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revision 1.2078 by gforget, Mon Oct 6 14:12:28 2014 UTC revision 1.2322 by jmc, Thu Apr 6 16:29:09 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint66f (2017/04/06)
8    o model/src:
9      - add specific run-time param to select level of printed plot-field-maps,
10        set by default to debugLevel. Remove internal param "printDomain".
11    o pkg/seaice:
12      - add flag to add snow mass to seaiceMassC/U/V, the default is
13        SEAICEaddSnowMass=.FALSE., not to change previous results
14    o pkg/bling
15      - Bug fix in bling_production regarding unit conversion for diagnostics
16        being put in the wrong place
17    o model/src:
18      - add back recomputation of rSurfW & S to ensure consistent column thickness
19        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
20        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
21        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
22    o pkg/autodiff:
23      - clean-up "checkpoint.flow"
24    o pkg/rw (Contribution from Jody Klymak):
25        option to set mds file suffix as function of time in simulation:
26        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
27           to select file suffix format; by default (=0), use iteration number;
28        *) add simple routine to return file suffix according to rwSuffixType;
29        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
30           use new S/R to get file suffix, except for debug output file (diagFreq)
31           and pkgs offline & rbcs input files.
32    o pkg/rw:
33      - uniform processing of "I10" suffix across writing fld routines; used to
34        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
35        (similar to cg3d.F, cg3d_ex0.F)
36    o pkg/mom_vecinv:
37      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
38        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
39    o pkg/bling:
40      - Many small changes intended to clean the code.
41        Unnecessary ADJOINT_SAFEs removed ;
42        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
43        diagnostics added.
44    
45    checkpoint66e (2017/03/14)
46    o pkg/exf:
47      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
48        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
49        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
50        avoid any dynamic allocation ;
51      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
52        read-in ; add warning when file is read-in but not used within pkg/exf ;
53        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
54      - update exf_summary.F (print {FLD}RepCycle).
55    o verification/global_with_exf:
56      - switch on exf interpolation in AD test (just like the forward test)
57    o pkg/mom_vecinv:
58      - add storage directives to avoid recomputations within mom_vecinv.F
59        which were generating seg. fault with gfortran -devel
60    o pkg/ctrl, pkg/smooth:
61      - initialize array halos which were generating seg. fault with
62        gfortran -devel in adjoint mode
63    o pkg/exf:
64      - for each input field, enable to specify a field specific repeat-cycle
65        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
66    o verification/lab_sea:
67      - update AD results of primary test and noseaicedyn test after switching
68        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
69        check stays about the same.
70    o pkg/exf:
71      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
72      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
73    o pkg/bling, USE_EXFCO2 code:
74      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
75      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
76    o pkg/exf:
77      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
78      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
79        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
80        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
81      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
82        EXF_INIT_FLD) and update calls in exf_init_varia.F
83      - For now, for backward compatibility, keep a simplified version of S/Rs
84        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
85      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
86        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
87    o tools/genmake2:
88      - replace "bc -l" (only used once) by "expr" (already used).
89    o verification/global_ocean.cs32x15:
90      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
91        Note: exf setting (data.exf) can be compared to other exf secondary exp
92        "seaice" (kept with useCAL=T) which has same time dependent forcing.
93    
94    checkpoint66d (2017/02/13)
95    o pkg/exf:
96      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
97        early on (in packages_boot.F) to stress this change in pkg setting.
98      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
99    o model/src:
100      - move call to ecco_phys to end of time step; this may induce minor
101        cost function changes by shifting time averages by one time step
102        for some variables; this revision resulted in changed adjoint results
103        in MITgcm_contrib/verification_other/global_oce_cs32
104    o pkg/exf:
105      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
106        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
107        e.g. precip, are not available.
108    o pkg/flt:
109      - flt_init_varia.F: use pickupSuff if specified
110      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
111        intermediate, step towards completing pkg/exch2 support within pkg/flt;
112        ifdef DEVEL_FLT_EXCH2 then:
113        - flt_init_fixed.F: comment out stop
114        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
115        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
116        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
117        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
118    o tools/genmake2 & pkg/pkg_depend:
119      - define new type of pkg dependency rule ("=pkg_x"), less strict than
120        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
121        (-pkg_x in packages.conf).
122      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
123      - add "+cal" to dependency list of pkg/ecco (needed to compile).
124      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
125    o utils/matlab:
126      - adding ocean_basin routines for defining basin masks.
127    o pkg/exf:
128      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
129        arguments, allowing to check (and stop) if parameter setting of
130         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
131        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
132        for backward compatibility.
133      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
134        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
135    o pkg/bling (USE_EXFCO2 code):
136      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
137        by adding a call to S/R EXF_GETFFIELD_START.
138    o pkg/exf:
139      - allows to compile without pkg/cal (but disabled by current dependency
140        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
141        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
142        of {FLD}startdate1 & date2 ; consistency check not yet coded.
143    o verification/global_ocean.cs32x15:
144      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
145        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
146    o pkg/exf:
147      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
148        calculations); change FWD experiment global_ocean.cs32x15
149        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
150    o pkg/exf:
151      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
152         {FIELD}startdate to {FIELD}StartTime
153        Note: new name also fit better the content, i.e, a start time in second.
154    o eesupp/src:
155      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
156    o pkg/exf:
157      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
158        to allow to read-in Sensible & Latent Heat flux ;
159      - simplify pkg/exf main options:
160        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
161           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
162           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
163        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
164           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
165        3) improve options documentation in EXF_OPTIONS.h.
166    o pkg/ecco:
167      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
168        ecco_summary.F: add passive tracer cost functions to gencost;
169        m_ptracer and m_boxmean_ptracer
170    o pkg/ctrl:
171      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
172        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
173        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
174        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
175    o model/src:
176      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
177        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
178    o pkg/exf:
179      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
180        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
181    
182    checkpoint66c (2017/01/19)
183    o verification:
184      - add new option "-src" to testreport to only produce source code (*.f),
185        including taf output src code (if using '-adm'/'-tlm' option).
186    o pkg/exf:
187      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
188    o pkg/diagnostics:
189      - add run-time variable diagMdsDir to specify a subdirectory for
190        diagnostic output when mds is being used and mdsioLocalDir is not.
