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revision 1.752 by jmc, Tue Dec 5 22:15:47 2006 UTC revision 1.842 by jmc, Thu Jun 21 00:53:20 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 standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
8     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
9     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
10    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
11     and change default value of parameter "GM_Small_Number";
12     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
13       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
14       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
15    o pkg/ecco: cost function when applying pkg/smooth to controls
16    o pkg/ctrl: add forcingPrecond run time parameter
17    o pkg/seaice:
18     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
19     - fix bug in metric terms of u-equation in LSR solver (implicit part),
20       changes verification/lab_sea
21     - rearrange implicit part of u-equation in LSR solver to make it easier to
22       read, understand, and debug. This causes changes at the truncation level.
23     - fix (serious) bug in the boundary conditions (sign error in the implicit
24       part) of the LSR solver. Changes all LSR results.
25     - fixed problem with HSNOW initialization to avoid thick snow when AREA
26       is initilized with small values - does not change lab_sea results.
27     - added HsnowFile initialization capability
28    o pkg/smooth: addition to model/src and pkg/ctrl so allow
29     initialization of pkg/smooth and application to control vector
30    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
31    o dependencies: pkg/profiles requires pkg/cal
32    o pkg/profiles:
33     - added option ALLOW_PROFILES_GENERICGRID
34         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
35         that interpolation information (grid points and coefficients) is provided
36         within the netcdf input files.
37         -> sample matlab scripts can be found in MITgcm_contrib/gael
38         that allow you to prepare netcdf input files.
39     - also modified: cleaner include statements, cleaner error print statements,
40       cleaner stops when error, and more tests of the netcdf input files consistency.
41    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
42    o pkg/seaice:
43     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
44       requires a new routine: seaice_diagnostics_fill.F
45     - make sure that seaice does not move if not forced (pressure replacement
46       method, Hibler and Ip, 1995), changes results
47     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
48     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
49       It is turned off by default (=-1.), because it changes the results.
50     - make it possible to read AREA from a file, too.
51    
52    checkpoint59c
53    o add S/R and diagnostics for oceanic mixed-layer depth
54    o move GMRedi call after all vertical mixing schemes (including KPP)
55    o pkg/thsice:
56     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
57      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
58    o pkg/obcs:
59     - bug fix for balance code
60    o pkg/seaice:
61      - allow values of SEAICE_elasticParm > 1
62      - add new parameter SEAICE_evpTauRelax as an alternative
63        to SEAICE_elasticParm
64      - make lsr boundary conditions free slip (by default), changes result
65      - add code for no slip boundary conditions for lsr
66      - set minimum of zeta to zero (and not 4e8) (changes results)
67      - add a cap on AREA after advecting AREA if seaice_growth is not called
68    o change calculation of Visbeck K:
69      - no longer depend on tapering scheme; instead, compute slope (limited
70        by GM_maxSlope). this is equivalent to what was comuted before with
71        clipping or linear tappering.
72      - fix vertical averaging (wrong by 1/2 level)
73      - leave the old version (but will not be maintained) within
74        #ifdef OLD_VISBECK_CALC / #endif
75      - update output of exp. ideal_2D_oce
76    o change error catch in calc_r_star to improve vectorization
77    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
78      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
79    o adjoint:
80      Re-organized adjoint checkpointing according to Matt Mazloff
81      (but with modifs/completions/cleanups)
82      Storing is now bundled into large arrays to optimized I/O
83      (and second step in cleanup of the_main_loop)
84    
85    checkpoint59b
86    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
87      - export/import (between ocean & coupler) fields needed for ocean DIC.
88    o pkg/seaice:
89      - get rid of three more exchanges seaice_calc_viscosities (required
90        different loop boundaries in seaice_lsr and seaice_ocean_stress)
91      - bug fix in seaice_ocean_stress (update of lab_sea required)
92      - reduce loop boundaries to necessary minimum also in seaice_evp
93      - go back to the old way of computing deltaC/Z as the adjoint likes that
94        better
95    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
96      passive tracer to an Age Tracer) + update output.txt
97    o pkg/exf:
98      - implement A-grid / C-grid selection for wind-stress input files.
99      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
100      for now, in exf_bulk_largeyeager04.F only :
101      - change implementation for case where windspeed + 2. components wind-stress
102        are read-in. AND use rhoConstFresh to convert evap.
103    o pkg/seaice:
104      - use correct EXCH_UV for wind-forcing (on A-grid).
105      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
106        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
107    o pkg/exf:
108      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
109      EXF_INTERPOLATION:
110      - merge global_with_exf/code version of exf_interp_read.F
111        to the main code ;
112      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
113        reading the file ; Important: This options needs to be defined to recover
114        previous code.
115        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
116      - no longer loose real*8 precision along the way when using exf_iprec=64.
