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revision 1.2179 by mlosch, Thu Sep 10 15:58:25 2015 UTC revision 1.2355 by dimitri, Tue Sep 26 15:52:52 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 eesupp:
8      - shift standardMessageUnit in eeboot.F and I/O units in mdsfindunit.F
9        for coupling to GEOS AGCM: HACK_FOR_GMAO_CPL option in CPP_EEOPTIONS.h
10    
11    checkpoint66k (2017/09/20)
12    o model/src:
13      - add missing CPP brackets (ALLOW_COST, ALLOW_CTRL in load_fields_driver.F
14        and the_model_main.F)
15    o ctrl:
16      - use zeroRL in place of fc when ALLOW_COST is not compiled (in ctrl_pack.F)
17      - call MDS_READ_FIELD / MDS_WRITE_FIELD instead of deprecated
18        mdsreadfield / mdswritefield (in ctrl_get_gen.F, ctrl_map_ini_gen.F,
19        ctrl_map_ini_genarr.F, and ctrl_map_ini_gentim2d.F )
20    o eesupp:
21      - add CPP option to activate some pieces of code for coupling to GEOS AGCM;
22      - shift commonly used IO unit (in eeboot.F) for coupling to GEOS AGCM.
23    o pkg/bling:
24      - bling_production: Fix typo in calcium carbonate uptake. Also rearranging
25        and cleaning
26    o model/src:
27      - move k loop inside correction_step.F (+ update calling S/R)
28      - collect implicit pressure gradient tendencies in local 2-D array;
29        affect results (at machine truncation level) when using 3-D solver; update
30        output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
31                        rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
32                        & tutorial_plume_on_slope.
33    
34    checkpoint66j (2017/08/15)
35    o pkg/ptracers:
36      - fix surface forcing under ice-shelf (useShelfIce=T).
37    o pkg/atm_phys:
38      - use hFac weighted average when applying A-grid atm-phys momentum tendency
39        to C-grid dynamics; this ensures wind-stress match mom tendency.
40    o eesupp/src:
41      - change default for opening scratch files to avoid STATUS='SCRATCH'
42      - close scratch files with STATUS='DELETE'
43      - changes affect eeset_parms.F and open_copy_data_file.F and many routines
44        that read namelists (because they close the scratch files)
45      - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
46        in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
47    o pkg/atm_phys:
48      - fix unset arguments in (unused) S/R surface_flux_0d.
49    o eesupp/src:
50      - add argument "procId" to S/R EESET_PARMS to fix  scratchFile1 & 2 setting
51        (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
52        called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
53    o pkg/streamice:
54      - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
55        preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
56        streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
57    o pkg/diagnostics:
58      - new option to allow to cumulate thickness-factor (hFac) weighted field
59        (if field permitted); implemented by changing sign of "jdiag" pointer
60        (> 0: cumlulate field, < 0: cumulate hFac weighted field).
61        a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
62           center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
63        b) for now, activated by setting fileFlags 3rd character to 'h'.
64    
65    checkpoint66i (2017/07/18)
66    o pkg/cheapaml:
67      - add parameter "useRelativeWind", default set to False; this change the
68        previous setting which was always using relative wind.
69    o add hooks for the Parallel Data Assimilation Framework PDAF
70        (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
71        to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
72    o pkg/exf:
73      - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
74        of South-Pole mean value.  
75      - interpolation near the poles, case where second additional row is at the
76        pole (or beyond the pole and moved to the pole): change first addition row
77        value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
78        row (instead of just a copy of it).
79    o pkg/seaice:
80      - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
81      - add the option to compute no-slip du/dy, dv/dx (i.e.
82        the offdiagonal strain rate e12) by a second order approximation
83        on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
84        it is too messy to implement for the implicit LSR matrix.
85        SEAICE_2ndOrderBC = .FALSE. by default
86    
87    checkpoint66h (2017/06/02)
88    o pkg/seaice:
89      - add new routines to compute stress tensor components and stress tensor
90        divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
91      - change names of diagnostics SIsigI/II (commonly used for invariants)
92        to SIsig1/sig2 (more common for principal components) to avoid confusion
93    o pkf/exf:
94      - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
95        similarly, stop if rotateStressOnAgrid with constant wind-stress.
96    o pkg/seaice:
97      - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
98        EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
99      - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
100        fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
101    o pkg/diagnostics:
102      - small piece of code to rename (old) diagnostics, when namelist is processed.