191    o pkg/mnc:
192      - mnc_utils.F: edit stop message
193    o pkg/autodiff:
194      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
195        add HAVE_SYSTEM bracket around system call to mkdir
196    o pkg/profiles:
197      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
198        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
199      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
200        add HAVE_SYSTEM bracket around system call to mkdir
201    o pkg/smooth:
202      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
203      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
204      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
205    o pkg/exf:
206      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
207        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
208        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
209      - summary: skip detailed field report if not used (empty file-name).
210    o tools/xmakedepend:
211      - In case line editor "ed" is missing, switch to "sed" command to clean-up
212        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
213    o pkg/exf:
214      - change definition of "hflux" input file to always include Short-Wave;
215        this is now consistent with hflux computation (if using bulk-formulae)
216        and hflux diagnostic & documentation (in EXF_FIELDS.h).
217    
218    checkpoint66b (2016/12/01)
219    o model & momentum pkgs:
220      - implement fully implicit bottom friction combined with implicit surf.
221        pressure, for now, only in hydrostic formulation:
222        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
223          and run with selectImplicitDrag=2 ;
224        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
225      - partial implicit time-stepping (bot. friction + vert. visc first, then
226        surf. press) corresponding to selectImplicitDrag=1 should be applicable
227        to NH formulation but not available until we solve for surf. pressure
228        increment (instead of full etaN).
229      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
230        with implicit vertical viscosity.
231    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
232      - this is a first version that includes many regularisations that may
233        not all be necessary, to be sorted out,
234      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
235      - change one verification experiment in seaice_itd to use and test new code
236      - seaice_growth: catch a case where the argument of log can be zero
237        or smaller (important for code stability)
238    o model/src:
239      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
240        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
241        similar A.X'=Y' system (with same matrix A) in subsequent calls;
242        switch based on errCode (In/Out) argument value; in calling routines,
243        initialise errCode before first call.
244    
245    checkpoint66a (2016/10/18)
246    o pkg/bling:
247      - BLING package now loads in atmospheric pCO2 file using exf package routines
248        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
249    o model/src & pkg/ptracers:
250      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
251        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
252        implicitDiffusion (respectively) are used (even without momImplVertAdv
253        or temp,salt,PTRACERS_ImplVertAdv).
254    o model/src & generic_advdiff:
255      - add parenthesis in main diagonal calculation of implicit vertical
256        diffusion matrix (impldiff.F & gad_implicit_r.F).
257        This affects results at machine truncation level; update output of many
258        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
259    o pkg/mom_commom & generic_advdiff:
260      - add deep atmosphere and anelastic scaling factor in implicit vertical
261        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
262    o model/src:
263      - remove few unnecessary temp array copies in solve_tridiagonal.F
264        & solve_pentadiagonal.F
265    
266    checkpoint65z (2016/09/28)
267    o pkg/seaice: fix multithreading for seaice_fgmres.F
268      - remove unecessary variables from common blocks
269      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
270        basis, that are stored in commom blocks (including integer variable i1)
271      - clean up code a little by removing commented lines that refer to
272        original code
273      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
274    o MITgcm manual:
275      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
276        preliminary documentation for generic controls (8.3; ctrl.tex),
277        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
278        ecco_costfunction.tex
279    o pkg/ecco:
280      - update and cleanup list of CCP options
281      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
282        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
283      - add checks that retired run-time options are not used, and in relation
284        to gencost_mask and gencost_errfile
285      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
286        gencost_nrecperiod
287      - fix m_eta computation for virtual salt flux case
288      - add m_horflux_vol case (selected via gencost_barfile) that computes
289        transports via cost_gencost_boxmean (gencost_flag=-3)
290      - use gencost_flag more systematically (i.e., avoid using gencost_name)
291        for code switches (aside from physical variable selection)
292    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
293      attempt appears to be a bit of a hack and my need some repair down the road
294    o pkg/exf:
295      - interpolation near South Pole: fix criteria on input field latitude.
296    o pkg/icefront & pkg/exf:
297      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
298        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
299    o pkg/exf:
300      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
301        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
302        (add suffix "_out" instead of a prefix); keep same record number as in
303        input file but always write record 1 first (to avoid a STOP in I/O S/R).
304        Change output file content by writing interpolated field before applying
305        land-sea mask (helpful for debug).
306      - 2 compon. vector interpolation with rotation: apply scaling factor on
307        each compon. (Eastward and Northward) just before rotation.
308    o pkg/bling:
309      - Cleaned package. Removed not needed code and comments.
310      - adjoint example now works
311        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
312    o pkg/ptracers:
313      - add Bruno Deremble's code to complete the linear surface correction
314        for tracer conservation;
315      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
316    
317    checkpoint65y (2016/07/29)
318    o pkg/debug (stats):
319      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
320        proc/thread mapping);
321      - fix Min & Max for case where 1 thread has only empty tiles;
322      - use RL variable to count number of wet grid points (with big domain,
323        can be too large to fit into integer*4).
324    o pkg/monitor:
325      - use RL variable to count number of wet grid points (but used only for del2)
326      - add new routine to compute Advective CFL within tracer time-stepping with
327        writing delayed until next monitor output.
328    o pkg/obcs:
329      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
330    o pkg/cal:
331      - calandar-dump: treat case myTime < timePhase in the same way as in
332        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
333    o pkg/dic & seaice:
334      - fix compilation of ocean component for coupled atm+ocn model with
335        seaice dynamics & dic.
336    
337    checkpoint65x (2016/06/11)
338    o add a license text file in main MITgcm tree.
339    o added pkg/bling:
340      - intermediate complexity biogeochemical model
341      - see bling_description.txt for details
342      - verification experiment is global_oce_biogeo_bling (for now, in
343        Contrib/verification_other/); tested daily on baudelaire with gfortran.
344      - add entry point in pkg/gchem for new pkg "bling".
345    o pkg/seaice: fix tensile stength computation
346      - replace global field tensileStrength by tensileStrFac
347      - tensileStrFac can be computed once in S/R seaice_init_varia
348      - fortunately that does not affect any verification results
349    
350    checkpoint65w (2016/05/12)
351    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
352         with ECCO_CTRL_DEPRECATED defined
353    o verification/global_ocean.cs32x15:
354      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
355        with "selectNHfreeSurf=1".
356    o model/src (non-hydrostatic free-surface):
357      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
358        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
359      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
360        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
361        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
362        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
363      - Update output (changes at machine truncation level) of verification exp:
364        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
365        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
366    o pkg/seaice: ITD code
367      - fix picking up from a single category model by initialising
368        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
369      - split a long warning message in seaice_check_pickup.F into two lines,
370        because NEC SX-ACE cannot deal with the long line.
