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revision 1.813 by mlosch, Thu May 10 20:02:36 2007 UTC revision 1.904 by jmc, Mon Nov 5 19:38:59 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 split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
8     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
9      to allow to compile customized code before the update)
10    o cleaning-up:
11      - fix CPP instruction syntax in pkg/obcs
12      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
13        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
14      - fix some threads issue in IO parts.
15    o pkg/dic:
16      - add tons of "_d 0" (--> much better testreports !)
17       and then update outputs of tutorial_global_oce_biogeo
18    o pkg/mom_fluxform:
19      add a special version of momentum advection intended to conserve momentum
20      next to a bathymetry step or a coastline edge. (default = off = #undef)
21    o new read/write pickup version:
22      - for now, only implemented for main (mdsio) pickup file.
23      - write out only what is needed to restart; merge pickup_nh , pickup_ph
24        and main pickup together.
25      - read meta file; read only what is needed to restart; stop if a field
26        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
27        if it make sense (even if the restart is not perfect).
28      - if no meta file, assume that pickup to read corresponds exactly to
29        a pickup that would currently be written.
30      - read pickup written in the old format (until checkpoint59i) if it
31        recognizes an old meta file (no field-list).
32      - add a meta file in exp. which starts from a pickup: 2 cases:
33        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
34         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
35        b) a meta file describing the content of the associated pickup file
36         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
37    o pkg/mdsio & pkg/rw:
38      - new routine to read a meta file ; new set of routine to read
39        Multiple-fields file (with meta file).
40    o added open boundary conditions capability for seaice
41        HSNOW, HSALT, UICE, and VICE
42    
43    checkpoint59i
44    o adjoint:
45      * fix multiDimAdvection adjoint
46        (partial recomputation problem by TAF for fVerT(:,:,kDown)
47        and comlev1 size definition (maxpass vs. max. number of tracers)
48      * verification/global_ocean.90x45x15 adjoint now tests
49        NLFS and multiDimAdvection using DST3 (=30)
50      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
51    o pkg/kpp: add "_d 0" to real constant (if missing);
52      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
53      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
54    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
55      for internal parameters related to restart process (formerly from PARAMS.h)
56      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
57    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
58      as argument. (only atm2d & obcs write_pickup have not yet been updated)
59    o pkg/monitor:
60      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
61      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
62      - account for deep Atmosphere factor and density factor (anelastic)
63    o added open boundary conditions capability for seaice HEFF and AREA
64    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
65      thermodynamics
66      - requires a little reorganization, which affects the testreport results
67        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
68        so that now the conservative form is tested
69      - add a few comments
70    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
71    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
72    o add new diagnostics to seaice: advective, diffusive fluxes (only for
73      multidim-advection, for scheme 2 they are not filled) and transports,
74      thermodynamic growth rates
75    o change units of EmPmR (inside the code, + within coupling interface)
76      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
77      Affects results @ truncation level (cg2d match) and update output of
78       experiments: lab_sea(6), global_ocean.90x40x15(10),
79      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
80      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
81      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
82      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
83    
84    checkpoint59h
85    o pkg/exf:
86      - improve vectorization by moving if-statement out of loops in
87        exf_mapfields, exf_radiation
88      - exf_bulkformulae.F: introduce 2D fields and vectorize code
89    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
90    o testreport:
91      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
92        monitor & update offline_exf_seaice exp. output.
93      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
94    o pkg/seaice:
95      - bug fix in the evp solver: boundary conditions were affected be
96        masking of zMax/zMin (changes results)
97      - minor bug fix in boundary conditions in seaice_calc_strainrates
98        (changes results for no_slip)
99      - seaice_lsr.F: make interpolation of eta dependent on boundaries
100      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
101      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
102        stress formulation and no-slip boundary conditions
103    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
104      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
105    o pkg/seaice: a first HSALT time stepping equation has been checked in
106    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
107      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
108      without requiring DO-IF statements
109    o pkg/thsice:
110      use continuous power-law function for partition of energy between lateral
111      melting/freezing and thinning/thickening ; old code using step function
112      still available with #undef THSICE_FRACEN_POWERLAW
113      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
114    o testreport: change AD testing : check against results/output_adm.txt
115      using same scripts as for forward test.
