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revision 1.740 by heimbach, Fri Oct 27 05:19:42 2006 UTC revision 1.830 by mlosch, Tue Jun 5 10:46:27 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     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
9     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
10       It is turned off by default (=-1.), because it changes the results.
11    
12    checkpoint59c
13    o add S/R and diagnostics for oceanic mixed-layer depth
14    o move GMRedi call after all vertical mixing schemes (including KPP)
15    o pkg/thsice:
16     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
17      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
18    o pkg/obcs:
19     - bug fix for balance code
20    o pkg/seaice:
21      - allow values of SEAICE_elasticParm > 1
22      - add new parameter SEAICE_evpTauRelax as an alternative
23        to SEAICE_elasticParm
24      - make lsr boundary conditions free slip (by default), changes result
25      - add code for no slip boundary conditions for lsr
26      - set minimum of zeta to zero (and not 4e8) (changes results)
27      - add a cap on AREA after advecting AREA if seaice_growth is not called
28    o change calculation of Visbeck K:
29      - no longer depend on tapering scheme; instead, compute slope (limited
30        by GM_maxSlope). this is equivalent to what was comuted before with
31        clipping or linear tappering.
32      - fix vertical averaging (wrong by 1/2 level)
33      - leave the old version (but will not be maintained) within
34        #ifdef OLD_VISBECK_CALC / #endif
35      - update output of exp. ideal_2D_oce
36    o change error catch in calc_r_star to improve vectorization
37    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
38      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
39    o adjoint:
40      Re-organized adjoint checkpointing according to Matt Mazloff
41      (but with modifs/completions/cleanups)
42      Storing is now bundled into large arrays to optimized I/O
43      (and second step in cleanup of the_main_loop)
44    
45    checkpoint59b
46    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
47      - export/import (between ocean & coupler) fields needed for ocean DIC.
48    o pkg/seaice:
49      - get rid of three more exchanges seaice_calc_viscosities (required
50        different loop boundaries in seaice_lsr and seaice_ocean_stress)
51      - bug fix in seaice_ocean_stress (update of lab_sea required)
52      - reduce loop boundaries to necessary minimum also in seaice_evp
53      - go back to the old way of computing deltaC/Z as the adjoint likes that
54        better
55    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
56      passive tracer to an Age Tracer) + update output.txt
57    o pkg/exf:
58      - implement A-grid / C-grid selection for wind-stress input files.
59      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
60      for now, in exf_bulk_largeyeager04.F only :
61      - change implementation for case where windspeed + 2. components wind-stress
62        are read-in. AND use rhoConstFresh to convert evap.
63    o pkg/seaice:
64      - use correct EXCH_UV for wind-forcing (on A-grid).
65      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
66        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
67    o pkg/exf:
68      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
69      EXF_INTERPOLATION:
70      - merge global_with_exf/code version of exf_interp_read.F
71        to the main code ;
72      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
73        reading the file ; Important: This options needs to be defined to recover
74        previous code.
75        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
76      - no longer loose real*8 precision along the way when using exf_iprec=64.
77    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
78      - change discretisation of evp-solver in order to avoid another exchange
79        (changes lab_sea) and clean up a little
80      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
81        help the adjoint (this also changes the results slightly)
82      - add a few "_d 0" where they had been missing in seaice_evp.F
83      - cleaning up: remove unused seaice_calc_rhs.F
84    o pkg/exf: some cleaning-up:
85      - change various "constants" into runtime parameters
86      - cleaned-up Large&Yeager04 routine which should eventually
87        replace exf_bulkformulae.F (changed names of S/R and CPP)
88        and merged various ALLOW_ATM_WIND options
89     only used with thsice pkg (in thsice_get_exf.F):
90      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
91        which are used when useStabilityFct_overIce=TRUE (= the default)
92      - change default values of ice & snow emissivity and scale downward LW
93        by ice & snow emissivity.
94    o pkg/thsice:
95     fix few little problems, in thsice_calc_thickn.F:
96      - growth vertically (and not laterally) if iceFrac == iceMaskMax
97      - melt only laterally if hIce < hThinIce (as the comments say)
98      and in thsice_extend.F:
99      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
100      - start to form ice as soon as the minimum ice-volume is reachable.
101     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
102      and cpl_aim+ocn
103    o pkg/kpp
104     - move computation of surface related input fields to KPP into a new
105       subroutine kpp_forcing_surf.F
106     - remove wrong (within bi,bj loops) EXCH calls.
107     - little cleaning (add argument myThid in last position, cvs header ...)
