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revision 1.803 by mlosch, Mon Apr 30 22:48:52 2007 UTC revision 1.889 by jmc, Tue Oct 9 02:43:45 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 add missing cvs $Header$ or $Name$ in eesupp/*, pkg/* & verification/code*
8    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
9    o add new diagnostics to seaice: advective, diffusive fluxes (only for
10      multidim-advection, for scheme 2 they are not filled) and transports,
11      thermodynamic growth rates
12    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
13      leave input file unchanged. Affects results @ truncation level (cg2d match)
14      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
15      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
16      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
17      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
18    
19    checkpoint59h
20    o pkg/exf:
21      - improve vectorization by moving if-statement out of loops in
22        exf_mapfields, exf_radiation
23      - exf_bulkformulae.F: introduce 2D fields and vectorize code
24    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
25    o testreport:
26      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
27        monitor & update offline_exf_seaice exp. output.
28      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
29    o pkg/seaice:
30      - bug fix in the evp solver: boundary conditions were affected be
31        masking of zMax/zMin (changes results)
32      - minor bug fix in boundary conditions in seaice_calc_strainrates
33        (changes results for no_slip)
34      - seaice_lsr.F: make interpolation of eta dependent on boundaries
35      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
36      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
37        stress formulation and no-slip boundary conditions
38    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
39      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
40    o pkg/seaice: a first HSALT time stepping equation has been checked in
41    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
42      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
43      without requiring DO-IF statements
44    o pkg/thsice:
45      use continuous power-law function for partition of energy between lateral
46      melting/freezing and thinning/thickening ; old code using step function
47      still available with #undef THSICE_FRACEN_POWERLAW
48      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
49    o testreport: change AD testing : check against results/output_adm.txt
50      using same scripts as for forward test.
51    
52    checkpoint59g
53    o adjoint testing: in preparation for changing testreport:
54      - output format: cost and grad written on separated lines
55      - ad output results in directory "results" (instead of "results_ad")
56    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
57    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
58    o pkg/ecco: allow user defined cost function contributions
59    o testreport:
60      Allow to choose (per experiment) the list of tested output variables
61       and the main variable (used to issue a pass/FAIL ) ;
62      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
63      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
64      Also modify printing of summary:
65       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
66       b) echo the list of tested variables in the individual summary.txt of
67          each experiment.
68    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
69      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
70      (but still depend on the tile decompostion of the domain).
71    o pkg/seaice: change a discretization detail to make the B-grid code
72      "more symmetric". This change is likely to remove all "ridges/leads" that
73      where quasi-aligned with the grid in B-grid solutions. It may also be
74      the solution to the stress coupling issues with the B-grid.
75    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
76      remove .cvsignore from input dir. (since testreport no longer run here).
77    o pkg/thsice:
78     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
79     - fix reshaping of sea-ice just after advection:
80       melt all the ice only if ice-volume is too small.
81     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
82       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
83     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
84    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
85      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
86    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
87      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
88      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
89      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
90      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
91      -> update output.txt
92    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
93     this affects truncation error: -> update output.txt of exp:
94      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
95      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
96    
97    checkpoint59f
98    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
99    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
100      a bounded range (in forward mode)
101    o pkg/ecco, ctrl, autodiff and mom_common:
102     internal parameter controls, completements of implementations
103    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
104    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
105      (not seem any difference in testing results).
106    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
107       at face corners.
108    o pkg/generic_advdiff:
109     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
110      loop range indices for computing vertical advection tendency
111      and do the calculation in the interior only (no overlap) ;
112      for now, only implemented for SOM advection (to save CPU time).
113     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
114    o exch2 adjoint
115      First set of changes:
116      - add exch2 hand-written adjoint templates
117      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
118        This will require cleanup in pkg/autodiff/*.F
119        (changed routines currently kept separate in verif. code/)
120      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
121        that used to hide exch2 or cubed-sphere specific code
122        (commented via 'cph-exch2')
123    o pkg/seaice
124      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
125    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
126       output of global_ocean.cs32x15.thsice .
