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revision 1.2179 by mlosch, Thu Sep 10 15:58:25 2015 UTC revision 1.2288 by gforget, Mon Jan 9 19:28:21 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/exf:
8      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
9        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc.EQ.UNSET_RL;
10        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
11      - summary: skip detailed field report if not used (empty file-name).
12    o tools/xmakedepend:
13      - In case line editor "ed" is missing, switch to "sed" command to clean-up
14        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
15    o pkg/exf:
16      - change definition of "hflux" input file to always include Short-Wave;
17        this is now consistent with hflux computation (if using bulk-formulae)
18        and hflux diagnostic & documentation (in EXF_FIELDS.h).
19    
20    checkpoint66b (2016/12/01)
21    o model & momentum pkgs:
22      - implement fully implicit bottom friction combined with implicit surf.
23        pressure, for now, only in hydrostic formulation:
24        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
25          and run with selectImplicitDrag=2 ;
26        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
27      - partial implicit time-stepping (bot. friction + vert. visc first, then
28        surf. press) corresponding to selectImplicitDrag=1 should be applicable
29        to NH formulation but not available until we solve for surf. pressure
30        increment (instead of full etaN).
31      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
32        with implicit vertical viscosity.
33    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
34      - this is a first version that includes many regularisations that may
35        not all be necessary, to be sorted out,
36      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
37      - change one verification experiment in seaice_itd to use and test new code
38      - seaice_growth: catch a case where the argument of log can be zero
39        or smaller (important for code stability)
40    o model/src:
41      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
42        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
43        similar A.X'=Y' system (with same matrix A) in subsequent calls;
44        switch based on errCode (In/Out) argument value; in calling routines,
45        initialise errCode before first call.
46    
47    checkpoint66a (2016/10/18)
48    o pkg/bling:
49      - BLING package now loads in atmospheric pCO2 file using exf package routines
50        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
51    o model/src & pkg/ptracers:
52      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
53        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
54        implicitDiffusion (respectively) are used (even without momImplVertAdv
55        or temp,salt,PTRACERS_ImplVertAdv).
56    o model/src & generic_advdiff:
57      - add parenthesis in main diagonal calculation of implicit vertical
58        diffusion matrix (impldiff.F & gad_implicit_r.F).
59        This affects results at machine truncation level; update output of many
60        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
61    o pkg/mom_commom & generic_advdiff:
62      - add deep atmosphere and anelastic scaling factor in implicit vertical
63        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
64    o model/src:
65      - remove few unnecessary temp array copies in solve_tridiagonal.F
66        & solve_pentadiagonal.F
67    
68    checkpoint65z (2016/09/28)
69    o pkg/seaice: fix multithreading for seaice_fgmres.F
70      - remove unecessary variables from common blocks
71      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
72        basis, that are stored in commom blocks (including integer variable i1)
73      - clean up code a little by removing commented lines that refer to
74        original code
75      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
76    o MITgcm manual:
77      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
78        preliminary documentation for generic controls (8.3; ctrl.tex),
79        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
80        ecco_costfunction.tex
81    o pkg/ecco:
82      - update and cleanup list of CCP options
83      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
84        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
85      - add checks that retired run-time options are not used, and in relation
86        to gencost_mask and gencost_errfile
87      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
88        gencost_nrecperiod
89      - fix m_eta computation for virtual salt flux case
90      - add m_horflux_vol case (selected via gencost_barfile) that computes
91        transports via cost_gencost_boxmean (gencost_flag=-3)
92      - use gencost_flag more systematically (i.e., avoid using gencost_name)
93        for code switches (aside from physical variable selection)
94    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
95      attempt appears to be a bit of a hack and my need some repair down the road
96    o pkg/exf:
97      - interpolation near South Pole: fix criteria on input field latitude.
