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revision 1.596 by jmc, Sat Dec 31 01:21:41 2005 UTC revision 1.707 by jmc, Sun Jul 16 03:59:39 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
8       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
9    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
10       keep global_ocean.90x40x15 (for AD testing) with former secondary test
11       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
12    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
13        add MITgcm_tutorials (= code + all the tutorials)
14    o ecco, option to compute cost for total ssh (mean+anom)
15    o consistent with addition of ptracer and ssh in pkg/profiles
16    o profiles: adding ptracer and ssh
17    o testreport: change multi-test output-file name
18      (from output.txt.{name} to output.{name}.txt)
19    o profiles: now ok for mutli-threaded case
20    o seaice: add 4 parameters for different advection schemes for area,
21      (effective) seaice thickness, enthalphy, and snow height. Their default
22      is the standard parameter SEAICEadvScheme
23    o calc_gw:
24     - add cosFacU in zonal viscous flux (harmonic.visc.).
25     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
26       of tutorial_plume_on_slope.
27    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
28    o calc_gw: true flux-form, account for horizontal grid spacing.
29      update rotating_tank results, but not plume_on_slope (affected at
30      truncation level, 11 digits).
31    
32    checkpoint58l_post
33    o calc_gw:
34     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
35     - remove side-drag for now (need to fix it); update plume_on_slope results.
36     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
37    o commit code to make SST/SSS weights spatially variable
38      (based on either variable in-situ or variable initial T/S weights)
39    o pkg/ecco:
40      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
41        now based on horizontally varying weights wthetaLev, wsaltLev
42      * cost_averagesflags now returns year indices in addition to day, month
43      * sflux balance is performed on annual basis
44        (sflxumm, sfluxmm2, bal_sfluxmm)
45      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
46        including separate counting and multipliers
47    o pkg/rbcs
48      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
49    
50    checkpoint58k_post
51    o testreport:
52     - always build in dir. "build" (if not there, mkdir build instead of building
53       & running in input)
54     - run in dir run (if it exists), in build otherwise.
55     - call prepare_run (if input/prepare_run exists)
56     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
57    o pkg/exf modifications to interpolation and rotation routines for more
58       reasonable treatment of North Pole singularity: for tracers North Pole
59       value is set to northernmost zonal-mean value, for zonal velocity it is
60       set to zero, and for meridional velocity it is set to northernmost value.
61    o pkg/exf/exf_check_range.F
62     - add tile index to diagnostics and move stop statement to the very
63       end of the routine.
64    o pkg/diagnostics: (diagnostics_main_init.F)
65      define title of isomorphic variables according to the current config.
66    o pkg/thsice with pkg/seaice dynamics:
67    - fix domain of computation (interior only, required for exf) and do exchanges
68    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
69    o towards a standard way of dealing with multi-threading in MONITOR
70      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
71    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
72       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
73    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
74    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
75    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
76       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
77    o tracer advection:
78     - clean-up and simplify calc_common_factors.F
79     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
80       advection subroutine (but still not used within DST advection S/R)
81    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
82    
83    checkpoint58j_post
84    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
85      from file (collects calls previously in FORWARD_STEP)
86    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
87    o adjoint store dir. adjusted accordingly
88    o genmake2
89      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
90    
91    checkpoint58i_post
92    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
93      on wind stress (SEAICEstressFactor defaults to 1.)
94    o Total number of Timers is finite (<=40): comment out 2 non-essential one
95      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
96    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
97      on CS-grid: no longer loosing mass.
98    o exf & curvilinear-grid: no longer modify longitude xC & xG.
99    o pkg/ggl90: fix sloppy output and fix a bug
100    o pkg/seaice: added SEAICEuseEVPpickup parameter
101      - Set to false in order to start EVP solver with
102        non-EVP pickup files when using SEAICEuseEVP
103      - fix sign error in diffusion in seaice_calc_rhs
104    
105    checkpoint58h_post
106    * Modifications for bottom topography control
107      o replace hFacC by _hFacC at various places
108      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
109      o add non-self-adjoint cg2d_nsa
110      o update autodiff support routines
111      o re-initialise hfac after ctrl_depth_ini
112      o works for 5x5 box, doesnt work for global_ocean.90x40x15
113    * Adding verification for 5x5 box (4-layer) bottom topography control
114    
115    checkpoint58g_post
116    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
117       used for mean seasonal cycle, mean diurnal cycle); add an example
118       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
119    o pkg/ggl90:
120      - add parameter (minimum surface kinetic energy)
121      - fix bug (avoiding division by zero)
122    o couple pkg/thsice to pkg/seaice:
123      - modify advection in seaice to accomodate new scalar fields to be advected
124      - only muliDimAdection scheme work with seaice/thsice
125      - mapping of thsice-variables to seaice-variables, back and forth
126      - does not break the verification experiments, but does not give the
127        desired results either
128    o pkg/seaice
129      - make (default) second order advection a bit less confusing?
