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revision 1.2170 by heimbach, Sun Jul 5 02:06:23 2015 UTC revision 1.2325 by jmc, Wed Apr 12 18:50:25 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
9        to get same expression (regarding machine truncation) in different places
10        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
11        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
12        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
13    o pkg/shelfice:
14      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
15        to shelfice_init_fixed.F
16      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
17        ini_masks_etc.F for now) to update ocean upper boundary position according
18        to ice-shelf topography (instead of directly updating hFacC).
19    o model/src:
20      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
21        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
22    
23    checkpoint66f (2017/04/06)
24    o model/src:
25      - add specific run-time param to select level of printed plot-field-maps,
26        set by default to debugLevel. Remove internal param "printDomain".
27    o pkg/seaice:
28      - add flag to add snow mass to seaiceMassC/U/V, the default is
29        SEAICEaddSnowMass=.FALSE., not to change previous results
30    o pkg/bling
31      - Bug fix in bling_production regarding unit conversion for diagnostics
32        being put in the wrong place
33    o model/src:
34      - add back recomputation of rSurfW & S to ensure consistent column thickness
35        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
36        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
37        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
38    o pkg/autodiff:
39      - clean-up "checkpoint.flow"
40    o pkg/rw (Contribution from Jody Klymak):
41        option to set mds file suffix as function of time in simulation:
42        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
43           to select file suffix format; by default (=0), use iteration number;
44        *) add simple routine to return file suffix according to rwSuffixType;
45        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
46           use new S/R to get file suffix, except for debug output file (diagFreq)
47           and pkgs offline & rbcs input files.
48    o pkg/rw:
49      - uniform processing of "I10" suffix across writing fld routines; used to
50        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
51        (similar to cg3d.F, cg3d_ex0.F)
52    o pkg/mom_vecinv:
53      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
54        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
55    o pkg/bling:
56      - Many small changes intended to clean the code.
57        Unnecessary ADJOINT_SAFEs removed ;
58        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
59        diagnostics added.
60    
61    checkpoint66e (2017/03/14)
62    o pkg/exf:
63      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
64        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
65        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
66        avoid any dynamic allocation ;
67      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
68        read-in ; add warning when file is read-in but not used within pkg/exf ;
69        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
70      - update exf_summary.F (print {FLD}RepCycle).
71    o verification/global_with_exf:
72      - switch on exf interpolation in AD test (just like the forward test)
73    o pkg/mom_vecinv:
74      - add storage directives to avoid recomputations within mom_vecinv.F
75        which were generating seg. fault with gfortran -devel
76    o pkg/ctrl, pkg/smooth:
77      - initialize array halos which were generating seg. fault with
78        gfortran -devel in adjoint mode
79    o pkg/exf:
80      - for each input field, enable to specify a field specific repeat-cycle
81        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
82    o verification/lab_sea:
83      - update AD results of primary test and noseaicedyn test after switching
84        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
85        check stays about the same.
86    o pkg/exf:
87      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
88      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
89    o pkg/bling, USE_EXFCO2 code:
90      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
91      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
92    o pkg/exf:
93      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
94      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
95        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
96        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
97      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
98        EXF_INIT_FLD) and update calls in exf_init_varia.F
99      - For now, for backward compatibility, keep a simplified version of S/Rs
100        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
101      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
102        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
103    o tools/genmake2:
104      - replace "bc -l" (only used once) by "expr" (already used).
105    o verification/global_ocean.cs32x15:
106      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
107        Note: exf setting (data.exf) can be compared to other exf secondary exp
108        "seaice" (kept with useCAL=T) which has same time dependent forcing.
109    
110    checkpoint66d (2017/02/13)
111    o pkg/exf:
112      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
113        early on (in packages_boot.F) to stress this change in pkg setting.
114      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
115    o model/src:
116      - move call to ecco_phys to end of time step; this may induce minor
117        cost function changes by shifting time averages by one time step
118        for some variables; this revision resulted in changed adjoint results
119        in MITgcm_contrib/verification_other/global_oce_cs32
120    o pkg/exf:
121      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
122        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
123        e.g. precip, are not available.
