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revision 1.2183 by mlosch, Thu Sep 24 08:17:32 2015 UTC revision 1.2307 by jmc, Thu Feb 23 20:50:12 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/bling, USE_EXFCO2 code:
8      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
9      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
10    o pkg/exf:
11      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
12      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
13        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
14        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
15      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
16        EXF_INIT_FLD) and update calls in exf_init_varia.F
17      - For now, for backward compatibility, keep a simplified version of S/Rs
18        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
19      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
20        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
21    o tools/genmake2:
22      - replace "bc -l" (only used once) by "expr" (already used).
23    o verification/global_ocean.cs32x15:
24      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
25        Note: exf setting (data.exf) can be compared to other exf secondary exp
26        "seaice" (kept with useCAL=T) which has same time dependent forcing.
27    
28    checkpoint66d (2017/02/13)
29    o pkg/exf:
30      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
31        early on (in packages_boot.F) to stress this change in pkg setting.
32      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
33    o model/src:
34      - move call to ecco_phys to end of time step; this may induce minor
35        cost function changes by shifting time averages by one time step
36        for some variables; this revision resulted in changed adjoint results
37        in MITgcm_contrib/verification_other/global_oce_cs32
38    o pkg/exf:
39      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
40        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
41        e.g. precip, are not available.
42    o pkg/flt:
43      - flt_init_varia.F: use pickupSuff if specified
44      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
45        intermediate, step towards completing pkg/exch2 support within pkg/flt;
46        ifdef DEVEL_FLT_EXCH2 then:
47        - flt_init_fixed.F: comment out stop
48        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
49        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
50        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
51        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
52    o tools/genmake2 & pkg/pkg_depend:
53      - define new type of pkg dependency rule ("=pkg_x"), less strict than
54        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
55        (-pkg_x in packages.conf).
56      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
57      - add "+cal" to dependency list of pkg/ecco (needed to compile).
58      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
59    o utils/matlab:
60      - adding ocean_basin routines for defining basin masks.
61    o pkg/exf:
62      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
63        arguments, allowing to check (and stop) if parameter setting of
64         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
65        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
66        for backward compatibility.
67      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
68        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
69    o pkg/bling (USE_EXFCO2 code):
70      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
71        by adding a call to S/R EXF_GETFFIELD_START.
72    o pkg/exf:
73      - allows to compile without pkg/cal (but disabled by current dependency
74        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
75        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
76        of {FLD}startdate1 & date2 ; consistency check not yet coded.
77    o verification/global_ocean.cs32x15:
78      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
79        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
80    o pkg/exf:
81      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
82        calculations); change FWD experiment global_ocean.cs32x15
83        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
84    o pkg/exf:
85      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
86         {FIELD}startdate to {FIELD}StartTime
87        Note: new name also fit better the content, i.e, a start time in second.
88    o eesupp/src:
89      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
90    o pkg/exf:
91      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
92        to allow to read-in Sensible & Latent Heat flux ;
93      - simplify pkg/exf main options:
94        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
95           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
96           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
97        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
98           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
99        3) improve options documentation in EXF_OPTIONS.h.
100    o pkg/ecco:
101      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
102        ecco_summary.F: add passive tracer cost functions to gencost;
103        m_ptracer and m_boxmean_ptracer
104    o pkg/ctrl:
105      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
106        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
107        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
108        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
109    o model/src:
110      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
111        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
112    o pkg/exf:
113      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
114        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
115    
116    checkpoint66c (2017/01/19)
117    o verification:
118      - add new option "-src" to testreport to only produce source code (*.f),
119        including taf output src code (if using '-adm'/'-tlm' option).
120    o pkg/exf:
121      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
122    o pkg/diagnostics:
123      - add run-time variable diagMdsDir to specify a subdirectory for
124        diagnostic output when mds is being used and mdsioLocalDir is not.
