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revision 1.724 by heimbach, Wed Sep 6 18:31:32 2006 UTC revision 1.823 by mlosch, Fri May 25 14:52:27 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      - allow values of SEAICE_elaticParm > 1
9      - make lsr boundary conditions free slip (by default)
10      - add code for no slip boundary conditions for lsr
11      - set minimum of zeta to zero (and not 4e8) (changes results)
12    o change calculation of Visbeck K:
13      - no longer depend on tapering scheme; instead, compute slope (limited
14        by GM_maxSlope). this is equivalent to what was comuted before with
15        clipping or linear tappering.
16      - fix vertical averaging (wrong by 1 level)
17      - leave the old version (but will not be maintained) within
18        #ifdef OLD_VISBECK_CALC / #endif
19    o change error catch in calc_r_star to improve vectorization
20    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
21      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
22    
23    checkpoint59b
24    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
25      - export/import (between ocean & coupler) fields needed for ocean DIC.
26    o pkg/seaice:
27      - get rid of three more exchanges seaice_calc_viscosities (required
28        different loop boundaries in seaice_lsr and seaice_ocean_stress)
29      - bug fix in seaice_ocean_stress (update of lab_sea required)
30      - reduce loop boundaries to necessary minimum also in seaice_evp
31      - go back to the old way of computing deltaC/Z as the adjoint likes that
32        better
33    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
34      passive tracer to an Age Tracer) + update output.txt
35    o pkg/exf:
36      - implement A-grid / C-grid selection for wind-stress input files.
37      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
38      for now, in exf_bulk_largeyeager04.F only :
39      - change implementation for case where windspeed + 2. components wind-stress
40        are read-in. AND use rhoConstFresh to convert evap.
41    o pkg/seaice:
42      - use correct EXCH_UV for wind-forcing (on A-grid).
43      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
44        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
45    o pkg/exf:
46      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
47      EXF_INTERPOLATION:
48      - merge global_with_exf/code version of exf_interp_read.F
49        to the main code ;
50      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
51        reading the file ; Important: This options needs to be defined to recover
52        previous code.
53        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
54      - no longer loose real*8 precision along the way when using exf_iprec=64.
55    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
56      - change discretisation of evp-solver in order to avoid another exchange
57        (changes lab_sea) and clean up a little
58      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
59        help the adjoint (this also changes the results slightly)
60      - add a few "_d 0" where they had been missing in seaice_evp.F
61      - cleaning up: remove unused seaice_calc_rhs.F
62    o pkg/exf: some cleaning-up:
63      - change various "constants" into runtime parameters
64      - cleaned-up Large&Yeager04 routine which should eventually
65        replace exf_bulkformulae.F (changed names of S/R and CPP)
66        and merged various ALLOW_ATM_WIND options
67     only used with thsice pkg (in thsice_get_exf.F):
68      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
69        which are used when useStabilityFct_overIce=TRUE (= the default)
70      - change default values of ice & snow emissivity and scale downward LW
71        by ice & snow emissivity.
72    o pkg/thsice:
73     fix few little problems, in thsice_calc_thickn.F:
74      - growth vertically (and not laterally) if iceFrac == iceMaskMax
75      - melt laterally only if hIce < hThinIce (as the comments say)
76      and in thsice_extend.F:
77      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
78      - start to form ice as soon as the minimum ice-volume is reachable.
79     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
80      and cpl_aim+ocn
81    o pkg/kpp
82     - move computation of surface related input fields to KPP into a new
83       subroutine kpp_forcing_surf.F
84     - remove wrong (within bi,bj loops) EXCH calls.
85     - little cleaning (add argument myThid in last position, cvs header ...)
86     - for now, fix conservation problem by exchanging KPPviscAz (may not
87       be the best fix)
88    o pkg/seaice
89     - check for inconsistent evp parameter/cpp-flag combination
90     - remove leftover errIO flat for obsolete name list error handling
91    o OpenAD
92     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
93    
94    checkpoint59a
95    o pkg/seaice: some parameter clarifications and a little bit of clean up
96    o pkg/thsice: rename run-time parameters:
97       himin       -> hIceMin
98       himin0      -> hThinIce
99       hihig       -> hThickIce
100       i0          -> i0swFrac
101       transCoef   -> bMeltCoef
102       frac_energy -> fracMelting
103      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
104       with default values (for now) that do not change the results.
105      remove old version of thsice vars advection in pkg/seaice.
106    o in FFIELDS.h:
107      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
108      - make pLoad & sIceLoad always available (but still only used if
109         ATMOSPHERIC_LOADING is #define).
110    o pkg/kpp: replaced _KPP_RL with _RL
111    o bug fixes for vertical diffusivity computations when both KPP and
112        3D diffusivity arrays are used.