124    o pkg/flt:
125      - flt_init_varia.F: use pickupSuff if specified
126      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
127        intermediate, step towards completing pkg/exch2 support within pkg/flt;
128        ifdef DEVEL_FLT_EXCH2 then:
129        - flt_init_fixed.F: comment out stop
130        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
131        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
132        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
133        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
134    o tools/genmake2 & pkg/pkg_depend:
135      - define new type of pkg dependency rule ("=pkg_x"), less strict than
136        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
137        (-pkg_x in packages.conf).
138      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
139      - add "+cal" to dependency list of pkg/ecco (needed to compile).
140      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
141    o utils/matlab:
142      - adding ocean_basin routines for defining basin masks.
143    o pkg/exf:
144      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
145        arguments, allowing to check (and stop) if parameter setting of
146         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
147        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
148        for backward compatibility.
149      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
150        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
151    o pkg/bling (USE_EXFCO2 code):
152      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
153        by adding a call to S/R EXF_GETFFIELD_START.
154    o pkg/exf:
155      - allows to compile without pkg/cal (but disabled by current dependency
156        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
157        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
158        of {FLD}startdate1 & date2 ; consistency check not yet coded.
159    o verification/global_ocean.cs32x15:
160      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
161        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
162    o pkg/exf:
163      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
164        calculations); change FWD experiment global_ocean.cs32x15
165        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
166    o pkg/exf:
167      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
168         {FIELD}startdate to {FIELD}StartTime
169        Note: new name also fit better the content, i.e, a start time in second.
170    o eesupp/src:
171      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
172    o pkg/exf:
173      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
174        to allow to read-in Sensible & Latent Heat flux ;
175      - simplify pkg/exf main options:
176        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
177           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
178           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
179        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
180           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
181        3) improve options documentation in EXF_OPTIONS.h.
182    o pkg/ecco:
183      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
184        ecco_summary.F: add passive tracer cost functions to gencost;
185        m_ptracer and m_boxmean_ptracer
186    o pkg/ctrl:
187      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
188        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
189        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
190        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
191    o model/src:
192      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
193        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
194    o pkg/exf:
195      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
196        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
197    
198    checkpoint66c (2017/01/19)
199    o verification:
200      - add new option "-src" to testreport to only produce source code (*.f),
201        including taf output src code (if using '-adm'/'-tlm' option).
202    o pkg/exf:
203      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
204    o pkg/diagnostics:
205      - add run-time variable diagMdsDir to specify a subdirectory for
206        diagnostic output when mds is being used and mdsioLocalDir is not.
207    o pkg/mnc:
208      - mnc_utils.F: edit stop message
209    o pkg/autodiff:
210      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
211        add HAVE_SYSTEM bracket around system call to mkdir
212    o pkg/profiles:
213      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
214        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
215      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
216        add HAVE_SYSTEM bracket around system call to mkdir
217    o pkg/smooth:
218      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
219      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
220      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
221    o pkg/exf:
222      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
223        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
224        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
225      - summary: skip detailed field report if not used (empty file-name).
226    o tools/xmakedepend:
227      - In case line editor "ed" is missing, switch to "sed" command to clean-up
228        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
229    o pkg/exf:
230      - change definition of "hflux" input file to always include Short-Wave;
231        this is now consistent with hflux computation (if using bulk-formulae)
232        and hflux diagnostic & documentation (in EXF_FIELDS.h).
233    
234    checkpoint66b (2016/12/01)
235    o model & momentum pkgs:
236      - implement fully implicit bottom friction combined with implicit surf.
237        pressure, for now, only in hydrostic formulation:
238        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
239          and run with selectImplicitDrag=2 ;
240        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
241      - partial implicit time-stepping (bot. friction + vert. visc first, then
242        surf. press) corresponding to selectImplicitDrag=1 should be applicable
243        to NH formulation but not available until we solve for surf. pressure
244        increment (instead of full etaN).
245      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
246        with implicit vertical viscosity.