130    
131    checkpoint58f_post
132    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
133      to pkg/seaice):
134      - new routines thsice_map_exf and thsice_get_exf provide the interface
135      - add an additional formal parameter to thsice_solve4temp
136    o pkg/exf:
137      - add new fields wspeed, snowprecip (to be able to couple to thsice)
138      - correct Stefan-Boltzmann constant
139      - new parameter for longwave surface emittance
140      - separate some stuff from exf_bulkformulae into new routines  
141        exf_radiation, exf_wind
142      - add new parameters and constants: longwave emissivity for ocean, ice
143        and snow, evaporation parameters over ice
144      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
145        either wind from stress or stress from wind
146    o pkg/thSIce:
147    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
148    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
149       and THSICE_CALC_THICKN
150    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
151    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
152      to make debugging easier.
153    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
154    o pkg/bulk_force:
155      - clean-up comments and parameters ;
156      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
157    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
158      generate new output for test-experiment: aim.5l_cs.thSI
159    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
160      testreport accordingly
161    
162    checkpoint58e_post
163    o SEAICE_CGRID adjoint done
164    o R_STAR adjoint implemented.
165      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
166      * need to sort out init. of h0facc, etc.
167    o Make pkg/profile fully independent of ecco,cost, etc. stuff
168      to be able to use it in pure forward.
169    
170    checkpoint58d_post
171    o upgrade simple test-experiment to tutorial example:
172     step.1: duplicate the experiment and (step.2) will remove the old copy.
173      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
174      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
175      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
176      tutorial_global_oce_biogeo    <- copy of dic_example
177      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
178      tutorial_plume_on_slope       <- copy of plume_on_slope
179      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
180      tutorial_global_oce_optim     <- empty for now (David ?)
181      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
182     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
183    o correct a sign problem in cost_scat.F
184    o obcs and ptracers: fix boundary conditions for advections schemes
185      with larger stencil
186    o thsice adjoint: start
187    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
188      completeness
189    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
190      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
191    o ptracers adjoint:
192      * avoid extensive recomputatations
193      * fix missing re-init. of gptr (missed by TAF)
194    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
195      me to turn off the excessive output to STDOUT that this package produces
196    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
197      and add those terms in Vector-Invariant formulation.
198    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
199      if the control period (xx_hfluxperiod etc) is 0
200    o in profiles pkg, clean routines and fix details
201    o in ecco pkg, reading ssh data:
202      fix problem in case the model does not start at iter0=0
203    o fix mnc-pickup/restart for ptracers
204    o new package prifiles:
205      code to compute profile-based cost by Gael Forget
206      (modifs in ecco, ctrl, autodiff)
207    o Benign bug fix in initialization (spotted by M. Mazloff) of
208      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
209    
210    checkpoint58c_post
211    o adjoint: finish NLFS adjoint and provide reference output in
212      verification/global_ocean.90x40x15/results_ad_nlfs
213    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
214      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
215      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
216      with SEAICE_CGRID defined.
217    o move calendarDumps from "data" to "data.cal" and clean-up the code
218      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
219    o add useEXF & useCAL flags (for now, set in hard-coded way)
220    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
221      (were missing in NH mode, and wrong in quasihydrostatic mode).
222      waiting for Chris updated version of calc_gw to add those CALLs.
223    o fix bug in quasihydrostatic S/R ;
224      add a test for this option: global_ocean.90x40x15.qshyd
225    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
226      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
227    o add on/off flag useOffLine for package OFFLINE
228    o seaice:
229      - modify advection so that it works also on the C-grid
230      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
231        problem in multi-tile runs with C-grid
232      - add flags for clipping ice velocities and/or masking solver forcing
233      - fix drag (ocean on ice) formulation and a bug that caused noise in the
234        C-grid solver
235      - added a few comments to seaice_diffusion.F
236      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
237        are now exclusive)
238      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
239        required re-ordering the code a little:
240       + make DAIRN global variable (defined in SEAICE)
241       + move computation of the viscosities eta and zeta into a new separate
242         routine (because I need to recompute them in seaice_ocean_stress.F)
243    
244    checkpoint58b_post
245    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
246      update output.txt of exp. aim.5l_cs.thSI
247    o various mnc cleanups and improvements:
248      + shrink lookup tables by factor of ~4
249      + better error reporting when running out of lookup space
250      + able to handle longer path/file names (up to 500 chars)
251    o adjoint:
252      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
253      - TBD: "hidden" mom_vecinv recomp. in dynamics
254    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
255     (allow to differentiate between forcing components using new integer flags:
256      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
257     and add new flag to put Dissipation tendency out of Adams-Bashforth.
258    o ecco
259      - enable trend removal from SSH anomaly obs.
