat unclear so far
7744      * no area weighting was included since no other cost term does so far
7745    
7746    checkpoint57y_post (2005/12/08)
7747    First step for a NLFS adjoint
7748    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
7749    o new init. routines for calc_r_star, calc_surf_dr
7750    o still need to deal with ini_masks_etc
7751    o testreport seemed happy
7752    checkpoint57y_pre (2005/12/08)
7753    
7754    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
7755    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
7756    o add new offset feature to offline pkg (plus minor cleanup)
7757    o cfc fixes for final year of integration
7758    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
7759      be in GCHEM_OPTIONS).
7760    
7761    checkpoint57x_post (2005/12/04)
7762    o fix testreport Pb in multiple test experiment.
7763    o cleanup our namelist syntax in verification:
7764      - make it more F95 standards compliant (some work still needed)
7765      - allows the vast majority of our tests to work with gfortran
7766    o Non-Hydrostatic:
7767     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
7768     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
7769    o Allow to apply AB on T,S rather than on AB(gT,gS):
7770     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
7771     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
7772       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
7773     - need a "clever" read_pickup to restart from the other AB formulation
7774    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
7775    o remove some unused variables (reduces number of compiler warnings)
7776    o adjoint
7777      * Disable useVariableViscosity for adjoint for time being
7778        (there are a number of extensive recomputations)
7779      * Initialize certain variables needed for adjoint
7780    
7781    checkpoint57w_post (2005/11/03)
7782    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
7783                 fix the singleCpuIO RS version of MDSWRITEFIELD
7784       and add a WARNING if using globalFiles=T with multi-processors.
7785    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
7786      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
7787    o tracer advection scheme:
7788      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
7789       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
7790       was not very convenient).
7791      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
7792       (further tests needed for the implicit DST & Flux-Limiter schemes).
7793    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
7794      and sRef for convenience, handy, when you want to initialize
7795      ptracers in a large domain with a constant non-zero value. Also,
7796      untangle ptracers_init.F a little.
7797    
7798    checkpoint57v_post (2005/10/13)
7799    o change dome exp. to use variable viscosity in side-drag terms.
7800    o remove all the files from the cfc_offline test since they are now
7801      incorporated into tutorial_cfc_offline which has been producing
7802      identical results for a few days of testing
7803    o add new parameter: sideDragFactor to enable half-slip-side BC
7804      and change side-drag S/R to use viscosity from mom_calc_visc
7805      (can switch back by setting sideDragFactor=0.); affects results at
7806      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
7807       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
7808    o vorticity & strain are now computed without masking, to account for
7809      no-slip-side BC in variable viscosity calculation ; mask is applied
7810      anyway later on, before computing advection/coriolis terms.
7811    o modify exp4 to test new obcs support for reading from external files
7812      and for passive tracers
7813    o fix behavior of ptracers_monitor when monitor output is written to a
7814      netcdf-file; still not independent of monitor.F (writes in the same
7815      file).
7816    o change default value of tRef (put a uniform, meaningful value for ocean
7817      & atmos) and initialize sRef (was missing, as Martin mentioned).
7818    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
7819      to be proportional to enstrophy dissipation length.  Thus,
7820       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
7821      This is now consistent with Smagorinsky and with the manual.
7822    
7823    checkpoint57u_post
7824    o OBCS and PTRACERS: add open boundary support for passive tracers
7825      - either use homogenous (pseudo) v.Neumann conditions or prescribe
7826        OB-values from file; this is not different from the way theta and salinity
7827        are treated
7828      - however, Orlanski-radiation conditions are not supported, and the model
7829        will stop if you use pTracers and Orlanski at the same time.
7830      - beefed up the rountine obcs_external_fields_load: now only those open
7831        boundary values are overwritten with values from files for which there
7832        are really files, otherwise the OB-fields remain untouched. This makes
7833        it possible to use different OBs at different ends of the domain (as
7834        with EXF)
7835    o reduce number of exch calls in shap_filt (s2).
7836    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
7837      truncation level) 4/5 MLAdjust test results (11&12 digits match).
7838    
7839    checkpoint57t_post (2005/10/03)
7840    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
7841    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
7842      same truncation, independent of the face number: affects affects several
7843      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
7844    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
7845      note that biharmonic viscosity + no-slip was not tested in any experiment.
7846    o fix bug in non-linear free-surf side-drag ; generate new output for
7847      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
7848    o make mnc honor the writeBinaryPrec flag for most kinds of output
7849    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
7850    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
7851      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
7852    o add brackets in multi-terms sum to get same truncation, independent of
7853      the face number (manage to get exactly same value of gU,gV at the cs-edge)
7854      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
7855    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
7856      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
7857      a maximum grid-scale Reynolds number.  Also, changes all length calculations
7858      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
7859      Suggested values of viscosity parameters found in mom_calc_visc.
7860      Many new viscosity diagnostics available.
7861    
7862    checkpoint57s_post (2005/09/20)
7863    o Add clearing-house for viscosity calculations, mom_calc_visc and
7864      correct numerous bugs in LeithD and Smagorinsky discretizations.  
7865      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
7866      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
7867      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
7868      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
7869      The Strain-Tension form is now called with useStrainTensonVisc=.true.
7870      ViscAhStrain and viscAhTension are now retired.
7871    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
7872    o In response to JMC's bug report, genmake2 now ignores any soft-links
7873      that it finds in the *current* directory when searching for files.
7874      Soft-links found in any other source directories will still work as
7875      they did before.
7876    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
7877      a C routine to unlimit the stack size
7878    o mnc-ify pkg/aim snapshot vars
7879    o mnc-ify pkg/land as requested by Daniel
7880    o various changes to mnc including:
7881      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
7882      - output can now be grouped so that all files within a group
7883          change the ITER portion of their names in lock-step together
7884      - can now read ("global") PER-FACE (in addition to PER-TILE) files
7885          and works with both EXCH1 and EXCH2 (but needs more testing)
7886      - writing works for all verification test cases w/ g77 on Linux
7887    
7888    checkpoint57r_post (2005/09/07)
7889    o make MNC variable initialization happen earlier
7890    o add diagnostics for (almost) each term of the momentum Eq.
7891    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
7892    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
7893    o remove MINIMAL_TAVE_OUTPUT option ;
7894      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
7895    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
7896      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
7897    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
7898    o add time-dependent SST, SSS control
7899    o cost terms in ecco/ modularized (new cost_generic.F)
7900    o cost_averages routines are modularized (new cost_averagesgeneric.F)
7901    o new infrastructure for seaice model vs. obs misfits in seaice/
7902      * driver from the_main_loop.F is seaice_cost_driver.F
7903      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
7904      * gradient check in Exp. 6a of natl_box_adjoint/
7905    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
7906      (see README file)
7907    
7908    checkpoint57q_post (2005/08/19)
7909    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
7910    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
7911      - bug was reported by Jean-Michel and Ian Fenty
7912    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
7913      update exp. cpl_aim+ocn output.
7914    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
7915      Needed for high-res. runs with large global files
7916      to be able to limit tapelev size
7917    o Changed some tests for adjoint:
7918      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
7919      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
7920      * global_ocean.90x40x15/ back to default 3-level checkpointing
7921    o Modifications to enable scripted COMMON to MODULE conversion
7922      * verification/OpenAD/code/ has necessary scripts and description;
7923      * converts, compiles and runs successfully;
7924    
7925    checkpoint57p_post (2005/08/01)
7926    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
7927    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
7928      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
7929    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
7930    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
7931      (was already the case for dissipation with mom_vecinv,
7932       and also the case for grad.PhiHyd when staggered-timeStep)
7933      This will allow to put dissipation out-off the AB time-stepping.
7934     Unfortunately, affects truncation error. Update output of exp. that "fails"
7935      (cg2d matching number) and leave the others for later: front_relax(10),
7936      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
7937      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
7938    
7939    checkpoint57o_post (2005/07/30)
7940    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
7941      (2) its ready to be documented during the 20050801 DocFest
7942    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
7943      for ideal_2D_oce and lab_sea on linux_ia32_g77
7944    o set to #undef CTRL_SET_OLD_MAXCVARS_30
7945      in global1x1_tot/code_seaice_adj to access indices 32, 33
7946      (worth another tag)
7947    
7948    checkpoint57n_post (2005/07/29)
7949    o adding precip control xx_precip 32
7950    o adding swflux control xx_swflux 33
7951    o Replacing 10 forcing penalty cost routines by 1 generic.
7952    o Implementing partitioning in time-mean and variable adjustment
7953      for atmos. state.
7954    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
7955    o in natl_box_adjoint:
7956      * updated exp 1 to 10
7957        (but does not have time-mean vs. variable split results yet)
7958    o updated global1x1/*_seaice_adj/
7959      to incorporate latest changes
7960    o enable useSingleCpuIO for mdsio vector routines
7961      (applies in particular to tapelev I/O)
7962    o removed inefficient K-loop in all active_file*control*.F
7963    
7964    checkpoint57m_post (2005/07/28)
7965    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
7966      and advect_cs (use EXCH-2 and standard cs-32 grid files).
7967    o pkg/exch2: filling of face-corner halo regions is optional
7968      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
7969    
7970    checkpoint57l_post (2005/07/14)
7971     tag before updating tutorials (pre-release-2)
7972    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
7973       for output and interpolation of input fields onto model grid)
7974    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
7975       Affects results of exp. rotating_tank ; update output.txt.
7976    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
7977          and taking the square quantity and/or using a fraction-weight field.
7978    o fix aim_diagnostics_init.F mate numbers.
7979    o add mnc output capability to diagnostics/diagstat and update
7980      our cvsignore files for the ACSII output generated
7981    
7982    checkpoint57k_post (2005/07/02)
7983    o lab_sea now uses diagnostics package and provides a suite of
7984      new EXF diagnostics output.
7985    
7986    checkpoint57j_post (2005/06/30)
7987    o exf
7988      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
7989        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
7990        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
7991      * extended diagnostics output
7992        - now includes all EXF variables
7993        - hs, hl moved to common block
7994        - separate S/R for diagnostics, called after ctrl vector is added
7995        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
7996        - EXFqnet contains true Qnet (i.e. includes qsw)
7997      * updated verif. lab_sea, global_with_exf
7998      * Rearranging hflux (exf_mapfields -> exf_getforcing)
7999        to ensure that diagnostics sees a true EXFqnet
8000    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
8001    o diagnostics pkg: change pointers so that 1 diagnostic can be used
8002      several times with different frequencies.
8003    o mnc-ify the thsice package as requested by Daniel Enderton
8004      - the monitor--MNC output needs work
8005      - many attributes need to be added (most are currently blank)
8006    o mnc-ify theaim_v23 package as requested by Daniel Enderton
8007      - many attributes need to be added (most are currently blank)
8008    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
8009    o add Sadourny like discretization to the 4th.O vorticity advection scheme
8010    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
8011      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
8012         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
8013    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
8014     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
8015    
8016    checkpoint57i_post (2005/06/19)
8017    o Diagnostics package was changed: diagnostic allocation is now deactivated
8018      by setting an empty file name in the namelist (used to be by setting 0 frequency)
8019    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
8020      add 1rst Order upwind vertical Shear.
8021    o add a quick fix for A/B checkpointing in OFFLINE mode
8022    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
8023      end-run around the C/Fortran linking horror in eesup/src/timers.F
8024    o added pkg/runclock: allows user to terminate run based on wall clock
8025    o added non-hydrostatic scaling parameter: nh_am2
8026    o pkg/my82: futile attempt to make results compiler-independent by adding
8027      some "_d 0", etc. no effect.
8028    o for mnc output, fill the 'T' coordinate var with myTime and create a
8029      separate 'iter' variable for iteration count
8030    o pkg/diagnostics:
8031      add new capability: output of Global/Regional & per-level statistics ;
8032      tested against monitor output (including land & thSIce) on various exp.
8033    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
8034    
8035    checkpoint57h_done (2005/05/19)
8036      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
8037      data.diagnostics, data.gchem, data.ptracers) is done.
8038    
8039    o pkg/diagnostics: prepare for Global/Regional statistics.
8040      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
8041    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
8042      and rename it: DIFFERENT_MULTIPLE
8043    
8044    checkpoint57h_post (2005/05/14)
8045    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
8046    o pkg/diagnostics: change output frequency, now in seconds (instead
8047      of Nb of iterations). This requires to change data.diagnostics.