125    o pkg/mnc:
126      - mnc_utils.F: edit stop message
127    o pkg/autodiff:
128      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
129        add HAVE_SYSTEM bracket around system call to mkdir
130    o pkg/profiles:
131      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
132        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
133      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
134        add HAVE_SYSTEM bracket around system call to mkdir
135    o pkg/smooth:
136      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
137      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
138      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
139    o pkg/exf:
140      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
141        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
142        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
143      - summary: skip detailed field report if not used (empty file-name).
144    o tools/xmakedepend:
145      - In case line editor "ed" is missing, switch to "sed" command to clean-up
146        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
147    o pkg/exf:
148      - change definition of "hflux" input file to always include Short-Wave;
149        this is now consistent with hflux computation (if using bulk-formulae)
150        and hflux diagnostic & documentation (in EXF_FIELDS.h).
151    
152    checkpoint66b (2016/12/01)
153    o model & momentum pkgs:
154      - implement fully implicit bottom friction combined with implicit surf.
155        pressure, for now, only in hydrostic formulation:
156        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
157          and run with selectImplicitDrag=2 ;
158        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
159      - partial implicit time-stepping (bot. friction + vert. visc first, then
160        surf. press) corresponding to selectImplicitDrag=1 should be applicable
161        to NH formulation but not available until we solve for surf. pressure
162        increment (instead of full etaN).
163      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
164        with implicit vertical viscosity.
165    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
166      - this is a first version that includes many regularisations that may
167        not all be necessary, to be sorted out,
168      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
169      - change one verification experiment in seaice_itd to use and test new code
170      - seaice_growth: catch a case where the argument of log can be zero
171        or smaller (important for code stability)
172    o model/src:
173      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
174        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
175        similar A.X'=Y' system (with same matrix A) in subsequent calls;
176        switch based on errCode (In/Out) argument value; in calling routines,
177        initialise errCode before first call.
178    
179    checkpoint66a (2016/10/18)
180    o pkg/bling:
181      - BLING package now loads in atmospheric pCO2 file using exf package routines
182        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
183    o model/src & pkg/ptracers:
184      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
185        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
186        implicitDiffusion (respectively) are used (even without momImplVertAdv
187        or temp,salt,PTRACERS_ImplVertAdv).
188    o model/src & generic_advdiff:
189      - add parenthesis in main diagonal calculation of implicit vertical
190        diffusion matrix (impldiff.F & gad_implicit_r.F).
191        This affects results at machine truncation level; update output of many
192        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
193    o pkg/mom_commom & generic_advdiff:
194      - add deep atmosphere and anelastic scaling factor in implicit vertical
195        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
196    o model/src:
197      - remove few unnecessary temp array copies in solve_tridiagonal.F
198        & solve_pentadiagonal.F
199    
200    checkpoint65z (2016/09/28)
201    o pkg/seaice: fix multithreading for seaice_fgmres.F
202      - remove unecessary variables from common blocks
203      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
204        basis, that are stored in commom blocks (including integer variable i1)
205      - clean up code a little by removing commented lines that refer to
206        original code
207      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
208    o MITgcm manual:
209      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
210        preliminary documentation for generic controls (8.3; ctrl.tex),
211        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
212        ecco_costfunction.tex
213    o pkg/ecco:
214      - update and cleanup list of CCP options
215      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
216        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
217      - add checks that retired run-time options are not used, and in relation
218        to gencost_mask and gencost_errfile
219      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
220        gencost_nrecperiod
221      - fix m_eta computation for virtual salt flux case
222      - add m_horflux_vol case (selected via gencost_barfile) that computes
223        transports via cost_gencost_boxmean (gencost_flag=-3)
224      - use gencost_flag more systematically (i.e., avoid using gencost_name)
225        for code switches (aside from physical variable selection)
226    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
227      attempt appears to be a bit of a hack and my need some repair down the road
228    o pkg/exf:
229      - interpolation near South Pole: fix criteria on input field latitude.
230    o pkg/icefront & pkg/exf:
231      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
232        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
233    o pkg/exf:
234      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
235        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
236        (add suffix "_out" instead of a prefix); keep same record number as in
237        input file but always write record 1 first (to avoid a STOP in I/O S/R).
