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revision 1.742 by mlosch, Wed Nov 1 09:50:43 2006 UTC revision 1.829 by jmc, Mon Jun 4 00:51:28 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    checkpoint59c
8    o add S/R and diagnostics for oceanic mixed-layer depth
9    o move GMRedi call after all vertical mixing schemes (including KPP)
10    o pkg/thsice:
11     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
12      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
13    o pkg/obcs:
14     - bug fix for balance code
15    o pkg/seaice:
16      - allow values of SEAICE_elasticParm > 1
17      - add new parameter SEAICE_evpTauRelax as an alternative
18        to SEAICE_elasticParm
19      - make lsr boundary conditions free slip (by default), changes result
20      - add code for no slip boundary conditions for lsr
21      - set minimum of zeta to zero (and not 4e8) (changes results)
22      - add a cap on AREA after advecting AREA if seaice_growth is not called
23    o change calculation of Visbeck K:
24      - no longer depend on tapering scheme; instead, compute slope (limited
25        by GM_maxSlope). this is equivalent to what was comuted before with
26        clipping or linear tappering.
27      - fix vertical averaging (wrong by 1/2 level)
28      - leave the old version (but will not be maintained) within
29        #ifdef OLD_VISBECK_CALC / #endif
30      - update output of exp. ideal_2D_oce
31    o change error catch in calc_r_star to improve vectorization
32    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
33      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
34    o adjoint:
35      Re-organized adjoint checkpointing according to Matt Mazloff
36      (but with modifs/completions/cleanups)
37      Storing is now bundled into large arrays to optimized I/O
38      (and second step in cleanup of the_main_loop)
39    
40    checkpoint59b
41    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
42      - export/import (between ocean & coupler) fields needed for ocean DIC.
43    o pkg/seaice:
44      - get rid of three more exchanges seaice_calc_viscosities (required
45        different loop boundaries in seaice_lsr and seaice_ocean_stress)
46      - bug fix in seaice_ocean_stress (update of lab_sea required)
47      - reduce loop boundaries to necessary minimum also in seaice_evp
48      - go back to the old way of computing deltaC/Z as the adjoint likes that
49        better
50    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
51      passive tracer to an Age Tracer) + update output.txt
52    o pkg/exf:
53      - implement A-grid / C-grid selection for wind-stress input files.
54      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
55      for now, in exf_bulk_largeyeager04.F only :
56      - change implementation for case where windspeed + 2. components wind-stress
57        are read-in. AND use rhoConstFresh to convert evap.
58    o pkg/seaice:
59      - use correct EXCH_UV for wind-forcing (on A-grid).
60      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
61        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
62    o pkg/exf:
63      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
64      EXF_INTERPOLATION:
65      - merge global_with_exf/code version of exf_interp_read.F
66        to the main code ;
67      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
68        reading the file ; Important: This options needs to be defined to recover
69        previous code.
70        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
71      - no longer loose real*8 precision along the way when using exf_iprec=64.
72    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
73      - change discretisation of evp-solver in order to avoid another exchange
74        (changes lab_sea) and clean up a little
75      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
76        help the adjoint (this also changes the results slightly)
77      - add a few "_d 0" where they had been missing in seaice_evp.F
78      - cleaning up: remove unused seaice_calc_rhs.F
79    o pkg/exf: some cleaning-up:
80      - change various "constants" into runtime parameters
81      - cleaned-up Large&Yeager04 routine which should eventually
82        replace exf_bulkformulae.F (changed names of S/R and CPP)
83        and merged various ALLOW_ATM_WIND options
84     only used with thsice pkg (in thsice_get_exf.F):
85      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
86        which are used when useStabilityFct_overIce=TRUE (= the default)
87      - change default values of ice & snow emissivity and scale downward LW
88        by ice & snow emissivity.
89    o pkg/thsice:
90     fix few little problems, in thsice_calc_thickn.F:
91      - growth vertically (and not laterally) if iceFrac == iceMaskMax
92      - melt only laterally if hIce < hThinIce (as the comments say)
93      and in thsice_extend.F:
94      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
95      - start to form ice as soon as the minimum ice-volume is reachable.
96     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
97      and cpl_aim+ocn
98    o pkg/kpp
99     - move computation of surface related input fields to KPP into a new
100       subroutine kpp_forcing_surf.F
101     - remove wrong (within bi,bj loops) EXCH calls.
102     - little cleaning (add argument myThid in last position, cvs header ...)