247    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
248      - this is a first version that includes many regularisations that may
249        not all be necessary, to be sorted out,
250      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
251      - change one verification experiment in seaice_itd to use and test new code
252      - seaice_growth: catch a case where the argument of log can be zero
253        or smaller (important for code stability)
254    o model/src:
255      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
256        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
257        similar A.X'=Y' system (with same matrix A) in subsequent calls;
258        switch based on errCode (In/Out) argument value; in calling routines,
259        initialise errCode before first call.
260    
261    checkpoint66a (2016/10/18)
262    o pkg/bling:
263      - BLING package now loads in atmospheric pCO2 file using exf package routines
264        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
265    o model/src & pkg/ptracers:
266      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
267        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
268        implicitDiffusion (respectively) are used (even without momImplVertAdv
269        or temp,salt,PTRACERS_ImplVertAdv).
270    o model/src & generic_advdiff:
271      - add parenthesis in main diagonal calculation of implicit vertical
272        diffusion matrix (impldiff.F & gad_implicit_r.F).
273        This affects results at machine truncation level; update output of many
274        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
275    o pkg/mom_commom & generic_advdiff:
276      - add deep atmosphere and anelastic scaling factor in implicit vertical
277        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
278    o model/src:
279      - remove few unnecessary temp array copies in solve_tridiagonal.F
280        & solve_pentadiagonal.F
281    
282    checkpoint65z (2016/09/28)
283    o pkg/seaice: fix multithreading for seaice_fgmres.F
284      - remove unecessary variables from common blocks
285      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
286        basis, that are stored in commom blocks (including integer variable i1)
287      - clean up code a little by removing commented lines that refer to
288        original code
289      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
290    o MITgcm manual:
291      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
292        preliminary documentation for generic controls (8.3; ctrl.tex),
293        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
294        ecco_costfunction.tex
295    o pkg/ecco:
296      - update and cleanup list of CCP options
297      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
298        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
299      - add checks that retired run-time options are not used, and in relation
300        to gencost_mask and gencost_errfile
301      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
302        gencost_nrecperiod
303      - fix m_eta computation for virtual salt flux case
304      - add m_horflux_vol case (selected via gencost_barfile) that computes
305        transports via cost_gencost_boxmean (gencost_flag=-3)
306      - use gencost_flag more systematically (i.e., avoid using gencost_name)
307        for code switches (aside from physical variable selection)
308    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
309      attempt appears to be a bit of a hack and my need some repair down the road
310    o pkg/exf:
311      - interpolation near South Pole: fix criteria on input field latitude.
312    o pkg/icefront & pkg/exf:
313      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
314        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
315    o pkg/exf:
316      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
317        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
318        (add suffix "_out" instead of a prefix); keep same record number as in
319        input file but always write record 1 first (to avoid a STOP in I/O S/R).
320        Change output file content by writing interpolated field before applying
321        land-sea mask (helpful for debug).
322      - 2 compon. vector interpolation with rotation: apply scaling factor on
323        each compon. (Eastward and Northward) just before rotation.
324    o pkg/bling:
325      - Cleaned package. Removed not needed code and comments.
326      - adjoint example now works
327        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
328    o pkg/ptracers:
329      - add Bruno Deremble's code to complete the linear surface correction
330        for tracer conservation;
331      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
332    
333    checkpoint65y (2016/07/29)
334    o pkg/debug (stats):
335      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
336        proc/thread mapping);
337      - fix Min & Max for case where 1 thread has only empty tiles;
338      - use RL variable to count number of wet grid points (with big domain,
339        can be too large to fit into integer*4).
340    o pkg/monitor:
341      - use RL variable to count number of wet grid points (but used only for del2)
342      - add new routine to compute Advective CFL within tracer time-stepping with
343        writing delayed until next monitor output.
344    o pkg/obcs:
345      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
346    o pkg/cal:
347      - calandar-dump: treat case myTime < timePhase in the same way as in
348        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
349    o pkg/dic & seaice:
350      - fix compilation of ocean component for coupled atm+ocn model with
351        seaice dynamics & dic.
352    
353    checkpoint65x (2016/06/11)
354    o add a license text file in main MITgcm tree.
