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revision 1.747 by dimitri, Mon Nov 20 20:06:43 2006 UTC revision 1.838 by gforget, Tue Jun 19 03:44:19 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/smooth: addition to model/src and pkg/ctrl so allow
8     initialization of pkg/smooth and application to control vector
9    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
10    o dependencies: pkg/profiles requires pkg/cal
11    o pkg/profiles:
12     - added option ALLOW_PROFILES_GENERICGRID
13         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
14         that interpolation information (grid points and coefficients) is provided
15         within the netcdf input files.
16         -> sample matlab scripts can be found in MITgcm_contrib/gael
17         that allow you to prepare netcdf input files.
18     - also modified: cleaner include statements, cleaner error print statements,
19       cleaner stops when error, and more tests of the netcdf input files consistency.
20    
21    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
22    o pkg/seaice:
23     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
24       requires a new routine: seaice_diagnostics_fill.F
25     - make sure that seaice does not move if not forced (pressure replacement
26       method, Hibler and Ip, 1995), changes results
27     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
28     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
29       It is turned off by default (=-1.), because it changes the results.
30     - make it possible to read AREA from a file, too.
31    
32    checkpoint59c
33    o add S/R and diagnostics for oceanic mixed-layer depth
34    o move GMRedi call after all vertical mixing schemes (including KPP)
35    o pkg/thsice:
36     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
37      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
38    o pkg/obcs:
39     - bug fix for balance code
40    o pkg/seaice:
41      - allow values of SEAICE_elasticParm > 1
42      - add new parameter SEAICE_evpTauRelax as an alternative
43        to SEAICE_elasticParm
44      - make lsr boundary conditions free slip (by default), changes result
45      - add code for no slip boundary conditions for lsr
46      - set minimum of zeta to zero (and not 4e8) (changes results)
47      - add a cap on AREA after advecting AREA if seaice_growth is not called
48    o change calculation of Visbeck K:
49      - no longer depend on tapering scheme; instead, compute slope (limited
50        by GM_maxSlope). this is equivalent to what was comuted before with
51        clipping or linear tappering.
52      - fix vertical averaging (wrong by 1/2 level)
53      - leave the old version (but will not be maintained) within
54        #ifdef OLD_VISBECK_CALC / #endif
55      - update output of exp. ideal_2D_oce
56    o change error catch in calc_r_star to improve vectorization
57    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
58      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
59    o adjoint:
60      Re-organized adjoint checkpointing according to Matt Mazloff
61      (but with modifs/completions/cleanups)
62      Storing is now bundled into large arrays to optimized I/O
63      (and second step in cleanup of the_main_loop)
64    
65    checkpoint59b
66    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
67      - export/import (between ocean & coupler) fields needed for ocean DIC.
68    o pkg/seaice:
69      - get rid of three more exchanges seaice_calc_viscosities (required
70        different loop boundaries in seaice_lsr and seaice_ocean_stress)
71      - bug fix in seaice_ocean_stress (update of lab_sea required)
72      - reduce loop boundaries to necessary minimum also in seaice_evp
73      - go back to the old way of computing deltaC/Z as the adjoint likes that
74        better
75    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
76      passive tracer to an Age Tracer) + update output.txt
77    o pkg/exf:
78      - implement A-grid / C-grid selection for wind-stress input files.
79      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
80      for now, in exf_bulk_largeyeager04.F only :
81      - change implementation for case where windspeed + 2. components wind-stress
82        are read-in. AND use rhoConstFresh to convert evap.
83    o pkg/seaice:
84      - use correct EXCH_UV for wind-forcing (on A-grid).
85      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
86        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
87    o pkg/exf:
88      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
89      EXF_INTERPOLATION:
90      - merge global_with_exf/code version of exf_interp_read.F
91        to the main code ;
92      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
93        reading the file ; Important: This options needs to be defined to recover
94        previous code.
95        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
96      - no longer loose real*8 precision along the way when using exf_iprec=64.
97    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
98      - change discretisation of evp-solver in order to avoid another exchange
99        (changes lab_sea) and clean up a little
100      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
101        help the adjoint (this also changes the results slightly)
102      - add a few "_d 0" where they had been missing in seaice_evp.F
103      - cleaning up: remove unused seaice_calc_rhs.F
104    o pkg/exf: some cleaning-up:
105      - change various "constants" into runtime parameters
106      - cleaned-up Large&Yeager04 routine which should eventually
107        replace exf_bulkformulae.F (changed names of S/R and CPP)
108        and merged various ALLOW_ATM_WIND options
109     only used with thsice pkg (in thsice_get_exf.F):
110      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
111        which are used when useStabilityFct_overIce=TRUE (= the default)
112      - change default values of ice & snow emissivity and scale downward LW
113        by ice & snow emissivity.
