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revision 1.2173 by jmc, Sat Jul 18 22:15:07 2015 UTC revision 1.2350 by jmc, Tue Aug 22 03:02:30 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - move k loop inside correction_step.F (+ update calling S/R)
9      - collect implicit pressure gradient tendencies in local 2-D array;
10        affect results (at machine truncation level) when using 3-D solver; update
11        output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
12                        rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
13                        & tutorial_plume_on_slope.
14    
15    checkpoint66j (2017/08/15)
16    o pkg/ptracers:
17      - fix surface forcing under ice-shelf (useShelfIce=T).
18    o pkg/atm_phys:
19      - use hFac weighted average when applying A-grid atm-phys momentum tendency
20        to C-grid dynamics; this ensures wind-stress match mom tendency.
21    o eesupp/src:
22      - change default for opening scratch files to avoid STATUS='SCRATCH'
23      - close scratch files with STATUS='DELETE'
24      - changes affect eeset_parms.F and open_copy_data_file.F and many routines
25        that read namelists (because they close the scratch files)
26      - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
27        in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
28    o pkg/atm_phys:
29      - fix unset arguments in (unused) S/R surface_flux_0d.
30    o eesupp/src:
31      - add argument "procId" to S/R EESET_PARMS to fix  scratchFile1 & 2 setting
32        (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
33        called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
34    o pkg/streamice:
35      - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
36        preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
37        streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
38    o pkg/diagnostics:
39      - new option to allow to cumulate thickness-factor (hFac) weighted field
40        (if field permitted); implemented by changing sign of "jdiag" pointer
41        (> 0: cumlulate field, < 0: cumulate hFac weighted field).
42        a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
43           center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
44        b) for now, activated by setting fileFlags 3rd character to 'h'.
45    
46    checkpoint66i (2017/07/18)
47    o pkg/cheapaml:
48      - add parameter "useRelativeWind", default set to False; this change the
49        previous setting which was always using relative wind.
50    o add hooks for the Parallel Data Assimilation Framework PDAF
51        (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
52        to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
53    o pkg/exf:
54      - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
55        of South-Pole mean value.  
56      - interpolation near the poles, case where second additional row is at the
57        pole (or beyond the pole and moved to the pole): change first addition row
58        value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
59        row (instead of just a copy of it).
60    o pkg/seaice:
61      - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
62      - add the option to compute no-slip du/dy, dv/dx (i.e.
63        the offdiagonal strain rate e12) by a second order approximation
64        on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
65        it is too messy to implement for the implicit LSR matrix.
66        SEAICE_2ndOrderBC = .FALSE. by default
67    
68    checkpoint66h (2017/06/02)
69    o pkg/seaice:
70      - add new routines to compute stress tensor components and stress tensor
71        divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
72      - change names of diagnostics SIsigI/II (commonly used for invariants)
73        to SIsig1/sig2 (more common for principal components) to avoid confusion
74    o pkf/exf:
75      - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
76        similarly, stop if rotateStressOnAgrid with constant wind-stress.
77    o pkg/seaice:
78      - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
79        EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
80      - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
81        fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
82    o pkg/diagnostics:
83      - small piece of code to rename (old) diagnostics, when namelist is processed.
84    o model/src:
85      - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
86        originally, set as minimum of adjacent hFacC factor ; now (new default)
87        computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
88        Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
89    o pkg/seaice:
90      - add momemtum advection, off by default, still in test phase
91        most of the momentum advection code is adapted and reused from mom_vecinv
92    o pkg/mom_vecinv:
93      - pass these runtime flags:
94        selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
95        as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
96        so that these routines can also be used in pkg/seaice.
97    
98    checkpoint66g (2017/04/24)
99    o model/src:
100      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
101        to get same expression (regarding machine truncation) in different places
102        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
103        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
104        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
105    o pkg/shelfice:
106      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
107        to shelfice_init_fixed.F
108      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
109        ini_masks_etc.F for now) to update ocean upper boundary position according
110        to ice-shelf topography (instead of directly updating hFacC).
111    o model/src:
112      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
113        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
114    
115    checkpoint66f (2017/04/06)
116    o model/src:
117      - add specific run-time param to select level of printed plot-field-maps,
118        set by default to debugLevel. Remove internal param "printDomain".
