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revision 1.2170 by heimbach, Sun Jul 5 02:06:23 2015 UTC revision 1.2326 by jmc, Mon Apr 24 12:43:21 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint66g (2017/04/24)
8    o model/src:
9      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
10        to get same expression (regarding machine truncation) in different places
11        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
12        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
13        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
14    o pkg/shelfice:
15      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
16        to shelfice_init_fixed.F
17      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
18        ini_masks_etc.F for now) to update ocean upper boundary position according
19        to ice-shelf topography (instead of directly updating hFacC).
20    o model/src:
21      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
22        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
23    
24    checkpoint66f (2017/04/06)
25    o model/src:
26      - add specific run-time param to select level of printed plot-field-maps,
27        set by default to debugLevel. Remove internal param "printDomain".
28    o pkg/seaice:
29      - add flag to add snow mass to seaiceMassC/U/V, the default is
30        SEAICEaddSnowMass=.FALSE., not to change previous results
31    o pkg/bling
32      - Bug fix in bling_production regarding unit conversion for diagnostics
33        being put in the wrong place
34    o model/src:
35      - add back recomputation of rSurfW & S to ensure consistent column thickness
36        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
37        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
38        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
39    o pkg/autodiff:
40      - clean-up "checkpoint.flow"
41    o pkg/rw (Contribution from Jody Klymak):
42        option to set mds file suffix as function of time in simulation:
43        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
44           to select file suffix format; by default (=0), use iteration number;
45        *) add simple routine to return file suffix according to rwSuffixType;
46        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
47           use new S/R to get file suffix, except for debug output file (diagFreq)
48           and pkgs offline & rbcs input files.
49    o pkg/rw:
50      - uniform processing of "I10" suffix across writing fld routines; used to
51        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
52        (similar to cg3d.F, cg3d_ex0.F)
53    o pkg/mom_vecinv:
54      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
55        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
56    o pkg/bling:
57      - Many small changes intended to clean the code.
58        Unnecessary ADJOINT_SAFEs removed ;
59        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
60        diagnostics added.
61    
62    checkpoint66e (2017/03/14)
63    o pkg/exf:
64      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
65        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
66        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
67        avoid any dynamic allocation ;
68      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
69        read-in ; add warning when file is read-in but not used within pkg/exf ;
70        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
71      - update exf_summary.F (print {FLD}RepCycle).
72    o verification/global_with_exf:
73      - switch on exf interpolation in AD test (just like the forward test)
74    o pkg/mom_vecinv:
75      - add storage directives to avoid recomputations within mom_vecinv.F
76        which were generating seg. fault with gfortran -devel
77    o pkg/ctrl, pkg/smooth:
78      - initialize array halos which were generating seg. fault with
79        gfortran -devel in adjoint mode
80    o pkg/exf:
81      - for each input field, enable to specify a field specific repeat-cycle
82        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
83    o verification/lab_sea:
84      - update AD results of primary test and noseaicedyn test after switching
85        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
86        check stays about the same.
87    o pkg/exf:
88      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
89      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
90    o pkg/bling, USE_EXFCO2 code:
91      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
92      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
93    o pkg/exf:
94      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
95      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
96        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
97        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
98      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
99        EXF_INIT_FLD) and update calls in exf_init_varia.F
100      - For now, for backward compatibility, keep a simplified version of S/Rs
101        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
102      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
103        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
104    o tools/genmake2:
105      - replace "bc -l" (only used once) by "expr" (already used).
106    o verification/global_ocean.cs32x15:
107      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
108        Note: exf setting (data.exf) can be compared to other exf secondary exp
109        "seaice" (kept with useCAL=T) which has same time dependent forcing.
110    
111    checkpoint66d (2017/02/13)
112    o pkg/exf:
113      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
114        early on (in packages_boot.F) to stress this change in pkg setting.
115      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
116    o model/src:
117      - move call to ecco_phys to end of time step; this may induce minor
118        cost function changes by shifting time averages by one time step
119        for some variables; this revision resulted in changed adjoint results
120        in MITgcm_contrib/verification_other/global_oce_cs32
121    o pkg/exf:
122      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
123        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
124        e.g. precip, are not available.