371    o model/src:
372      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
373    o pkg/seaice:
374      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
375    o pkg/seaice:
376      - add basal stress as parameterisation for grounding ice
377        following Lemieux et al. (2015)
378      - turn on by setting new parameter SEAICEbasalDragK2 to a value
379        larger than 0. Lemieux et al. (2015) recommend 15.
380      - The adjoint complains with extra recomputations so there is also a
381        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
382        order to postpone the problem
383      - compile the new code in lab_sea
384    o verification/halfpipe_streamice:
385      - update both TAF and OpenAD adm output (machine truncation differences)
386    
387    checkpoint65v (2016/04/08)
388    o verification/advect_xz:
389      - increase overlap size from 3 to 4 and add new secondary test for PQM
390        advection scheme (with mono & wino limiter).
391      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
392    o model/src:
393      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
394        added phi0Ref) to set vertical axis origin and phiRef origin;
395        keep Ro_SeaLevel for backward compatibility (with a warning).
396       According to coordinate and fluid type:
397        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
398        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
399        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
400        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
401      - remove Ro_SeaLevel from ATM experiment parameter files;
402      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
403        complement; update output.txt (changes at machine truncation level).
404    o pkg/seaice/seaice_evp.F
405      - simplify computation of deltaZ and zetaZ to simple averaging following
406        Bouillon et al. (2013). This removes a lot of code, but also changes
407        verification experiment lab_sea.hb87 -> updated
408    
409    checkpoint65u (2016/03/14)
410    o pkg/generic_advdiff:
411      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
412        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
413        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
414        testing and not for actual use.
415    o model/src:
416      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
417        origin r = rF(1);
418      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
419        in EOS for height coordinate: enable to include NH Pressure or to use
420        more accurate pressure vertical profile; options not linked to EOS type
421        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
422      - start to implement variable gravity (along vertical): for now, only with
423        z-coords (not even z*).
424      - add Ideal Gas equation of state for height coordinate.
425      - update OpenAD output (affected at machine truncation level) of exp:
426        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
427    o pkg/exf:
428      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
429        of exf interpolation (before any rescaling, rotation or interpolation
430        to velocity point) for each field that gets loaded from file. This option
431        identically mimics the input file organization (e.g. record numbers in year
432        by year input files) besides the change in horizontal grid.
433      - add rotateStressOnAgrid run-time switch so that wind stress fields
434        can be provided on the A-grid in zonal/meridional direction and
435        rotated on the fly. This only applies to the case when the exf
436        interpolation is off and rotateStressOnAgrid is false by default.
437    o model/src:
438      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
439        it's also used with pkg/atm_phys) and add few more parameters (but still
440        inactive, src code yet to come)
441    
442    checkpoint65t (2016/02/10)
443    o pkg/atm_phys:
444      - from Ruth Geen: add optical depth dependence on CO2 concentration.
445    o model/src:
446      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
447        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
448        Update output of exp. deep_anelastic (changes at truncation level).
449    o tools:
450      - add a hack in "remove_comments_sed" (used only with TAF) for recent
451        version of OpenMPI (shipped with FC.23): comment out the new header
452        file "mpif-sizeof.h" which causes problems to TAF.
453    o pkg/seaice:
454      - change the termination criterion so that maxits (SEAICElinearIterMax)
455        has an effect
456      - unify iteration parameters for implicit solvers (JFNK and Picard)
457        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
458        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
459        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
460        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
461        SEAICEnonLinTol     replaces JFNKgamma_nonlin
462      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
463      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
464        use with SEAICEuseKrylov
465    o pkg/seaice/seaice_lsr.F
466        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
467        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
468        an effect.
469    o pkg/seaice: add two new parameters
470      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
471        parameter is not in any namelist)
472      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
473        a preconditioner for the non-linear Newton iteration of the JFNK
474        solver
475    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
476      affects some experiments at truncation level:
477      - global_ocean.cs32x15.icedyn (11 digits),
478      - global_ocean.cs32x15.seaice (11 digits),
479      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
480      - also update global_ocean.cs32x15 adjoint and tangent-linear results
481    o pkg/salt_plume & pkg/thsice:
482      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
483        connect salt_plume flux to ATM-OCN coupling pkgs interface:
484       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
485         export to coupler interface) even without compiling pkg/salt_plume ;
486       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
487         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
488    o pkg/dic:
489      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
490        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
491        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
492      - move also update with values from ATM-OCN Coupler in the same new S/R
493        (previously done in ocn_apply_import.F).
494    o tools/adjoint_options:
495      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
496        has been changed on Jan 14, 2016.
497    o pkg/ggl90:
498      - add alternative discretisation of vertical shear (off by default), to
499        compute the mean (@ grid-cell center) of vertical shear compon instead of
500        vertical shear of mean flow (@ grid-cell center).
501      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
502        results on adjacent faces of cubed-sphere grids; this fix the restart.
503    o pkg/atm_compon_interf:
504      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
505        pass last value, stored directly before export to CPL ;
506        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
507      - remove atmSLPr from pickup files (no longer needed for restart)
508    
509    checkpoint65s (2016/01/13)
510    o eesupp & genmake2:
511       - first check for Function ETIME and, if it fails, then check for subroutine
512         ETIME and consistent output; use the appropriate version in timers.F
513    o model/src:
514      - to check restart test, add option to apply EXCH to U,V earlier, just before
515        integr_continuity; turned off by default.
516    o pkg/dic:
517      - remove CPP option USE_ATMOSCO2 (not needed)
518    o tools/tst_2+2:
519      - try to ignore difference between +0 and -0 in binary file, causing test
520        to fail for no good reason.
521    o eesupp & genmake2:
522      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
523        but also check (in genmake2) that test runs and returns meaningful results.
524    o coupler pkgs:
525      Finish implementation of optionally-exchanged variable switches (started on
526       Nov 12) with addition of few more exchanged fields, including 2-way exchange
527       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
528       advection in OCN component; this requires sequential coupling.
529      coupler (pkg/atm_ocn_coupler):
530      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
531        routines (useful for debug).
532      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
533         flux, DIC fields) if corresponding switch is ON.
534      - add option to export RunOff to OCN (to use for DIC river input)
535      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
536      components (pkg/atm_ & ocn_compon_interf):
537      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
538        optionally exchanged fields; add a check & stop in cpl_readparms.F.