117    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
118      - change discretisation of evp-solver in order to avoid another exchange
119        (changes lab_sea) and clean up a little
120      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
121        help the adjoint (this also changes the results slightly)
122      - add a few "_d 0" where they had been missing in seaice_evp.F
123      - cleaning up: remove unused seaice_calc_rhs.F
124    o pkg/exf: some cleaning-up:
125      - change various "constants" into runtime parameters
126      - cleaned-up Large&Yeager04 routine which should eventually
127        replace exf_bulkformulae.F (changed names of S/R and CPP)
128        and merged various ALLOW_ATM_WIND options
129     only used with thsice pkg (in thsice_get_exf.F):
130      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
131        which are used when useStabilityFct_overIce=TRUE (= the default)
132      - change default values of ice & snow emissivity and scale downward LW
133        by ice & snow emissivity.
134    o pkg/thsice:
135     fix few little problems, in thsice_calc_thickn.F:
136      - growth vertically (and not laterally) if iceFrac == iceMaskMax
137      - melt only laterally if hIce < hThinIce (as the comments say)
138      and in thsice_extend.F:
139      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
140      - start to form ice as soon as the minimum ice-volume is reachable.
141     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
142      and cpl_aim+ocn
143    o pkg/kpp
144     - move computation of surface related input fields to KPP into a new
145       subroutine kpp_forcing_surf.F
146     - remove wrong (within bi,bj loops) EXCH calls.
147     - little cleaning (add argument myThid in last position, cvs header ...)
148     - for now, fix conservation problem by exchanging KPPviscAz (may not
149       be the best fix)
150    o pkg/seaice
151     - check for inconsistent evp parameter/cpp-flag combination
152     - remove leftover errIO flat for obsolete name list error handling
153    o OpenAD
154     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
155    
156    checkpoint59a
157    o pkg/seaice: some parameter clarifications and a little bit of clean up
158    o pkg/thsice: rename run-time parameters:
159       himin       -> hIceMin
160       himin0      -> hThinIce
161       hihig       -> hThickIce
162       i0          -> i0swFrac
163       transCoef   -> bMeltCoef
164       frac_energy -> fracMelting
165      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
166       with default values (for now) that do not change the results.
167      remove old version of thsice vars advection in pkg/seaice.
168    o in FFIELDS.h:
169      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
170      - make pLoad & sIceLoad always available (but still only used if
171         ATMOSPHERIC_LOADING is #define).
172    o pkg/kpp: replaced _KPP_RL with _RL
173    o bug fixes for vertical diffusivity computations when both KPP and
174        3D diffusivity arrays are used.
175    o pkg/seaice: fix bug in evp solver, while doing that
176      - change (improve?) discretization of stress computations for both
177        cgrid-lsr and evp solver
178      - add a new routine to compute strain rates
179      - the above changes lab_sea results
180      - add no slip conditions for evp solver (off by default), lsr-version
181        may follow
182      - fix exchange for shear at Z-points (does not change lab_sea)
183      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
184        (to force the user to pick a time step since there is not "safe" way
185        of choosing it)
186      - add principal stress diagnostics
187      - rearrange fields for evp a little to avoid having to call a: too many
188        exchanges and b: exchanges for stress trensor components which we do
189        not have.
190      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
191        of evp, complete rewrite for lsr case (latter is does not yet work
192        in all cases)
193    o pkg/kpp: add code to have mixing in shelf ice caverns
194      - add myThid to all kpp routines (long overdue)
195    
196    checkpoint59
197    o pkg/exf:
198      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
199        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
200      - move exf header files from lower_case.h to UPPER_CASE.h ;
201        add missing cvs Header & Name
202      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
203      - add namelist param. selectStressGridPosition, exf_monFreq
204      - retire many _CLIM routines, and remove data.exf_clim
205        + params moved to data.exf
206        + climsst, climsss now handled by exf_set_gen, i.e.
207          climss?period=0 refers to constant field,
208          climss?period=-12 to monthly forcing
209      - split up namelists in data.exf
210    o pkg/seaice:
211      - remove seaice_exch and seaice_exch_uv
212      - remove superfluous exchange of theta
213      - add myThid to seaice_budget_ocean/ice
214      - add new interface for atmospheric wind forcing (C-grid only)
215        + new routine
216        + two new field (taux, tauy for stress over ice)
217        + removed one global field (DAIRN) for C-grid case only
218    o pkg/thsise
219      - 2nd set of modifs for thsice adjoint in conjunction with exf
220    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
221    
222    checkpoint58y_post
223    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
224      vertical diffusivity, similar to that in MOM4; turned on using
225      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
226      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
227    o Added capability for 3D specification of background vertical diffusion
228      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
229      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
230      "data" file that contains the 3D vertical diffusivity coefficients.