103    o model/src:
104      - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
105        originally, set as minimum of adjacent hFacC factor ; now (new default)
106        computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
107        Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
108    o pkg/seaice:
109      - add momemtum advection, off by default, still in test phase
110        most of the momentum advection code is adapted and reused from mom_vecinv
111    o pkg/mom_vecinv:
112      - pass these runtime flags:
113        selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
114        as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
115        so that these routines can also be used in pkg/seaice.
116    
117    checkpoint66g (2017/04/24)
118    o model/src:
119      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
120        to get same expression (regarding machine truncation) in different places
121        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
122        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
123        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
124    o pkg/shelfice:
125      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
126        to shelfice_init_fixed.F
127      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
128        ini_masks_etc.F for now) to update ocean upper boundary position according
129        to ice-shelf topography (instead of directly updating hFacC).
130    o model/src:
131      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
132        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
133    
134    checkpoint66f (2017/04/06)
135    o model/src:
136      - add specific run-time param to select level of printed plot-field-maps,
137        set by default to debugLevel. Remove internal param "printDomain".
138    o pkg/seaice:
139      - add flag to add snow mass to seaiceMassC/U/V, the default is
140        SEAICEaddSnowMass=.FALSE., not to change previous results
141    o pkg/bling
142      - Bug fix in bling_production regarding unit conversion for diagnostics
143        being put in the wrong place
144    o model/src:
145      - add back recomputation of rSurfW & S to ensure consistent column thickness
146        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
147        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
148        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
149    o pkg/autodiff:
150      - clean-up "checkpoint.flow"
151    o pkg/rw (Contribution from Jody Klymak):
152        option to set mds file suffix as function of time in simulation:
153        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
154           to select file suffix format; by default (=0), use iteration number;
155        *) add simple routine to return file suffix according to rwSuffixType;
156        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
157           use new S/R to get file suffix, except for debug output file (diagFreq)
158           and pkgs offline & rbcs input files.
159    o pkg/rw:
160      - uniform processing of "I10" suffix across writing fld routines; used to
161        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
162        (similar to cg3d.F, cg3d_ex0.F)
163    o pkg/mom_vecinv:
164      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
165        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
166    o pkg/bling:
167      - Many small changes intended to clean the code.
168        Unnecessary ADJOINT_SAFEs removed ;
169        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
170        diagnostics added.
171    
172    checkpoint66e (2017/03/14)
173    o pkg/exf:
174      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
175        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
176        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
177        avoid any dynamic allocation ;
178      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
179        read-in ; add warning when file is read-in but not used within pkg/exf ;
180        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
181      - update exf_summary.F (print {FLD}RepCycle).
182    o verification/global_with_exf:
183      - switch on exf interpolation in AD test (just like the forward test)
184    o pkg/mom_vecinv:
185      - add storage directives to avoid recomputations within mom_vecinv.F
186        which were generating seg. fault with gfortran -devel
187    o pkg/ctrl, pkg/smooth:
188      - initialize array halos which were generating seg. fault with
189        gfortran -devel in adjoint mode
190    o pkg/exf:
191      - for each input field, enable to specify a field specific repeat-cycle
192        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
193    o verification/lab_sea:
194      - update AD results of primary test and noseaicedyn test after switching
195        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
196        check stays about the same.
197    o pkg/exf:
198      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
199      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
200    o pkg/bling, USE_EXFCO2 code:
201      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
202      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
203    o pkg/exf:
204      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
205      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
206        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
207        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
208      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
209        EXF_INIT_FLD) and update calls in exf_init_varia.F
210      - For now, for backward compatibility, keep a simplified version of S/Rs
211        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
212      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
213        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
214    o tools/genmake2:
215      - replace "bc -l" (only used once) by "expr" (already used).
216    o verification/global_ocean.cs32x15:
217      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
218        Note: exf setting (data.exf) can be compared to other exf secondary exp
219        "seaice" (kept with useCAL=T) which has same time dependent forcing.
220    
221    checkpoint66d (2017/02/13)
222    o pkg/exf:
223      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
224        early on (in packages_boot.F) to stress this change in pkg setting.
225      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
226    o model/src:
227      - move call to ecco_phys to end of time step; this may induce minor
228        cost function changes by shifting time averages by one time step
229        for some variables; this revision resulted in changed adjoint results
230        in MITgcm_contrib/verification_other/global_oce_cs32
231    o pkg/exf:
232      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
233        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
234        e.g. precip, are not available.
