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revision 1.599 by jmc, Thu Jan 12 16:49:07 2006 UTC revision 1.703 by gforget, Fri Jul 14 22:14:28 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 profiles: adding ptracer and ssh
8    o testreport: change multi-test output-file name
9      (from output.txt.{name} to output.{name}.txt)
10    o profiles: now ok for mutli-threaded case
11    o seaice: add 4 parameters for different advection schemes for area,
12      (effective) seaice thickness, enthalphy, and snow height. Their default
13      is the standard parameter SEAICEadvScheme
14    o calc_gw:
15     - add cosFacU in zonal viscous flux (harmonic.visc.).
16     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
17       of tutorial_plume_on_slope.
18    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
19    o calc_gw: true flux-form, account for horizontal grid spacing.
20      update rotating_tank results, but not plume_on_slope (affected at
21      truncation level, 11 digits).
22    
23    checkpoint58l_post
24    o calc_gw:
25     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
26     - remove side-drag for now (need to fix it); update plume_on_slope results.
27     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
28    o commit code to make SST/SSS weights spatially variable
29      (based on either variable in-situ or variable initial T/S weights)
30    o pkg/ecco:
31      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
32        now based on horizontally varying weights wthetaLev, wsaltLev
33      * cost_averagesflags now returns year indices in addition to day, month
34      * sflux balance is performed on annual basis
35        (sflxumm, sfluxmm2, bal_sfluxmm)
36      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
37        including separate counting and multipliers
38    o pkg/rbcs
39      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
40    
41    checkpoint58k_post
42    o testreport:
43     - always build in dir. "build" (if not there, mkdir build instead of building
44       & running in input)
45     - run in dir run (if it exists), in build otherwise.
46     - call prepare_run (if input/prepare_run exists)
47     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
48    o pkg/exf modifications to interpolation and rotation routines for more
49       reasonable treatment of North Pole singularity: for tracers North Pole
50       value is set to northernmost zonal-mean value, for zonal velocity it is
51       set to zero, and for meridional velocity it is set to northernmost value.
52    o pkg/exf/exf_check_range.F
53     - add tile index to diagnostics and move stop statement to the very
54       end of the routine.
55    o pkg/diagnostics: (diagnostics_main_init.F)
56      define title of isomorphic variables according to the current config.
57    o pkg/thsice with pkg/seaice dynamics:
58    - fix domain of computation (interior only, required for exf) and do exchanges
59    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
60    o towards a standard way of dealing with multi-threading in MONITOR
61      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
62    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
63       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
64    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
65    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
66    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
67       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
68    o tracer advection:
69     - clean-up and simplify calc_common_factors.F
70     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
71       advection subroutine (but still not used within DST advection S/R)
72    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
73    
74    checkpoint58j_post
75    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
76      from file (collects calls previously in FORWARD_STEP)
77    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
78    o adjoint store dir. adjusted accordingly
79    o genmake2
80      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
81    
82    checkpoint58i_post
83    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
84      on wind stress (SEAICEstressFactor defaults to 1.)
85    o Total number of Timers is finite (<=40): comment out 2 non-essential one
86      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
87    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
88      on CS-grid: no longer loosing mass.
89    o exf & curvilinear-grid: no longer modify longitude xC & xG.
90    o pkg/ggl90: fix sloppy output and fix a bug
91    o pkg/seaice: added SEAICEuseEVPpickup parameter
92      - Set to false in order to start EVP solver with
93        non-EVP pickup files when using SEAICEuseEVP
94      - fix sign error in diffusion in seaice_calc_rhs
95    
96    checkpoint58h_post
97    * Modifications for bottom topography control
98      o replace hFacC by _hFacC at various places
99      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
100      o add non-self-adjoint cg2d_nsa
101      o update autodiff support routines
102      o re-initialise hfac after ctrl_depth_ini
103      o works for 5x5 box, doesnt work for global_ocean.90x40x15
104    * Adding verification for 5x5 box (4-layer) bottom topography control
105    
106    checkpoint58g_post
107    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
108       used for mean seasonal cycle, mean diurnal cycle); add an example
109       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
110    o pkg/ggl90:
111      - add parameter (minimum surface kinetic energy)
112      - fix bug (avoiding division by zero)
113    o couple pkg/thsice to pkg/seaice:
114      - modify advection in seaice to accomodate new scalar fields to be advected
115      - only muliDimAdection scheme work with seaice/thsice
116      - mapping of thsice-variables to seaice-variables, back and forth
117      - does not break the verification experiments, but does not give the
118        desired results either
119    o pkg/seaice
120      - make (default) second order advection a bit less confusing?
