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revision 1.2183 by mlosch, Thu Sep 24 08:17:32 2015 UTC revision 1.2330 by jmc, Tue May 9 03:25:45 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      - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
9        EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
10      - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
11        fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
12    o pkg/diagnostics:
13      - small piece of code to rename (old) diagnostics, when namelist is processed.
14    o model/src:
15      - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
16        originally, set as minimum of adjacent hFacC factor ; now (new default)
17        computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
18        Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
19    o pkg/seaice:
20      - add momemtum advection, off by default, still in test phase
21        most of the momentum advection code is adapted and reused from mom_vecinv
22    o pkg/mom_vecinv:
23      - pass these runtime flags:
24        selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
25        as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
26        so that these routines can also be used in pkg/seaice.
27    
28    checkpoint66g (2017/04/24)
29    o model/src:
30      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
31        to get same expression (regarding machine truncation) in different places
32        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
33        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
34        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
35    o pkg/shelfice:
36      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
37        to shelfice_init_fixed.F
38      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
39        ini_masks_etc.F for now) to update ocean upper boundary position according
40        to ice-shelf topography (instead of directly updating hFacC).
41    o model/src:
42      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
43        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
44    
45    checkpoint66f (2017/04/06)
46    o model/src:
47      - add specific run-time param to select level of printed plot-field-maps,
48        set by default to debugLevel. Remove internal param "printDomain".
49    o pkg/seaice:
50      - add flag to add snow mass to seaiceMassC/U/V, the default is
51        SEAICEaddSnowMass=.FALSE., not to change previous results
52    o pkg/bling
53      - Bug fix in bling_production regarding unit conversion for diagnostics
54        being put in the wrong place
55    o model/src:
56      - add back recomputation of rSurfW & S to ensure consistent column thickness
57        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
58        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
59        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
60    o pkg/autodiff:
61      - clean-up "checkpoint.flow"
62    o pkg/rw (Contribution from Jody Klymak):
63        option to set mds file suffix as function of time in simulation:
64        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
65           to select file suffix format; by default (=0), use iteration number;
66        *) add simple routine to return file suffix according to rwSuffixType;
67        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
68           use new S/R to get file suffix, except for debug output file (diagFreq)
69           and pkgs offline & rbcs input files.
70    o pkg/rw:
71      - uniform processing of "I10" suffix across writing fld routines; used to
72        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
73        (similar to cg3d.F, cg3d_ex0.F)
74    o pkg/mom_vecinv:
75      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
76        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
77    o pkg/bling:
78      - Many small changes intended to clean the code.
79        Unnecessary ADJOINT_SAFEs removed ;
80        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
81        diagnostics added.
82    
83    checkpoint66e (2017/03/14)
84    o pkg/exf:
85      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
86        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
87        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
88        avoid any dynamic allocation ;
89      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
90        read-in ; add warning when file is read-in but not used within pkg/exf ;
91        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
92      - update exf_summary.F (print {FLD}RepCycle).
93    o verification/global_with_exf:
94      - switch on exf interpolation in AD test (just like the forward test)
95    o pkg/mom_vecinv:
96      - add storage directives to avoid recomputations within mom_vecinv.F
97        which were generating seg. fault with gfortran -devel
98    o pkg/ctrl, pkg/smooth:
99      - initialize array halos which were generating seg. fault with
100        gfortran -devel in adjoint mode
101    o pkg/exf:
102      - for each input field, enable to specify a field specific repeat-cycle
103        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
104    o verification/lab_sea:
105      - update AD results of primary test and noseaicedyn test after switching
106        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
107        check stays about the same.
108    o pkg/exf:
109      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
110      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
111    o pkg/bling, USE_EXFCO2 code:
112      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
113      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
114    o pkg/exf:
115      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
116      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
117        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
118        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
119      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
120        EXF_INIT_FLD) and update calls in exf_init_varia.F
121      - For now, for backward compatibility, keep a simplified version of S/Rs
122        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
123      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
124        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
125    o tools/genmake2:
126      - replace "bc -l" (only used once) by "expr" (already used).