98    o pkg/icefront & pkg/exf:
99      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
100        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
101    o pkg/exf:
102      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
103        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
104        (add suffix "_out" instead of a prefix); keep same record number as in
105        input file but always write record 1 first (to avoid a STOP in I/O S/R).
106        Change output file content by writing interpolated field before applying
107        land-sea mask (helpful for debug).
108      - 2 compon. vector interpolation with rotation: apply scaling factor on
109        each compon. (Eastward and Northward) just before rotation.
110    o pkg/bling:
111      - Cleaned package. Removed not needed code and comments.
112      - adjoint example now works
113        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
114    o pkg/ptracers:
115      - add Bruno Deremble's code to complete the linear surface correction
116        for tracer conservation;
117      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
118    
119    checkpoint65y (2016/07/29)
120    o pkg/debug (stats):
121      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
122        proc/thread mapping);
123      - fix Min & Max for case where 1 thread has only empty tiles;
124      - use RL variable to count number of wet grid points (with big domain,
125        can be too large to fit into integer*4).
126    o pkg/monitor:
127      - use RL variable to count number of wet grid points (but used only for del2)
128      - add new routine to compute Advective CFL within tracer time-stepping with
129        writing delayed until next monitor output.
130    o pkg/obcs:
131      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
132    o pkg/cal:
133      - calandar-dump: treat case myTime < timePhase in the same way as in
134        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
135    o pkg/dic & seaice:
136      - fix compilation of ocean component for coupled atm+ocn model with
137        seaice dynamics & dic.
138    
139    checkpoint65x (2016/06/11)
140    o add a license text file in main MITgcm tree.
141    o added pkg/bling:
142      - intermediate complexity biogeochemical model
143      - see bling_description.txt for details
144      - verification experiment is global_oce_biogeo_bling (for now, in
145        Contrib/verification_other/); tested daily on baudelaire with gfortran.
146      - add entry point in pkg/gchem for new pkg "bling".
147    o pkg/seaice: fix tensile stength computation
148      - replace global field tensileStrength by tensileStrFac
149      - tensileStrFac can be computed once in S/R seaice_init_varia
150      - fortunately that does not affect any verification results
151    
152    checkpoint65w (2016/05/12)
153    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
154         with ECCO_CTRL_DEPRECATED defined
155    o verification/global_ocean.cs32x15:
156      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
157        with "selectNHfreeSurf=1".
158    o model/src (non-hydrostatic free-surface):
159      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
160        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
161      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
162        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
163        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
164        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
165      - Update output (changes at machine truncation level) of verification exp:
166        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
167        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
168    o pkg/seaice: ITD code
169      - fix picking up from a single category model by initialising
170        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
171      - split a long warning message in seaice_check_pickup.F into two lines,
172        because NEC SX-ACE cannot deal with the long line.
173    o model/src:
174      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
175    o pkg/seaice:
176      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
177    o pkg/seaice:
178      - add basal stress as parameterisation for grounding ice
179        following Lemieux et al. (2015)
180      - turn on by setting new parameter SEAICEbasalDragK2 to a value
181        larger than 0. Lemieux et al. (2015) recommend 15.
182      - The adjoint complains with extra recomputations so there is also a
183        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
184        order to postpone the problem
185      - compile the new code in lab_sea
186    o verification/halfpipe_streamice:
187      - update both TAF and OpenAD adm output (machine truncation differences)
188    
189    checkpoint65v (2016/04/08)
190    o verification/advect_xz:
191      - increase overlap size from 3 to 4 and add new secondary test for PQM
192        advection scheme (with mono & wino limiter).
193      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
194    o model/src:
195      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
196        added phi0Ref) to set vertical axis origin and phiRef origin;
197        keep Ro_SeaLevel for backward compatibility (with a warning).
198       According to coordinate and fluid type:
199        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
200        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
201        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
202        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
203      - remove Ro_SeaLevel from ATM experiment parameter files;
204      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
205        complement; update output.txt (changes at machine truncation level).