113    o pkg/seaice: fix bug in evp solver, while doing that
114      - change (improve?) discretization of stress computations for both
115        cgrid-lsr and evp solver
116      - add a new routine to compute strain rates
117      - the above changes lab_sea results
118      - add no slip conditions for evp solver (off by default), lsr-version
119        may follow
120      - fix exchange for shear at Z-points (does not change lab_sea)
121      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
122        (to force the user to pick a time step since there is not "safe" way
123        of choosing it)
124      - add principal stress diagnostics
125      - rearrange fields for evp a little to avoid having to call a: too many
126        exchanges and b: exchanges for stress trensor components which we do
127        not have.
128      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
129        of evp, complete rewrite for lsr case (latter is does not yet work
130        in all cases)
131    o pkg/kpp: add code to have mixing in shelf ice caverns
132      - add myThid to all kpp routines (long overdue)
133    
134    checkpoint59
135    o pkg/exf:
136      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
137        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
138      - move exf header files from lower_case.h to UPPER_CASE.h ;
139        add missing cvs Header & Name
140      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
141      - add namelist param. selectStressGridPosition, exf_monFreq
142      - retire many _CLIM routines, and remove data.exf_clim
143        + params moved to data.exf
144        + climsst, climsss now handled by exf_set_gen, i.e.
145          climss?period=0 refers to constant field,
146          climss?period=-12 to monthly forcing
147      - split up namelists in data.exf
148    o pkg/seaice:
149      - remove seaice_exch and seaice_exch_uv
150      - remove superfluous exchange of theta
151      - add myThid to seaice_budget_ocean/ice
152      - add new interface for atmospheric wind forcing (C-grid only)
153        + new routine
154        + two new field (taux, tauy for stress over ice)
155        + removed one global field (DAIRN) for C-grid case only
156    o pkg/thsise
157      - 2nd set of modifs for thsice adjoint in conjunction with exf
158    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
159    
160    checkpoint58y_post
161    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
162      vertical diffusivity, similar to that in MOM4; turned on using
163      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
164      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
165    o Added capability for 3D specification of background vertical diffusion
166      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
167      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
168      "data" file that contains the 3D vertical diffusivity coefficients.
169    o ice dynamics (pkg/seaice) with thsice thermodynamics:
170      - add code within pkg thsice to advect & diffuse sea-ice fields
171      similar to (and will replace) what has been added in  seaice_advdiff.F,
172      but: - conserving Mass, Heat & Salt.
173           - better when using non-linear advection scheme (not yet fully tested)
174           - can also be used in atmospheric set-up (for now, only the diffusion).
175    
176    checkpoint58x_post
177    o IO option for global-file compact format:
178      - add options when generating topology (utils/exch2/matlab-topology-generator)
179      - add I/O capability (pkg/mdsio).
180      - adapt utils/matlab/rdmds.m to read this format.
181      for now long-line format not yet supported by pkg/mdsio (& exch2).
182    o shelfice: add a few diagnostics
183    
184    checkpoint58w_post
185    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
186      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
187      (and replace horiVertRatio in NH code).
188      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
189                         and tutorial_plume_on_slope (sensitive to truncation)
190    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
191      directly to drive seaice model (C-grid only)
192    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
193     - reintroduce computation of wind from stress,
194     - compute tau (in exf_bulkformulae.F) from windstress averaged to
195       mass points to avoid tau = 0
196     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
197    o rdmnc.m: make it work with "global" files created with gluemnc
198    o rdmnc.m : some improvements in dealing with singleton dimension
199      (tested on all testreport mnc output files).
200    o genmake2: disable pkg/profiles if netcdf test fails.
201    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
202    o move call to cal_readparms up to make calendar parameters/variable available
203      to all packages
204    
205    checkpoint58v_post
206    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
207      useDynP_inEos_Zc tested.
208    o pkg/exf: changes to properly interpolate/mask/scale initial fields
209    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
210      and portions thereof.  See read_cs.txt for description and examples.
211    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
212      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
213      following the great-circle arc between those 2 points.
214    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
215      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
216    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
217     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
218     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
219     - still needs work (not working with some options ; efficiency to improve)
220       and serious testing.
221     - use this scheme for temperature & salinity in 2 advection test exp.:
222       advect_xy & advect_xz, respectively.
223    
224    checkpoint58u_post
225    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
226    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
227    o testreport: add option "-skipdir" to skip some test.
228    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
229      momentum calculation.
230    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
231    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
232      remove checkpoint.F and the_correction_step.F (no longer used);
233      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
234    o add option (linFSConserveTr) to correct for tracer source/sink due to
235      Linear Free surface
236    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
237    o pkg/thsice: fix reading mnc-pickups
238    
239    checkpoint58t_post
240    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
241    o pkg/mdsio:
242     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
243       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
244       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
245     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
246     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
247       either MDS_READ_FIELD or MDS_WRITE_FIELD )
248     - new S/R (to replace MDSWRITEMETA), which allows to write more
249       informations (variable names, time ...) to meta files.