238        Change output file content by writing interpolated field before applying
239        land-sea mask (helpful for debug).
240      - 2 compon. vector interpolation with rotation: apply scaling factor on
241        each compon. (Eastward and Northward) just before rotation.
242    o pkg/bling:
243      - Cleaned package. Removed not needed code and comments.
244      - adjoint example now works
245        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
246    o pkg/ptracers:
247      - add Bruno Deremble's code to complete the linear surface correction
248        for tracer conservation;
249      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
250    
251    checkpoint65y (2016/07/29)
252    o pkg/debug (stats):
253      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
254        proc/thread mapping);
255      - fix Min & Max for case where 1 thread has only empty tiles;
256      - use RL variable to count number of wet grid points (with big domain,
257        can be too large to fit into integer*4).
258    o pkg/monitor:
259      - use RL variable to count number of wet grid points (but used only for del2)
260      - add new routine to compute Advective CFL within tracer time-stepping with
261        writing delayed until next monitor output.
262    o pkg/obcs:
263      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
264    o pkg/cal:
265      - calandar-dump: treat case myTime < timePhase in the same way as in
266        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
267    o pkg/dic & seaice:
268      - fix compilation of ocean component for coupled atm+ocn model with
269        seaice dynamics & dic.
270    
271    checkpoint65x (2016/06/11)
272    o add a license text file in main MITgcm tree.
273    o added pkg/bling:
274      - intermediate complexity biogeochemical model
275      - see bling_description.txt for details
276      - verification experiment is global_oce_biogeo_bling (for now, in
277        Contrib/verification_other/); tested daily on baudelaire with gfortran.
278      - add entry point in pkg/gchem for new pkg "bling".
279    o pkg/seaice: fix tensile stength computation
280      - replace global field tensileStrength by tensileStrFac
281      - tensileStrFac can be computed once in S/R seaice_init_varia
282      - fortunately that does not affect any verification results
283    
284    checkpoint65w (2016/05/12)
285    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
286         with ECCO_CTRL_DEPRECATED defined
287    o verification/global_ocean.cs32x15:
288      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
289        with "selectNHfreeSurf=1".
290    o model/src (non-hydrostatic free-surface):
291      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
292        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
293      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
294        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
295        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
296        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
297      - Update output (changes at machine truncation level) of verification exp:
298        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
299        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
300    o pkg/seaice: ITD code
301      - fix picking up from a single category model by initialising
302        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
303      - split a long warning message in seaice_check_pickup.F into two lines,
304        because NEC SX-ACE cannot deal with the long line.
305    o model/src:
306      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
307    o pkg/seaice:
308      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
309    o pkg/seaice:
310      - add basal stress as parameterisation for grounding ice
311        following Lemieux et al. (2015)
312      - turn on by setting new parameter SEAICEbasalDragK2 to a value
313        larger than 0. Lemieux et al. (2015) recommend 15.
314      - The adjoint complains with extra recomputations so there is also a
315        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
316        order to postpone the problem
317      - compile the new code in lab_sea
318    o verification/halfpipe_streamice:
319      - update both TAF and OpenAD adm output (machine truncation differences)
320    
321    checkpoint65v (2016/04/08)
322    o verification/advect_xz:
323      - increase overlap size from 3 to 4 and add new secondary test for PQM
324        advection scheme (with mono & wino limiter).
325      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
326    o model/src:
327      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
328        added phi0Ref) to set vertical axis origin and phiRef origin;
329        keep Ro_SeaLevel for backward compatibility (with a warning).
330       According to coordinate and fluid type:
331        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
332        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
333        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
334        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
335      - remove Ro_SeaLevel from ATM experiment parameter files;
336      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
337        complement; update output.txt (changes at machine truncation level).
