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revision 1.2211 by mlosch, Wed Dec 16 12:16:46 2015 UTC revision 1.2333 by jmc, Fri Jun 2 17:50:35 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 pkg/seaice: fix a bug computing areaS in seaice_calc_lhs/rhs (J-J -> J-1)  checkpoint66h (2017/06/02)
8    that affects runs when SEAICEscaleSurfStress=.TRUE. (only for JFNK)  o pkg/seaice:
9      - add new routines to compute stress tensor components and stress tensor
10        divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
11      - change names of diagnostics SIsigI/II (commonly used for invariants)
12        to SIsig1/sig2 (more common for principal components) to avoid confusion
13    o pkf/exf:
14      - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
15        similarly, stop if rotateStressOnAgrid with constant wind-stress.
16    o pkg/seaice:
17      - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
18        EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
19      - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
20        fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
21    o pkg/diagnostics:
22      - small piece of code to rename (old) diagnostics, when namelist is processed.
23    o model/src:
24      - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
25        originally, set as minimum of adjacent hFacC factor ; now (new default)
26        computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
27        Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
28    o pkg/seaice:
29      - add momemtum advection, off by default, still in test phase
30        most of the momentum advection code is adapted and reused from mom_vecinv
31    o pkg/mom_vecinv:
32      - pass these runtime flags:
33        selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
34        as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
35        so that these routines can also be used in pkg/seaice.
36    
37    checkpoint66g (2017/04/24)
38    o model/src:
39      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
40        to get same expression (regarding machine truncation) in different places
41        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
42        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
43        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
44    o pkg/shelfice:
45      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
46        to shelfice_init_fixed.F
47      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
48        ini_masks_etc.F for now) to update ocean upper boundary position according
49        to ice-shelf topography (instead of directly updating hFacC).
50    o model/src:
51      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
52        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
53    
54    checkpoint66f (2017/04/06)
55    o model/src:
56      - add specific run-time param to select level of printed plot-field-maps,
57        set by default to debugLevel. Remove internal param "printDomain".
58    o pkg/seaice:
59      - add flag to add snow mass to seaiceMassC/U/V, the default is
60        SEAICEaddSnowMass=.FALSE., not to change previous results
61    o pkg/bling
62      - Bug fix in bling_production regarding unit conversion for diagnostics
63        being put in the wrong place
64    o model/src:
65      - add back recomputation of rSurfW & S to ensure consistent column thickness
66        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
67        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
68        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
69    o pkg/autodiff:
70      - clean-up "checkpoint.flow"
71    o pkg/rw (Contribution from Jody Klymak):
72        option to set mds file suffix as function of time in simulation:
73        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
74           to select file suffix format; by default (=0), use iteration number;
75        *) add simple routine to return file suffix according to rwSuffixType;
76        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
77           use new S/R to get file suffix, except for debug output file (diagFreq)
78           and pkgs offline & rbcs input files.
79    o pkg/rw:
80      - uniform processing of "I10" suffix across writing fld routines; used to
81        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
82        (similar to cg3d.F, cg3d_ex0.F)
83    o pkg/mom_vecinv:
84      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
85        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
86    o pkg/bling:
87      - Many small changes intended to clean the code.
88        Unnecessary ADJOINT_SAFEs removed ;
89        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
90        diagnostics added.
91    
92    checkpoint66e (2017/03/14)
93    o pkg/exf:
94      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
95        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
96        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
97        avoid any dynamic allocation ;
98      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
99        read-in ; add warning when file is read-in but not used within pkg/exf ;
100        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
101      - update exf_summary.F (print {FLD}RepCycle).