125    o pkg/flt:
126      - flt_init_varia.F: use pickupSuff if specified
127      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
128        intermediate, step towards completing pkg/exch2 support within pkg/flt;
129        ifdef DEVEL_FLT_EXCH2 then:
130        - flt_init_fixed.F: comment out stop
131        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
132        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
133        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
134        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
135    o tools/genmake2 & pkg/pkg_depend:
136      - define new type of pkg dependency rule ("=pkg_x"), less strict than
137        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
138        (-pkg_x in packages.conf).
139      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
140      - add "+cal" to dependency list of pkg/ecco (needed to compile).
141      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
142    o utils/matlab:
143      - adding ocean_basin routines for defining basin masks.
144    o pkg/exf:
145      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
146        arguments, allowing to check (and stop) if parameter setting of
147         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
148        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
149        for backward compatibility.
150      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
151        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
152    o pkg/bling (USE_EXFCO2 code):
153      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
154        by adding a call to S/R EXF_GETFFIELD_START.
155    o pkg/exf:
156      - allows to compile without pkg/cal (but disabled by current dependency
157        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
158        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
159        of {FLD}startdate1 & date2 ; consistency check not yet coded.
160    o verification/global_ocean.cs32x15:
161      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
162        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
163    o pkg/exf:
164      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
165        calculations); change FWD experiment global_ocean.cs32x15
166        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
167    o pkg/exf:
168      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
169         {FIELD}startdate to {FIELD}StartTime
170        Note: new name also fit better the content, i.e, a start time in second.
171    o eesupp/src:
172      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
173    o pkg/exf:
174      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
175        to allow to read-in Sensible & Latent Heat flux ;
176      - simplify pkg/exf main options:
177        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
178           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
179           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
180        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
181           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
182        3) improve options documentation in EXF_OPTIONS.h.
183    o pkg/ecco:
184      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
185        ecco_summary.F: add passive tracer cost functions to gencost;
186        m_ptracer and m_boxmean_ptracer
187    o pkg/ctrl:
188      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
189        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
190        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
191        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
192    o model/src:
193      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
194        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
195    o pkg/exf:
196      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
197        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
198    
199    checkpoint66c (2017/01/19)
200    o verification:
201      - add new option "-src" to testreport to only produce source code (*.f),
202        including taf output src code (if using '-adm'/'-tlm' option).
203    o pkg/exf:
204      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
205    o pkg/diagnostics:
206      - add run-time variable diagMdsDir to specify a subdirectory for
207        diagnostic output when mds is being used and mdsioLocalDir is not.
208    o pkg/mnc:
209      - mnc_utils.F: edit stop message
210    o pkg/autodiff:
211      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
212        add HAVE_SYSTEM bracket around system call to mkdir
213    o pkg/profiles:
214      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
215        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
216      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
217        add HAVE_SYSTEM bracket around system call to mkdir
218    o pkg/smooth:
219      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
220      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
221      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
222    o pkg/exf:
223      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
224        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
225        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
226      - summary: skip detailed field report if not used (empty file-name).
227    o tools/xmakedepend:
228      - In case line editor "ed" is missing, switch to "sed" command to clean-up
229        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
230    o pkg/exf:
231      - change definition of "hflux" input file to always include Short-Wave;
232        this is now consistent with hflux computation (if using bulk-formulae)
233        and hflux diagnostic & documentation (in EXF_FIELDS.h).
234    
235    checkpoint66b (2016/12/01)
236    o model & momentum pkgs:
237      - implement fully implicit bottom friction combined with implicit surf.
238        pressure, for now, only in hydrostic formulation:
239        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
240          and run with selectImplicitDrag=2 ;
241        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
242      - partial implicit time-stepping (bot. friction + vert. visc first, then
243        surf. press) corresponding to selectImplicitDrag=1 should be applicable
244        to NH formulation but not available until we solve for surf. pressure
245        increment (instead of full etaN).
246      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
247        with implicit vertical viscosity.