127    o verification/global_ocean.cs32x15:
128      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
129        Note: exf setting (data.exf) can be compared to other exf secondary exp
130        "seaice" (kept with useCAL=T) which has same time dependent forcing.
131    
132    checkpoint66d (2017/02/13)
133    o pkg/exf:
134      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
135        early on (in packages_boot.F) to stress this change in pkg setting.
136      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
137    o model/src:
138      - move call to ecco_phys to end of time step; this may induce minor
139        cost function changes by shifting time averages by one time step
140        for some variables; this revision resulted in changed adjoint results
141        in MITgcm_contrib/verification_other/global_oce_cs32
142    o pkg/exf:
143      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
144        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
145        e.g. precip, are not available.
146    o pkg/flt:
147      - flt_init_varia.F: use pickupSuff if specified
148      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
149        intermediate, step towards completing pkg/exch2 support within pkg/flt;
150        ifdef DEVEL_FLT_EXCH2 then:
151        - flt_init_fixed.F: comment out stop
152        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
153        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
154        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
155        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
156    o tools/genmake2 & pkg/pkg_depend:
157      - define new type of pkg dependency rule ("=pkg_x"), less strict than
158        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
159        (-pkg_x in packages.conf).
160      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
161      - add "+cal" to dependency list of pkg/ecco (needed to compile).
162      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
163    o utils/matlab:
164      - adding ocean_basin routines for defining basin masks.
165    o pkg/exf:
166      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
167        arguments, allowing to check (and stop) if parameter setting of
168         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
169        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
170        for backward compatibility.
171      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
172        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
173    o pkg/bling (USE_EXFCO2 code):
174      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
175        by adding a call to S/R EXF_GETFFIELD_START.
176    o pkg/exf:
177      - allows to compile without pkg/cal (but disabled by current dependency
178        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
179        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
180        of {FLD}startdate1 & date2 ; consistency check not yet coded.
181    o verification/global_ocean.cs32x15:
182      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
183        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
184    o pkg/exf:
185      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
186        calculations); change FWD experiment global_ocean.cs32x15
187        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
188    o pkg/exf:
189      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
190         {FIELD}startdate to {FIELD}StartTime
191        Note: new name also fit better the content, i.e, a start time in second.
192    o eesupp/src:
193      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
194    o pkg/exf:
195      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
196        to allow to read-in Sensible & Latent Heat flux ;
197      - simplify pkg/exf main options:
198        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
199           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
200           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
201        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
202           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
203        3) improve options documentation in EXF_OPTIONS.h.
204    o pkg/ecco:
205      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
206        ecco_summary.F: add passive tracer cost functions to gencost;
207        m_ptracer and m_boxmean_ptracer
208    o pkg/ctrl:
209      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
210        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
211        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
212        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
213    o model/src:
214      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
215        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
216    o pkg/exf:
217      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
218        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
219    
220    checkpoint66c (2017/01/19)
221    o verification:
222      - add new option "-src" to testreport to only produce source code (*.f),
223        including taf output src code (if using '-adm'/'-tlm' option).
224    o pkg/exf:
225      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
226    o pkg/diagnostics:
227      - add run-time variable diagMdsDir to specify a subdirectory for
228        diagnostic output when mds is being used and mdsioLocalDir is not.
229    o pkg/mnc:
230      - mnc_utils.F: edit stop message
231    o pkg/autodiff:
232      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
233        add HAVE_SYSTEM bracket around system call to mkdir
234    o pkg/profiles:
235      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
236        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
237      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
238        add HAVE_SYSTEM bracket around system call to mkdir
239    o pkg/smooth:
240      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
241      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
242      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
243    o pkg/exf:
244      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
245        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
246        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
247      - summary: skip detailed field report if not used (empty file-name).