102    o verification/global_with_exf:
103      - switch on exf interpolation in AD test (just like the forward test)
104    o pkg/mom_vecinv:
105      - add storage directives to avoid recomputations within mom_vecinv.F
106        which were generating seg. fault with gfortran -devel
107    o pkg/ctrl, pkg/smooth:
108      - initialize array halos which were generating seg. fault with
109        gfortran -devel in adjoint mode
110    o pkg/exf:
111      - for each input field, enable to specify a field specific repeat-cycle
112        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
113    o verification/lab_sea:
114      - update AD results of primary test and noseaicedyn test after switching
115        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
116        check stays about the same.
117    o pkg/exf:
118      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
119      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
120    o pkg/bling, USE_EXFCO2 code:
121      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
122      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
123    o pkg/exf:
124      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
125      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
126        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
127        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
128      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
129        EXF_INIT_FLD) and update calls in exf_init_varia.F
130      - For now, for backward compatibility, keep a simplified version of S/Rs
131        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
132      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
133        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
134    o tools/genmake2:
135      - replace "bc -l" (only used once) by "expr" (already used).
136    o verification/global_ocean.cs32x15:
137      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
138        Note: exf setting (data.exf) can be compared to other exf secondary exp
139        "seaice" (kept with useCAL=T) which has same time dependent forcing.
140    
141    checkpoint66d (2017/02/13)
142    o pkg/exf:
143      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
144        early on (in packages_boot.F) to stress this change in pkg setting.
145      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
146    o model/src:
147      - move call to ecco_phys to end of time step; this may induce minor
148        cost function changes by shifting time averages by one time step
149        for some variables; this revision resulted in changed adjoint results
150        in MITgcm_contrib/verification_other/global_oce_cs32
151    o pkg/exf:
152      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
153        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
154        e.g. precip, are not available.
155    o pkg/flt:
156      - flt_init_varia.F: use pickupSuff if specified
157      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
158        intermediate, step towards completing pkg/exch2 support within pkg/flt;
159        ifdef DEVEL_FLT_EXCH2 then:
160        - flt_init_fixed.F: comment out stop
161        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
162        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
163        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
164        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
165    o tools/genmake2 & pkg/pkg_depend:
166      - define new type of pkg dependency rule ("=pkg_x"), less strict than
167        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
168        (-pkg_x in packages.conf).
169      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
170      - add "+cal" to dependency list of pkg/ecco (needed to compile).
171      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
172    o utils/matlab:
173      - adding ocean_basin routines for defining basin masks.
174    o pkg/exf:
175      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
176        arguments, allowing to check (and stop) if parameter setting of
177         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
178        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
179        for backward compatibility.
180      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
181        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
182    o pkg/bling (USE_EXFCO2 code):
183      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
184        by adding a call to S/R EXF_GETFFIELD_START.
185    o pkg/exf:
186      - allows to compile without pkg/cal (but disabled by current dependency
187        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
188        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
189        of {FLD}startdate1 & date2 ; consistency check not yet coded.
190    o verification/global_ocean.cs32x15:
191      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
192        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
193    o pkg/exf:
194      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
195        calculations); change FWD experiment global_ocean.cs32x15
196        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
197    o pkg/exf:
198      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
199         {FIELD}startdate to {FIELD}StartTime
200        Note: new name also fit better the content, i.e, a start time in second.
201    o eesupp/src:
202      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
203    o pkg/exf:
204      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
205        to allow to read-in Sensible & Latent Heat flux ;
206      - simplify pkg/exf main options:
207        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
208           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
209           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
210        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
211           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
212        3) improve options documentation in EXF_OPTIONS.h.
213    o pkg/ecco:
214      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
215        ecco_summary.F: add passive tracer cost functions to gencost;
216        m_ptracer and m_boxmean_ptracer
217    o pkg/ctrl:
218      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
219        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
220        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
221        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
222    o model/src:
223      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
224        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
225    o pkg/exf:
226      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
227        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
228    
229    checkpoint66c (2017/01/19)
230    o verification:
231      - add new option "-src" to testreport to only produce source code (*.f),
232        including taf output src code (if using '-adm'/'-tlm' option).