8048    checkpoint57h_pre (2005/05/12)
8049    
8050    o in mnc, let the user create the output dir if both mnc_outdir_date
8051      and mnc_outdir_num are false
8052    o add fflags() to pkg/diagnostics which allows one to specify, on a
8053      per-file basis, the file precision [default behavior is unchanged]
8054    o added diagnostics to pkg/kpp, including computation of mixed layer
8055      depth based on a temperature/density criterion
8056    o updated verification/natl_box to test the new pkg/kpp diagnostics
8057    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
8058    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
8059    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
8060      not mnc -- this mistake was found by JMC and is now corrected
8061    
8062    checkpoint57g_post (2005/04/15)
8063    o add Adams-Bashforth 3rd Order time stepping:
8064      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
8065      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
8066    checkpoint57g_pre (2005/04/15)
8067    
8068    o make lambda[Theta,Salt]ClimRelax spatially varying
8069      (default remains spatially uniform constant based on tau)
8070    o added new control variables
8071      * init. uVel, vVel, etanN
8072      * lambda[Theta,Salt]ClimRelax
8073    o separate masks used for ctrl_pack/unpack 'from write_grid' output
8074      (suggested by G. Forget)
8075    
8076    checkpoint57f_post (2005/04/06)
8077    o add parameter "baseTime" = model base time = time at iteration zero
8078      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
8079      account for baseTime shift
8080    o move Coriolis arrays from PARAMS.h to GRID.h
8081    checkpoint57f_pre (2005/04/06)
8082    
8083    o mnc-ifying the seaice package
8084    o introduced an alternative length scale calculation for use in the limiting
8085      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
8086    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
8087    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
8088      as well as grad(vort3).  Made it compatible with both approximate form
8089      for the cubed sphere and full form of these gradients.  Added flag
8090      useFullLeith to select between approximate and full form.  
8091    o add "d0" in getcon.F to reduce differences between compilers/platforms
8092      update output.txt of exp. fizhi-gridalt-hs
8093    o change port_rand funtion to allow to set the seed.
8094    o fix obscure MNC bug involving conversion between reals and integers
8095      - it caused no problems with certain (eg. gcc, ifc) compilers but the
8096        new version is now more standards-compliant
8097    o adjoint-related modifications
8098      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
8099      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
8100      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
8101    
8102    checkpoint57e_post (2005/02/28)
8103    o Adding eddy stress controls a la Ferreira et al.
8104    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
8105    
8106    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
8107      update output.txt of exp. fizhi-gridalt-hs
8108    o add more "Z" dimensions and associated coordinate vars to MNC
8109    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
8110    o parameter calendarDumps: when set, approximate months (30-31 days) and years
8111      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
8112      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
8113      months and years.  Requires pkg/cal.
8114    o diagnostics: add pickup functionality
8115      - off by default for backwards compatibility
8116      - current version only uses MDSIO -- MNC will be added
8117    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
8118    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
8119    
8120    checkpoint57d_post (2005/02/11)
8121    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
8122    o modify verification/ideal_2D_oce so that it tests the creation of mnc
8123      output from the diagnostics package
8124    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
8125    o make genmake2 more portable by using ".$FS" instead of ".f" for more
8126      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
8127    o add coordinate variables to the MNC output from the diagnostics package
8128    o change MNC-flags default value: true when useMNC=TRUE
8129    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
8130      the ability (off by default) to read the grid information using MNC
8131    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
8132    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
8133    o do snap-shot diagnostics at the middle of the time-interval (instead of
8134      at the end).
8135    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
8136      new test for AIM with thSIce + slab-ocean
8137    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
8138    o move state variable diagnostics to the beginning of the time step ;
8139      (note: still needs some work specially for snap-shot diagnostics)
8140      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
8141    
8142    checkpoint57c_post (2005/01/27)
8143    o Change testing option (-ieee) to get closer agreement between g77 & ifort
8144    o generate new output.txt files on faulks with g77 & the new -ieee option
8145    checkpoint57c_pre (2005/01/27)
8146    
8147    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
8148      update output.txt of exp. global_ocean.90x40x15
8149    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
8150      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
8151    o add saltFlux(+File) forcing capability with periodicExternalForcing
8152    o allow to use pkg diagnostics for GM-Redi & ThSIce output
8153    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
8154    o improvements for the MNC output from DIAGNOSTICS:
8155      - correct handling of the unlimitied dimension
8156      - all dims now have associated coordinate variables
8157      - variables located at U, V, and Corner ("Z") points are now written
8158        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
8159        *all* data points are output
8160    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
8161    o added pkg/seaice/seaice_monitor.F
8162    o mdsio_readfield.F can now read files visible only to master MPI process.
8163    o pkg/seaice: some test code for ice-modified ocean stress
8164    o exf_getffields interpolation defaults to bilinear for all scalar forcing
8165      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
8166      spurious negative numbers for precipitation and humidity.  Will cause
8167      some small numerical differences for integrations using pkg/exf/exf_interp.F.
8168    o pkg/ctrl/
8169      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
8170        May be enabled via doPackDiag
8171      *  introduce z-scaling of
8172         + gradient (doZscalePack) and
8173         + control (doZscaleUnpack)
8174    o pkg/mdsio/
8175      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
8176      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
8177    
8178    checkpoint57b_post (2004/12/20)
8179    o simplify options in diagnostics_fill arguments (remove weird combinations)
8180    o fix MNC coordinate variables so that they now contain per-face index
8181      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
8182      general, EXCH2 grids are only aligned to a "local" coordinate system
8183    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
8184    o Implement instantaneous output within pkg diagnostics:
8185      setting a negative frequency in data.diagnostics produces
8186     "snap-shot" output (as opposed to time-average if freq > 0)
8187    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
8188      NOTE: change ptracer diagnostics name: use 2 characters to work with
8189            more than 9 tracers. Add also diagnostics of advect & diffus flux.
8190    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
8191      becomes the coordinate variable for the 'T' dimension
8192    o add CF-style coordinate variables to MNC
8193      - just a first cut:  numbers are meaningless on the cubesphere and
8194        missing along the T axis but otherwise it works!
8195    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
8196    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
8197    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
8198      this is based directly on what the model compute, so that the content of
8199      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
8200    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
8201    o clean up build options files for SunOS, in particular
8202      - remove -traditional from xmakedepend
8203      - change -xarch=v9 to -xarch=native for f77
8204      - restore use of make (not gmake)
8205      - add CC=gcc if using g77
8206    o changes per discussion of AM, JMC, & EH3 today:
8207      - move redundant "grid" variables out of "state" -- in preparation of
8208        creating proper CF-style coordinate variables and in recognition
8209        that any/all grid variables can be easily copied (eg. w/NCO) from
8210        the grid files into any of the other NetCDF files
8211      - *always* output grid variables with MDSIO (this will eventually be
8212        changed)
8213      - output MNC grid file if useMNC is true
8214    o every instance of _END_MASTER() has been found and replaced with
8215      _END_MASTER( myThid ) in order to satisfy certain picky Sun
8216      preprocessors
8217    o re-arrange diagnostics pkg initialisation:
8218     - allow each package to extend the available diagnostics list
8219     - add some checking and fix small problems (multi-threaded, ...)
8220     - new S/R diagnostics_fill (replace fill_diagnostics):
8221       look through the short list of active diag. (instead of the long list)
8222       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
8223    
8224    checkpoint57a_post (2004/12/10)
8225    o this set of changes restores TAMC compatibility
8226      tested for global_ocean.90x40x15 adjoint on trough
8227      (what a pain)
8228    
8229    checkpoint57a_pre (2004/12/10)
8230    o some modifs in tools/build_options for sunos
8231    o call ctrl_pack for ctrl at end for optimcycle=0
8232    
8233    checkpoint57 (2004/12/09)
8234    o add horizontal bi-harmonic viscosity for vertical velocity
8235      - new parameter viscA4W (defaults to viscA4)
8236      - affects only non-hydrostatic code
8237      - to be done: no-slip lateral boundary conditions
8238    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
8239    o implement Implicit Vertical advection for pTracers
8240    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
8241      (implemented also for implicit vertical diffusion & advection)
8242    o OBCS: extend application of tracer open boundary conditions
8243      to a strip beyond the boundary of width Olx/Oly
8244    o add call monitor to TAF set of required calls (flow directives)
8245      and include in natl_box_adjoint
8246    o untangle a few ifdefs related to cost, ctrl, autodiff
8247      untangel a few ALLOW_ECCO_OPTIMIZATION
8248    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
8249      (theta2, salt2 in ecco_cost_weights)
8250    
8251    checkpoint56c_post (2004/12/03)
8252    o OBCS as control variables
8253      - update ctrl_ad_diff.list, obcs_ad_diff.list
8254      - remove balance of obcs controls from default
8255      - fix index bug nobcs in ctrl_init
8256      - fix dummy fields filen in ctrl_pack
8257      - add dummy weights for obcs
8258    o lsopt: comment out fort.94 output
8259    o optim:
8260      - remove unnecessary header files
8261      - adjusted namelists
8262      - add xerbla.F to Makefile
8263    o exf:
8264      - multiple modifications of exf_check_range
8265      - unit change in exf_init_runoff from [m/year] to [m/s]
8266    o mdsio:
8267      - i/o-vector change debugLevel from debLevA to debLevB
8268    
8269    checkpoint56b_post (2004/12/01)
8270    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
8271      is called from DO_THE_MODEL_IO
8272      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
8273      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
8274      - clean up PTRACERS_WRITE_TIMEAVE a little
8275    o add another verification experiment that tests both the cfc-pkg and
8276      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
8277      reactive tendencies treated inline with regular timestepping
8278    o testreport previously did a lousy job of comparing small numbers, so
8279      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
8280      implemented in the little c-progam tmp_cmpnum.c which is embedded in
8281      testreport.
8282    o ptracers_monitor: bug fix for MPI
8283    
8284    checkpoint56a_post (2004/11/28)
8285    o GCHEM: finish reorganizating the package
8286      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
8287        (introduces another 3D-array for each passive tracer, but only if
8288        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
8289        gchemTendency is not needed because the timestep is done separately)
8290      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
8291      - GCHEM is now---more or less cleanly---separate from PTRACERS
8292      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
8293        so clear to me how that should be done in a general way.
8294    o CFC: improve formatting of output in CFC_ATMOS
8295    o PTRACERS:
8296      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
8297        that ALL experiments with ptracers enable can be checked. This makes
8298        GCHEM_MONITOR obsolete.
8299      - include a runtime parameter PTRACERS_monitorFreq that defaults to
8300        monitorFreq
8301      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
8302    o add PTRACERS (PTR0[1-5]) to testreport output
8303    o exf_check_range:
8304      * default changed to .TRUE.
8305      * will check values for niter0 if debLevA, every timestep if debLevB
8306      * STOP in exf_check_range if 'out of range'
8307      * range chosen generous to allow for potential extema
8308      TBD: a version with stricter range
8309           permitted range would be runtime parameters
8310    o GMredi:
8311      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
8312      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
8313      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
8314    o GCHEM:
8315      - move call to GCHEM_FORCING_SEP, so that it is now called before
8316        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
8317      - introduced a useGCHEM runtime flag and applied it everywhere.
8318      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
8319        this flag is now only visible within GCHEM-pkg routines.
8320      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
8321        be replaced by a 3D array that is computed before thermodynamics; for
8322        this, the tracer ID iTracer had to be included into the parameter list
8323        of ptracers_forcing
8324      - set up forward_step to call gchem_forcing, that will replace
8325        gchem_forcing_int in ptracers_forcing
8326      - cleaning up
8327    o small cleaning of exch2: remove files that are also in eesupp/src
8328    
8329    checkpoint56 (2004/11/17)
8330    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
8331    o mnc: cleanup "full" files--fixes out-of-memory problem
8332    o ECCO-GODAE
8333      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
8334      * fully merged and updated from SIO code
8335        windstress sign change affects
8336        - exf_inscal_[u/v]stress
8337        - sign of xx_tau[u/v] adjustments
8338        - signs in cost_scat
8339      * ctrl_get_gen: avoid update of tau[u/v] for first few days
8340      * natl_box_adjoint updated and compressed
8341      * 2-level checkpoint switch added
8342        (tested in EXP. 1 of natl_box_adjoint)
8343      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
8344    o SVD
8345      * first complete, non-hacked version for SVD calculations
8346      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
8347        performed via direct access files admtlm_vector.it????
8348        (via ctrl_[un]pack)
8349      * optimcycle is used for ARPACK iteration counter
8350        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
8351      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
8352        and add linear transforms where necessary
8353      * controls are initial/final SST, SSS (can be extended; need to check
8354        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
8355    o mdsio: filename info to both stderr, stdout
8356    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
8357      from sign change
8358    
8359    checkpoint55j_post (2004/11/10)
8360    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
8361      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
8362    o add consistent build directories and .cvsignore files to verification
8363    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
8364    o make all subroutines 30 or less characters in length for certain older
8365      compilers to work (a thorough search only turns up two routines in
8366      pkg/ptracers)
8367    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
8368      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
8369    
8370    checkpoint55i_post (2004/10/28)
8371    o change arrays for total vertical diffusivity (2.D if explicit,
8372      3.D if implicit) ; each ptracer uses its own background value.