539        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
540        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
541      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
542        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
543      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
544      - hold in common block coupler optionally-exchanged variable switch
545        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
546      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
547        this is intended to replace the OCN cplFldtave.* output files (not updated
548        to contain new additional exchanged fields).
549    o pkg/dic:
550      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
551    o pkg/thsice:
552      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
553        and writing of thsice pickup files.
554    o pkg/atm_compon_interf:
555      - move all field individual export-call out of cpl_export_import_data.F
556        into new S/R ATM_EXPORT_FIELDS
557    o pkg/atm_compon_interf:
558      - store state variables (for now, only thSIce fields) just before beeing
559        exported (in cpl_export_import_data.F, like on ocean side) instead of from
560        atm_store_my_data.F like all exported fluxes.
561      - new version of pickup_cpl: write field names into meta file and read meta
562        file to find field postion in pickup. Also only write/read fields meeded for
563        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
564    o pkg/dic:
565      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
566    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
567        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
568        value can be from domain [0,1] to average between the two methods
569    o pkg/atm_phys:
570      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
571        hold fixed in time).
572    
573    checkpoint65r (2015/12/21)
574    o pkg/seaice:
575        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
576        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
577    o pkg/seaice:
578      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
579        when SEAICEscaleSurfStress=.TRUE.,
580      - apply areaW and areaS in S/R seaice_calc_lhs
581    o pkg/atm_phys:
582      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
583        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
584        for individual contribution (convection, LSC cond, radiation)
585      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
586        information); activated with: solar_exponent=0. and wv_exponent=-1.
587    o pkg/ggl90:
588      - within IDEMIX add upper limit for horizontal group velocity to
589        avoid instability problems in the explicit horizontal diffusion term for
590        long time steps or high resolution
591    o pkg/diagnostics:
592      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
593        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
594    o testreport:
595      - remove "-v" (verbose option) in default mpirun command.
596    o pkg/seaice/seaice_growth:
597      - catch potential division by zero in ITD code, does not change
598        verification results
599    o pkg/ecco:
600      - retire old codes to the Attic. The calls to retired functions are
601        left in a commented form in case they ever need to be re-activated.
602      - ecco_check.F: issue warning if any old CPP option is
603        defined that corresponds to retired codes -- then stop.
604    o pkg/atm_compon_interf:
605      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
606        coupler: use last time-step value instead of average over cplSendFrq_iter
607        time-step, similar to what is done for seaIceMass.
608        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
609    o eesupp & genmake2:
610      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
611        <= remove until a fix is found for some ifort version on ia32 machine.
612    o pkg/seaice/seaice_evp:
613      - refine residual computation
614    
615    checkpoint65q (2015/11/18)
616    o pkg/seaice/seaice_evp:
617      - fix residual computations so that they no longer affect the actual
618        simulation code
619      - fix seaice_readparams to be able to actually set new parameters
620        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
621    o model/src:
622      - fix wrong truncation (single prec) from "FLOAT" function in expressions
623        like: deltaT*FLOAT(myIter) when myIter is large:
624         a) replaced by DFLOAT (if not seen by TAF);
625         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
626    o pkg/aim_v23:
627      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
628        when pickupSuff is set ; do write rolling pickups + at the end of the run.
629    o pkg/atm_ocn_coupler + ocn_compon_interf:
630      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
631        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
632        add corresponding call in DO_OCEANIC_PHYS.
633    o coupler pkgs:
634      Start a new way to set-up optionally-exchanged variables (previously, only
635       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
636       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
637       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
638       compononent param default can be set accordingly).
639      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
640       but rather applies to a group a fields (going both ways like for DIC)
641       and corresponds to an option of coupling config.
642      coupler (pkg/atm_ocn_coupler):
643      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
644        and read namelist directly (without eessup S/R calls) instead of
645        in the very un-flexible old way, 1 param per line, in fixed order;
646      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
647        cleanly in CPL_CHECK_CPLCONFIG
648      - add new coupling-exchange selectors (some not yet active) including
649        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
650                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
651      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
652        component ; called directly from coupler.F, after comp. registrations;
653      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
654         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
655          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
656      components (pkg/atm_ & ocn_compon_interf):
657      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
658        CPP header file in all pkg source files.
659      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
660        ATM/OCN_CHECK_CPLCONFIG;
661      - add error-counter to track errors (e.g., in "data.cpl") and to stop
662        cleanly in ATM/OCN_CHECK_CPLCONFIG;
663      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
664        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
665        before PACKAGES_READPARMS;
666      verification/cpl_aim+ocn/:
667      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
668        "data.cpl" for coupler (in input_cpl).
669    o eesupp/inc:
670      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
671        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
672        to always cumulate tile local-sum in the same order (still uses
673        MPI_Allreduce like standard code).
674      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
675        that are now identical to standard version (in eesupp/inc).
676    o pkg/shelfice:
677      - add SHELFICETransCoeffTFile for initializing spatially varying
678        heat and salt transfer coefficients
679    o pkg/atm_compon_interf & ocn_compon_interf:
680      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
681        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
682      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
683    o pkg/atm_ocn_coupler:
684      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
685    o pkg/rbcs:
686      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
687        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
688      - add a short report (to STDOUT) about RBCS-mask settings.
689    
690    checkpoint65p (2015/10/23)
691    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
692        there is no adjoint test for EVP, we don't know what it does to the adjoint
693        solution, but at least there are no more recomputation warnings left
694    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
695        a chance of giving the same results as a fully converged VP (JFNK) solver
696    o tools/adjoint_options/adjoint_diva:
697      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
698    o pkg/streamice:
699      - spotted bug in streamice_driving_stress using dyG where should have been dxG
700    o pkg/exf:
701      - remove STOP statement that prevented to use wind or (wind-)stress
702        interpolation for constant-in-time forcing fields (wind/stress period = 0).
703    o pkg/seaice:
704      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
705        5 additionals 2D fields and 6 new store directives
706      - change logic in seaice_readparms.F: EVP code can now be turned on in
707        various ways, setting SEAICE_deltaTev is no longer required,
708        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
709        or SEAICEaEVPcoeff
710    o pkg/shelfice/shelfice_thermodynamics.F
711      - redefining uLoc/vLoc to u/v, instead of 2u/v
712    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
713      - this is an intermediate state of a truely converging EVP that has
714        the potential of outperforming implicit VP methods, I do not recommend
715        using it yet.