206    o pkg/seaice/seaice_evp.F
207      - simplify computation of deltaZ and zetaZ to simple averaging following
208        Bouillon et al. (2013). This removes a lot of code, but also changes
209        verification experiment lab_sea.hb87 -> updated
210    
211    checkpoint65u (2016/03/14)
212    o pkg/generic_advdiff:
213      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
214        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
215        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
216        testing and not for actual use.
217    o model/src:
218      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
219        origin r = rF(1);
220      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
221        in EOS for height coordinate: enable to include NH Pressure or to use
222        more accurate pressure vertical profile; options not linked to EOS type
223        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
224      - start to implement variable gravity (along vertical): for now, only with
225        z-coords (not even z*).
226      - add Ideal Gas equation of state for height coordinate.
227      - update OpenAD output (affected at machine truncation level) of exp:
228        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
229    o pkg/exf:
230      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
231        of exf interpolation (before any rescaling, rotation or interpolation
232        to velocity point) for each field that gets loaded from file. This option
233        identically mimics the input file organization (e.g. record numbers in year
234        by year input files) besides the change in horizontal grid.
235      - add rotateStressOnAgrid run-time switch so that wind stress fields
236        can be provided on the A-grid in zonal/meridional direction and
237        rotated on the fly. This only applies to the case when the exf
238        interpolation is off and rotateStressOnAgrid is false by default.
239    o model/src:
240      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
241        it's also used with pkg/atm_phys) and add few more parameters (but still
242        inactive, src code yet to come)
243    
244    checkpoint65t (2016/02/10)
245    o pkg/atm_phys:
246      - from Ruth Geen: add optical depth dependence on CO2 concentration.
247    o model/src:
248      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
249        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
250        Update output of exp. deep_anelastic (changes at truncation level).
251    o tools:
252      - add a hack in "remove_comments_sed" (used only with TAF) for recent
253        version of OpenMPI (shipped with FC.23): comment out the new header
254        file "mpif-sizeof.h" which causes problems to TAF.
255    o pkg/seaice:
256      - change the termination criterion so that maxits (SEAICElinearIterMax)
257        has an effect
258      - unify iteration parameters for implicit solvers (JFNK and Picard)
259        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
260        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
261        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
262        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
263        SEAICEnonLinTol     replaces JFNKgamma_nonlin
264      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
265      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
266        use with SEAICEuseKrylov
267    o pkg/seaice/seaice_lsr.F
268        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
269        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
270        an effect.
271    o pkg/seaice: add two new parameters
272      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
273        parameter is not in any namelist)
274      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
275        a preconditioner for the non-linear Newton iteration of the JFNK
276        solver
277    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
278      affects some experiments at truncation level:
279      - global_ocean.cs32x15.icedyn (11 digits),
280      - global_ocean.cs32x15.seaice (11 digits),
281      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
282      - also update global_ocean.cs32x15 adjoint and tangent-linear results
283    o pkg/salt_plume & pkg/thsice:
284      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
285        connect salt_plume flux to ATM-OCN coupling pkgs interface:
286       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
287         export to coupler interface) even without compiling pkg/salt_plume ;
288       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
289         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
290    o pkg/dic:
291      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
292        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
293        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
294      - move also update with values from ATM-OCN Coupler in the same new S/R
295        (previously done in ocn_apply_import.F).
296    o tools/adjoint_options:
297      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
298        has been changed on Jan 14, 2016.
299    o pkg/ggl90:
300      - add alternative discretisation of vertical shear (off by default), to
301        compute the mean (@ grid-cell center) of vertical shear compon instead of
302        vertical shear of mean flow (@ grid-cell center).
303      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
304        results on adjacent faces of cubed-sphere grids; this fix the restart.