355    o added pkg/bling:
356      - intermediate complexity biogeochemical model
357      - see bling_description.txt for details
358      - verification experiment is global_oce_biogeo_bling (for now, in
359        Contrib/verification_other/); tested daily on baudelaire with gfortran.
360      - add entry point in pkg/gchem for new pkg "bling".
361    o pkg/seaice: fix tensile stength computation
362      - replace global field tensileStrength by tensileStrFac
363      - tensileStrFac can be computed once in S/R seaice_init_varia
364      - fortunately that does not affect any verification results
365    
366    checkpoint65w (2016/05/12)
367    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
368         with ECCO_CTRL_DEPRECATED defined
369    o verification/global_ocean.cs32x15:
370      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
371        with "selectNHfreeSurf=1".
372    o model/src (non-hydrostatic free-surface):
373      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
374        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
375      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
376        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
377        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
378        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
379      - Update output (changes at machine truncation level) of verification exp:
380        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
381        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
382    o pkg/seaice: ITD code
383      - fix picking up from a single category model by initialising
384        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
385      - split a long warning message in seaice_check_pickup.F into two lines,
386        because NEC SX-ACE cannot deal with the long line.
387    o model/src:
388      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
389    o pkg/seaice:
390      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
391    o pkg/seaice:
392      - add basal stress as parameterisation for grounding ice
393        following Lemieux et al. (2015)
394      - turn on by setting new parameter SEAICEbasalDragK2 to a value
395        larger than 0. Lemieux et al. (2015) recommend 15.
396      - The adjoint complains with extra recomputations so there is also a
397        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
398        order to postpone the problem
399      - compile the new code in lab_sea
400    o verification/halfpipe_streamice:
401      - update both TAF and OpenAD adm output (machine truncation differences)
402    
403    checkpoint65v (2016/04/08)
404    o verification/advect_xz:
405      - increase overlap size from 3 to 4 and add new secondary test for PQM
406        advection scheme (with mono & wino limiter).
407      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
408    o model/src:
409      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
410        added phi0Ref) to set vertical axis origin and phiRef origin;
411        keep Ro_SeaLevel for backward compatibility (with a warning).
412       According to coordinate and fluid type:
413        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
414        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
415        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
416        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
417      - remove Ro_SeaLevel from ATM experiment parameter files;
418      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
419        complement; update output.txt (changes at machine truncation level).
420    o pkg/seaice/seaice_evp.F
421      - simplify computation of deltaZ and zetaZ to simple averaging following
422        Bouillon et al. (2013). This removes a lot of code, but also changes
423        verification experiment lab_sea.hb87 -> updated
424    
425    checkpoint65u (2016/03/14)
426    o pkg/generic_advdiff:
427      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
428        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
429        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
430        testing and not for actual use.
431    o model/src:
432      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
433        origin r = rF(1);
434      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
435        in EOS for height coordinate: enable to include NH Pressure or to use
436        more accurate pressure vertical profile; options not linked to EOS type
437        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
438      - start to implement variable gravity (along vertical): for now, only with
439        z-coords (not even z*).
440      - add Ideal Gas equation of state for height coordinate.
441      - update OpenAD output (affected at machine truncation level) of exp:
442        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
443    o pkg/exf:
444      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
445        of exf interpolation (before any rescaling, rotation or interpolation
446        to velocity point) for each field that gets loaded from file. This option
447        identically mimics the input file organization (e.g. record numbers in year
448        by year input files) besides the change in horizontal grid.
449      - add rotateStressOnAgrid run-time switch so that wind stress fields
450        can be provided on the A-grid in zonal/meridional direction and
451        rotated on the fly. This only applies to the case when the exf
452        interpolation is off and rotateStressOnAgrid is false by default.
453    o model/src:
454      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
455        it's also used with pkg/atm_phys) and add few more parameters (but still
456        inactive, src code yet to come)
457    
458    checkpoint65t (2016/02/10)
459    o pkg/atm_phys:
460      - from Ruth Geen: add optical depth dependence on CO2 concentration.
