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revision 1.600 by jmc, Sun Jan 22 16:49:26 2006 UTC revision 1.716 by mlosch, Mon Aug 14 17:29:53 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 shelfice:
8     - add a simple boundary layer scheme to reduce noise
9     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
10    checkpoint58n_post
11    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
12       local variable (not in common block).
13    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
14      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
15      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
16        to work with SingleCpuIO.
17    o add "_d 0" to real constant of pkg/cfc subroutines ;
18       update exp. cfc_exemple & tutorial_cfc_offline output files.
19    o multi-threading and IO:
20      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
21        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
22      - barrier before and after reading.
23      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
24      - avoid using MDS_WRITELOCAL for LAND pkg output.
25      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
26        common-block variables ; Allows multi-threading with master-thread IO.
27    o change default MAX_NO_THREADS from 32 to 4 ;
28      and stop cleanly when MAX_NO_THREADS is too small.
29    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
30    
31    checkpoint58m_post
32    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
33       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
34    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
35       keep global_ocean.90x40x15 (for AD testing) with former secondary test
36       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
37    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
38        add MITgcm_tutorials (= code + all the tutorials)
39    o ecco, option to compute cost for total ssh (mean+anom)
40    o consistent with addition of ptracer and ssh in pkg/profiles
41    o profiles: adding ptracer and ssh
42    o testreport: change multi-test output-file name
43      (from output.txt.{name} to output.{name}.txt)
44    o profiles: now ok for mutli-tiles case
45    o seaice: add 4 parameters for different advection schemes for area,
46      (effective) seaice thickness, enthalphy, and snow height. Their default
47      is the standard parameter SEAICEadvScheme
48    o calc_gw:
49     - add cosFacU in zonal viscous flux (harmonic.visc.).
50     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
51       of tutorial_plume_on_slope.
52    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
53    o calc_gw: true flux-form, account for horizontal grid spacing.
54      update rotating_tank results, but not plume_on_slope (affected at
55      truncation level, 11 digits).
56    
57    checkpoint58l_post
58    o calc_gw:
59     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
60     - remove side-drag for now (need to fix it); update plume_on_slope results.
61     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
62    o commit code to make SST/SSS weights spatially variable
63      (based on either variable in-situ or variable initial T/S weights)
64    o pkg/ecco:
65      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
66        now based on horizontally varying weights wthetaLev, wsaltLev
67      * cost_averagesflags now returns year indices in addition to day, month
68      * sflux balance is performed on annual basis
69        (sflxumm, sfluxmm2, bal_sfluxmm)
70      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
71        including separate counting and multipliers
72    o pkg/rbcs
73      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
74    
75    checkpoint58k_post
76    o testreport:
77     - always build in dir. "build" (if not there, mkdir build instead of building
78       & running in input)
79     - run in dir run (if it exists), in build otherwise.
80     - call prepare_run (if input/prepare_run exists)
81     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
82    o pkg/exf modifications to interpolation and rotation routines for more
83       reasonable treatment of North Pole singularity: for tracers North Pole
84       value is set to northernmost zonal-mean value, for zonal velocity it is
85       set to zero, and for meridional velocity it is set to northernmost value.
86    o pkg/exf/exf_check_range.F
87     - add tile index to diagnostics and move stop statement to the very
88       end of the routine.
89    o pkg/diagnostics: (diagnostics_main_init.F)
90      define title of isomorphic variables according to the current config.
91    o pkg/thsice with pkg/seaice dynamics:
92    - fix domain of computation (interior only, required for exf) and do exchanges
93    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
94    o towards a standard way of dealing with multi-threading in MONITOR
95      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
96    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
97       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
98    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
99    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
100    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
101       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
102    o tracer advection:
103     - clean-up and simplify calc_common_factors.F
104     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
105       advection subroutine (but still not used within DST advection S/R)
106    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
107    
108    checkpoint58j_post
109    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
110      from file (collects calls previously in FORWARD_STEP)
111    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
112    o adjoint store dir. adjusted accordingly
113    o genmake2
114      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
115    
116    checkpoint58i_post
117    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
118      on wind stress (SEAICEstressFactor defaults to 1.)
119    o Total number of Timers is finite (<=40): comment out 2 non-essential one
120      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
121    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
122      on CS-grid: no longer loosing mass.
123    o exf & curvilinear-grid: no longer modify longitude xC & xG.
