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revision 1.742 by mlosch, Wed Nov 1 09:50:43 2006 UTC revision 1.838 by gforget, Tue Jun 19 03:44:19 2007 UTC
# Line 3  $Name$ Line 3  $Name$
3    
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:
344      s/'PRESSURE'/'RCENTER '/g
345      s/'TICE    '/'oceFreez'/g
346      s/'TAUX    '/'oceTAUX '/g
347      s/'TAUY    '/'oceTAUY '/g
348      s/'SWFLUX  '/'oceQsw  '/g
349      s/DIFx/DFxE/g
350      s/DIFy/DFyE/g
351      and add few ocean-forcing diagnostics:
352      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
353    o modifications to pkg/seaice/growth.F and budget.F, which change results of
354      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
355      as actual snow thickness.  It now refers everywhere to effective snow
356      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
357    
358    checkpoint58r_post
359    o modifications to pkg/seaice/growth.F, which change results of
360      lab_sea experiment: fixes pertain to melting snow over open water, to
361      masking EVAP under sea ice, and to using the correct AREA variable for
362      computations of EVAP, PRECIP, HSNOW, and GHEFF
363    o add ability to read bathy, salt, and theta using MNC (off by def)
364  o add flooding algorithm and advection of HSNOW for pkg/seaice;  o add flooding algorithm and advection of HSNOW for pkg/seaice;
365    both are turned off by default and do no change any results    both are turned off by default and do no change any results
366  o seaice advection with pkg/thsice: a step toward the use of non-linear  o seaice advection with pkg/thsice: a step toward the use of non-linear

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