8373    o added mnc/NetCDF output capability to ocn_compon_interf
8374      - added bits to verification/cpl_aim+ocn so that it can run on
8375        ITRDA and other clusters without the mpirun "-wd" option
8376    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
8377      configuration
8378    o give MNC the ability to create additional files rather than
8379      exceeding a specified file size limit "MNC_MAX_FILESIZE"
8380      - the default is just less than 2GB which is a practical limit
8381        on many systems
8382    o Compute the non-local term using either KPP vertical diffusivity (=default)
8383       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
8384    
8385    checkpoint55h_post (2004/10/20)
8386    o add verification test "vermix"
8387    o remove all the *_ioinc flags and replace with the single global
8388      outputTypesInclusive flag
8389    o allow to set a vertical profile of vertical diffusivity for T & S
8390    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
8391    o useMNC moved from data.mnc to data.pkg
8392    
8393    checkpoint55g_post (2004/10/14)
8394    o Renaming carbon AD experiments to comply with testreport conventions
8395    o Updating adjoint of Held-Suarez hs94.1x64x5
8396    o Fixing directives for non-ECCO forward_step, after ECCO directives
8397      have been fixed to avoid recomp. of do_oceanic_phys
8398      Works well for global_ocean.90x40x15,
8399      but recomp. issue remains for carbon
8400    o Updating adjoint output for natl_box_adjoint after
8401      pkg/ecco has been modified (see taga c55d_post)
8402    
8403    checkpoint55f_post (2004/10/13)
8404    o rename to timeave_init_fixed
8405    
8406    checkpoint55e_post (2004/10/13)
8407    o some delicate re-shuffle of store directives to avoid one
8408      extra call of do_oceanic_physics
8409      affects ecco_the_main_loop.F, do_oceanic_physics.F
8410      checkpoint_lev1_directives.h
8411    o NB: this may break global_ocean adjoint temporarily,
8412      but it is clear how to fix it. Will do later, need this now.
8413    
8414    checkpoint55d_post (2004/10/11)
8415    o ECCO specific cost function terms (up-to-date with 1x1 runs)
8416    o ecco_cost_weights is modified to 1x1 runs
8417    o modifs to allow observations to be read in as
8418      single file or yearly files
8419    o enable to read exf forcing fields as either
8420      single file or yearly files (flag useExfYearlyFields)
8421    checkpoint55d_pre (2004/10/08)
8422    
8423    o switch between 2-level and 3-level checkpointing
8424    o add ability of MNC to write local and "partial" (eg. 2D slices where
8425      the full 3D field is never actually stored) arrays to NetCDF files
8426      with the correct (that is, the complete multi-dimensional) set of
8427      array indicies
8428      - used in mom_vecinv() to write the diagFreq output
8429      - tested (demonstrated) in verification/aim.5l_cs
8430    o further mnc-ification
8431      - add verification/lab_sea to the list with mnc setups
8432      - fix undefined mnc v-names in cd_code
8433      - add kpp to mnc output (both snapshot and timeave)
8434    o non-hydrostatic code
8435      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
8436        in calc_gw.F
8437      - defaults to viscAh
8438      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
8439        friction or Leith) in non-hydrostatic mode, as long as there is
8440        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
8441    o pkg/cost
8442      extend simple cost functions to treat time mean quantities
8443      (T,U,V) via cost_accumulate_state from cost_tile
8444    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
8445        be 2 times larger than the minimum size the advection scheme requires.
8446        now get a perfect conservation of salt in advect_cs test-exp (updated)
8447    o GGL90 (Gaspar's TKE mixed layer)
8448      - add horizontal diffusion of TKE, requires exchanges in
8449        do_fields_blocking_exchanges, horizontal diffusivity is zero by
8450        default. In OPA there is no horizontal diffusion of TKE but the
8451        mixing coefficients are computed from a horizontal average of TKE of
8452        6 points or so. I think that diffusion has a little more physical
8453        justification.
8454      - clean up ggl90_calc in the hope of reducing memory usage (this hope
8455        was in vain)
8456      - mask tke-variable in ggl90_init
8457    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
8458    o fix biharmonic diffusion on CS-grid.
8459    o more obcs stuff
8460      - added obcs_external_fields_load as an alternative to the EXF-pkg option
8461        for reading boundary values. This routine is called from
8462        obcs_prescribe_read
8463      - updated obcs_check
8464      - changed sponge layer relaxation parameter units for days to seconds
8465      - turned off sponge layer by default
8466      - changed argument list of OBCS_CALC to myTime+deltaTclock
8467      - fixed about 35 bugs in obcs_external_fields_load
8468    
8469    checkpoint55c_post (2004/09/23)
8470    o obcs stuff
8471      - new runtime flags useOBCSprescribe, useOBCSbalance
8472      - re-arranged obcs_calc
8473      - moved exf_getobcs to obcs_prescibe_read
8474        obcs_prescibe_read is called after ORLANSKI stuff
8475        and independent of it (executable can contain all).
8476      - updated obcs_check
8477      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
8478        These may be necessary only if tangential velocities are
8479        prescribed at OB, not sure, needs testing.
8480    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
8481      which simplifies the calls and passes the ifc check-bounds test
8482    
8483    checkpoint55b_post (2004/09/22)
8484    o add a 2D scalar, Z location, exchange_2 routine.
8485    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
8486      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
8487      affects advect_cs results (for the wrong reason): update output.txt
8488    o use a more standard discretization for biharmonic viscosity ;
8489     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
8490      affects results of dome set-up: update output.txt
8491    o fix gad_advection.F (CubedSphere part), back to version 1.23
8492    o fix bug in mom_vi_del2uv.F (CubedSphere part).
8493    
8494    checkpoint55a_post (2004/09/20)
8495    o merged code to
8496      * prescribe/read time-dependent open boundaries
8497        (works in conjunction with exf, cal)
8498      * sponge layer code for open boundaries
8499      * each boundary N/S/E/W now has its own CPP option
8500        (healthy for the adjoint)
8501    
8502    checkpoint55 (2004/09/17)
8503    o up-to-date adjoint of previous breaks
8504      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
8505      - global_ocean_ebm: adjoint still needs fix (TLM ok)
8506      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
8507      - carbon: * remove tr1-related adjoint verification
8508                * add ptracer as control variable
8509    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
8510      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
8511    
8512    checkpoint54f_post (2004/09/16)
8513    o in verification/carbin/ remove experiment related to
8514      ALLOW_PASSIVE_TRACER (array tr1 etc)
8515      code_ad/ input_ad/ results_ad
8516    
8517    o add two new packages
8518      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
8519        + subject to optimization (memory)
8520      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
8521        + subject to reordering (many GOTOs in the original code)
8522        + so far opps is called for every (i,j) point, and then operates in
8523          the vertical; one may want to reorder the scheme in order operate in
8524          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
8525          fields)
8526    o overhaul of IO so that we now have flags for MDSIO and/or MNC
8527      - all verification tests compile and run with linux_ia32_g77
8528      - defaults are compatible with current input files--nothing
8529        should change if you were not previously using MNC
8530      - MNC output has been added in numerous places (eg. timeave)
8531        but there are still a few writes not yet do-able with MNC
8532        (this is in progress)
8533      - flags now allow for either/or/both use of MDSIO and MNC and
8534        documentation will soon follow
8535      - numerous small formatting cleanups for ProTeX
8536    o add version info (via BUILD_INFO.h) to MNC and stdout
8537    
8538    checkpoint54e_post (2004/09/02)
8539    o add two new packages
8540      - pp81 (Packanowski and Philander, 1981), Richardson number and
8541        stratification dependent mixing
8542      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
8543      - these scheme operate in a similar manner as KPP (without ghat, of
8544        course), however there is only one diffusivity that is used for both
8545        temperature and salinity (and passive tracers)
8546    o add offline package
8547    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
8548      provided by Stephanie Dutkiewicz
8549    o genmake2: add ability to search for C compilers and cleanup test output
8550      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
8551    
8552    checkpoint54d_post (2004/07/27)
8553    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
8554    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
8555      leading to additional shift by 5 days each year of integration
8556       (i.e. leading to considerable offset over the years)
8557    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
8558    o start with no AB and no initial filtering (staggerTimeStep):
8559      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
8560    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
8561      (external loading & cpl import/export stay in forward_step.F)
8562    o update coupling interface to work with new staggerTimeStep
8563    o change MDSIO ptracers_pickup.
8564    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
8565    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
8566    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
8567    
8568    checkpoint54c_post (2004/07/18)
8569    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
8570      this affects (truncation error) output.txt of test-exp:
8571       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
8572    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
8573    o change Qnet to always be the net heat flux, (+upward).
8574      affects (truncation error) output of natl_box exp.: updated
8575    o define the max number of passive tracers in PTRACERS_SIZE.h
8576    o start to test mnc routinely in exp0
8577    o add sea-ice loading (sIceLoad) as a new forcing field.
8578    
8579    checkpoint54b_post (2004/07/08)
8580    o add testreport "-j JOBS" option for parallel builds (tested and pretty
8581       impressive on Altix and Opteron systems)
8582    o diagnostics can now write NetCDF files through the mnc package
8583    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
8584    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
8585    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
8586      affects (truncation error) output of lab_sea & natl_box exp.: updated
8587    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
8588    
8589    checkpoint54a_post (2004/07/06)
8590    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
8591    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
8592    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
8593    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
8594      + internal_wave (shift in writing cg2d_ini_res)
8595    checkpoint54a_pre (2004/07/05)
8596    
8597    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
8598      - modified verification/lab_sea and natl_box_adjoint accordingly
8599    
8600    checkpoint54 (2004/07/02)
8601    checkpoint53g_post (2004/07/02)
8602    o prepare splitting of thermodynamics: store convect.counter in common block
8603    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
8604      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
8605    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
8606    o new parameter "nShapS": allow to treat differently S from T (nShapT)
8607    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
8608    o restore adjointability
8609    
8610    checkpoint53f_post (2004/06/25)
8611    o modifications that affect AIM experiment results (update output.txt):
8612      - no advection of S at top interface Nr (pkg/generic_advdiff)
8613      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
8614    o AIM pkg:
8615      - include stability function into surf.Flux derivative relative to Tsurf
8616      - calculate clear-sky radiation & surface temp. change (for diagnostics)
8617    
8618    checkpoint53e_post
8619    o merged cylindrical coord configuration
8620    o added rotating_tank experiment
8621    checkpoint53e_pre
8622    
8623    checkpoint53d_post (2004/06/14)
8624    o faulks upgraded: re-generate output.txt that have changed:
8625       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
8626    o Added Bryan and Lewis, 1979, vertical diffusivity profile
8627    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
8628    o added Sadourny discretization of Coriolis
8629      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
8630      - re-enabled use of omega3 (useAbsVorticity)
8631    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
8632      vector-invariant equations
8633      - note: does *NOT* yet use same variable visc. for no-slip BC's.
8634    o recoded the lateral boundary conditions for non-hydrostatic w, this time
8635      hopefully without new bugs
8636      - still to do: biharmonic friction for non-hydrostatic w
8637    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
8638    o regenerated output for global_ocean_ebm (using -ieee)
8639    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
8640      of mom_common/
8641      - simple re-arrangement of instructions within computing loop
8642    checkpoint53d_pre (2004/05/21)
8643    
8644    checkpoint53c_post (2004/05/21)
8645    o new version of coupler for AIM+thSIce and Ocean models
8646     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
8647     - land: change Evaporation of snow
8648     - aim with thSIce: fix bug in snow-precip.
8649    o changes to calc_gw.F
8650     - bug fix for w^2 term near the bottom boundary
8651     - (hopefully) improve the lateral slip boundary condtions for use with
8652        partial/looped cells
8653      - because the bug fix changes two verification experiments anyway (exp5
8654        and plume on slope), change the lateral boundary condition from half slip
8655        to the value of no_slip_sides
8656    o ebm package wasnt quite up to the parallel task. Fixed that.
8657    o Adjoint of EBM package + verification
8658      * TLM OK
8659      * ADM not sufficient accuracy yet (needs further testing)
8660    
8661    checkpoint53b_post (2004/05/14)
8662    o Commiting new energy balance model to repository
8663      * package is pkg/ebm
8664      * verif. is verification/global_ocean_ebm
8665      * references are in ebm_driver.F
8666    C      * X. Wang, P. Stone and J. Marotzke, 1999:
8667    C        Global thermohaline circulation. Part I:
8668    C        Sensitivity to atmospheric moisture transport.
8669    C        J. Climate 12(1), 71-82
8670    C      * X. Wang, P. Stone and J. Marotzke, 1999:
8671    C        Global thermohaline circulation. Part II:
8672    C        Sensitivity with interactive transport.
8673    C        J. Climate 12(1), 83-91
8674    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
8675    C        Destabilization of the thermohaline circulation
8676    C        by atmospheric eddy transports.
8677    C        J. Climate 7(12), 1870-1882
8678    o Will need long integration testing.