248    o tools/xmakedepend:
249      - In case line editor "ed" is missing, switch to "sed" command to clean-up
250        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
251    o pkg/exf:
252      - change definition of "hflux" input file to always include Short-Wave;
253        this is now consistent with hflux computation (if using bulk-formulae)
254        and hflux diagnostic & documentation (in EXF_FIELDS.h).
255    
256    checkpoint66b (2016/12/01)
257    o model & momentum pkgs:
258      - implement fully implicit bottom friction combined with implicit surf.
259        pressure, for now, only in hydrostic formulation:
260        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
261          and run with selectImplicitDrag=2 ;
262        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
263      - partial implicit time-stepping (bot. friction + vert. visc first, then
264        surf. press) corresponding to selectImplicitDrag=1 should be applicable
265        to NH formulation but not available until we solve for surf. pressure
266        increment (instead of full etaN).
267      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
268        with implicit vertical viscosity.
269    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
270      - this is a first version that includes many regularisations that may
271        not all be necessary, to be sorted out,
272      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
273      - change one verification experiment in seaice_itd to use and test new code
274      - seaice_growth: catch a case where the argument of log can be zero
275        or smaller (important for code stability)
276    o model/src:
277      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
278        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
279        similar A.X'=Y' system (with same matrix A) in subsequent calls;
280        switch based on errCode (In/Out) argument value; in calling routines,
281        initialise errCode before first call.
282    
283    checkpoint66a (2016/10/18)
284    o pkg/bling:
285      - BLING package now loads in atmospheric pCO2 file using exf package routines
286        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
287    o model/src & pkg/ptracers:
288      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
289        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
290        implicitDiffusion (respectively) are used (even without momImplVertAdv
291        or temp,salt,PTRACERS_ImplVertAdv).
292    o model/src & generic_advdiff:
293      - add parenthesis in main diagonal calculation of implicit vertical
294        diffusion matrix (impldiff.F & gad_implicit_r.F).
295        This affects results at machine truncation level; update output of many
296        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
297    o pkg/mom_commom & generic_advdiff:
298      - add deep atmosphere and anelastic scaling factor in implicit vertical
299        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
300    o model/src:
301      - remove few unnecessary temp array copies in solve_tridiagonal.F
302        & solve_pentadiagonal.F
303    
304    checkpoint65z (2016/09/28)
305    o pkg/seaice: fix multithreading for seaice_fgmres.F
306      - remove unecessary variables from common blocks
307      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
308        basis, that are stored in commom blocks (including integer variable i1)
309      - clean up code a little by removing commented lines that refer to
310        original code
311      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
312    o MITgcm manual:
313      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
314        preliminary documentation for generic controls (8.3; ctrl.tex),
315        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
316        ecco_costfunction.tex
317    o pkg/ecco:
318      - update and cleanup list of CCP options
319      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
320        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
321      - add checks that retired run-time options are not used, and in relation
322        to gencost_mask and gencost_errfile
323      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
324        gencost_nrecperiod
325      - fix m_eta computation for virtual salt flux case
326      - add m_horflux_vol case (selected via gencost_barfile) that computes
327        transports via cost_gencost_boxmean (gencost_flag=-3)
328      - use gencost_flag more systematically (i.e., avoid using gencost_name)
329        for code switches (aside from physical variable selection)
330    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
331      attempt appears to be a bit of a hack and my need some repair down the road
332    o pkg/exf:
333      - interpolation near South Pole: fix criteria on input field latitude.
334    o pkg/icefront & pkg/exf:
335      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
336        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
337    o pkg/exf:
338      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
339        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
340        (add suffix "_out" instead of a prefix); keep same record number as in
341        input file but always write record 1 first (to avoid a STOP in I/O S/R).
342        Change output file content by writing interpolated field before applying
343        land-sea mask (helpful for debug).