233    o pkg/exf:
234      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
235    o pkg/diagnostics:
236      - add run-time variable diagMdsDir to specify a subdirectory for
237        diagnostic output when mds is being used and mdsioLocalDir is not.
238    o pkg/mnc:
239      - mnc_utils.F: edit stop message
240    o pkg/autodiff:
241      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
242        add HAVE_SYSTEM bracket around system call to mkdir
243    o pkg/profiles:
244      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
245        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
246      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
247        add HAVE_SYSTEM bracket around system call to mkdir
248    o pkg/smooth:
249      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
250      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
251      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
252    o pkg/exf:
253      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
254        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
255        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
256      - summary: skip detailed field report if not used (empty file-name).
257    o tools/xmakedepend:
258      - In case line editor "ed" is missing, switch to "sed" command to clean-up
259        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
260    o pkg/exf:
261      - change definition of "hflux" input file to always include Short-Wave;
262        this is now consistent with hflux computation (if using bulk-formulae)
263        and hflux diagnostic & documentation (in EXF_FIELDS.h).
264    
265    checkpoint66b (2016/12/01)
266    o model & momentum pkgs:
267      - implement fully implicit bottom friction combined with implicit surf.
268        pressure, for now, only in hydrostic formulation:
269        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
270          and run with selectImplicitDrag=2 ;
271        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
272      - partial implicit time-stepping (bot. friction + vert. visc first, then
273        surf. press) corresponding to selectImplicitDrag=1 should be applicable
274        to NH formulation but not available until we solve for surf. pressure
275        increment (instead of full etaN).
276      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
277        with implicit vertical viscosity.
278    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
279      - this is a first version that includes many regularisations that may
280        not all be necessary, to be sorted out,
281      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
282      - change one verification experiment in seaice_itd to use and test new code
283      - seaice_growth: catch a case where the argument of log can be zero
284        or smaller (important for code stability)
285    o model/src:
286      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
287        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
288        similar A.X'=Y' system (with same matrix A) in subsequent calls;
289        switch based on errCode (In/Out) argument value; in calling routines,
290        initialise errCode before first call.
291    
292    checkpoint66a (2016/10/18)
293    o pkg/bling:
294      - BLING package now loads in atmospheric pCO2 file using exf package routines
295        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
296    o model/src & pkg/ptracers:
297      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
298        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
299        implicitDiffusion (respectively) are used (even without momImplVertAdv
300        or temp,salt,PTRACERS_ImplVertAdv).
301    o model/src & generic_advdiff:
302      - add parenthesis in main diagonal calculation of implicit vertical
303        diffusion matrix (impldiff.F & gad_implicit_r.F).
304        This affects results at machine truncation level; update output of many
305        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
306    o pkg/mom_commom & generic_advdiff:
307      - add deep atmosphere and anelastic scaling factor in implicit vertical
308        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
309    o model/src:
310      - remove few unnecessary temp array copies in solve_tridiagonal.F
311        & solve_pentadiagonal.F
312    
313    checkpoint65z (2016/09/28)
314    o pkg/seaice: fix multithreading for seaice_fgmres.F
315      - remove unecessary variables from common blocks
316      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
317        basis, that are stored in commom blocks (including integer variable i1)
318      - clean up code a little by removing commented lines that refer to
319        original code
320      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
321    o MITgcm manual:
322      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
323        preliminary documentation for generic controls (8.3; ctrl.tex),
324        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
325        ecco_costfunction.tex
326    o pkg/ecco:
327      - update and cleanup list of CCP options
328      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
329        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
330      - add checks that retired run-time options are not used, and in relation
331        to gencost_mask and gencost_errfile
332      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
333        gencost_nrecperiod
334      - fix m_eta computation for virtual salt flux case
335      - add m_horflux_vol case (selected via gencost_barfile) that computes
336        transports via cost_gencost_boxmean (gencost_flag=-3)
337      - use gencost_flag more systematically (i.e., avoid using gencost_name)
338        for code switches (aside from physical variable selection)
339    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
340      attempt appears to be a bit of a hack and my need some repair down the road
341    o pkg/exf:
342      - interpolation near South Pole: fix criteria on input field latitude.