116    
117    checkpoint59g
118    o adjoint testing: in preparation for changing testreport:
119      - output format: cost and grad written on separated lines
120      - ad output results in directory "results" (instead of "results_ad")
121    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
122    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
123    o pkg/ecco: allow user defined cost function contributions
124    o testreport:
125      Allow to choose (per experiment) the list of tested output variables
126       and the main variable (used to issue a pass/FAIL ) ;
127      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
128      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
129      Also modify printing of summary:
130       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
131       b) echo the list of tested variables in the individual summary.txt of
132          each experiment.
133    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
134      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
135      (but still depend on the tile decompostion of the domain).
136    o pkg/seaice: change a discretization detail to make the B-grid code
137      "more symmetric". This change is likely to remove all "ridges/leads" that
138      where quasi-aligned with the grid in B-grid solutions. It may also be
139      the solution to the stress coupling issues with the B-grid.
140    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
141      remove .cvsignore from input dir. (since testreport no longer run here).
142    o pkg/thsice:
143     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
144     - fix reshaping of sea-ice just after advection:
145       melt all the ice only if ice-volume is too small.
146     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
147       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
148     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
149    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
150      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
151    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
152      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
153      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
154      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
155      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
156      -> update output.txt
157    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
158     this affects truncation error: -> update output.txt of exp:
159      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
160      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
161    
162    checkpoint59f
163    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
164    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
165      a bounded range (in forward mode)
166    o pkg/ecco, ctrl, autodiff and mom_common:
167     internal parameter controls, completements of implementations
168    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
169    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
170      (not seem any difference in testing results).
171    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
172       at face corners.
173    o pkg/generic_advdiff:
174     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
175      loop range indices for computing vertical advection tendency
176      and do the calculation in the interior only (no overlap) ;
177      for now, only implemented for SOM advection (to save CPU time).
178     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
179    o exch2 adjoint
180      First set of changes:
181      - add exch2 hand-written adjoint templates
182      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
183        This will require cleanup in pkg/autodiff/*.F
184        (changed routines currently kept separate in verif. code/)
185      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
186        that used to hide exch2 or cubed-sphere specific code
187        (commented via 'cph-exch2')
188    o pkg/seaice
189      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
190    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
191       output of global_ocean.cs32x15.thsice .
192    
193    checkpoint59e
194    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
195      for B-grid vector (not yet tested) and C-grid vector (<- only used
196      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
197    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
198      (#ifdef ALLOW_SALT_PLUME)
199    o gather_2d/scatter_2d: removed halo regions
200    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
201      scheme and the corresponding test case (under front_relax dir). For now,
202      only available with Skew-flux form and not yet tested in realistic set-up.
203      adjoint: store directives updated, but gradient checks deteriorated,
204      so maybe GM/Redi adjoint is now broken.
205    o seaice adjoint
206      * add AREA, HEFF, HSNOW as control variable
207        (should not change lab_sea results)
208      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
209    o pkg/seaice:
210      * added computation of saltFlux in seaice_growth;
211        For time being, sea ice salinity is assumed constant
212        contribution of snow flooding to freshening of sea ice is neglected.
213        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
214        defaults to 0.0 in order to maintain backward compatibility.
215        Typical values for SEAICE_salinity are 4 to 10 g/kg.
216      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
217      * added SEAICE_availHeatFrac, which specifies fraction of surface level
218        heat content used to melt or grow ice
219      * commented out cap of HICE: it helps keep ice thinner
220      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
221      * applied OBCS T/S mask to HEFFM sea ice mask
222    
223    checkpoint59d
224    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
225     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
226     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
227    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
228     and change default value of parameter "GM_Small_Number";
229     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
230       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
231       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
232    o pkg/ecco: cost function when applying pkg/smooth to controls
233    o pkg/ctrl: add forcingPrecond run time parameter
234    o pkg/seaice:
235     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
236     - fix bug in metric terms of u-equation in LSR solver (implicit part),
237       changes verification/lab_sea
238     - rearrange implicit part of u-equation in LSR solver to make it easier to
239       read, understand, and debug. This causes changes at the truncation level.
240     - fix (serious) bug in the boundary conditions (sign error in the implicit
241       part) of the LSR solver. Changes all LSR results.
242     - fixed problem with HSNOW initialization to avoid thick snow when AREA
243       is initilized with small values - does not change lab_sea results.
