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revision 1.2189 by jmc, Tue Oct 20 13:43:32 2015 UTC revision 1.2335 by mlosch, Thu Jun 8 15:35:52 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:
8      - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
9      - add the option to compute no-slip du/dy, dv/dx (i.e.
10        the offdiagonal strain rate e12) by a second order approximation
11        on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
12        it is too messy to implement for the implicit LSR matrix.
13        SEAICE_2ndOrderBC = .FALSE. by default
14    
15    checkpoint66h (2017/06/02)
16    o pkg/seaice:
17      - add new routines to compute stress tensor components and stress tensor
18        divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
19      - change names of diagnostics SIsigI/II (commonly used for invariants)
20        to SIsig1/sig2 (more common for principal components) to avoid confusion
21    o pkf/exf:
22      - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
23        similarly, stop if rotateStressOnAgrid with constant wind-stress.
24    o pkg/seaice:
25      - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
26        EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
27      - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
28        fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
29    o pkg/diagnostics:
30      - small piece of code to rename (old) diagnostics, when namelist is processed.
31    o model/src:
32      - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
33        originally, set as minimum of adjacent hFacC factor ; now (new default)
34        computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
35        Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
36    o pkg/seaice:
37      - add momemtum advection, off by default, still in test phase
38        most of the momentum advection code is adapted and reused from mom_vecinv
39    o pkg/mom_vecinv:
40      - pass these runtime flags:
41        selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
42        as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
43        so that these routines can also be used in pkg/seaice.
44    
45    checkpoint66g (2017/04/24)
46    o model/src:
47      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
48        to get same expression (regarding machine truncation) in different places
49        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
50        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
51        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
52    o pkg/shelfice:
53      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
54        to shelfice_init_fixed.F
55      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
56        ini_masks_etc.F for now) to update ocean upper boundary position according
57        to ice-shelf topography (instead of directly updating hFacC).
58    o model/src:
59      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
60        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
61    
62    checkpoint66f (2017/04/06)
63    o model/src:
64      - add specific run-time param to select level of printed plot-field-maps,
65        set by default to debugLevel. Remove internal param "printDomain".
66    o pkg/seaice:
67      - add flag to add snow mass to seaiceMassC/U/V, the default is
68        SEAICEaddSnowMass=.FALSE., not to change previous results
69    o pkg/bling
70      - Bug fix in bling_production regarding unit conversion for diagnostics
71        being put in the wrong place
72    o model/src:
73      - add back recomputation of rSurfW & S to ensure consistent column thickness
74        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
75        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
76        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
77    o pkg/autodiff:
78      - clean-up "checkpoint.flow"
79    o pkg/rw (Contribution from Jody Klymak):
80        option to set mds file suffix as function of time in simulation:
81        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
82           to select file suffix format; by default (=0), use iteration number;
83        *) add simple routine to return file suffix according to rwSuffixType;
84        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
85           use new S/R to get file suffix, except for debug output file (diagFreq)
86           and pkgs offline & rbcs input files.
87    o pkg/rw:
88      - uniform processing of "I10" suffix across writing fld routines; used to
89        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
90        (similar to cg3d.F, cg3d_ex0.F)
91    o pkg/mom_vecinv:
92      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
93        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
94    o pkg/bling:
95      - Many small changes intended to clean the code.
96        Unnecessary ADJOINT_SAFEs removed ;
97        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
98        diagnostics added.
99    
100    checkpoint66e (2017/03/14)
101    o pkg/exf:
102      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
103        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
104        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
105        avoid any dynamic allocation ;
106      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
107        read-in ; add warning when file is read-in but not used within pkg/exf ;
108        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
109      - update exf_summary.F (print {FLD}RepCycle).