235    o pkg/flt:
236      - flt_init_varia.F: use pickupSuff if specified
237      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
238        intermediate, step towards completing pkg/exch2 support within pkg/flt;
239        ifdef DEVEL_FLT_EXCH2 then:
240        - flt_init_fixed.F: comment out stop
241        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
242        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
243        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
244        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
245    o tools/genmake2 & pkg/pkg_depend:
246      - define new type of pkg dependency rule ("=pkg_x"), less strict than
247        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
248        (-pkg_x in packages.conf).
249      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
250      - add "+cal" to dependency list of pkg/ecco (needed to compile).
251      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
252    o utils/matlab:
253      - adding ocean_basin routines for defining basin masks.
254    o pkg/exf:
255      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
256        arguments, allowing to check (and stop) if parameter setting of
257         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
258        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
259        for backward compatibility.
260      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
261        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
262    o pkg/bling (USE_EXFCO2 code):
263      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
264        by adding a call to S/R EXF_GETFFIELD_START.
265    o pkg/exf:
266      - allows to compile without pkg/cal (but disabled by current dependency
267        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
268        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
269        of {FLD}startdate1 & date2 ; consistency check not yet coded.
270    o verification/global_ocean.cs32x15:
271      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
272        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
273    o pkg/exf:
274      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
275        calculations); change FWD experiment global_ocean.cs32x15
276        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
277    o pkg/exf:
278      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
279         {FIELD}startdate to {FIELD}StartTime
280        Note: new name also fit better the content, i.e, a start time in second.
281    o eesupp/src:
282      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
283    o pkg/exf:
284      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
285        to allow to read-in Sensible & Latent Heat flux ;
286      - simplify pkg/exf main options:
287        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
288           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
289           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
290        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
291           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
292        3) improve options documentation in EXF_OPTIONS.h.
293    o pkg/ecco:
294      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
295        ecco_summary.F: add passive tracer cost functions to gencost;
296        m_ptracer and m_boxmean_ptracer
297    o pkg/ctrl:
298      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
299        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
300        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
301        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
302    o model/src:
303      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
304        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
305    o pkg/exf:
306      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
307        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
308    
309    checkpoint66c (2017/01/19)
310    o verification:
311      - add new option "-src" to testreport to only produce source code (*.f),
312        including taf output src code (if using '-adm'/'-tlm' option).
313    o pkg/exf:
314      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
315    o pkg/diagnostics:
316      - add run-time variable diagMdsDir to specify a subdirectory for
317        diagnostic output when mds is being used and mdsioLocalDir is not.
318    o pkg/mnc:
319      - mnc_utils.F: edit stop message
320    o pkg/autodiff:
321      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
322        add HAVE_SYSTEM bracket around system call to mkdir
323    o pkg/profiles:
324      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
325        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
326      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
327        add HAVE_SYSTEM bracket around system call to mkdir
328    o pkg/smooth:
329      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
330      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
331      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
332    o pkg/exf:
333      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
334        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
335        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
336      - summary: skip detailed field report if not used (empty file-name).
337    o tools/xmakedepend:
338      - In case line editor "ed" is missing, switch to "sed" command to clean-up
339        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
340    o pkg/exf:
341      - change definition of "hflux" input file to always include Short-Wave;
342        this is now consistent with hflux computation (if using bulk-formulae)
343        and hflux diagnostic & documentation (in EXF_FIELDS.h).
344    
345    checkpoint66b (2016/12/01)
346    o model & momentum pkgs:
347      - implement fully implicit bottom friction combined with implicit surf.
348        pressure, for now, only in hydrostic formulation:
349        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
350          and run with selectImplicitDrag=2 ;
351        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
352      - partial implicit time-stepping (bot. friction + vert. visc first, then
353        surf. press) corresponding to selectImplicitDrag=1 should be applicable
354        to NH formulation but not available until we solve for surf. pressure
355        increment (instead of full etaN).
356      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
357        with implicit vertical viscosity.
358    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
359      - this is a first version that includes many regularisations that may
360        not all be necessary, to be sorted out,
361      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
362      - change one verification experiment in seaice_itd to use and test new code
363      - seaice_growth: catch a case where the argument of log can be zero
364        or smaller (important for code stability)
365    o model/src:
366      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
367        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
368        similar A.X'=Y' system (with same matrix A) in subsequent calls;
369        switch based on errCode (In/Out) argument value; in calling routines,
370        initialise errCode before first call.