108     - for now, fix conservation problem by exchanging KPPviscAz (may not
109       be the best fix)
110    o pkg/seaice
111     - check for inconsistent evp parameter/cpp-flag combination
112     - remove leftover errIO flat for obsolete name list error handling
113    o OpenAD
114     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
115    
116    checkpoint59a
117    o pkg/seaice: some parameter clarifications and a little bit of clean up
118    o pkg/thsice: rename run-time parameters:
119       himin       -> hIceMin
120       himin0      -> hThinIce
121       hihig       -> hThickIce
122       i0          -> i0swFrac
123       transCoef   -> bMeltCoef
124       frac_energy -> fracMelting
125      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
126       with default values (for now) that do not change the results.
127      remove old version of thsice vars advection in pkg/seaice.
128    o in FFIELDS.h:
129      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
130      - make pLoad & sIceLoad always available (but still only used if
131         ATMOSPHERIC_LOADING is #define).
132    o pkg/kpp: replaced _KPP_RL with _RL
133    o bug fixes for vertical diffusivity computations when both KPP and
134        3D diffusivity arrays are used.
135    o pkg/seaice: fix bug in evp solver, while doing that
136      - change (improve?) discretization of stress computations for both
137        cgrid-lsr and evp solver
138      - add a new routine to compute strain rates
139      - the above changes lab_sea results
140      - add no slip conditions for evp solver (off by default), lsr-version
141        may follow
142      - fix exchange for shear at Z-points (does not change lab_sea)
143      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
144        (to force the user to pick a time step since there is not "safe" way
145        of choosing it)
146      - add principal stress diagnostics
147      - rearrange fields for evp a little to avoid having to call a: too many
148        exchanges and b: exchanges for stress trensor components which we do
149        not have.
150      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
151        of evp, complete rewrite for lsr case (latter is does not yet work
152        in all cases)
153    o pkg/kpp: add code to have mixing in shelf ice caverns
154      - add myThid to all kpp routines (long overdue)
155    
156    checkpoint59
157    o pkg/exf:
158      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
159        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
160      - move exf header files from lower_case.h to UPPER_CASE.h ;
161        add missing cvs Header & Name
162      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
163      - add namelist param. selectStressGridPosition, exf_monFreq
164      - retire many _CLIM routines, and remove data.exf_clim
165        + params moved to data.exf
166        + climsst, climsss now handled by exf_set_gen, i.e.
167          climss?period=0 refers to constant field,
168          climss?period=-12 to monthly forcing
169      - split up namelists in data.exf
170    o pkg/seaice:
171      - remove seaice_exch and seaice_exch_uv
172      - remove superfluous exchange of theta
173      - add myThid to seaice_budget_ocean/ice
174      - add new interface for atmospheric wind forcing (C-grid only)
175        + new routine
176        + two new field (taux, tauy for stress over ice)
177        + removed one global field (DAIRN) for C-grid case only
178    o pkg/thsise
179      - 2nd set of modifs for thsice adjoint in conjunction with exf
180    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
181    
182    checkpoint58y_post
183    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
184      vertical diffusivity, similar to that in MOM4; turned on using
185      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
186      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
187    o Added capability for 3D specification of background vertical diffusion
188      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
189      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
190      "data" file that contains the 3D vertical diffusivity coefficients.
191    o ice dynamics (pkg/seaice) with thsice thermodynamics:
192      - add code within pkg thsice to advect & diffuse sea-ice fields
193      similar to (and will replace) what has been added in  seaice_advdiff.F,
194      but: - conserving Mass, Heat & Salt.
195           - better when using non-linear advection scheme (not yet fully tested)
196           - can also be used in atmospheric set-up (for now, only the diffusion).
197    
198    checkpoint58x_post
199    o IO option for global-file compact format:
200      - add options when generating topology (utils/exch2/matlab-topology-generator)
201      - add I/O capability (pkg/mdsio).
202      - adapt utils/matlab/rdmds.m to read this format.
203      for now long-line format not yet supported by pkg/mdsio (& exch2).
204    o shelfice: add a few diagnostics
205    
206    checkpoint58w_post
207    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
208      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
209      (and replace horiVertRatio in NH code).
210      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
211                         and tutorial_plume_on_slope (sensitive to truncation)
212    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
213      directly to drive seaice model (C-grid only)
214    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
215     - reintroduce computation of wind from stress,
216     - compute tau (in exf_bulkformulae.F) from windstress averaged to
217       mass points to avoid tau = 0
218     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
219    o rdmnc.m: make it work with "global" files created with gluemnc
220    o rdmnc.m : some improvements in dealing with singleton dimension
221      (tested on all testreport mnc output files).
222    o genmake2: disable pkg/profiles if netcdf test fails.
223    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
224    o move call to cal_readparms up to make calendar parameters/variable available
225      to all packages
226    
227    checkpoint58v_post
228    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
229      useDynP_inEos_Zc tested.