119    o pkg/seaice:
120      - add flag to add snow mass to seaiceMassC/U/V, the default is
121        SEAICEaddSnowMass=.FALSE., not to change previous results
122    o pkg/bling
123      - Bug fix in bling_production regarding unit conversion for diagnostics
124        being put in the wrong place
125    o model/src:
126      - add back recomputation of rSurfW & S to ensure consistent column thickness
127        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
128        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
129        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
130    o pkg/autodiff:
131      - clean-up "checkpoint.flow"
132    o pkg/rw (Contribution from Jody Klymak):
133        option to set mds file suffix as function of time in simulation:
134        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
135           to select file suffix format; by default (=0), use iteration number;
136        *) add simple routine to return file suffix according to rwSuffixType;
137        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
138           use new S/R to get file suffix, except for debug output file (diagFreq)
139           and pkgs offline & rbcs input files.
140    o pkg/rw:
141      - uniform processing of "I10" suffix across writing fld routines; used to
142        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
143        (similar to cg3d.F, cg3d_ex0.F)
144    o pkg/mom_vecinv:
145      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
146        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
147    o pkg/bling:
148      - Many small changes intended to clean the code.
149        Unnecessary ADJOINT_SAFEs removed ;
150        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
151        diagnostics added.
152    
153    checkpoint66e (2017/03/14)
154    o pkg/exf:
155      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
156        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
157        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
158        avoid any dynamic allocation ;
159      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
160        read-in ; add warning when file is read-in but not used within pkg/exf ;
161        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
162      - update exf_summary.F (print {FLD}RepCycle).
163    o verification/global_with_exf:
164      - switch on exf interpolation in AD test (just like the forward test)
165    o pkg/mom_vecinv:
166      - add storage directives to avoid recomputations within mom_vecinv.F
167        which were generating seg. fault with gfortran -devel
168    o pkg/ctrl, pkg/smooth:
169      - initialize array halos which were generating seg. fault with
170        gfortran -devel in adjoint mode
171    o pkg/exf:
172      - for each input field, enable to specify a field specific repeat-cycle
173        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
174    o verification/lab_sea:
175      - update AD results of primary test and noseaicedyn test after switching
176        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
177        check stays about the same.
178    o pkg/exf:
179      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
180      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
181    o pkg/bling, USE_EXFCO2 code:
182      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
183      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
184    o pkg/exf:
185      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
186      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
187        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
188        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
189      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
190        EXF_INIT_FLD) and update calls in exf_init_varia.F
191      - For now, for backward compatibility, keep a simplified version of S/Rs
192        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
193      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
194        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
195    o tools/genmake2:
196      - replace "bc -l" (only used once) by "expr" (already used).
197    o verification/global_ocean.cs32x15:
198      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
199        Note: exf setting (data.exf) can be compared to other exf secondary exp
200        "seaice" (kept with useCAL=T) which has same time dependent forcing.
201    
202    checkpoint66d (2017/02/13)
203    o pkg/exf:
204      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
205        early on (in packages_boot.F) to stress this change in pkg setting.
206      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
207    o model/src:
208      - move call to ecco_phys to end of time step; this may induce minor
209        cost function changes by shifting time averages by one time step
210        for some variables; this revision resulted in changed adjoint results
211        in MITgcm_contrib/verification_other/global_oce_cs32
212    o pkg/exf:
213      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
214        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
215        e.g. precip, are not available.
216    o pkg/flt:
217      - flt_init_varia.F: use pickupSuff if specified
218      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
219        intermediate, step towards completing pkg/exch2 support within pkg/flt;
220        ifdef DEVEL_FLT_EXCH2 then:
221        - flt_init_fixed.F: comment out stop
222        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
223        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
224        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
225        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
226    o tools/genmake2 & pkg/pkg_depend:
227      - define new type of pkg dependency rule ("=pkg_x"), less strict than
228        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
229        (-pkg_x in packages.conf).
230      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
231      - add "+cal" to dependency list of pkg/ecco (needed to compile).
232      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
233    o utils/matlab:
234      - adding ocean_basin routines for defining basin masks.
