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revision 1.794 by mlosch, Thu Apr 19 15:49:24 2007 UTC revision 1.892 by jmc, Mon Oct 15 00:30:04 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/monitor:
8      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
9      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
10      - account for deep Atmosphere factor and density factor (anelastic)
11    o added open boundary conditions capability for seaice HEFF and AREA
12    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
13      thermodynamics
14      - requires a little reorganization, which affects the testreport results
15        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
16        so that now the conservative form is tested
17      - add a few comments
18    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
19    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
20    o add new diagnostics to seaice: advective, diffusive fluxes (only for
21      multidim-advection, for scheme 2 they are not filled) and transports,
22      thermodynamic growth rates
23    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
24      leave input file unchanged. Affects results @ truncation level (cg2d match)
25      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
26      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
27      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
28      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
29    
30    checkpoint59h
31    o pkg/exf:
32      - improve vectorization by moving if-statement out of loops in
33        exf_mapfields, exf_radiation
34      - exf_bulkformulae.F: introduce 2D fields and vectorize code
35    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
36    o testreport:
37      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
38        monitor & update offline_exf_seaice exp. output.
39      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
40    o pkg/seaice:
41      - bug fix in the evp solver: boundary conditions were affected be
42        masking of zMax/zMin (changes results)
43      - minor bug fix in boundary conditions in seaice_calc_strainrates
44        (changes results for no_slip)
45      - seaice_lsr.F: make interpolation of eta dependent on boundaries
46      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
47      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
48        stress formulation and no-slip boundary conditions
49    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
50      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
51    o pkg/seaice: a first HSALT time stepping equation has been checked in
52    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
53      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
54      without requiring DO-IF statements
55    o pkg/thsice:
56      use continuous power-law function for partition of energy between lateral
57      melting/freezing and thinning/thickening ; old code using step function
58      still available with #undef THSICE_FRACEN_POWERLAW
59      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
60    o testreport: change AD testing : check against results/output_adm.txt
61      using same scripts as for forward test.
62    
63    checkpoint59g
64    o adjoint testing: in preparation for changing testreport:
65      - output format: cost and grad written on separated lines
66      - ad output results in directory "results" (instead of "results_ad")
67    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
68    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
69    o pkg/ecco: allow user defined cost function contributions
70    o testreport:
71      Allow to choose (per experiment) the list of tested output variables
72       and the main variable (used to issue a pass/FAIL ) ;
73      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
74      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
75      Also modify printing of summary:
76       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
77       b) echo the list of tested variables in the individual summary.txt of
78          each experiment.
79    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
80      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
81      (but still depend on the tile decompostion of the domain).
82    o pkg/seaice: change a discretization detail to make the B-grid code
83      "more symmetric". This change is likely to remove all "ridges/leads" that
84      where quasi-aligned with the grid in B-grid solutions. It may also be
85      the solution to the stress coupling issues with the B-grid.
86    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
87      remove .cvsignore from input dir. (since testreport no longer run here).
88    o pkg/thsice:
89     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
90     - fix reshaping of sea-ice just after advection:
91       melt all the ice only if ice-volume is too small.
92     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
93       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
94     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
95    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
96      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
97    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
98      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
99      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
100      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
101      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
102      -> update output.txt
103    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
104     this affects truncation error: -> update output.txt of exp:
105      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
106      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
107    
108    checkpoint59f
109    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
110    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
111      a bounded range (in forward mode)
112    o pkg/ecco, ctrl, autodiff and mom_common:
113     internal parameter controls, completements of implementations
114    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
115    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
116      (not seem any difference in testing results).
117    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
118       at face corners.
119    o pkg/generic_advdiff:
120     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
121      loop range indices for computing vertical advection tendency
122      and do the calculation in the interior only (no overlap) ;
123      for now, only implemented for SOM advection (to save CPU time).
124     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
125    o exch2 adjoint
126      First set of changes:
127      - add exch2 hand-written adjoint templates
128      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
129        This will require cleanup in pkg/autodiff/*.F
130        (changed routines currently kept separate in verif. code/)
131      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
132        that used to hide exch2 or cubed-sphere specific code
133        (commented via 'cph-exch2')
134    o pkg/seaice
135      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
136    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
137       output of global_ocean.cs32x15.thsice .
138    
139    checkpoint59e
140    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
141      for B-grid vector (not yet tested) and C-grid vector (<- only used
142      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
143    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
144      (#ifdef ALLOW_SALT_PLUME)
145    o gather_2d/scatter_2d: removed halo regions
146    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
147      scheme and the corresponding test case (under front_relax dir). For now,
148      only available with Skew-flux form and not yet tested in realistic set-up.