371    
372    checkpoint66a (2016/10/18)
373    o pkg/bling:
374      - BLING package now loads in atmospheric pCO2 file using exf package routines
375        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
376    o model/src & pkg/ptracers:
377      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
378        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
379        implicitDiffusion (respectively) are used (even without momImplVertAdv
380        or temp,salt,PTRACERS_ImplVertAdv).
381    o model/src & generic_advdiff:
382      - add parenthesis in main diagonal calculation of implicit vertical
383        diffusion matrix (impldiff.F & gad_implicit_r.F).
384        This affects results at machine truncation level; update output of many
385        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
386    o pkg/mom_commom & generic_advdiff:
387      - add deep atmosphere and anelastic scaling factor in implicit vertical
388        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
389    o model/src:
390      - remove few unnecessary temp array copies in solve_tridiagonal.F
391        & solve_pentadiagonal.F
392    
393    checkpoint65z (2016/09/28)
394    o pkg/seaice: fix multithreading for seaice_fgmres.F
395      - remove unecessary variables from common blocks
396      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
397        basis, that are stored in commom blocks (including integer variable i1)
398      - clean up code a little by removing commented lines that refer to
399        original code
400      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
401    o MITgcm manual:
402      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
403        preliminary documentation for generic controls (8.3; ctrl.tex),
404        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
405        ecco_costfunction.tex
406    o pkg/ecco:
407      - update and cleanup list of CCP options
408      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
409        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
410      - add checks that retired run-time options are not used, and in relation
411        to gencost_mask and gencost_errfile
412      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
413        gencost_nrecperiod
414      - fix m_eta computation for virtual salt flux case
415      - add m_horflux_vol case (selected via gencost_barfile) that computes
416        transports via cost_gencost_boxmean (gencost_flag=-3)
417      - use gencost_flag more systematically (i.e., avoid using gencost_name)
418        for code switches (aside from physical variable selection)
419    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
420      attempt appears to be a bit of a hack and my need some repair down the road
421    o pkg/exf:
422      - interpolation near South Pole: fix criteria on input field latitude.
423    o pkg/icefront & pkg/exf:
424      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
425        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
426    o pkg/exf:
427      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
428        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
429        (add suffix "_out" instead of a prefix); keep same record number as in
430        input file but always write record 1 first (to avoid a STOP in I/O S/R).
431        Change output file content by writing interpolated field before applying
432        land-sea mask (helpful for debug).
433      - 2 compon. vector interpolation with rotation: apply scaling factor on
434        each compon. (Eastward and Northward) just before rotation.
435    o pkg/bling:
436      - Cleaned package. Removed not needed code and comments.
437      - adjoint example now works
438        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
439    o pkg/ptracers:
440      - add Bruno Deremble's code to complete the linear surface correction
441        for tracer conservation;
442      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
443    
444    checkpoint65y (2016/07/29)
445    o pkg/debug (stats):
446      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
447        proc/thread mapping);
448      - fix Min & Max for case where 1 thread has only empty tiles;
449      - use RL variable to count number of wet grid points (with big domain,
450        can be too large to fit into integer*4).
451    o pkg/monitor:
452      - use RL variable to count number of wet grid points (but used only for del2)
453      - add new routine to compute Advective CFL within tracer time-stepping with
454        writing delayed until next monitor output.
455    o pkg/obcs:
456      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
457    o pkg/cal:
458      - calandar-dump: treat case myTime < timePhase in the same way as in
459        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
460    o pkg/dic & seaice:
461      - fix compilation of ocean component for coupled atm+ocn model with
462        seaice dynamics & dic.
463    
464    checkpoint65x (2016/06/11)
465    o add a license text file in main MITgcm tree.
466    o added pkg/bling:
467      - intermediate complexity biogeochemical model
468      - see bling_description.txt for details
469      - verification experiment is global_oce_biogeo_bling (for now, in
470        Contrib/verification_other/); tested daily on baudelaire with gfortran.
471      - add entry point in pkg/gchem for new pkg "bling".