110    o verification/global_with_exf:
111      - switch on exf interpolation in AD test (just like the forward test)
112    o pkg/mom_vecinv:
113      - add storage directives to avoid recomputations within mom_vecinv.F
114        which were generating seg. fault with gfortran -devel
115    o pkg/ctrl, pkg/smooth:
116      - initialize array halos which were generating seg. fault with
117        gfortran -devel in adjoint mode
118    o pkg/exf:
119      - for each input field, enable to specify a field specific repeat-cycle
120        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
121    o verification/lab_sea:
122      - update AD results of primary test and noseaicedyn test after switching
123        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
124        check stays about the same.
125    o pkg/exf:
126      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
127      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
128    o pkg/bling, USE_EXFCO2 code:
129      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
130      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
131    o pkg/exf:
132      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
133      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
134        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
135        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
136      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
137        EXF_INIT_FLD) and update calls in exf_init_varia.F
138      - For now, for backward compatibility, keep a simplified version of S/Rs
139        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
140      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
141        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
142    o tools/genmake2:
143      - replace "bc -l" (only used once) by "expr" (already used).
144    o verification/global_ocean.cs32x15:
145      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
146        Note: exf setting (data.exf) can be compared to other exf secondary exp
147        "seaice" (kept with useCAL=T) which has same time dependent forcing.
148    
149    checkpoint66d (2017/02/13)
150    o pkg/exf:
151      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
152        early on (in packages_boot.F) to stress this change in pkg setting.
153      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
154    o model/src:
155      - move call to ecco_phys to end of time step; this may induce minor
156        cost function changes by shifting time averages by one time step
157        for some variables; this revision resulted in changed adjoint results
158        in MITgcm_contrib/verification_other/global_oce_cs32
159    o pkg/exf:
160      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
161        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
162        e.g. precip, are not available.
163    o pkg/flt:
164      - flt_init_varia.F: use pickupSuff if specified
165      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
166        intermediate, step towards completing pkg/exch2 support within pkg/flt;
167        ifdef DEVEL_FLT_EXCH2 then:
168        - flt_init_fixed.F: comment out stop
169        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
170        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
171        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
172        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
173    o tools/genmake2 & pkg/pkg_depend:
174      - define new type of pkg dependency rule ("=pkg_x"), less strict than
175        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
176        (-pkg_x in packages.conf).
177      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
178      - add "+cal" to dependency list of pkg/ecco (needed to compile).
179      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
180    o utils/matlab:
181      - adding ocean_basin routines for defining basin masks.
182    o pkg/exf:
183      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
184        arguments, allowing to check (and stop) if parameter setting of
185         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
186        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
187        for backward compatibility.
188      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
189        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
190    o pkg/bling (USE_EXFCO2 code):
191      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
192        by adding a call to S/R EXF_GETFFIELD_START.
193    o pkg/exf:
194      - allows to compile without pkg/cal (but disabled by current dependency
195        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
196        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
197        of {FLD}startdate1 & date2 ; consistency check not yet coded.
198    o verification/global_ocean.cs32x15:
199      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
200        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
201    o pkg/exf:
202      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
203        calculations); change FWD experiment global_ocean.cs32x15
204        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
205    o pkg/exf:
206      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
207         {FIELD}startdate to {FIELD}StartTime
208        Note: new name also fit better the content, i.e, a start time in second.
209    o eesupp/src:
210      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
211    o pkg/exf:
212      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
213        to allow to read-in Sensible & Latent Heat flux ;
214      - simplify pkg/exf main options:
215        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
216           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
217           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
218        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
219           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
220        3) improve options documentation in EXF_OPTIONS.h.
221    o pkg/ecco:
222      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
223        ecco_summary.F: add passive tracer cost functions to gencost;
224        m_ptracer and m_boxmean_ptracer
225    o pkg/ctrl:
226      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
227        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
228        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
229        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
230    o model/src:
231      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
232        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
233    o pkg/exf:
234      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
235        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
236    
237    checkpoint66c (2017/01/19)
238    o verification:
239      - add new option "-src" to testreport to only produce source code (*.f),
240        including taf output src code (if using '-adm'/'-tlm' option).