248    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
249      - this is a first version that includes many regularisations that may
250        not all be necessary, to be sorted out,
251      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
252      - change one verification experiment in seaice_itd to use and test new code
253      - seaice_growth: catch a case where the argument of log can be zero
254        or smaller (important for code stability)
255    o model/src:
256      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
257        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
258        similar A.X'=Y' system (with same matrix A) in subsequent calls;
259        switch based on errCode (In/Out) argument value; in calling routines,
260        initialise errCode before first call.
261    
262    checkpoint66a (2016/10/18)
263    o pkg/bling:
264      - BLING package now loads in atmospheric pCO2 file using exf package routines
265        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
266    o model/src & pkg/ptracers:
267      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
268        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
269        implicitDiffusion (respectively) are used (even without momImplVertAdv
270        or temp,salt,PTRACERS_ImplVertAdv).
271    o model/src & generic_advdiff:
272      - add parenthesis in main diagonal calculation of implicit vertical
273        diffusion matrix (impldiff.F & gad_implicit_r.F).
274        This affects results at machine truncation level; update output of many
275        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
276    o pkg/mom_commom & generic_advdiff:
277      - add deep atmosphere and anelastic scaling factor in implicit vertical
278        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
279    o model/src:
280      - remove few unnecessary temp array copies in solve_tridiagonal.F
281        & solve_pentadiagonal.F
282    
283    checkpoint65z (2016/09/28)
284    o pkg/seaice: fix multithreading for seaice_fgmres.F
285      - remove unecessary variables from common blocks
286      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
287        basis, that are stored in commom blocks (including integer variable i1)
288      - clean up code a little by removing commented lines that refer to
289        original code
290      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
291    o MITgcm manual:
292      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
293        preliminary documentation for generic controls (8.3; ctrl.tex),
294        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
295        ecco_costfunction.tex
296    o pkg/ecco:
297      - update and cleanup list of CCP options
298      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
299        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
300      - add checks that retired run-time options are not used, and in relation
301        to gencost_mask and gencost_errfile
302      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
303        gencost_nrecperiod
304      - fix m_eta computation for virtual salt flux case
305      - add m_horflux_vol case (selected via gencost_barfile) that computes
306        transports via cost_gencost_boxmean (gencost_flag=-3)
307      - use gencost_flag more systematically (i.e., avoid using gencost_name)
308        for code switches (aside from physical variable selection)
309    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
310      attempt appears to be a bit of a hack and my need some repair down the road
311    o pkg/exf:
312      - interpolation near South Pole: fix criteria on input field latitude.
313    o pkg/icefront & pkg/exf:
314      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
315        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
316    o pkg/exf:
317      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
318        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
319        (add suffix "_out" instead of a prefix); keep same record number as in
320        input file but always write record 1 first (to avoid a STOP in I/O S/R).
321        Change output file content by writing interpolated field before applying
322        land-sea mask (helpful for debug).
323      - 2 compon. vector interpolation with rotation: apply scaling factor on
324        each compon. (Eastward and Northward) just before rotation.
325    o pkg/bling:
326      - Cleaned package. Removed not needed code and comments.
327      - adjoint example now works
328        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
329    o pkg/ptracers:
330      - add Bruno Deremble's code to complete the linear surface correction
331        for tracer conservation;
332      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
333    
334    checkpoint65y (2016/07/29)
335    o pkg/debug (stats):
336      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
337        proc/thread mapping);
338      - fix Min & Max for case where 1 thread has only empty tiles;
339      - use RL variable to count number of wet grid points (with big domain,
340        can be too large to fit into integer*4).
341    o pkg/monitor:
342      - use RL variable to count number of wet grid points (but used only for del2)
343      - add new routine to compute Advective CFL within tracer time-stepping with
344        writing delayed until next monitor output.
345    o pkg/obcs:
346      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
347    o pkg/cal:
348      - calandar-dump: treat case myTime < timePhase in the same way as in
349        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
350    o pkg/dic & seaice:
351      - fix compilation of ocean component for coupled atm+ocn model with
352        seaice dynamics & dic.
353    
354    checkpoint65x (2016/06/11)
355    o add a license text file in main MITgcm tree.
