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revision 1.733 by jmc, Tue Oct 17 19:08:57 2006 UTC revision 1.822 by mlosch, Fri May 25 12:53:44 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      - allow values of SEAICE_elaticParm > 1
9      - make lsr boundary conditions free slip (by default, changes results of
10        lsr solver)
11      - no slip boundary conditions for lsr will follow
12      - set minimum of zeta to zero (and not 4e8) (changes results)
13    o change calculation of Visbeck K:
14      - no longer depend on tapering scheme; instead, compute slope (limited
15        by GM_maxSlope). this is equivalent to what was comuted before with
16        clipping or linear tappering.
17      - fix vertical averaging (wrong by 1 level)
18      - leave the old version (but will not be maintained) within
19        #ifdef OLD_VISBECK_CALC / #endif
20    o change error catch in calc_r_star to improve vectorization
21    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
22      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
23    
24    checkpoint59b
25    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
26      - export/import (between ocean & coupler) fields needed for ocean DIC.
27    o pkg/seaice:
28      - get rid of three more exchanges seaice_calc_viscosities (required
29        different loop boundaries in seaice_lsr and seaice_ocean_stress)
30      - bug fix in seaice_ocean_stress (update of lab_sea required)
31      - reduce loop boundaries to necessary minimum also in seaice_evp
32      - go back to the old way of computing deltaC/Z as the adjoint likes that
33        better
34    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
35      passive tracer to an Age Tracer) + update output.txt
36    o pkg/exf:
37      - implement A-grid / C-grid selection for wind-stress input files.
38      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
39      for now, in exf_bulk_largeyeager04.F only :
40      - change implementation for case where windspeed + 2. components wind-stress
41        are read-in. AND use rhoConstFresh to convert evap.
42    o pkg/seaice:
43      - use correct EXCH_UV for wind-forcing (on A-grid).
44      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
45        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
46    o pkg/exf:
47      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
48      EXF_INTERPOLATION:
49      - merge global_with_exf/code version of exf_interp_read.F
50        to the main code ;
51      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
52        reading the file ; Important: This options needs to be defined to recover
53        previous code.
54        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
55      - no longer loose real*8 precision along the way when using exf_iprec=64.
56    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
57      - change discretisation of evp-solver in order to avoid another exchange
58        (changes lab_sea) and clean up a little
59      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
60        help the adjoint (this also changes the results slightly)
61      - add a few "_d 0" where they had been missing in seaice_evp.F
62      - cleaning up: remove unused seaice_calc_rhs.F
63    o pkg/exf: some cleaning-up:
64      - change various "constants" into runtime parameters
65      - cleaned-up Large&Yeager04 routine which should eventually
66        replace exf_bulkformulae.F (changed names of S/R and CPP)
67        and merged various ALLOW_ATM_WIND options
68     only used with thsice pkg (in thsice_get_exf.F):
69      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
70        which are used when useStabilityFct_overIce=TRUE (= the default)
71      - change default values of ice & snow emissivity and scale downward LW
72        by ice & snow emissivity.
73    o pkg/thsice:
74     fix few little problems, in thsice_calc_thickn.F:
75      - growth vertically (and not laterally) if iceFrac == iceMaskMax
76      - melt laterally only if hIce < hThinIce (as the comments say)
77      and in thsice_extend.F:
78      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
79      - start to form ice as soon as the minimum ice-volume is reachable.
80     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
81      and cpl_aim+ocn
82    o pkg/kpp
83     - move computation of surface related input fields to KPP into a new
84       subroutine kpp_forcing_surf.F
85     - remove wrong (within bi,bj loops) EXCH calls.
86     - little cleaning (add argument myThid in last position, cvs header ...)
87     - for now, fix conservation problem by exchanging KPPviscAz (may not
88       be the best fix)
89    o pkg/seaice
90     - check for inconsistent evp parameter/cpp-flag combination
91     - remove leftover errIO flat for obsolete name list error handling
92    o OpenAD
93     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
94    
95    checkpoint59a
96    o pkg/seaice: some parameter clarifications and a little bit of clean up
97    o pkg/thsice: rename run-time parameters:
98       himin       -> hIceMin
99       himin0      -> hThinIce
100       hihig       -> hThickIce
101       i0          -> i0swFrac
102       transCoef   -> bMeltCoef
103       frac_energy -> fracMelting
104      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
105       with default values (for now) that do not change the results.
106      remove old version of thsice vars advection in pkg/seaice.
107    o in FFIELDS.h:
108      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
109      - make pLoad & sIceLoad always available (but still only used if
110         ATMOSPHERIC_LOADING is #define).
111    o pkg/kpp: replaced _KPP_RL with _RL
112    o bug fixes for vertical diffusivity computations when both KPP and
113        3D diffusivity arrays are used.