716      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
717        and all parameters are hardwired
718      - for convergence it still requires very smooth regularisations, that means,
719        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
720        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
721        specific averaging appears to be required, still subject to tuning
722      - still needs cleaning and I need to turn parameter into runtime parameters
723      - add code to compute and print residuals of iteration, compile with
724        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
725    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
726      that entered with r1.54 on Sep04, 2015, -> update results
727    
728    checkpoint65o (2015/09/14)
729    o pkg/mom_vecinv & mom_common:
730      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
731        called from there.
732      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
733        allows to use Vector-Invariant form in deep atmos and anelastic formulation
734    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
735      and Koenig-Beatty+Holland (2012)
736      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
737      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
738      - requires an extra input argument for S/R seaice_calc_viscosities
739      - tensileStrength's depth dependence is different from Itkin et al. (2015)
740        (to be changed and played with, for now exponential)
741    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
742      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
743        by AREA according to Connelly et al. (2004), JPO.
744      - For EVP and the LSR solver, the implicit part of the drag term is
745        the only non-zero term in the denominator when there is no ice (which
746        prevented running the model with zero ice-ocean drag). If
747        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
748        (or zero main diagonals BU/BV) which need to be caught. A practical
749        consequence is that for open water, the momentum equation reduce
750        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
751        they happen to be zero, often leading to a non-zero solution over
752        open water.
753    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
754        efficient EVP method.
755      - introduce area-weighted averages for e12 (analogously to
756        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
757        remain, but also changing the order of terms in the previous average
758        changed the results as much) -> update experiment
759      - add SEAICE_DELTA_SMOOTHREG code
760      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
761        TEM-code
762      - adjust loop bounds so that only required fields are computed
763      - add new averaging code for zetaZ/deltaZ (again similar to
764        seaice_calc_viscosities.F), inactive by default for now (will change
765        results again), but will replace old code eventually
766    o eesupp/src:
767      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
768        to always cumulate tile local-sum in the same order
769        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
770        Still uses MPI_Allreduce (like standard code) but on array of tiles
771        and should be faster than GLOBAL_SUM_SEND_RECV code.
772      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
773        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
774      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
775         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
776         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
777         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
778         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
779    
780    checkpoint65n (2015/07/29)
781    o pkg/thsice:
782      - add a warning when used with pkg/aim but without updating SST
783        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
784    o pkg/offline:
785      - change where Offline-Fields are loaded, from load_fields_driver.F to
786        directly within FORWARD_STEP, just after updating iter number and time;
787      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
788        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
789       These changes allow:
790        a) to recover exactly on-line results using deltaToffline=deltaTClock,
791        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
792        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
793        time-step, both with GM & KPP files and with recomputing these fields;
794        b) no needs to switch on staggerTimeStep anymore;
795        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
796      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
797    o pkg/offline:
798      - change (rarely used) offset-iteration parameter to an offset time (in s):
799        can easily recover previous offset-iter effect by setting offset-time
800        (offlineTimeOffset) to offset-iter x deltaToffline;
801      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
802        in KPP as part of surface buoyancy forcing) in offline run.
803      - fix ptracers KPP non-local term in the case where KPP is re-computed.
804    o OpenAD
805      - Adding preliminary ggl90 test to OpenAD verification.
806        Config. with ggl90 currently diverges after 64 time steps
807        so will need more work to become more stable
808      - Adding preliminary kpp test to OpenAD verification.
809        required small tweakes in kpp_routines.F
810      - Merge and update from Krishna Narayanan's contrib area:
811        * Add one variable for preliminary OpenAD DIVA
812        * Add replacement time-stepping for OpenAD DIVA
813        * genmake2 flag -diva (but only for OpenAD; preliminary)
814        * required modifs for OAD_support
815        successful preliminary test for tutorial_global_oce_biogeo/
816    o pkg/seaice:
817      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
818      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
819        delta with a smooth function in s/r seaice_calc_viscosity
820        (no effect on EVP)
821      - rename local suffix "sqr" into "sq" for more consistent variable names
822    o pkg/seaice:
823        add new parameter SEAICE_deltaMin that is used ***only***
824        for regularizing Delta (and nothing else, like the parameter
825        which is also used for all sorts of things SEAICE_EPS).
826        Defaults to SEAICE_EPS for backward compatibility only.
827    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
828        the wrong key by inialising it before use -> fixes a recomputation
829        problem but does not fix the gradient
830    o pkg/layers:
831      - move resetting of flux arrays to outside the iLa loop
832        (this caused layers_diapycnal to not work with more than one layer coord.)
833      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
834    o pkg/layers:
835      - remove from common block 3D layers fields (used to diagnose transport
836        in tracer coords) and declare them as local arrays in layers_calc.F
837    o pkg/seaice:
838      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
839        in lab_sea forward experiment (changes results -> updated)
840      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
841    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
842       computations; for SEAICE_VECTORIZE_LSR
843      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
844        sweep to the outside,
845      - remove store directives and add "CADJ loop sequential" directives
846        in analogy to model/src/solve_tridiagonal.F
847      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
848        boundaries to yield more readable code. This has also the charming side
849        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
850        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
851        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
852        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
853        an additional option)
854       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
855       but the adjoint gradients (which are affected by this change) still explode.
856    o coupler (atm & ocn _compon_interf):
857      - avoid using Exch2 IO mapping if not suitable.
858    
859    checkpoint65m (2015/06/15)
860    o pkg/layers:
861      - clean-up old parameters setting (from Sep 2012):
862        + remove old parameters setting from common block (declared locally);
863        + stop if any old parameter is mixed with new parameters;
864        + check for valid or consistent parameter setting (e.g., layers_name)
865      - check that layers_bounds for Pot.Density are in the right range;
866        this is supposed to catch un-updated setting after recently shifting
867        potential density field "prho" by -1000 (now in "sigma" scale).
868    o pkg/layers:
869      - Added missing call to layers_fill for keeping track of tottend in
870        pkg/diagnostics/diagnostics_fill_state.F
871    o pkg/layers:
872      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
873        of diapycnal fluxes
874    o pkg/layers:
875      - reverted changes to interpolation to previous treatment; there
876        was never actually a problem
877    o pkg/layers:
878      - fix interpolation of layers tracers in the presence of partial cells
879      - add lots of new functionality to compute water mass transformation
880        (enabled by CPP flag LAYERS_THERMODYNAMICS)
881      - add new calls from main code (diags_oceanic_surf_flux.F,
882        thermodynamics.F, impldiff.F) and gad to save the necessary fields
883        for layers_thermodynamics calculations
884    o pkg/ptracers:
885      - add capability of stepping a passive tracer forward without advection
886        by setting PTRACERS_advScheme to 0.
