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revision 1.819 by jmc, Fri May 18 03:02:47 2007 UTC revision 1.906 by jmc, Thu Nov 8 23:01:44 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 in pkgs: dic, obcs, offline, rbcs:
8      standard way to compute coeff. for time interpolation between 2 time reccords
9      which retains full precision (& make results less dependent on compiler).
10      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
11    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
12      packages instead of reading ice cover and wind speed separately
13    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
14     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
15      to allow to compile customized code before the update)
16    o cleaning-up:
17      - fix CPP instruction syntax in pkg/obcs
18      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
19        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
20      - fix some threads issue in IO parts.
21    o pkg/dic:
22      - add tons of "_d 0" (--> much better testreports !)
23       and then update outputs of tutorial_global_oce_biogeo
24    o pkg/mom_fluxform:
25      add a special version of momentum advection intended to conserve momentum
26      next to a bathymetry step or a coastline edge. (default = off = #undef)
27    o new read/write pickup version:
28      - for now, only implemented for main (mdsio) pickup file.
29      - write out only what is needed to restart; merge pickup_nh , pickup_ph
30        and main pickup together.
31      - read meta file; read only what is needed to restart; stop if a field
32        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
33        if it make sense (even if the restart is not perfect).
34      - if no meta file, assume that pickup to read corresponds exactly to
35        a pickup that would currently be written.
36      - read pickup written in the old format (until checkpoint59i) if it
37        recognizes an old meta file (no field-list).
38      - add a meta file in exp. which starts from a pickup: 2 cases:
39        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
40         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
41        b) a meta file describing the content of the associated pickup file
42         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
43    o pkg/mdsio & pkg/rw:
44      - new routine to read a meta file ; new set of routine to read
45        Multiple-fields file (with meta file).
46    o added open boundary conditions capability for seaice
47        HSNOW, HSALT, UICE, and VICE
48    
49    checkpoint59i
50    o adjoint:
51      * fix multiDimAdvection adjoint
52        (partial recomputation problem by TAF for fVerT(:,:,kDown)
53        and comlev1 size definition (maxpass vs. max. number of tracers)
54      * verification/global_ocean.90x45x15 adjoint now tests
55        NLFS and multiDimAdvection using DST3 (=30)
56      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
57    o pkg/kpp: add "_d 0" to real constant (if missing);
58      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
59      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
60    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
61      for internal parameters related to restart process (formerly from PARAMS.h)
62      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
63    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
64      as argument. (only atm2d & obcs write_pickup have not yet been updated)
65    o pkg/monitor:
66      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
67      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
68      - account for deep Atmosphere factor and density factor (anelastic)
69    o added open boundary conditions capability for seaice HEFF and AREA
70    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
71      thermodynamics
72      - requires a little reorganization, which affects the testreport results
73        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
74        so that now the conservative form is tested
75      - add a few comments
76    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
77    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
78    o add new diagnostics to seaice: advective, diffusive fluxes (only for
79      multidim-advection, for scheme 2 they are not filled) and transports,
80      thermodynamic growth rates
81    o change units of EmPmR (inside the code, + within coupling interface)
82      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
83      Affects results @ truncation level (cg2d match) and update output of
84       experiments: lab_sea(6), global_ocean.90x40x15(10),
85      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
86      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
87      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
88      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
89    
90    checkpoint59h
91    o pkg/exf:
92      - improve vectorization by moving if-statement out of loops in
93        exf_mapfields, exf_radiation
94      - exf_bulkformulae.F: introduce 2D fields and vectorize code
95    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
96    o testreport:
97      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
98        monitor & update offline_exf_seaice exp. output.