8679    checkpoint53b_pre (2004/05/14)
8680    
8681    o created pkg/mom_common in preparation for variable viscosity code
8682    o renamed and split ini_mnc_io
8683    o pkg/land: only liquid water can diffuse or run-off
8684    o AIM using land: soil wetness availability account for snow
8685    o added printMapIncludesZeros to EEPARMS namelist
8686    
8687    checkpoint53a_post (2004/05/11)
8688    o restore TAMC compatiility for exf_constants.h
8689      (no usage of _d in .h)
8690    o Additional storing in KPP in an attempt to fix
8691      TAMC problem with adjoint of KPP code.
8692      (no success...)
8693      Identical code works fine with TAF.
8694    o Fixed verification/natl_box_adjoint experiments.
8695      Initial conditions for Experiments 4 and 5 are now
8696      set to "SEAICE_initialHEFF=0", which is more reasonable,
8697      and hence gives results closer to that of Experiment 2.
8698      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
8699    
8700    checkpoint53 (2004/05/06)
8701    o stable checkpoint with up to date adjoint
8702      TLM tests only run for 1st grdchk at the moment. Its unclear if
8703      this is a code problem or a problem with resetting code for g_
8704      variables that is being autogenerated wrong.
8705      Otherwise:
8706       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
8707       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
8708         are both still in chaos following their security messes.
8709    
8710    checkpoint52n_post (2004/05/06)
8711    o various build (mostly genmake2) changes including:
8712      - ability to build/run more easily within Cygwin and MacOS X
8713      - more complicated Makefiles with a stronger dependence on Gnu Make
8714    o pkg/seaice modifications
8715      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
8716        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
8717        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
8718      - changed proxy for geostrophic velocity and updated
8719        verification/lab_sea/results/* accordingly
8720      - removed ADI dynamic solver from pkg/seaice
8721      - replaced all occurrences of 1/CSTICE or 1/CSUICE
8722        they caused a segmentation fault under certain circumstances
8723      - removed unused field WATR
8724    o bug fix in exf-package:
8725      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
8726         now reflect that.
8727    o small fixes in the cal-package:
8728      - set reference date to first of January for the 'model'-calendar
8729      - failing of cal_CheckDate in cal_FullDate now actually results in a
8730        warning
8731    o small modifications in exf-package to increase flexibility:
8732      - change climtempfreeze from a constant to a runtime parameter that
8733        is specified in data.exf_clim (default = -1.9)
8734      - introduce runtime parameter windstressmax (default = 2.0) that is
8735        specified in data.exf
8736    o fix in pkg/thsice:
8737      - update Evap (Tsf changes) to be consistent with Latent heat flux
8738      - maintain snow precipitation unchanged (even if Tsf >=0).
8739     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
8740    
8741    checkpoint52m_post (2004/04/18)
8742    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
8743      this does not change any of the results, because myIter=0 in swfrac always
8744      lead to jwtype=2 (the default anyway), but the call makes little sense
8745      as a default
8746    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
8747    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
8748      atmospheric model (AIM) to use it ; add a "slab ocean" component.
8749    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
8750    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
8751    o extending useSingleCpuIO option to work with new exch2 I/O format
8752      - old-style, missing-tile I/O is still accessible by defining CPP
8753        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
8754    o monitor package can write to NetCDF files and/or STDOUT
8755    o fix re-definition bug in MNC_GRID_INIT_ALL()
8756    o doc/api_reference added
8757      - a framework for building an API Reference Manual using all
8758        the "protex" comments embedded in the code
8759      - see pkg/generic_advdiff, pkg/mnc for examples
8760    o MNC:
8761      - make myThid the last argument for all subroutines
8762      - new default for the grid files: NO halos
8763      - add useMNC and other run-time flags
8764      - separate per-file-group handling of the unlimited dimension
8765      - early initialization of MNC w/ flags read at the eeboot stage
8766        and lookup tables set in initialize_fixed
8767      - write all MNC output to a freshly-created directory
8768    o thermodynamics sea-ice (thsice) is now tested with testreport.
8769    o test exp. advect_cs: use the standard cs32 grid ; update output.
8770    o Added functionality to grdchk:
8771      pick global i,j,k position (or nearest wet) where to perform check.
8772    
8773    checkpoint52l_post (2004/03/11)
8774    o new land formulation:
8775      a) use ground enthalpy as prognostic variable to ensure exact
8776         energy conservation.
8777      b) account for water temperature and for latent heat of freezing
8778         in all processes (rain, run-off, ground storage)
8779      c) compute surface and ground temperature implicitly.
8780    o aim_v23 modification for new land model:
8781      a) Treat separately land / ocean / sea-ice surface fluxes
8782         to allow implicit computation of land & sea-ice surface temp.
8783      b) add snow precipitation.
8784    checkpoint52l_pre (2004/03/11)
8785    
8786    o fix problem (when 1 tile is empty) in min/max monitor.
8787    o fix bug in timeAve (u,vZetatave in common block)
8788    o no restoring terms under ice for pkg/seaice
8789    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
8790    o bug fix for pkg/seaice pickups
8791    o change MNC call locations and add coordinate attributes
8792    o mask vorticity at the corner ; affects global_ocean.cs output
8793    o fix ini_curvilinear_grid ; test CS experiments with mpi
8794    o aim.5l_cs: modify sea-ice fraction input file ; update output
8795    o exf: Adding simple range check routine for exf fields after read
8796    
8797    checkpoint52k_post (2004/02/23)
8798    o removed top-level directory "diags"
8799      - we migrated these functions to pkg/timeave a long time ago
8800    o fixed bug introduced in pkg/monitor
8801    o accuracy ctrlprec = 32 insuffient for gradient checks using
8802      averaged fields (I/O via cost_averages)
8803      -> use ctrl.h in active_file*.F to control I/O precision.
8804    o paramter list of CALL ADTHE_MAIN_LOOP
8805    o added initial do_the_model_io to ecco
8806    o set all ...Freq to zero after cost_final
8807      taveFreq, dumpFreq, pChkptFreq
8808    o MAIN and ECCO differentiability restored
8809    
8810    checkpoint52j_post (2004/02/18)
8811    o fix nchklev in tamc.h for global_ocean...
8812    o Bringing flow and store directives up-to-date
8813    o Really weird thing!
8814      call do_the_model_io from the_main_loop with parameters
8815      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
8816      TAF places a faulty re-call of initialise_varia
8817      after cost_final call which should not be there!
8818    checkpoint52j_pre (2004/02/03)
8819    
8820    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
8821      error messages
8822    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
8823    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
8824      debug output
8825    o modfied mdsio_writefield.F to handle non-global files under exch2
8826    o update AIM Cubed-Sphere exp (aim.5l_cs):
8827      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
8828    o update AIM Equatorial Channel exp:
8829      use standard aim_v23 pkg and change the SST fields to be more realistic.
8830    o globalFile now works with exch2
8831    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
8832      mon_vort3.F to make exch2 friendly with >1 tile per cube face
8833    o limit timeave output for hi-res integrations
8834    
8835    checkpoint52i_post (2004/01/21)
8836    o removed CPP_EEOPTIONS.h from verification/*/code
8837    o updated the tiling for global_ocean_pressure
8838    checkpoint52i_pre (2004/01/20)
8839    
8840    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
8841      the old pkg/aim).
8842    
8843    checkpoint52h_pre (2004/01/20)
8844    o shortened offending lines in exch2_send_rx?.template
8845    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
8846    o genmake2: add build & execute test for NetCDF code
8847    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
8848      old grid files, moved CPP_EEMACROS.h to pkg/exch2
8849    o added useSingleCPUIO flag to monitor.F and mon_out.F
8850    o added temporary hack for sea-ice dynamics on the cube:
8851      metric terms are ignored and it is assumed that
8852      there is no sea-ice on cube faces 1, 2, 4, and 5.
8853    
8854    checkpoint52f_post (2004/01/09)
8855    o added exch2 cube routines to pkg/exch2
8856    o modified hs94.cs-32x32x5 to use it
8857    o added new grid files to hs94.cs-32x32x5
8858    checkpoint52f_pre (2004/01/07)
8859    
8860    checkpoint52e_post (2004/01/07)
8861    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
8862      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
8863    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
8864      to work with implicit vertical advection and AB ;
8865    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
8866    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
8867     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
8868    checkpoint52e_pre (2004/01/02)
8869    
8870    o fix bug in impldiff when Nr=1 or Nr=2.
8871    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
8872    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
8873    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
8874      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
8875    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
8876    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
8877    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
8878    
8879    checkpoint52d_post (2003/12/16)
8880    o re-tiled many expts to allow comparison in multi-processor mode
8881      - updated output accordingly
8882      - changed hs94.128x64x5 to use intial T from file rather than use the
8883        random number generator
8884    o add infrastructure in model routines for fizhi and gridalt packages
8885    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
8886    o changes to permit hi-res, cubed-sphere, configuration
8887      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
8888      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
8889      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
8890        of surface winds for the cube
8891      (A verification experiment, based on global_ocean.cs32x15, but with
8892       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
8893       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
8894       complete with example surface forcing files and matlab scripts to look
8895       at the output and compare it with that of global_ocean.cs32x15.)
8896    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
8897       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
8898       to conform to the common rule.
8899    o check-in the first version of the coupler + interfaces for multi-components
8900       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
8901       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
8902       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
8903       - ocean and atmos. share the same horizontal grid (no interpolation).
8904       - exchanges between component and coupler is done in forward_step
8905    o new verification experiment, cpl_aim+ocn:
8906       coupled ocean - AIM atmosphere on cs32 grid.
8907    
8908    checkpoint52d_pre (2003/12/06)
8909    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
8910    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
8911    
8912    checkpoint52c_post (2003/11/25)
8913    o Fixing OPTIONS files for use of exf:
8914      - ALLOW_ECCO not needed
8915      - ECCO_CPPOPTIONS.h should not be included from
8916        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
8917        as has been the case in the past
8918      - All cal/exf related options are currently set in
8919        single header file. Should remain so until we
8920        agree on a consistent new policy.
8921    o Removed all CPP options for cal package.
8922      cal has no more CPP options.
8923    o modified STOREs in GAD_ADVECTION
8924    o corrected key comp. for passkey
8925    
8926    checkpoint52b_post (2003/11/23)
8927    o new version: "thsice" of thermodynamic sea-ice pkg:
8928     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
8929     - modify fluxes but do not change theta directly;
8930     - light cleaning of bulk_force pkg (still needed with thsice).
8931     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
8932       + output_thsice.txt to test thsice & bulk_force pkgs.
8933    o put back grid & coriolis monitor output.
8934    checkpoint52b_pre (2003/11/23)
8935    
8936    o call "do_the_model_io" at the beginning (=> dump initial state)
8937    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
8938    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
8939      (need info on NUMBER_OF_PTRACERS)
8940    o missing PTRACERS headers in some routines
8941    o default tamc.h in pkg/autodiff supposed to crash
8942      to ensure proper customization
8943    
8944    checkpoint52a_post (2003/11/17)
8945    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
8946      - moved surfaceTendencyTice from pkg/seaice to main code
8947      - subroutine FREEZE_SURFACE now limits only surface temperature
8948        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
8949        => new output.txt for global_ocean.cs32x15 & global_with_exf
8950      - keep the old version of FREEZE for backward compatibility;
8951        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
8952      - corresponding modifs for TAF directives
8953    o added surface flux output variables to TIMEAVE_STATVARS
8954    o time-averaged output for pkg/ptracers
8955    o fix problem with ECCO-related divided adjoint
8956      snapshot file was missing some ad-variables,
8957      but no warning issued by TAF
8958    
8959    checkpoint52a_pre (2003/11/12)
8960    o some bug fixes for #undef REAL4_IS_SLOW
8961    
8962    checkpoint52 = ecco_c52_e35
8963    o after testing adjoints of checkpoint51u_post
8964    
8965    checkpoint51u_post (2003/11/06)
8966    o this is the post-merge tag of the ecco-branch
8967      (needs another clean checkout and re-testing)
8968    o various natl_box_adjoint configs and results
8969      but no input fields
8970    o obcs adjoint not yet merged!