472    o pkg/seaice: fix tensile stength computation
473      - replace global field tensileStrength by tensileStrFac
474      - tensileStrFac can be computed once in S/R seaice_init_varia
475      - fortunately that does not affect any verification results
476    
477    checkpoint65w (2016/05/12)
478    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
479         with ECCO_CTRL_DEPRECATED defined
480    o verification/global_ocean.cs32x15:
481      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
482        with "selectNHfreeSurf=1".
483    o model/src (non-hydrostatic free-surface):
484      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
485        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
486      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
487        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
488        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
489        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
490      - Update output (changes at machine truncation level) of verification exp:
491        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
492        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
493    o pkg/seaice: ITD code
494      - fix picking up from a single category model by initialising
495        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
496      - split a long warning message in seaice_check_pickup.F into two lines,
497        because NEC SX-ACE cannot deal with the long line.
498    o model/src:
499      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
500    o pkg/seaice:
501      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
502    o pkg/seaice:
503      - add basal stress as parameterisation for grounding ice
504        following Lemieux et al. (2015)
505      - turn on by setting new parameter SEAICEbasalDragK2 to a value
506        larger than 0. Lemieux et al. (2015) recommend 15.
507      - The adjoint complains with extra recomputations so there is also a
508        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
509        order to postpone the problem
510      - compile the new code in lab_sea
511    o verification/halfpipe_streamice:
512      - update both TAF and OpenAD adm output (machine truncation differences)
513    
514    checkpoint65v (2016/04/08)
515    o verification/advect_xz:
516      - increase overlap size from 3 to 4 and add new secondary test for PQM
517        advection scheme (with mono & wino limiter).
518      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
519    o model/src:
520      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
521        added phi0Ref) to set vertical axis origin and phiRef origin;
522        keep Ro_SeaLevel for backward compatibility (with a warning).
523       According to coordinate and fluid type:
524        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
525        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
526        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
527        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
528      - remove Ro_SeaLevel from ATM experiment parameter files;
529      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
530        complement; update output.txt (changes at machine truncation level).
531    o pkg/seaice/seaice_evp.F
532      - simplify computation of deltaZ and zetaZ to simple averaging following
533        Bouillon et al. (2013). This removes a lot of code, but also changes
534        verification experiment lab_sea.hb87 -> updated
535    
536    checkpoint65u (2016/03/14)
537    o pkg/generic_advdiff:
538      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
539        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
540        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
541        testing and not for actual use.
542    o model/src:
543      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
544        origin r = rF(1);
545      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
546        in EOS for height coordinate: enable to include NH Pressure or to use
547        more accurate pressure vertical profile; options not linked to EOS type
548        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
549      - start to implement variable gravity (along vertical): for now, only with
550        z-coords (not even z*).
551      - add Ideal Gas equation of state for height coordinate.
552      - update OpenAD output (affected at machine truncation level) of exp:
553        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
554    o pkg/exf:
555      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
556        of exf interpolation (before any rescaling, rotation or interpolation
557        to velocity point) for each field that gets loaded from file. This option
558        identically mimics the input file organization (e.g. record numbers in year
559        by year input files) besides the change in horizontal grid.
560      - add rotateStressOnAgrid run-time switch so that wind stress fields
561        can be provided on the A-grid in zonal/meridional direction and
562        rotated on the fly. This only applies to the case when the exf
563        interpolation is off and rotateStressOnAgrid is false by default.
564    o model/src:
565      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
566        it's also used with pkg/atm_phys) and add few more parameters (but still
567        inactive, src code yet to come)
568    
569    checkpoint65t (2016/02/10)
570    o pkg/atm_phys:
571      - from Ruth Geen: add optical depth dependence on CO2 concentration.
572    o model/src:
573      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
574        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
575        Update output of exp. deep_anelastic (changes at truncation level).
576    o tools:
577      - add a hack in "remove_comments_sed" (used only with TAF) for recent
578        version of OpenMPI (shipped with FC.23): comment out the new header
579        file "mpif-sizeof.h" which causes problems to TAF.
580    o pkg/seaice:
581      - change the termination criterion so that maxits (SEAICElinearIterMax)
582        has an effect
583      - unify iteration parameters for implicit solvers (JFNK and Picard)
584        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
585        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
586        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
587        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
588        SEAICEnonLinTol     replaces JFNKgamma_nonlin
589      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
590      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
591        use with SEAICEuseKrylov
592    o pkg/seaice/seaice_lsr.F
593        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
594        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
595        an effect.