235    o pkg/exf:
236      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
237        arguments, allowing to check (and stop) if parameter setting of
238         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
239        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
240        for backward compatibility.
241      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
242        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
243    o pkg/bling (USE_EXFCO2 code):
244      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
245        by adding a call to S/R EXF_GETFFIELD_START.
246    o pkg/exf:
247      - allows to compile without pkg/cal (but disabled by current dependency
248        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
249        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
250        of {FLD}startdate1 & date2 ; consistency check not yet coded.
251    o verification/global_ocean.cs32x15:
252      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
253        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
254    o pkg/exf:
255      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
256        calculations); change FWD experiment global_ocean.cs32x15
257        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
258    o pkg/exf:
259      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
260         {FIELD}startdate to {FIELD}StartTime
261        Note: new name also fit better the content, i.e, a start time in second.
262    o eesupp/src:
263      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
264    o pkg/exf:
265      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
266        to allow to read-in Sensible & Latent Heat flux ;
267      - simplify pkg/exf main options:
268        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
269           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
270           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
271        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
272           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
273        3) improve options documentation in EXF_OPTIONS.h.
274    o pkg/ecco:
275      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
276        ecco_summary.F: add passive tracer cost functions to gencost;
277        m_ptracer and m_boxmean_ptracer
278    o pkg/ctrl:
279      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
280        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
281        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
282        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
283    o model/src:
284      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
285        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
286    o pkg/exf:
287      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
288        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
289    
290    checkpoint66c (2017/01/19)
291    o verification:
292      - add new option "-src" to testreport to only produce source code (*.f),
293        including taf output src code (if using '-adm'/'-tlm' option).
294    o pkg/exf:
295      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
296    o pkg/diagnostics:
297      - add run-time variable diagMdsDir to specify a subdirectory for
298        diagnostic output when mds is being used and mdsioLocalDir is not.
299    o pkg/mnc:
300      - mnc_utils.F: edit stop message
301    o pkg/autodiff:
302      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
303        add HAVE_SYSTEM bracket around system call to mkdir
304    o pkg/profiles:
305      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
306        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
307      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
308        add HAVE_SYSTEM bracket around system call to mkdir
309    o pkg/smooth:
310      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
311      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
312      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
313    o pkg/exf:
314      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
315        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
316        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
317      - summary: skip detailed field report if not used (empty file-name).
318    o tools/xmakedepend:
319      - In case line editor "ed" is missing, switch to "sed" command to clean-up
320        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
321    o pkg/exf:
322      - change definition of "hflux" input file to always include Short-Wave;
323        this is now consistent with hflux computation (if using bulk-formulae)
324        and hflux diagnostic & documentation (in EXF_FIELDS.h).
325    
326    checkpoint66b (2016/12/01)
327    o model & momentum pkgs:
328      - implement fully implicit bottom friction combined with implicit surf.
329        pressure, for now, only in hydrostic formulation:
330        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
331          and run with selectImplicitDrag=2 ;
332        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
333      - partial implicit time-stepping (bot. friction + vert. visc first, then
334        surf. press) corresponding to selectImplicitDrag=1 should be applicable
335        to NH formulation but not available until we solve for surf. pressure
336        increment (instead of full etaN).
337      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
338        with implicit vertical viscosity.
339    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
340      - this is a first version that includes many regularisations that may
341        not all be necessary, to be sorted out,
342      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
343      - change one verification experiment in seaice_itd to use and test new code
344      - seaice_growth: catch a case where the argument of log can be zero
345        or smaller (important for code stability)
346    o model/src:
347      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
348        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
349        similar A.X'=Y' system (with same matrix A) in subsequent calls;
350        switch based on errCode (In/Out) argument value; in calling routines,
351        initialise errCode before first call.
352    
353    checkpoint66a (2016/10/18)
354    o pkg/bling:
355      - BLING package now loads in atmospheric pCO2 file using exf package routines
356        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
357    o model/src & pkg/ptracers:
358      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
359        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
360        implicitDiffusion (respectively) are used (even without momImplVertAdv
361        or temp,salt,PTRACERS_ImplVertAdv).
362    o model/src & generic_advdiff:
363      - add parenthesis in main diagonal calculation of implicit vertical
364        diffusion matrix (impldiff.F & gad_implicit_r.F).