121    
122    checkpoint58f_post
123    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
124      to pkg/seaice):
125      - new routines thsice_map_exf and thsice_get_exf provide the interface
126      - add an additional formal parameter to thsice_solve4temp
127    o pkg/exf:
128      - add new fields wspeed, snowprecip (to be able to couple to thsice)
129      - correct Stefan-Boltzmann constant
130      - new parameter for longwave surface emittance
131      - separate some stuff from exf_bulkformulae into new routines  
132        exf_radiation, exf_wind
133      - add new parameters and constants: longwave emissivity for ocean, ice
134        and snow, evaporation parameters over ice
135      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
136        either wind from stress or stress from wind
137    o pkg/thSIce:
138    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
139    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
140       and THSICE_CALC_THICKN
141    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
142    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
143      to make debugging easier.
144    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
145    o pkg/bulk_force:
146      - clean-up comments and parameters ;
147      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
148    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
149      generate new output for test-experiment: aim.5l_cs.thSI
150    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
151      testreport accordingly
152    
153    checkpoint58e_post
154    o SEAICE_CGRID adjoint done
155    o R_STAR adjoint implemented.
156      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
157      * need to sort out init. of h0facc, etc.
158    o Make pkg/profile fully independent of ecco,cost, etc. stuff
159      to be able to use it in pure forward.
160    
161    checkpoint58d_post
162    o upgrade simple test-experiment to tutorial example:
163     step.1: duplicate the experiment and (step.2) will remove the old copy.
164      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
165      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
166      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
167      tutorial_global_oce_biogeo    <- copy of dic_example
168      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
169      tutorial_plume_on_slope       <- copy of plume_on_slope
170      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
171      tutorial_global_oce_optim     <- empty for now (David ?)
172      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
173     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
174    o correct a sign problem in cost_scat.F
175    o obcs and ptracers: fix boundary conditions for advections schemes
176      with larger stencil
177    o thsice adjoint: start
178    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
179      completeness
180    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
181      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
182    o ptracers adjoint:
183      * avoid extensive recomputatations
184      * fix missing re-init. of gptr (missed by TAF)
185    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
186      me to turn off the excessive output to STDOUT that this package produces
187    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
188      and add those terms in Vector-Invariant formulation.
189    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
190      if the control period (xx_hfluxperiod etc) is 0
191    o in profiles pkg, clean routines and fix details
192    o in ecco pkg, reading ssh data:
193      fix problem in case the model does not start at iter0=0
194    o fix mnc-pickup/restart for ptracers
195    o new package prifiles:
196      code to compute profile-based cost by Gael Forget
197      (modifs in ecco, ctrl, autodiff)
198    o Benign bug fix in initialization (spotted by M. Mazloff) of
199      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
200    
201    checkpoint58c_post
202    o adjoint: finish NLFS adjoint and provide reference output in
203      verification/global_ocean.90x40x15/results_ad_nlfs
204    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
205      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
206      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
207      with SEAICE_CGRID defined.
208    o move calendarDumps from "data" to "data.cal" and clean-up the code
209      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
210    o add useEXF & useCAL flags (for now, set in hard-coded way)
211    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
212      (were missing in NH mode, and wrong in quasihydrostatic mode).
213      waiting for Chris updated version of calc_gw to add those CALLs.
214    o fix bug in quasihydrostatic S/R ;
215      add a test for this option: global_ocean.90x40x15.qshyd
216    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
217      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
218    o add on/off flag useOffLine for package OFFLINE
219    o seaice:
220      - modify advection so that it works also on the C-grid
221      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
222        problem in multi-tile runs with C-grid
223      - add flags for clipping ice velocities and/or masking solver forcing
224      - fix drag (ocean on ice) formulation and a bug that caused noise in the
225        C-grid solver
226      - added a few comments to seaice_diffusion.F
227      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
228        are now exclusive)
229      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
230        required re-ordering the code a little:
231       + make DAIRN global variable (defined in SEAICE)
232       + move computation of the viscosities eta and zeta into a new separate
233         routine (because I need to recompute them in seaice_ocean_stress.F)
234    
235    checkpoint58b_post
236    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
237      update output.txt of exp. aim.5l_cs.thSI
238    o various mnc cleanups and improvements:
239      + shrink lookup tables by factor of ~4
240      + better error reporting when running out of lookup space
241      + able to handle longer path/file names (up to 500 chars)
242    o adjoint:
243      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
244      - TBD: "hidden" mom_vecinv recomp. in dynamics
245    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
246     (allow to differentiate between forcing components using new integer flags:
247      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
248     and add new flag to put Dissipation tendency out of Adams-Bashforth.