260    o adjoint
261      - a fix for PmEpR when #undef EXACT_CONSERV
262      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
263      - try to fix "hidden" recomp. in forward_step for NLFS
264        (NLFS seems broken sometimes after I checked it in)
265    o seaice:
266     - add c-grid version of the dynamic solver:
267       + three new routines that are the c-grid substitute lsr, dynsolver
268         and ostres
269       + put a few fields that were local to dynsolver into global common
270         blocks, so that I can move the computation of stresses etc into
271         seaice_lsr (saves coding but may break the adjoint).
272     - replace more hardwired parameters by runtime parameters
273     - add ice masks that mask the rhs of the implicit solvers where there
274       is no ice (commented out in seaice_dynsolver, because i am not sure
275       if this works properly), eventually this should replace the clipping
276       of ice velocities in seaice_dynsolver to +/-40cm/s.
277    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
278      include it only where its needed
279    o move balancing of fluxes before the call of external_forcing_surf
280    o seaice:
281      - correct units of turning angles (now they are really in degrees)
282      - move computation of GWATX/Y out of main routine into dynsolver
283      - initialize GWATX/Y in seaice_init
284    o Apply mask on Fresh-Water flux (needed for SSH forcing).
285      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
286    o seaice: add runtime flags for turning angles (default to zero)
287    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
288      and trend from exf forcing and ctrl control adjustments
289    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
290      (since checkpoint57x_post)
291    o change the default rotation period to 86164.s = the Earth rotation
292    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
293      and based on a reference stratification. Tested within hs94.cs-32x32x5.
294    o seaice advection: add code for choosing between the default (2nd order
295      central differences) and multiDim advection schemes provided by
296      pkg/generic_advdiff
297    o seaice:
298      - removed all references to SEAICE_GRID.h fields from
299        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
300        (cubed-sphere configuration will change a little)
301      - grid computations in seaice_init are obsolete now.
302      - cleaned up code a little so that is easier to read (hopefully).
303      - added new (better?) discretizations of default advection and diffusion
304        (turn on with SEAICEuseFluxForm)
305      - replace 1 in 3d global fields by kSurface in growth.F
306      
307    checkpoint58a_post
308    o seaice:
309      - bug fix in advect.F
310    o shelfice:
311      - separate shelfice load anomaly from pload (breaks with time
312        dependent forcing), => introduce constant field shelficeLoadAnomaly.
313        Its default is 0., but it may be computed more cleverly from (unknown)
314        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
315        done offline. A good approximation of the pressure load anomaly is
316        necessary to avoid large initial adjustment processes underneath
317        deep-reaching shelfice.
318      - small fix in ISOMIP shelfice_thermodynamics
319      - add more sophisticated thermodynamics of Hellmer (1989), this is
320        now the default
321      - give a few constants more intuitive names
322    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
323      if bulk formulae are used in long integration (especially EmPmR). Turn
324      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
325      if balancePrintMean, the imbalance that is substracted is printed to
326      STDOUT.
327    o fix bug (typo) in obcs_apply_eta.F
328    o add a new package shelfice which enables us to model the circulation
329      underneath shelf-ice with draughts of hundreds of meters.
330     - works
331     - to do: + include improved thermodynamics
332              + check whether kSurfC (from model/inc/SURFACE.h) can be used
333                instead of new field kTopC
334              + can we use topoFile, Ro_surf and existing code in ini_depth.F
335                instead of new field R_shelfIce and new code in ini_depth.F
336                and ini_mask_etc.F?
337              + adjust vertical mixing schemes?
338    o seaice pkg:
339     - add a cpp-flag to include a simple formula for a salinity dependent
340       freezing point of sea water at the surface
341     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
342       meridional stresses are now different (and hopefully correct)
343    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
344       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
345       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
346    o pkg/diagnostics: add options and parameters for regional-statistics
347       diagnostics ; define regions by reading a region-mask from a file
348       (might add other options later)
349    o pkg/bulk_force:
350     - add option and parameters to use AIM surface-flux formulae.
351     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
352       others forcing fields (defined in PARM05, parameter file "data") are loaded
353       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
354     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
355     - use the right EXCH call for uwind,vwind (to work on CS-grid).
356     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
357       and parameters (note: calcWindStress replaces .NOT.readwindstress).
358     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
359    
360    checkpoint58
361    o add "--embed-source" option to genmake2 which, when the supporting
362      tools can be compiled (as determined by genmake2) will turn on the
363      embed_files package which then embeds the entire MITgcm source code
364      (*.[fFhc] + Makefile) used for the build within the executable
365      - requested by CNH but off by default
366      - adds a paltry <9MB to the mitgcmuv executable in most cases
367      - only writes the output when useEMBEDSRC in eedata is true
368    o clean up 3-dim. relaxation codes:
369      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
370      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
371      * Thanks to Tom Haine for testing!
372    
373  checkpoint57z_post  checkpoint57z_post
374  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
375    affects output (@ truncation level) of exp. plume_on_slope ; updated.    affects output (@ truncation level) of exp. plume_on_slope ; updated.

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