365        This affects results at machine truncation level; update output of many
366        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
367    o pkg/mom_commom & generic_advdiff:
368      - add deep atmosphere and anelastic scaling factor in implicit vertical
369        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
370    o model/src:
371      - remove few unnecessary temp array copies in solve_tridiagonal.F
372        & solve_pentadiagonal.F
373    
374    checkpoint65z (2016/09/28)
375    o pkg/seaice: fix multithreading for seaice_fgmres.F
376      - remove unecessary variables from common blocks
377      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
378        basis, that are stored in commom blocks (including integer variable i1)
379      - clean up code a little by removing commented lines that refer to
380        original code
381      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
382    o MITgcm manual:
383      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
384        preliminary documentation for generic controls (8.3; ctrl.tex),
385        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
386        ecco_costfunction.tex
387    o pkg/ecco:
388      - update and cleanup list of CCP options
389      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
390        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
391      - add checks that retired run-time options are not used, and in relation
392        to gencost_mask and gencost_errfile
393      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
394        gencost_nrecperiod
395      - fix m_eta computation for virtual salt flux case
396      - add m_horflux_vol case (selected via gencost_barfile) that computes
397        transports via cost_gencost_boxmean (gencost_flag=-3)
398      - use gencost_flag more systematically (i.e., avoid using gencost_name)
399        for code switches (aside from physical variable selection)
400    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
401      attempt appears to be a bit of a hack and my need some repair down the road
402    o pkg/exf:
403      - interpolation near South Pole: fix criteria on input field latitude.
404    o pkg/icefront & pkg/exf:
405      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
406        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
407    o pkg/exf:
408      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
409        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
410        (add suffix "_out" instead of a prefix); keep same record number as in
411        input file but always write record 1 first (to avoid a STOP in I/O S/R).
412        Change output file content by writing interpolated field before applying
413        land-sea mask (helpful for debug).
414      - 2 compon. vector interpolation with rotation: apply scaling factor on
415        each compon. (Eastward and Northward) just before rotation.
416    o pkg/bling:
417      - Cleaned package. Removed not needed code and comments.
418      - adjoint example now works
419        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
420    o pkg/ptracers:
421      - add Bruno Deremble's code to complete the linear surface correction
422        for tracer conservation;
423      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
424    
425    checkpoint65y (2016/07/29)
426    o pkg/debug (stats):
427      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
428        proc/thread mapping);
429      - fix Min & Max for case where 1 thread has only empty tiles;
430      - use RL variable to count number of wet grid points (with big domain,
431        can be too large to fit into integer*4).
432    o pkg/monitor:
433      - use RL variable to count number of wet grid points (but used only for del2)
434      - add new routine to compute Advective CFL within tracer time-stepping with
435        writing delayed until next monitor output.
436    o pkg/obcs:
437      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
438    o pkg/cal:
439      - calandar-dump: treat case myTime < timePhase in the same way as in
440        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
441    o pkg/dic & seaice:
442      - fix compilation of ocean component for coupled atm+ocn model with
443        seaice dynamics & dic.
444    
445    checkpoint65x (2016/06/11)
446    o add a license text file in main MITgcm tree.
447    o added pkg/bling:
448      - intermediate complexity biogeochemical model
449      - see bling_description.txt for details
450      - verification experiment is global_oce_biogeo_bling (for now, in
451        Contrib/verification_other/); tested daily on baudelaire with gfortran.
452      - add entry point in pkg/gchem for new pkg "bling".
453    o pkg/seaice: fix tensile stength computation
454      - replace global field tensileStrength by tensileStrFac
455      - tensileStrFac can be computed once in S/R seaice_init_varia
456      - fortunately that does not affect any verification results
457    
458    checkpoint65w (2016/05/12)
459    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
460         with ECCO_CTRL_DEPRECATED defined
461    o verification/global_ocean.cs32x15:
462      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
463        with "selectNHfreeSurf=1".
