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revision 1.632 by mlosch, Wed Mar 15 19:52:16 2006 UTC revision 1.839 by mlosch, Tue Jun 19 12:39:54 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice:
8     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
9     - fix bug in metric terms of u-equation in LSR solver (implicit part),
10       changes verification/lab_sea
11     - rearrange implicit part of u-equation in LSR solver to make it easier to
12       read, understand, and debug. This causes changes at the truncation level.
13     - fix (serious) bug in the boundary conditions (sign error in the implicit
14       part) of the LSR solver. Changes all LSR results.
15    o pkg/smooth: addition to model/src and pkg/ctrl so allow
16     initialization of pkg/smooth and application to control vector
17    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
18    o dependencies: pkg/profiles requires pkg/cal
19    o pkg/profiles:
20     - added option ALLOW_PROFILES_GENERICGRID
21         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
22         that interpolation information (grid points and coefficients) is provided
23         within the netcdf input files.
24         -> sample matlab scripts can be found in MITgcm_contrib/gael
25         that allow you to prepare netcdf input files.
26     - also modified: cleaner include statements, cleaner error print statements,
27       cleaner stops when error, and more tests of the netcdf input files consistency.
28    
29    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
30    o pkg/seaice:
31     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
32       requires a new routine: seaice_diagnostics_fill.F
33     - make sure that seaice does not move if not forced (pressure replacement
34       method, Hibler and Ip, 1995), changes results
35     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
36     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
37       It is turned off by default (=-1.), because it changes the results.
38     - make it possible to read AREA from a file, too.
39    
40    checkpoint59c
41    o add S/R and diagnostics for oceanic mixed-layer depth
42    o move GMRedi call after all vertical mixing schemes (including KPP)
43    o pkg/thsice:
44     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
45      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
46    o pkg/obcs:
47     - bug fix for balance code
48    o pkg/seaice:
49      - allow values of SEAICE_elasticParm > 1
50      - add new parameter SEAICE_evpTauRelax as an alternative
51        to SEAICE_elasticParm
52      - make lsr boundary conditions free slip (by default), changes result
53      - add code for no slip boundary conditions for lsr
54      - set minimum of zeta to zero (and not 4e8) (changes results)
55      - add a cap on AREA after advecting AREA if seaice_growth is not called
56    o change calculation of Visbeck K:
57      - no longer depend on tapering scheme; instead, compute slope (limited
58        by GM_maxSlope). this is equivalent to what was comuted before with
59        clipping or linear tappering.
60      - fix vertical averaging (wrong by 1/2 level)
61      - leave the old version (but will not be maintained) within
62        #ifdef OLD_VISBECK_CALC / #endif
63      - update output of exp. ideal_2D_oce
64    o change error catch in calc_r_star to improve vectorization
65    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
66      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
67    o adjoint:
68      Re-organized adjoint checkpointing according to Matt Mazloff
69      (but with modifs/completions/cleanups)
70      Storing is now bundled into large arrays to optimized I/O
71      (and second step in cleanup of the_main_loop)
72    
73    checkpoint59b
74    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
75      - export/import (between ocean & coupler) fields needed for ocean DIC.
76    o pkg/seaice:
77      - get rid of three more exchanges seaice_calc_viscosities (required
78        different loop boundaries in seaice_lsr and seaice_ocean_stress)
79      - bug fix in seaice_ocean_stress (update of lab_sea required)
80      - reduce loop boundaries to necessary minimum also in seaice_evp
81      - go back to the old way of computing deltaC/Z as the adjoint likes that
82        better
83    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
84      passive tracer to an Age Tracer) + update output.txt
85    o pkg/exf:
86      - implement A-grid / C-grid selection for wind-stress input files.
87      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
88      for now, in exf_bulk_largeyeager04.F only :
89      - change implementation for case where windspeed + 2. components wind-stress
90        are read-in. AND use rhoConstFresh to convert evap.
91    o pkg/seaice:
92      - use correct EXCH_UV for wind-forcing (on A-grid).
93      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
94        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
95    o pkg/exf:
96      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
97      EXF_INTERPOLATION:
98      - merge global_with_exf/code version of exf_interp_read.F
99        to the main code ;
100      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
101        reading the file ; Important: This options needs to be defined to recover
102        previous code.
103        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
104      - no longer loose real*8 precision along the way when using exf_iprec=64.