344      - 2 compon. vector interpolation with rotation: apply scaling factor on
345        each compon. (Eastward and Northward) just before rotation.
346    o pkg/bling:
347      - Cleaned package. Removed not needed code and comments.
348      - adjoint example now works
349        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
350    o pkg/ptracers:
351      - add Bruno Deremble's code to complete the linear surface correction
352        for tracer conservation;
353      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
354    
355    checkpoint65y (2016/07/29)
356    o pkg/debug (stats):
357      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
358        proc/thread mapping);
359      - fix Min & Max for case where 1 thread has only empty tiles;
360      - use RL variable to count number of wet grid points (with big domain,
361        can be too large to fit into integer*4).
362    o pkg/monitor:
363      - use RL variable to count number of wet grid points (but used only for del2)
364      - add new routine to compute Advective CFL within tracer time-stepping with
365        writing delayed until next monitor output.
366    o pkg/obcs:
367      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
368    o pkg/cal:
369      - calandar-dump: treat case myTime < timePhase in the same way as in
370        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
371    o pkg/dic & seaice:
372      - fix compilation of ocean component for coupled atm+ocn model with
373        seaice dynamics & dic.
374    
375    checkpoint65x (2016/06/11)
376    o add a license text file in main MITgcm tree.
377    o added pkg/bling:
378      - intermediate complexity biogeochemical model
379      - see bling_description.txt for details
380      - verification experiment is global_oce_biogeo_bling (for now, in
381        Contrib/verification_other/); tested daily on baudelaire with gfortran.
382      - add entry point in pkg/gchem for new pkg "bling".
383    o pkg/seaice: fix tensile stength computation
384      - replace global field tensileStrength by tensileStrFac
385      - tensileStrFac can be computed once in S/R seaice_init_varia
386      - fortunately that does not affect any verification results
387    
388    checkpoint65w (2016/05/12)
389    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
390         with ECCO_CTRL_DEPRECATED defined
391    o verification/global_ocean.cs32x15:
392      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
393        with "selectNHfreeSurf=1".
394    o model/src (non-hydrostatic free-surface):
395      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
396        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
397      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
398        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
399        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
400        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
401      - Update output (changes at machine truncation level) of verification exp:
402        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
403        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
404    o pkg/seaice: ITD code
405      - fix picking up from a single category model by initialising
406        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
407      - split a long warning message in seaice_check_pickup.F into two lines,
408        because NEC SX-ACE cannot deal with the long line.
409    o model/src:
410      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
411    o pkg/seaice:
412      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
413    o pkg/seaice:
414      - add basal stress as parameterisation for grounding ice
415        following Lemieux et al. (2015)
416      - turn on by setting new parameter SEAICEbasalDragK2 to a value
417        larger than 0. Lemieux et al. (2015) recommend 15.
418      - The adjoint complains with extra recomputations so there is also a
419        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
420        order to postpone the problem
421      - compile the new code in lab_sea
422    o verification/halfpipe_streamice:
423      - update both TAF and OpenAD adm output (machine truncation differences)
424    
425    checkpoint65v (2016/04/08)
426    o verification/advect_xz:
427      - increase overlap size from 3 to 4 and add new secondary test for PQM
428        advection scheme (with mono & wino limiter).
429      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
430    o model/src:
431      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
432        added phi0Ref) to set vertical axis origin and phiRef origin;
433        keep Ro_SeaLevel for backward compatibility (with a warning).
434       According to coordinate and fluid type:
435        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
436        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
437        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
438        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
439      - remove Ro_SeaLevel from ATM experiment parameter files;
440      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
441        complement; update output.txt (changes at machine truncation level).
442    o pkg/seaice/seaice_evp.F
443      - simplify computation of deltaZ and zetaZ to simple averaging following
444        Bouillon et al. (2013). This removes a lot of code, but also changes
445        verification experiment lab_sea.hb87 -> updated
446    
447    checkpoint65u (2016/03/14)
448    o pkg/generic_advdiff:
449      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
450        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
451        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
452        testing and not for actual use.