149      adjoint: store directives updated, but gradient checks deteriorated,
150      so maybe GM/Redi adjoint is now broken.
151    o seaice adjoint
152      * add AREA, HEFF, HSNOW as control variable
153        (should not change lab_sea results)
154      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
155    o pkg/seaice:
156      * added computation of saltFlux in seaice_growth;
157        For time being, sea ice salinity is assumed constant
158        contribution of snow flooding to freshening of sea ice is neglected.
159        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
160        defaults to 0.0 in order to maintain backward compatibility.
161        Typical values for SEAICE_salinity are 4 to 10 g/kg.
162      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
163      * added SEAICE_availHeatFrac, which specifies fraction of surface level
164        heat content used to melt or grow ice
165      * commented out cap of HICE: it helps keep ice thinner
166      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
167      * applied OBCS T/S mask to HEFFM sea ice mask
168    
169    checkpoint59d
170    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
171     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
172     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
173    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
174     and change default value of parameter "GM_Small_Number";
175     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
176       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
177       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
178    o pkg/ecco: cost function when applying pkg/smooth to controls
179    o pkg/ctrl: add forcingPrecond run time parameter
180    o pkg/seaice:
181     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
182     - fix bug in metric terms of u-equation in LSR solver (implicit part),
183       changes verification/lab_sea
184     - rearrange implicit part of u-equation in LSR solver to make it easier to
185       read, understand, and debug. This causes changes at the truncation level.
186     - fix (serious) bug in the boundary conditions (sign error in the implicit
187       part) of the LSR solver. Changes all LSR results.
188     - fixed problem with HSNOW initialization to avoid thick snow when AREA
189       is initilized with small values - does not change lab_sea results.
190     - added HsnowFile initialization capability
191    o pkg/smooth: addition to model/src and pkg/ctrl so allow
192     initialization of pkg/smooth and application to control vector
193    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
194    o dependencies: pkg/profiles requires pkg/cal
195    o pkg/profiles:
196     - added option ALLOW_PROFILES_GENERICGRID
197         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
198         that interpolation information (grid points and coefficients) is provided
199         within the netcdf input files.
200         -> sample matlab scripts can be found in MITgcm_contrib/gael
201         that allow you to prepare netcdf input files.
202     - also modified: cleaner include statements, cleaner error print statements,
203       cleaner stops when error, and more tests of the netcdf input files consistency.
204    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
205    o pkg/seaice:
206     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
207       requires a new routine: seaice_diagnostics_fill.F
208     - make sure that seaice does not move if not forced (pressure replacement
209       method, Hibler and Ip, 1995), changes results
210     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
211     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
212       It is turned off by default (=-1.), because it changes the results.
213     - make it possible to read AREA from a file, too.
214    
215    checkpoint59c
216    o add S/R and diagnostics for oceanic mixed-layer depth
217    o move GMRedi call after all vertical mixing schemes (including KPP)
218    o pkg/thsice:
219     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
220      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
221    o pkg/obcs:
222     - bug fix for balance code
223    o pkg/seaice:
224      - allow values of SEAICE_elasticParm > 1
225      - add new parameter SEAICE_evpTauRelax as an alternative
226        to SEAICE_elasticParm
227      - make lsr boundary conditions free slip (by default), changes result
228      - add code for no slip boundary conditions for lsr
229      - set minimum of zeta to zero (and not 4e8) (changes results)
230      - add a cap on AREA after advecting AREA if seaice_growth is not called
231    o change calculation of Visbeck K:
232      - no longer depend on tapering scheme; instead, compute slope (limited
233        by GM_maxSlope). this is equivalent to what was comuted before with
234        clipping or linear tappering.
235      - fix vertical averaging (wrong by 1/2 level)
236      - leave the old version (but will not be maintained) within
237        #ifdef OLD_VISBECK_CALC / #endif
238      - update output of exp. ideal_2D_oce
239    o change error catch in calc_r_star to improve vectorization
240    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
241      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
242    o adjoint:
243      Re-organized adjoint checkpointing according to Matt Mazloff
244      (but with modifs/completions/cleanups)
245      Storing is now bundled into large arrays to optimized I/O
246      (and second step in cleanup of the_main_loop)
247    
248    checkpoint59b
249    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
250      - export/import (between ocean & coupler) fields needed for ocean DIC.