103     - for now, fix conservation problem by exchanging KPPviscAz (may not
104       be the best fix)
105    o pkg/seaice
106     - check for inconsistent evp parameter/cpp-flag combination
107     - remove leftover errIO flat for obsolete name list error handling
108    o OpenAD
109     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
110    
111    checkpoint59a
112    o pkg/seaice: some parameter clarifications and a little bit of clean up
113    o pkg/thsice: rename run-time parameters:
114       himin       -> hIceMin
115       himin0      -> hThinIce
116       hihig       -> hThickIce
117       i0          -> i0swFrac
118       transCoef   -> bMeltCoef
119       frac_energy -> fracMelting
120      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
121       with default values (for now) that do not change the results.
122      remove old version of thsice vars advection in pkg/seaice.
123    o in FFIELDS.h:
124      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
125      - make pLoad & sIceLoad always available (but still only used if
126         ATMOSPHERIC_LOADING is #define).
127    o pkg/kpp: replaced _KPP_RL with _RL
128    o bug fixes for vertical diffusivity computations when both KPP and
129        3D diffusivity arrays are used.
130    o pkg/seaice: fix bug in evp solver, while doing that
131      - change (improve?) discretization of stress computations for both
132        cgrid-lsr and evp solver
133      - add a new routine to compute strain rates
134      - the above changes lab_sea results
135      - add no slip conditions for evp solver (off by default), lsr-version
136        may follow
137      - fix exchange for shear at Z-points (does not change lab_sea)
138      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
139        (to force the user to pick a time step since there is not "safe" way
140        of choosing it)
141      - add principal stress diagnostics
142      - rearrange fields for evp a little to avoid having to call a: too many
143        exchanges and b: exchanges for stress trensor components which we do
144        not have.
145      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
146        of evp, complete rewrite for lsr case (latter is does not yet work
147        in all cases)
148    o pkg/kpp: add code to have mixing in shelf ice caverns
149      - add myThid to all kpp routines (long overdue)
150    
151    checkpoint59
152    o pkg/exf:
153      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
154        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
155      - move exf header files from lower_case.h to UPPER_CASE.h ;
156        add missing cvs Header & Name
157      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
158      - add namelist param. selectStressGridPosition, exf_monFreq
159      - retire many _CLIM routines, and remove data.exf_clim
160        + params moved to data.exf
161        + climsst, climsss now handled by exf_set_gen, i.e.
162          climss?period=0 refers to constant field,
163          climss?period=-12 to monthly forcing
164      - split up namelists in data.exf
165    o pkg/seaice:
166      - remove seaice_exch and seaice_exch_uv
167      - remove superfluous exchange of theta
168      - add myThid to seaice_budget_ocean/ice
169      - add new interface for atmospheric wind forcing (C-grid only)
170        + new routine
171        + two new field (taux, tauy for stress over ice)
172        + removed one global field (DAIRN) for C-grid case only
173    o pkg/thsise
174      - 2nd set of modifs for thsice adjoint in conjunction with exf
175    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
176    
177    checkpoint58y_post
178    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
179      vertical diffusivity, similar to that in MOM4; turned on using
180      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
181      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
182    o Added capability for 3D specification of background vertical diffusion
183      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
184      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
185      "data" file that contains the 3D vertical diffusivity coefficients.
186    o ice dynamics (pkg/seaice) with thsice thermodynamics:
187      - add code within pkg thsice to advect & diffuse sea-ice fields
188      similar to (and will replace) what has been added in  seaice_advdiff.F,
189      but: - conserving Mass, Heat & Salt.
190           - better when using non-linear advection scheme (not yet fully tested)
191           - can also be used in atmospheric set-up (for now, only the diffusion).
192    
193    checkpoint58x_post
194    o IO option for global-file compact format:
195      - add options when generating topology (utils/exch2/matlab-topology-generator)
196      - add I/O capability (pkg/mdsio).
197      - adapt utils/matlab/rdmds.m to read this format.
198      for now long-line format not yet supported by pkg/mdsio (& exch2).
199    o shelfice: add a few diagnostics
200    
201    checkpoint58w_post
202    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
203      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
204      (and replace horiVertRatio in NH code).
205      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
206                         and tutorial_plume_on_slope (sensitive to truncation)
207    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
208      directly to drive seaice model (C-grid only)
209    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
210     - reintroduce computation of wind from stress,
211     - compute tau (in exf_bulkformulae.F) from windstress averaged to
212       mass points to avoid tau = 0
213     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
214    o rdmnc.m: make it work with "global" files created with gluemnc
215    o rdmnc.m : some improvements in dealing with singleton dimension
216      (tested on all testreport mnc output files).
217    o genmake2: disable pkg/profiles if netcdf test fails.