241    o pkg/exf:
242      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
243    o pkg/diagnostics:
244      - add run-time variable diagMdsDir to specify a subdirectory for
245        diagnostic output when mds is being used and mdsioLocalDir is not.
246    o pkg/mnc:
247      - mnc_utils.F: edit stop message
248    o pkg/autodiff:
249      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
250        add HAVE_SYSTEM bracket around system call to mkdir
251    o pkg/profiles:
252      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
253        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
254      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
255        add HAVE_SYSTEM bracket around system call to mkdir
256    o pkg/smooth:
257      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
258      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
259      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
260    o pkg/exf:
261      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
262        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
263        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
264      - summary: skip detailed field report if not used (empty file-name).
265    o tools/xmakedepend:
266      - In case line editor "ed" is missing, switch to "sed" command to clean-up
267        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
268    o pkg/exf:
269      - change definition of "hflux" input file to always include Short-Wave;
270        this is now consistent with hflux computation (if using bulk-formulae)
271        and hflux diagnostic & documentation (in EXF_FIELDS.h).
272    
273    checkpoint66b (2016/12/01)
274    o model & momentum pkgs:
275      - implement fully implicit bottom friction combined with implicit surf.
276        pressure, for now, only in hydrostic formulation:
277        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
278          and run with selectImplicitDrag=2 ;
279        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
280      - partial implicit time-stepping (bot. friction + vert. visc first, then
281        surf. press) corresponding to selectImplicitDrag=1 should be applicable
282        to NH formulation but not available until we solve for surf. pressure
283        increment (instead of full etaN).
284      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
285        with implicit vertical viscosity.
286    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
287      - this is a first version that includes many regularisations that may
288        not all be necessary, to be sorted out,
289      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
290      - change one verification experiment in seaice_itd to use and test new code
291      - seaice_growth: catch a case where the argument of log can be zero
292        or smaller (important for code stability)
293    o model/src:
294      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
295        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
296        similar A.X'=Y' system (with same matrix A) in subsequent calls;
297        switch based on errCode (In/Out) argument value; in calling routines,
298        initialise errCode before first call.
299    
300    checkpoint66a (2016/10/18)
301    o pkg/bling:
302      - BLING package now loads in atmospheric pCO2 file using exf package routines
303        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
304    o model/src & pkg/ptracers:
305      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
306        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
307        implicitDiffusion (respectively) are used (even without momImplVertAdv
308        or temp,salt,PTRACERS_ImplVertAdv).
309    o model/src & generic_advdiff:
310      - add parenthesis in main diagonal calculation of implicit vertical
311        diffusion matrix (impldiff.F & gad_implicit_r.F).
312        This affects results at machine truncation level; update output of many
313        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
314    o pkg/mom_commom & generic_advdiff:
315      - add deep atmosphere and anelastic scaling factor in implicit vertical
316        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
317    o model/src:
318      - remove few unnecessary temp array copies in solve_tridiagonal.F
319        & solve_pentadiagonal.F
320    
321    checkpoint65z (2016/09/28)
322    o pkg/seaice: fix multithreading for seaice_fgmres.F
323      - remove unecessary variables from common blocks
324      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
325        basis, that are stored in commom blocks (including integer variable i1)
326      - clean up code a little by removing commented lines that refer to
327        original code
328      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
329    o MITgcm manual:
330      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
331        preliminary documentation for generic controls (8.3; ctrl.tex),
332        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
333        ecco_costfunction.tex
334    o pkg/ecco:
335      - update and cleanup list of CCP options
336      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
337        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
338      - add checks that retired run-time options are not used, and in relation
339        to gencost_mask and gencost_errfile
340      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
341        gencost_nrecperiod
342      - fix m_eta computation for virtual salt flux case
343      - add m_horflux_vol case (selected via gencost_barfile) that computes
344        transports via cost_gencost_boxmean (gencost_flag=-3)
345      - use gencost_flag more systematically (i.e., avoid using gencost_name)
346        for code switches (aside from physical variable selection)
347    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
348      attempt appears to be a bit of a hack and my need some repair down the road
349    o pkg/exf:
350      - interpolation near South Pole: fix criteria on input field latitude.