464    o model/src (non-hydrostatic free-surface):
465      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
466        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
467      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
468        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
469        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
470        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
471      - Update output (changes at machine truncation level) of verification exp:
472        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
473        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
474    o pkg/seaice: ITD code
475      - fix picking up from a single category model by initialising
476        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
477      - split a long warning message in seaice_check_pickup.F into two lines,
478        because NEC SX-ACE cannot deal with the long line.
479    o model/src:
480      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
481    o pkg/seaice:
482      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
483    o pkg/seaice:
484      - add basal stress as parameterisation for grounding ice
485        following Lemieux et al. (2015)
486      - turn on by setting new parameter SEAICEbasalDragK2 to a value
487        larger than 0. Lemieux et al. (2015) recommend 15.
488      - The adjoint complains with extra recomputations so there is also a
489        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
490        order to postpone the problem
491      - compile the new code in lab_sea
492    o verification/halfpipe_streamice:
493      - update both TAF and OpenAD adm output (machine truncation differences)
494    
495    checkpoint65v (2016/04/08)
496    o verification/advect_xz:
497      - increase overlap size from 3 to 4 and add new secondary test for PQM
498        advection scheme (with mono & wino limiter).
499      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
500    o model/src:
501      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
502        added phi0Ref) to set vertical axis origin and phiRef origin;
503        keep Ro_SeaLevel for backward compatibility (with a warning).
504       According to coordinate and fluid type:
505        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
506        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
507        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
508        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
509      - remove Ro_SeaLevel from ATM experiment parameter files;
510      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
511        complement; update output.txt (changes at machine truncation level).
512    o pkg/seaice/seaice_evp.F
513      - simplify computation of deltaZ and zetaZ to simple averaging following
514        Bouillon et al. (2013). This removes a lot of code, but also changes
515        verification experiment lab_sea.hb87 -> updated
516    
517    checkpoint65u (2016/03/14)
518    o pkg/generic_advdiff:
519      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
520        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
521        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
522        testing and not for actual use.
523    o model/src:
524      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
525        origin r = rF(1);
526      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
527        in EOS for height coordinate: enable to include NH Pressure or to use
528        more accurate pressure vertical profile; options not linked to EOS type
529        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
530      - start to implement variable gravity (along vertical): for now, only with
531        z-coords (not even z*).
532      - add Ideal Gas equation of state for height coordinate.
533      - update OpenAD output (affected at machine truncation level) of exp:
534        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
535    o pkg/exf:
536      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
537        of exf interpolation (before any rescaling, rotation or interpolation
538        to velocity point) for each field that gets loaded from file. This option
539        identically mimics the input file organization (e.g. record numbers in year
540        by year input files) besides the change in horizontal grid.
541      - add rotateStressOnAgrid run-time switch so that wind stress fields
542        can be provided on the A-grid in zonal/meridional direction and
543        rotated on the fly. This only applies to the case when the exf
544        interpolation is off and rotateStressOnAgrid is false by default.
545    o model/src:
546      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
547        it's also used with pkg/atm_phys) and add few more parameters (but still
548        inactive, src code yet to come)
549    
550    checkpoint65t (2016/02/10)
551    o pkg/atm_phys:
552      - from Ruth Geen: add optical depth dependence on CO2 concentration.
553    o model/src:
554      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
555        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
556        Update output of exp. deep_anelastic (changes at truncation level).
557    o tools:
558      - add a hack in "remove_comments_sed" (used only with TAF) for recent
559        version of OpenMPI (shipped with FC.23): comment out the new header
560        file "mpif-sizeof.h" which causes problems to TAF.
561    o pkg/seaice:
562      - change the termination criterion so that maxits (SEAICElinearIterMax)
563        has an effect
564      - unify iteration parameters for implicit solvers (JFNK and Picard)
565        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
566        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
567        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
568        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
569        SEAICEnonLinTol     replaces JFNKgamma_nonlin
570      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
571      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
572        use with SEAICEuseKrylov
573    o pkg/seaice/seaice_lsr.F
574        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
575        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
576        an effect.
