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revision 1.598 by edhill, Wed Jan 11 06:04:11 2006 UTC revision 1.709 by jmc, Sun Jul 30 01:04:07 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 change default MAX_NO_THREADS from 32 to 4 ;
8      and stop cleanly when MAX_NO_THREADS is too small.
9    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
10    
11    checkpoint58m_post
12    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
13       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
14    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
15       keep global_ocean.90x40x15 (for AD testing) with former secondary test
16       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
17    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
18        add MITgcm_tutorials (= code + all the tutorials)
19    o ecco, option to compute cost for total ssh (mean+anom)
20    o consistent with addition of ptracer and ssh in pkg/profiles
21    o profiles: adding ptracer and ssh
22    o testreport: change multi-test output-file name
23      (from output.txt.{name} to output.{name}.txt)
24    o profiles: now ok for mutli-threaded case
25    o seaice: add 4 parameters for different advection schemes for area,
26      (effective) seaice thickness, enthalphy, and snow height. Their default
27      is the standard parameter SEAICEadvScheme
28    o calc_gw:
29     - add cosFacU in zonal viscous flux (harmonic.visc.).
30     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
31       of tutorial_plume_on_slope.
32    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
33    o calc_gw: true flux-form, account for horizontal grid spacing.
34      update rotating_tank results, but not plume_on_slope (affected at
35      truncation level, 11 digits).
36    
37    checkpoint58l_post
38    o calc_gw:
39     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
40     - remove side-drag for now (need to fix it); update plume_on_slope results.
41     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
42    o commit code to make SST/SSS weights spatially variable
43      (based on either variable in-situ or variable initial T/S weights)
44    o pkg/ecco:
45      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
46        now based on horizontally varying weights wthetaLev, wsaltLev
47      * cost_averagesflags now returns year indices in addition to day, month
48      * sflux balance is performed on annual basis
49        (sflxumm, sfluxmm2, bal_sfluxmm)
50      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
51        including separate counting and multipliers
52    o pkg/rbcs
53      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
54    
55    checkpoint58k_post
56    o testreport:
57     - always build in dir. "build" (if not there, mkdir build instead of building
58       & running in input)
59     - run in dir run (if it exists), in build otherwise.
60     - call prepare_run (if input/prepare_run exists)
61     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
62    o pkg/exf modifications to interpolation and rotation routines for more
63       reasonable treatment of North Pole singularity: for tracers North Pole
64       value is set to northernmost zonal-mean value, for zonal velocity it is
65       set to zero, and for meridional velocity it is set to northernmost value.
66    o pkg/exf/exf_check_range.F
67     - add tile index to diagnostics and move stop statement to the very
68       end of the routine.
69    o pkg/diagnostics: (diagnostics_main_init.F)
70      define title of isomorphic variables according to the current config.
71    o pkg/thsice with pkg/seaice dynamics:
72    - fix domain of computation (interior only, required for exf) and do exchanges
73    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
74    o towards a standard way of dealing with multi-threading in MONITOR
75      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
76    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
77       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
78    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
79    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
80    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
81       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
82    o tracer advection:
83     - clean-up and simplify calc_common_factors.F
84     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
85       advection subroutine (but still not used within DST advection S/R)
86    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
87    
88    checkpoint58j_post
89    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
90      from file (collects calls previously in FORWARD_STEP)
91    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
92    o adjoint store dir. adjusted accordingly
93    o genmake2
94      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
95    
96    checkpoint58i_post
97    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
98      on wind stress (SEAICEstressFactor defaults to 1.)
99    o Total number of Timers is finite (<=40): comment out 2 non-essential one
100      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
101    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
102      on CS-grid: no longer loosing mass.
103    o exf & curvilinear-grid: no longer modify longitude xC & xG.
104    o pkg/ggl90: fix sloppy output and fix a bug
105    o pkg/seaice: added SEAICEuseEVPpickup parameter
106      - Set to false in order to start EVP solver with
107        non-EVP pickup files when using SEAICEuseEVP
108      - fix sign error in diffusion in seaice_calc_rhs
109    
110    checkpoint58h_post
111    * Modifications for bottom topography control
112      o replace hFacC by _hFacC at various places
113      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
114      o add non-self-adjoint cg2d_nsa
115      o update autodiff support routines
116      o re-initialise hfac after ctrl_depth_ini
117      o works for 5x5 box, doesnt work for global_ocean.90x40x15
118    * Adding verification for 5x5 box (4-layer) bottom topography control
119    
120    checkpoint58g_post
121    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
122       used for mean seasonal cycle, mean diurnal cycle); add an example
123       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
124    o pkg/ggl90:
125      - add parameter (minimum surface kinetic energy)
126      - fix bug (avoiding division by zero)
127    o couple pkg/thsice to pkg/seaice:
128      - modify advection in seaice to accomodate new scalar fields to be advected
129      - only muliDimAdection scheme work with seaice/thsice
130      - mapping of thsice-variables to seaice-variables, back and forth
131      - does not break the verification experiments, but does not give the
132        desired results either
133    o pkg/seaice
134      - make (default) second order advection a bit less confusing?
