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revision 1.861 by gforget, Mon Aug 20 17:44:38 2007 UTC revision 1.956 by jmc, Tue Feb 12 23:18:18 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 generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
8      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
9      - modify verification advect_cs test to test SOM-advection on CS-grid.
10    o pkg/ctrl:
11      - Rewrite of ctrl_map_ini_ecco.F,
12        introducing a generic routine (ctrl_map_ini_gen.F).
13      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
14    
15    checkpoint59n
16    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
17      number in dedicate array "hdiag":
18      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
19        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
20      - many small changes (integer format) for large number of diagnostics
21      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
22        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
23    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
24      usingSphericalGrid, this allows to define the rotated grid coordinates
25      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
26      geographical coordinates according to the inverse of the rotation defined
27      by the Euler angles, so that Coriolis parameter and online-interpolation by
28      exf works with the geographical coordinates on XC/YC/XG/YG.
29      Naturally, this feature does not work with all packages, so some
30      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
31      profiles), because there the coordinates are assumed to be regular
32      spherical grid coordinates.
33    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
34      - introduce isopycnal diffusion coefficient control.
35    o tools/adjoint_options:
36      - additional control vector components.
37    o pkg/mnc: have mnc create marginally meaning full coordinate variables
38      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
39    o pkg/mypackage:
40      - add example of read/write pickup for state-var ;
41      - add entry points to the main code for state-vars diags & write-pickup.
42    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
43      transitions for useExfYearlyFields
44      - add new subroutine that determines the file to read from for
45        use*YearlyFields = .TRUE. and .FALSE.
46      - add a verification experiment to global_with_exf that tests
47        useExfYearlyFields with USE_EXF_INTERPOLATION defined
48    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
49      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
50      subroutines (which could be generated from a template, because they are
51      almost identical), for now they are included in obcs_prescribe_read.F for
52      simplicity
53    o pkg/exf:
54      - add a little more diagnostic to exf_interp_read (in analogy to
55        mds_read_field, can be turned off with debugLevel < debugLevA=1)
56      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
57        ugly but fast by unrolling short inner loops, inserting a unroll=8
58        directive in routine lagran, and splitting a loop and making do while the
59        outermost loop (the latter requires the intoduction of index arrays)
60    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
61    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
62      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
63    o verification/seaice_obcs: updated for restart test and latest options
64    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
65      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
66      for now this is only available for the C-grid code and also within
67      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
68    
69    checkpoint59m
70    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
71      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
72    o gad_som : fix flux output (& diagnostics) to have same units as other  
73      advection scheme fluxes (was previously multiplied by deltaT).  
74    o added verification/seaice_obcs both to test seaice open boundaries
75      and to provide an example matlab scrpt for generating them
76    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
77    o pkg/salt_plume: clean up salt_plume_frac.F to
78      remove redundancy in PlumeMethod 1 and 4
79    o pkg/kpp: added saltplume diagnostics
80    o pkg/obcs and pkg/seaice:
81      - do not set uice and vice to zero when OB*icefile are unspecified
82      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
83      - moved seaice tracer obcs after call to seaice_growth
84    o pkg/salt_plume: added various options for salt plume depth
85      criterion and for vertical distribution of the salt
86    
87    checkpoint59l
88    o pkg/ptracers: new version of ptracers pickup:
89      read meta file and write only fields which are needed to restart.
90      ( same logic as main pickup file ; also using pickupStrictlyMatch )
91    o pkg/seaice:
92      - add timescale for melting due to warm mixed layer as a means of
93        setting SEAICE_availHeatFrac more conveniently
94      - add a CPP-flag/runtime parameter check for flooding algorithm
95      - reformulated availHeat in seaice_growth.F to be independent of AREA
96    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
97      unit changes
98    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
99    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
100      SX vector computer.
101    o pkg/seaice:
102      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
103        seaice forcing fields can now be read only through pkg/exf
104      - removed some unused halos
105    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
106    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
107      or U/VICE from U/VWIND before computing U/VSTRESS
108    
109    checkpoint59k
110    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
111      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
112    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
113      all experiments pass when compile with un-initialised var. checking option.
114    o added pkg/salt_plume
115    o script to test restart (for now, in MITgcm_contrib/jmc_script)
116    o pkg/seaice: new read/write pickup version.
117      read meta file and write only fields which are needed to restart.
118      ( same logic as main pickup file ; also using pickupStrictlyMatch )
119    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
120    o lab_sea.hb87: modify the domain & update output.hb87.txt :
121      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
122      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
123      process. Fixed here by closing the domain at the Northern boundary.
124    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
125    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
126      a set of consecutive levels in/from a 3-D array.
127    o pkg/ptracers:
128      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
129      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
130    
131    checkpoint59j
132    o in pkgs: dic, obcs, offline, rbcs:
133      standard way to compute coeff. for time interpolation between 2 time reccords
134      which retains full precision (& make results less dependent on compiler).
135      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
136    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
137      packages instead of reading ice cover and wind speed separately
138    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
139     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
140      to allow to compile customized code before the update)
141    o cleaning-up:
142      - fix CPP instruction syntax in pkg/obcs
143      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
144        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
145      - fix some threads issue in IO parts.
146    o pkg/dic:
147      - add tons of "_d 0" (--> much better testreports !)
148       and then update outputs of tutorial_global_oce_biogeo
149    o pkg/mom_fluxform:
150      add a special version of momentum advection intended to conserve momentum
151      next to a bathymetry step or a coastline edge. (default = off = #undef)
152    o new read/write pickup version:
153      - for now, only implemented for main (mdsio) pickup file.