249    o ecco
250      - enable trend removal from SSH anomaly obs.
251    o adjoint
252      - a fix for PmEpR when #undef EXACT_CONSERV
253      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
254      - try to fix "hidden" recomp. in forward_step for NLFS
255        (NLFS seems broken sometimes after I checked it in)
256    o seaice:
257     - add c-grid version of the dynamic solver:
258       + three new routines that are the c-grid substitute lsr, dynsolver
259         and ostres
260       + put a few fields that were local to dynsolver into global common
261         blocks, so that I can move the computation of stresses etc into
262         seaice_lsr (saves coding but may break the adjoint).
263     - replace more hardwired parameters by runtime parameters
264     - add ice masks that mask the rhs of the implicit solvers where there
265       is no ice (commented out in seaice_dynsolver, because i am not sure
266       if this works properly), eventually this should replace the clipping
267       of ice velocities in seaice_dynsolver to +/-40cm/s.
268    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
269      include it only where its needed
270    o move balancing of fluxes before the call of external_forcing_surf
271    o seaice:
272      - correct units of turning angles (now they are really in degrees)
273      - move computation of GWATX/Y out of main routine into dynsolver
274      - initialize GWATX/Y in seaice_init
275    o Apply mask on Fresh-Water flux (needed for SSH forcing).
276      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
277    o seaice: add runtime flags for turning angles (default to zero)
278    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
279      and trend from exf forcing and ctrl control adjustments
280    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
281      (since checkpoint57x_post)
282    o change the default rotation period to 86164.s = the Earth rotation
283    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
284      and based on a reference stratification. Tested within hs94.cs-32x32x5.
285    o seaice advection: add code for choosing between the default (2nd order
286      central differences) and multiDim advection schemes provided by
287      pkg/generic_advdiff
288    o seaice:
289      - removed all references to SEAICE_GRID.h fields from
290        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
291        (cubed-sphere configuration will change a little)
292      - grid computations in seaice_init are obsolete now.
293      - cleaned up code a little so that is easier to read (hopefully).
294      - added new (better?) discretizations of default advection and diffusion
295        (turn on with SEAICEuseFluxForm)
296      - replace 1 in 3d global fields by kSurface in growth.F
297      
298    checkpoint58a_post
299    o seaice:
300      - bug fix in advect.F
301    o shelfice:
302      - separate shelfice load anomaly from pload (breaks with time
303        dependent forcing), => introduce constant field shelficeLoadAnomaly.
304        Its default is 0., but it may be computed more cleverly from (unknown)
305        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
306        done offline. A good approximation of the pressure load anomaly is
307        necessary to avoid large initial adjustment processes underneath
308        deep-reaching shelfice.
309      - small fix in ISOMIP shelfice_thermodynamics
310      - add more sophisticated thermodynamics of Hellmer (1989), this is
311        now the default
312      - give a few constants more intuitive names
313    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
314      if bulk formulae are used in long integration (especially EmPmR). Turn
315      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
316      if balancePrintMean, the imbalance that is substracted is printed to
317      STDOUT.
318    o fix bug (typo) in obcs_apply_eta.F
319    o add a new package shelfice which enables us to model the circulation
320      underneath shelf-ice with draughts of hundreds of meters.
321     - works
322     - to do: + include improved thermodynamics
323              + check whether kSurfC (from model/inc/SURFACE.h) can be used
324                instead of new field kTopC
325              + can we use topoFile, Ro_surf and existing code in ini_depth.F
326                instead of new field R_shelfIce and new code in ini_depth.F
327                and ini_mask_etc.F?
328              + adjust vertical mixing schemes?
329    o seaice pkg:
330     - add a cpp-flag to include a simple formula for a salinity dependent
331       freezing point of sea water at the surface
332     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
333       meridional stresses are now different (and hopefully correct)
334    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
335       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
336       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
337    o pkg/diagnostics: add options and parameters for regional-statistics
338       diagnostics ; define regions by reading a region-mask from a file
339       (might add other options later)
340    o pkg/bulk_force:
341     - add option and parameters to use AIM surface-flux formulae.
342     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
343       others forcing fields (defined in PARM05, parameter file "data") are loaded
344       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
345     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
346     - use the right EXCH call for uwind,vwind (to work on CS-grid).
347     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
348       and parameters (note: calcWindStress replaces .NOT.readwindstress).
349     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
350    
351  checkpoint58  checkpoint58
352  o add "--embed-source" option to genmake2 which, when the supporting  o add "--embed-source" option to genmake2 which, when the supporting
353    tools can be compiled (as determined by genmake2) will turn on the    tools can be compiled (as determined by genmake2) will turn on the

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