124    o pkg/ggl90: fix sloppy output and fix a bug
125    o pkg/seaice: added SEAICEuseEVPpickup parameter
126      - Set to false in order to start EVP solver with
127        non-EVP pickup files when using SEAICEuseEVP
128      - fix sign error in diffusion in seaice_calc_rhs
129    
130    checkpoint58h_post
131    * Modifications for bottom topography control
132      o replace hFacC by _hFacC at various places
133      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
134      o add non-self-adjoint cg2d_nsa
135      o update autodiff support routines
136      o re-initialise hfac after ctrl_depth_ini
137      o works for 5x5 box, doesnt work for global_ocean.90x40x15
138    * Adding verification for 5x5 box (4-layer) bottom topography control
139    
140    checkpoint58g_post
141    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
142       used for mean seasonal cycle, mean diurnal cycle); add an example
143       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
144    o pkg/ggl90:
145      - add parameter (minimum surface kinetic energy)
146      - fix bug (avoiding division by zero)
147    o couple pkg/thsice to pkg/seaice:
148      - modify advection in seaice to accomodate new scalar fields to be advected
149      - only muliDimAdection scheme work with seaice/thsice
150      - mapping of thsice-variables to seaice-variables, back and forth
151      - does not break the verification experiments, but does not give the
152        desired results either
153    o pkg/seaice
154      - make (default) second order advection a bit less confusing?
155    
156    checkpoint58f_post
157    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
158      to pkg/seaice):
159      - new routines thsice_map_exf and thsice_get_exf provide the interface
160      - add an additional formal parameter to thsice_solve4temp
161    o pkg/exf:
162      - add new fields wspeed, snowprecip (to be able to couple to thsice)
163      - correct Stefan-Boltzmann constant
164      - new parameter for longwave surface emittance
165      - separate some stuff from exf_bulkformulae into new routines  
166        exf_radiation, exf_wind
167      - add new parameters and constants: longwave emissivity for ocean, ice
168        and snow, evaporation parameters over ice
169      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
170        either wind from stress or stress from wind
171    o pkg/thSIce:
172    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
173    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
174       and THSICE_CALC_THICKN
175    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
176    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
177      to make debugging easier.
178    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
179    o pkg/bulk_force:
180      - clean-up comments and parameters ;
181      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
182    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
183      generate new output for test-experiment: aim.5l_cs.thSI
184    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
185      testreport accordingly
186    
187    checkpoint58e_post
188    o SEAICE_CGRID adjoint done
189    o R_STAR adjoint implemented.
190      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
191      * need to sort out init. of h0facc, etc.
192    o Make pkg/profile fully independent of ecco,cost, etc. stuff
193      to be able to use it in pure forward.
194    
195    checkpoint58d_post
196    o upgrade simple test-experiment to tutorial example:
197     step.1: duplicate the experiment and (step.2) will remove the old copy.
198      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
199      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
200      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
201      tutorial_global_oce_biogeo    <- copy of dic_example
202      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
203      tutorial_plume_on_slope       <- copy of plume_on_slope
204      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
205      tutorial_global_oce_optim     <- empty for now (David ?)
206      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
207     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
208    o correct a sign problem in cost_scat.F
209    o obcs and ptracers: fix boundary conditions for advections schemes
210      with larger stencil
211    o thsice adjoint: start
212    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
213      completeness
214    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
215      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
216    o ptracers adjoint:
217      * avoid extensive recomputatations
218      * fix missing re-init. of gptr (missed by TAF)
219    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
220      me to turn off the excessive output to STDOUT that this package produces
221    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
222      and add those terms in Vector-Invariant formulation.
223    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
224      if the control period (xx_hfluxperiod etc) is 0
225    o in profiles pkg, clean routines and fix details
226    o in ecco pkg, reading ssh data:
227      fix problem in case the model does not start at iter0=0
228    o fix mnc-pickup/restart for ptracers
229    o new package prifiles:
230      code to compute profile-based cost by Gael Forget
231      (modifs in ecco, ctrl, autodiff)
232    o Benign bug fix in initialization (spotted by M. Mazloff) of
233      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
234    
235    checkpoint58c_post
236    o adjoint: finish NLFS adjoint and provide reference output in
237      verification/global_ocean.90x40x15/results_ad_nlfs
238    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
239      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
240      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
241      with SEAICE_CGRID defined.
242    o move calendarDumps from "data" to "data.cal" and clean-up the code
243      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
244    o add useEXF & useCAL flags (for now, set in hard-coded way)
245    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
246      (were missing in NH mode, and wrong in quasihydrostatic mode).
247      waiting for Chris updated version of calc_gw to add those CALLs.
248    o fix bug in quasihydrostatic S/R ;
249      add a test for this option: global_ocean.90x40x15.qshyd
250    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
251      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
252    o add on/off flag useOffLine for package OFFLINE
253    o seaice:
254      - modify advection so that it works also on the C-grid
255      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
256        problem in multi-tile runs with C-grid
257      - add flags for clipping ice velocities and/or masking solver forcing
258      - fix drag (ocean on ice) formulation and a bug that caused noise in the
259        C-grid solver
260      - added a few comments to seaice_diffusion.F
261      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
262        are now exclusive)
263      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
264        required re-ordering the code a little:
265       + make DAIRN global variable (defined in SEAICE)
266       + move computation of the viscosities eta and zeta into a new separate
267         routine (because I need to recompute them in seaice_ocean_stress.F)
268    
269    checkpoint58b_post
270    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
271      update output.txt of exp. aim.5l_cs.thSI
272    o various mnc cleanups and improvements:
273      + shrink lookup tables by factor of ~4
274      + better error reporting when running out of lookup space
275      + able to handle longer path/file names (up to 500 chars)
276    o adjoint:
277      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
278      - TBD: "hidden" mom_vecinv recomp. in dynamics
279    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
280     (allow to differentiate between forcing components using new integer flags:
281      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
282     and add new flag to put Dissipation tendency out of Adams-Bashforth.