343    o pkg/icefront & pkg/exf:
344      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
345        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
346    o pkg/exf:
347      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
348        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
349        (add suffix "_out" instead of a prefix); keep same record number as in
350        input file but always write record 1 first (to avoid a STOP in I/O S/R).
351        Change output file content by writing interpolated field before applying
352        land-sea mask (helpful for debug).
353      - 2 compon. vector interpolation with rotation: apply scaling factor on
354        each compon. (Eastward and Northward) just before rotation.
355    o pkg/bling:
356      - Cleaned package. Removed not needed code and comments.
357      - adjoint example now works
358        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
359    o pkg/ptracers:
360      - add Bruno Deremble's code to complete the linear surface correction
361        for tracer conservation;
362      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
363    
364    checkpoint65y (2016/07/29)
365    o pkg/debug (stats):
366      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
367        proc/thread mapping);
368      - fix Min & Max for case where 1 thread has only empty tiles;
369      - use RL variable to count number of wet grid points (with big domain,
370        can be too large to fit into integer*4).
371    o pkg/monitor:
372      - use RL variable to count number of wet grid points (but used only for del2)
373      - add new routine to compute Advective CFL within tracer time-stepping with
374        writing delayed until next monitor output.
375    o pkg/obcs:
376      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
377    o pkg/cal:
378      - calandar-dump: treat case myTime < timePhase in the same way as in
379        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
380    o pkg/dic & seaice:
381      - fix compilation of ocean component for coupled atm+ocn model with
382        seaice dynamics & dic.
383    
384    checkpoint65x (2016/06/11)
385    o add a license text file in main MITgcm tree.
386    o added pkg/bling:
387      - intermediate complexity biogeochemical model
388      - see bling_description.txt for details
389      - verification experiment is global_oce_biogeo_bling (for now, in
390        Contrib/verification_other/); tested daily on baudelaire with gfortran.
391      - add entry point in pkg/gchem for new pkg "bling".
392    o pkg/seaice: fix tensile stength computation
393      - replace global field tensileStrength by tensileStrFac
394      - tensileStrFac can be computed once in S/R seaice_init_varia
395      - fortunately that does not affect any verification results
396    
397    checkpoint65w (2016/05/12)
398    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
399         with ECCO_CTRL_DEPRECATED defined
400    o verification/global_ocean.cs32x15:
401      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
402        with "selectNHfreeSurf=1".
403    o model/src (non-hydrostatic free-surface):
404      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
405        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
406      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
407        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
408        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
409        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
410      - Update output (changes at machine truncation level) of verification exp:
411        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
412        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
413    o pkg/seaice: ITD code
414      - fix picking up from a single category model by initialising
415        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
416      - split a long warning message in seaice_check_pickup.F into two lines,
417        because NEC SX-ACE cannot deal with the long line.
418    o model/src:
419      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
420    o pkg/seaice:
421      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
422    o pkg/seaice:
423      - add basal stress as parameterisation for grounding ice
424        following Lemieux et al. (2015)
425      - turn on by setting new parameter SEAICEbasalDragK2 to a value
426        larger than 0. Lemieux et al. (2015) recommend 15.
427      - The adjoint complains with extra recomputations so there is also a
428        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
429        order to postpone the problem
430      - compile the new code in lab_sea
431    o verification/halfpipe_streamice:
432      - update both TAF and OpenAD adm output (machine truncation differences)
433    
434    checkpoint65v (2016/04/08)
435    o verification/advect_xz:
436      - increase overlap size from 3 to 4 and add new secondary test for PQM
437        advection scheme (with mono & wino limiter).
438      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
439    o model/src:
440      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
441        added phi0Ref) to set vertical axis origin and phiRef origin;
442        keep Ro_SeaLevel for backward compatibility (with a warning).
