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revision 1.846 by dimitri, Fri Jun 22 06:41:09 2007 UTC revision 1.942 by dimitri, Fri Jan 18 01:38:33 2008 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/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
8    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
9      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
10    o verification/seaice_obcs: updated for restart test and latest options
11    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
12      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
13      for now this is only available for the C-grid code and also within
14      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
15    
16    checkpoint59m
17    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
18      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
19    o gad_som : fix flux output (& diagnostics) to have same units as other  
20      advection scheme fluxes (was previously multiplied by deltaT).  
21    o added verification/seaice_obcs both to test seaice open boundaries
22      and to provide an example matlab scrpt for generating them
23    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
24    o pkg/salt_plume: clean up salt_plume_frac.F to
25      remove redundancy in PlumeMethod 1 and 4
26    o pkg/kpp: added saltplume diagnostics
27    o pkg/obcs and pkg/seaice:
28      - do not set uice and vice to zero when OB*icefile are unspecified
29      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
30      - moved seaice tracer obcs after call to seaice_growth
31    o pkg/salt_plume: added various options for salt plume depth
32      criterion and for vertical distribution of the salt
33    
34    checkpoint59l
35    o pkg/ptracers: new version of ptracers pickup:
36      read meta file and write only fields which are needed to restart.
37      ( same logic as main pickup file ; also using pickupStrictlyMatch )
38    o pkg/seaice:
39      - add timescale for melting due to warm mixed layer as a means of
40        setting SEAICE_availHeatFrac more conveniently
41      - add a CPP-flag/runtime parameter check for flooding algorithm
42      - reformulated availHeat in seaice_growth.F to be independent of AREA
43    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
44      unit changes
45    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
46    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
47      SX vector computer.
48    o pkg/seaice:
49      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
50        seaice forcing fields can now be read only through pkg/exf
51      - removed some unused halos
52    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
53    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
54      or U/VICE from U/VWIND before computing U/VSTRESS
55    
56    checkpoint59k
57    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
58      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
59    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
60      all experiments pass when compile with un-initialised var. checking option.
61    o added pkg/salt_plume
62    o script to test restart (for now, in MITgcm_contrib/jmc_script)
63    o pkg/seaice: new read/write pickup version.
64      read meta file and write only fields which are needed to restart.
65      ( same logic as main pickup file ; also using pickupStrictlyMatch )
66    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
67    o lab_sea.hb87: modify the domain & update output.hb87.txt :
68      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
69      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
70      process. Fixed here by closing the domain at the Northern boundary.
71    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
72    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
73      a set of consecutive levels in/from a 3-D array.
74    o pkg/ptracers:
75      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
76      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
77    
78    checkpoint59j
79    o in pkgs: dic, obcs, offline, rbcs:
80      standard way to compute coeff. for time interpolation between 2 time reccords
81      which retains full precision (& make results less dependent on compiler).
82      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
83    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
84      packages instead of reading ice cover and wind speed separately
85    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
86     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
87      to allow to compile customized code before the update)
88    o cleaning-up:
89      - fix CPP instruction syntax in pkg/obcs
90      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
91        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
92      - fix some threads issue in IO parts.
93    o pkg/dic:
94      - add tons of "_d 0" (--> much better testreports !)
95       and then update outputs of tutorial_global_oce_biogeo
96    o pkg/mom_fluxform:
97      add a special version of momentum advection intended to conserve momentum
98      next to a bathymetry step or a coastline edge. (default = off = #undef)
99    o new read/write pickup version:
100      - for now, only implemented for main (mdsio) pickup file.
101      - write out only what is needed to restart; merge pickup_nh , pickup_ph
102        and main pickup together.
103      - read meta file; read only what is needed to restart; stop if a field
104        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
105        if it make sense (even if the restart is not perfect).
106      - if no meta file, assume that pickup to read corresponds exactly to
107        a pickup that would currently be written.
108      - read pickup written in the old format (until checkpoint59i) if it
109        recognizes an old meta file (no field-list).
110      - add a meta file in exp. which starts from a pickup: 2 cases:
111        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
112         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
113        b) a meta file describing the content of the associated pickup file
114         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
115    o pkg/mdsio & pkg/rw:
116      - new routine to read a meta file ; new set of routine to read
117        Multiple-fields file (with meta file).
118    o added open boundary conditions capability for seaice
119        HSNOW, HSALT, UICE, and VICE
120    
121    checkpoint59i
122    o adjoint:
123      * fix multiDimAdvection adjoint
124        (partial recomputation problem by TAF for fVerT(:,:,kDown)
125        and comlev1 size definition (maxpass vs. max. number of tracers)
126      * verification/global_ocean.90x45x15 adjoint now tests
127        NLFS and multiDimAdvection using DST3 (=30)
128      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
129    o pkg/kpp: add "_d 0" to real constant (if missing);
130      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
131      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
132    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
133      for internal parameters related to restart process (formerly from PARAMS.h)
134      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
135    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
136      as argument. (only atm2d & obcs write_pickup have not yet been updated)
137    o pkg/monitor:
138      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
139      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
140      - account for deep Atmosphere factor and density factor (anelastic)
141    o added open boundary conditions capability for seaice HEFF and AREA
142    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
143      thermodynamics
144      - requires a little reorganization, which affects the testreport results
145        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
146        so that now the conservative form is tested
147      - add a few comments
148    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
149    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
150    o add new diagnostics to seaice: advective, diffusive fluxes (only for
151      multidim-advection, for scheme 2 they are not filled) and transports,
152      thermodynamic growth rates
153    o change units of EmPmR (inside the code, + within coupling interface)
154      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
155      Affects results @ truncation level (cg2d match) and update output of
156       experiments: lab_sea(6), global_ocean.90x40x15(10),
157      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
158      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
159      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
160      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
161    
162    checkpoint59h
163    o pkg/exf:
164      - improve vectorization by moving if-statement out of loops in
165        exf_mapfields, exf_radiation
166      - exf_bulkformulae.F: introduce 2D fields and vectorize code
167    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
168    o testreport:
169      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
170        monitor & update offline_exf_seaice exp. output.