305    o pkg/atm_compon_interf:
306      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
307        pass last value, stored directly before export to CPL ;
308        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
309      - remove atmSLPr from pickup files (no longer needed for restart)
310    
311    checkpoint65s (2016/01/13)
312    o eesupp & genmake2:
313       - first check for Function ETIME and, if it fails, then check for subroutine
314         ETIME and consistent output; use the appropriate version in timers.F
315    o model/src:
316      - to check restart test, add option to apply EXCH to U,V earlier, just before
317        integr_continuity; turned off by default.
318    o pkg/dic:
319      - remove CPP option USE_ATMOSCO2 (not needed)
320    o tools/tst_2+2:
321      - try to ignore difference between +0 and -0 in binary file, causing test
322        to fail for no good reason.
323    o eesupp & genmake2:
324      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
325        but also check (in genmake2) that test runs and returns meaningful results.
326    o coupler pkgs:
327      Finish implementation of optionally-exchanged variable switches (started on
328       Nov 12) with addition of few more exchanged fields, including 2-way exchange
329       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
330       advection in OCN component; this requires sequential coupling.
331      coupler (pkg/atm_ocn_coupler):
332      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
333        routines (useful for debug).
334      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
335         flux, DIC fields) if corresponding switch is ON.
336      - add option to export RunOff to OCN (to use for DIC river input)
337      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
338      components (pkg/atm_ & ocn_compon_interf):
339      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
340        optionally exchanged fields; add a check & stop in cpl_readparms.F.
341        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
342        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
343      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
344        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
345      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
346      - hold in common block coupler optionally-exchanged variable switch
347        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
348      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
349        this is intended to replace the OCN cplFldtave.* output files (not updated
350        to contain new additional exchanged fields).
351    o pkg/dic:
352      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
353    o pkg/thsice:
354      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
355        and writing of thsice pickup files.
356    o pkg/atm_compon_interf:
357      - move all field individual export-call out of cpl_export_import_data.F
358        into new S/R ATM_EXPORT_FIELDS
359    o pkg/atm_compon_interf:
360      - store state variables (for now, only thSIce fields) just before beeing
361        exported (in cpl_export_import_data.F, like on ocean side) instead of from
362        atm_store_my_data.F like all exported fluxes.
363      - new version of pickup_cpl: write field names into meta file and read meta
364        file to find field postion in pickup. Also only write/read fields meeded for
365        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
366    o pkg/dic:
367      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
368    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
369        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
370        value can be from domain [0,1] to average between the two methods
371    o pkg/atm_phys:
372      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
373        hold fixed in time).
374    
375    checkpoint65r (2015/12/21)
376    o pkg/seaice:
377        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
378        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
379    o pkg/seaice:
380      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
381        when SEAICEscaleSurfStress=.TRUE.,
382      - apply areaW and areaS in S/R seaice_calc_lhs
383    o pkg/atm_phys:
384      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
385        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
386        for individual contribution (convection, LSC cond, radiation)
387      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
388        information); activated with: solar_exponent=0. and wv_exponent=-1.
389    o pkg/ggl90:
390      - within IDEMIX add upper limit for horizontal group velocity to
391        avoid instability problems in the explicit horizontal diffusion term for
392        long time steps or high resolution
393    o pkg/diagnostics:
394      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
395        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
396    o testreport:
397      - remove "-v" (verbose option) in default mpirun command.
398    o pkg/seaice/seaice_growth:
399      - catch potential division by zero in ITD code, does not change
400        verification results
401    o pkg/ecco:
402      - retire old codes to the Attic. The calls to retired functions are
403        left in a commented form in case they ever need to be re-activated.
404      - ecco_check.F: issue warning if any old CPP option is
405        defined that corresponds to retired codes -- then stop.
406    o pkg/atm_compon_interf:
407      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
408        coupler: use last time-step value instead of average over cplSendFrq_iter
409        time-step, similar to what is done for seaIceMass.
410        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
411    o eesupp & genmake2:
412      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
413        <= remove until a fix is found for some ifort version on ia32 machine.