351    o pkg/icefront & pkg/exf:
352      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
353        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
354    o pkg/exf:
355      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
356        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
357        (add suffix "_out" instead of a prefix); keep same record number as in
358        input file but always write record 1 first (to avoid a STOP in I/O S/R).
359        Change output file content by writing interpolated field before applying
360        land-sea mask (helpful for debug).
361      - 2 compon. vector interpolation with rotation: apply scaling factor on
362        each compon. (Eastward and Northward) just before rotation.
363    o pkg/bling:
364      - Cleaned package. Removed not needed code and comments.
365      - adjoint example now works
366        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
367    o pkg/ptracers:
368      - add Bruno Deremble's code to complete the linear surface correction
369        for tracer conservation;
370      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
371    
372    checkpoint65y (2016/07/29)
373    o pkg/debug (stats):
374      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
375        proc/thread mapping);
376      - fix Min & Max for case where 1 thread has only empty tiles;
377      - use RL variable to count number of wet grid points (with big domain,
378        can be too large to fit into integer*4).
379    o pkg/monitor:
380      - use RL variable to count number of wet grid points (but used only for del2)
381      - add new routine to compute Advective CFL within tracer time-stepping with
382        writing delayed until next monitor output.
383    o pkg/obcs:
384      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
385    o pkg/cal:
386      - calandar-dump: treat case myTime < timePhase in the same way as in
387        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
388    o pkg/dic & seaice:
389      - fix compilation of ocean component for coupled atm+ocn model with
390        seaice dynamics & dic.
391    
392    checkpoint65x (2016/06/11)
393    o add a license text file in main MITgcm tree.
394    o added pkg/bling:
395      - intermediate complexity biogeochemical model
396      - see bling_description.txt for details
397      - verification experiment is global_oce_biogeo_bling (for now, in
398        Contrib/verification_other/); tested daily on baudelaire with gfortran.
399      - add entry point in pkg/gchem for new pkg "bling".
400    o pkg/seaice: fix tensile stength computation
401      - replace global field tensileStrength by tensileStrFac
402      - tensileStrFac can be computed once in S/R seaice_init_varia
403      - fortunately that does not affect any verification results
404    
405    checkpoint65w (2016/05/12)
406    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
407         with ECCO_CTRL_DEPRECATED defined
408    o verification/global_ocean.cs32x15:
409      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
410        with "selectNHfreeSurf=1".
411    o model/src (non-hydrostatic free-surface):
412      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
413        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
414      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
415        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
416        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
417        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
418      - Update output (changes at machine truncation level) of verification exp:
419        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
420        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
421    o pkg/seaice: ITD code
422      - fix picking up from a single category model by initialising
423        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
424      - split a long warning message in seaice_check_pickup.F into two lines,
425        because NEC SX-ACE cannot deal with the long line.
426    o model/src:
427      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
428    o pkg/seaice:
429      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
430    o pkg/seaice:
431      - add basal stress as parameterisation for grounding ice
432        following Lemieux et al. (2015)
433      - turn on by setting new parameter SEAICEbasalDragK2 to a value
434        larger than 0. Lemieux et al. (2015) recommend 15.
435      - The adjoint complains with extra recomputations so there is also a
436        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
437        order to postpone the problem
438      - compile the new code in lab_sea
439    o verification/halfpipe_streamice:
440      - update both TAF and OpenAD adm output (machine truncation differences)
441    
442    checkpoint65v (2016/04/08)
443    o verification/advect_xz:
444      - increase overlap size from 3 to 4 and add new secondary test for PQM
445        advection scheme (with mono & wino limiter).