8971    o adding ECCO global 1x1 and 2x2 degree configs
8972    o updated/extended some store directives for seaice
8973    o pkg/ecco now containes ecco-specific part of cost function
8974    o top level routines the_main_loop, forward_step
8975      supersede those in model/src/
8976      previous input data.cost now in data.ecco
8977      (new namelist ecco_cost_nml)
8978    o in ctrl/ cleaned some cross-dependencies and updated CPP options
8979    
8980    checkpoint51t_post (2003/11/04)
8981    o this is the pre-merge tag of the ecco-branch
8982    
8983    checkpoint51s_post (2003/11/04)
8984    o cleanup: removed various obsolete #define-s
8985    o pkg/grdchk
8986      - renamed 'ph-grd 3' to 'grad-res'
8987      - merged from ecco-branch
8988        (remaining bug fixes for obcs gradient checks)
8989      - additional high-precision output for testreport
8990        (grep for 'precision_grdchk_result')
8991    
8992    checkpoint51r_post (2003/11/03)
8993    o cleaned up or removed CPP_OPTIONS.h files
8994    o updated results for some of the tests to reflect the new
8995      optfiles (-ieee: -O0 instead of -O3)
8996    
8997    checkpoint51q_post (2003/10/30)
8998    o cd_code:
8999      - moved cd_scheme.F -> cd_code_scheme.F
9000      - separate read_checkpoint from cd_code_ini_vars.F
9001      - separated cd_code part from write_checkpoint
9002      - updated AD_SOURCE, generated .flow
9003      - added CD_CODE_VARS.h to the_main_loop
9004      - Moving cd_code specific store dir.s to pkg/cd_code
9005    o ctrl package totally restructured
9006      - pack/unpack now optional and decoupled from
9007        xx_/adxx_ I/O
9008      - ctrl_pack/unpack cleaned
9009        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
9010      - confined inclusion of AD_CONFIG.h to where necessary.
9011    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
9012    
9013    checkpoint51p_post (2003/10/30)
9014    o create initial cd_code package
9015      - WARNING: the initialization of fields within packages
9016        is broken because INI_FIELDS (where READ_CHECKPOINT is
9017        called) is called *before* PACKAGES_INIT_VARIABLES.
9018        This seems to be backwards since
9019        1) its important to initially zero the entire field including
9020           the "halo" region
9021        2) zeroing needs to be done *before* reading pickup info
9022           and the pickup call might or might not happen in any
9023           particular run
9024      - this needs an overhaul for R2
9025    o cleanup verification/*/code/GMREDI_OPTIONS.h
9026    o cleanup testreport
9027    
9028    checkpoint51o_post (2003/10/27)
9029    o bringing AD-related verif's up to date with genmake2
9030      - carbon/
9031      - global_ocean.90x40x15/
9032      - hs.94.1x64x5/
9033      - (front_relax/ )
9034    o (more) consistent directory structure for AD-related verif.'s
9035    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
9036    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
9037    o bug fix in find_alpha.F for MDJWF:
9038      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
9039        change rho -> rho-rhoConst
9040      - replace call find_rho to find_rhonum
9041    o initialisation of rFlx extended to full array (required by TAF)
9042      and shifted to thermodynamics
9043    o removed PTRACERS.h in ptracers routine
9044    o added surfacetendencyPtr to S/R parameter list pracers_forcing
9045    o Correcting initialisations for fVerU, fVerV.
9046    o helping TAF to recognize dependency on kUp for
9047      fVerU, fVerV
9048    o Replacing delZ by delR in pkg/ctrl/
9049    checkpoint51o_pre (2003/10/24)
9050    
9051    o undid all of cp51 pending some cleanups and discussion
9052    o added the [#include "AD_CONFIG.h"] statement to all files that need
9053       it for adjoint/tl #defines
9054     o re-worked the build logic in genmake2 to support AD_CONFIG.h
9055     o removed tools/genmake since it no longer works
9056    
9057    checkpoint51n_post (2003/10/23)
9058    o modifications to make FREEZE flux visible to pkg/kpp
9059      - moved surfaceTendencyTice from pkg/seaice to main code
9060      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
9061      - subroutine FREEZE now limits only surface temperature
9062        (this means new output.txt for global_ocean.90x40x15,
9063         global_ocean.cs32x15, and global_with_exf)
9064    o added surface flux output variables to TIMEAVE_STATVARS
9065    
9066    checkpoint51n_pre (2003/10/23)
9067    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
9068    o added [#include "AD_CONFIG.h"] to all files that use the following
9069      defines:
9070      - ALLOW_ADJOINT_RUN
9071      - ALLOW_TANGENTLINEAR_RUN
9072      - ALLOW_ECCO_OPTIMIZATION
9073    
9074    checkpoint51m_post (2003/10/21)
9075    o incorporating changes to get TAMC/TAF working in genmake2
9076      - added new TAMC/TAF targets to the Makefile
9077      - various cleanups related to package handling
9078      - these changes should have no impact on the forward model
9079    
9080    checkpoint51l_post (2003/10/20)
9081    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
9082     - faster algorithm for cal_addtime.F
9083     - higher precision arithmetic, where needed
9084     - pkg/exf *startdate variables changed from calendar date to
9085       model integration time
9086    
9087    checkpoint51l_pre (2003/10/17)
9088    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
9089    o enable to apply restoring on S & T only in a latitude band.
9090    o update output (external_forcing_surf modif. change truncation errors)
9091       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
9092    
9093    checkpoint51k_post (2003/10/16)
9094    o change default to: useNHMTerms=.FALSE.
9095     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
9096       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
9097     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
9098        exp1, ideal_2D_oce
9099     - change data file of oceanic exp (leave the results unchanged for now)
9100       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
9101    o set gravitySign automatically according to the vertical coordinate used
9102      (and change sign: back to "logical" value: +1 when R increases downward)
9103    o added an include barrier to the default CPP_OPTIONS.h and
9104      removed the #include "PACKAGES_CONFIG.h" from it
9105    o fix a bug in mom_fluxform (from chk51j_post)
9106    
9107    checkpoint51j_post (2003/10/10)
9108    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
9109    o adjusted some flow directives (dynamics, thermodynamics)
9110    o added cubed-sphere case to test cost function
9111    o heckpoint_lev?_directives.h now include
9112      pkg-specific directives, whenever those are enabled.
9113    o Moving pkg-specific flow directives to corresponding pkg
9114      Moving pkg-specific differentiation list to corresponding pkg
9115      Moving pkg-specific checkpoint-lev storing to corresponding pkg
9116      ---> conventions are
9117           - pkg_ad.flow
9118           - pkg_ad_diff.list
9119           - pkg_ad_check_lev?_dir.h
9120    
9121    checkpoint51i_post (2003/10/09)
9122    o merge of the branch-genmake2
9123      - knowingly breaks the older genmake
9124      - automatic generation of all ALLOW_${PKG_NAME} defines
9125      - new testreport supersedes older testscript
9126    o large number of package inclusion and header cleanups
9127    checkpoint51i_pre (2003/10/08)
9128    
9129    o new output for adjoin of global ocean vector invariant
9130    o fix for checkpoint of thermodynamic seaice and bulk_force
9131    o Steph gchem various cleanups
9132    
9133    checkpoint 51h_pre
9134    o fixed some single quotes
9135    o modify gchem pkg to be more versatile
9136    o modifications to clean up dic pkg
9137    o add pkg/cfc
9138    
9139    checkpoint51g_post (2003/10/02)
9140    o provide links for ARPACK and ADM*TLM
9141    o start removing verification/vero/
9142    o update AD-related stuff
9143      (in particular some IF-statements in model/src/ routines)
9144    o adding to verification/global_ocean.90x40x15/ adjoint of
9145      vector invariant setup
9146    
9147    checkpoint51f_post (2003/10/02)
9148    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
9149    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
9150      of tracer Green's fucntions for ocean inversion project.
9151    
9152    checkpoint51f_pre (2003/08/07)
9153    o Added on-the-fly spatial interpolation capability
9154        "USE_EXF_INTERPOLATION" to pkg/exf.
9155      - This is a temporary Cartesian-grid hack until
9156        the super-duper ESMF coupler becomes available.
9157      - See verification/global_with_exf/README for usage example.
9158      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
9159        flags and modified pkg/seaice accordingly.
9160    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
9161        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
9162        non-local transport term.
9163    
9164    checkpoint51e_post (2003/08/03)
9165    o pkg/mom_vecinv:
9166      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
9167      - add time-ave diagnostic of vorticity advection.
9168    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
9169    o atmospheric geopotential: - include water vapor effect;
9170                                - use p^kappa in p* scaling.
9171    o land pkg: read initial state from files.
9172    o AIM : add stratospheric drag in the upper level
9173    
9174    checkpoint51d_post (2003/07/18)
9175    o change function ILNBLNK (=> last non-blank char.) to return zero
9176      (instead of the string length) when the string. char is empty
9177    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
9178    o modif's to restore TAMC compatibility
9179      - avoid "_d" constructs in PARAMETER declarations
9180      - avoid interrupting lines by comment lines
9181    o Use cluster local disks for purely local I/O
9182      vs. globally visible disks needed for ctrl stuff
9183      (merged from ecco-branch)
9184      - new active_file_loc... and mdsio_..._loc routines
9185      - affected packages: autodiff, ctrl, grdchk, mdsio
9186    
9187    checkpoint51c_post (2003/07/08)
9188    o introducing integer flag debugLevel
9189      - debLevZero: suppress all output
9190      - debLevA: standard
9191      - debLevB: equivalent to current debugMode=.TRUE.
9192    o introducing pathname variable mdsioLocalDir for mdsio
9193      that can be specified at runtime
9194      (relevant for cluster I/O to local disk)
9195    `
9196    >>>checkpoint51b_post
9197    adjoint of ptracers
9198    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
9199    o extended state in checkpoint_lev?, etc.
9200    o alternative ctrl/cost with tr1 or ptracer
9201    o new comlev1_bibj_ptracers
9202    o new ptracers.flow
9203    o made ptracers_forcing same as external_forcing_s
9204    o added verification for adjoint with ptracers
9205      - adm. grdchk fail so far
9206      - tlm. grdchk OK
9207      - checked tapelev/comlev recomputations: OK
9208    <<<checkpoint51b_pre
9209    
9210    checkpoint51a_post (2003/06/25)
9211    o added code for biogeochemistry package
9212      - new pkgs: dic, gchem
9213      - new subroutine in ptracers
9214    o modify code for biogeo packages
9215      - in model/src and pkg/ptracers
9216    
9217    checkpoint51 (2003/06/24)
9218    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
9219      - autodiff, ctrl, exf, grdchk, seaice
9220      kept separate packages
9221      - cost, ecco, obcs
9222    o updating verification/internal_wave, verification/lab_sea
9223      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
9224    
9225    checkpoint50i_post (2003/06/23)
9226    o Preparing next differentiable checkpoint and sync
9227      of MAIN vs. ecco-branch
9228      - 1st step: this one is differentiable
9229      - 2nd step: next(! not this) checkpoint will have updated packages
9230                  from ecco-branch)
9231    
9232    checkpoint50h_post (2003/06/20)
9233    o new package "land": provide surface BC for AIM.
9234    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
9235    o AIM: use true log-P extrapolation for near surface temp (= as in
9236        F.Molteni paper) ; update aim.5l_cs output.
9237    o New variable in PARM03 for more flexible pickups
9238    o somewhat cleaned package initialisation sequence for
9239      ctrl/ cost/ ecco/ in packages_... routines
9240    
9241    checkpoint50g_post (2003/05/23)
9242    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
9243      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
9244      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
9245        made the default because of faster convergence than ADI
9246    
9247    checkpoint50f_post (2003/05/23)
9248    o exf totally restructured
9249      - replaced all exf_set_ routines by one generic exf_set_gen.F
9250        and made sure it's still differentiable
9251      - split exf_getffields.F into new exf_bulkformulae.F
9252      - exf_inscal_/exf_outscal_ suffixes consistent with field names
9253      - updated adjoint/makefile and relevant verif. accordingly
9254    
9255    checkpoint50f_pre (2003/05/23)
9256     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
9257          + change Evap over land. (update aim.5l_cs output)
9258     o added missing .cvsignores and made uniform across expts
9259     o changed configuration of tidal_basin_2d expt
9260     o added pkg/debug functions for tracing code in fatal crashes
9261     o tidied pkg/monitor to use MONITOR_OPTIONS.h
9262     o new fn in pkg/monitor to stop model if solution grows too big
9263     o removed lots of single quotes from comments
9264    
9265    checkpoint50e_post (2003/05/14)
9266    o make KPP work with PTRACERS
9267     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
9268       nearly a copy of kpp_transport_s
9269     - there is no analogue to SurfaceTendencyS, so I have to use
9270       gPtr(of the surface layer) instead
9271    o add a new platform SunFire+mpi (SunFire 15000) to genmake
9272    checkpoint50e_pre (2003/05/13)
9273    
9274    checkpoint50d_post (2003/05/13)
9275    o change kpp output from multiple-record state files to single-record state
9276      files analogous to write_state.F
9277    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
9278      analogous to the cg2d-related output.
9279    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
9280      so that writing to internal file fn (with length 512) fails.
