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revision 1.730 by cnh, Wed Oct 11 19:30:01 2006 UTC revision 1.818 by jmc, Wed May 16 13:39:57 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint59b
8    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
9      - export/import (between ocean & coupler) fields needed for ocean DIC.
10    o pkg/seaice:
11      - get rid of three more exchanges seaice_calc_viscosities (required
12        different loop boundaries in seaice_lsr and seaice_ocean_stress)
13      - bug fix in seaice_ocean_stress (update of lab_sea required)
14      - reduce loop boundaries to necessary minimum also in seaice_evp
15      - go back to the old way of computing deltaC/Z as the adjoint likes that
16        better
17    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
18      passive tracer to an Age Tracer) + update output.txt
19    o pkg/exf:
20      - implement A-grid / C-grid selection for wind-stress input files.
21      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
22      for now, in exf_bulk_largeyeager04.F only :
23      - change implementation for case where windspeed + 2. components wind-stress
24        are read-in. AND use rhoConstFresh to convert evap.
25    o pkg/seaice:
26      - use correct EXCH_UV for wind-forcing (on A-grid).
27      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
28        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
29    o pkg/exf:
30      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
31      EXF_INTERPOLATION:
32      - merge global_with_exf/code version of exf_interp_read.F
33        to the main code ;
34      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
35        reading the file ; Important: This options needs to be defined to recover
36        previous code.
37        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
38      - no longer loose real*8 precision along the way when using exf_iprec=64.
39    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
40      - change discretisation of evp-solver in order to avoid another exchange
41        (changes lab_sea) and clean up a little
42      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
43        help the adjoint (this also changes the results slightly)
44      - add a few "_d 0" where they had been missing in seaice_evp.F
45      - cleaning up: remove unused seaice_calc_rhs.F
46    o pkg/exf: some cleaning-up:
47      - change various "constants" into runtime parameters
48      - cleaned-up Large&Yeager04 routine which should eventually
49        replace exf_bulkformulae.F (changed names of S/R and CPP)
50        and merged various ALLOW_ATM_WIND options
51     only used with thsice pkg (in thsice_get_exf.F):
52      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
53        which are used when useStabilityFct_overIce=TRUE (= the default)
54      - change default values of ice & snow emissivity and scale downward LW
55        by ice & snow emissivity.
56    o pkg/thsice:
57     fix few little problems, in thsice_calc_thickn.F:
58      - growth vertically (and not laterally) if iceFrac == iceMaskMax
59      - melt laterally only if hIce < hThinIce (as the comments say)
60      and in thsice_extend.F:
61      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
62      - start to form ice as soon as the minimum ice-volume is reachable.
63     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
64      and cpl_aim+ocn
65    o pkg/kpp
66     - move computation of surface related input fields to KPP into a new
67       subroutine kpp_forcing_surf.F
68     - remove wrong (within bi,bj loops) EXCH calls.
69     - little cleaning (add argument myThid in last position, cvs header ...)
70     - for now, fix conservation problem by exchanging KPPviscAz (may not
71       be the best fix)
72    o pkg/seaice
73     - check for inconsistent evp parameter/cpp-flag combination
74     - remove leftover errIO flat for obsolete name list error handling
75    o OpenAD
76     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
77    
78    checkpoint59a
79    o pkg/seaice: some parameter clarifications and a little bit of clean up
80    o pkg/thsice: rename run-time parameters:
81       himin       -> hIceMin
82       himin0      -> hThinIce
83       hihig       -> hThickIce
84       i0          -> i0swFrac
85       transCoef   -> bMeltCoef
86       frac_energy -> fracMelting
87      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
88       with default values (for now) that do not change the results.
89      remove old version of thsice vars advection in pkg/seaice.
90    o in FFIELDS.h:
91      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
92      - make pLoad & sIceLoad always available (but still only used if
93         ATMOSPHERIC_LOADING is #define).
94    o pkg/kpp: replaced _KPP_RL with _RL
95    o bug fixes for vertical diffusivity computations when both KPP and
96        3D diffusivity arrays are used.
97    o pkg/seaice: fix bug in evp solver, while doing that
98      - change (improve?) discretization of stress computations for both
99        cgrid-lsr and evp solver
100      - add a new routine to compute strain rates
101      - the above changes lab_sea results
102      - add no slip conditions for evp solver (off by default), lsr-version
103        may follow
104      - fix exchange for shear at Z-points (does not change lab_sea)
105      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
106        (to force the user to pick a time step since there is not "safe" way
107        of choosing it)
108      - add principal stress diagnostics
109      - rearrange fields for evp a little to avoid having to call a: too many
110        exchanges and b: exchanges for stress trensor components which we do
111        not have.