461    o model/src:
462      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
463        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
464        Update output of exp. deep_anelastic (changes at truncation level).
465    o tools:
466      - add a hack in "remove_comments_sed" (used only with TAF) for recent
467        version of OpenMPI (shipped with FC.23): comment out the new header
468        file "mpif-sizeof.h" which causes problems to TAF.
469    o pkg/seaice:
470      - change the termination criterion so that maxits (SEAICElinearIterMax)
471        has an effect
472      - unify iteration parameters for implicit solvers (JFNK and Picard)
473        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
474        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
475        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
476        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
477        SEAICEnonLinTol     replaces JFNKgamma_nonlin
478      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
479      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
480        use with SEAICEuseKrylov
481    o pkg/seaice/seaice_lsr.F
482        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
483        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
484        an effect.
485    o pkg/seaice: add two new parameters
486      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
487        parameter is not in any namelist)
488      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
489        a preconditioner for the non-linear Newton iteration of the JFNK
490        solver
491    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
492      affects some experiments at truncation level:
493      - global_ocean.cs32x15.icedyn (11 digits),
494      - global_ocean.cs32x15.seaice (11 digits),
495      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
496      - also update global_ocean.cs32x15 adjoint and tangent-linear results
497    o pkg/salt_plume & pkg/thsice:
498      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
499        connect salt_plume flux to ATM-OCN coupling pkgs interface:
500       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
501         export to coupler interface) even without compiling pkg/salt_plume ;
502       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
503         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
504    o pkg/dic:
505      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
506        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
507        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
508      - move also update with values from ATM-OCN Coupler in the same new S/R
509        (previously done in ocn_apply_import.F).
510    o tools/adjoint_options:
511      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
512        has been changed on Jan 14, 2016.
513    o pkg/ggl90:
514      - add alternative discretisation of vertical shear (off by default), to
515        compute the mean (@ grid-cell center) of vertical shear compon instead of
516        vertical shear of mean flow (@ grid-cell center).
517      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
518        results on adjacent faces of cubed-sphere grids; this fix the restart.
519    o pkg/atm_compon_interf:
520      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
521        pass last value, stored directly before export to CPL ;
522        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
523      - remove atmSLPr from pickup files (no longer needed for restart)
524    
525    checkpoint65s (2016/01/13)
526    o eesupp & genmake2:
527       - first check for Function ETIME and, if it fails, then check for subroutine
528         ETIME and consistent output; use the appropriate version in timers.F
529    o model/src:
530      - to check restart test, add option to apply EXCH to U,V earlier, just before
531        integr_continuity; turned off by default.
532    o pkg/dic:
533      - remove CPP option USE_ATMOSCO2 (not needed)
534    o tools/tst_2+2:
535      - try to ignore difference between +0 and -0 in binary file, causing test
536        to fail for no good reason.
537    o eesupp & genmake2:
538      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
539        but also check (in genmake2) that test runs and returns meaningful results.
540    o coupler pkgs:
541      Finish implementation of optionally-exchanged variable switches (started on
542       Nov 12) with addition of few more exchanged fields, including 2-way exchange
543       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
544       advection in OCN component; this requires sequential coupling.
545      coupler (pkg/atm_ocn_coupler):
546      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
547        routines (useful for debug).
548      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
549         flux, DIC fields) if corresponding switch is ON.
550      - add option to export RunOff to OCN (to use for DIC river input)
551      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
552      components (pkg/atm_ & ocn_compon_interf):
553      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
554        optionally exchanged fields; add a check & stop in cpl_readparms.F.
555        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
556        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
557      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
558        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
559      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
560      - hold in common block coupler optionally-exchanged variable switch
561        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
562      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
563        this is intended to replace the OCN cplFldtave.* output files (not updated
564        to contain new additional exchanged fields).
565    o pkg/dic:
566      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
567    o pkg/thsice:
568      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
569        and writing of thsice pickup files.