114    o pkg/thsice:
115     fix few little problems, in thsice_calc_thickn.F:
116      - growth vertically (and not laterally) if iceFrac == iceMaskMax
117      - melt only laterally if hIce < hThinIce (as the comments say)
118      and in thsice_extend.F:
119      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
120      - start to form ice as soon as the minimum ice-volume is reachable.
121     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
122      and cpl_aim+ocn
123    o pkg/kpp
124     - move computation of surface related input fields to KPP into a new
125       subroutine kpp_forcing_surf.F
126     - remove wrong (within bi,bj loops) EXCH calls.
127     - little cleaning (add argument myThid in last position, cvs header ...)
128     - for now, fix conservation problem by exchanging KPPviscAz (may not
129       be the best fix)
130    o pkg/seaice
131     - check for inconsistent evp parameter/cpp-flag combination
132     - remove leftover errIO flat for obsolete name list error handling
133    o OpenAD
134     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
135    
136    checkpoint59a
137    o pkg/seaice: some parameter clarifications and a little bit of clean up
138    o pkg/thsice: rename run-time parameters:
139       himin       -> hIceMin
140       himin0      -> hThinIce
141       hihig       -> hThickIce
142       i0          -> i0swFrac
143       transCoef   -> bMeltCoef
144       frac_energy -> fracMelting
145      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
146       with default values (for now) that do not change the results.
147      remove old version of thsice vars advection in pkg/seaice.
148    o in FFIELDS.h:
149      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
150      - make pLoad & sIceLoad always available (but still only used if
151         ATMOSPHERIC_LOADING is #define).
152    o pkg/kpp: replaced _KPP_RL with _RL
153    o bug fixes for vertical diffusivity computations when both KPP and
154        3D diffusivity arrays are used.
155    o pkg/seaice: fix bug in evp solver, while doing that
156      - change (improve?) discretization of stress computations for both
157        cgrid-lsr and evp solver
158      - add a new routine to compute strain rates
159      - the above changes lab_sea results
160      - add no slip conditions for evp solver (off by default), lsr-version
161        may follow
162      - fix exchange for shear at Z-points (does not change lab_sea)
163      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
164        (to force the user to pick a time step since there is not "safe" way
165        of choosing it)
166      - add principal stress diagnostics
167      - rearrange fields for evp a little to avoid having to call a: too many
168        exchanges and b: exchanges for stress trensor components which we do
169        not have.
170      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
171        of evp, complete rewrite for lsr case (latter is does not yet work
172        in all cases)
173    o pkg/kpp: add code to have mixing in shelf ice caverns
174      - add myThid to all kpp routines (long overdue)
175    
176    checkpoint59
177    o pkg/exf:
178      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
179        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
180      - move exf header files from lower_case.h to UPPER_CASE.h ;
181        add missing cvs Header & Name
182      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
183      - add namelist param. selectStressGridPosition, exf_monFreq
184      - retire many _CLIM routines, and remove data.exf_clim
185        + params moved to data.exf
186        + climsst, climsss now handled by exf_set_gen, i.e.
187          climss?period=0 refers to constant field,
188          climss?period=-12 to monthly forcing
189      - split up namelists in data.exf
190    o pkg/seaice:
191      - remove seaice_exch and seaice_exch_uv
192      - remove superfluous exchange of theta
193      - add myThid to seaice_budget_ocean/ice
194      - add new interface for atmospheric wind forcing (C-grid only)
195        + new routine
196        + two new field (taux, tauy for stress over ice)
197        + removed one global field (DAIRN) for C-grid case only
198    o pkg/thsise
199      - 2nd set of modifs for thsice adjoint in conjunction with exf
200    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
201    
202    checkpoint58y_post
203    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
204      vertical diffusivity, similar to that in MOM4; turned on using
205      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
206      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
207    o Added capability for 3D specification of background vertical diffusion
208      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
209      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
210      "data" file that contains the 3D vertical diffusivity coefficients.
211    o ice dynamics (pkg/seaice) with thsice thermodynamics:
212      - add code within pkg thsice to advect & diffuse sea-ice fields
213      similar to (and will replace) what has been added in  seaice_advdiff.F,
214      but: - conserving Mass, Heat & Salt.
215           - better when using non-linear advection scheme (not yet fully tested)
216           - can also be used in atmospheric set-up (for now, only the diffusion).
217    
218    checkpoint58x_post
219    o IO option for global-file compact format:
220      - add options when generating topology (utils/exch2/matlab-topology-generator)
221      - add I/O capability (pkg/mdsio).