112      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
113        of evp, complete rewrite for lsr case (latter is does not yet work
114        in all cases)
115    o pkg/kpp: add code to have mixing in shelf ice caverns
116      - add myThid to all kpp routines (long overdue)
117    
118    checkpoint59
119    o pkg/exf:
120      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
121        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
122      - move exf header files from lower_case.h to UPPER_CASE.h ;
123        add missing cvs Header & Name
124      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
125      - add namelist param. selectStressGridPosition, exf_monFreq
126      - retire many _CLIM routines, and remove data.exf_clim
127        + params moved to data.exf
128        + climsst, climsss now handled by exf_set_gen, i.e.
129          climss?period=0 refers to constant field,
130          climss?period=-12 to monthly forcing
131      - split up namelists in data.exf
132    o pkg/seaice:
133      - remove seaice_exch and seaice_exch_uv
134      - remove superfluous exchange of theta
135      - add myThid to seaice_budget_ocean/ice
136      - add new interface for atmospheric wind forcing (C-grid only)
137        + new routine
138        + two new field (taux, tauy for stress over ice)
139        + removed one global field (DAIRN) for C-grid case only
140    o pkg/thsise
141      - 2nd set of modifs for thsice adjoint in conjunction with exf
142    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
143    
144    checkpoint58y_post
145    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
146      vertical diffusivity, similar to that in MOM4; turned on using
147      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
148      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
149    o Added capability for 3D specification of background vertical diffusion
150      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
151      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
152      "data" file that contains the 3D vertical diffusivity coefficients.
153    o ice dynamics (pkg/seaice) with thsice thermodynamics:
154      - add code within pkg thsice to advect & diffuse sea-ice fields
155      similar to (and will replace) what has been added in  seaice_advdiff.F,
156      but: - conserving Mass, Heat & Salt.
157           - better when using non-linear advection scheme (not yet fully tested)
158           - can also be used in atmospheric set-up (for now, only the diffusion).
159    
160    checkpoint58x_post
161    o IO option for global-file compact format:
162      - add options when generating topology (utils/exch2/matlab-topology-generator)
163      - add I/O capability (pkg/mdsio).
164      - adapt utils/matlab/rdmds.m to read this format.
165      for now long-line format not yet supported by pkg/mdsio (& exch2).
166    o shelfice: add a few diagnostics
167    
168    checkpoint58w_post
169    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
170      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
171      (and replace horiVertRatio in NH code).
172      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
173                         and tutorial_plume_on_slope (sensitive to truncation)
174    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
175      directly to drive seaice model (C-grid only)
176    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
177     - reintroduce computation of wind from stress,
178     - compute tau (in exf_bulkformulae.F) from windstress averaged to
179       mass points to avoid tau = 0
180     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
181    o rdmnc.m: make it work with "global" files created with gluemnc
182    o rdmnc.m : some improvements in dealing with singleton dimension
183      (tested on all testreport mnc output files).
184    o genmake2: disable pkg/profiles if netcdf test fails.
185    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
186    o move call to cal_readparms up to make calendar parameters/variable available
187      to all packages
188    
189    checkpoint58v_post
190    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
191      useDynP_inEos_Zc tested.
192    o pkg/exf: changes to properly interpolate/mask/scale initial fields
193    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
194      and portions thereof.  See read_cs.txt for description and examples.
195    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
196      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
197      following the great-circle arc between those 2 points.
198    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
199      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
200    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
201     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
202     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
203     - still needs work (not working with some options ; efficiency to improve)
204       and serious testing.
205     - use this scheme for temperature & salinity in 2 advection test exp.:
206       advect_xy & advect_xz, respectively.
207    
208    checkpoint58u_post
209    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
210    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
211    o testreport: add option "-skipdir" to skip some test.
212    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
213      momentum calculation.
214    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
215    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
216      remove checkpoint.F and the_correction_step.F (no longer used);
217      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
218    o add option (linFSConserveTr) to correct for tracer source/sink due to
219      Linear Free surface
220    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
221    o pkg/thsice: fix reading mnc-pickups
222    
223    checkpoint58t_post
224    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
225    o pkg/mdsio:
226     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
227       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
228       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
229     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
230     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
231       either MDS_READ_FIELD or MDS_WRITE_FIELD )
232     - new S/R (to replace MDSWRITEMETA), which allows to write more
233       informations (variable names, time ...) to meta files.
