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revision 1.800 by mlosch, Tue Apr 24 11:24:37 2007 UTC revision 1.891 by dimitri, Thu Oct 11 10:30:34 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 added open boundary conditions capability for seaice HEFF and AREA
8    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
9      thermodynamics
10      - requires a little reorganization, which affects the testreport results
11        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
12        so that now the conservative form is tested
13      - add a few comments
14    o add missing cvs $Header$ or $Name$ in eesupp/*, pkg/* & verification/code*
15    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
16    o add new diagnostics to seaice: advective, diffusive fluxes (only for
17      multidim-advection, for scheme 2 they are not filled) and transports,
18      thermodynamic growth rates
19    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
20      leave input file unchanged. Affects results @ truncation level (cg2d match)
21      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
22      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
23      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
24      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
25    
26    checkpoint59h
27    o pkg/exf:
28      - improve vectorization by moving if-statement out of loops in
29        exf_mapfields, exf_radiation
30      - exf_bulkformulae.F: introduce 2D fields and vectorize code
31    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
32    o testreport:
33      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
34        monitor & update offline_exf_seaice exp. output.
35      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
36    o pkg/seaice:
37      - bug fix in the evp solver: boundary conditions were affected be
38        masking of zMax/zMin (changes results)
39      - minor bug fix in boundary conditions in seaice_calc_strainrates
40        (changes results for no_slip)
41      - seaice_lsr.F: make interpolation of eta dependent on boundaries
42      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
43      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
44        stress formulation and no-slip boundary conditions
45    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
46      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
47    o pkg/seaice: a first HSALT time stepping equation has been checked in
48    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
49      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
50      without requiring DO-IF statements
51    o pkg/thsice:
52      use continuous power-law function for partition of energy between lateral
53      melting/freezing and thinning/thickening ; old code using step function
54      still available with #undef THSICE_FRACEN_POWERLAW
55      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
56    o testreport: change AD testing : check against results/output_adm.txt
57      using same scripts as for forward test.
58    
59    checkpoint59g
60    o adjoint testing: in preparation for changing testreport:
61      - output format: cost and grad written on separated lines
62      - ad output results in directory "results" (instead of "results_ad")
63    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
64    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
65    o pkg/ecco: allow user defined cost function contributions
66    o testreport:
67      Allow to choose (per experiment) the list of tested output variables
68       and the main variable (used to issue a pass/FAIL ) ;
69      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
70      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
71      Also modify printing of summary:
72       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
73       b) echo the list of tested variables in the individual summary.txt of
74          each experiment.
75    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
76      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
77      (but still depend on the tile decompostion of the domain).
78    o pkg/seaice: change a discretization detail to make the B-grid code
79      "more symmetric". This change is likely to remove all "ridges/leads" that
80      where quasi-aligned with the grid in B-grid solutions. It may also be
81      the solution to the stress coupling issues with the B-grid.
82    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
83      remove .cvsignore from input dir. (since testreport no longer run here).
84    o pkg/thsice:
85     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
86     - fix reshaping of sea-ice just after advection:
87       melt all the ice only if ice-volume is too small.
88     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
89       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
90     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
91    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
92      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
93    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
94      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
95      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
96      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
97      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
98      -> update output.txt
99    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
100     this affects truncation error: -> update output.txt of exp:
101      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
102      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
103    
104    checkpoint59f
105    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
106    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
107      a bounded range (in forward mode)
108    o pkg/ecco, ctrl, autodiff and mom_common:
109     internal parameter controls, completements of implementations
110    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
111    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
112      (not seem any difference in testing results).
113    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
114       at face corners.
115    o pkg/generic_advdiff:
116     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
117      loop range indices for computing vertical advection tendency
118      and do the calculation in the interior only (no overlap) ;
119      for now, only implemented for SOM advection (to save CPU time).
120     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
121    o exch2 adjoint
122      First set of changes:
123      - add exch2 hand-written adjoint templates
124      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
125        This will require cleanup in pkg/autodiff/*.F
126        (changed routines currently kept separate in verif. code/)
127      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
128        that used to hide exch2 or cubed-sphere specific code
129        (commented via 'cph-exch2')
130    o pkg/seaice
131      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
132    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
133       output of global_ocean.cs32x15.thsice .
