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revision 1.849 by dimitri, Wed Jul 18 22:26:05 2007 UTC revision 1.951 by gforget, Sat Feb 2 02:41:43 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/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
8      - introduce isopycnal diffusion coefficient control.
9    o tools/adjoint_options:
10      - additional control vector components.
11    o pkg/mnc: have mnc create marginally meaning full coordinate variables
12      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
13    o pkg/mypackage:
14      - add example of read/write pickup for state-var ;
15      - add entry points to the main code for state-vars diags & write-pickup.
16    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
17      transitions for useExfYearlyFields
18      - add new subroutine that determines the file to read from for
19        use*YearlyFields = .TRUE. and .FALSE.
20      - add a verification experiment to global_with_exf that tests
21        useExfYearlyFields with USE_EXF_INTERPOLATION defined
22    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
23      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
24      subroutines (which could be generated from a template, because they are
25      almost identical), for now they are included in obcs_prescribe_read.F for
26      simplicity
27    o pkg/exf:
28      - add a little more diagnostic to exf_interp_read (in analogy to
29        mds_read_field, can be turned off with debugLevel < debugLevA=1)
30      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
31        ugly but fast by unrolling short inner loops, inserting a unroll=8
32        directive in routine lagran, and splitting a loop and making do while the
33        outermost loop (the latter requires the intoduction of index arrays)
34    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
35    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
36      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
37    o verification/seaice_obcs: updated for restart test and latest options
38    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
39      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
40      for now this is only available for the C-grid code and also within
41      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
42    
43    checkpoint59m
44    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
45      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
46    o gad_som : fix flux output (& diagnostics) to have same units as other  
47      advection scheme fluxes (was previously multiplied by deltaT).  
48    o added verification/seaice_obcs both to test seaice open boundaries
49      and to provide an example matlab scrpt for generating them
50    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
51    o pkg/salt_plume: clean up salt_plume_frac.F to
52      remove redundancy in PlumeMethod 1 and 4
53    o pkg/kpp: added saltplume diagnostics
54    o pkg/obcs and pkg/seaice:
55      - do not set uice and vice to zero when OB*icefile are unspecified
56      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
57      - moved seaice tracer obcs after call to seaice_growth
58    o pkg/salt_plume: added various options for salt plume depth
59      criterion and for vertical distribution of the salt
60    
61    checkpoint59l
62    o pkg/ptracers: new version of ptracers pickup:
63      read meta file and write only fields which are needed to restart.
64      ( same logic as main pickup file ; also using pickupStrictlyMatch )
65    o pkg/seaice:
66      - add timescale for melting due to warm mixed layer as a means of
67        setting SEAICE_availHeatFrac more conveniently
68      - add a CPP-flag/runtime parameter check for flooding algorithm
69      - reformulated availHeat in seaice_growth.F to be independent of AREA
70    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
71      unit changes
72    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
73    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
74      SX vector computer.
75    o pkg/seaice:
76      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
77        seaice forcing fields can now be read only through pkg/exf
78      - removed some unused halos
79    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
80    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
81      or U/VICE from U/VWIND before computing U/VSTRESS
82    
83    checkpoint59k
84    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
85      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
86    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
87      all experiments pass when compile with un-initialised var. checking option.
88    o added pkg/salt_plume
89    o script to test restart (for now, in MITgcm_contrib/jmc_script)
90    o pkg/seaice: new read/write pickup version.
91      read meta file and write only fields which are needed to restart.
92      ( same logic as main pickup file ; also using pickupStrictlyMatch )
93    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
94    o lab_sea.hb87: modify the domain & update output.hb87.txt :
95      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
96      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
97      process. Fixed here by closing the domain at the Northern boundary.
98    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
99    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
100      a set of consecutive levels in/from a 3-D array.
101    o pkg/ptracers:
102      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
103      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
104    
105    checkpoint59j
106    o in pkgs: dic, obcs, offline, rbcs:
107      standard way to compute coeff. for time interpolation between 2 time reccords
108      which retains full precision (& make results less dependent on compiler).
109      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
110    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
111      packages instead of reading ice cover and wind speed separately
112    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
113     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
114      to allow to compile customized code before the update)
115    o cleaning-up:
116      - fix CPP instruction syntax in pkg/obcs
117      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
118        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
119      - fix some threads issue in IO parts.
120    o pkg/dic:
121      - add tons of "_d 0" (--> much better testreports !)
122       and then update outputs of tutorial_global_oce_biogeo
123    o pkg/mom_fluxform:
124      add a special version of momentum advection intended to conserve momentum
125      next to a bathymetry step or a coastline edge. (default = off = #undef)
126    o new read/write pickup version:
127      - for now, only implemented for main (mdsio) pickup file.
128      - write out only what is needed to restart; merge pickup_nh , pickup_ph
129        and main pickup together.
130      - read meta file; read only what is needed to restart; stop if a field
131        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
132        if it make sense (even if the restart is not perfect).
133      - if no meta file, assume that pickup to read corresponds exactly to
134        a pickup that would currently be written.
135      - read pickup written in the old format (until checkpoint59i) if it
136        recognizes an old meta file (no field-list).