577    o pkg/seaice: add two new parameters
578      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
579        parameter is not in any namelist)
580      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
581        a preconditioner for the non-linear Newton iteration of the JFNK
582        solver
583    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
584      affects some experiments at truncation level:
585      - global_ocean.cs32x15.icedyn (11 digits),
586      - global_ocean.cs32x15.seaice (11 digits),
587      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
588      - also update global_ocean.cs32x15 adjoint and tangent-linear results
589    o pkg/salt_plume & pkg/thsice:
590      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
591        connect salt_plume flux to ATM-OCN coupling pkgs interface:
592       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
593         export to coupler interface) even without compiling pkg/salt_plume ;
594       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
595         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
596    o pkg/dic:
597      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
598        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
599        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
600      - move also update with values from ATM-OCN Coupler in the same new S/R
601        (previously done in ocn_apply_import.F).
602    o tools/adjoint_options:
603      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
604        has been changed on Jan 14, 2016.
605    o pkg/ggl90:
606      - add alternative discretisation of vertical shear (off by default), to
607        compute the mean (@ grid-cell center) of vertical shear compon instead of
608        vertical shear of mean flow (@ grid-cell center).
609      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
610        results on adjacent faces of cubed-sphere grids; this fix the restart.
611    o pkg/atm_compon_interf:
612      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
613        pass last value, stored directly before export to CPL ;
614        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
615      - remove atmSLPr from pickup files (no longer needed for restart)
616    
617    checkpoint65s (2016/01/13)
618    o eesupp & genmake2:
619       - first check for Function ETIME and, if it fails, then check for subroutine
620         ETIME and consistent output; use the appropriate version in timers.F
621    o model/src:
622      - to check restart test, add option to apply EXCH to U,V earlier, just before
623        integr_continuity; turned off by default.
624    o pkg/dic:
625      - remove CPP option USE_ATMOSCO2 (not needed)
626    o tools/tst_2+2:
627      - try to ignore difference between +0 and -0 in binary file, causing test
628        to fail for no good reason.
629    o eesupp & genmake2:
630      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
631        but also check (in genmake2) that test runs and returns meaningful results.
632    o coupler pkgs:
633      Finish implementation of optionally-exchanged variable switches (started on
634       Nov 12) with addition of few more exchanged fields, including 2-way exchange
635       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
636       advection in OCN component; this requires sequential coupling.
637      coupler (pkg/atm_ocn_coupler):
638      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
639        routines (useful for debug).
640      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
641         flux, DIC fields) if corresponding switch is ON.
642      - add option to export RunOff to OCN (to use for DIC river input)
643      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
644      components (pkg/atm_ & ocn_compon_interf):
645      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
646        optionally exchanged fields; add a check & stop in cpl_readparms.F.
647        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
648        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
649      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
650        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
651      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
652      - hold in common block coupler optionally-exchanged variable switch
653        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
654      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
655        this is intended to replace the OCN cplFldtave.* output files (not updated
656        to contain new additional exchanged fields).
657    o pkg/dic:
658      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
659    o pkg/thsice:
660      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
661        and writing of thsice pickup files.
662    o pkg/atm_compon_interf:
663      - move all field individual export-call out of cpl_export_import_data.F
664        into new S/R ATM_EXPORT_FIELDS
665    o pkg/atm_compon_interf:
666      - store state variables (for now, only thSIce fields) just before beeing
667        exported (in cpl_export_import_data.F, like on ocean side) instead of from
668        atm_store_my_data.F like all exported fluxes.
669      - new version of pickup_cpl: write field names into meta file and read meta
670        file to find field postion in pickup. Also only write/read fields meeded for
671        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
672    o pkg/dic:
673      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
674    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
675        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
676        value can be from domain [0,1] to average between the two methods
677    o pkg/atm_phys:
678      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
679        hold fixed in time).
680    
681    checkpoint65r (2015/12/21)
682    o pkg/seaice:
683        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
684        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
685    o pkg/seaice:
686      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
687        when SEAICEscaleSurfStress=.TRUE.,
688      - apply areaW and areaS in S/R seaice_calc_lhs
689    o pkg/atm_phys:
690      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
691        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
692        for individual contribution (convection, LSC cond, radiation)
693      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
694        information); activated with: solar_exponent=0. and wv_exponent=-1.
695    o pkg/ggl90:
696      - within IDEMIX add upper limit for horizontal group velocity to
697        avoid instability problems in the explicit horizontal diffusion term for
698        long time steps or high resolution
699    o pkg/diagnostics:
700      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
701        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
702    o testreport:
703      - remove "-v" (verbose option) in default mpirun command.