105    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
106      - change discretisation of evp-solver in order to avoid another exchange
107        (changes lab_sea) and clean up a little
108      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
109        help the adjoint (this also changes the results slightly)
110      - add a few "_d 0" where they had been missing in seaice_evp.F
111      - cleaning up: remove unused seaice_calc_rhs.F
112    o pkg/exf: some cleaning-up:
113      - change various "constants" into runtime parameters
114      - cleaned-up Large&Yeager04 routine which should eventually
115        replace exf_bulkformulae.F (changed names of S/R and CPP)
116        and merged various ALLOW_ATM_WIND options
117     only used with thsice pkg (in thsice_get_exf.F):
118      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
119        which are used when useStabilityFct_overIce=TRUE (= the default)
120      - change default values of ice & snow emissivity and scale downward LW
121        by ice & snow emissivity.
122    o pkg/thsice:
123     fix few little problems, in thsice_calc_thickn.F:
124      - growth vertically (and not laterally) if iceFrac == iceMaskMax
125      - melt only laterally if hIce < hThinIce (as the comments say)
126      and in thsice_extend.F:
127      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
128      - start to form ice as soon as the minimum ice-volume is reachable.
129     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
130      and cpl_aim+ocn
131    o pkg/kpp
132     - move computation of surface related input fields to KPP into a new
133       subroutine kpp_forcing_surf.F
134     - remove wrong (within bi,bj loops) EXCH calls.
135     - little cleaning (add argument myThid in last position, cvs header ...)
136     - for now, fix conservation problem by exchanging KPPviscAz (may not
137       be the best fix)
138    o pkg/seaice
139     - check for inconsistent evp parameter/cpp-flag combination
140     - remove leftover errIO flat for obsolete name list error handling
141    o OpenAD
142     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
143    
144    checkpoint59a
145    o pkg/seaice: some parameter clarifications and a little bit of clean up
146    o pkg/thsice: rename run-time parameters:
147       himin       -> hIceMin
148       himin0      -> hThinIce
149       hihig       -> hThickIce
150       i0          -> i0swFrac
151       transCoef   -> bMeltCoef
152       frac_energy -> fracMelting
153      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
154       with default values (for now) that do not change the results.
155      remove old version of thsice vars advection in pkg/seaice.
156    o in FFIELDS.h:
157      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
158      - make pLoad & sIceLoad always available (but still only used if
159         ATMOSPHERIC_LOADING is #define).
160    o pkg/kpp: replaced _KPP_RL with _RL
161    o bug fixes for vertical diffusivity computations when both KPP and
162        3D diffusivity arrays are used.
163    o pkg/seaice: fix bug in evp solver, while doing that
164      - change (improve?) discretization of stress computations for both
165        cgrid-lsr and evp solver
166      - add a new routine to compute strain rates
167      - the above changes lab_sea results
168      - add no slip conditions for evp solver (off by default), lsr-version
169        may follow
170      - fix exchange for shear at Z-points (does not change lab_sea)
171      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
172        (to force the user to pick a time step since there is not "safe" way
173        of choosing it)
174      - add principal stress diagnostics
175      - rearrange fields for evp a little to avoid having to call a: too many
176        exchanges and b: exchanges for stress trensor components which we do
177        not have.
178      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
179        of evp, complete rewrite for lsr case (latter is does not yet work
180        in all cases)
181    o pkg/kpp: add code to have mixing in shelf ice caverns
182      - add myThid to all kpp routines (long overdue)
183    
184    checkpoint59
185    o pkg/exf:
186      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
187        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
188      - move exf header files from lower_case.h to UPPER_CASE.h ;
189        add missing cvs Header & Name
190      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
191      - add namelist param. selectStressGridPosition, exf_monFreq
192      - retire many _CLIM routines, and remove data.exf_clim
193        + params moved to data.exf
194        + climsst, climsss now handled by exf_set_gen, i.e.
195          climss?period=0 refers to constant field,
196          climss?period=-12 to monthly forcing
197      - split up namelists in data.exf
198    o pkg/seaice:
199      - remove seaice_exch and seaice_exch_uv
200      - remove superfluous exchange of theta
201      - add myThid to seaice_budget_ocean/ice
202      - add new interface for atmospheric wind forcing (C-grid only)
203        + new routine
204        + two new field (taux, tauy for stress over ice)
205        + removed one global field (DAIRN) for C-grid case only
206    o pkg/thsise
207      - 2nd set of modifs for thsice adjoint in conjunction with exf
208    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
209    
210    checkpoint58y_post
211    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
212      vertical diffusivity, similar to that in MOM4; turned on using
213      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
214      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
215    o Added capability for 3D specification of background vertical diffusion
216      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
217      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
218      "data" file that contains the 3D vertical diffusivity coefficients.