9281    checkpoint50d_pre (2003/05/12)
9282    
9283    checkpoint50c_post (2003/05/12)
9284    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
9285    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
9286    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
9287    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
9288    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
9289    
9290    checkpoint50c_pre (2003/04/30)
9291    Merging from release1_p13:
9292    o bug fix for pkg/seaice dynamic solver
9293    o Added SEAICE_initialHEFF to pkg/seaice
9294    
9295    checkpoint50b_post (2003/04/17)
9296    o store u*,v* in gU,V instead of in guNm1,gvNm1
9297    o in order to put the momForcing out of the Adams-Bashforth:
9298      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
9299      to timestep.F
9300    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
9301    o re-generate output for highly sensitive test-exp:
9302       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
9303    
9304    checkpoint50b_pre (2003/04/17)
9305    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
9306    o corrected CPP option mismatch in exf_Bulk... functions for case
9307      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
9308    
9309    checkpoint50a_post (2003/03/21)
9310    o Bug fix for merging between c50 and KPP.
9311      ikey was passed from thermodynamics to kpp_calc via
9312      common block rather than being recomputed in kpp_calc,
9313      in contradiction with new key itdkey.
9314      New key ikppkey created, and tamc.h headers updated.
9315    
9316    checkpoint50 (2003/03/08)
9317    - 2nd step of merge with ecco-branch:
9318      merge changes in ecco-branch back into main trunk
9319    - bug fix in find_alpha
9320    - more storing in gmredi_calc_tensor.F, kpp_routines.F
9321    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
9322    - merged some sliced AD support routines
9323    
9324    checkpoint49 (2003/03/06)
9325    merged from ecco-branch:
9326    o exf:
9327      - Enable initialisation of forcing fields to constant
9328        (runtime) values.
9329      - in exf_getffields.F
9330        Reduce i-/j-loop to interior domain, discarding overlaps.
9331        That also fixes wrong TAF-key computations for key_1, key_2
9332        with bulf formulae.
9333      - exf_init.F modify #ifdef for exf_init_evap
9334      - exf_getffieldrec.F, ctrl_getrec.F
9335        The following INT-usages are not safe:
9336          fldsecs  = int(fldsecs/fldperiod)*fldperiod
9337          fldcount = int(fldsecs/fldperiod) + 1
9338        and were modified.
9339    o autodiff: checkpoint_lev...
9340      - updated storing for bulk formulae (some arrays were missing)
9341      - added state for seaice package
9342      - synchronized with main branch
9343    o DIVA:
9344      Modif.s in
9345      - the_main_loop.F
9346      - the_model_main.F
9347      and added cost_final_restore.F cost_final_store.F
9348      o With these changes, it is possible to fully separate
9349        the first forward run to compute the cost function (mdthe_main_loop)
9350        and adjoint runs over individual DIVA intervals (adthe_main_loop)
9351        into separate model executions.
9352        This enables better tuning of DIVA to given queue sizes.
9353      o Loss of cost function value in consecutive DIVA runs is
9354        fixed by storing to 'costfinal' file.
9355      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
9356        beginning/end of adjoint integration is accounted for.
9357      The current changes apply to TAF-1.4.26.
9358      TAF has one remaining bug, requiring one manual change
9359      (see MITgcm manual).
9360    o cal: synchronized between MAIN and ecco-branch
9361    
9362    checkpoint48i_post (2003/03/05)
9363    o Changes to restore differentiability of code w.r.t. previous tag
9364      (mostly adding new routines to make list and replacing
9365      pressure by totPhiHyd).
9366    o Updated and merged grdchk package
9367      - has both ADM and TLM checks
9368      - works for single- and multi-proc.
9369      - output cleaned
9370      - worked successfully for parallel DIVA
9371    o genmake:
9372      - Adding -platform=SP4
9373      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
9374    o Modif. for DIVA:
9375      ctrl_unpack should not be called in intermediate DIVA interval.
9376      (similar thing would apply for active files such as
9377      tbar, sbar, psbar, which should not be reinitialised;
9378      only relevant for ecco-branch)
9379    
9380    checkpoint48h_post (2003/02/28)
9381    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
9382    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
9383    o Added SEAICE_initialHEFF to pkg/seaice
9384    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
9385    
9386    checkpoint48g_post (2003/02/18)
9387    --- EOS:
9388    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
9389      store total Potential in totPhyHyd for diagnostics & EOS.
9390    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
9391    --- Pressure/geopotential gradient:
9392    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
9393    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
9394      ( changes results of global_ocean_pressure )
9395    o NLFS + z-coord.: add eta*Rho' contribution.
9396    o accurate phiHyd when using interface-W at the middle between 2 centers
9397     ( changes results of ideal_2D_oce )
9398    o includes r* 2nd term in potential gradient.
9399    
9400    checkpoint48f_post (2003/02/18)
9401    Merging from release1_p12:
9402    o Modifications for using pkg/exf with pkg/seaice
9403      - improved description of the various forcing configurations
9404      - added basic radiation bulk formulae to pkg/exf
9405      - units/sign fix for evap computation in exf_getffields.F
9406      - updated verification/global_with_exf/results/output.txt
9407    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
9408      (SBO) core products, including oceanic mass, center-of-mass,
9409      angular, and bottom pressure (see pkg/sbo/README.sbo).
9410    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
9411      to avoid negative values in shallow regions.
9412      - updated verification/natl_box/results/output.txt
9413      - updated verification/lab_sea/results/output.txt
9414    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
9415    o Added useSingleCpuIO option (see PARAMS.h).
9416    o Updated useSingleCpuIO option in mdsio_writefield.F to
9417      work with multi-field files, e.g., for single-file pickup.
9418    o pkg/seaice:
9419      - bug fix in growth.F: QNET for no shortwave case
9420      - added HeffFile for specifying initial sea-ice thickness
9421      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
9422    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
9423      kpp_transport_t.F, forward_step.F, and the_main_loop.F
9424    o pkg/seaice:
9425      - adjoint-friendly modifications
9426      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
9427    
9428    checkpoint48e_post (2003/02/12)
9429    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
9430    o dynamics: change definition of computational domain & adapt mom_fluxform
9431      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
9432    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
9433        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
9434        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
9435        global_ocean.90x40x15 global_with_exf global_ocean_pressure
9436        inverted_barometer solid-body.cs-32x32x1
9437      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
9438    
9439    checkpoint48d_post (2003/02/09)
9440    o in preparation for r*:
9441     a) use pre-computed gradient of hydrostatic potential:
9442        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
9443     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
9444        => affects results of glob_oce_pressure (different truncation error)  
9445      update output.txt of ideal_2D_oce & global_ocean_pressure
9446    
9447    checkpoint48d_pre (2003/02/08)
9448    o in preparation for r*:
9449      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
9450      pass the 2 comp. of the grad. as arguments to momentum S/R.
9451      but for the moment, only used if it does not change the results.
9452    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
9453    
9454    checkpoint48c_post (2003/02/06)
9455    Modifications in treatment of initial flux forcing controls
9456    to avoid extra storing of flux fields.
9457    
9458    checkpoint48c_pre (2003/01/21)
9459    o Added tidal_basin_2d experiment (currently 1D!)
9460    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
9461    
9462    checkpoint48b_post (2003/01/27)
9463    o r* coordinate added in #ifdef NONLIN_FRSURF block.
9464     (modification to pressure gradient not yet implemented)
9465    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
9466      (for U & V) that are used for vertical advection of momentum.
9467    
9468    checkpoint48a_post (2003/01/24)
9469    o In preparation for r*, use temp. array to compute vertical transport
9470       in flux-form momentum pkg. => change results of few test-exp.
9471      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
9472                        lab_sea, natl_box & plume_on_slope
9473    
9474    checkpoint48 (2003/01/23)
9475    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
9476    
9477    checkpoint47j_post (2003/01/21)
9478    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
9479    o moved adexch from forward_step to addummy_in_stepping
9480    o added exch in ctrl_map_...
9481    o aveFreq.=0. at end of cost_final to avoid overwrite in
9482      reverse checkpointing loop
9483    o Yet more changes in gmredi:
9484      * adgmredi_calc_tensor
9485        avoiding all recomputation of gmredi_slope_limit
9486      * adgmredi_x/y/rtransport
9487        added flag for excessive storing to avoid recomp. of
9488        u/v/rtans, dTdx/y/z
9489        -> this is not really necessary and very memory-consuming
9490      * adgmredi_slope_psi:
9491        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
9492      * gmredi_slope_limit
9493        re-activated full calculation of taperfct for case 'ac02'
9494    o updating verification/ adjoints of carbon, global_ocean.90x40x15
9495    
9496    checkpoint47i_post (2003/01/13)
9497    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
9498    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
9499      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
9500    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
9501    o gmredi: fix few bugs.
9502    
9503    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
9504    This will be a good checkpoint to plug into the ecco-branch.
9505    o few modif.'s to get latest version adjointed
9506      (mainly kick out code in ini_linear_phisurf)
9507    o modif's to run adjoint with exactConserv
9508    o case GM_BOLUS_ADVEC should be cleaned
9509      S/R gmredi_slope_psi should be cleaned
9510    o verification/carbon now has exactConserv=.TRUE.
9511    
9512    checkpoint47g_post (2003/01/10)
9513    o time-average AIM output: becomes independent from statvars time-average
9514      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
9515    o After TAF bug fix:
9516      Tested adjoint of gmredi package.
9517      Tests were done with checkpoint47 rather than with latest
9518      checkpoint47f_post since the latter is broken for the adjoint
9519      verification/carbon/ contains both ADM and TLM gradient checks.
9520    Here they are, before they get changed/lost/stolen.
9521    Mostly modif.'s to fix numerical sensitivities.
9522    Gradient checks OK for
9523    - GM_taper_scheme:
9524      * clipping
9525      * ac02
9526      * linear
9527      * glw91
9528      * dm95
9529      * ldd97
9530    - GMREDI_OPTIONS:
9531      * GM_VISBECK_VARIABLE_K
9532      * GM_NON_UNITY_DIAGONAL
9533      * GM_EXTRA_DIAGONAL
9534      * GM_BOLUS_ADVEC
9535    in conjunction with data.gmredi parameters to be checked in
9536    in a few minutes under verification/carbon/code/
9537    
9538    checkpoint47f_post (2002/12/28)
9539    Merging from release1_p10:
9540    o modifications for using pkg/exf with pkg/seaice
9541      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
9542        and SEAICE_EXTERNAL_FLUXES
9543      - pkg/exf CPP options EXF_READ_EVAP and
9544        EXF_NO_BULK_COMPUTATIONS
9545      - usage examples are Experiments 8 and 9 in
9546        verification/lab_sea/README
9547      - verification/lab_sea default experiment now uses
9548        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
9549    
9550    checkpoint47e_post (2002/12/27)
9551    o created a tag prior to creating a branch
9552    
9553    checkpoint47d_post (2002/12/16)
9554    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
9555      at the bottom boundary had an erroneous half slip boundary condition
9556    o added bottom drag and no slip boundary condition capabilities to
9557      oceanic pressure coordinates code
9558    o added new verification experiment global_ocean_pressure, this experiment is
9559      also described in the tutorial section of the manual
9560    checkpoint47d_pre (2002/12/16)
9561    
9562    checkpoint47c_post (2002/12/16)
9563    o Added a verification experiment for a global cubed-sphere ocean run
9564      -  verification/global_ocean.cubed32x32x30
9565      -  uses pkg/therm_seaice and pkg/bulk_forcing
9566    
9567    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
9568    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
9569      when using P-coordinate; only implemented for atmospheric config.
9570    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
9571      NOTES: requires option NONLIN_FRSURF to be "#define".
9572    o update advect_xz/results/output.txt (left from checkpoint44g_post)
9573    
9574    checkpoint47b_post (2002/12/05)
9575    Merging from release1_p9:
9576    o pkg/seaice
9577      - removed GOTO's and added taf directives
9578      - double precision constants to reduce the g77 (Linux)
9579        to F77 (SGI) differences reported in release1_p8
9580    o tools/genmake
9581      - added SGI options
9582    o verification/testscript
9583      - updated to that of checkpoint47a_post
9584    o verification/global_ocean.90x40x15/input/eedata
9585      - modified for SGI f77 compatibility
9586    o verification/lab_sea
9587      - added description of sea-ice model
9588      - added missing matlab routines
9589      - added test of thermodynamics parallelization
9590    
9591    checkpoint47a_post (2002/11/23)
9592    o new pkg: aim_v23
9593     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
9594       for now, keep the same surface forcing as before.
9595     - Part-Cell implemented into AIM; check that Heat & Water are conserved
9596     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
9597     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
9598    o add diagnostic of surface correction term in monitor output
9599    
9600    o bulk_force and therm_seaice
9601    - Two packages:  bulk_force (Bulk forcing)
9602      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
9603    - Earlier integration from Stephaine Dutkiewicz
9604      and Patrick Heimbach.