135    
136    checkpoint58f_post
137    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
138      to pkg/seaice):
139      - new routines thsice_map_exf and thsice_get_exf provide the interface
140      - add an additional formal parameter to thsice_solve4temp
141    o pkg/exf:
142      - add new fields wspeed, snowprecip (to be able to couple to thsice)
143      - correct Stefan-Boltzmann constant
144      - new parameter for longwave surface emittance
145      - separate some stuff from exf_bulkformulae into new routines  
146        exf_radiation, exf_wind
147      - add new parameters and constants: longwave emissivity for ocean, ice
148        and snow, evaporation parameters over ice
149      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
150        either wind from stress or stress from wind
151    o pkg/thSIce:
152    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
153    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
154       and THSICE_CALC_THICKN
155    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
156    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
157      to make debugging easier.
158    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
159    o pkg/bulk_force:
160      - clean-up comments and parameters ;
161      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
162    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
163      generate new output for test-experiment: aim.5l_cs.thSI
164    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
165      testreport accordingly
166    
167    checkpoint58e_post
168    o SEAICE_CGRID adjoint done
169    o R_STAR adjoint implemented.
170      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
171      * need to sort out init. of h0facc, etc.
172    o Make pkg/profile fully independent of ecco,cost, etc. stuff
173      to be able to use it in pure forward.
174    
175    checkpoint58d_post
176    o upgrade simple test-experiment to tutorial example:
177     step.1: duplicate the experiment and (step.2) will remove the old copy.
178      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
179      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
180      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
181      tutorial_global_oce_biogeo    <- copy of dic_example
182      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
183      tutorial_plume_on_slope       <- copy of plume_on_slope
184      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
185      tutorial_global_oce_optim     <- empty for now (David ?)
186      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
187     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
188    o correct a sign problem in cost_scat.F
189    o obcs and ptracers: fix boundary conditions for advections schemes
190      with larger stencil
191    o thsice adjoint: start
192    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
193      completeness
194    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
195      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
196    o ptracers adjoint:
197      * avoid extensive recomputatations
198      * fix missing re-init. of gptr (missed by TAF)
199    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
200      me to turn off the excessive output to STDOUT that this package produces
201    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
202      and add those terms in Vector-Invariant formulation.
203    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
204      if the control period (xx_hfluxperiod etc) is 0
205    o in profiles pkg, clean routines and fix details
206    o in ecco pkg, reading ssh data:
207      fix problem in case the model does not start at iter0=0
208    o fix mnc-pickup/restart for ptracers
209    o new package prifiles:
210      code to compute profile-based cost by Gael Forget
211      (modifs in ecco, ctrl, autodiff)
212    o Benign bug fix in initialization (spotted by M. Mazloff) of
213      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
214    
215    checkpoint58c_post
216    o adjoint: finish NLFS adjoint and provide reference output in
217      verification/global_ocean.90x40x15/results_ad_nlfs
218    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
219      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
220      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
221      with SEAICE_CGRID defined.
222    o move calendarDumps from "data" to "data.cal" and clean-up the code
223      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
224    o add useEXF & useCAL flags (for now, set in hard-coded way)
225    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
226      (were missing in NH mode, and wrong in quasihydrostatic mode).
227      waiting for Chris updated version of calc_gw to add those CALLs.
228    o fix bug in quasihydrostatic S/R ;
229      add a test for this option: global_ocean.90x40x15.qshyd
230    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
231      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
232    o add on/off flag useOffLine for package OFFLINE
233    o seaice:
234      - modify advection so that it works also on the C-grid
235      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
236        problem in multi-tile runs with C-grid
237      - add flags for clipping ice velocities and/or masking solver forcing
238      - fix drag (ocean on ice) formulation and a bug that caused noise in the
239        C-grid solver
240      - added a few comments to seaice_diffusion.F
241      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
242        are now exclusive)
243      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
244        required re-ordering the code a little:
245       + make DAIRN global variable (defined in SEAICE)
246       + move computation of the viscosities eta and zeta into a new separate
247         routine (because I need to recompute them in seaice_ocean_stress.F)
248    
249    checkpoint58b_post
250    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
251      update output.txt of exp. aim.5l_cs.thSI
252    o various mnc cleanups and improvements:
253      + shrink lookup tables by factor of ~4
254      + better error reporting when running out of lookup space
255      + able to handle longer path/file names (up to 500 chars)
256    o adjoint:
257      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
258      - TBD: "hidden" mom_vecinv recomp. in dynamics
259    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
260     (allow to differentiate between forcing components using new integer flags:
261      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
262     and add new flag to put Dissipation tendency out of Adams-Bashforth.