114    o pkg/seaice: fix bug in evp solver, while doing that
115      - change (improve?) discretization of stress computations for both
116        cgrid-lsr and evp solver
117      - add a new routine to compute strain rates
118      - the above changes lab_sea results
119      - add no slip conditions for evp solver (off by default), lsr-version
120        may follow
121      - fix exchange for shear at Z-points (does not change lab_sea)
122      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
123        (to force the user to pick a time step since there is not "safe" way
124        of choosing it)
125      - add principal stress diagnostics
126      - rearrange fields for evp a little to avoid having to call a: too many
127        exchanges and b: exchanges for stress trensor components which we do
128        not have.
129      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
130        of evp, complete rewrite for lsr case (latter is does not yet work
131        in all cases)
132    o pkg/kpp: add code to have mixing in shelf ice caverns
133      - add myThid to all kpp routines (long overdue)
134    
135    checkpoint59
136    o pkg/exf:
137      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
138        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
139      - move exf header files from lower_case.h to UPPER_CASE.h ;
140        add missing cvs Header & Name
141      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
142      - add namelist param. selectStressGridPosition, exf_monFreq
143      - retire many _CLIM routines, and remove data.exf_clim
144        + params moved to data.exf
145        + climsst, climsss now handled by exf_set_gen, i.e.
146          climss?period=0 refers to constant field,
147          climss?period=-12 to monthly forcing
148      - split up namelists in data.exf
149    o pkg/seaice:
150      - remove seaice_exch and seaice_exch_uv
151      - remove superfluous exchange of theta
152      - add myThid to seaice_budget_ocean/ice
153      - add new interface for atmospheric wind forcing (C-grid only)
154        + new routine
155        + two new field (taux, tauy for stress over ice)
156        + removed one global field (DAIRN) for C-grid case only
157    o pkg/thsise
158      - 2nd set of modifs for thsice adjoint in conjunction with exf
159    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
160    
161    checkpoint58y_post
162    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
163      vertical diffusivity, similar to that in MOM4; turned on using
164      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
165      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
166    o Added capability for 3D specification of background vertical diffusion
167      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
168      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
169      "data" file that contains the 3D vertical diffusivity coefficients.
170    o ice dynamics (pkg/seaice) with thsice thermodynamics:
171      - add code within pkg thsice to advect & diffuse sea-ice fields
172      similar to (and will replace) what has been added in  seaice_advdiff.F,
173      but: - conserving Mass, Heat & Salt.
174           - better when using non-linear advection scheme (not yet fully tested)
175           - can also be used in atmospheric set-up (for now, only the diffusion).
176    
177    checkpoint58x_post
178    o IO option for global-file compact format:
179      - add options when generating topology (utils/exch2/matlab-topology-generator)
180      - add I/O capability (pkg/mdsio).
181      - adapt utils/matlab/rdmds.m to read this format.
182      for now long-line format not yet supported by pkg/mdsio (& exch2).
183    o shelfice: add a few diagnostics
184    
185    checkpoint58w_post
186    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
187      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
188      (and replace horiVertRatio in NH code).
189      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
190                         and tutorial_plume_on_slope (sensitive to truncation)
191    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
192      directly to drive seaice model (C-grid only)
193    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
194     - reintroduce computation of wind from stress,
195     - compute tau (in exf_bulkformulae.F) from windstress averaged to
196       mass points to avoid tau = 0
197     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
198    o rdmnc.m: make it work with "global" files created with gluemnc
199    o rdmnc.m : some improvements in dealing with singleton dimension
200      (tested on all testreport mnc output files).
201    o genmake2: disable pkg/profiles if netcdf test fails.
202    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
203    o move call to cal_readparms up to make calendar parameters/variable available
204      to all packages
205    
206    checkpoint58v_post
207    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
208      useDynP_inEos_Zc tested.
209    o pkg/exf: changes to properly interpolate/mask/scale initial fields
210    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
211      and portions thereof.  See read_cs.txt for description and examples.
212    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
213      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
214      following the great-circle arc between those 2 points.
215    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
216      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
217    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
218     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
219     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
220     - still needs work (not working with some options ; efficiency to improve)
221       and serious testing.
222     - use this scheme for temperature & salinity in 2 advection test exp.:
223       advect_xy & advect_xz, respectively.
224    
225    checkpoint58u_post
226    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
227    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
228    o testreport: add option "-skipdir" to skip some test.
229    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
230      momentum calculation.