9605    - Two ifdef statements for compile time,
9606       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
9607    
9608    checkpoint47 (2002/11/15)
9609    differentiable version of checkpoint46n_post
9610    o bug fix in quasihydrostaticterms
9611    o * "clean" adjoint code (in terms of extensive recomputations)
9612        can now be obtained for all GMREDI options (i.e. for
9613        - GM_VISBECK_VARIABLE_K
9614        - GM_NON_UNITY_DIAGONAL
9615        - GM_EXTRA_DIAGONAL
9616        - GM_BOLUS_ADVEC )
9617      * However, wrong gradient check problem remains unsolved.
9618      * New CPP options have been introduced for different
9619        tapering schemes
9620    o external_fields_load now part of differentiation list
9621    o pressure needs multiple storing;
9622      would be nice to have store_pressure at beginning or
9623      end of forward_step, e.g. by having phiHyd global (5-dim.)
9624      (NB: pressure is needed for certain cases in find_rho,
9625      which is also invoked through convective_adjustment).
9626    o recomputations in find_rho for cases
9627     'JMD95'/'UNESCO' or 'MDJWF' are OK.
9628    o #define ATMOSPHERIC_LOADING should be differentiable
9629    o ini_forcing shifted to begining of initialise_varia
9630    o Incorporating QNVS line search routines into MITgcm
9631      (this is separate code, and therefore not under pkg)
9632      lsopt/, optim/
9633    o Updated verification/carbon/
9634      - #define GM_VISBECK_VARIABLE_K
9635      - GM_taper_scheme    = 'ldd97'    
9636    
9637    checkpoint46n_post (2002/11/12)
9638    Merging from release1_p8:
9639    o verification/natl_box:
9640      updating new external_fields_load routine
9641    o New package: pkg/seaice
9642      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
9643      The sea-ice code is based on Hibler (1979-1980).
9644      Two sea-ice dynamic solvers, ADI and LSR, are included.
9645      In addition to computing prognostic sea-ice variables and diagnosing
9646      the forcing/external data fields that drive the ocean model,
9647      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
9648      The implied surface heat flux is then stored in variable
9649      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
9650      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
9651      non-local transport term.  Because this call precedes model
9652      thermodynamics, temperature under sea-ice may not be "exactly" at
9653      the freezing point by the time theta is dumped or time-averaged.
9654      N.B.: fairly large differences in accuracy occur across
9655            different platforms/compilers; comparison between
9656            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
9657            generated output gives:
9658       T           S           U           V
9659      C D M    c        m  s        m  s        m  s        m  s
9660      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
9661      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
9662      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
9663    
9664      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
9665    o GAD:
9666      - generated new common blocks to account for call of
9667        same gad routines with differing traceridentities
9668        (needed to modify tracerIdentity indices in GAD.h)
9669      - generated separate common blocks for case useCubedSphereExchange
9670        (Department of Futurology)
9671      - parameter lists to gmredi_?transport: added tracerIdentity
9672      - added new key indices to tamc.h
9673    o external_fields_load:
9674      - added this routine to TAF list
9675      - needed to make some common blocks global and additional storing
9676        along the same lines as exf package (checkpoint_lev?_directives.h)
9677    o exf:
9678      updated external forcing package
9679      - bug fixes carried over from ecco-branch
9680        (missing OBCS_OPTIONS.h in two routines)
9681      - enable easy to use "no forcing".
9682      - added exf I/O for atmospheric loading
9683      - added exf I/O for runoff data
9684      - transfered scaling between exf <-> MITgcm to exf namelist
9685    o Adding new verification experiment global_with_exf.
9686      This verification experiment is almost identical to the
9687      global_ocean.90x40x15 experiment, except that it uses
9688      the exf (and cal) package instead of the
9689      external_fields_load routine (cf README file).
9690    
9691    checkpoint46m_post (2002/11/07)
9692    o modified testscript to return -- when there are no lines of "%MON" output
9693    o added new flag "quasiHydrostatic" for QH mode
9694      and new routine quasihydrostaticterms()
9695    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
9696      New routine: mom_u_coriolis_nh()
9697    o fixed sign of non-hydrostatic metric terms in u and v equations.
9698      Depend on correct sign of gravitySign.
9699    o added work.pc* to .cvsignore in aim directories using ifc
9700    o introduced flag for controllin non-hydrostatic metric terms
9701    o removed gravitySign from PARM04
9702    o switched to g77/ifc from pgf77 in aim experiments
9703    
9704    checkpoint46l_post (2002/11/01)
9705    o made convective adjustment work with pressure coordinates:
9706     - changed the direction of k-loop in convective_adjustment.F for the
9707       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
9708     - adjusted the reference pressure k-index in convective_adjustment.F
9709     - adjusted the convection condition in convect.F (in analogy to
9710       calc_ivdc.F)
9711     - convective_adjustment no longer computes anything on the halos
9712     - removed the warnings about negative salinity from find_rho.F and
9713       find_alpha.F; instead the new routine look_for_neg_salinity, called
9714       at the beginning of find_rho, find_alpha, and find_beta, does a
9715       check of the entire slice, if CPP-option
9716       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
9717    checkpoint46l_pre (2002/10/23)
9718    
9719    checkpoint46k_post (2002/10/23)
9720    o fixed the verification/global_ocean.90x40x15 experiment:
9721     - new bathymetry (the world according to A., JMC, and M.)
9722     - new initial fields and forcing fields (*.bin files)
9723     - new POLY3.COEFFS (for the next release one should switch to a full
9724       equation of state: JMD95P or MDJWF)
9725     - fixed several errors and redundancies in the data file
9726     - experiment uses looped cells
9727     - added matlab directory with diagnostic scripts for plotting of output
9728    
9729    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
9730     - read AIM physics parameters from a file (data.aimphys)
9731     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
9732    
9733    checkpoint46j_post (2002/10/07)
9734    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
9735    o move wVel computation at the end of the time step, in S/R integr_continuity
9736    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
9737    o update timeave pkg for wVel diagnostic.
9738    checkpoint46j_pre (2002/09/27)
9739    
9740    checkpoint46i_post (2002/09/25)
9741    o Clean up AIM package (and keep the results unchanged):
9742      include CPP_OPTION and use IMPLICT NONE in all routines ;
9743      declare all the variables _RL ; use _d 0 for all numerical constants.
9744      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
9745    
9746    checkpoint46h_post (2002/09/25)
9747    o cleaned up the use of rhoNil and rhoConst.
9748      - rhoNil should only appear in the LINEAR equation of state, everywhere
9749        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
9750        and the dynamical equations are all divided by rhoConst
9751    o introduced new parameter rhoConstFresh, a reference density of fresh
9752      water, to remove the fresh water flux's dependence on rhoNil. The default
9753      value is 999.8 kg/m^3
9754    o cleanup up external_forcing.F and external_forcing_surf.F
9755      - can now be used by both OCEANIC and OCEANICP
9756    checkpoint46h_pre (2002/09/18)
9757    
9758     Added code to convert surface volume flux (fresh water) into
9759     a mass flux when using P coordinates in the ocean (OCEANICP).
9760     Note: It assumes you have set rho0=rhoConst=density of fresh water.
9761    
9762    checkpoint46g_post (2002/09/18)
9763    o Include a new diagnostic variable phiHydLow for the ocean model
9764      - in z-coordinates, it is the bottom pressure anomaly
9765      - in p-coordinates, it is the sea surface elevation
9766      - in both cases, these variable have global drift, reflecting the mass
9767        drift in z-coordinates and the volume drift in p-coordinates
9768      - included time averaging for phiHydLow, be aware of the drift!
9769    o depth-dependent computation of Bo_surf for pressure coordinates
9770      in the ocean (buoyancyRelation='OCEANICP')
9771      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
9772        Theta, Salinity, and Pressure in the parameter list. This routine is
9773        presently contained in find_rho.F. This routine does not give the
9774        correct density for 'POLY3', which would be a z-dependent reference
9775        density.
9776    o cleaned up find_rho
9777      - removed obsolete 'eqn' from the parameter list.
9778    o added two new verification experiments: gop and goz
9779      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
9780    checkpoint46g_pre (2002/09/16)
9781    
9782    checkpoint46f_post (2002/09/16)
9783    o Enable tangent linear (forward mode) gradient checks:
9784      - extended active file handling to g_... files
9785      - added TANGENT_SIMULATION to theSimulationMode
9786      - extended grdchk package accordingly
9787    o added tangent linear setup in verification/carbon/code_ftl
9788    o added adjoint setup in verification/front_relax/code_ad
9789    
9790    checkpoint46e_post (2002/09/05)
9791    o Added new equation of state -> MDJWF
9792      - EOS of McDougall et al., 2002, JAOT, submitted
9793      - caveat: the equation of state is only valid for a smaller (more
9794        realistic?) range of values than JMD95P/Z and UNESCO
9795      - added masks to the calculation of pressure in store_pressure
9796      - added more check values for density in check_eos (ini_eos.F), some of
9797        the old check values are out of the range of the MDJWF-eos, so don't
9798        expect perfect matches for those
9799    checkpoint46e_pre (2002/08/19)
9800    
9801    checkpoint46d_post (2002/08/19)
9802    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
9803      'OCEANICP', also initialised field pressure correctly in ini_eos in the
9804      case of pressure coordinates. eosType='JMD95Z' in
9805      combination with buoyancyRelation='OCEANICP' now causes an error.
9806    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
9807      in find_alpha/beta.
9808    checkpoint46d_pre (2002/08/15)
9809    
9810    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
9811      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
9812    
9813    checkpoint46c_post (2002/08/15)
9814    o Changes necessary for ocean in p-coordinates
9815     -  Added new buoyancy relation = 'OCEANICP'
9816     -  Added new parameters = gravitySign (this used to be contained inside
9817        the factor dRdZ which I added when we first switched to R coordinates).
9818     X GM/Redi is not compatible (yet)
9819     X bottom drag and no-slip need to be debugged.
9820    checkpoint46c_pre (2002/08/07)
9821    
9822    checkpoint46b_post (2002/08/07)
9823    o Added new equation of state -> JMD95Z and JMD95P
9824      - EOS of Jackett and McDougall, 1995, JAOT
9825      - moved all EOS parameters into EOS.h
9826      - new routines ini_eos.F, store_pressure.F
9827    o Added UNESCO EOS, but not recommended because it requires
9828      in-situ temperature (see JMD95)
9829    o Modified formatting for knudsen2.f in utils/knudsen2 and added
9830      unesco.f to be used with POLY3
9831    checkpoint46b_pre (2002/07/31)
9832    
9833    checkpoint46a_post (2002/07/31)
9834    o Added (atmospheric) pressure loading
9835      - new field in FFIELDS.h, etc...
9836      - new cpp flag ATMOSPHERIC_LOADING
9837    o Changed hFacC to _hFacC in calc_phi_hyd.F
9838    o Added SHORTWAVE_HEATING to some files for consistency
9839    checkpoint46a_pre (2002/07/13)
9840    
9841    checkpoint46 (2002/07/13)
9842    further merges from release1_p5
9843    o new ctrl package
9844      - adopted from ECCO environment to enable optimization
9845      - added Eliassen Palm fluxes to controls
9846    o added Eliassen Palm flux controls to gradient check package
9847    o cost package
9848      - Compatible with new ctrl package
9849      - added Eliassen Palm cost hooks
9850      - modif's of existing cost functions
9851    o Adjoint-related bug fixes in kpp:
9852      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
9853      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
9854    o autodiff package
9855      - flow directives:
9856        + new for S/R do_the_model_io
9857        + enhanced for S/R checkpoint
9858        + new gmredi.flow
9859      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
9860        disable adcommon.h/g_common.h by default.
9861      - fixed problem for adjoint of global_max
9862    o modified verification/carbon/
9863    o New setup for adjoint of global_ocean
9864    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
9865    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
9866    o incorporated hooks for sponge layer code (external_forcing.F)
9867    
9868    checkpoint45d_post (2002/07/12)
9869    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
9870    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
9871      (affects plume_on_slope "cg2d" output)
9872    o add new parameter deltaTfreesurf for free-surface time stepping
9873    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
9874    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
9875    o change phiMin in exp1 (to agree with documentation)
9876    o add new flags:
9877     - T,S forcing inside/outside Adams-Bashforth
9878     - turn off temp,salt advection and/or forcing
9879     - for each tracer, define internal flag for multiDimAdvection & A-B
9880    o monitor: change definition of KE to check conservation of Energy
9881    
9882    checkpoint45c_post (2002/05/30)
9883    o Removed f90 comments ("!")
9884    o Modified initialisations to enable exf package for MITgcm
9885      (without invoking ECCO_PACKAGE).