596    o pkg/seaice: add two new parameters
597      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
598        parameter is not in any namelist)
599      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
600        a preconditioner for the non-linear Newton iteration of the JFNK
601        solver
602    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
603      affects some experiments at truncation level:
604      - global_ocean.cs32x15.icedyn (11 digits),
605      - global_ocean.cs32x15.seaice (11 digits),
606      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
607      - also update global_ocean.cs32x15 adjoint and tangent-linear results
608    o pkg/salt_plume & pkg/thsice:
609      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
610        connect salt_plume flux to ATM-OCN coupling pkgs interface:
611       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
612         export to coupler interface) even without compiling pkg/salt_plume ;
613       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
614         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
615    o pkg/dic:
616      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
617        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
618        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
619      - move also update with values from ATM-OCN Coupler in the same new S/R
620        (previously done in ocn_apply_import.F).
621    o tools/adjoint_options:
622      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
623        has been changed on Jan 14, 2016.
624    o pkg/ggl90:
625      - add alternative discretisation of vertical shear (off by default), to
626        compute the mean (@ grid-cell center) of vertical shear compon instead of
627        vertical shear of mean flow (@ grid-cell center).
628      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
629        results on adjacent faces of cubed-sphere grids; this fix the restart.
630    o pkg/atm_compon_interf:
631      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
632        pass last value, stored directly before export to CPL ;
633        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
634      - remove atmSLPr from pickup files (no longer needed for restart)
635    
636    checkpoint65s (2016/01/13)
637    o eesupp & genmake2:
638       - first check for Function ETIME and, if it fails, then check for subroutine
639         ETIME and consistent output; use the appropriate version in timers.F
640    o model/src:
641      - to check restart test, add option to apply EXCH to U,V earlier, just before
642        integr_continuity; turned off by default.
643    o pkg/dic:
644      - remove CPP option USE_ATMOSCO2 (not needed)
645    o tools/tst_2+2:
646      - try to ignore difference between +0 and -0 in binary file, causing test
647        to fail for no good reason.
648    o eesupp & genmake2:
649      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
650        but also check (in genmake2) that test runs and returns meaningful results.
651    o coupler pkgs:
652      Finish implementation of optionally-exchanged variable switches (started on
653       Nov 12) with addition of few more exchanged fields, including 2-way exchange
654       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
655       advection in OCN component; this requires sequential coupling.
656      coupler (pkg/atm_ocn_coupler):
657      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
658        routines (useful for debug).
659      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
660         flux, DIC fields) if corresponding switch is ON.
661      - add option to export RunOff to OCN (to use for DIC river input)
662      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
663      components (pkg/atm_ & ocn_compon_interf):
664      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
665        optionally exchanged fields; add a check & stop in cpl_readparms.F.
666        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
667        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
668      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
669        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
670      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
671      - hold in common block coupler optionally-exchanged variable switch
672        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
673      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
674        this is intended to replace the OCN cplFldtave.* output files (not updated
675        to contain new additional exchanged fields).
676    o pkg/dic:
677      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
678    o pkg/thsice:
679      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
680        and writing of thsice pickup files.
681    o pkg/atm_compon_interf:
682      - move all field individual export-call out of cpl_export_import_data.F
683        into new S/R ATM_EXPORT_FIELDS
684    o pkg/atm_compon_interf:
685      - store state variables (for now, only thSIce fields) just before beeing
686        exported (in cpl_export_import_data.F, like on ocean side) instead of from
687        atm_store_my_data.F like all exported fluxes.
688      - new version of pickup_cpl: write field names into meta file and read meta
689        file to find field postion in pickup. Also only write/read fields meeded for
690        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
691    o pkg/dic:
692      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
693    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
694        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
695        value can be from domain [0,1] to average between the two methods
696    o pkg/atm_phys:
697      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
698        hold fixed in time).
699    
700    checkpoint65r (2015/12/21)
701    o pkg/seaice:
702        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
703        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
704    o pkg/seaice:
705      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
706        when SEAICEscaleSurfStress=.TRUE.,
707      - apply areaW and areaS in S/R seaice_calc_lhs
708    o pkg/atm_phys:
709      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
710        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
711        for individual contribution (convection, LSC cond, radiation)
712      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
713        information); activated with: solar_exponent=0. and wv_exponent=-1.