234     - modify rdmds.m to give back the meta file content.
235    o pkg/diagnostics: change vertical interpolation to be safer, and more
236       flexible (define p-levels to interpolate to in data.diagnostics);
237      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
238       diagnostic pointer.
239    o pkg/seaice: more cleaning up of seaice_growth, added many comments
240    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
241    o fix multi-category seaice:
242     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
243       SEAICE_MULTICATEGORY
244     - fix short wave heat flux
245    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
246       and allow to use EVP solver. Change forward lab_sea: test both EVP
247       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
248    o Initial check-in of lab_sea adjoint
249      (very similar to natl_box_adjoint/code_seaice)
250      * used C-grid and EVP solver
251      * used KPP, GM/Redi
252      * uses inAdExact=.TRUE.
253      * gradient checks fail for both ADM and TLM
254        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
255        f.d. gradients actually seem more problematic than ADM, TLM gradients;
256        issue is related to forward mismatch between g77 an ifort
257    o pkg/seaice: overhaul of thermodynamics
258     - growth.F and groatb.F are replaced by new routine seaice_growth.F
259     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
260     - move a few global fields out of SEAICE.h into seaice_growth.F and
261       make them 2D (FICE/QNETO/ ...)
262     - remove FO (it is the same as QNETO)
263     - introduce a few local fields to avoid modifying external fields such
264       as atemp, etc.
265    
266    checkpoint58s_post
267    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
268      changed exf_set_gen.F so that
269        genperiod=0 means input file is one time-constant field and
270        genperiod=-12 means input file contains 12 monthly means
271    o CG2D: use pre-computed solver main-diagonal (stored in common block);
272      this affects truncation error ; generate new output file for exp. which
273      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
274        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
275        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
276        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
277        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
278        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
279    o start implementation of deep-atmosphere and anelastic formulation
280    o verification: remove 2nd copy of input files and use script "prepare_run"
281      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
282    o mom_common/vecinv/fluxform: fix a few initialisation isssues
283    o profiles: fix for multithreaded case
284    
285    o diagnostics: rename few diags:
286      s/'PRESSURE'/'RCENTER '/g
287      s/'TICE    '/'oceFreez'/g
288      s/'TAUX    '/'oceTAUX '/g
289      s/'TAUY    '/'oceTAUY '/g
290      s/'SWFLUX  '/'oceQsw  '/g
291      s/DIFx/DFxE/g
292      s/DIFy/DFyE/g
293      and add few ocean-forcing diagnostics:
294      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
295    o modifications to pkg/seaice/growth.F and budget.F, which change results of
296      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
297      as actual snow thickness.  It now refers everywhere to effective snow
298      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
299    
300    checkpoint58r_post
301    o modifications to pkg/seaice/growth.F, which change results of
302      lab_sea experiment: fixes pertain to melting snow over open water, to
303      masking EVAP under sea ice, and to using the correct AREA variable for
304      computations of EVAP, PRECIP, HSNOW, and GHEFF
305    o add ability to read bathy, salt, and theta using MNC (off by def)
306    o add flooding algorithm and advection of HSNOW for pkg/seaice;
307      both are turned off by default and do no change any results
308    o seaice advection with pkg/thsice: a step toward the use of non-linear
309      advection scheme, but #ifdef or commented out for now (requires more EXCH).
310    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
311      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
312      in natl_box (affects results @ truncation level: update output.txt)
313    o multi-threading and IO:
314      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
315      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
316        (needed to work with SingleCpuIO): tested in all verif. exp.
317    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
318      affects the results (but none of the verification test uses this scheme).
319    o Adding some pkg/diagnostics capability to pkg/seaice
320      (will certainly be subject to changes)
321    o ctrl: adding new control variables:
322      lwflux, lwdown, evap, snowprecip, apressure, runoff
323    
324    checkpoint58q_post
325    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
326      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
327      high_res_cube configuration by 4% on Columbia.
328    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
329      add (in global_with_exf/code) a version of EXF_INTERP_READ without
330      dynamical allocation (seems to work in multi-threaded).
331    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
332      single CPU io) so that TAF does not have to see EESUPPORT.h
333  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
334    
335  checkpoint58p_post  checkpoint58p_post

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