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revision 1.840 by dimitri, Wed Jun 20 14:08:22 2007 UTC revision 1.944 by mlosch, Thu Jan 24 08:30:07 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/exf:
8      - add a little more diagnostic to exf_interp_read (in analogy to
9        mds_read_field, can be turned off with debugLevel < debugLevA=1)
10      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
11        ugly but fast by unrolling short inner loops, inserting a unroll=8
12        directive in routine lagran, and splitting a loop and making do while the
13        outermost loop (the latter requires the intoduction of index arrays)
14    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
15    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
16      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
17    o verification/seaice_obcs: updated for restart test and latest options
18    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
19      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
20      for now this is only available for the C-grid code and also within
21      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
22    
23    checkpoint59m
24    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
25      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
26    o gad_som : fix flux output (& diagnostics) to have same units as other  
27      advection scheme fluxes (was previously multiplied by deltaT).  
28    o added verification/seaice_obcs both to test seaice open boundaries
29      and to provide an example matlab scrpt for generating them
30    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
31    o pkg/salt_plume: clean up salt_plume_frac.F to
32      remove redundancy in PlumeMethod 1 and 4
33    o pkg/kpp: added saltplume diagnostics
34    o pkg/obcs and pkg/seaice:
35      - do not set uice and vice to zero when OB*icefile are unspecified
36      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
37      - moved seaice tracer obcs after call to seaice_growth
38    o pkg/salt_plume: added various options for salt plume depth
39      criterion and for vertical distribution of the salt
40    
41    checkpoint59l
42    o pkg/ptracers: new version of ptracers pickup:
43      read meta file and write only fields which are needed to restart.
44      ( same logic as main pickup file ; also using pickupStrictlyMatch )
45    o pkg/seaice:
46      - add timescale for melting due to warm mixed layer as a means of
47        setting SEAICE_availHeatFrac more conveniently
48      - add a CPP-flag/runtime parameter check for flooding algorithm
49      - reformulated availHeat in seaice_growth.F to be independent of AREA
50    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
51      unit changes
52    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
53    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
54      SX vector computer.
55    o pkg/seaice:
56      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
57        seaice forcing fields can now be read only through pkg/exf
58      - removed some unused halos
59    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
60    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
61      or U/VICE from U/VWIND before computing U/VSTRESS
62    
63    checkpoint59k
64    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
65      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
66    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
67      all experiments pass when compile with un-initialised var. checking option.
68    o added pkg/salt_plume
69    o script to test restart (for now, in MITgcm_contrib/jmc_script)
70    o pkg/seaice: new read/write pickup version.
71      read meta file and write only fields which are needed to restart.
72      ( same logic as main pickup file ; also using pickupStrictlyMatch )
73    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
74    o lab_sea.hb87: modify the domain & update output.hb87.txt :
75      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
76      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
77      process. Fixed here by closing the domain at the Northern boundary.
78    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
79    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
80      a set of consecutive levels in/from a 3-D array.
81    o pkg/ptracers:
82      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
83      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
84    
85    checkpoint59j
86    o in pkgs: dic, obcs, offline, rbcs:
87      standard way to compute coeff. for time interpolation between 2 time reccords
88      which retains full precision (& make results less dependent on compiler).
89      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
90    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
91      packages instead of reading ice cover and wind speed separately
92    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
93     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
94      to allow to compile customized code before the update)
95    o cleaning-up:
96      - fix CPP instruction syntax in pkg/obcs
97      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
98        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
99      - fix some threads issue in IO parts.
100    o pkg/dic:
101      - add tons of "_d 0" (--> much better testreports !)
102       and then update outputs of tutorial_global_oce_biogeo
103    o pkg/mom_fluxform:
104      add a special version of momentum advection intended to conserve momentum
105      next to a bathymetry step or a coastline edge. (default = off = #undef)
106    o new read/write pickup version:
107      - for now, only implemented for main (mdsio) pickup file.
108      - write out only what is needed to restart; merge pickup_nh , pickup_ph
109        and main pickup together.