453    o model/src:
454      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
455        origin r = rF(1);
456      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
457        in EOS for height coordinate: enable to include NH Pressure or to use
458        more accurate pressure vertical profile; options not linked to EOS type
459        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
460      - start to implement variable gravity (along vertical): for now, only with
461        z-coords (not even z*).
462      - add Ideal Gas equation of state for height coordinate.
463      - update OpenAD output (affected at machine truncation level) of exp:
464        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
465    o pkg/exf:
466      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
467        of exf interpolation (before any rescaling, rotation or interpolation
468        to velocity point) for each field that gets loaded from file. This option
469        identically mimics the input file organization (e.g. record numbers in year
470        by year input files) besides the change in horizontal grid.
471      - add rotateStressOnAgrid run-time switch so that wind stress fields
472        can be provided on the A-grid in zonal/meridional direction and
473        rotated on the fly. This only applies to the case when the exf
474        interpolation is off and rotateStressOnAgrid is false by default.
475    o model/src:
476      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
477        it's also used with pkg/atm_phys) and add few more parameters (but still
478        inactive, src code yet to come)
479    
480    checkpoint65t (2016/02/10)
481    o pkg/atm_phys:
482      - from Ruth Geen: add optical depth dependence on CO2 concentration.
483    o model/src:
484      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
485        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
486        Update output of exp. deep_anelastic (changes at truncation level).
487    o tools:
488      - add a hack in "remove_comments_sed" (used only with TAF) for recent
489        version of OpenMPI (shipped with FC.23): comment out the new header
490        file "mpif-sizeof.h" which causes problems to TAF.
491    o pkg/seaice:
492      - change the termination criterion so that maxits (SEAICElinearIterMax)
493        has an effect
494      - unify iteration parameters for implicit solvers (JFNK and Picard)
495        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
496        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
497        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
498        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
499        SEAICEnonLinTol     replaces JFNKgamma_nonlin
500      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
501      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
502        use with SEAICEuseKrylov
503    o pkg/seaice/seaice_lsr.F
504        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
505        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
506        an effect.
507    o pkg/seaice: add two new parameters
508      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
509        parameter is not in any namelist)
510      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
511        a preconditioner for the non-linear Newton iteration of the JFNK
512        solver
513    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
514      affects some experiments at truncation level:
515      - global_ocean.cs32x15.icedyn (11 digits),
516      - global_ocean.cs32x15.seaice (11 digits),
517      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
518      - also update global_ocean.cs32x15 adjoint and tangent-linear results
519    o pkg/salt_plume & pkg/thsice:
520      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
521        connect salt_plume flux to ATM-OCN coupling pkgs interface:
522       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
523         export to coupler interface) even without compiling pkg/salt_plume ;
524       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
525         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
526    o pkg/dic:
527      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
528        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
529        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
530      - move also update with values from ATM-OCN Coupler in the same new S/R
531        (previously done in ocn_apply_import.F).
532    o tools/adjoint_options:
533      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
534        has been changed on Jan 14, 2016.
535    o pkg/ggl90:
536      - add alternative discretisation of vertical shear (off by default), to
537        compute the mean (@ grid-cell center) of vertical shear compon instead of
538        vertical shear of mean flow (@ grid-cell center).
539      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
540        results on adjacent faces of cubed-sphere grids; this fix the restart.
541    o pkg/atm_compon_interf:
542      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
543        pass last value, stored directly before export to CPL ;
544        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
545      - remove atmSLPr from pickup files (no longer needed for restart)
546    
547    checkpoint65s (2016/01/13)
548    o eesupp & genmake2:
549       - first check for Function ETIME and, if it fails, then check for subroutine
550         ETIME and consistent output; use the appropriate version in timers.F
551    o model/src:
552      - to check restart test, add option to apply EXCH to U,V earlier, just before
553        integr_continuity; turned off by default.