127    
128    checkpoint59e
129    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
130      for B-grid vector (not yet tested) and C-grid vector (<- only used
131      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
132    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
133      (#ifdef ALLOW_SALT_PLUME)
134    o gather_2d/scatter_2d: removed halo regions
135    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
136      scheme and the corresponding test case (under front_relax dir). For now,
137      only available with Skew-flux form and not yet tested in realistic set-up.
138      adjoint: store directives updated, but gradient checks deteriorated,
139      so maybe GM/Redi adjoint is now broken.
140    o seaice adjoint
141      * add AREA, HEFF, HSNOW as control variable
142        (should not change lab_sea results)
143      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
144    o pkg/seaice:
145      * added computation of saltFlux in seaice_growth;
146        For time being, sea ice salinity is assumed constant
147        contribution of snow flooding to freshening of sea ice is neglected.
148        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
149        defaults to 0.0 in order to maintain backward compatibility.
150        Typical values for SEAICE_salinity are 4 to 10 g/kg.
151      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
152      * added SEAICE_availHeatFrac, which specifies fraction of surface level
153        heat content used to melt or grow ice
154      * commented out cap of HICE: it helps keep ice thinner
155      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
156      * applied OBCS T/S mask to HEFFM sea ice mask
157    
158    checkpoint59d
159    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
160     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
161     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
162    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
163     and change default value of parameter "GM_Small_Number";
164     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
165       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
166       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
167    o pkg/ecco: cost function when applying pkg/smooth to controls
168    o pkg/ctrl: add forcingPrecond run time parameter
169    o pkg/seaice:
170     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
171     - fix bug in metric terms of u-equation in LSR solver (implicit part),
172       changes verification/lab_sea
173     - rearrange implicit part of u-equation in LSR solver to make it easier to
174       read, understand, and debug. This causes changes at the truncation level.
175     - fix (serious) bug in the boundary conditions (sign error in the implicit
176       part) of the LSR solver. Changes all LSR results.
177     - fixed problem with HSNOW initialization to avoid thick snow when AREA
178       is initilized with small values - does not change lab_sea results.
179     - added HsnowFile initialization capability
180    o pkg/smooth: addition to model/src and pkg/ctrl so allow
181     initialization of pkg/smooth and application to control vector
182    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
183    o dependencies: pkg/profiles requires pkg/cal
184    o pkg/profiles:
185     - added option ALLOW_PROFILES_GENERICGRID
186         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
187         that interpolation information (grid points and coefficients) is provided
188         within the netcdf input files.
189         -> sample matlab scripts can be found in MITgcm_contrib/gael
190         that allow you to prepare netcdf input files.
191     - also modified: cleaner include statements, cleaner error print statements,
192       cleaner stops when error, and more tests of the netcdf input files consistency.
193    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
194    o pkg/seaice:
195     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
196       requires a new routine: seaice_diagnostics_fill.F
197     - make sure that seaice does not move if not forced (pressure replacement
198       method, Hibler and Ip, 1995), changes results
199     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
200     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
201       It is turned off by default (=-1.), because it changes the results.
202     - make it possible to read AREA from a file, too.
203    
204    checkpoint59c
205    o add S/R and diagnostics for oceanic mixed-layer depth
206    o move GMRedi call after all vertical mixing schemes (including KPP)
207    o pkg/thsice:
208     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
209      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
210    o pkg/obcs:
211     - bug fix for balance code
212    o pkg/seaice:
213      - allow values of SEAICE_elasticParm > 1
214      - add new parameter SEAICE_evpTauRelax as an alternative
215        to SEAICE_elasticParm
216      - make lsr boundary conditions free slip (by default), changes result
217      - add code for no slip boundary conditions for lsr
218      - set minimum of zeta to zero (and not 4e8) (changes results)
219      - add a cap on AREA after advecting AREA if seaice_growth is not called
220    o change calculation of Visbeck K:
221      - no longer depend on tapering scheme; instead, compute slope (limited
222        by GM_maxSlope). this is equivalent to what was comuted before with
223        clipping or linear tappering.