219    o ice dynamics (pkg/seaice) with thsice thermodynamics:
220      - add code within pkg thsice to advect & diffuse sea-ice fields
221      similar to (and will replace) what has been added in  seaice_advdiff.F,
222      but: - conserving Mass, Heat & Salt.
223           - better when using non-linear advection scheme (not yet fully tested)
224           - can also be used in atmospheric set-up (for now, only the diffusion).
225    
226    checkpoint58x_post
227    o IO option for global-file compact format:
228      - add options when generating topology (utils/exch2/matlab-topology-generator)
229      - add I/O capability (pkg/mdsio).
230      - adapt utils/matlab/rdmds.m to read this format.
231      for now long-line format not yet supported by pkg/mdsio (& exch2).
232    o shelfice: add a few diagnostics
233    
234    checkpoint58w_post
235    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
236      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
237      (and replace horiVertRatio in NH code).
238      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
239                         and tutorial_plume_on_slope (sensitive to truncation)
240    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
241      directly to drive seaice model (C-grid only)
242    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
243     - reintroduce computation of wind from stress,
244     - compute tau (in exf_bulkformulae.F) from windstress averaged to
245       mass points to avoid tau = 0
246     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
247    o rdmnc.m: make it work with "global" files created with gluemnc
248    o rdmnc.m : some improvements in dealing with singleton dimension
249      (tested on all testreport mnc output files).
250    o genmake2: disable pkg/profiles if netcdf test fails.
251    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
252    o move call to cal_readparms up to make calendar parameters/variable available
253      to all packages
254    
255    checkpoint58v_post
256    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
257      useDynP_inEos_Zc tested.
258    o pkg/exf: changes to properly interpolate/mask/scale initial fields
259    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
260      and portions thereof.  See read_cs.txt for description and examples.
261    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
262      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
263      following the great-circle arc between those 2 points.
264    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
265      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
266    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
267     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
268     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
269     - still needs work (not working with some options ; efficiency to improve)
270       and serious testing.
271     - use this scheme for temperature & salinity in 2 advection test exp.:
272       advect_xy & advect_xz, respectively.
273    
274    checkpoint58u_post
275    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
276    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
277    o testreport: add option "-skipdir" to skip some test.
278    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
279      momentum calculation.
280    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
281    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
282      remove checkpoint.F and the_correction_step.F (no longer used);
283      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
284    o add option (linFSConserveTr) to correct for tracer source/sink due to
285      Linear Free surface
286    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
287    o pkg/thsice: fix reading mnc-pickups
288    
289    checkpoint58t_post
290    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
291    o pkg/mdsio:
292     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
293       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
294       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
295     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
296     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
297       either MDS_READ_FIELD or MDS_WRITE_FIELD )
298     - new S/R (to replace MDSWRITEMETA), which allows to write more
299       informations (variable names, time ...) to meta files.
300     - modify rdmds.m to give back the meta file content.
301    o pkg/diagnostics: change vertical interpolation to be safer, and more
302       flexible (define p-levels to interpolate to in data.diagnostics);
303      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
304       diagnostic pointer.
305    o pkg/seaice: more cleaning up of seaice_growth, added many comments
306    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
307    o fix multi-category seaice:
308     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
309       SEAICE_MULTICATEGORY
310     - fix short wave heat flux
311    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
312       and allow to use EVP solver. Change forward lab_sea: test both EVP
313       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
314    o Initial check-in of lab_sea adjoint
315      (very similar to natl_box_adjoint/code_seaice)
316      * used C-grid and EVP solver
317      * used KPP, GM/Redi
318      * uses inAdExact=.TRUE.
319      * gradient checks fail for both ADM and TLM
320        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
321        f.d. gradients actually seem more problematic than ADM, TLM gradients;
322        issue is related to forward mismatch between g77 an ifort
323    o pkg/seaice: overhaul of thermodynamics
324     - growth.F and groatb.F are replaced by new routine seaice_growth.F
325     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
326     - move a few global fields out of SEAICE.h into seaice_growth.F and
327       make them 2D (FICE/QNETO/ ...)
328     - remove FO (it is the same as QNETO)
329     - introduce a few local fields to avoid modifying external fields such
330       as atemp, etc.