570    o pkg/atm_compon_interf:
571      - move all field individual export-call out of cpl_export_import_data.F
572        into new S/R ATM_EXPORT_FIELDS
573    o pkg/atm_compon_interf:
574      - store state variables (for now, only thSIce fields) just before beeing
575        exported (in cpl_export_import_data.F, like on ocean side) instead of from
576        atm_store_my_data.F like all exported fluxes.
577      - new version of pickup_cpl: write field names into meta file and read meta
578        file to find field postion in pickup. Also only write/read fields meeded for
579        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
580    o pkg/dic:
581      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
582    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
583        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
584        value can be from domain [0,1] to average between the two methods
585    o pkg/atm_phys:
586      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
587        hold fixed in time).
588    
589    checkpoint65r (2015/12/21)
590    o pkg/seaice:
591        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
592        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
593    o pkg/seaice:
594      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
595        when SEAICEscaleSurfStress=.TRUE.,
596      - apply areaW and areaS in S/R seaice_calc_lhs
597    o pkg/atm_phys:
598      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
599        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
600        for individual contribution (convection, LSC cond, radiation)
601      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
602        information); activated with: solar_exponent=0. and wv_exponent=-1.
603    o pkg/ggl90:
604      - within IDEMIX add upper limit for horizontal group velocity to
605        avoid instability problems in the explicit horizontal diffusion term for
606        long time steps or high resolution
607    o pkg/diagnostics:
608      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
609        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
610    o testreport:
611      - remove "-v" (verbose option) in default mpirun command.
612    o pkg/seaice/seaice_growth:
613      - catch potential division by zero in ITD code, does not change
614        verification results
615    o pkg/ecco:
616      - retire old codes to the Attic. The calls to retired functions are
617        left in a commented form in case they ever need to be re-activated.
618      - ecco_check.F: issue warning if any old CPP option is
619        defined that corresponds to retired codes -- then stop.
620    o pkg/atm_compon_interf:
621      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
622        coupler: use last time-step value instead of average over cplSendFrq_iter
623        time-step, similar to what is done for seaIceMass.
624        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
625    o eesupp & genmake2:
626      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
627        <= remove until a fix is found for some ifort version on ia32 machine.
628    o pkg/seaice/seaice_evp:
629      - refine residual computation
630    
631    checkpoint65q (2015/11/18)
632    o pkg/seaice/seaice_evp:
633      - fix residual computations so that they no longer affect the actual
634        simulation code
635      - fix seaice_readparams to be able to actually set new parameters
636        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
637    o model/src:
638      - fix wrong truncation (single prec) from "FLOAT" function in expressions
639        like: deltaT*FLOAT(myIter) when myIter is large:
640         a) replaced by DFLOAT (if not seen by TAF);
641         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
642    o pkg/aim_v23:
643      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
644        when pickupSuff is set ; do write rolling pickups + at the end of the run.
645    o pkg/atm_ocn_coupler + ocn_compon_interf:
646      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
647        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
648        add corresponding call in DO_OCEANIC_PHYS.
649    o coupler pkgs:
650      Start a new way to set-up optionally-exchanged variables (previously, only
651       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
652       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
653       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
654       compononent param default can be set accordingly).
655      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
656       but rather applies to a group a fields (going both ways like for DIC)
657       and corresponds to an option of coupling config.
658      coupler (pkg/atm_ocn_coupler):
659      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
660        and read namelist directly (without eessup S/R calls) instead of
661        in the very un-flexible old way, 1 param per line, in fixed order;
662      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
663        cleanly in CPL_CHECK_CPLCONFIG
664      - add new coupling-exchange selectors (some not yet active) including
665        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
666                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
667      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
668        component ; called directly from coupler.F, after comp. registrations;
669      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
670         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
671          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
672      components (pkg/atm_ & ocn_compon_interf):
673      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
674        CPP header file in all pkg source files.
675      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
676        ATM/OCN_CHECK_CPLCONFIG;
677      - add error-counter to track errors (e.g., in "data.cpl") and to stop
678        cleanly in ATM/OCN_CHECK_CPLCONFIG;
679      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
680        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
681        before PACKAGES_READPARMS;
682      verification/cpl_aim+ocn/:
683      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
684        "data.cpl" for coupler (in input_cpl).