554    o pkg/dic:
555      - remove CPP option USE_ATMOSCO2 (not needed)
556    o tools/tst_2+2:
557      - try to ignore difference between +0 and -0 in binary file, causing test
558        to fail for no good reason.
559    o eesupp & genmake2:
560      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
561        but also check (in genmake2) that test runs and returns meaningful results.
562    o coupler pkgs:
563      Finish implementation of optionally-exchanged variable switches (started on
564       Nov 12) with addition of few more exchanged fields, including 2-way exchange
565       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
566       advection in OCN component; this requires sequential coupling.
567      coupler (pkg/atm_ocn_coupler):
568      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
569        routines (useful for debug).
570      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
571         flux, DIC fields) if corresponding switch is ON.
572      - add option to export RunOff to OCN (to use for DIC river input)
573      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
574      components (pkg/atm_ & ocn_compon_interf):
575      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
576        optionally exchanged fields; add a check & stop in cpl_readparms.F.
577        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
578        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
579      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
580        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
581      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
582      - hold in common block coupler optionally-exchanged variable switch
583        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
584      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
585        this is intended to replace the OCN cplFldtave.* output files (not updated
586        to contain new additional exchanged fields).
587    o pkg/dic:
588      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
589    o pkg/thsice:
590      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
591        and writing of thsice pickup files.
592    o pkg/atm_compon_interf:
593      - move all field individual export-call out of cpl_export_import_data.F
594        into new S/R ATM_EXPORT_FIELDS
595    o pkg/atm_compon_interf:
596      - store state variables (for now, only thSIce fields) just before beeing
597        exported (in cpl_export_import_data.F, like on ocean side) instead of from
598        atm_store_my_data.F like all exported fluxes.
599      - new version of pickup_cpl: write field names into meta file and read meta
600        file to find field postion in pickup. Also only write/read fields meeded for
601        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
602    o pkg/dic:
603      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
604    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
605        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
606        value can be from domain [0,1] to average between the two methods
607    o pkg/atm_phys:
608      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
609        hold fixed in time).
610    
611    checkpoint65r (2015/12/21)
612    o pkg/seaice:
613        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
614        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
615    o pkg/seaice:
616      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
617        when SEAICEscaleSurfStress=.TRUE.,
618      - apply areaW and areaS in S/R seaice_calc_lhs
619    o pkg/atm_phys:
620      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
621        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
622        for individual contribution (convection, LSC cond, radiation)
623      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
624        information); activated with: solar_exponent=0. and wv_exponent=-1.
625    o pkg/ggl90:
626      - within IDEMIX add upper limit for horizontal group velocity to
627        avoid instability problems in the explicit horizontal diffusion term for
628        long time steps or high resolution
629    o pkg/diagnostics:
630      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
631        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
632    o testreport:
633      - remove "-v" (verbose option) in default mpirun command.
634    o pkg/seaice/seaice_growth:
635      - catch potential division by zero in ITD code, does not change
636        verification results
637    o pkg/ecco:
638      - retire old codes to the Attic. The calls to retired functions are
639        left in a commented form in case they ever need to be re-activated.
640      - ecco_check.F: issue warning if any old CPP option is
641        defined that corresponds to retired codes -- then stop.
642    o pkg/atm_compon_interf:
643      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
644        coupler: use last time-step value instead of average over cplSendFrq_iter
645        time-step, similar to what is done for seaIceMass.
646        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
647    o eesupp & genmake2:
648      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
649        <= remove until a fix is found for some ifort version on ia32 machine.
650    o pkg/seaice/seaice_evp:
651      - refine residual computation
652    
653    checkpoint65q (2015/11/18)
654    o pkg/seaice/seaice_evp:
655      - fix residual computations so that they no longer affect the actual
656        simulation code
657      - fix seaice_readparams to be able to actually set new parameters
658        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
659    o model/src:
660      - fix wrong truncation (single prec) from "FLOAT" function in expressions
661        like: deltaT*FLOAT(myIter) when myIter is large:
662         a) replaced by DFLOAT (if not seen by TAF);
663         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
664    o pkg/aim_v23:
665      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
666        when pickupSuff is set ; do write rolling pickups + at the end of the run.