99      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
100    o pkg/seaice:
101      - bug fix in the evp solver: boundary conditions were affected be
102        masking of zMax/zMin (changes results)
103      - minor bug fix in boundary conditions in seaice_calc_strainrates
104        (changes results for no_slip)
105      - seaice_lsr.F: make interpolation of eta dependent on boundaries
106      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
107      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
108        stress formulation and no-slip boundary conditions
109    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
110      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
111    o pkg/seaice: a first HSALT time stepping equation has been checked in
112    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
113      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
114      without requiring DO-IF statements
115    o pkg/thsice:
116      use continuous power-law function for partition of energy between lateral
117      melting/freezing and thinning/thickening ; old code using step function
118      still available with #undef THSICE_FRACEN_POWERLAW
119      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
120    o testreport: change AD testing : check against results/output_adm.txt
121      using same scripts as for forward test.
122    
123    checkpoint59g
124    o adjoint testing: in preparation for changing testreport:
125      - output format: cost and grad written on separated lines
126      - ad output results in directory "results" (instead of "results_ad")
127    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
128    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
129    o pkg/ecco: allow user defined cost function contributions
130    o testreport:
131      Allow to choose (per experiment) the list of tested output variables
132       and the main variable (used to issue a pass/FAIL ) ;
133      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
134      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
135      Also modify printing of summary:
136       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
137       b) echo the list of tested variables in the individual summary.txt of
138          each experiment.
139    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
140      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
141      (but still depend on the tile decompostion of the domain).
142    o pkg/seaice: change a discretization detail to make the B-grid code
143      "more symmetric". This change is likely to remove all "ridges/leads" that
144      where quasi-aligned with the grid in B-grid solutions. It may also be
145      the solution to the stress coupling issues with the B-grid.
146    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
147      remove .cvsignore from input dir. (since testreport no longer run here).
148    o pkg/thsice:
149     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
150     - fix reshaping of sea-ice just after advection:
151       melt all the ice only if ice-volume is too small.
152     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
153       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
154     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
155    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
156      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
157    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
158      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
159      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
160      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
161      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
162      -> update output.txt
163    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
164     this affects truncation error: -> update output.txt of exp:
165      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
166      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
167    
168    checkpoint59f
169    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
170    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
171      a bounded range (in forward mode)
172    o pkg/ecco, ctrl, autodiff and mom_common:
173     internal parameter controls, completements of implementations
174    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
175    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
176      (not seem any difference in testing results).
177    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
178       at face corners.
179    o pkg/generic_advdiff:
180     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
181      loop range indices for computing vertical advection tendency
182      and do the calculation in the interior only (no overlap) ;
183      for now, only implemented for SOM advection (to save CPU time).
184     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
185    o exch2 adjoint
186      First set of changes:
187      - add exch2 hand-written adjoint templates
188      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
189        This will require cleanup in pkg/autodiff/*.F
190        (changed routines currently kept separate in verif. code/)
191      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
192        that used to hide exch2 or cubed-sphere specific code
193        (commented via 'cph-exch2')
194    o pkg/seaice
195      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
196    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
197       output of global_ocean.cs32x15.thsice .
198    
199    checkpoint59e
200    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
201      for B-grid vector (not yet tested) and C-grid vector (<- only used
202      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
203    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
204      (#ifdef ALLOW_SALT_PLUME)
205    o gather_2d/scatter_2d: removed halo regions
206    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
207      scheme and the corresponding test case (under front_relax dir). For now,
208      only available with Skew-flux form and not yet tested in realistic set-up.
209      adjoint: store directives updated, but gradient checks deteriorated,
210      so maybe GM/Redi adjoint is now broken.
211    o seaice adjoint
212      * add AREA, HEFF, HSNOW as control variable
213        (should not change lab_sea results)
214      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
215    o pkg/seaice:
216      * added computation of saltFlux in seaice_growth;
217        For time being, sea ice salinity is assumed constant
218        contribution of snow flooding to freshening of sea ice is neglected.
219        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
220        defaults to 0.0 in order to maintain backward compatibility.