331    
332    checkpoint58s_post
333    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
334      changed exf_set_gen.F so that
335        genperiod=0 means input file is one time-constant field and
336        genperiod=-12 means input file contains 12 monthly means
337    o CG2D: use pre-computed solver main-diagonal (stored in common block);
338      this affects truncation error ; generate new output file for exp. which
339      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
340        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
341        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
342        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
343        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
344        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
345    o start implementation of deep-atmosphere and anelastic formulation
346    o verification: remove 2nd copy of input files and use script "prepare_run"
347      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
348    o mom_common/vecinv/fluxform: fix a few initialisation isssues
349    o profiles: fix for multithreaded case
350    
351    o diagnostics: rename few diags:
352      s/'PRESSURE'/'RCENTER '/g
353      s/'TICE    '/'oceFreez'/g
354      s/'TAUX    '/'oceTAUX '/g
355      s/'TAUY    '/'oceTAUY '/g
356      s/'SWFLUX  '/'oceQsw  '/g
357      s/DIFx/DFxE/g
358      s/DIFy/DFyE/g
359      and add few ocean-forcing diagnostics:
360      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
361    o modifications to pkg/seaice/growth.F and budget.F, which change results of
362      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
363      as actual snow thickness.  It now refers everywhere to effective snow
364      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
365    
366    checkpoint58r_post
367    o modifications to pkg/seaice/growth.F, which change results of
368      lab_sea experiment: fixes pertain to melting snow over open water, to
369      masking EVAP under sea ice, and to using the correct AREA variable for
370      computations of EVAP, PRECIP, HSNOW, and GHEFF
371    o add ability to read bathy, salt, and theta using MNC (off by def)
372    o add flooding algorithm and advection of HSNOW for pkg/seaice;
373      both are turned off by default and do no change any results
374    o seaice advection with pkg/thsice: a step toward the use of non-linear
375      advection scheme, but #ifdef or commented out for now (requires more EXCH).
376    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
377      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
378      in natl_box (affects results @ truncation level: update output.txt)
379    o multi-threading and IO:
380      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
381      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
382        (needed to work with SingleCpuIO): tested in all verif. exp.
383    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
384      affects the results (but none of the verification test uses this scheme).
385    o Adding some pkg/diagnostics capability to pkg/seaice
386      (will certainly be subject to changes)
387    o ctrl: adding new control variables:
388      lwflux, lwdown, evap, snowprecip, apressure, runoff
389    
390    checkpoint58q_post
391    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
392      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
393      high_res_cube configuration by 4% on Columbia.
394    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
395      add (in global_with_exf/code) a version of EXF_INTERP_READ without
396      dynamical allocation (seems to work in multi-threaded).
397    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
398      single CPU io) so that TAF does not have to see EESUPPORT.h
399    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
400    
401    checkpoint58p_post
402    o obcs: stop if obcs is used with useCDscheme = .true.
403    o shelfice:
404     - fix a sign error so that no slip at shelfice interface works
405     - remove stop for combination non-hydrostatic code and shelfice. That does
406       not mean, that the results are correct, but at least they are numerically
407       stable
408    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
409    o added adjoint exch routined for all exch*3d* routines
410      and updated flow directives
411    
412    checkpoint58o_post
413    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
414      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
415    o change controling S/R for writing pickup file (new S/R do_write_pickup)
416      and clean-up reading/writing of pickup files.
417    o fix local version of read/write pickup (NH part) in rotating_tank/code
418    o simplify EXCH interface:
419     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
420     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
421    o added the regrid package
422    o shelfice:
423     - add a simple boundary layer scheme to reduce noise
424     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
425    
426    checkpoint58n_post
427    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
428       local variable (not in common block).
429    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
430      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
431      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
432        to work with SingleCpuIO.
433    o add "_d 0" to real constant of pkg/cfc subroutines ;
434       update exp. cfc_exemple & tutorial_cfc_offline output files.
435    o multi-threading and IO:
436      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
437        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
438      - barrier before and after reading.
439      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
440      - avoid using MDS_WRITELOCAL for LAND pkg output.
441      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
442        common-block variables ; Allows multi-threading with master-thread IO.
443    o change default MAX_NO_THREADS from 32 to 4 ;
444      and stop cleanly when MAX_NO_THREADS is too small.