414    o pkg/seaice/seaice_evp:
415      - refine residual computation
416    
417    checkpoint65q (2015/11/18)
418    o pkg/seaice/seaice_evp:
419      - fix residual computations so that they no longer affect the actual
420        simulation code
421      - fix seaice_readparams to be able to actually set new parameters
422        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
423    o model/src:
424      - fix wrong truncation (single prec) from "FLOAT" function in expressions
425        like: deltaT*FLOAT(myIter) when myIter is large:
426         a) replaced by DFLOAT (if not seen by TAF);
427         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
428    o pkg/aim_v23:
429      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
430        when pickupSuff is set ; do write rolling pickups + at the end of the run.
431    o pkg/atm_ocn_coupler + ocn_compon_interf:
432      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
433        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
434        add corresponding call in DO_OCEANIC_PHYS.
435    o coupler pkgs:
436      Start a new way to set-up optionally-exchanged variables (previously, only
437       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
438       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
439       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
440       compononent param default can be set accordingly).
441      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
442       but rather applies to a group a fields (going both ways like for DIC)
443       and corresponds to an option of coupling config.
444      coupler (pkg/atm_ocn_coupler):
445      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
446        and read namelist directly (without eessup S/R calls) instead of
447        in the very un-flexible old way, 1 param per line, in fixed order;
448      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
449        cleanly in CPL_CHECK_CPLCONFIG
450      - add new coupling-exchange selectors (some not yet active) including
451        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
452                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
453      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
454        component ; called directly from coupler.F, after comp. registrations;
455      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
456         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
457          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
458      components (pkg/atm_ & ocn_compon_interf):
459      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
460        CPP header file in all pkg source files.
461      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
462        ATM/OCN_CHECK_CPLCONFIG;
463      - add error-counter to track errors (e.g., in "data.cpl") and to stop
464        cleanly in ATM/OCN_CHECK_CPLCONFIG;
465      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
466        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
467        before PACKAGES_READPARMS;
468      verification/cpl_aim+ocn/:
469      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
470        "data.cpl" for coupler (in input_cpl).
471    o eesupp/inc:
472      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
473        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
474        to always cumulate tile local-sum in the same order (still uses
475        MPI_Allreduce like standard code).
476      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
477        that are now identical to standard version (in eesupp/inc).
478    o pkg/shelfice:
479      - add SHELFICETransCoeffTFile for initializing spatially varying
480        heat and salt transfer coefficients
481    o pkg/atm_compon_interf & ocn_compon_interf:
482      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
483        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
484      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
485    o pkg/atm_ocn_coupler:
486      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
487    o pkg/rbcs:
488      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
489        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
490      - add a short report (to STDOUT) about RBCS-mask settings.
491    
492    checkpoint65p (2015/10/23)
493    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
494        there is no adjoint test for EVP, we don't know what it does to the adjoint
495        solution, but at least there are no more recomputation warnings left
496    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
497        a chance of giving the same results as a fully converged VP (JFNK) solver
498    o tools/adjoint_options/adjoint_diva:
499      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
500    o pkg/streamice:
501      - spotted bug in streamice_driving_stress using dyG where should have been dxG
502    o pkg/exf:
503      - remove STOP statement that prevented to use wind or (wind-)stress
504        interpolation for constant-in-time forcing fields (wind/stress period = 0).
505    o pkg/seaice:
506      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
507        5 additionals 2D fields and 6 new store directives
508      - change logic in seaice_readparms.F: EVP code can now be turned on in
509        various ways, setting SEAICE_deltaTev is no longer required,
510        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
511        or SEAICEaEVPcoeff
512    o pkg/shelfice/shelfice_thermodynamics.F
513      - redefining uLoc/vLoc to u/v, instead of 2u/v
514    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
515      - this is an intermediate state of a truely converging EVP that has
516        the potential of outperforming implicit VP methods, I do not recommend
517        using it yet.