263    o ecco
264      - enable trend removal from SSH anomaly obs.
265    o adjoint
266      - a fix for PmEpR when #undef EXACT_CONSERV
267      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
268      - try to fix "hidden" recomp. in forward_step for NLFS
269        (NLFS seems broken sometimes after I checked it in)
270    o seaice:
271     - add c-grid version of the dynamic solver:
272       + three new routines that are the c-grid substitute lsr, dynsolver
273         and ostres
274       + put a few fields that were local to dynsolver into global common
275         blocks, so that I can move the computation of stresses etc into
276         seaice_lsr (saves coding but may break the adjoint).
277     - replace more hardwired parameters by runtime parameters
278     - add ice masks that mask the rhs of the implicit solvers where there
279       is no ice (commented out in seaice_dynsolver, because i am not sure
280       if this works properly), eventually this should replace the clipping
281       of ice velocities in seaice_dynsolver to +/-40cm/s.
282    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
283      include it only where its needed
284    o move balancing of fluxes before the call of external_forcing_surf
285    o seaice:
286      - correct units of turning angles (now they are really in degrees)
287      - move computation of GWATX/Y out of main routine into dynsolver
288      - initialize GWATX/Y in seaice_init
289    o Apply mask on Fresh-Water flux (needed for SSH forcing).
290      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
291    o seaice: add runtime flags for turning angles (default to zero)
292    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
293      and trend from exf forcing and ctrl control adjustments
294    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
295      (since checkpoint57x_post)
296    o change the default rotation period to 86164.s = the Earth rotation
297    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
298      and based on a reference stratification. Tested within hs94.cs-32x32x5.
299    o seaice advection: add code for choosing between the default (2nd order
300      central differences) and multiDim advection schemes provided by
301      pkg/generic_advdiff
302    o seaice:
303      - removed all references to SEAICE_GRID.h fields from
304        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
305        (cubed-sphere configuration will change a little)
306      - grid computations in seaice_init are obsolete now.
307      - cleaned up code a little so that is easier to read (hopefully).
308      - added new (better?) discretizations of default advection and diffusion
309        (turn on with SEAICEuseFluxForm)
310      - replace 1 in 3d global fields by kSurface in growth.F
311      
312    checkpoint58a_post
313    o seaice:
314      - bug fix in advect.F
315    o shelfice:
316      - separate shelfice load anomaly from pload (breaks with time
317        dependent forcing), => introduce constant field shelficeLoadAnomaly.
318        Its default is 0., but it may be computed more cleverly from (unknown)
319        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
320        done offline. A good approximation of the pressure load anomaly is
321        necessary to avoid large initial adjustment processes underneath
322        deep-reaching shelfice.
323      - small fix in ISOMIP shelfice_thermodynamics
324      - add more sophisticated thermodynamics of Hellmer (1989), this is
325        now the default
326      - give a few constants more intuitive names
327    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
328      if bulk formulae are used in long integration (especially EmPmR). Turn
329      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
330      if balancePrintMean, the imbalance that is substracted is printed to
331      STDOUT.
332    o fix bug (typo) in obcs_apply_eta.F
333    o add a new package shelfice which enables us to model the circulation
334      underneath shelf-ice with draughts of hundreds of meters.
335     - works
336     - to do: + include improved thermodynamics
337              + check whether kSurfC (from model/inc/SURFACE.h) can be used
338                instead of new field kTopC
339              + can we use topoFile, Ro_surf and existing code in ini_depth.F
340                instead of new field R_shelfIce and new code in ini_depth.F
341                and ini_mask_etc.F?
342              + adjust vertical mixing schemes?
343    o seaice pkg:
344     - add a cpp-flag to include a simple formula for a salinity dependent
345       freezing point of sea water at the surface
346     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
347       meridional stresses are now different (and hopefully correct)
348    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
349       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
350       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
351    o pkg/diagnostics: add options and parameters for regional-statistics
352       diagnostics ; define regions by reading a region-mask from a file
353       (might add other options later)
354    o pkg/bulk_force:
355     - add option and parameters to use AIM surface-flux formulae.
356     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
357       others forcing fields (defined in PARM05, parameter file "data") are loaded
358       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
359     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
360     - use the right EXCH call for uwind,vwind (to work on CS-grid).
361     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
362       and parameters (note: calcWindStress replaces .NOT.readwindstress).
363     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
364    
365    checkpoint58
366  o add "--embed-source" option to genmake2 which, when the supporting  o add "--embed-source" option to genmake2 which, when the supporting
367    tools can be compiled (as determined by genmake2) will turn on the    tools can be compiled (as determined by genmake2) will turn on the
368    embed_files package which then embeds the entire MITgcm source code    embed_files package which then embeds the entire MITgcm source code

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