338    o pkg/seaice/seaice_evp.F
339      - simplify computation of deltaZ and zetaZ to simple averaging following
340        Bouillon et al. (2013). This removes a lot of code, but also changes
341        verification experiment lab_sea.hb87 -> updated
342    
343    checkpoint65u (2016/03/14)
344    o pkg/generic_advdiff:
345      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
346        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
347        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
348        testing and not for actual use.
349    o model/src:
350      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
351        origin r = rF(1);
352      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
353        in EOS for height coordinate: enable to include NH Pressure or to use
354        more accurate pressure vertical profile; options not linked to EOS type
355        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
356      - start to implement variable gravity (along vertical): for now, only with
357        z-coords (not even z*).
358      - add Ideal Gas equation of state for height coordinate.
359      - update OpenAD output (affected at machine truncation level) of exp:
360        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
361    o pkg/exf:
362      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
363        of exf interpolation (before any rescaling, rotation or interpolation
364        to velocity point) for each field that gets loaded from file. This option
365        identically mimics the input file organization (e.g. record numbers in year
366        by year input files) besides the change in horizontal grid.
367      - add rotateStressOnAgrid run-time switch so that wind stress fields
368        can be provided on the A-grid in zonal/meridional direction and
369        rotated on the fly. This only applies to the case when the exf
370        interpolation is off and rotateStressOnAgrid is false by default.
371    o model/src:
372      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
373        it's also used with pkg/atm_phys) and add few more parameters (but still
374        inactive, src code yet to come)
375    
376    checkpoint65t (2016/02/10)
377    o pkg/atm_phys:
378      - from Ruth Geen: add optical depth dependence on CO2 concentration.
379    o model/src:
380      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
381        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
382        Update output of exp. deep_anelastic (changes at truncation level).
383    o tools:
384      - add a hack in "remove_comments_sed" (used only with TAF) for recent
385        version of OpenMPI (shipped with FC.23): comment out the new header
386        file "mpif-sizeof.h" which causes problems to TAF.
387    o pkg/seaice:
388      - change the termination criterion so that maxits (SEAICElinearIterMax)
389        has an effect
390      - unify iteration parameters for implicit solvers (JFNK and Picard)
391        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
392        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
393        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
394        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
395        SEAICEnonLinTol     replaces JFNKgamma_nonlin
396      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
397      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
398        use with SEAICEuseKrylov
399    o pkg/seaice/seaice_lsr.F
400        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
401        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
402        an effect.
403    o pkg/seaice: add two new parameters
404      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
405        parameter is not in any namelist)
406      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
407        a preconditioner for the non-linear Newton iteration of the JFNK
408        solver
409    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
410      affects some experiments at truncation level:
411      - global_ocean.cs32x15.icedyn (11 digits),
412      - global_ocean.cs32x15.seaice (11 digits),
413      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
414      - also update global_ocean.cs32x15 adjoint and tangent-linear results
415    o pkg/salt_plume & pkg/thsice:
416      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
417        connect salt_plume flux to ATM-OCN coupling pkgs interface:
418       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
419         export to coupler interface) even without compiling pkg/salt_plume ;
420       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
421         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
422    o pkg/dic:
423      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
424        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
425        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
426      - move also update with values from ATM-OCN Coupler in the same new S/R
427        (previously done in ocn_apply_import.F).
428    o tools/adjoint_options:
429      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
430        has been changed on Jan 14, 2016.
431    o pkg/ggl90:
432      - add alternative discretisation of vertical shear (off by default), to
433        compute the mean (@ grid-cell center) of vertical shear compon instead of
434        vertical shear of mean flow (@ grid-cell center).
435      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
436        results on adjacent faces of cubed-sphere grids; this fix the restart.
437    o pkg/atm_compon_interf:
438      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
439        pass last value, stored directly before export to CPL ;
440        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
441      - remove atmSLPr from pickup files (no longer needed for restart)
442    
443    checkpoint65s (2016/01/13)
444    o eesupp & genmake2:
445       - first check for Function ETIME and, if it fails, then check for subroutine
446         ETIME and consistent output; use the appropriate version in timers.F
447    o model/src:
448      - to check restart test, add option to apply EXCH to U,V earlier, just before
449        integr_continuity; turned off by default.