446      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
447    o model/src:
448      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
449        added phi0Ref) to set vertical axis origin and phiRef origin;
450        keep Ro_SeaLevel for backward compatibility (with a warning).
451       According to coordinate and fluid type:
452        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
453        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
454        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
455        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
456      - remove Ro_SeaLevel from ATM experiment parameter files;
457      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
458        complement; update output.txt (changes at machine truncation level).
459    o pkg/seaice/seaice_evp.F
460      - simplify computation of deltaZ and zetaZ to simple averaging following
461        Bouillon et al. (2013). This removes a lot of code, but also changes
462        verification experiment lab_sea.hb87 -> updated
463    
464    checkpoint65u (2016/03/14)
465    o pkg/generic_advdiff:
466      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
467        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
468        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
469        testing and not for actual use.
470    o model/src:
471      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
472        origin r = rF(1);
473      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
474        in EOS for height coordinate: enable to include NH Pressure or to use
475        more accurate pressure vertical profile; options not linked to EOS type
476        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
477      - start to implement variable gravity (along vertical): for now, only with
478        z-coords (not even z*).
479      - add Ideal Gas equation of state for height coordinate.
480      - update OpenAD output (affected at machine truncation level) of exp:
481        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
482    o pkg/exf:
483      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
484        of exf interpolation (before any rescaling, rotation or interpolation
485        to velocity point) for each field that gets loaded from file. This option
486        identically mimics the input file organization (e.g. record numbers in year
487        by year input files) besides the change in horizontal grid.
488      - add rotateStressOnAgrid run-time switch so that wind stress fields
489        can be provided on the A-grid in zonal/meridional direction and
490        rotated on the fly. This only applies to the case when the exf
491        interpolation is off and rotateStressOnAgrid is false by default.
492    o model/src:
493      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
494        it's also used with pkg/atm_phys) and add few more parameters (but still
495        inactive, src code yet to come)
496    
497    checkpoint65t (2016/02/10)
498    o pkg/atm_phys:
499      - from Ruth Geen: add optical depth dependence on CO2 concentration.
500    o model/src:
501      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
502        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
503        Update output of exp. deep_anelastic (changes at truncation level).
504    o tools:
505      - add a hack in "remove_comments_sed" (used only with TAF) for recent
506        version of OpenMPI (shipped with FC.23): comment out the new header
507        file "mpif-sizeof.h" which causes problems to TAF.
508    o pkg/seaice:
509      - change the termination criterion so that maxits (SEAICElinearIterMax)
510        has an effect
511      - unify iteration parameters for implicit solvers (JFNK and Picard)
512        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
513        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
514        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
515        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
516        SEAICEnonLinTol     replaces JFNKgamma_nonlin
517      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
518      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
519        use with SEAICEuseKrylov
520    o pkg/seaice/seaice_lsr.F
521        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
522        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
523        an effect.
524    o pkg/seaice: add two new parameters
525      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
526        parameter is not in any namelist)
527      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
528        a preconditioner for the non-linear Newton iteration of the JFNK
529        solver
530    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
531      affects some experiments at truncation level:
532      - global_ocean.cs32x15.icedyn (11 digits),
533      - global_ocean.cs32x15.seaice (11 digits),
534      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
535      - also update global_ocean.cs32x15 adjoint and tangent-linear results
536    o pkg/salt_plume & pkg/thsice:
537      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
538        connect salt_plume flux to ATM-OCN coupling pkgs interface:
539       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
540         export to coupler interface) even without compiling pkg/salt_plume ;
541       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
542         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
543    o pkg/dic:
544      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
545        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
546        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
547      - move also update with values from ATM-OCN Coupler in the same new S/R
548        (previously done in ocn_apply_import.F).
549    o tools/adjoint_options:
550      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
551        has been changed on Jan 14, 2016.