134    
135    checkpoint59e
136    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
137      for B-grid vector (not yet tested) and C-grid vector (<- only used
138      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
139    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
140      (#ifdef ALLOW_SALT_PLUME)
141    o gather_2d/scatter_2d: removed halo regions
142    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
143      scheme and the corresponding test case (under front_relax dir). For now,
144      only available with Skew-flux form and not yet tested in realistic set-up.
145      adjoint: store directives updated, but gradient checks deteriorated,
146      so maybe GM/Redi adjoint is now broken.
147    o seaice adjoint
148      * add AREA, HEFF, HSNOW as control variable
149        (should not change lab_sea results)
150      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
151    o pkg/seaice:
152      * added computation of saltFlux in seaice_growth;
153        For time being, sea ice salinity is assumed constant
154        contribution of snow flooding to freshening of sea ice is neglected.
155        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
156        defaults to 0.0 in order to maintain backward compatibility.
157        Typical values for SEAICE_salinity are 4 to 10 g/kg.
158      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
159      * added SEAICE_availHeatFrac, which specifies fraction of surface level
160        heat content used to melt or grow ice
161      * commented out cap of HICE: it helps keep ice thinner
162      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
163      * applied OBCS T/S mask to HEFFM sea ice mask
164    
165    checkpoint59d
166    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
167     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
168     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
169    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
170     and change default value of parameter "GM_Small_Number";
171     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
172       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
173       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
174    o pkg/ecco: cost function when applying pkg/smooth to controls
175    o pkg/ctrl: add forcingPrecond run time parameter
176    o pkg/seaice:
177     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
178     - fix bug in metric terms of u-equation in LSR solver (implicit part),
179       changes verification/lab_sea
180     - rearrange implicit part of u-equation in LSR solver to make it easier to
181       read, understand, and debug. This causes changes at the truncation level.
182     - fix (serious) bug in the boundary conditions (sign error in the implicit
183       part) of the LSR solver. Changes all LSR results.
184     - fixed problem with HSNOW initialization to avoid thick snow when AREA
185       is initilized with small values - does not change lab_sea results.
186     - added HsnowFile initialization capability
187    o pkg/smooth: addition to model/src and pkg/ctrl so allow
188     initialization of pkg/smooth and application to control vector
189    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
190    o dependencies: pkg/profiles requires pkg/cal
191    o pkg/profiles:
192     - added option ALLOW_PROFILES_GENERICGRID
193         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
194         that interpolation information (grid points and coefficients) is provided
195         within the netcdf input files.
196         -> sample matlab scripts can be found in MITgcm_contrib/gael
197         that allow you to prepare netcdf input files.
198     - also modified: cleaner include statements, cleaner error print statements,
199       cleaner stops when error, and more tests of the netcdf input files consistency.
200    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
201    o pkg/seaice:
202     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
203       requires a new routine: seaice_diagnostics_fill.F
204     - make sure that seaice does not move if not forced (pressure replacement
205       method, Hibler and Ip, 1995), changes results
206     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
207     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
208       It is turned off by default (=-1.), because it changes the results.
209     - make it possible to read AREA from a file, too.
210    
211    checkpoint59c
212    o add S/R and diagnostics for oceanic mixed-layer depth
213    o move GMRedi call after all vertical mixing schemes (including KPP)
214    o pkg/thsice:
215     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
216      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
217    o pkg/obcs:
218     - bug fix for balance code
219    o pkg/seaice:
220      - allow values of SEAICE_elasticParm > 1
221      - add new parameter SEAICE_evpTauRelax as an alternative
222        to SEAICE_elasticParm
223      - make lsr boundary conditions free slip (by default), changes result
224      - add code for no slip boundary conditions for lsr
225      - set minimum of zeta to zero (and not 4e8) (changes results)
226      - add a cap on AREA after advecting AREA if seaice_growth is not called
227    o change calculation of Visbeck K:
228      - no longer depend on tapering scheme; instead, compute slope (limited
229        by GM_maxSlope). this is equivalent to what was comuted before with
230        clipping or linear tappering.
231      - fix vertical averaging (wrong by 1/2 level)
232      - leave the old version (but will not be maintained) within
233        #ifdef OLD_VISBECK_CALC / #endif
234      - update output of exp. ideal_2D_oce
235    o change error catch in calc_r_star to improve vectorization
236    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
237      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
238    o adjoint:
239      Re-organized adjoint checkpointing according to Matt Mazloff
240      (but with modifs/completions/cleanups)
241      Storing is now bundled into large arrays to optimized I/O
242      (and second step in cleanup of the_main_loop)
243    
244    checkpoint59b
245    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
246      - export/import (between ocean & coupler) fields needed for ocean DIC.