704    o pkg/seaice/seaice_growth:
705      - catch potential division by zero in ITD code, does not change
706        verification results
707    o pkg/ecco:
708      - retire old codes to the Attic. The calls to retired functions are
709        left in a commented form in case they ever need to be re-activated.
710      - ecco_check.F: issue warning if any old CPP option is
711        defined that corresponds to retired codes -- then stop.
712    o pkg/atm_compon_interf:
713      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
714        coupler: use last time-step value instead of average over cplSendFrq_iter
715        time-step, similar to what is done for seaIceMass.
716        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
717    o eesupp & genmake2:
718      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
719        <= remove until a fix is found for some ifort version on ia32 machine.
720    o pkg/seaice/seaice_evp:
721      - refine residual computation
722    
723    checkpoint65q (2015/11/18)
724    o pkg/seaice/seaice_evp:
725      - fix residual computations so that they no longer affect the actual
726        simulation code
727      - fix seaice_readparams to be able to actually set new parameters
728        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
729    o model/src:
730      - fix wrong truncation (single prec) from "FLOAT" function in expressions
731        like: deltaT*FLOAT(myIter) when myIter is large:
732         a) replaced by DFLOAT (if not seen by TAF);
733         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
734    o pkg/aim_v23:
735      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
736        when pickupSuff is set ; do write rolling pickups + at the end of the run.
737    o pkg/atm_ocn_coupler + ocn_compon_interf:
738      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
739        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
740        add corresponding call in DO_OCEANIC_PHYS.
741    o coupler pkgs:
742      Start a new way to set-up optionally-exchanged variables (previously, only
743       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
744       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
745       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
746       compononent param default can be set accordingly).
747      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
748       but rather applies to a group a fields (going both ways like for DIC)
749       and corresponds to an option of coupling config.
750      coupler (pkg/atm_ocn_coupler):
751      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
752        and read namelist directly (without eessup S/R calls) instead of
753        in the very un-flexible old way, 1 param per line, in fixed order;
754      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
755        cleanly in CPL_CHECK_CPLCONFIG
756      - add new coupling-exchange selectors (some not yet active) including
757        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
758                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
759      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
760        component ; called directly from coupler.F, after comp. registrations;
761      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
762         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
763          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
764      components (pkg/atm_ & ocn_compon_interf):
765      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
766        CPP header file in all pkg source files.
767      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
768        ATM/OCN_CHECK_CPLCONFIG;
769      - add error-counter to track errors (e.g., in "data.cpl") and to stop
770        cleanly in ATM/OCN_CHECK_CPLCONFIG;
771      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
772        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
773        before PACKAGES_READPARMS;
774      verification/cpl_aim+ocn/:
775      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
776        "data.cpl" for coupler (in input_cpl).
777    o eesupp/inc:
778      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
779        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
780        to always cumulate tile local-sum in the same order (still uses
781        MPI_Allreduce like standard code).
782      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
783        that are now identical to standard version (in eesupp/inc).
784    o pkg/shelfice:
785      - add SHELFICETransCoeffTFile for initializing spatially varying
786        heat and salt transfer coefficients
787    o pkg/atm_compon_interf & ocn_compon_interf:
788      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
789        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
790      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
791    o pkg/atm_ocn_coupler:
792      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
793    o pkg/rbcs:
794      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
795        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
796      - add a short report (to STDOUT) about RBCS-mask settings.
797    
798    checkpoint65p (2015/10/23)
799    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
800        there is no adjoint test for EVP, we don't know what it does to the adjoint
801        solution, but at least there are no more recomputation warnings left
802    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
803        a chance of giving the same results as a fully converged VP (JFNK) solver
804    o tools/adjoint_options/adjoint_diva:
805      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
806    o pkg/streamice:
807      - spotted bug in streamice_driving_stress using dyG where should have been dxG
808    o pkg/exf:
809      - remove STOP statement that prevented to use wind or (wind-)stress
810        interpolation for constant-in-time forcing fields (wind/stress period = 0).