552    o pkg/ggl90:
553      - add alternative discretisation of vertical shear (off by default), to
554        compute the mean (@ grid-cell center) of vertical shear compon instead of
555        vertical shear of mean flow (@ grid-cell center).
556      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
557        results on adjacent faces of cubed-sphere grids; this fix the restart.
558    o pkg/atm_compon_interf:
559      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
560        pass last value, stored directly before export to CPL ;
561        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
562      - remove atmSLPr from pickup files (no longer needed for restart)
563    
564    checkpoint65s (2016/01/13)
565    o eesupp & genmake2:
566       - first check for Function ETIME and, if it fails, then check for subroutine
567         ETIME and consistent output; use the appropriate version in timers.F
568    o model/src:
569      - to check restart test, add option to apply EXCH to U,V earlier, just before
570        integr_continuity; turned off by default.
571    o pkg/dic:
572      - remove CPP option USE_ATMOSCO2 (not needed)
573    o tools/tst_2+2:
574      - try to ignore difference between +0 and -0 in binary file, causing test
575        to fail for no good reason.
576    o eesupp & genmake2:
577      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
578        but also check (in genmake2) that test runs and returns meaningful results.
579    o coupler pkgs:
580      Finish implementation of optionally-exchanged variable switches (started on
581       Nov 12) with addition of few more exchanged fields, including 2-way exchange
582       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
583       advection in OCN component; this requires sequential coupling.
584      coupler (pkg/atm_ocn_coupler):
585      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
586        routines (useful for debug).
587      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
588         flux, DIC fields) if corresponding switch is ON.
589      - add option to export RunOff to OCN (to use for DIC river input)
590      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
591      components (pkg/atm_ & ocn_compon_interf):
592      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
593        optionally exchanged fields; add a check & stop in cpl_readparms.F.
594        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
595        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
596      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
597        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
598      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
599      - hold in common block coupler optionally-exchanged variable switch
600        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
601      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
602        this is intended to replace the OCN cplFldtave.* output files (not updated
603        to contain new additional exchanged fields).
604    o pkg/dic:
605      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
606    o pkg/thsice:
607      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
608        and writing of thsice pickup files.
609    o pkg/atm_compon_interf:
610      - move all field individual export-call out of cpl_export_import_data.F
611        into new S/R ATM_EXPORT_FIELDS
612    o pkg/atm_compon_interf:
613      - store state variables (for now, only thSIce fields) just before beeing
614        exported (in cpl_export_import_data.F, like on ocean side) instead of from
615        atm_store_my_data.F like all exported fluxes.
616      - new version of pickup_cpl: write field names into meta file and read meta
617        file to find field postion in pickup. Also only write/read fields meeded for
618        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
619    o pkg/dic:
620      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
621    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
622        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
623        value can be from domain [0,1] to average between the two methods
624    o pkg/atm_phys:
625      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
626        hold fixed in time).
627    
628    checkpoint65r (2015/12/21)
629    o pkg/seaice:
630        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
631        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
632    o pkg/seaice:
633      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
634        when SEAICEscaleSurfStress=.TRUE.,
635      - apply areaW and areaS in S/R seaice_calc_lhs
636    o pkg/atm_phys:
637      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
638        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
639        for individual contribution (convection, LSC cond, radiation)
640      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
641        information); activated with: solar_exponent=0. and wv_exponent=-1.
642    o pkg/ggl90:
643      - within IDEMIX add upper limit for horizontal group velocity to
644        avoid instability problems in the explicit horizontal diffusion term for
645        long time steps or high resolution
646    o pkg/diagnostics:
647      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
648        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
649    o testreport:
650      - remove "-v" (verbose option) in default mpirun command.
651    o pkg/seaice/seaice_growth:
652      - catch potential division by zero in ITD code, does not change
653        verification results
654    o pkg/ecco:
655      - retire old codes to the Attic. The calls to retired functions are
656        left in a commented form in case they ever need to be re-activated.