443       According to coordinate and fluid type:
444        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
445        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
446        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
447        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
448      - remove Ro_SeaLevel from ATM experiment parameter files;
449      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
450        complement; update output.txt (changes at machine truncation level).
451    o pkg/seaice/seaice_evp.F
452      - simplify computation of deltaZ and zetaZ to simple averaging following
453        Bouillon et al. (2013). This removes a lot of code, but also changes
454        verification experiment lab_sea.hb87 -> updated
455    
456    checkpoint65u (2016/03/14)
457    o pkg/generic_advdiff:
458      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
459        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
460        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
461        testing and not for actual use.
462    o model/src:
463      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
464        origin r = rF(1);
465      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
466        in EOS for height coordinate: enable to include NH Pressure or to use
467        more accurate pressure vertical profile; options not linked to EOS type
468        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
469      - start to implement variable gravity (along vertical): for now, only with
470        z-coords (not even z*).
471      - add Ideal Gas equation of state for height coordinate.
472      - update OpenAD output (affected at machine truncation level) of exp:
473        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
474    o pkg/exf:
475      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
476        of exf interpolation (before any rescaling, rotation or interpolation
477        to velocity point) for each field that gets loaded from file. This option
478        identically mimics the input file organization (e.g. record numbers in year
479        by year input files) besides the change in horizontal grid.
480      - add rotateStressOnAgrid run-time switch so that wind stress fields
481        can be provided on the A-grid in zonal/meridional direction and
482        rotated on the fly. This only applies to the case when the exf
483        interpolation is off and rotateStressOnAgrid is false by default.
484    o model/src:
485      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
486        it's also used with pkg/atm_phys) and add few more parameters (but still
487        inactive, src code yet to come)
488    
489    checkpoint65t (2016/02/10)
490    o pkg/atm_phys:
491      - from Ruth Geen: add optical depth dependence on CO2 concentration.
492    o model/src:
493      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
494        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
495        Update output of exp. deep_anelastic (changes at truncation level).
496    o tools:
497      - add a hack in "remove_comments_sed" (used only with TAF) for recent
498        version of OpenMPI (shipped with FC.23): comment out the new header
499        file "mpif-sizeof.h" which causes problems to TAF.
500    o pkg/seaice:
501      - change the termination criterion so that maxits (SEAICElinearIterMax)
502        has an effect
503      - unify iteration parameters for implicit solvers (JFNK and Picard)
504        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
505        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
506        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
507        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
508        SEAICEnonLinTol     replaces JFNKgamma_nonlin
509      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
510      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
511        use with SEAICEuseKrylov
512    o pkg/seaice/seaice_lsr.F
513        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
514        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
515        an effect.
516    o pkg/seaice: add two new parameters
517      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
518        parameter is not in any namelist)
519      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
520        a preconditioner for the non-linear Newton iteration of the JFNK
521        solver
522    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
523      affects some experiments at truncation level:
524      - global_ocean.cs32x15.icedyn (11 digits),
525      - global_ocean.cs32x15.seaice (11 digits),
526      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
527      - also update global_ocean.cs32x15 adjoint and tangent-linear results
528    o pkg/salt_plume & pkg/thsice:
529      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
530        connect salt_plume flux to ATM-OCN coupling pkgs interface:
531       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
532         export to coupler interface) even without compiling pkg/salt_plume ;
533       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
534         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
535    o pkg/dic:
536      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
537        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
538        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
539      - move also update with values from ATM-OCN Coupler in the same new S/R
540        (previously done in ocn_apply_import.F).
541    o tools/adjoint_options:
542      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
543        has been changed on Jan 14, 2016.
544    o pkg/ggl90:
545      - add alternative discretisation of vertical shear (off by default), to
546        compute the mean (@ grid-cell center) of vertical shear compon instead of
547        vertical shear of mean flow (@ grid-cell center).