221        Typical values for SEAICE_salinity are 4 to 10 g/kg.
222      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
223      * added SEAICE_availHeatFrac, which specifies fraction of surface level
224        heat content used to melt or grow ice
225      * commented out cap of HICE: it helps keep ice thinner
226      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
227      * applied OBCS T/S mask to HEFFM sea ice mask
228    
229    checkpoint59d
230    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
231     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
232     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
233    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
234     and change default value of parameter "GM_Small_Number";
235     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
236       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
237       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
238    o pkg/ecco: cost function when applying pkg/smooth to controls
239    o pkg/ctrl: add forcingPrecond run time parameter
240    o pkg/seaice:
241     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
242     - fix bug in metric terms of u-equation in LSR solver (implicit part),
243       changes verification/lab_sea
244     - rearrange implicit part of u-equation in LSR solver to make it easier to
245       read, understand, and debug. This causes changes at the truncation level.
246     - fix (serious) bug in the boundary conditions (sign error in the implicit
247       part) of the LSR solver. Changes all LSR results.
248     - fixed problem with HSNOW initialization to avoid thick snow when AREA
249       is initilized with small values - does not change lab_sea results.
250     - added HsnowFile initialization capability
251    o pkg/smooth: addition to model/src and pkg/ctrl so allow
252     initialization of pkg/smooth and application to control vector
253    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
254    o dependencies: pkg/profiles requires pkg/cal
255    o pkg/profiles:
256     - added option ALLOW_PROFILES_GENERICGRID
257         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
258         that interpolation information (grid points and coefficients) is provided
259         within the netcdf input files.
260         -> sample matlab scripts can be found in MITgcm_contrib/gael
261         that allow you to prepare netcdf input files.
262     - also modified: cleaner include statements, cleaner error print statements,
263       cleaner stops when error, and more tests of the netcdf input files consistency.
264    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
265    o pkg/seaice:
266     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
267       requires a new routine: seaice_diagnostics_fill.F
268     - make sure that seaice does not move if not forced (pressure replacement
269       method, Hibler and Ip, 1995), changes results
270     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
271     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
272       It is turned off by default (=-1.), because it changes the results.
273     - make it possible to read AREA from a file, too.
274    
275    checkpoint59c
276    o add S/R and diagnostics for oceanic mixed-layer depth
277    o move GMRedi call after all vertical mixing schemes (including KPP)
278    o pkg/thsice:
279     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
280      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
281    o pkg/obcs:
282     - bug fix for balance code
283    o pkg/seaice:
284      - allow values of SEAICE_elasticParm > 1
285      - add new parameter SEAICE_evpTauRelax as an alternative
286        to SEAICE_elasticParm
287      - make lsr boundary conditions free slip (by default), changes result
288      - add code for no slip boundary conditions for lsr
289      - set minimum of zeta to zero (and not 4e8) (changes results)
290      - add a cap on AREA after advecting AREA if seaice_growth is not called
291    o change calculation of Visbeck K:
292      - no longer depend on tapering scheme; instead, compute slope (limited
293        by GM_maxSlope). this is equivalent to what was comuted before with
294        clipping or linear tappering.
295      - fix vertical averaging (wrong by 1/2 level)
296      - leave the old version (but will not be maintained) within
297        #ifdef OLD_VISBECK_CALC / #endif
298      - update output of exp. ideal_2D_oce
299    o change error catch in calc_r_star to improve vectorization
300  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
301    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
302    o adjoint:
303      Re-organized adjoint checkpointing according to Matt Mazloff
304      (but with modifs/completions/cleanups)
305      Storing is now bundled into large arrays to optimized I/O
306      (and second step in cleanup of the_main_loop)
307    
308  checkpoint59b  checkpoint59b
309  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
# Line 59  o pkg/exf: some cleaning-up: Line 357  o pkg/exf: some cleaning-up:
357  o pkg/thsice:  o pkg/thsice:
358   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
359    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
360    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
361    and in thsice_extend.F:    and in thsice_extend.F:
362    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
363    - start to form ice as soon as the minimum ice-volume is reachable.    - start to form ice as soon as the minimum ice-volume is reachable.
# Line 96  o in FFIELDS.h: Line 394  o in FFIELDS.h:
394       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
395  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
396  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
397      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
398        are no longer updating the vertical diffusivity array
399        (passed as argument) but are (re-) setting those arrays.
400  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
401    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
402      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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