518      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
519        and all parameters are hardwired
520      - for convergence it still requires very smooth regularisations, that means,
521        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
522        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
523        specific averaging appears to be required, still subject to tuning
524      - still needs cleaning and I need to turn parameter into runtime parameters
525      - add code to compute and print residuals of iteration, compile with
526        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
527    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
528      that entered with r1.54 on Sep04, 2015, -> update results
529    
530    checkpoint65o (2015/09/14)
531    o pkg/mom_vecinv & mom_common:
532      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
533        called from there.
534      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
535        allows to use Vector-Invariant form in deep atmos and anelastic formulation
536  o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)  o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
537    and Koenig-Beatty+Holland (2012)    and Koenig-Beatty+Holland (2012)
538    - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth    - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
# Line 15  o pkg/seaice: introduce new parameter SE Line 544  o pkg/seaice: introduce new parameter SE
544    - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice    - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
545      by AREA according to Connelly et al. (2004), JPO.      by AREA according to Connelly et al. (2004), JPO.
546    - For EVP and the LSR solver, the implicit part of the drag term is    - For EVP and the LSR solver, the implicit part of the drag term is
547      the only non-zero term in the denominator when there is no ice (which      the only non-zero term in the denominator when there is no ice (which
548      prevented running the model with zero ice-ocean drag). If      prevented running the model with zero ice-ocean drag). If
549      SEAICEscaleSurfStress = .TRUE., this results in a division by zero      SEAICEscaleSurfStress = .TRUE., this results in a division by zero
550      (or zero main diagonals BU/BV) which need to be caught. A practical      (or zero main diagonals BU/BV) which need to be caught. A practical
551      consequence is that for open water, the momentum equation reduce      consequence is that for open water, the momentum equation reduce
552      to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if      to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
553      they happen to be zero, often leading to a non-zero solution over      they happen to be zero, often leading to a non-zero solution over
554      open water.      open water.
555  o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more  o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
556      efficient EVP method.      efficient EVP method.
557    - introduce area-weighted averages for e12 (analogously to    - introduce area-weighted averages for e12 (analogously to
558      seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits      seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
559      remain, but also changing the order of terms in the previous average      remain, but also changing the order of terms in the previous average
560      changed the results as much) -> update experiment      changed the results as much) -> update experiment
561    - add SEAICE_DELTA_SMOOTHREG code    - add SEAICE_DELTA_SMOOTHREG code
562    - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for    - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
563      TEM-code      TEM-code
564    - adjust loop bounds so that only required fields are computed    - adjust loop bounds so that only required fields are computed
565    - add new averaging code for zetaZ/deltaZ (again similar to    - add new averaging code for zetaZ/deltaZ (again similar to
566      seaice_calc_viscosities.F), inactive by default for now (will change      seaice_calc_viscosities.F), inactive by default for now (will change
567      results again), but will replace old code eventually      results again), but will replace old code eventually
568  o eesupp/src:  o eesupp/src:
# Line 44  o eesupp/src: Line 573  o eesupp/src:
573      and should be faster than GLOBAL_SUM_SEND_RECV code.      and should be faster than GLOBAL_SUM_SEND_RECV code.
574    - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV    - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
575      (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.      (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
576    - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 13 more exp.:    - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
577       aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,       aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
578       fizhi-cs-aqualev20, global_ocean_ebm, matrix_example, natl_box,       fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
579       solid-body.cs-32x32x1, tutorial_advection_in_gyre, tutorial_baroclinic_gyre       natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
580       and tutorial_held_suarez_cs.       tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
581    
582  checkpoint65n (2015/07/29)  checkpoint65n (2015/07/29)
583  o pkg/thsice:  o pkg/thsice:
# Line 378  o model/src & mom pkgs: Line 907  o model/src & mom pkgs:
907      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
908  o doc:  o doc:
909    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
910  o pkg/streamice:  o pkg/shelfice:
911    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
912      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
913      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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