356    o added pkg/bling:
357      - intermediate complexity biogeochemical model
358      - see bling_description.txt for details
359      - verification experiment is global_oce_biogeo_bling (for now, in
360        Contrib/verification_other/); tested daily on baudelaire with gfortran.
361      - add entry point in pkg/gchem for new pkg "bling".
362    o pkg/seaice: fix tensile stength computation
363      - replace global field tensileStrength by tensileStrFac
364      - tensileStrFac can be computed once in S/R seaice_init_varia
365      - fortunately that does not affect any verification results
366    
367    checkpoint65w (2016/05/12)
368    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
369         with ECCO_CTRL_DEPRECATED defined
370    o verification/global_ocean.cs32x15:
371      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
372        with "selectNHfreeSurf=1".
373    o model/src (non-hydrostatic free-surface):
374      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
375        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
376      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
377        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
378        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
379        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
380      - Update output (changes at machine truncation level) of verification exp:
381        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
382        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
383    o pkg/seaice: ITD code
384      - fix picking up from a single category model by initialising
385        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
386      - split a long warning message in seaice_check_pickup.F into two lines,
387        because NEC SX-ACE cannot deal with the long line.
388    o model/src:
389      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
390    o pkg/seaice:
391      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
392    o pkg/seaice:
393      - add basal stress as parameterisation for grounding ice
394        following Lemieux et al. (2015)
395      - turn on by setting new parameter SEAICEbasalDragK2 to a value
396        larger than 0. Lemieux et al. (2015) recommend 15.
397      - The adjoint complains with extra recomputations so there is also a
398        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
399        order to postpone the problem
400      - compile the new code in lab_sea
401    o verification/halfpipe_streamice:
402      - update both TAF and OpenAD adm output (machine truncation differences)
403    
404    checkpoint65v (2016/04/08)
405    o verification/advect_xz:
406      - increase overlap size from 3 to 4 and add new secondary test for PQM
407        advection scheme (with mono & wino limiter).
408      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
409    o model/src:
410      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
411        added phi0Ref) to set vertical axis origin and phiRef origin;
412        keep Ro_SeaLevel for backward compatibility (with a warning).
413       According to coordinate and fluid type:
414        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
415        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
416        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
417        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
418      - remove Ro_SeaLevel from ATM experiment parameter files;
419      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
420        complement; update output.txt (changes at machine truncation level).
421    o pkg/seaice/seaice_evp.F
422      - simplify computation of deltaZ and zetaZ to simple averaging following
423        Bouillon et al. (2013). This removes a lot of code, but also changes
424        verification experiment lab_sea.hb87 -> updated
425    
426    checkpoint65u (2016/03/14)
427    o pkg/generic_advdiff:
428      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
429        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
430        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
431        testing and not for actual use.
432    o model/src:
433      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
434        origin r = rF(1);
435      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
436        in EOS for height coordinate: enable to include NH Pressure or to use
437        more accurate pressure vertical profile; options not linked to EOS type
438        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
439      - start to implement variable gravity (along vertical): for now, only with
440        z-coords (not even z*).
441      - add Ideal Gas equation of state for height coordinate.
442      - update OpenAD output (affected at machine truncation level) of exp:
443        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
444    o pkg/exf:
445      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
446        of exf interpolation (before any rescaling, rotation or interpolation
447        to velocity point) for each field that gets loaded from file. This option
448        identically mimics the input file organization (e.g. record numbers in year
449        by year input files) besides the change in horizontal grid.
450      - add rotateStressOnAgrid run-time switch so that wind stress fields
451        can be provided on the A-grid in zonal/meridional direction and
452        rotated on the fly. This only applies to the case when the exf
453        interpolation is off and rotateStressOnAgrid is false by default.
454    o model/src:
455      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
456        it's also used with pkg/atm_phys) and add few more parameters (but still
457        inactive, src code yet to come)
458    
459    checkpoint65t (2016/02/10)
460    o pkg/atm_phys:
461      - from Ruth Geen: add optical depth dependence on CO2 concentration.
462    o model/src:
463      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
464        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
465        Update output of exp. deep_anelastic (changes at truncation level).
466    o tools:
467      - add a hack in "remove_comments_sed" (used only with TAF) for recent
468        version of OpenMPI (shipped with FC.23): comment out the new header
469        file "mpif-sizeof.h" which causes problems to TAF.