247    o pkg/seaice:
248      - get rid of three more exchanges seaice_calc_viscosities (required
249        different loop boundaries in seaice_lsr and seaice_ocean_stress)
250      - bug fix in seaice_ocean_stress (update of lab_sea required)
251      - reduce loop boundaries to necessary minimum also in seaice_evp
252      - go back to the old way of computing deltaC/Z as the adjoint likes that
253        better
254    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
255      passive tracer to an Age Tracer) + update output.txt
256    o pkg/exf:
257      - implement A-grid / C-grid selection for wind-stress input files.
258      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
259      for now, in exf_bulk_largeyeager04.F only :
260      - change implementation for case where windspeed + 2. components wind-stress
261        are read-in. AND use rhoConstFresh to convert evap.
262    o pkg/seaice:
263      - use correct EXCH_UV for wind-forcing (on A-grid).
264      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
265        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
266    o pkg/exf:
267      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
268      EXF_INTERPOLATION:
269      - merge global_with_exf/code version of exf_interp_read.F
270        to the main code ;
271      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
272        reading the file ; Important: This options needs to be defined to recover
273        previous code.
274        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
275      - no longer loose real*8 precision along the way when using exf_iprec=64.
276    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
277      - change discretisation of evp-solver in order to avoid another exchange
278        (changes lab_sea) and clean up a little
279      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
280        help the adjoint (this also changes the results slightly)
281      - add a few "_d 0" where they had been missing in seaice_evp.F
282      - cleaning up: remove unused seaice_calc_rhs.F
283    o pkg/exf: some cleaning-up:
284      - change various "constants" into runtime parameters
285      - cleaned-up Large&Yeager04 routine which should eventually
286        replace exf_bulkformulae.F (changed names of S/R and CPP)
287        and merged various ALLOW_ATM_WIND options
288     only used with thsice pkg (in thsice_get_exf.F):
289      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
290        which are used when useStabilityFct_overIce=TRUE (= the default)
291      - change default values of ice & snow emissivity and scale downward LW
292        by ice & snow emissivity.
293    o pkg/thsice:
294     fix few little problems, in thsice_calc_thickn.F:
295      - growth vertically (and not laterally) if iceFrac == iceMaskMax
296      - melt only laterally if hIce < hThinIce (as the comments say)
297      and in thsice_extend.F:
298      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
299      - start to form ice as soon as the minimum ice-volume is reachable.
300     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
301      and cpl_aim+ocn
302    o pkg/kpp
303     - move computation of surface related input fields to KPP into a new
304       subroutine kpp_forcing_surf.F
305     - remove wrong (within bi,bj loops) EXCH calls.
306     - little cleaning (add argument myThid in last position, cvs header ...)
307     - for now, fix conservation problem by exchanging KPPviscAz (may not
308       be the best fix)
309    o pkg/seaice
310     - check for inconsistent evp parameter/cpp-flag combination
311     - remove leftover errIO flat for obsolete name list error handling
312    o OpenAD
313     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
314    
315    checkpoint59a
316    o pkg/seaice: some parameter clarifications and a little bit of clean up
317    o pkg/thsice: rename run-time parameters:
318       himin       -> hIceMin
319       himin0      -> hThinIce
320       hihig       -> hThickIce
321       i0          -> i0swFrac
322       transCoef   -> bMeltCoef
323       frac_energy -> fracMelting
324      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
325       with default values (for now) that do not change the results.
326      remove old version of thsice vars advection in pkg/seaice.
327    o in FFIELDS.h:
328      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
329      - make pLoad & sIceLoad always available (but still only used if
330         ATMOSPHERIC_LOADING is #define).
331  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
332  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
333      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
334        are no longer updating the vertical diffusivity array
335        (passed as argument) but are (re-) setting those arrays.
336  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
337    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
338      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 26  o pkg/seaice: fix bug in evp solver, whi Line 352  o pkg/seaice: fix bug in evp solver, whi
352      of evp, complete rewrite for lsr case (latter is does not yet work      of evp, complete rewrite for lsr case (latter is does not yet work
353      in all cases)      in all cases)
354  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
355      - add myThid to all kpp routines (long overdue)
356    
357  checkpoint59  checkpoint59
358  o pkg/exf:  o pkg/exf:

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