714    o pkg/ggl90:
715      - within IDEMIX add upper limit for horizontal group velocity to
716        avoid instability problems in the explicit horizontal diffusion term for
717        long time steps or high resolution
718    o pkg/diagnostics:
719      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
720        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
721    o testreport:
722      - remove "-v" (verbose option) in default mpirun command.
723    o pkg/seaice/seaice_growth:
724      - catch potential division by zero in ITD code, does not change
725        verification results
726    o pkg/ecco:
727      - retire old codes to the Attic. The calls to retired functions are
728        left in a commented form in case they ever need to be re-activated.
729      - ecco_check.F: issue warning if any old CPP option is
730        defined that corresponds to retired codes -- then stop.
731    o pkg/atm_compon_interf:
732      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
733        coupler: use last time-step value instead of average over cplSendFrq_iter
734        time-step, similar to what is done for seaIceMass.
735        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
736    o eesupp & genmake2:
737      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
738        <= remove until a fix is found for some ifort version on ia32 machine.
739    o pkg/seaice/seaice_evp:
740      - refine residual computation
741    
742    checkpoint65q (2015/11/18)
743    o pkg/seaice/seaice_evp:
744      - fix residual computations so that they no longer affect the actual
745        simulation code
746      - fix seaice_readparams to be able to actually set new parameters
747        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
748    o model/src:
749      - fix wrong truncation (single prec) from "FLOAT" function in expressions
750        like: deltaT*FLOAT(myIter) when myIter is large:
751         a) replaced by DFLOAT (if not seen by TAF);
752         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
753    o pkg/aim_v23:
754      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
755        when pickupSuff is set ; do write rolling pickups + at the end of the run.
756    o pkg/atm_ocn_coupler + ocn_compon_interf:
757      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
758        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
759        add corresponding call in DO_OCEANIC_PHYS.
760    o coupler pkgs:
761      Start a new way to set-up optionally-exchanged variables (previously, only
762       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
763       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
764       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
765       compononent param default can be set accordingly).
766      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
767       but rather applies to a group a fields (going both ways like for DIC)
768       and corresponds to an option of coupling config.
769      coupler (pkg/atm_ocn_coupler):
770      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
771        and read namelist directly (without eessup S/R calls) instead of
772        in the very un-flexible old way, 1 param per line, in fixed order;
773      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
774        cleanly in CPL_CHECK_CPLCONFIG
775      - add new coupling-exchange selectors (some not yet active) including
776        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
777                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
778      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
779        component ; called directly from coupler.F, after comp. registrations;
780      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
781         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
782          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
783      components (pkg/atm_ & ocn_compon_interf):
784      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
785        CPP header file in all pkg source files.
786      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
787        ATM/OCN_CHECK_CPLCONFIG;
788      - add error-counter to track errors (e.g., in "data.cpl") and to stop
789        cleanly in ATM/OCN_CHECK_CPLCONFIG;
790      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
791        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
792        before PACKAGES_READPARMS;
793      verification/cpl_aim+ocn/:
794      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
795        "data.cpl" for coupler (in input_cpl).
796    o eesupp/inc:
797      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
798        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
799        to always cumulate tile local-sum in the same order (still uses
800        MPI_Allreduce like standard code).
801      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
802        that are now identical to standard version (in eesupp/inc).
803    o pkg/shelfice:
804      - add SHELFICETransCoeffTFile for initializing spatially varying
805        heat and salt transfer coefficients
806    o pkg/atm_compon_interf & ocn_compon_interf:
807      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
808        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
809      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
810    o pkg/atm_ocn_coupler:
811      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
812    o pkg/rbcs:
813      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
814        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
815      - add a short report (to STDOUT) about RBCS-mask settings.
816    
817    checkpoint65p (2015/10/23)
818    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
819        there is no adjoint test for EVP, we don't know what it does to the adjoint
820        solution, but at least there are no more recomputation warnings left
821    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
822        a chance of giving the same results as a fully converged VP (JFNK) solver
823    o tools/adjoint_options/adjoint_diva:
824      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
825    o pkg/streamice:
826      - spotted bug in streamice_driving_stress using dyG where should have been dxG
827    o pkg/exf:
828      - remove STOP statement that prevented to use wind or (wind-)stress
829        interpolation for constant-in-time forcing fields (wind/stress period = 0).