154      - write out only what is needed to restart; merge pickup_nh , pickup_ph
155        and main pickup together.
156      - read meta file; read only what is needed to restart; stop if a field
157        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
158        if it make sense (even if the restart is not perfect).
159      - if no meta file, assume that pickup to read corresponds exactly to
160        a pickup that would currently be written.
161      - read pickup written in the old format (until checkpoint59i) if it
162        recognizes an old meta file (no field-list).
163      - add a meta file in exp. which starts from a pickup: 2 cases:
164        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
165         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
166        b) a meta file describing the content of the associated pickup file
167         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
168    o pkg/mdsio & pkg/rw:
169      - new routine to read a meta file ; new set of routine to read
170        Multiple-fields file (with meta file).
171    o added open boundary conditions capability for seaice
172        HSNOW, HSALT, UICE, and VICE
173    
174    checkpoint59i
175    o adjoint:
176      * fix multiDimAdvection adjoint
177        (partial recomputation problem by TAF for fVerT(:,:,kDown)
178        and comlev1 size definition (maxpass vs. max. number of tracers)
179      * verification/global_ocean.90x45x15 adjoint now tests
180        NLFS and multiDimAdvection using DST3 (=30)
181      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
182    o pkg/kpp: add "_d 0" to real constant (if missing);
183      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
184      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
185    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
186      for internal parameters related to restart process (formerly from PARAMS.h)
187      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
188    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
189      as argument. (only atm2d & obcs write_pickup have not yet been updated)
190    o pkg/monitor:
191      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
192      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
193      - account for deep Atmosphere factor and density factor (anelastic)
194    o added open boundary conditions capability for seaice HEFF and AREA
195    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
196      thermodynamics
197      - requires a little reorganization, which affects the testreport results
198        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
199        so that now the conservative form is tested
200      - add a few comments
201    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
202    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
203    o add new diagnostics to seaice: advective, diffusive fluxes (only for
204      multidim-advection, for scheme 2 they are not filled) and transports,
205      thermodynamic growth rates
206    o change units of EmPmR (inside the code, + within coupling interface)
207      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
208      Affects results @ truncation level (cg2d match) and update output of
209       experiments: lab_sea(6), global_ocean.90x40x15(10),
210      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
211      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
212      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
213      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
214    
215    checkpoint59h
216    o pkg/exf:
217      - improve vectorization by moving if-statement out of loops in
218        exf_mapfields, exf_radiation
219      - exf_bulkformulae.F: introduce 2D fields and vectorize code
220    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
221    o testreport:
222      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
223        monitor & update offline_exf_seaice exp. output.
224      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
225    o pkg/seaice:
226      - bug fix in the evp solver: boundary conditions were affected be
227        masking of zMax/zMin (changes results)
228      - minor bug fix in boundary conditions in seaice_calc_strainrates
229        (changes results for no_slip)
230      - seaice_lsr.F: make interpolation of eta dependent on boundaries
231      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
232      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
233        stress formulation and no-slip boundary conditions
234    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
235      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
236    o pkg/seaice: a first HSALT time stepping equation has been checked in
237    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
238      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
239      without requiring DO-IF statements
240    o pkg/thsice:
241      use continuous power-law function for partition of energy between lateral
242      melting/freezing and thinning/thickening ; old code using step function
243      still available with #undef THSICE_FRACEN_POWERLAW
244      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
245    o testreport: change AD testing : check against results/output_adm.txt
246      using same scripts as for forward test.
247    
248    checkpoint59g
249    o adjoint testing: in preparation for changing testreport:
250      - output format: cost and grad written on separated lines
251      - ad output results in directory "results" (instead of "results_ad")
252    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
253    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
254    o pkg/ecco: allow user defined cost function contributions
255    o testreport:
256      Allow to choose (per experiment) the list of tested output variables
257       and the main variable (used to issue a pass/FAIL ) ;
258      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
259      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
260      Also modify printing of summary:
261       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
262       b) echo the list of tested variables in the individual summary.txt of
263          each experiment.
264    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
265      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
266      (but still depend on the tile decompostion of the domain).
267    o pkg/seaice: change a discretization detail to make the B-grid code
268      "more symmetric". This change is likely to remove all "ridges/leads" that
269      where quasi-aligned with the grid in B-grid solutions. It may also be
270      the solution to the stress coupling issues with the B-grid.
271    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
272      remove .cvsignore from input dir. (since testreport no longer run here).
273    o pkg/thsice:
274     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
275     - fix reshaping of sea-ice just after advection:
276       melt all the ice only if ice-volume is too small.
277     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
278       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
279     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
280    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
281      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
282    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
283      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
284      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
285      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
286      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
287      -> update output.txt
288    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
289     this affects truncation error: -> update output.txt of exp:
290      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
291      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
292    
293    checkpoint59f
294  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
295  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
296    a bounded range (in forward mode)    a bounded range (in forward mode)
297  o pkg/ecco, ctrl, autodiff and mom_common:  o pkg/ecco, ctrl, autodiff and mom_common:
298   internal parameter controls, completements of implementations   internal parameter controls, completements of implementations
299  o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.  o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
300    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
301      (not seem any difference in testing results).
302  o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains  o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
303     at face corners.     at face corners.
304  o pkg/generic_advdiff:  o pkg/generic_advdiff:
# Line 230  o in FFIELDS.h: Line 519  o in FFIELDS.h:
519       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
520  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
521  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
522      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
523        are no longer updating the vertical diffusivity array
524        (passed as argument) but are (re-) setting those arrays.
525  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
526    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
527      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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