470    o pkg/seaice:
471      - change the termination criterion so that maxits (SEAICElinearIterMax)
472        has an effect
473      - unify iteration parameters for implicit solvers (JFNK and Picard)
474        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
475        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
476        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
477        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
478        SEAICEnonLinTol     replaces JFNKgamma_nonlin
479      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
480      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
481        use with SEAICEuseKrylov
482    o pkg/seaice/seaice_lsr.F
483        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
484        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
485        an effect.
486    o pkg/seaice: add two new parameters
487      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
488        parameter is not in any namelist)
489      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
490        a preconditioner for the non-linear Newton iteration of the JFNK
491        solver
492    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
493      affects some experiments at truncation level:
494      - global_ocean.cs32x15.icedyn (11 digits),
495      - global_ocean.cs32x15.seaice (11 digits),
496      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
497      - also update global_ocean.cs32x15 adjoint and tangent-linear results
498    o pkg/salt_plume & pkg/thsice:
499      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
500        connect salt_plume flux to ATM-OCN coupling pkgs interface:
501       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
502         export to coupler interface) even without compiling pkg/salt_plume ;
503       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
504         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
505    o pkg/dic:
506      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
507        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
508        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
509      - move also update with values from ATM-OCN Coupler in the same new S/R
510        (previously done in ocn_apply_import.F).
511    o tools/adjoint_options:
512      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
513        has been changed on Jan 14, 2016.
514    o pkg/ggl90:
515      - add alternative discretisation of vertical shear (off by default), to
516        compute the mean (@ grid-cell center) of vertical shear compon instead of
517        vertical shear of mean flow (@ grid-cell center).
518      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
519        results on adjacent faces of cubed-sphere grids; this fix the restart.
520    o pkg/atm_compon_interf:
521      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
522        pass last value, stored directly before export to CPL ;
523        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
524      - remove atmSLPr from pickup files (no longer needed for restart)
525    
526    checkpoint65s (2016/01/13)
527    o eesupp & genmake2:
528       - first check for Function ETIME and, if it fails, then check for subroutine
529         ETIME and consistent output; use the appropriate version in timers.F
530    o model/src:
531      - to check restart test, add option to apply EXCH to U,V earlier, just before
532        integr_continuity; turned off by default.
533    o pkg/dic:
534      - remove CPP option USE_ATMOSCO2 (not needed)
535    o tools/tst_2+2:
536      - try to ignore difference between +0 and -0 in binary file, causing test
537        to fail for no good reason.
538    o eesupp & genmake2:
539      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
540        but also check (in genmake2) that test runs and returns meaningful results.
541    o coupler pkgs:
542      Finish implementation of optionally-exchanged variable switches (started on
543       Nov 12) with addition of few more exchanged fields, including 2-way exchange
544       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
545       advection in OCN component; this requires sequential coupling.
546      coupler (pkg/atm_ocn_coupler):
547      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
548        routines (useful for debug).
549      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
550         flux, DIC fields) if corresponding switch is ON.
551      - add option to export RunOff to OCN (to use for DIC river input)
552      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
553      components (pkg/atm_ & ocn_compon_interf):
554      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
555        optionally exchanged fields; add a check & stop in cpl_readparms.F.
556        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
557        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
558      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
559        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
560      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
561      - hold in common block coupler optionally-exchanged variable switch
562        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
563      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
564        this is intended to replace the OCN cplFldtave.* output files (not updated
565        to contain new additional exchanged fields).
566    o pkg/dic:
567      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
568    o pkg/thsice:
569      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
570        and writing of thsice pickup files.
571    o pkg/atm_compon_interf:
572      - move all field individual export-call out of cpl_export_import_data.F
573        into new S/R ATM_EXPORT_FIELDS
574    o pkg/atm_compon_interf:
575      - store state variables (for now, only thSIce fields) just before beeing
576        exported (in cpl_export_import_data.F, like on ocean side) instead of from
577        atm_store_my_data.F like all exported fluxes.