830    o pkg/seaice:
831      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
832        5 additionals 2D fields and 6 new store directives
833      - change logic in seaice_readparms.F: EVP code can now be turned on in
834        various ways, setting SEAICE_deltaTev is no longer required,
835        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
836        or SEAICEaEVPcoeff
837    o pkg/shelfice/shelfice_thermodynamics.F
838      - redefining uLoc/vLoc to u/v, instead of 2u/v
839    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
840      - this is an intermediate state of a truely converging EVP that has
841        the potential of outperforming implicit VP methods, I do not recommend
842        using it yet.
843      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
844        and all parameters are hardwired
845      - for convergence it still requires very smooth regularisations, that means,
846        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
847        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
848        specific averaging appears to be required, still subject to tuning
849      - still needs cleaning and I need to turn parameter into runtime parameters
850      - add code to compute and print residuals of iteration, compile with
851        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
852    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
853      that entered with r1.54 on Sep04, 2015, -> update results
854    
855    checkpoint65o (2015/09/14)
856    o pkg/mom_vecinv & mom_common:
857      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
858        called from there.
859      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
860        allows to use Vector-Invariant form in deep atmos and anelastic formulation
861  o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)  o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
862    and Koenig-Beatty+Holland (2012)    and Koenig-Beatty+Holland (2012)
863    - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth    - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
# Line 15  o pkg/seaice: introduce new parameter SE Line 869  o pkg/seaice: introduce new parameter SE
869    - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice    - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
870      by AREA according to Connelly et al. (2004), JPO.      by AREA according to Connelly et al. (2004), JPO.
871    - For EVP and the LSR solver, the implicit part of the drag term is    - For EVP and the LSR solver, the implicit part of the drag term is
872      the only non-zero term in the denominator when there is no ice (which      the only non-zero term in the denominator when there is no ice (which
873      prevented running the model with zero ice-ocean drag). If      prevented running the model with zero ice-ocean drag). If
874      SEAICEscaleSurfStress = .TRUE., this results in a division by zero      SEAICEscaleSurfStress = .TRUE., this results in a division by zero
875      (or zero main diagonals BU/BV) which need to be caught. A practical      (or zero main diagonals BU/BV) which need to be caught. A practical
876      consequence is that for open water, the momentum equation reduce      consequence is that for open water, the momentum equation reduce
877      to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if      to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
878      they happen to be zero, often leading to a non-zero solution over      they happen to be zero, often leading to a non-zero solution over
879      open water.      open water.
880  o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more  o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
881      efficient EVP method.      efficient EVP method.
882    - introduce area-weighted averages for e12 (analogously to    - introduce area-weighted averages for e12 (analogously to
883      seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits      seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
884      remain, but also changing the order of terms in the previous average      remain, but also changing the order of terms in the previous average
885      changed the results as much) -> update experiment      changed the results as much) -> update experiment
886    - add SEAICE_DELTA_SMOOTHREG code    - add SEAICE_DELTA_SMOOTHREG code
887    - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for    - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
888      TEM-code      TEM-code
889    - adjust loop bounds so that only required fields are computed    - adjust loop bounds so that only required fields are computed
890    - add new averaging code for zetaZ/deltaZ (again similar to    - add new averaging code for zetaZ/deltaZ (again similar to
891      seaice_calc_viscosities.F), inactive by default for now (will change      seaice_calc_viscosities.F), inactive by default for now (will change
892      results again), but will replace old code eventually      results again), but will replace old code eventually
893  o eesupp/src:  o eesupp/src:
# Line 44  o eesupp/src: Line 898  o eesupp/src:
898      and should be faster than GLOBAL_SUM_SEND_RECV code.      and should be faster than GLOBAL_SUM_SEND_RECV code.
899    - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV    - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
900      (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.      (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
901    - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 13 more exp.:    - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
902       aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,       aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
903       fizhi-cs-aqualev20, global_ocean_ebm, matrix_example, natl_box,       fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
904       solid-body.cs-32x32x1, tutorial_advection_in_gyre, tutorial_baroclinic_gyre       natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
905       and tutorial_held_suarez_cs.       tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
906    
907  checkpoint65n (2015/07/29)  checkpoint65n (2015/07/29)
908  o pkg/thsice:  o pkg/thsice:
# Line 378  o model/src & mom pkgs: Line 1232  o model/src & mom pkgs:
1232      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1233  o doc:  o doc:
1234    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1235  o pkg/streamice:  o pkg/shelfice:
1236    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1237      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1238      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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