445    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
446    
447    checkpoint58m_post
448    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
449       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
450    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
451       keep global_ocean.90x40x15 (for AD testing) with former secondary test
452       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
453    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
454        add MITgcm_tutorials (= code + all the tutorials)
455    o ecco, option to compute cost for total ssh (mean+anom)
456    o consistent with addition of ptracer and ssh in pkg/profiles
457    o profiles: adding ptracer and ssh
458    o testreport: change multi-test output-file name
459      (from output.txt.{name} to output.{name}.txt)
460    o profiles: now ok for mutli-tiles case
461    o seaice: add 4 parameters for different advection schemes for area,
462      (effective) seaice thickness, enthalphy, and snow height. Their default
463      is the standard parameter SEAICEadvScheme
464    o calc_gw:
465     - add cosFacU in zonal viscous flux (harmonic.visc.).
466     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
467       of tutorial_plume_on_slope.
468    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
469    o calc_gw: true flux-form, account for horizontal grid spacing.
470      update rotating_tank results, but not plume_on_slope (affected at
471      truncation level, 11 digits).
472    
473    checkpoint58l_post
474    o calc_gw:
475     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
476     - remove side-drag for now (need to fix it); update plume_on_slope results.
477     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
478    o commit code to make SST/SSS weights spatially variable
479      (based on either variable in-situ or variable initial T/S weights)
480    o pkg/ecco:
481      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
482        now based on horizontally varying weights wthetaLev, wsaltLev
483      * cost_averagesflags now returns year indices in addition to day, month
484      * sflux balance is performed on annual basis
485        (sflxumm, sfluxmm2, bal_sfluxmm)
486      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
487        including separate counting and multipliers
488    o pkg/rbcs
489      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
490    
491    checkpoint58k_post
492    o testreport:
493     - always build in dir. "build" (if not there, mkdir build instead of building
494       & running in input)
495     - run in dir run (if it exists), in build otherwise.
496     - call prepare_run (if input/prepare_run exists)
497     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
498    o pkg/exf modifications to interpolation and rotation routines for more
499       reasonable treatment of North Pole singularity: for tracers North Pole
500       value is set to northernmost zonal-mean value, for zonal velocity it is
501       set to zero, and for meridional velocity it is set to northernmost value.
502    o pkg/exf/exf_check_range.F
503     - add tile index to diagnostics and move stop statement to the very
504       end of the routine.
505    o pkg/diagnostics: (diagnostics_main_init.F)
506      define title of isomorphic variables according to the current config.
507    o pkg/thsice with pkg/seaice dynamics:
508    - fix domain of computation (interior only, required for exf) and do exchanges
509    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
510    o towards a standard way of dealing with multi-threading in MONITOR
511      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
512    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
513       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
514    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
515    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
516    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
517       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
518    o tracer advection:
519     - clean-up and simplify calc_common_factors.F
520     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
521       advection subroutine (but still not used within DST advection S/R)
522    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
523    
524    checkpoint58j_post
525    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
526      from file (collects calls previously in FORWARD_STEP)
527    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
528    o adjoint store dir. adjusted accordingly
529    o genmake2
530      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
531    
532    checkpoint58i_post
533    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
534      on wind stress (SEAICEstressFactor defaults to 1.)
535    o Total number of Timers is finite (<=40): comment out 2 non-essential one
536      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
537    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
538      on CS-grid: no longer loosing mass.
539    o exf & curvilinear-grid: no longer modify longitude xC & xG.
540    o pkg/ggl90: fix sloppy output and fix a bug
541    o pkg/seaice: added SEAICEuseEVPpickup parameter
542      - Set to false in order to start EVP solver with
543        non-EVP pickup files when using SEAICEuseEVP
544      - fix sign error in diffusion in seaice_calc_rhs
545    
546    checkpoint58h_post
547    * Modifications for bottom topography control
548      o replace hFacC by _hFacC at various places
549      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
550      o add non-self-adjoint cg2d_nsa
551      o update autodiff support routines
552      o re-initialise hfac after ctrl_depth_ini
553      o works for 5x5 box, doesnt work for global_ocean.90x40x15
554    * Adding verification for 5x5 box (4-layer) bottom topography control
555    
556    checkpoint58g_post
557    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
558       used for mean seasonal cycle, mean diurnal cycle); add an example
559       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
560    o pkg/ggl90:
561      - add parameter (minimum surface kinetic energy)
562      - fix bug (avoiding division by zero)
563    o couple pkg/thsice to pkg/seaice:
564      - modify advection in seaice to accomodate new scalar fields to be advected
565      - only muliDimAdection scheme work with seaice/thsice
566      - mapping of thsice-variables to seaice-variables, back and forth
567      - does not break the verification experiments, but does not give the
568        desired results either
569    o pkg/seaice
570      - make (default) second order advection a bit less confusing?