9886    o modifications to gradient check package (Martin Losch)
9887      - enable centered differences
9888      - modified format of standard output
9889    
9890    checkpoint45b_post (2002/05/30)
9891    o cleaned exchange calls in cg2d
9892    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
9893    o included CPP option SINGLE_LAYER_MODE in thermodynamics
9894      to configure barotropic setup (Martin Losch)
9895    o moved some initialisations within bi,bj loop in dynamics
9896      (TAF flow dependency)
9897    o in initialise_varia, moved call packages_init_variables
9898      before convective_adjustment_init
9899      (corresponding adjustment of TAF tape initialisation).
9900    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
9901    
9902    checkpoint45a_post (2002/05/01)
9903    o compute Rho over the whole domain (extend iMin,jMin indices)
9904    o specific exchange for X-slice domain (case Ny=1)
9905    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
9906    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
9907    
9908    checkpoint44h_post = checkpoint45
9909    o Fix to restore differentiability:
9910      place at which packages_init_variables is called in
9911      initialise_varia is crucial for reverse control flow.
9912    o modifications in GMRedi to enable stable adjoint
9913      (corresponding modif's in thermodynamics, dynamics)
9914    o added missing hook for sponge layer code in external_forcing
9915    o modified test cost functions
9916    o storing in gad_advection (plus removal of write(0,*)!
9917    o missing headers TR1.h added in convective_adjustment routines
9918    o errorMessageUnit set non-equal zero in eeboot
9919      (conflict on some platforms, e.g. IBM SP3)
9920    o modified carbon verif.
9921    
9922    checkpoint44h_pre (2002/03/14)
9923    o vertical grid option: allow to put the Interface at the middle between
9924      2 cell-centers ; replace delZ in pkg/kpp by drF.
9925    o GM Advective form: Tracers are advected using the residual transport (=
9926      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
9927    
9928    checkpoint44g_post (2002/03/05)
9929  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
9930    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
9931    
# Line 68  o merge of relevant stuff from the ecco- Line 9990  o merge of relevant stuff from the ecco-
9990  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
9991  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
9992    
9993  checkpoint44  checkpoint44 (2002/01/18)
9994  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
9995  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
9996  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 76  o update AIM experiments (NCEP input fil Line 9998  o update AIM experiments (NCEP input fil
9998  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
9999  o added some stuff for AD  o added some stuff for AD
10000    
10001  checkpoint43  checkpoint43 (2001/09/28)
10002  o added two new advection tests  o added two new advection tests
10003  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
10004  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
10005  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
10006    
10007  checkpoint42  checkpoint42 (2001/09/27)
10008    Fixed AD-related problems:    Fixed AD-related problems:
10009  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
10010    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 94  o Modified store directives for split of Line 10016  o Modified store directives for split of
10016    for the case ALLOW_KPP    for the case ALLOW_KPP
10017  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
10018    
10019  checkpoint41  checkpoint41 (2001/09/27)
10020  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
10021    to work with protex    to work with protex
10022    
10023  checkpoint40  checkpoint40 (2001/09/27)
10024  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
10025  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
10026  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 107  o more mods for non-linear free-surface Line 10029  o more mods for non-linear free-surface
10029  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
10030  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
10031    
10032  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
10033  o added DST advection schemes  o added DST advection schemes
10034  o fix MPI bug on SGI's  o fix MPI bug on SGI's
10035  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 117  o changes to commenting of arguments for Line 10039  o changes to commenting of arguments for
10039  o added/updated many matlab scripts  o added/updated many matlab scripts
10040  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
10041        
10042  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
10043  o new package rw/  o new package rw/
10044    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
10045    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 136  o TAMC-related update to cope with mom_f Line 10058  o TAMC-related update to cope with mom_f
10058    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
10059    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
10060    
10061  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
10062  o bug fix in dynamics.F  o bug fix in dynamics.F
10063    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
10064  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
10065  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
10066    related to TAF    related to TAF
10067    
10068  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
10069  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
10070  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
10071    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 151  o corresponding split of calc_diffusivit Line 10073  o corresponding split of calc_diffusivit
10073  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
10074  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
10075    
10076  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
10077  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
10078    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
10079  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 165  o added new expt "solid-body.cs-32x32x1" Line 10087  o added new expt "solid-body.cs-32x32x1"
10087    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
10088      is not necessarily any better than the current one...      is not necessarily any better than the current one...
10089    
10090  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
10091  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
10092    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
10093  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 173  o extended iMin,jMin range for calc_comm Line 10095  o extended iMin,jMin range for calc_comm
10095  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
10096  o a few minor updates and fixes  o a few minor updates and fixes
10097    
10098  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
10099  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
10100  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
10101  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
10102    
10103  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
10104  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
10105  o Added gradient check package  o Added gradient check package
10106  o Added routines for passive tracer handling  o Added routines for passive tracer handling
10107  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
10108    
10109  checkpoint39  checkpoint39 (2001/05/14)
10110   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
10111     (mainly missing or wrong directives)     (mainly missing or wrong directives)
10112   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 198  checkpoint39 Line 10120  checkpoint39
10120           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
10121   o disabled some packages by default in genmake   o disabled some packages by default in genmake
10122    
10123  checkpoint38  checkpoint38 (2001/04/10)
10124   o see notes_c37_adj.txt   o see notes_c37_adj.txt
10125   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
10126   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 206  checkpoint38 Line 10128  checkpoint38
10128     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
10129   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
10130    
10131  checkpoint37  checkpoint37 (2001/03/13)
10132   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
10133     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
10134      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 223  checkpoint37 Line 10145  checkpoint37
10145   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
10146   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
10147    
10148  checkpoint36  checkpoint36 (2001/02/20)
10149   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
10150   o recover Time-Average diagnostics   o recover Time-Average diagnostics
10151   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
10152   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
10153    
10154  checkpoint35  checkpoint35 (2001/02/08)
10155   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
10156   o allows staggered time-stepping   o allows staggered time-stepping
10157   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
10158   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
10159    
10160  checkpoint34  checkpoint34 (2001/01/30)
10161   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
10162   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
10163     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 246  checkpoint34 Line 10168  checkpoint34
10168   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
10169   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
10170    
10171  checkpoint33  checkpoint33 (2000/11/30)
10172   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
10173   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
10174     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 264  checkpoint33 Line 10186  checkpoint33
10186       possibly use them.       possibly use them.
10187   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
10188    
10189  checkpoint32  checkpoint32 (2000/11/13)
10190   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
10191     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
10192   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 275  checkpoint32 Line 10197  checkpoint32
10197   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
10198   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
10199    
10200  checkpoint31  checkpoint31 (2000/09/11)
10201   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
10202     -> new routines packages_...F     -> new routines packages_...F
10203     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 292  checkpoint31 Line 10214  checkpoint31
10214     - not yet tested for GMRedi.     - not yet tested for GMRedi.
10215     - not yet tested for KPP.     - not yet tested for KPP.
10216    
10217  checkpoint30  checkpoint30 (2000/07/13)
10218   o Updates for OBCs   o Updates for OBCs
10219   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
10220   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 301  checkpoint30 Line 10223  checkpoint30
10223   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
10224     and entry for T90 in genmake     and entry for T90 in genmake
10225    
10226  checkpoint29  checkpoint29 (2000/06/21)
10227   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
10228    
10229  checkpoint28  checkpoint28 (2000/06/09)
10230   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
10231   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
10232   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 317  checkpoint28 Line 10239  checkpoint28
10239     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
10240   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
10241    
10242  checkpoint27  checkpoint27 (2000/04/10)
10243   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
10244     formulation works properly with variable resolution.     formulation works properly with variable resolution.
10245   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 325  checkpoint27 Line 10247  checkpoint27
10247   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
10248     in new routine ini_psurf()     in new routine ini_psurf()
10249    
10250  checkpoint26  checkpoint26 (2000/04/05)
10251   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
10252     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
10253   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 335  checkpoint26 Line 10257  checkpoint26
10257     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
10258   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
10259    
10260  checkpoint25  checkpoint25 (2000/03/15)
10261   o updates for OBCs and NH   o updates for OBCs and NH
10262   o dramatically reduced memory usage   o dramatically reduced memory usage
10263   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 346  checkpoint25 Line 10268  checkpoint25
10268      an explicit free-surface option)      an explicit free-surface option)
10269   o initial state input files for U and V   o initial state input files for U and V
10270    
10271  checkpoint24  checkpoint24 (1999/08/02)
10272   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
10273   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
10274   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
10275    
10276  checkpoint23  checkpoint23 (1999/05/26)
10277   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
10278   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
10279    
10280  checkpoint22  checkpoint22 (1999/05/18)
10281   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
10282   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
10283    
10284  checkpoint21  checkpoint21 (1999/05/18)
10285   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
10286   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
10287   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
10288   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
10289    
10290  checkpoint20  checkpoint20 (1999/03/22)
10291   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
10292   o Added non-hydrostatic code   o Added non-hydrostatic code
10293   o Fixed some input data   o Fixed some input data
10294   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
10295    
10296  checkpoint19  checkpoint19 (1998/12/15)
10297   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
10298   o Added new code for open boundaries.   o Added new code for open boundaries.
10299   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 379  checkpoint19 Line 10301  checkpoint19
10301   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
10302   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
10303    
10304  checkpoint18  checkpoint18 (1998/11/30)
10305   o Further changes for optional code generation with   o Further changes for optional code generation with
10306     CPP - ugh!     CPP - ugh!
10307    
10308  checkpoint17  checkpoint17 (1998/11/03)
10309   o Beginning to incorporating modularity   o Beginning to incorporating modularity
10310     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
10311   o Small changes for TAMC complinace   o Small changes for TAMC complinace
10312   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
10313     configuration "exp0".     configuration "exp0".
10314    
10315  checkpoint16  checkpoint16 (1998/10/28)
10316   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
10317     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
10318     assignment is an addition.     assignment is an addition.
# Line 398  checkpoint16 Line 10320  checkpoint16
10320     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
10321     limit ).     limit ).
10322    
10323  checkpoint15  checkpoint15 (1998/09/29)
10324   Rewrote exchange routines to allow   Rewrote exchange routines to allow
10325   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
10326   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 407  checkpoint15 Line 10329  checkpoint15
10329     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
10330     communication method.     communication method.
10331    
10332  checkpoint14  checkpoint14 (1998/09/09)
10333   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
10334   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
10335    
10336  checkpoint13  checkpoint13 (1998/07/17)
10337   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
10338   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
10339   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 426  branch-point-rdot Line 10348  branch-point-rdot
10348   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
10349   we've actually tested it...   we've actually tested it...
10350    
10351  checkpoint12  checkpoint12 (1998/07/08)
10352   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
10353   configure script).   configure script).
10354   Released to testers.   Released to testers.
10355    
10356  checkpoint11  checkpoint11 (1998/07/02)
10357   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
10358   and ini_masks_etc().   and ini_masks_etc().
10359    
10360  checkpoint10  checkpoint10 (1998/07/01)
10361   Introduced the configure script.   Introduced the configure script.
10362   Separated out the diags package.   Separated out the diags package.
10363   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
10364   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
10365    
10366  checkpoint9  checkpoint9 (1998/06/22)
10367   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
10368   General tidy-up.   General tidy-up.
10369   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
10370    
10371  checkpoint8  checkpoint8 (1998/06/22)
10372   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
10373   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
10374    
# Line 456  checkpoint7-4degree-ref Line 10378  checkpoint7-4degree-ref
10378   model etc..   model etc..
10379   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
10380    
10381  checkpoint7  checkpoint7 (1998/06/15)
10382   Created by cnh   Created by cnh
10383   Simple 4 degree global simulation   Simple 4 degree global simulation
10384   configuration.   configuration.
# Line 464  checkpoint7 Line 10386  checkpoint7
10386   hydrography, bathymetry etc   hydrography, bathymetry etc
10387   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
10388    
10389  checkpoint6  checkpoint6 (1998/06/08)
10390   Created by cnh   Created by cnh
10391   merged checkpoint5 with CD and   merged checkpoint5 with CD and
10392   spherical polar code.   spherical polar code.
10393   Still some problems with GM Redi   Still some problems with GM Redi
10394   abd full topography.   abd full topography.
10395    
10396  checkpoint5  checkpoint5 (1998/06/08)
10397   Created by AJA   Created by AJA
10398   contains updates to GM Redi   contains updates to GM Redi
10399   and reordered timestepping loop   and reordered timestepping loop
10400   for Implicit Diffusion.   for Implicit Diffusion.
10401    
10402  checkpoint4  checkpoint4 (1998/05/30)
10403   Created by cnh   Created by cnh
10404   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
10405   grid variations are limited.   grid variations are limited.
10406   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
10407   for generation.   for generation.
10408    
10409  checkpoint3  checkpoint3 (1998/05/26)
10410   Created by cnh   Created by cnh
10411   Added extra flags for runtime options   Added extra flags for runtime options
10412   Added this file   Added this file

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