218    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
219    o move call to cal_readparms up to make calendar parameters/variable available
220      to all packages
221    
222    checkpoint58v_post
223    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
224      useDynP_inEos_Zc tested.
225    o pkg/exf: changes to properly interpolate/mask/scale initial fields
226    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
227      and portions thereof.  See read_cs.txt for description and examples.
228    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
229      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
230      following the great-circle arc between those 2 points.
231    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
232      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
233    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
234     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
235     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
236     - still needs work (not working with some options ; efficiency to improve)
237       and serious testing.
238     - use this scheme for temperature & salinity in 2 advection test exp.:
239       advect_xy & advect_xz, respectively.
240    
241    checkpoint58u_post
242    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
243    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
244    o testreport: add option "-skipdir" to skip some test.
245    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
246      momentum calculation.
247    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
248    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
249      remove checkpoint.F and the_correction_step.F (no longer used);
250      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
251    o add option (linFSConserveTr) to correct for tracer source/sink due to
252      Linear Free surface
253    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
254    o pkg/thsice: fix reading mnc-pickups
255    
256    checkpoint58t_post
257    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
258    o pkg/mdsio:
259     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
260       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
261       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
262     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
263     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
264       either MDS_READ_FIELD or MDS_WRITE_FIELD )
265     - new S/R (to replace MDSWRITEMETA), which allows to write more
266       informations (variable names, time ...) to meta files.
267     - modify rdmds.m to give back the meta file content.
268    o pkg/diagnostics: change vertical interpolation to be safer, and more
269       flexible (define p-levels to interpolate to in data.diagnostics);
270      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
271       diagnostic pointer.
272    o pkg/seaice: more cleaning up of seaice_growth, added many comments
273    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
274    o fix multi-category seaice:
275     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
276       SEAICE_MULTICATEGORY
277     - fix short wave heat flux
278    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
279       and allow to use EVP solver. Change forward lab_sea: test both EVP
280       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
281    o Initial check-in of lab_sea adjoint
282      (very similar to natl_box_adjoint/code_seaice)
283      * used C-grid and EVP solver
284      * used KPP, GM/Redi
285      * uses inAdExact=.TRUE.
286      * gradient checks fail for both ADM and TLM
287        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
288        f.d. gradients actually seem more problematic than ADM, TLM gradients;
289        issue is related to forward mismatch between g77 an ifort
290    o pkg/seaice: overhaul of thermodynamics
291     - growth.F and groatb.F are replaced by new routine seaice_growth.F
292     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
293     - move a few global fields out of SEAICE.h into seaice_growth.F and
294       make them 2D (FICE/QNETO/ ...)
295     - remove FO (it is the same as QNETO)
296     - introduce a few local fields to avoid modifying external fields such
297       as atemp, etc.
298    
299    checkpoint58s_post
300    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
301      changed exf_set_gen.F so that
302        genperiod=0 means input file is one time-constant field and
303        genperiod=-12 means input file contains 12 monthly means
304    o CG2D: use pre-computed solver main-diagonal (stored in common block);
305      this affects truncation error ; generate new output file for exp. which
306      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
307        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
308        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
309        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
310        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
311        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
312    o start implementation of deep-atmosphere and anelastic formulation
313    o verification: remove 2nd copy of input files and use script "prepare_run"
314      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
315    o mom_common/vecinv/fluxform: fix a few initialisation isssues
316    o profiles: fix for multithreaded case
317    
318    o diagnostics: rename few diags:
319      s/'PRESSURE'/'RCENTER '/g
320      s/'TICE    '/'oceFreez'/g
321      s/'TAUX    '/'oceTAUX '/g
322      s/'TAUY    '/'oceTAUY '/g
323      s/'SWFLUX  '/'oceQsw  '/g
324      s/DIFx/DFxE/g
325      s/DIFy/DFyE/g
326      and add few ocean-forcing diagnostics:
327      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
328    o modifications to pkg/seaice/growth.F and budget.F, which change results of
329      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
330      as actual snow thickness.  It now refers everywhere to effective snow
331      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
332    
333    checkpoint58r_post
334    o modifications to pkg/seaice/growth.F, which change results of
335      lab_sea experiment: fixes pertain to melting snow over open water, to
336      masking EVAP under sea ice, and to using the correct AREA variable for
337      computations of EVAP, PRECIP, HSNOW, and GHEFF
338    o add ability to read bathy, salt, and theta using MNC (off by def)
339  o add flooding algorithm and advection of HSNOW for pkg/seaice;  o add flooding algorithm and advection of HSNOW for pkg/seaice;
340    both are turned off by default and do no change any results    both are turned off by default and do no change any results
341  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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