811    o pkg/seaice:
812      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
813        5 additionals 2D fields and 6 new store directives
814      - change logic in seaice_readparms.F: EVP code can now be turned on in
815        various ways, setting SEAICE_deltaTev is no longer required,
816        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
817        or SEAICEaEVPcoeff
818    o pkg/shelfice/shelfice_thermodynamics.F
819      - redefining uLoc/vLoc to u/v, instead of 2u/v
820    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
821      - this is an intermediate state of a truely converging EVP that has
822        the potential of outperforming implicit VP methods, I do not recommend
823        using it yet.
824      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
825        and all parameters are hardwired
826      - for convergence it still requires very smooth regularisations, that means,
827        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
828        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
829        specific averaging appears to be required, still subject to tuning
830      - still needs cleaning and I need to turn parameter into runtime parameters
831      - add code to compute and print residuals of iteration, compile with
832        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
833    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
834      that entered with r1.54 on Sep04, 2015, -> update results
835    
836    checkpoint65o (2015/09/14)
837    o pkg/mom_vecinv & mom_common:
838      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
839        called from there.
840      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
841        allows to use Vector-Invariant form in deep atmos and anelastic formulation
842    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
843      and Koenig-Beatty+Holland (2012)
844      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
845      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
846      - requires an extra input argument for S/R seaice_calc_viscosities
847      - tensileStrength's depth dependence is different from Itkin et al. (2015)
848        (to be changed and played with, for now exponential)
849    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
850      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
851        by AREA according to Connelly et al. (2004), JPO.
852      - For EVP and the LSR solver, the implicit part of the drag term is
853        the only non-zero term in the denominator when there is no ice (which
854        prevented running the model with zero ice-ocean drag). If
855        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
856        (or zero main diagonals BU/BV) which need to be caught. A practical
857        consequence is that for open water, the momentum equation reduce
858        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
859        they happen to be zero, often leading to a non-zero solution over
860        open water.
861    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
862        efficient EVP method.
863      - introduce area-weighted averages for e12 (analogously to
864        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
865        remain, but also changing the order of terms in the previous average
866        changed the results as much) -> update experiment
867      - add SEAICE_DELTA_SMOOTHREG code
868      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
869        TEM-code
870      - adjust loop bounds so that only required fields are computed
871      - add new averaging code for zetaZ/deltaZ (again similar to
872        seaice_calc_viscosities.F), inactive by default for now (will change
873        results again), but will replace old code eventually
874    o eesupp/src:
875      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
876        to always cumulate tile local-sum in the same order
877        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
878        Still uses MPI_Allreduce (like standard code) but on array of tiles
879        and should be faster than GLOBAL_SUM_SEND_RECV code.
880      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
881        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
882      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
883         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
884         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
885         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
886         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
887    
888    checkpoint65n (2015/07/29)
889    o pkg/thsice:
890      - add a warning when used with pkg/aim but without updating SST
891        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
892  o pkg/offline:  o pkg/offline:
893    - change where Offline-Fields are loaded, from load_fields_driver.F to    - change where Offline-Fields are loaded, from load_fields_driver.F to
894      directly within FORWARD_STEP, just after updating iter number and time;      directly within FORWARD_STEP, just after updating iter number and time;
# Line 16  o pkg/offline: Line 901  o pkg/offline:
901      time-step, both with GM & KPP files and with recomputing these fields;      time-step, both with GM & KPP files and with recomputing these fields;
902      b) no needs to switch on staggerTimeStep anymore;      b) no needs to switch on staggerTimeStep anymore;
903      c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.      c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
904    - update output of experiments tutorial_cfc_offline (11 to 13 digits left)    - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
     and tutorial_dic_adjoffline (only 3 digits left).  
905  o pkg/offline:  o pkg/offline:
906    - change (rarely used) offset-iteration parameter to an offset time (in s):    - change (rarely used) offset-iteration parameter to an offset time (in s):
907      can easily recover previous offset-iter effect by setting offset-time      can easily recover previous offset-iter effect by setting offset-time
# Line 329  o model/src & mom pkgs: Line 1213  o model/src & mom pkgs:
1213      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1214  o doc:  o doc:
1215    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1216  o pkg/streamice:  o pkg/shelfice:
1217    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1218      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1219      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and

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