224      - fix vertical averaging (wrong by 1/2 level)
225      - leave the old version (but will not be maintained) within
226        #ifdef OLD_VISBECK_CALC / #endif
227      - update output of exp. ideal_2D_oce
228    o change error catch in calc_r_star to improve vectorization
229    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
230      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
231    o adjoint:
232      Re-organized adjoint checkpointing according to Matt Mazloff
233      (but with modifs/completions/cleanups)
234      Storing is now bundled into large arrays to optimized I/O
235      (and second step in cleanup of the_main_loop)
236    
237    checkpoint59b
238    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
239      - export/import (between ocean & coupler) fields needed for ocean DIC.
240    o pkg/seaice:
241      - get rid of three more exchanges seaice_calc_viscosities (required
242        different loop boundaries in seaice_lsr and seaice_ocean_stress)
243      - bug fix in seaice_ocean_stress (update of lab_sea required)
244      - reduce loop boundaries to necessary minimum also in seaice_evp
245      - go back to the old way of computing deltaC/Z as the adjoint likes that
246        better
247    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
248      passive tracer to an Age Tracer) + update output.txt
249    o pkg/exf:
250      - implement A-grid / C-grid selection for wind-stress input files.
251      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
252      for now, in exf_bulk_largeyeager04.F only :
253      - change implementation for case where windspeed + 2. components wind-stress
254        are read-in. AND use rhoConstFresh to convert evap.
255    o pkg/seaice:
256      - use correct EXCH_UV for wind-forcing (on A-grid).
257      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
258        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
259    o pkg/exf:
260      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
261      EXF_INTERPOLATION:
262      - merge global_with_exf/code version of exf_interp_read.F
263        to the main code ;
264      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
265        reading the file ; Important: This options needs to be defined to recover
266        previous code.
267        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
268      - no longer loose real*8 precision along the way when using exf_iprec=64.
269    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
270      - change discretisation of evp-solver in order to avoid another exchange
271        (changes lab_sea) and clean up a little
272      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
273        help the adjoint (this also changes the results slightly)
274      - add a few "_d 0" where they had been missing in seaice_evp.F
275      - cleaning up: remove unused seaice_calc_rhs.F
276    o pkg/exf: some cleaning-up:
277      - change various "constants" into runtime parameters
278      - cleaned-up Large&Yeager04 routine which should eventually
279        replace exf_bulkformulae.F (changed names of S/R and CPP)
280        and merged various ALLOW_ATM_WIND options
281     only used with thsice pkg (in thsice_get_exf.F):
282      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
283        which are used when useStabilityFct_overIce=TRUE (= the default)
284      - change default values of ice & snow emissivity and scale downward LW
285        by ice & snow emissivity.
286    o pkg/thsice:
287     fix few little problems, in thsice_calc_thickn.F:
288      - growth vertically (and not laterally) if iceFrac == iceMaskMax
289      - melt only laterally if hIce < hThinIce (as the comments say)
290      and in thsice_extend.F:
291      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
292      - start to form ice as soon as the minimum ice-volume is reachable.
293     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
294      and cpl_aim+ocn
295    o pkg/kpp
296     - move computation of surface related input fields to KPP into a new
297       subroutine kpp_forcing_surf.F
298     - remove wrong (within bi,bj loops) EXCH calls.
299     - little cleaning (add argument myThid in last position, cvs header ...)
300     - for now, fix conservation problem by exchanging KPPviscAz (may not
301       be the best fix)
302    o pkg/seaice
303     - check for inconsistent evp parameter/cpp-flag combination
304     - remove leftover errIO flat for obsolete name list error handling
305    o OpenAD
306     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
307    
308    checkpoint59a
309  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
310  o pkg/thsice: rename run-time parameters:  o pkg/thsice: rename run-time parameters:
311     himin       -> hIceMin     himin       -> hIceMin
# Line 21  o in FFIELDS.h: Line 323  o in FFIELDS.h:
323       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
324  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
325  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
326      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
327        are no longer updating the vertical diffusivity array
328        (passed as argument) but are (re-) setting those arrays.
329  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
330    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
331      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 41  o pkg/seaice: fix bug in evp solver, whi Line 345  o pkg/seaice: fix bug in evp solver, whi
345      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
346      in all cases)      in all cases)
347  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
348      - add myThid to all kpp routines (long overdue)
349    
350  checkpoint59  checkpoint59
351  o pkg/exf:  o pkg/exf:

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