283    o ecco
284      - enable trend removal from SSH anomaly obs.
285    o adjoint
286      - a fix for PmEpR when #undef EXACT_CONSERV
287      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
288      - try to fix "hidden" recomp. in forward_step for NLFS
289        (NLFS seems broken sometimes after I checked it in)
290    o seaice:
291     - add c-grid version of the dynamic solver:
292       + three new routines that are the c-grid substitute lsr, dynsolver
293         and ostres
294       + put a few fields that were local to dynsolver into global common
295         blocks, so that I can move the computation of stresses etc into
296         seaice_lsr (saves coding but may break the adjoint).
297     - replace more hardwired parameters by runtime parameters
298     - add ice masks that mask the rhs of the implicit solvers where there
299       is no ice (commented out in seaice_dynsolver, because i am not sure
300       if this works properly), eventually this should replace the clipping
301       of ice velocities in seaice_dynsolver to +/-40cm/s.
302    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
303      include it only where its needed
304    o move balancing of fluxes before the call of external_forcing_surf
305    o seaice:
306      - correct units of turning angles (now they are really in degrees)
307      - move computation of GWATX/Y out of main routine into dynsolver
308      - initialize GWATX/Y in seaice_init
309    o Apply mask on Fresh-Water flux (needed for SSH forcing).
310      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
311    o seaice: add runtime flags for turning angles (default to zero)
312    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
313      and trend from exf forcing and ctrl control adjustments
314    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
315      (since checkpoint57x_post)
316    o change the default rotation period to 86164.s = the Earth rotation
317    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
318      and based on a reference stratification. Tested within hs94.cs-32x32x5.
319    o seaice advection: add code for choosing between the default (2nd order
320      central differences) and multiDim advection schemes provided by
321      pkg/generic_advdiff
322    o seaice:
323      - removed all references to SEAICE_GRID.h fields from
324        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
325        (cubed-sphere configuration will change a little)
326      - grid computations in seaice_init are obsolete now.
327      - cleaned up code a little so that is easier to read (hopefully).
328      - added new (better?) discretizations of default advection and diffusion
329        (turn on with SEAICEuseFluxForm)
330      - replace 1 in 3d global fields by kSurface in growth.F
331      
332    checkpoint58a_post
333    o seaice:
334      - bug fix in advect.F
335    o shelfice:
336      - separate shelfice load anomaly from pload (breaks with time
337        dependent forcing), => introduce constant field shelficeLoadAnomaly.
338        Its default is 0., but it may be computed more cleverly from (unknown)
339        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
340        done offline. A good approximation of the pressure load anomaly is
341        necessary to avoid large initial adjustment processes underneath
342        deep-reaching shelfice.
343      - small fix in ISOMIP shelfice_thermodynamics
344      - add more sophisticated thermodynamics of Hellmer (1989), this is
345        now the default
346      - give a few constants more intuitive names
347    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
348      if bulk formulae are used in long integration (especially EmPmR). Turn
349      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
350      if balancePrintMean, the imbalance that is substracted is printed to
351      STDOUT.
352    o fix bug (typo) in obcs_apply_eta.F
353    o add a new package shelfice which enables us to model the circulation
354      underneath shelf-ice with draughts of hundreds of meters.
355     - works
356     - to do: + include improved thermodynamics
357              + check whether kSurfC (from model/inc/SURFACE.h) can be used
358                instead of new field kTopC
359              + can we use topoFile, Ro_surf and existing code in ini_depth.F
360                instead of new field R_shelfIce and new code in ini_depth.F
361                and ini_mask_etc.F?
362              + adjust vertical mixing schemes?
363    o seaice pkg:
364     - add a cpp-flag to include a simple formula for a salinity dependent
365       freezing point of sea water at the surface
366     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
367       meridional stresses are now different (and hopefully correct)
368    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
369       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
370       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
371    o pkg/diagnostics: add options and parameters for regional-statistics
372       diagnostics ; define regions by reading a region-mask from a file
373       (might add other options later)
374  o pkg/bulk_force:  o pkg/bulk_force:
375   - add option and parameters to use AIM surface-flux formulae.   - add option and parameters to use AIM surface-flux formulae.
376   - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;   - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;

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