251    o pkg/seaice:
252      - get rid of three more exchanges seaice_calc_viscosities (required
253        different loop boundaries in seaice_lsr and seaice_ocean_stress)
254      - bug fix in seaice_ocean_stress (update of lab_sea required)
255      - reduce loop boundaries to necessary minimum also in seaice_evp
256      - go back to the old way of computing deltaC/Z as the adjoint likes that
257        better
258    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
259      passive tracer to an Age Tracer) + update output.txt
260    o pkg/exf:
261      - implement A-grid / C-grid selection for wind-stress input files.
262      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
263      for now, in exf_bulk_largeyeager04.F only :
264      - change implementation for case where windspeed + 2. components wind-stress
265        are read-in. AND use rhoConstFresh to convert evap.
266    o pkg/seaice:
267      - use correct EXCH_UV for wind-forcing (on A-grid).
268      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
269        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
270    o pkg/exf:
271      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
272      EXF_INTERPOLATION:
273      - merge global_with_exf/code version of exf_interp_read.F
274        to the main code ;
275      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
276        reading the file ; Important: This options needs to be defined to recover
277        previous code.
278        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
279      - no longer loose real*8 precision along the way when using exf_iprec=64.
280    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
281      - change discretisation of evp-solver in order to avoid another exchange
282        (changes lab_sea) and clean up a little
283      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
284        help the adjoint (this also changes the results slightly)
285      - add a few "_d 0" where they had been missing in seaice_evp.F
286      - cleaning up: remove unused seaice_calc_rhs.F
287    o pkg/exf: some cleaning-up:
288      - change various "constants" into runtime parameters
289      - cleaned-up Large&Yeager04 routine which should eventually
290        replace exf_bulkformulae.F (changed names of S/R and CPP)
291        and merged various ALLOW_ATM_WIND options
292     only used with thsice pkg (in thsice_get_exf.F):
293      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
294        which are used when useStabilityFct_overIce=TRUE (= the default)
295      - change default values of ice & snow emissivity and scale downward LW
296        by ice & snow emissivity.
297    o pkg/thsice:
298     fix few little problems, in thsice_calc_thickn.F:
299      - growth vertically (and not laterally) if iceFrac == iceMaskMax
300      - melt only laterally if hIce < hThinIce (as the comments say)
301      and in thsice_extend.F:
302      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
303      - start to form ice as soon as the minimum ice-volume is reachable.
304     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
305      and cpl_aim+ocn
306    o pkg/kpp
307     - move computation of surface related input fields to KPP into a new
308       subroutine kpp_forcing_surf.F
309     - remove wrong (within bi,bj loops) EXCH calls.
310     - little cleaning (add argument myThid in last position, cvs header ...)
311     - for now, fix conservation problem by exchanging KPPviscAz (may not
312       be the best fix)
313    o pkg/seaice
314     - check for inconsistent evp parameter/cpp-flag combination
315     - remove leftover errIO flat for obsolete name list error handling
316    o OpenAD
317     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
318    
319    checkpoint59a
320    o pkg/seaice: some parameter clarifications and a little bit of clean up
321    o pkg/thsice: rename run-time parameters:
322       himin       -> hIceMin
323       himin0      -> hThinIce
324       hihig       -> hThickIce
325       i0          -> i0swFrac
326       transCoef   -> bMeltCoef
327       frac_energy -> fracMelting
328      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
329       with default values (for now) that do not change the results.
330      remove old version of thsice vars advection in pkg/seaice.
331    o in FFIELDS.h:
332      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
333      - make pLoad & sIceLoad always available (but still only used if
334         ATMOSPHERIC_LOADING is #define).
335    o pkg/kpp: replaced _KPP_RL with _RL
336    o bug fixes for vertical diffusivity computations when both KPP and
337        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
338        are no longer updating the vertical diffusivity array
339        (passed as argument) but are (re-) setting those arrays.
340    o pkg/seaice: fix bug in evp solver, while doing that
341      - change (improve?) discretization of stress computations for both
342        cgrid-lsr and evp solver
343      - add a new routine to compute strain rates
344      - the above changes lab_sea results
345      - add no slip conditions for evp solver (off by default), lsr-version
346        may follow
347      - fix exchange for shear at Z-points (does not change lab_sea)
348      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
349        (to force the user to pick a time step since there is not "safe" way
350        of choosing it)
351      - add principal stress diagnostics
352      - rearrange fields for evp a little to avoid having to call a: too many
353        exchanges and b: exchanges for stress trensor components which we do
354        not have.
355      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
356        of evp, complete rewrite for lsr case (latter is does not yet work
357        in all cases)
358  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
359      - add myThid to all kpp routines (long overdue)
360    
361  checkpoint59  checkpoint59
362  o pkg/exf:  o pkg/exf:

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