450    o pkg/dic:
451      - remove CPP option USE_ATMOSCO2 (not needed)
452    o tools/tst_2+2:
453      - try to ignore difference between +0 and -0 in binary file, causing test
454        to fail for no good reason.
455    o eesupp & genmake2:
456      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
457        but also check (in genmake2) that test runs and returns meaningful results.
458    o coupler pkgs:
459      Finish implementation of optionally-exchanged variable switches (started on
460       Nov 12) with addition of few more exchanged fields, including 2-way exchange
461       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
462       advection in OCN component; this requires sequential coupling.
463      coupler (pkg/atm_ocn_coupler):
464      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
465        routines (useful for debug).
466      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
467         flux, DIC fields) if corresponding switch is ON.
468      - add option to export RunOff to OCN (to use for DIC river input)
469      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
470      components (pkg/atm_ & ocn_compon_interf):
471      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
472        optionally exchanged fields; add a check & stop in cpl_readparms.F.
473        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
474        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
475      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
476        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
477      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
478      - hold in common block coupler optionally-exchanged variable switch
479        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
480      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
481        this is intended to replace the OCN cplFldtave.* output files (not updated
482        to contain new additional exchanged fields).
483    o pkg/dic:
484      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
485    o pkg/thsice:
486      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
487        and writing of thsice pickup files.
488    o pkg/atm_compon_interf:
489      - move all field individual export-call out of cpl_export_import_data.F
490        into new S/R ATM_EXPORT_FIELDS
491    o pkg/atm_compon_interf:
492      - store state variables (for now, only thSIce fields) just before beeing
493        exported (in cpl_export_import_data.F, like on ocean side) instead of from
494        atm_store_my_data.F like all exported fluxes.
495      - new version of pickup_cpl: write field names into meta file and read meta
496        file to find field postion in pickup. Also only write/read fields meeded for
497        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
498    o pkg/dic:
499      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
500    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
501        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
502        value can be from domain [0,1] to average between the two methods
503    o pkg/atm_phys:
504      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
505        hold fixed in time).
506    
507    checkpoint65r (2015/12/21)
508    o pkg/seaice:
509        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
510        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
511    o pkg/seaice:
512      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
513        when SEAICEscaleSurfStress=.TRUE.,
514      - apply areaW and areaS in S/R seaice_calc_lhs
515    o pkg/atm_phys:
516      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
517        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
518        for individual contribution (convection, LSC cond, radiation)
519      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
520        information); activated with: solar_exponent=0. and wv_exponent=-1.
521    o pkg/ggl90:
522      - within IDEMIX add upper limit for horizontal group velocity to
523        avoid instability problems in the explicit horizontal diffusion term for
524        long time steps or high resolution
525    o pkg/diagnostics:
526      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
527        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
528    o testreport:
529      - remove "-v" (verbose option) in default mpirun command.
530    o pkg/seaice/seaice_growth:
531      - catch potential division by zero in ITD code, does not change
532        verification results
533    o pkg/ecco:
534      - retire old codes to the Attic. The calls to retired functions are
535        left in a commented form in case they ever need to be re-activated.
536      - ecco_check.F: issue warning if any old CPP option is
537        defined that corresponds to retired codes -- then stop.
538    o pkg/atm_compon_interf:
539      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
540        coupler: use last time-step value instead of average over cplSendFrq_iter
541        time-step, similar to what is done for seaIceMass.
542        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
543    o eesupp & genmake2:
544      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
545        <= remove until a fix is found for some ifort version on ia32 machine.