578      - new version of pickup_cpl: write field names into meta file and read meta
579        file to find field postion in pickup. Also only write/read fields meeded for
580        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
581    o pkg/dic:
582      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
583    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
584        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
585        value can be from domain [0,1] to average between the two methods
586    o pkg/atm_phys:
587      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
588        hold fixed in time).
589    
590    checkpoint65r (2015/12/21)
591    o pkg/seaice:
592        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
593        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
594    o pkg/seaice:
595      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
596        when SEAICEscaleSurfStress=.TRUE.,
597      - apply areaW and areaS in S/R seaice_calc_lhs
598    o pkg/atm_phys:
599      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
600        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
601        for individual contribution (convection, LSC cond, radiation)
602      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
603        information); activated with: solar_exponent=0. and wv_exponent=-1.
604    o pkg/ggl90:
605      - within IDEMIX add upper limit for horizontal group velocity to
606        avoid instability problems in the explicit horizontal diffusion term for
607        long time steps or high resolution
608    o pkg/diagnostics:
609      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
610        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
611    o testreport:
612      - remove "-v" (verbose option) in default mpirun command.
613    o pkg/seaice/seaice_growth:
614      - catch potential division by zero in ITD code, does not change
615        verification results
616    o pkg/ecco:
617      - retire old codes to the Attic. The calls to retired functions are
618        left in a commented form in case they ever need to be re-activated.
619      - ecco_check.F: issue warning if any old CPP option is
620        defined that corresponds to retired codes -- then stop.
621    o pkg/atm_compon_interf:
622      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
623        coupler: use last time-step value instead of average over cplSendFrq_iter
624        time-step, similar to what is done for seaIceMass.
625        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
626    o eesupp & genmake2:
627      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
628        <= remove until a fix is found for some ifort version on ia32 machine.
629    o pkg/seaice/seaice_evp:
630      - refine residual computation
631    
632    checkpoint65q (2015/11/18)
633    o pkg/seaice/seaice_evp:
634      - fix residual computations so that they no longer affect the actual
635        simulation code
636      - fix seaice_readparams to be able to actually set new parameters
637        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
638    o model/src:
639      - fix wrong truncation (single prec) from "FLOAT" function in expressions
640        like: deltaT*FLOAT(myIter) when myIter is large:
641         a) replaced by DFLOAT (if not seen by TAF);
642         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
643    o pkg/aim_v23:
644      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
645        when pickupSuff is set ; do write rolling pickups + at the end of the run.
646    o pkg/atm_ocn_coupler + ocn_compon_interf:
647      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
648        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
649        add corresponding call in DO_OCEANIC_PHYS.
650    o coupler pkgs:
651      Start a new way to set-up optionally-exchanged variables (previously, only
652       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
653       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
654       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
655       compononent param default can be set accordingly).
656      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
657       but rather applies to a group a fields (going both ways like for DIC)
658       and corresponds to an option of coupling config.
659      coupler (pkg/atm_ocn_coupler):
660      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
661        and read namelist directly (without eessup S/R calls) instead of
662        in the very un-flexible old way, 1 param per line, in fixed order;
663      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
664        cleanly in CPL_CHECK_CPLCONFIG
665      - add new coupling-exchange selectors (some not yet active) including
666        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
667                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
668      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
669        component ; called directly from coupler.F, after comp. registrations;
670      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
671         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
672          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
673      components (pkg/atm_ & ocn_compon_interf):
674      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
675        CPP header file in all pkg source files.
676      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
677        ATM/OCN_CHECK_CPLCONFIG;
678      - add error-counter to track errors (e.g., in "data.cpl") and to stop
679        cleanly in ATM/OCN_CHECK_CPLCONFIG;
680      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
681        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
682        before PACKAGES_READPARMS;
683      verification/cpl_aim+ocn/:
684      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
685        "data.cpl" for coupler (in input_cpl).
686    o eesupp/inc:
687      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
688        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
689        to always cumulate tile local-sum in the same order (still uses
690        MPI_Allreduce like standard code).
691      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
692        that are now identical to standard version (in eesupp/inc).