571    
572    checkpoint58f_post
573    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
574      to pkg/seaice):
575      - new routines thsice_map_exf and thsice_get_exf provide the interface
576      - add an additional formal parameter to thsice_solve4temp
577    o pkg/exf:
578      - add new fields wspeed, snowprecip (to be able to couple to thsice)
579      - correct Stefan-Boltzmann constant
580      - new parameter for longwave surface emittance
581      - separate some stuff from exf_bulkformulae into new routines  
582        exf_radiation, exf_wind
583      - add new parameters and constants: longwave emissivity for ocean, ice
584        and snow, evaporation parameters over ice
585      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
586        either wind from stress or stress from wind
587    o pkg/thSIce:
588    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
589    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
590       and THSICE_CALC_THICKN
591    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
592    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
593      to make debugging easier.
594    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
595    o pkg/bulk_force:
596      - clean-up comments and parameters ;
597      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
598    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
599      generate new output for test-experiment: aim.5l_cs.thSI
600    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
601      testreport accordingly
602    
603    checkpoint58e_post
604    o SEAICE_CGRID adjoint done
605    o R_STAR adjoint implemented.
606      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
607      * need to sort out init. of h0facc, etc.
608    o Make pkg/profile fully independent of ecco,cost, etc. stuff
609      to be able to use it in pure forward.
610    
611    checkpoint58d_post
612    o upgrade simple test-experiment to tutorial example:
613     step.1: duplicate the experiment and (step.2) will remove the old copy.
614      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
615      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
616      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
617      tutorial_global_oce_biogeo    <- copy of dic_example
618      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
619      tutorial_plume_on_slope       <- copy of plume_on_slope
620      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
621      tutorial_global_oce_optim     <- empty for now (David ?)
622      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
623     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
624    o correct a sign problem in cost_scat.F
625    o obcs and ptracers: fix boundary conditions for advections schemes
626      with larger stencil
627    o thsice adjoint: start
628    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
629      completeness
630    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
631      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
632    o ptracers adjoint:
633      * avoid extensive recomputatations
634      * fix missing re-init. of gptr (missed by TAF)
635    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
636      me to turn off the excessive output to STDOUT that this package produces
637    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
638      and add those terms in Vector-Invariant formulation.
639    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
640      if the control period (xx_hfluxperiod etc) is 0
641    o in profiles pkg, clean routines and fix details
642    o in ecco pkg, reading ssh data:
643      fix problem in case the model does not start at iter0=0
644    o fix mnc-pickup/restart for ptracers
645    o new package prifiles:
646      code to compute profile-based cost by Gael Forget
647      (modifs in ecco, ctrl, autodiff)
648    o Benign bug fix in initialization (spotted by M. Mazloff) of
649      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
650    
651    checkpoint58c_post
652    o adjoint: finish NLFS adjoint and provide reference output in
653      verification/global_ocean.90x40x15/results_ad_nlfs
654    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
655      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
656      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
657      with SEAICE_CGRID defined.
658    o move calendarDumps from "data" to "data.cal" and clean-up the code
659      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
660    o add useEXF & useCAL flags (for now, set in hard-coded way)
661    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
662      (were missing in NH mode, and wrong in quasihydrostatic mode).
663      waiting for Chris updated version of calc_gw to add those CALLs.
664    o fix bug in quasihydrostatic S/R ;
665      add a test for this option: global_ocean.90x40x15.qshyd
666    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
667      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
668    o add on/off flag useOffLine for package OFFLINE
669  o seaice:  o seaice:
670    - modify advection so that it works also on the C-grid    - modify advection so that it works also on the C-grid
671    - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes    - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
672      problem in multi-tile runs with C-grid      problem in multi-tile runs with C-grid
673    - remove velocity clipping from seaice_dynsolver with C-grid    - add flags for clipping ice velocities and/or masking solver forcing
674    - fix drag (ocean on ice) formulation and a bug that caused noise in the    - fix drag (ocean on ice) formulation and a bug that caused noise in the
675      C-grid solver      C-grid solver
676    - added a few comments to seaice_diffusion.F    - added a few comments to seaice_diffusion.F

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