110      - read meta file; read only what is needed to restart; stop if a field
111        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
112        if it make sense (even if the restart is not perfect).
113      - if no meta file, assume that pickup to read corresponds exactly to
114        a pickup that would currently be written.
115      - read pickup written in the old format (until checkpoint59i) if it
116        recognizes an old meta file (no field-list).
117      - add a meta file in exp. which starts from a pickup: 2 cases:
118        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
119         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
120        b) a meta file describing the content of the associated pickup file
121         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
122    o pkg/mdsio & pkg/rw:
123      - new routine to read a meta file ; new set of routine to read
124        Multiple-fields file (with meta file).
125    o added open boundary conditions capability for seaice
126        HSNOW, HSALT, UICE, and VICE
127    
128    checkpoint59i
129    o adjoint:
130      * fix multiDimAdvection adjoint
131        (partial recomputation problem by TAF for fVerT(:,:,kDown)
132        and comlev1 size definition (maxpass vs. max. number of tracers)
133      * verification/global_ocean.90x45x15 adjoint now tests
134        NLFS and multiDimAdvection using DST3 (=30)
135      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
136    o pkg/kpp: add "_d 0" to real constant (if missing);
137      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
138      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
139    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
140      for internal parameters related to restart process (formerly from PARAMS.h)
141      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
142    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
143      as argument. (only atm2d & obcs write_pickup have not yet been updated)
144    o pkg/monitor:
145      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
146      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
147      - account for deep Atmosphere factor and density factor (anelastic)
148    o added open boundary conditions capability for seaice HEFF and AREA
149    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
150      thermodynamics
151      - requires a little reorganization, which affects the testreport results
152        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
153        so that now the conservative form is tested
154      - add a few comments
155    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
156    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
157    o add new diagnostics to seaice: advective, diffusive fluxes (only for
158      multidim-advection, for scheme 2 they are not filled) and transports,
159      thermodynamic growth rates
160    o change units of EmPmR (inside the code, + within coupling interface)
161      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
162      Affects results @ truncation level (cg2d match) and update output of
163       experiments: lab_sea(6), global_ocean.90x40x15(10),
164      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
165      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
166      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
167      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
168    
169    checkpoint59h
170    o pkg/exf:
171      - improve vectorization by moving if-statement out of loops in
172        exf_mapfields, exf_radiation
173      - exf_bulkformulae.F: introduce 2D fields and vectorize code
174    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
175    o testreport:
176      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
177        monitor & update offline_exf_seaice exp. output.
178      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
179    o pkg/seaice:
180      - bug fix in the evp solver: boundary conditions were affected be
181        masking of zMax/zMin (changes results)
182      - minor bug fix in boundary conditions in seaice_calc_strainrates
183        (changes results for no_slip)
184      - seaice_lsr.F: make interpolation of eta dependent on boundaries
185      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
186      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
187        stress formulation and no-slip boundary conditions
188    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
189      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
190    o pkg/seaice: a first HSALT time stepping equation has been checked in
191    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
192      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
193      without requiring DO-IF statements
194    o pkg/thsice:
195      use continuous power-law function for partition of energy between lateral
196      melting/freezing and thinning/thickening ; old code using step function
197      still available with #undef THSICE_FRACEN_POWERLAW
198      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
199    o testreport: change AD testing : check against results/output_adm.txt
200      using same scripts as for forward test.
201    
202    checkpoint59g
203    o adjoint testing: in preparation for changing testreport:
204      - output format: cost and grad written on separated lines
205      - ad output results in directory "results" (instead of "results_ad")
206    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
207    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
208    o pkg/ecco: allow user defined cost function contributions
209    o testreport:
210      Allow to choose (per experiment) the list of tested output variables
211       and the main variable (used to issue a pass/FAIL ) ;
212      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
213      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
214      Also modify printing of summary:
215       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
216       b) echo the list of tested variables in the individual summary.txt of
217          each experiment.
218    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
219      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
220      (but still depend on the tile decompostion of the domain).