685    o eesupp/inc:
686      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
687        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
688        to always cumulate tile local-sum in the same order (still uses
689        MPI_Allreduce like standard code).
690      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
691        that are now identical to standard version (in eesupp/inc).
692    o pkg/shelfice:
693      - add SHELFICETransCoeffTFile for initializing spatially varying
694        heat and salt transfer coefficients
695    o pkg/atm_compon_interf & ocn_compon_interf:
696      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
697        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
698      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
699    o pkg/atm_ocn_coupler:
700      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
701    o pkg/rbcs:
702      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
703        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
704      - add a short report (to STDOUT) about RBCS-mask settings.
705    
706    checkpoint65p (2015/10/23)
707    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
708        there is no adjoint test for EVP, we don't know what it does to the adjoint
709        solution, but at least there are no more recomputation warnings left
710    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
711        a chance of giving the same results as a fully converged VP (JFNK) solver
712    o tools/adjoint_options/adjoint_diva:
713      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
714    o pkg/streamice:
715      - spotted bug in streamice_driving_stress using dyG where should have been dxG
716    o pkg/exf:
717      - remove STOP statement that prevented to use wind or (wind-)stress
718        interpolation for constant-in-time forcing fields (wind/stress period = 0).
719    o pkg/seaice:
720      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
721        5 additionals 2D fields and 6 new store directives
722      - change logic in seaice_readparms.F: EVP code can now be turned on in
723        various ways, setting SEAICE_deltaTev is no longer required,
724        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
725        or SEAICEaEVPcoeff
726    o pkg/shelfice/shelfice_thermodynamics.F
727      - redefining uLoc/vLoc to u/v, instead of 2u/v
728    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
729      - this is an intermediate state of a truely converging EVP that has
730        the potential of outperforming implicit VP methods, I do not recommend
731        using it yet.
732      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
733        and all parameters are hardwired
734      - for convergence it still requires very smooth regularisations, that means,
735        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
736        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
737        specific averaging appears to be required, still subject to tuning
738      - still needs cleaning and I need to turn parameter into runtime parameters
739      - add code to compute and print residuals of iteration, compile with
740        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
741    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
742      that entered with r1.54 on Sep04, 2015, -> update results
743    
744    checkpoint65o (2015/09/14)
745    o pkg/mom_vecinv & mom_common:
746      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
747        called from there.
748      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
749        allows to use Vector-Invariant form in deep atmos and anelastic formulation
750    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
751      and Koenig-Beatty+Holland (2012)
752      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
753      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
754      - requires an extra input argument for S/R seaice_calc_viscosities
755      - tensileStrength's depth dependence is different from Itkin et al. (2015)
756        (to be changed and played with, for now exponential)
757    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
758      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
759        by AREA according to Connelly et al. (2004), JPO.
760      - For EVP and the LSR solver, the implicit part of the drag term is
761        the only non-zero term in the denominator when there is no ice (which
762        prevented running the model with zero ice-ocean drag). If
763        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
764        (or zero main diagonals BU/BV) which need to be caught. A practical
765        consequence is that for open water, the momentum equation reduce
766        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
767        they happen to be zero, often leading to a non-zero solution over
768        open water.
769    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
770        efficient EVP method.
771      - introduce area-weighted averages for e12 (analogously to
772        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
773        remain, but also changing the order of terms in the previous average
774        changed the results as much) -> update experiment
775      - add SEAICE_DELTA_SMOOTHREG code
776      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
777        TEM-code
778      - adjust loop bounds so that only required fields are computed
779      - add new averaging code for zetaZ/deltaZ (again similar to
780        seaice_calc_viscosities.F), inactive by default for now (will change
781        results again), but will replace old code eventually
782    o eesupp/src:
783      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
784        to always cumulate tile local-sum in the same order
785        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
786        Still uses MPI_Allreduce (like standard code) but on array of tiles
787        and should be faster than GLOBAL_SUM_SEND_RECV code.