222      - adapt utils/matlab/rdmds.m to read this format.
223      for now long-line format not yet supported by pkg/mdsio (& exch2).
224    o shelfice: add a few diagnostics
225    
226    checkpoint58w_post
227    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
228      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
229      (and replace horiVertRatio in NH code).
230      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
231                         and tutorial_plume_on_slope (sensitive to truncation)
232    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
233      directly to drive seaice model (C-grid only)
234    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
235     - reintroduce computation of wind from stress,
236     - compute tau (in exf_bulkformulae.F) from windstress averaged to
237       mass points to avoid tau = 0
238     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
239    o rdmnc.m: make it work with "global" files created with gluemnc
240    o rdmnc.m : some improvements in dealing with singleton dimension
241      (tested on all testreport mnc output files).
242    o genmake2: disable pkg/profiles if netcdf test fails.
243    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
244    o move call to cal_readparms up to make calendar parameters/variable available
245      to all packages
246    
247    checkpoint58v_post
248    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
249      useDynP_inEos_Zc tested.
250    o pkg/exf: changes to properly interpolate/mask/scale initial fields
251    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
252      and portions thereof.  See read_cs.txt for description and examples.
253    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
254      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
255      following the great-circle arc between those 2 points.
256    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
257      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
258    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
259     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
260     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
261     - still needs work (not working with some options ; efficiency to improve)
262       and serious testing.
263     - use this scheme for temperature & salinity in 2 advection test exp.:
264       advect_xy & advect_xz, respectively.
265    
266    checkpoint58u_post
267    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
268    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
269    o testreport: add option "-skipdir" to skip some test.
270    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
271      momentum calculation.
272    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
273    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
274      remove checkpoint.F and the_correction_step.F (no longer used);
275      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
276    o add option (linFSConserveTr) to correct for tracer source/sink due to
277      Linear Free surface
278    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
279    o pkg/thsice: fix reading mnc-pickups
280    
281    checkpoint58t_post
282    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
283    o pkg/mdsio:
284     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
285       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
286       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
287     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
288     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
289       either MDS_READ_FIELD or MDS_WRITE_FIELD )
290     - new S/R (to replace MDSWRITEMETA), which allows to write more
291       informations (variable names, time ...) to meta files.
292     - modify rdmds.m to give back the meta file content.
293    o pkg/diagnostics: change vertical interpolation to be safer, and more
294       flexible (define p-levels to interpolate to in data.diagnostics);
295      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
296       diagnostic pointer.
297    o pkg/seaice: more cleaning up of seaice_growth, added many comments
298    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
299    o fix multi-category seaice:
300     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
301       SEAICE_MULTICATEGORY
302     - fix short wave heat flux
303    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
304       and allow to use EVP solver. Change forward lab_sea: test both EVP
305       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
306    o Initial check-in of lab_sea adjoint
307      (very similar to natl_box_adjoint/code_seaice)
308      * used C-grid and EVP solver
309      * used KPP, GM/Redi
310      * uses inAdExact=.TRUE.
311      * gradient checks fail for both ADM and TLM
312        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
313        f.d. gradients actually seem more problematic than ADM, TLM gradients;
314        issue is related to forward mismatch between g77 an ifort
315    o pkg/seaice: overhaul of thermodynamics
316     - growth.F and groatb.F are replaced by new routine seaice_growth.F
317     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
318     - move a few global fields out of SEAICE.h into seaice_growth.F and
319       make them 2D (FICE/QNETO/ ...)
320     - remove FO (it is the same as QNETO)
321     - introduce a few local fields to avoid modifying external fields such
322       as atemp, etc.
323    
324    checkpoint58s_post
325    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
326      changed exf_set_gen.F so that
327        genperiod=0 means input file is one time-constant field and
328        genperiod=-12 means input file contains 12 monthly means
329    o CG2D: use pre-computed solver main-diagonal (stored in common block);
330      this affects truncation error ; generate new output file for exp. which
331      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
332        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
333        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
334        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
335        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
336        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
337    o start implementation of deep-atmosphere and anelastic formulation
338    o verification: remove 2nd copy of input files and use script "prepare_run"
339      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
340    o mom_common/vecinv/fluxform: fix a few initialisation isssues
341    o profiles: fix for multithreaded case
342    
343  o diagnostics: rename few diags:  o diagnostics: rename few diags:
344    s/'PRESSURE'/'RCENTER '/g    s/'PRESSURE'/'RCENTER '/g
345    s/'TICE    '/'oceFreez'/g    s/'TICE    '/'oceFreez'/g

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