693    o pkg/shelfice:
694      - add SHELFICETransCoeffTFile for initializing spatially varying
695        heat and salt transfer coefficients
696    o pkg/atm_compon_interf & ocn_compon_interf:
697      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
698        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
699      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
700    o pkg/atm_ocn_coupler:
701      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
702    o pkg/rbcs:
703      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
704        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
705      - add a short report (to STDOUT) about RBCS-mask settings.
706    
707    checkpoint65p (2015/10/23)
708    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
709        there is no adjoint test for EVP, we don't know what it does to the adjoint
710        solution, but at least there are no more recomputation warnings left
711    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
712        a chance of giving the same results as a fully converged VP (JFNK) solver
713    o tools/adjoint_options/adjoint_diva:
714      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
715    o pkg/streamice:
716      - spotted bug in streamice_driving_stress using dyG where should have been dxG
717    o pkg/exf:
718      - remove STOP statement that prevented to use wind or (wind-)stress
719        interpolation for constant-in-time forcing fields (wind/stress period = 0).
720    o pkg/seaice:
721      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
722        5 additionals 2D fields and 6 new store directives
723      - change logic in seaice_readparms.F: EVP code can now be turned on in
724        various ways, setting SEAICE_deltaTev is no longer required,
725        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
726        or SEAICEaEVPcoeff
727    o pkg/shelfice/shelfice_thermodynamics.F
728      - redefining uLoc/vLoc to u/v, instead of 2u/v
729    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
730      - this is an intermediate state of a truely converging EVP that has
731        the potential of outperforming implicit VP methods, I do not recommend
732        using it yet.
733      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
734        and all parameters are hardwired
735      - for convergence it still requires very smooth regularisations, that means,
736        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
737        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
738        specific averaging appears to be required, still subject to tuning
739      - still needs cleaning and I need to turn parameter into runtime parameters
740      - add code to compute and print residuals of iteration, compile with
741        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
742    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
743      that entered with r1.54 on Sep04, 2015, -> update results
744    
745    checkpoint65o (2015/09/14)
746    o pkg/mom_vecinv & mom_common:
747      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
748        called from there.
749      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
750        allows to use Vector-Invariant form in deep atmos and anelastic formulation
751    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
752      and Koenig-Beatty+Holland (2012)
753      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
754      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
755      - requires an extra input argument for S/R seaice_calc_viscosities
756      - tensileStrength's depth dependence is different from Itkin et al. (2015)
757        (to be changed and played with, for now exponential)
758    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
759      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
760        by AREA according to Connelly et al. (2004), JPO.
761      - For EVP and the LSR solver, the implicit part of the drag term is
762        the only non-zero term in the denominator when there is no ice (which
763        prevented running the model with zero ice-ocean drag). If
764        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
765        (or zero main diagonals BU/BV) which need to be caught. A practical
766        consequence is that for open water, the momentum equation reduce
767        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
768        they happen to be zero, often leading to a non-zero solution over
769        open water.
770    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
771        efficient EVP method.
772      - introduce area-weighted averages for e12 (analogously to
773        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
774        remain, but also changing the order of terms in the previous average
775        changed the results as much) -> update experiment
776      - add SEAICE_DELTA_SMOOTHREG code
777      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
778        TEM-code
779      - adjust loop bounds so that only required fields are computed
780      - add new averaging code for zetaZ/deltaZ (again similar to
781        seaice_calc_viscosities.F), inactive by default for now (will change
782        results again), but will replace old code eventually
783    o eesupp/src:
784      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
785        to always cumulate tile local-sum in the same order
786        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
787        Still uses MPI_Allreduce (like standard code) but on array of tiles
788        and should be faster than GLOBAL_SUM_SEND_RECV code.