657      - ecco_check.F: issue warning if any old CPP option is
658        defined that corresponds to retired codes -- then stop.
659    o pkg/atm_compon_interf:
660      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
661        coupler: use last time-step value instead of average over cplSendFrq_iter
662        time-step, similar to what is done for seaIceMass.
663        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
664    o eesupp & genmake2:
665      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
666        <= remove until a fix is found for some ifort version on ia32 machine.
667    o pkg/seaice/seaice_evp:
668      - refine residual computation
669    
670    checkpoint65q (2015/11/18)
671    o pkg/seaice/seaice_evp:
672      - fix residual computations so that they no longer affect the actual
673        simulation code
674      - fix seaice_readparams to be able to actually set new parameters
675        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
676    o model/src:
677      - fix wrong truncation (single prec) from "FLOAT" function in expressions
678        like: deltaT*FLOAT(myIter) when myIter is large:
679         a) replaced by DFLOAT (if not seen by TAF);
680         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
681    o pkg/aim_v23:
682      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
683        when pickupSuff is set ; do write rolling pickups + at the end of the run.
684    o pkg/atm_ocn_coupler + ocn_compon_interf:
685      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
686        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
687        add corresponding call in DO_OCEANIC_PHYS.
688    o coupler pkgs:
689      Start a new way to set-up optionally-exchanged variables (previously, only
690       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
691       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
692       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
693       compononent param default can be set accordingly).
694      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
695       but rather applies to a group a fields (going both ways like for DIC)
696       and corresponds to an option of coupling config.
697      coupler (pkg/atm_ocn_coupler):
698      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
699        and read namelist directly (without eessup S/R calls) instead of
700        in the very un-flexible old way, 1 param per line, in fixed order;
701      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
702        cleanly in CPL_CHECK_CPLCONFIG
703      - add new coupling-exchange selectors (some not yet active) including
704        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
705                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
706      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
707        component ; called directly from coupler.F, after comp. registrations;
708      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
709         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
710          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
711      components (pkg/atm_ & ocn_compon_interf):
712      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
713        CPP header file in all pkg source files.
714      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
715        ATM/OCN_CHECK_CPLCONFIG;
716      - add error-counter to track errors (e.g., in "data.cpl") and to stop
717        cleanly in ATM/OCN_CHECK_CPLCONFIG;
718      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
719        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
720        before PACKAGES_READPARMS;
721      verification/cpl_aim+ocn/:
722      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
723        "data.cpl" for coupler (in input_cpl).
724    o eesupp/inc:
725      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
726        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
727        to always cumulate tile local-sum in the same order (still uses
728        MPI_Allreduce like standard code).
729      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
730        that are now identical to standard version (in eesupp/inc).
731    o pkg/shelfice:
732      - add SHELFICETransCoeffTFile for initializing spatially varying
733        heat and salt transfer coefficients
734    o pkg/atm_compon_interf & ocn_compon_interf:
735      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
736        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
737      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
738    o pkg/atm_ocn_coupler:
739      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
740    o pkg/rbcs:
741      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
742        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
743      - add a short report (to STDOUT) about RBCS-mask settings.
744    
745    checkpoint65p (2015/10/23)
746    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
747        there is no adjoint test for EVP, we don't know what it does to the adjoint
748        solution, but at least there are no more recomputation warnings left
749    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
750        a chance of giving the same results as a fully converged VP (JFNK) solver
751  o tools/adjoint_options/adjoint_diva:  o tools/adjoint_options/adjoint_diva:
752    - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA    - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
753  o pkg/streamice:  o pkg/streamice:
# Line 416  o model/src & mom pkgs: Line 1160  o model/src & mom pkgs:
1160      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1161  o doc:  o doc:
1162    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1163  o pkg/streamice:  o pkg/shelfice:
1164    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1165      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1166      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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