887    o pkg/diagnostics:
888      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
889    o pkg/layers:
890      - shift potential density field "prho" by -1000 for density layer averaging so
891        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
892        Note that density bin boundaries (layers_bounds in data.layers) have
893        to be set accordingly (i.e., shifted, in sigma scale).
894    o pkg/layers:
895      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
896      - fix calculation of layer non-weighted velocity and layer probability
897      - add diagnostics for pot.density used for layer averaging
898    o pkg/seaice:
899      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
900        positiveness, modify a few comments and improve variable names,
901      - the changed computation of deltaC affects most seaice-related
902        experiments at the truncation level.
903        seaice_itd.thermo is affected by far the most, with
904        only 7 digits of agreement remaining; update experiments.
905    
906    checkpoint65l (2015/05/04)
907    o pkg/shelfice:
908      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
909        factor drKp1 to zero where it is negative (ie. do not use
910        SHELFICEBoundaryLayer if hFacC>1)
911      - the same for factor drLoc in shelfice_forcing.F
912    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
913        with modules in ptracers, when using testreport option "-small_f"
914    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
915      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
916    o verification/testreport
917      - add new option -small_f
918        with this option testreport first makes the target small_f (*.f files)
919        before running make (all). This is useful for explicit inlining when
920        all sources need to be full available.
921    o pkg/exf/exf_interp.F:
922        remove previous changes related to reverse (decreasing) input grids latitude
923    
924    checkpoint65k (2015/04/01)
925    o pkg/ecco:
926        fix missing cosphi initialization; use eccoiter in place of optimcycle;
927        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
928        instead of active read/write
929    o pkg/ctrl:
930        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
931        instead of active read/write.
932    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
933        return if .NOT.useAUTODIFF
934    o pkg/seaice: add CPP brackets (cost function related).
935    o model/src:
936        add useAUTODIFF run time switch.
937    o pkg/exf/exf_interp.F:
938        add code to allow input grids with latitude starting in the north (i.e. when
939        j=1 corresponds to northern edge of field); modify global_with_exf to test
940        this feature.
941    o verification/testreport:
942      - replace "grep -A3" with POSIX conformal sed command, because there are
943        implementations of grep that cannot do contextual searches
944      - replace "cat -n" by "nl" (two occurrences), because not all implementations
945        of "cat" have the option "-n"
946    o model/src:
947        add new file gsw_teos10.F that contains 3 functions, more or less a copy
948        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
949        convert from conservative to potential temperature. For now they are not
950        called anywhere.
951    o pkg/ggl90: make "useIDEMIX" useful
952      - re-organize code in s/r ggl90_calc a little to move computations that
953        are different for idemix into separate loops (changes verification
954        experiment idemix at truncation level, 12 digits remain -> updated)
955      - requires 2 new 2D fields KappaM, verticalShear
956      - make hFacI and recip_hFacI local 3D variables that are passed to
957        s/r ggl90_idemix
958      - fix and improve some comments
959    
960    checkpoint65j (2015/02/25)
961    o pkg/openad
962      - synchronize seawater.F with version in model/src: replace routine
963        body of sw_temp by calling sw_ptmp and fix/add a few comments.
964    o pkg/mnc:
965      - change default value of pickup_read/write_mnc params to FALSE
966        (since few features are missing in reading MNC pickup files).
967    o model/src:
968      - change default (background) vertical diffusivity for salt to be the
969        temperature (background) vertical diffusivity.
970      - change background vertical diffusivity in vertical mixing pkgs ggl90,
971        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
972        This makes ptracers default diffusivity (that uses salt diffKr) more
973        consistent with vertical mixing schemes.
974    o verification/testreport:
975      - fix typo in "-pcls" option ;
976      - put temp files in /tmp (instead of in local dir)
977      - add option "-ncad" to use genmake2 new option "-nocat4ad"
978      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
979    o pkg/ggl90 (idemix code):
980      - apply few fixes ; add some missing "_d 0" ; update output of exp.
981        global_ocean.90x40x15.idemix
982    o OpenAD
983      - enable active file I/O and begin removal of work-around code
984        for OpenAD for handling control variables (memory vs. active files)
985      - new CPP options file OPENAD_OPTIONS.h
986      - revert to genarr2d gradient check for hs94.1x64x5
987      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
988      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
989    o tools/genmake2:
990      - add option for an alternative Makefile (from Martin) where multiple
991        source files are sent to TAF (instead of all in one file).
992    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
993      - code provided by Carsten Eden as an extension of ggl90
994      - so far the code is turned on within ggl90 by setting a CPP-flag at
995        compile time; a runtime flag implementation is not yet complete
996      - tested in new verification experiment global_ocean.90x40x15.idemix
997    o verification:
998      - reduce length of the AD test run by half for experiments
999        global_ocean.cs32x15 (std + thsice) and isomip
1000      - enable active file I/O for OpenAD, adjust verifications accordingly
1001      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
1002    o verification/testreport:
1003      - fix two non-POSIX sed statements so that there are no error messages
1004        on Mac OS X
1005      - replace hostname -s with hostname | sed 's/\..*$//'
1006    o model/src/seawater.F:
1007      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
1008        (following the matlab code), which would have avoided the bug caught
1009        by Matt (see below) in the first place
1010    o pkg/shelfice:
1011      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
1012        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
1013      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
1014        ice-shelf case (i.e., within surface level).
1015      - add config summary in shelfice_check.F
1016      - remove global variable recip_SHELFICElatentHeat and replace by a local
1017        variable recip_latentHeat
1018      - introduce diagnostics for friction velocity uStar (in case of
1019        SHELFICEuseGammaFrict)
1020      - change verification experiment isomip.htd:
1021        + start from pickup (as input_ad at nIter0=8640)
1022        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
1023        + test SHELFICEuseGammaFrict = .TRUE.
1024        + test SHELFICEadvDiffHeatFlux = .TRUE.
1025    o model/src:
1026      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
1027        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
1028        update output of experiments global_with_exf.yearly and isomip (all 6).
1029    o pkg/shelfice:
1030      - change setting of kTopC to also be zero where there is no ice-shelf.
1031      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
1032        ice-shelf is.