171      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
172    o pkg/seaice:
173      - bug fix in the evp solver: boundary conditions were affected be
174        masking of zMax/zMin (changes results)
175      - minor bug fix in boundary conditions in seaice_calc_strainrates
176        (changes results for no_slip)
177      - seaice_lsr.F: make interpolation of eta dependent on boundaries
178      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
179      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
180        stress formulation and no-slip boundary conditions
181    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
182      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
183    o pkg/seaice: a first HSALT time stepping equation has been checked in
184    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
185      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
186      without requiring DO-IF statements
187    o pkg/thsice:
188      use continuous power-law function for partition of energy between lateral
189      melting/freezing and thinning/thickening ; old code using step function
190      still available with #undef THSICE_FRACEN_POWERLAW
191      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
192    o testreport: change AD testing : check against results/output_adm.txt
193      using same scripts as for forward test.
194    
195    checkpoint59g
196    o adjoint testing: in preparation for changing testreport:
197      - output format: cost and grad written on separated lines
198      - ad output results in directory "results" (instead of "results_ad")
199    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
200    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
201    o pkg/ecco: allow user defined cost function contributions
202    o testreport:
203      Allow to choose (per experiment) the list of tested output variables
204       and the main variable (used to issue a pass/FAIL ) ;
205      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
206      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
207      Also modify printing of summary:
208       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
209       b) echo the list of tested variables in the individual summary.txt of
210          each experiment.
211    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
212      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
213      (but still depend on the tile decompostion of the domain).
214    o pkg/seaice: change a discretization detail to make the B-grid code
215      "more symmetric". This change is likely to remove all "ridges/leads" that
216      where quasi-aligned with the grid in B-grid solutions. It may also be
217      the solution to the stress coupling issues with the B-grid.
218    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
219      remove .cvsignore from input dir. (since testreport no longer run here).
220    o pkg/thsice:
221     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
222     - fix reshaping of sea-ice just after advection:
223       melt all the ice only if ice-volume is too small.
224     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
225       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
226     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
227    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
228      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
229    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
230      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
231      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
232      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
233      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
234      -> update output.txt
235    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
236     this affects truncation error: -> update output.txt of exp:
237      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
238      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
239    
240    checkpoint59f
241    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
242    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
243      a bounded range (in forward mode)
244    o pkg/ecco, ctrl, autodiff and mom_common:
245     internal parameter controls, completements of implementations
246    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
247    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
248      (not seem any difference in testing results).
249    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
250       at face corners.
251    o pkg/generic_advdiff:
252     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
253      loop range indices for computing vertical advection tendency
254      and do the calculation in the interior only (no overlap) ;
255      for now, only implemented for SOM advection (to save CPU time).
256     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
257    o exch2 adjoint
258      First set of changes:
259      - add exch2 hand-written adjoint templates
260      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
261        This will require cleanup in pkg/autodiff/*.F
262        (changed routines currently kept separate in verif. code/)
263      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
264        that used to hide exch2 or cubed-sphere specific code
265        (commented via 'cph-exch2')
266    o pkg/seaice
267      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
268    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
269       output of global_ocean.cs32x15.thsice .
270    
271    checkpoint59e
272    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
273      for B-grid vector (not yet tested) and C-grid vector (<- only used
274      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
275    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
276      (#ifdef ALLOW_SALT_PLUME)
277    o gather_2d/scatter_2d: removed halo regions
278  o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007  o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
279    scheme and the corresponding test case (under front_relax dir). For now,    scheme and the corresponding test case (under front_relax dir). For now,
280    only available with Skew-flux form and not yet tested in realistic set-up.    only available with Skew-flux form and not yet tested in realistic set-up.
281      adjoint: store directives updated, but gradient checks deteriorated,
282      so maybe GM/Redi adjoint is now broken.
283  o seaice adjoint  o seaice adjoint
284    * add AREA, HEFF, HSNOW as control variable    * add AREA, HEFF, HSNOW as control variable
285      (should not change lab_sea results)      (should not change lab_sea results)
286    * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40    * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
287  o pkg/seaice: added computation of saltFlux in seaice_growth;  o pkg/seaice:
288     For time being, sea ice salinity is assumed constant    * added computation of saltFlux in seaice_growth;
289     contribution of snow flooding to freshening of sea ice is neglected.      For time being, sea ice salinity is assumed constant
290     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it      contribution of snow flooding to freshening of sea ice is neglected.
291     defaults to 0.0 in order to maintain backward compatibility.      SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
292     Typical values for SEAICE_salinity are 4 to 10 g/kg.      defaults to 0.0 in order to maintain backward compatibility.
293        Typical values for SEAICE_salinity are 4 to 10 g/kg.
294      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
295      * added SEAICE_availHeatFrac, which specifies fraction of surface level
296        heat content used to melt or grow ice
297      * commented out cap of HICE: it helps keep ice thinner
298      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
299      * applied OBCS T/S mask to HEFFM sea ice mask
300    
301  checkpoint59d  checkpoint59d
302  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
# Line 186  o in FFIELDS.h: Line 466  o in FFIELDS.h:
466       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
467  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
468  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
469      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
470        are no longer updating the vertical diffusivity array
471        (passed as argument) but are (re-) setting those arrays.
472  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
473    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
474      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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