546    o pkg/seaice/seaice_evp:
547      - refine residual computation
548    
549    checkpoint65q (2015/11/18)
550    o pkg/seaice/seaice_evp:
551      - fix residual computations so that they no longer affect the actual
552        simulation code
553      - fix seaice_readparams to be able to actually set new parameters
554        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
555    o model/src:
556      - fix wrong truncation (single prec) from "FLOAT" function in expressions
557        like: deltaT*FLOAT(myIter) when myIter is large:
558         a) replaced by DFLOAT (if not seen by TAF);
559         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
560    o pkg/aim_v23:
561      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
562        when pickupSuff is set ; do write rolling pickups + at the end of the run.
563    o pkg/atm_ocn_coupler + ocn_compon_interf:
564      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
565        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
566        add corresponding call in DO_OCEANIC_PHYS.
567    o coupler pkgs:
568      Start a new way to set-up optionally-exchanged variables (previously, only
569       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
570       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
571       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
572       compononent param default can be set accordingly).
573      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
574       but rather applies to a group a fields (going both ways like for DIC)
575       and corresponds to an option of coupling config.
576      coupler (pkg/atm_ocn_coupler):
577      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
578        and read namelist directly (without eessup S/R calls) instead of
579        in the very un-flexible old way, 1 param per line, in fixed order;
580      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
581        cleanly in CPL_CHECK_CPLCONFIG
582      - add new coupling-exchange selectors (some not yet active) including
583        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
584                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
585      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
586        component ; called directly from coupler.F, after comp. registrations;
587      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
588         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
589          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
590      components (pkg/atm_ & ocn_compon_interf):
591      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
592        CPP header file in all pkg source files.
593      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
594        ATM/OCN_CHECK_CPLCONFIG;
595      - add error-counter to track errors (e.g., in "data.cpl") and to stop
596        cleanly in ATM/OCN_CHECK_CPLCONFIG;
597      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
598        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
599        before PACKAGES_READPARMS;
600      verification/cpl_aim+ocn/:
601      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
602        "data.cpl" for coupler (in input_cpl).
603    o eesupp/inc:
604      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
605        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
606        to always cumulate tile local-sum in the same order (still uses
607        MPI_Allreduce like standard code).
608      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
609        that are now identical to standard version (in eesupp/inc).
610    o pkg/shelfice:
611      - add SHELFICETransCoeffTFile for initializing spatially varying
612        heat and salt transfer coefficients
613    o pkg/atm_compon_interf & ocn_compon_interf:
614      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
615        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
616      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
617    o pkg/atm_ocn_coupler:
618      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
619    o pkg/rbcs:
620      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
621        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
622      - add a short report (to STDOUT) about RBCS-mask settings.
623    
624    checkpoint65p (2015/10/23)
625    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
626        there is no adjoint test for EVP, we don't know what it does to the adjoint
627        solution, but at least there are no more recomputation warnings left
628    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
629        a chance of giving the same results as a fully converged VP (JFNK) solver
630    o tools/adjoint_options/adjoint_diva:
631      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
632    o pkg/streamice:
633      - spotted bug in streamice_driving_stress using dyG where should have been dxG
634    o pkg/exf:
635      - remove STOP statement that prevented to use wind or (wind-)stress
636        interpolation for constant-in-time forcing fields (wind/stress period = 0).
637    o pkg/seaice:
638      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
639        5 additionals 2D fields and 6 new store directives
640      - change logic in seaice_readparms.F: EVP code can now be turned on in
641        various ways, setting SEAICE_deltaTev is no longer required,
642        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
643        or SEAICEaEVPcoeff
644    o pkg/shelfice/shelfice_thermodynamics.F
645      - redefining uLoc/vLoc to u/v, instead of 2u/v
646  o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz  o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
647    - this is an intermediate state of a truely converging EVP that has    - this is an intermediate state of a truely converging EVP that has
648      the potential of outperforming implicit VP methods, I do not recommend      the potential of outperforming implicit VP methods, I do not recommend
# Line 400  o model/src & mom pkgs: Line 1039  o model/src & mom pkgs:
1039      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1040  o doc:  o doc:
1041    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1042  o pkg/streamice:  o pkg/shelfice:
1043    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1044      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1045      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and

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