250     - modify rdmds.m to give back the meta file content.
251    o pkg/diagnostics: change vertical interpolation to be safer, and more
252       flexible (define p-levels to interpolate to in data.diagnostics);
253      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
254       diagnostic pointer.
255    o pkg/seaice: more cleaning up of seaice_growth, added many comments
256    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
257    o fix multi-category seaice:
258     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
259       SEAICE_MULTICATEGORY
260     - fix short wave heat flux
261    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
262       and allow to use EVP solver. Change forward lab_sea: test both EVP
263       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
264    o Initial check-in of lab_sea adjoint
265      (very similar to natl_box_adjoint/code_seaice)
266      * used C-grid and EVP solver
267      * used KPP, GM/Redi
268      * uses inAdExact=.TRUE.
269      * gradient checks fail for both ADM and TLM
270        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
271        f.d. gradients actually seem more problematic than ADM, TLM gradients;
272        issue is related to forward mismatch between g77 an ifort
273    o pkg/seaice: overhaul of thermodynamics
274     - growth.F and groatb.F are replaced by new routine seaice_growth.F
275     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
276     - move a few global fields out of SEAICE.h into seaice_growth.F and
277       make them 2D (FICE/QNETO/ ...)
278     - remove FO (it is the same as QNETO)
279     - introduce a few local fields to avoid modifying external fields such
280       as atemp, etc.
281    
282    checkpoint58s_post
283    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
284      changed exf_set_gen.F so that
285        genperiod=0 means input file is one time-constant field and
286        genperiod=-12 means input file contains 12 monthly means
287    o CG2D: use pre-computed solver main-diagonal (stored in common block);
288      this affects truncation error ; generate new output file for exp. which
289      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
290        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
291        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
292        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
293        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
294        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
295    o start implementation of deep-atmosphere and anelastic formulation
296    o verification: remove 2nd copy of input files and use script "prepare_run"
297      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
298    o mom_common/vecinv/fluxform: fix a few initialisation isssues
299    o profiles: fix for multithreaded case
300    
301    o diagnostics: rename few diags:
302      s/'PRESSURE'/'RCENTER '/g
303      s/'TICE    '/'oceFreez'/g
304      s/'TAUX    '/'oceTAUX '/g
305      s/'TAUY    '/'oceTAUY '/g
306      s/'SWFLUX  '/'oceQsw  '/g
307      s/DIFx/DFxE/g
308      s/DIFy/DFyE/g
309      and add few ocean-forcing diagnostics:
310      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
311    o modifications to pkg/seaice/growth.F and budget.F, which change results of
312      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
313      as actual snow thickness.  It now refers everywhere to effective snow
314      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
315    
316    checkpoint58r_post
317    o modifications to pkg/seaice/growth.F, which change results of
318      lab_sea experiment: fixes pertain to melting snow over open water, to
319      masking EVAP under sea ice, and to using the correct AREA variable for
320      computations of EVAP, PRECIP, HSNOW, and GHEFF
321    o add ability to read bathy, salt, and theta using MNC (off by def)
322    o add flooding algorithm and advection of HSNOW for pkg/seaice;
323      both are turned off by default and do no change any results
324    o seaice advection with pkg/thsice: a step toward the use of non-linear
325      advection scheme, but #ifdef or commented out for now (requires more EXCH).
326    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
327      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
328      in natl_box (affects results @ truncation level: update output.txt)
329    o multi-threading and IO:
330      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
331      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
332        (needed to work with SingleCpuIO): tested in all verif. exp.
333    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
334      affects the results (but none of the verification test uses this scheme).
335    o Adding some pkg/diagnostics capability to pkg/seaice
336      (will certainly be subject to changes)
337    o ctrl: adding new control variables:
338      lwflux, lwdown, evap, snowprecip, apressure, runoff
339    
340    checkpoint58q_post
341    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
342      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
343      high_res_cube configuration by 4% on Columbia.
344    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
345      add (in global_with_exf/code) a version of EXF_INTERP_READ without
346      dynamical allocation (seems to work in multi-threaded).
347    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
348      single CPU io) so that TAF does not have to see EESUPPORT.h
349    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
350    
351    checkpoint58p_post
352    o obcs: stop if obcs is used with useCDscheme = .true.
353  o shelfice:  o shelfice:
354   - fix a sign error so that no slip at shelfice interface works   - fix a sign error so that no slip at shelfice interface works
355   - remove stop for combination non-hydrostatic code and shelfice. That does   - remove stop for combination non-hydrostatic code and shelfice. That does

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