244     - added HsnowFile initialization capability
245    o pkg/smooth: addition to model/src and pkg/ctrl so allow
246     initialization of pkg/smooth and application to control vector
247    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
248    o dependencies: pkg/profiles requires pkg/cal
249    o pkg/profiles:
250     - added option ALLOW_PROFILES_GENERICGRID
251         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
252         that interpolation information (grid points and coefficients) is provided
253         within the netcdf input files.
254         -> sample matlab scripts can be found in MITgcm_contrib/gael
255         that allow you to prepare netcdf input files.
256     - also modified: cleaner include statements, cleaner error print statements,
257       cleaner stops when error, and more tests of the netcdf input files consistency.
258    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
259    o pkg/seaice:
260     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
261       requires a new routine: seaice_diagnostics_fill.F
262     - make sure that seaice does not move if not forced (pressure replacement
263       method, Hibler and Ip, 1995), changes results
264     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
265     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
266       It is turned off by default (=-1.), because it changes the results.
267     - make it possible to read AREA from a file, too.
268    
269    checkpoint59c
270    o add S/R and diagnostics for oceanic mixed-layer depth
271    o move GMRedi call after all vertical mixing schemes (including KPP)
272    o pkg/thsice:
273     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
274      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
275    o pkg/obcs:
276     - bug fix for balance code
277    o pkg/seaice:
278      - allow values of SEAICE_elasticParm > 1
279      - add new parameter SEAICE_evpTauRelax as an alternative
280        to SEAICE_elasticParm
281      - make lsr boundary conditions free slip (by default), changes result
282      - add code for no slip boundary conditions for lsr
283      - set minimum of zeta to zero (and not 4e8) (changes results)
284      - add a cap on AREA after advecting AREA if seaice_growth is not called
285    o change calculation of Visbeck K:
286      - no longer depend on tapering scheme; instead, compute slope (limited
287        by GM_maxSlope). this is equivalent to what was comuted before with
288        clipping or linear tappering.
289      - fix vertical averaging (wrong by 1/2 level)
290      - leave the old version (but will not be maintained) within
291        #ifdef OLD_VISBECK_CALC / #endif
292      - update output of exp. ideal_2D_oce
293    o change error catch in calc_r_star to improve vectorization
294    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
295      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
296    o adjoint:
297      Re-organized adjoint checkpointing according to Matt Mazloff
298      (but with modifs/completions/cleanups)
299      Storing is now bundled into large arrays to optimized I/O
300      (and second step in cleanup of the_main_loop)
301    
302    checkpoint59b
303    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
304      - export/import (between ocean & coupler) fields needed for ocean DIC.
305    o pkg/seaice:
306      - get rid of three more exchanges seaice_calc_viscosities (required
307        different loop boundaries in seaice_lsr and seaice_ocean_stress)
308      - bug fix in seaice_ocean_stress (update of lab_sea required)
309      - reduce loop boundaries to necessary minimum also in seaice_evp
310      - go back to the old way of computing deltaC/Z as the adjoint likes that
311        better
312    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
313      passive tracer to an Age Tracer) + update output.txt
314    o pkg/exf:
315      - implement A-grid / C-grid selection for wind-stress input files.
316      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
317      for now, in exf_bulk_largeyeager04.F only :
318      - change implementation for case where windspeed + 2. components wind-stress
319        are read-in. AND use rhoConstFresh to convert evap.
320    o pkg/seaice:
321      - use correct EXCH_UV for wind-forcing (on A-grid).
322      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
323        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
324    o pkg/exf:
325      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
326      EXF_INTERPOLATION:
327      - merge global_with_exf/code version of exf_interp_read.F
328        to the main code ;
329      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
330        reading the file ; Important: This options needs to be defined to recover
331        previous code.
332        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
333      - no longer loose real*8 precision along the way when using exf_iprec=64.
334  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
335    - change discretisation of evp-solver in order to avoid another exchange    - change discretisation of evp-solver in order to avoid another exchange
336      (changes lab_sea) and clean up a little      (changes lab_sea) and clean up a little
# Line 24  o pkg/exf: some cleaning-up: Line 351  o pkg/exf: some cleaning-up:
351  o pkg/thsice:  o pkg/thsice:
352   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
353    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
354    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
355    and in thsice_extend.F:    and in thsice_extend.F:
356    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
357    - 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 61  o in FFIELDS.h: Line 388  o in FFIELDS.h:
388       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
389  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
390  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
391      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
392        are no longer updating the vertical diffusivity array
393        (passed as argument) but are (re-) setting those arrays.
394  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
395    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
396      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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