137      - add a meta file in exp. which starts from a pickup: 2 cases:
138        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
139         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
140        b) a meta file describing the content of the associated pickup file
141         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
142    o pkg/mdsio & pkg/rw:
143      - new routine to read a meta file ; new set of routine to read
144        Multiple-fields file (with meta file).
145    o added open boundary conditions capability for seaice
146        HSNOW, HSALT, UICE, and VICE
147    
148    checkpoint59i
149    o adjoint:
150      * fix multiDimAdvection adjoint
151        (partial recomputation problem by TAF for fVerT(:,:,kDown)
152        and comlev1 size definition (maxpass vs. max. number of tracers)
153      * verification/global_ocean.90x45x15 adjoint now tests
154        NLFS and multiDimAdvection using DST3 (=30)
155      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
156    o pkg/kpp: add "_d 0" to real constant (if missing);
157      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
158      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
159    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
160      for internal parameters related to restart process (formerly from PARAMS.h)
161      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
162    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
163      as argument. (only atm2d & obcs write_pickup have not yet been updated)
164    o pkg/monitor:
165      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
166      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
167      - account for deep Atmosphere factor and density factor (anelastic)
168    o added open boundary conditions capability for seaice HEFF and AREA
169    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
170      thermodynamics
171      - requires a little reorganization, which affects the testreport results
172        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
173        so that now the conservative form is tested
174      - add a few comments
175    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
176    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
177    o add new diagnostics to seaice: advective, diffusive fluxes (only for
178      multidim-advection, for scheme 2 they are not filled) and transports,
179      thermodynamic growth rates
180    o change units of EmPmR (inside the code, + within coupling interface)
181      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
182      Affects results @ truncation level (cg2d match) and update output of
183       experiments: lab_sea(6), global_ocean.90x40x15(10),
184      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
185      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
186      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
187      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
188    
189    checkpoint59h
190    o pkg/exf:
191      - improve vectorization by moving if-statement out of loops in
192        exf_mapfields, exf_radiation
193      - exf_bulkformulae.F: introduce 2D fields and vectorize code
194    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
195    o testreport:
196      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
197        monitor & update offline_exf_seaice exp. output.
198      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
199    o pkg/seaice:
200      - bug fix in the evp solver: boundary conditions were affected be
201        masking of zMax/zMin (changes results)
202      - minor bug fix in boundary conditions in seaice_calc_strainrates
203        (changes results for no_slip)
204      - seaice_lsr.F: make interpolation of eta dependent on boundaries
205      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
206      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
207        stress formulation and no-slip boundary conditions
208    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
209      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
210    o pkg/seaice: a first HSALT time stepping equation has been checked in
211    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
212      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
213      without requiring DO-IF statements
214    o pkg/thsice:
215      use continuous power-law function for partition of energy between lateral
216      melting/freezing and thinning/thickening ; old code using step function
217      still available with #undef THSICE_FRACEN_POWERLAW
218      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
219    o testreport: change AD testing : check against results/output_adm.txt
220      using same scripts as for forward test.
221    
222    checkpoint59g
223    o adjoint testing: in preparation for changing testreport:
224      - output format: cost and grad written on separated lines
225      - ad output results in directory "results" (instead of "results_ad")
226    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
227    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
228    o pkg/ecco: allow user defined cost function contributions
229    o testreport:
230      Allow to choose (per experiment) the list of tested output variables
231       and the main variable (used to issue a pass/FAIL ) ;
232      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
233      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
234      Also modify printing of summary:
235       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
236       b) echo the list of tested variables in the individual summary.txt of
237          each experiment.
238    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
239      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
240      (but still depend on the tile decompostion of the domain).
241    o pkg/seaice: change a discretization detail to make the B-grid code
242      "more symmetric". This change is likely to remove all "ridges/leads" that
243      where quasi-aligned with the grid in B-grid solutions. It may also be
244      the solution to the stress coupling issues with the B-grid.
245    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
246      remove .cvsignore from input dir. (since testreport no longer run here).
247    o pkg/thsice:
248     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
249     - fix reshaping of sea-ice just after advection:
250       melt all the ice only if ice-volume is too small.
251     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
252       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
253     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
254    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
255      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
256    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
257      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
258      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
259      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
260      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
261      -> update output.txt
262    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
263     this affects truncation error: -> update output.txt of exp:
264      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
265      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
266    
267    checkpoint59f
268    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
269    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
270      a bounded range (in forward mode)
271    o pkg/ecco, ctrl, autodiff and mom_common:
272     internal parameter controls, completements of implementations
273    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
274    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
275      (not seem any difference in testing results).
276    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
277       at face corners.
278    o pkg/generic_advdiff:
279     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
280      loop range indices for computing vertical advection tendency
281      and do the calculation in the interior only (no overlap) ;
282      for now, only implemented for SOM advection (to save CPU time).
283     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
284    o exch2 adjoint
285      First set of changes:
286      - add exch2 hand-written adjoint templates
287      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
288        This will require cleanup in pkg/autodiff/*.F
289        (changed routines currently kept separate in verif. code/)
290      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
291        that used to hide exch2 or cubed-sphere specific code
292        (commented via 'cph-exch2')
293    o pkg/seaice
294      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
295    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
296       output of global_ocean.cs32x15.thsice .
297    
298    checkpoint59e
299    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
300      for B-grid vector (not yet tested) and C-grid vector (<- only used
301      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
302    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
303      (#ifdef ALLOW_SALT_PLUME)
304    o gather_2d/scatter_2d: removed halo regions
305  o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007  o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
306    scheme and the corresponding test case (under front_relax dir). For now,    scheme and the corresponding test case (under front_relax dir). For now,
307    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.
# Line 25  o pkg/seaice: Line 323  o pkg/seaice:
323      heat content used to melt or grow ice      heat content used to melt or grow ice
324    * commented out cap of HICE: it helps keep ice thinner    * commented out cap of HICE: it helps keep ice thinner
325    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
326      * applied OBCS T/S mask to HEFFM sea ice mask
327    
328  checkpoint59d  checkpoint59d
329  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
# Line 194  o in FFIELDS.h: Line 493  o in FFIELDS.h:
493       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
494  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
495  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
496      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
497        are no longer updating the vertical diffusivity array
498        (passed as argument) but are (re-) setting those arrays.
499  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
500    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
501      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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