788      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
789        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
790      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
791         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
792         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
793         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
794         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
795    
796    checkpoint65n (2015/07/29)
797    o pkg/thsice:
798      - add a warning when used with pkg/aim but without updating SST
799        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
800    o pkg/offline:
801      - change where Offline-Fields are loaded, from load_fields_driver.F to
802        directly within FORWARD_STEP, just after updating iter number and time;
803      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
804        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
805       These changes allow:
806        a) to recover exactly on-line results using deltaToffline=deltaTClock,
807        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
808        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
809        time-step, both with GM & KPP files and with recomputing these fields;
810        b) no needs to switch on staggerTimeStep anymore;
811        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
812      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
813    o pkg/offline:
814      - change (rarely used) offset-iteration parameter to an offset time (in s):
815        can easily recover previous offset-iter effect by setting offset-time
816        (offlineTimeOffset) to offset-iter x deltaToffline;
817      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
818        in KPP as part of surface buoyancy forcing) in offline run.
819      - fix ptracers KPP non-local term in the case where KPP is re-computed.
820  o OpenAD  o OpenAD
821   - Adding preliminary ggl90 test to OpenAD verification.    - Adding preliminary ggl90 test to OpenAD verification.
822     Config. with ggl90 currently diverges after 64 time steps      Config. with ggl90 currently diverges after 64 time steps
823     so will need more work to become more stable      so will need more work to become more stable
824   - Adding preliminary kpp test to OpenAD verification.    - Adding preliminary kpp test to OpenAD verification.
825     required small tweakes in kpp_routines.F      required small tweakes in kpp_routines.F
826   - Merge and update from Krishna Narayanan's contrib area:    - Merge and update from Krishna Narayanan's contrib area:
827     * Add one variable for preliminary OpenAD DIVA      * Add one variable for preliminary OpenAD DIVA
828     * Add replacement time-stepping for OpenAD DIVA      * Add replacement time-stepping for OpenAD DIVA
829     * genmake2 flag -diva (but only for OpenAD; preliminary)      * genmake2 flag -diva (but only for OpenAD; preliminary)
830     * required modifs for OAD_support      * required modifs for OAD_support
831     successful preliminary test for tutorial_global_oce_biogeo/      successful preliminary test for tutorial_global_oce_biogeo/
832  o pkg/seaice:  o pkg/seaice:
833   - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr    - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
834   - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising    - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
835     delta with a smooth function in s/r seaice_calc_viscosity      delta with a smooth function in s/r seaice_calc_viscosity
836     (no effect on EVP)      (no effect on EVP)
837   - rename local suffix "sqr" into "sq" for more consistent variable names    - rename local suffix "sqr" into "sq" for more consistent variable names
838  o pkg/seaice: add new parameter SEAICE_deltaMin that is used ***only***  o pkg/seaice:
839    for regularizing Delta (and nothing else, like the parameter      add new parameter SEAICE_deltaMin that is used ***only***
840    which is also used for all sorts of things SEAICE_EPS). Defaults to      for regularizing Delta (and nothing else, like the parameter
841    SEAICE_EPS for backward compatibility only.      which is also used for all sorts of things SEAICE_EPS).
842        Defaults to SEAICE_EPS for backward compatibility only.
843  o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with  o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
844    the wrong key by inialising it before use -> fixes a recomputation      the wrong key by inialising it before use -> fixes a recomputation
845    problem but does not fix the gradient      problem but does not fix the gradient
846  o pkg/layers:  o pkg/layers:
847    - move resetting of flux arrays to outside the iLa loop    - move resetting of flux arrays to outside the iLa loop
848      (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 854  o pkg/seaice:
854    - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it    - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
855      in lab_sea forward experiment (changes results -> updated)      in lab_sea forward experiment (changes results -> updated)
856    - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v    - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
857  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
858    computations; for SEAICE_VECTORIZE_LSR     computations; for SEAICE_VECTORIZE_LSR
859    - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)    - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
860      sweep to the outside,      sweep to the outside,
861    - 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 1121  o model/src & mom pkgs:
1121      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1122  o doc:  o doc:
1123    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1124  o pkg/streamice:  o pkg/shelfice:
1125    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1126      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1127      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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