667    o pkg/atm_ocn_coupler + ocn_compon_interf:
668      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
669        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
670        add corresponding call in DO_OCEANIC_PHYS.
671    o coupler pkgs:
672      Start a new way to set-up optionally-exchanged variables (previously, only
673       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
674       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
675       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
676       compononent param default can be set accordingly).
677      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
678       but rather applies to a group a fields (going both ways like for DIC)
679       and corresponds to an option of coupling config.
680      coupler (pkg/atm_ocn_coupler):
681      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
682        and read namelist directly (without eessup S/R calls) instead of
683        in the very un-flexible old way, 1 param per line, in fixed order;
684      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
685        cleanly in CPL_CHECK_CPLCONFIG
686      - add new coupling-exchange selectors (some not yet active) including
687        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
688                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
689      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
690        component ; called directly from coupler.F, after comp. registrations;
691      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
692         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
693          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
694      components (pkg/atm_ & ocn_compon_interf):
695      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
696        CPP header file in all pkg source files.
697      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
698        ATM/OCN_CHECK_CPLCONFIG;
699      - add error-counter to track errors (e.g., in "data.cpl") and to stop
700        cleanly in ATM/OCN_CHECK_CPLCONFIG;
701      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
702        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
703        before PACKAGES_READPARMS;
704      verification/cpl_aim+ocn/:
705      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
706        "data.cpl" for coupler (in input_cpl).
707    o eesupp/inc:
708      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
709        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
710        to always cumulate tile local-sum in the same order (still uses
711        MPI_Allreduce like standard code).
712      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
713        that are now identical to standard version (in eesupp/inc).
714    o pkg/shelfice:
715      - add SHELFICETransCoeffTFile for initializing spatially varying
716        heat and salt transfer coefficients
717    o pkg/atm_compon_interf & ocn_compon_interf:
718      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
719        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
720      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
721    o pkg/atm_ocn_coupler:
722      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
723    o pkg/rbcs:
724      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
725        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
726      - add a short report (to STDOUT) about RBCS-mask settings.
727    
728    checkpoint65p (2015/10/23)
729    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
730        there is no adjoint test for EVP, we don't know what it does to the adjoint
731        solution, but at least there are no more recomputation warnings left
732    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
733        a chance of giving the same results as a fully converged VP (JFNK) solver
734    o tools/adjoint_options/adjoint_diva:
735      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
736    o pkg/streamice:
737      - spotted bug in streamice_driving_stress using dyG where should have been dxG
738    o pkg/exf:
739      - remove STOP statement that prevented to use wind or (wind-)stress
740        interpolation for constant-in-time forcing fields (wind/stress period = 0).
741    o pkg/seaice:
742      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
743        5 additionals 2D fields and 6 new store directives
744      - change logic in seaice_readparms.F: EVP code can now be turned on in
745        various ways, setting SEAICE_deltaTev is no longer required,
746        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
747        or SEAICEaEVPcoeff
748    o pkg/shelfice/shelfice_thermodynamics.F
749      - redefining uLoc/vLoc to u/v, instead of 2u/v
750  o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz  o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
751    - this is an intermediate state of a truely converging EVP that has    - this is an intermediate state of a truely converging EVP that has
752      the potential of outperforming implicit VP methods, I do not recommend      the potential of outperforming implicit VP methods, I do not recommend
# Line 400  o model/src & mom pkgs: Line 1143  o model/src & mom pkgs:
1143      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1144  o doc:  o doc:
1145    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1146  o pkg/streamice:  o pkg/shelfice:
1147    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1148      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1149      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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