1033      - first attempt to get RealFreshWaterFlux effects: for now, only without
1034        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
1035    o pkg/seaice: add the option to prescribe a fixed thickness PDF
1036      for thermodynamic calculations
1037      - because of divisions of the type 7/7 not exactly equal to 1, this change
1038        affects results of some verification experiments by up to 4 digits:
1039        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
1040        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
1041        adjoint: lab_sea, lab_sea.noseaicedyn
1042        -> updated
1043    
1044    checkpoint65i (2015/01/23)
1045    o model/src:
1046      - change units of frictionHeating field from W to W/m^2
1047      - fix bug in frictional heating from stratospheric drag in
1048        S/R ATM_PHYS_TENDENCY_APPLY_V
1049      - with synchronous time-stepping: move resetting to zero of frictionHeating
1050        field from load_fields_driver.F to thermodynamics.F ;
1051      - add diagnostics for frictional heating.
1052    o model/src & gmredi K3D:
1053      - add frictionHeating field to pickup-files (for synchronous time-stepping)
1054      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
1055      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
1056        and name in pickup file).
1057      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
1058    o model/src:
1059      - move (from ini_forcing.F) initialisation of all arrays in header file
1060        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
1061        (since Nov 2012) with option selectAddFluid=1.
1062    o pkg/shelfice:
1063      - change units (+ document) of newly added field "shelfIceMassDynTendency"
1064      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
1065    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
1066    o pkg/seaice: two new runtime parameters:
1067      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
1068        long overdue
1069      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
1070        parameterization of tensil stress for fast ice (does not do anything yet)
1071    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
1072        for LSR: move checking overlaps out of JFNK-if-block
1073    o pkg/atm_phys:
1074      - move copy of grid and dynamical fields out of atm_phys_driver.F into
1075        new S/R ATM_PHYS_DYN2PHYS.
1076      - fix level height for Linear Free-Surf case (to be consistent with
1077        fixed-in-time pressure levels).
1078    o pkg/mom_common (bottomdrag):
1079      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
1080        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
1081        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
1082    o pkg/shelfice (u/v_drag):
1083      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
1084      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
1085        (now similar to shelfice_u_drag.F)
1086      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
1087        from mom_vecinv.F (similar to mom_fluxform calls).
1088    o pkg/mom_common (bottomdrag):
1089      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
1090      - add options for alternative discretisation of velocity norm in quadratic
1091        bottom drag: averaging of grid-cell-center KE to U.point and V.point
1092        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
1093        improves when averaging only the other component (e.g. vVel for U bottom
1094        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
1095      - add options (bottomVisc_pCell) to account for partial-cell in bottom
1096        friction (no-slip BC) thus getting the true distance from the bottom;
1097        off by default since this also reduces model stability (explicit bottom
1098        friction). Changes produce different machine truncation with linear-drag
1099        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
1100        front_relax (bvp & mxl, 10 & 11 digits).
1101    o model/src & mom pkgs:
1102      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
1103        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
1104      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
1105        just copy level Nr value to level Nr+1.
1106    o doc:
1107      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1108    o pkg/shelfice:
1109      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1110        SHELFICE.h: move array shelficemass to init_varia, initialise
1111        from array shelficemassinit, which is set in init_fixed and
1112        has option to be set from file; introduce array
1113        shelficeMassDynTend array, set thru file in init_fixed
1114      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
1115        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
1116        pkg/streamice
1117      - shelfice_thermodynamics.F: call shelfice_step_icemass if
1118        SHELFICEMassStepping = .true.
1119      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
1120    
1121    checkpoint65h (2014/12/17)
1122    o verification/global_ocean.90x40x15, global_ocean_ebm:
1123      - update to generic controls.
1124    o pkg/ctrl:
1125      - ctrl_map_ini_genarr.F: test for igen>0
1126      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
1127      - move gentim2d part of ctrl_map_ini_genarr.F to
1128        new separate routine : ctrl_map_ini_gentim2d.F
1129      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
1130        add time variable weights and cyclic controls (time mean,
1131        seasonal cycle, etc) capabilities to gentim2d
1132    o pkg/ecco:
1133      - move reading of error, conversion to weights from
1134        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
1135    o global_oce_llc90, cs32:
1136      - activte sbo.
1137      - CTRL_SIZE.h : add maxCtrlProc.
1138      - activate the new genctrl capabilities.
1139      - update following reorganization of global_oce_input_fields.tar.gz  
1140    o pkg/ctrl/ctrl_ad_diff.list:
1141      - add missing ctrl_init_rec.f
1142    o tools/OAD_support/keepOriginal:
1143      - add ctrl_init_rec.F
1144    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
1145      - avoid recomputations of xx_gentim2d_dummy.
1146    o momentum diagnostics:
1147      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
1148        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
1149    o pkg/seaice/seaice_lsr.F:
1150      - fix computation of BU/BV, make sure they are non-zero, only necessary
1151        for cubed sphere exchanges and SEAICE_OLx/y>0.
1152        This makes calling s/r fill_cs_corner_rl obsolete (removed).
1153    o verification/global_ocean.cs32x15/input.seaice
1154      - add test for strong implicit coupling and restricted addtive Schwarz
1155        methods for LSR
1156      - update results/output.seaice.txt
1157    o verification/tutorial_global_oce_biogeo:
1158      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
1159        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
1160        update output_adm,_oadm,_tlm.txt
1161    o pkg/dic:
1162      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
1163      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
1164        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
1165    o verification/tutorial_global_oce_biogeo:
1166      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
1167        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
1168        update output_adm,_oadm,_tlm.txt
1169    o eesupp/src:
1170      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
1171        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
1172    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
1173      LSR (following Hutchings et al. 2004)
1174      - introduce zetaZ as a global variable (requires adjustments in
1175        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
1176        in seaice_calc_viscosities.F
1177      - new flag SEAICEuseStrImpCpl (default off)
1178      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
1179        momentum equations
1180      - JFNK-solver (preconditioner) adjusted to allow using this method
1181        (where it does not have any positive effect)
1182    o pkg/seaice
1183      - add overlap for restrictive additive Schwartz method also to LSR, but
1184        turn it off by default (because it only seems to work for non-cubed
1185        sphere/llc topologies)
1186    o pkg/autodiff
1187      - add extra exchanges in addummy_in_steppging also for mnc output
1188    o pkg/seaice:
1189      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
1190        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
1191    o pkg/obcs:
1192      - add option to specify domain-connected piece Id along OB though files
1193        (for now, only used to diagnose PhiVel; default =1 -> global correction)
1194      - modify obcs_diag_balance.F to process each connected-part separately;
1195        exclude OB where Id = 0 but keep the full divergence there (-> constant
1196        Psi along this portion of OB and all inflow derived from grad(Phi))
1197      - add example of OB-conect files in verification/so_box_biogeo/input.