230    o pkg/exf: changes to properly interpolate/mask/scale initial fields
231    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
232      and portions thereof.  See read_cs.txt for description and examples.
233    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
234      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
235      following the great-circle arc between those 2 points.
236    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
237      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
238    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
239     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
240     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
241     - still needs work (not working with some options ; efficiency to improve)
242       and serious testing.
243     - use this scheme for temperature & salinity in 2 advection test exp.:
244       advect_xy & advect_xz, respectively.
245    
246    checkpoint58u_post
247    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
248    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
249    o testreport: add option "-skipdir" to skip some test.
250    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
251      momentum calculation.
252    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
253    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
254      remove checkpoint.F and the_correction_step.F (no longer used);
255      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
256    o add option (linFSConserveTr) to correct for tracer source/sink due to
257      Linear Free surface
258    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
259    o pkg/thsice: fix reading mnc-pickups
260    
261    checkpoint58t_post
262    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
263    o pkg/mdsio:
264     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
265       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
266       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
267     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
268     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
269       either MDS_READ_FIELD or MDS_WRITE_FIELD )
270     - new S/R (to replace MDSWRITEMETA), which allows to write more
271       informations (variable names, time ...) to meta files.
272     - modify rdmds.m to give back the meta file content.
273    o pkg/diagnostics: change vertical interpolation to be safer, and more
274       flexible (define p-levels to interpolate to in data.diagnostics);
275      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
276       diagnostic pointer.
277    o pkg/seaice: more cleaning up of seaice_growth, added many comments
278    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
279    o fix multi-category seaice:
280     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
281       SEAICE_MULTICATEGORY
282     - fix short wave heat flux
283    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
284       and allow to use EVP solver. Change forward lab_sea: test both EVP
285       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
286    o Initial check-in of lab_sea adjoint
287      (very similar to natl_box_adjoint/code_seaice)
288      * used C-grid and EVP solver
289      * used KPP, GM/Redi
290      * uses inAdExact=.TRUE.
291      * gradient checks fail for both ADM and TLM
292        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
293        f.d. gradients actually seem more problematic than ADM, TLM gradients;
294        issue is related to forward mismatch between g77 an ifort
295    o pkg/seaice: overhaul of thermodynamics
296     - growth.F and groatb.F are replaced by new routine seaice_growth.F
297     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
298     - move a few global fields out of SEAICE.h into seaice_growth.F and
299       make them 2D (FICE/QNETO/ ...)
300     - remove FO (it is the same as QNETO)
301     - introduce a few local fields to avoid modifying external fields such
302       as atemp, etc.
303    
304    checkpoint58s_post
305    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
306      changed exf_set_gen.F so that
307        genperiod=0 means input file is one time-constant field and
308        genperiod=-12 means input file contains 12 monthly means
309    o CG2D: use pre-computed solver main-diagonal (stored in common block);
310      this affects truncation error ; generate new output file for exp. which
311      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
312        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
313        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
314        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
315        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
316        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
317    o start implementation of deep-atmosphere and anelastic formulation
318    o verification: remove 2nd copy of input files and use script "prepare_run"
319      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
320    o mom_common/vecinv/fluxform: fix a few initialisation isssues
321    o profiles: fix for multithreaded case
322    
323    o diagnostics: rename few diags:
324      s/'PRESSURE'/'RCENTER '/g
325      s/'TICE    '/'oceFreez'/g
326      s/'TAUX    '/'oceTAUX '/g
327      s/'TAUY    '/'oceTAUY '/g
328      s/'SWFLUX  '/'oceQsw  '/g
329      s/DIFx/DFxE/g
330      s/DIFy/DFyE/g
331      and add few ocean-forcing diagnostics:
332      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
333    o modifications to pkg/seaice/growth.F and budget.F, which change results of
334      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
335      as actual snow thickness.  It now refers everywhere to effective snow
336      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
337    
338    checkpoint58r_post
339    o modifications to pkg/seaice/growth.F, which change results of
340      lab_sea experiment: fixes pertain to melting snow over open water, to
341      masking EVAP under sea ice, and to using the correct AREA variable for
342      computations of EVAP, PRECIP, HSNOW, and GHEFF
343    o add ability to read bathy, salt, and theta using MNC (off by def)
344    o add flooding algorithm and advection of HSNOW for pkg/seaice;
345      both are turned off by default and do no change any results
346    o seaice advection with pkg/thsice: a step toward the use of non-linear
347      advection scheme, but #ifdef or commented out for now (requires more EXCH).
348  o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens  o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
349    (identical results) and the standard version of EXTERNAL_FIELDS_LOAD    (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
350    in natl_box (affects results @ truncation level: update output.txt)    in natl_box (affects results @ truncation level: update output.txt)

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