789      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
790        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
791      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
792         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
793         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
794         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
795         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
796    
797    checkpoint65n (2015/07/29)
798    o pkg/thsice:
799      - add a warning when used with pkg/aim but without updating SST
800        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
801    o pkg/offline:
802      - change where Offline-Fields are loaded, from load_fields_driver.F to
803        directly within FORWARD_STEP, just after updating iter number and time;
804      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
805        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
806       These changes allow:
807        a) to recover exactly on-line results using deltaToffline=deltaTClock,
808        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
809        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
810        time-step, both with GM & KPP files and with recomputing these fields;
811        b) no needs to switch on staggerTimeStep anymore;
812        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
813      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
814    o pkg/offline:
815      - change (rarely used) offset-iteration parameter to an offset time (in s):
816        can easily recover previous offset-iter effect by setting offset-time
817        (offlineTimeOffset) to offset-iter x deltaToffline;
818      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
819        in KPP as part of surface buoyancy forcing) in offline run.
820      - fix ptracers KPP non-local term in the case where KPP is re-computed.
821  o OpenAD  o OpenAD
822   - Adding preliminary ggl90 test to OpenAD verification.    - Adding preliminary ggl90 test to OpenAD verification.
823     Config. with ggl90 currently diverges after 64 time steps      Config. with ggl90 currently diverges after 64 time steps
824     so will need more work to become more stable      so will need more work to become more stable
825   - Adding preliminary kpp test to OpenAD verification.    - Adding preliminary kpp test to OpenAD verification.
826     required small tweakes in kpp_routines.F      required small tweakes in kpp_routines.F
827   - Merge and update from Krishna Narayanan's contrib area:    - Merge and update from Krishna Narayanan's contrib area:
828     * Add one variable for preliminary OpenAD DIVA      * Add one variable for preliminary OpenAD DIVA
829     * Add replacement time-stepping for OpenAD DIVA      * Add replacement time-stepping for OpenAD DIVA
830     * genmake2 flag -diva (but only for OpenAD; preliminary)      * genmake2 flag -diva (but only for OpenAD; preliminary)
831     * required modifs for OAD_support      * required modifs for OAD_support
832     successful preliminary test for tutorial_global_oce_biogeo/      successful preliminary test for tutorial_global_oce_biogeo/
833  o pkg/seaice:  o pkg/seaice:
834   - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr    - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
835   - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising    - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
836     delta with a smooth function in s/r seaice_calc_viscosity      delta with a smooth function in s/r seaice_calc_viscosity
837     (no effect on EVP)      (no effect on EVP)
838   - rename local suffix "sqr" into "sq" for more consistent variable names    - rename local suffix "sqr" into "sq" for more consistent variable names
839  o pkg/seaice: add new parameter SEAICE_deltaMin that is used ***only***  o pkg/seaice:
840    for regularizing Delta (and nothing else, like the parameter      add new parameter SEAICE_deltaMin that is used ***only***
841    which is also used for all sorts of things SEAICE_EPS). Defaults to      for regularizing Delta (and nothing else, like the parameter
842    SEAICE_EPS for backward compatibility only.      which is also used for all sorts of things SEAICE_EPS).
843        Defaults to SEAICE_EPS for backward compatibility only.
844  o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with  o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
845    the wrong key by inialising it before use -> fixes a recomputation      the wrong key by inialising it before use -> fixes a recomputation
846    problem but does not fix the gradient      problem but does not fix the gradient
847  o pkg/layers:  o pkg/layers:
848    - move resetting of flux arrays to outside the iLa loop    - move resetting of flux arrays to outside the iLa loop
849      (this caused layers_diapycnal to not work with more than one layer coord.)      (this caused layers_diapycnal to not work with more than one layer coord.)
# Line 40  o pkg/seaice: Line 855  o pkg/seaice:
855    - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it    - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
856      in lab_sea forward experiment (changes results -> updated)      in lab_sea forward experiment (changes results -> updated)
857    - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v    - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
858  o pkg/seaice: modify seaice_lsr.F in order to improve the gradient  o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
859    computations; for SEAICE_VECTORIZE_LSR     computations; for SEAICE_VECTORIZE_LSR
860    - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)    - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
861      sweep to the outside,      sweep to the outside,
862    - remove store directives and add "CADJ loop sequential" directives    - remove store directives and add "CADJ loop sequential" directives
# Line 307  o model/src & mom pkgs: Line 1122  o model/src & mom pkgs:
1122      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1123  o doc:  o doc:
1124    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1125  o pkg/streamice:  o pkg/shelfice:
1126    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1127      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1128      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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