1198    o pkg/diagnostics:
1199      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
1200      a) use non zero matrix element across OB and solve for Phi 1 grid point
1201         outside OB (i.e, where tracer OBCS are applied).
1202      b) global imbalance of inFlow/outFlow across OB: instead of modifying
1203         velocity across OB, spread it uniformly along the OB in the RHS.
1204    
1205    checkpoint65g (2014/11/19)
1206    o pkg/diagnostcis:
1207      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
1208    o pkg/my82,pp81,kl10:
1209      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
1210        field diffKr as background diffusivity to set minimum diffusivity value.
1211    o pkg/seaice:
1212      - add new parameter SEAICEuseEVPrev (for revisited EVP by
1213        Bouillon et al 2013)
1214      - add SEAICE_evpAlpha/Beta to namelist
1215      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
1216        involve trivial re-ordering of divisions/multiplications that should not
1217        have any effects, but ... they do change the results of lab_sea.hb87 so
1218        that only 2 digits of agreement remain, in line with the general
1219        instability/fragility of the evp-code. For now, I do not care and just
1220        update the verification experiment
1221    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
1222      - remove xx_genarr2d_numsmooth etc
1223      - use xx_genarr2d_preproc etc instead
1224      - carry out smooth_correl2D at initialization stage rather than during
1225        time stepping.
1226      - get smoothOpNb from xx_gentim2d_preproc
1227    o global_oce_cs32 :
1228      - add test of generic ecco capabilities.
1229    o pkg/exf/exf_getsurfacefluxes.F :
1230      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
1231    o pkg/ctrl,ecco :
1232      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
1233        is defined.
1234    o pkg/seaice: add diagnostics for Delta (deformation parameter)
1235    o model/src:
1236      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
1237        diffusivity (background) is specified but ignored.
1238    o verification:
1239      - in testreport, convert hostname to lower case for default output dir name
1240    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
1241    o pkg/dic: add modifications from Hajoon:
1242      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
1243      - light attenuation: add self-shading effect by climatological Chlorophyll
1244        (read from file).
1245    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
1246        compiles when SEAICE_ALLOW_DYNAMICS is undefined
1247    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
1248        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
1249        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
1250        approach where CPP_OPTIONS.h includes an omnipotent
1251        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
1252    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
1253        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
1254    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
1255        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
1256        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
1257    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
1258      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
1259      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
1260      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
1261      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
1262    o pkg/ctrl,ecco,exf :
1263      - remove variables associated with NON-generic costs,
1264        unless ECCO_CTRL_DEPRECATED is defined.
1265      - remove NON-generic NON-obcs controls,
1266        unless ECCO_CTRL_DEPRECATED is defined.
1267    o pkg/ctrl : added ctrl_local_params.h
1268    o pkg/ecco : added ecco_local_params.h
1269    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
1270        experiments, which will progressively be removed once the
1271        experiments are revised to use only generic controls/costs.
1272    
1273    checkpoint65f (2014/10/13)
1274    o pkg/ctrl, ecco, seaice : minor changes in headers
1275    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
1276        cost function and control capabilities added since checkpoint65c.
1277    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
1278  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
1279    - ecco_toolbox.F (new) : basic operations that are often used    - ecco_toolbox.F (new) : basic operations that are often used,
1280       (for now, ecco_toolbox.F simply contains function ecco_zero).      including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
1281        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
1282    - cost_gencal.F (new) : determine filnames and records.    - cost_gencal.F (new) : determine filnames and records.
1283    - cost_gendif.F (new) : compute masked model-data difference.    - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
   - cost_genread.F : use ecco_zero to initialize field to 0s.  
1284    - cost_generic.F : use spzeroloc rather than hard-coded -9999,    - cost_generic.F : use spzeroloc rather than hard-coded -9999,
1285      and exploit the above functions leading to more compact code.      and exploit the above functions leading to more compact code.
1286      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
1287    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
1288      using_ers, using_gfo, using_mdt is now only defined within gencost)      using_ers, using_gfo, using_mdt is now only defined within gencost)
1289  o pkg/ecco: extend generic cost capabilities  o pkg/ecco: extend generic cost capabilities
1290    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
1291      capabilities via gencost_preproc (+ _c,_i,_r related params),      capabilities via gencost_preproc (+ _c,_i,_r related params),
1292      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
1293      gencost_outputlevel arguments to cost_generic      gencost_outputlevel arguments to cost_generic
1294    - pkg/ecco/cost_genread.F (new) : interface between cost_generic    - pkg/ecco/cost_genread.F (new) : interface between cost_generic
# Line 34  o pkg/ecco: extend generic cost capabili Line 1306  o pkg/ecco: extend generic cost capabili
1306    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
1307  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
1308  o pkg/ecco: internal re-organization  o pkg/ecco: internal re-organization
1309    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
1310      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
1311      mv relevant variables definition from ecco_cost.h to ecco.h,      mv relevant variables definition from ecco_cost.h to ecco.h,
1312      make sure gencost routines only include ecco.h)      make sure gencost routines only include ecco.h)
1313    - throughout : add missing CCP switches, rm unused variables,    - throughout : add missing CCP switches, rm unused variables,
1314      and rm un-necessary CPP switches      and rm un-necessary CPP switches
1315    - throughout gencost routines : replace modelstartdate with    - throughout gencost routines : replace modelstartdate with
1316      gencost_startdate when needed      gencost_startdate when needed
1317    - cost_bp_read.F : use arguments, instead of common blocs    - cost_bp_read.F : use arguments, instead of common blocs
1318      so that it can be used also by (new) cost_gencost_bpv4.F      so that it can be used also by (new) cost_gencost_bpv4.F
1319    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
1320    - ecco_phys.F : compute etanFull    - ecco_phys.F : compute etanFull
1321    - ecco_readparms.F : rename using_topex as using_tpj, add    - ecco_readparms.F : rename using_topex as using_tpj, add
# Line 361  o pkg/seaice: more clean up Line 1633  o pkg/seaice: more clean up
1633      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
1634      this experiment):      this experiment):
1635      > size mitgcmuv_ad      > size mitgcmuv_ad
1636      text    data        bss     dec        hex        text    data        bss     dec        hex
1637      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1638      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1639      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1640      text    data        bss     dec        hex      text    data        bss     dec        hex
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