221    o pkg/seaice: change a discretization detail to make the B-grid code
222      "more symmetric". This change is likely to remove all "ridges/leads" that
223      where quasi-aligned with the grid in B-grid solutions. It may also be
224      the solution to the stress coupling issues with the B-grid.
225    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
226      remove .cvsignore from input dir. (since testreport no longer run here).
227    o pkg/thsice:
228     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
229     - fix reshaping of sea-ice just after advection:
230       melt all the ice only if ice-volume is too small.
231     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
232       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
233     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
234    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
235      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
236    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
237      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
238      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
239      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
240      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
241      -> update output.txt
242    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
243     this affects truncation error: -> update output.txt of exp:
244      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
245      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
246    
247    checkpoint59f
248    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
249    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
250      a bounded range (in forward mode)
251    o pkg/ecco, ctrl, autodiff and mom_common:
252     internal parameter controls, completements of implementations
253    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
254    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
255      (not seem any difference in testing results).
256    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
257       at face corners.
258    o pkg/generic_advdiff:
259     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
260      loop range indices for computing vertical advection tendency
261      and do the calculation in the interior only (no overlap) ;
262      for now, only implemented for SOM advection (to save CPU time).
263     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
264    o exch2 adjoint
265      First set of changes:
266      - add exch2 hand-written adjoint templates
267      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
268        This will require cleanup in pkg/autodiff/*.F
269        (changed routines currently kept separate in verif. code/)
270      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
271        that used to hide exch2 or cubed-sphere specific code
272        (commented via 'cph-exch2')
273    o pkg/seaice
274      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
275    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
276       output of global_ocean.cs32x15.thsice .
277    
278    checkpoint59e
279    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
280      for B-grid vector (not yet tested) and C-grid vector (<- only used
281      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
282    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
283      (#ifdef ALLOW_SALT_PLUME)
284    o gather_2d/scatter_2d: removed halo regions
285    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
286      scheme and the corresponding test case (under front_relax dir). For now,
287      only available with Skew-flux form and not yet tested in realistic set-up.
288      adjoint: store directives updated, but gradient checks deteriorated,
289      so maybe GM/Redi adjoint is now broken.
290    o seaice adjoint
291      * add AREA, HEFF, HSNOW as control variable
292        (should not change lab_sea results)
293      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
294    o pkg/seaice:
295      * added computation of saltFlux in seaice_growth;
296        For time being, sea ice salinity is assumed constant
297        contribution of snow flooding to freshening of sea ice is neglected.
298        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
299        defaults to 0.0 in order to maintain backward compatibility.
300        Typical values for SEAICE_salinity are 4 to 10 g/kg.
301      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
302      * added SEAICE_availHeatFrac, which specifies fraction of surface level
303        heat content used to melt or grow ice
304      * commented out cap of HICE: it helps keep ice thinner
305      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
306      * applied OBCS T/S mask to HEFFM sea ice mask
307    
308    checkpoint59d
309    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
310     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
311     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
312    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
313     and change default value of parameter "GM_Small_Number";
314     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
315       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
316       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
317    o pkg/ecco: cost function when applying pkg/smooth to controls
318    o pkg/ctrl: add forcingPrecond run time parameter
319  o pkg/seaice:  o pkg/seaice:
320   - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code   - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
321   - fix bug in metric terms of u-equation in LSR solver (implicit part),   - fix bug in metric terms of u-equation in LSR solver (implicit part),
# Line 28  o pkg/profiles: Line 340  o pkg/profiles:
340       that allow you to prepare netcdf input files.       that allow you to prepare netcdf input files.
341   - also modified: cleaner include statements, cleaner error print statements,   - also modified: cleaner include statements, cleaner error print statements,
342     cleaner stops when error, and more tests of the netcdf input files consistency.     cleaner stops when error, and more tests of the netcdf input files consistency.
   
343  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
344  o pkg/seaice:  o pkg/seaice:
345   - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this   - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
# Line 162  o in FFIELDS.h: Line 473  o in FFIELDS.h:
473       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
474  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
475  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
476      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
477        are no longer updating the vertical diffusivity array
478        (passed as argument) but are (re-) setting those arrays.
479  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
480    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
481      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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