548      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
549        results on adjacent faces of cubed-sphere grids; this fix the restart.
550    o pkg/atm_compon_interf:
551      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
552        pass last value, stored directly before export to CPL ;
553        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
554      - remove atmSLPr from pickup files (no longer needed for restart)
555    
556    checkpoint65s (2016/01/13)
557    o eesupp & genmake2:
558       - first check for Function ETIME and, if it fails, then check for subroutine
559         ETIME and consistent output; use the appropriate version in timers.F
560    o model/src:
561      - to check restart test, add option to apply EXCH to U,V earlier, just before
562        integr_continuity; turned off by default.
563    o pkg/dic:
564      - remove CPP option USE_ATMOSCO2 (not needed)
565    o tools/tst_2+2:
566      - try to ignore difference between +0 and -0 in binary file, causing test
567        to fail for no good reason.
568    o eesupp & genmake2:
569      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
570        but also check (in genmake2) that test runs and returns meaningful results.
571    o coupler pkgs:
572      Finish implementation of optionally-exchanged variable switches (started on
573       Nov 12) with addition of few more exchanged fields, including 2-way exchange
574       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
575       advection in OCN component; this requires sequential coupling.
576      coupler (pkg/atm_ocn_coupler):
577      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
578        routines (useful for debug).
579      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
580         flux, DIC fields) if corresponding switch is ON.
581      - add option to export RunOff to OCN (to use for DIC river input)
582      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
583      components (pkg/atm_ & ocn_compon_interf):
584      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
585        optionally exchanged fields; add a check & stop in cpl_readparms.F.
586        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
587        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
588      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
589        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
590      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
591      - hold in common block coupler optionally-exchanged variable switch
592        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
593      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
594        this is intended to replace the OCN cplFldtave.* output files (not updated
595        to contain new additional exchanged fields).
596    o pkg/dic:
597      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
598    o pkg/thsice:
599      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
600        and writing of thsice pickup files.
601    o pkg/atm_compon_interf:
602      - move all field individual export-call out of cpl_export_import_data.F
603        into new S/R ATM_EXPORT_FIELDS
604    o pkg/atm_compon_interf:
605      - store state variables (for now, only thSIce fields) just before beeing
606        exported (in cpl_export_import_data.F, like on ocean side) instead of from
607        atm_store_my_data.F like all exported fluxes.
608      - new version of pickup_cpl: write field names into meta file and read meta
609        file to find field postion in pickup. Also only write/read fields meeded for
610        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
611    o pkg/dic:
612      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
613    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
614        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
615        value can be from domain [0,1] to average between the two methods
616    o pkg/atm_phys:
617      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
618        hold fixed in time).
619    
620    checkpoint65r (2015/12/21)
621    o pkg/seaice:
622        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
623        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
624    o pkg/seaice:
625      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
626        when SEAICEscaleSurfStress=.TRUE.,
627      - apply areaW and areaS in S/R seaice_calc_lhs
628  o pkg/atm_phys:  o pkg/atm_phys:
629    - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes    - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
630      (shortwave & longwave, net & downward) and diagnostics of temp. tendency      (shortwave & longwave, net & downward) and diagnostics of temp. tendency
631      for individual contribution (convection, LSC cond, radiation)      for individual contribution (convection, LSC cond, radiation)
632    - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.    - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
633      information); activated with: solar_exponent=0. and wv_exponent=-1.      information); activated with: solar_exponent=0. and wv_exponent=-1.
634  o pkg/ggl90:  o pkg/ggl90:
635    - within IDEMIX add upper limit for horizontal group velocity to    - within IDEMIX add upper limit for horizontal group velocity to
# Line 533  o model/src & mom pkgs: Line 1152  o model/src & mom pkgs:
1152      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1153  o doc:  o doc:
1154    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1155  o pkg/streamice:  o pkg/shelfice:
1156    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1157      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1158      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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