231    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
232    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
233      remove checkpoint.F and the_correction_step.F (no longer used);
234      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
235    o add option (linFSConserveTr) to correct for tracer source/sink due to
236      Linear Free surface
237    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
238    o pkg/thsice: fix reading mnc-pickups
239    
240    checkpoint58t_post
241    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
242    o pkg/mdsio:
243     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
244       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
245       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
246     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
247     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
248       either MDS_READ_FIELD or MDS_WRITE_FIELD )
249     - new S/R (to replace MDSWRITEMETA), which allows to write more
250       informations (variable names, time ...) to meta files.
251     - modify rdmds.m to give back the meta file content.
252    o pkg/diagnostics: change vertical interpolation to be safer, and more
253       flexible (define p-levels to interpolate to in data.diagnostics);
254      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
255       diagnostic pointer.
256    o pkg/seaice: more cleaning up of seaice_growth, added many comments
257    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
258    o fix multi-category seaice:
259     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
260       SEAICE_MULTICATEGORY
261     - fix short wave heat flux
262    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
263       and allow to use EVP solver. Change forward lab_sea: test both EVP
264       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
265    o Initial check-in of lab_sea adjoint
266      (very similar to natl_box_adjoint/code_seaice)
267      * used C-grid and EVP solver
268      * used KPP, GM/Redi
269      * uses inAdExact=.TRUE.
270      * gradient checks fail for both ADM and TLM
271        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
272        f.d. gradients actually seem more problematic than ADM, TLM gradients;
273        issue is related to forward mismatch between g77 an ifort
274    o pkg/seaice: overhaul of thermodynamics
275     - growth.F and groatb.F are replaced by new routine seaice_growth.F
276     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
277     - move a few global fields out of SEAICE.h into seaice_growth.F and
278       make them 2D (FICE/QNETO/ ...)
279     - remove FO (it is the same as QNETO)
280     - introduce a few local fields to avoid modifying external fields such
281       as atemp, etc.
282    
283    checkpoint58s_post
284    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
285      changed exf_set_gen.F so that
286        genperiod=0 means input file is one time-constant field and
287        genperiod=-12 means input file contains 12 monthly means
288    o CG2D: use pre-computed solver main-diagonal (stored in common block);
289      this affects truncation error ; generate new output file for exp. which
290      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
291        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
292        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
293        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
294        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
295        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
296    o start implementation of deep-atmosphere and anelastic formulation
297    o verification: remove 2nd copy of input files and use script "prepare_run"
298      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
299    o mom_common/vecinv/fluxform: fix a few initialisation isssues
300    o profiles: fix for multithreaded case
301    
302    o diagnostics: rename few diags:
303      s/'PRESSURE'/'RCENTER '/g
304      s/'TICE    '/'oceFreez'/g
305      s/'TAUX    '/'oceTAUX '/g
306      s/'TAUY    '/'oceTAUY '/g
307      s/'SWFLUX  '/'oceQsw  '/g
308      s/DIFx/DFxE/g
309      s/DIFy/DFyE/g
310      and add few ocean-forcing diagnostics:
311      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
312    o modifications to pkg/seaice/growth.F and budget.F, which change results of
313      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
314      as actual snow thickness.  It now refers everywhere to effective snow
315      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
316    
317    checkpoint58r_post
318    o modifications to pkg/seaice/growth.F, which change results of
319      lab_sea experiment: fixes pertain to melting snow over open water, to
320      masking EVAP under sea ice, and to using the correct AREA variable for
321      computations of EVAP, PRECIP, HSNOW, and GHEFF
322    o add ability to read bathy, salt, and theta using MNC (off by def)
323    o add flooding algorithm and advection of HSNOW for pkg/seaice;
324      both are turned off by default and do no change any results
325    o seaice advection with pkg/thsice: a step toward the use of non-linear
326      advection scheme, but #ifdef or commented out for now (requires more EXCH).
327    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
328      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
329      in natl_box (affects results @ truncation level: update output.txt)
330    o multi-threading and IO:
331      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
332      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
333        (needed to work with SingleCpuIO): tested in all verif. exp.
334    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
335      affects the results (but none of the verification test uses this scheme).
336    o Adding some pkg/diagnostics capability to pkg/seaice
337      (will certainly be subject to changes)
338    o ctrl: adding new control variables:
339      lwflux, lwdown, evap, snowprecip, apressure, runoff
340    
341    checkpoint58q_post
342    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
343      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
344      high_res_cube configuration by 4% on Columbia.
345  o clean-up multi-threaded problems (reported by debugger tcheck on ACES);  o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
346    add (in global_with_exf/code) a version of EXF_INTERP_READ without    add (in global_with_exf/code) a version of EXF_INTERP_READ without
347    dynamical allocation (seems to work in multi-threaded).    dynamical allocation (seems to work in multi-threaded).

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