231    o ice dynamics (pkg/seaice) with thsice thermodynamics:
232      - add code within pkg thsice to advect & diffuse sea-ice fields
233      similar to (and will replace) what has been added in  seaice_advdiff.F,
234      but: - conserving Mass, Heat & Salt.
235           - better when using non-linear advection scheme (not yet fully tested)
236           - can also be used in atmospheric set-up (for now, only the diffusion).
237    
238    checkpoint58x_post
239    o IO option for global-file compact format:
240      - add options when generating topology (utils/exch2/matlab-topology-generator)
241      - add I/O capability (pkg/mdsio).
242      - adapt utils/matlab/rdmds.m to read this format.
243      for now long-line format not yet supported by pkg/mdsio (& exch2).
244    o shelfice: add a few diagnostics
245    
246    checkpoint58w_post
247    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
248      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
249      (and replace horiVertRatio in NH code).
250      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
251                         and tutorial_plume_on_slope (sensitive to truncation)
252    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
253      directly to drive seaice model (C-grid only)
254    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
255     - reintroduce computation of wind from stress,
256     - compute tau (in exf_bulkformulae.F) from windstress averaged to
257       mass points to avoid tau = 0
258     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
259    o rdmnc.m: make it work with "global" files created with gluemnc
260    o rdmnc.m : some improvements in dealing with singleton dimension
261      (tested on all testreport mnc output files).
262    o genmake2: disable pkg/profiles if netcdf test fails.
263    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
264    o move call to cal_readparms up to make calendar parameters/variable available
265      to all packages
266    
267    checkpoint58v_post
268    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
269      useDynP_inEos_Zc tested.
270    o pkg/exf: changes to properly interpolate/mask/scale initial fields
271    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
272      and portions thereof.  See read_cs.txt for description and examples.
273    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
274      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
275      following the great-circle arc between those 2 points.
276    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
277      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
278    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
279     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
280     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
281     - still needs work (not working with some options ; efficiency to improve)
282       and serious testing.
283     - use this scheme for temperature & salinity in 2 advection test exp.:
284       advect_xy & advect_xz, respectively.
285    
286    checkpoint58u_post
287    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
288    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
289    o testreport: add option "-skipdir" to skip some test.
290    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
291      momentum calculation.
292    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
293    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
294      remove checkpoint.F and the_correction_step.F (no longer used);
295      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
296    o add option (linFSConserveTr) to correct for tracer source/sink due to
297      Linear Free surface
298    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
299    o pkg/thsice: fix reading mnc-pickups
300    
301    checkpoint58t_post
302    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
303    o pkg/mdsio:
304     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
305       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
306       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
307     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
308     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
309       either MDS_READ_FIELD or MDS_WRITE_FIELD )
310     - new S/R (to replace MDSWRITEMETA), which allows to write more
311       informations (variable names, time ...) to meta files.
312     - modify rdmds.m to give back the meta file content.
313    o pkg/diagnostics: change vertical interpolation to be safer, and more
314       flexible (define p-levels to interpolate to in data.diagnostics);
315      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
316       diagnostic pointer.
317    o pkg/seaice: more cleaning up of seaice_growth, added many comments
318    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
319    o fix multi-category seaice:
320     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
321       SEAICE_MULTICATEGORY
322     - fix short wave heat flux
323    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
324       and allow to use EVP solver. Change forward lab_sea: test both EVP
325       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
326    o Initial check-in of lab_sea adjoint
327      (very similar to natl_box_adjoint/code_seaice)
328      * used C-grid and EVP solver
329      * used KPP, GM/Redi
330      * uses inAdExact=.TRUE.
331      * gradient checks fail for both ADM and TLM
332        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
333        f.d. gradients actually seem more problematic than ADM, TLM gradients;
334        issue is related to forward mismatch between g77 an ifort
335    o pkg/seaice: overhaul of thermodynamics
336     - growth.F and groatb.F are replaced by new routine seaice_growth.F
337     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
338     - move a few global fields out of SEAICE.h into seaice_growth.F and
339       make them 2D (FICE/QNETO/ ...)
340     - remove FO (it is the same as QNETO)
341     - introduce a few local fields to avoid modifying external fields such
342       as atemp, etc.
343    
344    checkpoint58s_post
345    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
346      changed exf_set_gen.F so that
347        genperiod=0 means input file is one time-constant field and
348        genperiod=-12 means input file contains 12 monthly means
349  o CG2D: use pre-computed solver main-diagonal (stored in common block);  o CG2D: use pre-computed solver main-diagonal (stored in common block);
350    this affects truncation error ; generate new output file for exp. which    this affects truncation error ; generate new output file for exp. which
351    fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),    fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),

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