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revision 1.617 by mlosch, Thu Mar 2 16:10:08 2006 UTC revision 1.737 by jmc, Sun Oct 22 02:02:07 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 GAD: use simpler DST3 formulation as default (old version left within #ifdef)
8      affects the results (but none of the verification test uses this scheme).
9    o Adding some pkg/diagnostics capability to pkg/seaice
10      (will certainly be subject to changes)
11    
12    checkpoint58q_post
13    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
14      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
15      high_res_cube configuration by 4% on Columbia.
16    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
17      add (in global_with_exf/code) a version of EXF_INTERP_READ without
18      dynamical allocation (seems to work in multi-threaded).
19    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
20      single CPU io) so that TAF does not have to see EESUPPORT.h
21    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
22    
23    checkpoint58p_post
24    o obcs: stop if obcs is used with useCDscheme = .true.
25    o shelfice:
26     - fix a sign error so that no slip at shelfice interface works
27     - remove stop for combination non-hydrostatic code and shelfice. That does
28       not mean, that the results are correct, but at least they are numerically
29       stable
30    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
31    o added adjoint exch routined for all exch*3d* routines
32      and updated flow directives
33    
34    checkpoint58o_post
35    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
36      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
37    o change controling S/R for writing pickup file (new S/R do_write_pickup)
38      and clean-up reading/writing of pickup files.
39    o fix local version of read/write pickup (NH part) in rotating_tank/code
40    o simplify EXCH interface:
41     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
42     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
43    o added the regrid package
44    o shelfice:
45     - add a simple boundary layer scheme to reduce noise
46     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
47    
48    checkpoint58n_post
49    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
50       local variable (not in common block).
51    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
52      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
53      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
54        to work with SingleCpuIO.
55    o add "_d 0" to real constant of pkg/cfc subroutines ;
56       update exp. cfc_exemple & tutorial_cfc_offline output files.
57    o multi-threading and IO:
58      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
59        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
60      - barrier before and after reading.
61      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
62      - avoid using MDS_WRITELOCAL for LAND pkg output.
63      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
64        common-block variables ; Allows multi-threading with master-thread IO.
65    o change default MAX_NO_THREADS from 32 to 4 ;
66      and stop cleanly when MAX_NO_THREADS is too small.
67    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
68    
69    checkpoint58m_post
70    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
71       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
72    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
73       keep global_ocean.90x40x15 (for AD testing) with former secondary test
74       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
75    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
76        add MITgcm_tutorials (= code + all the tutorials)
77    o ecco, option to compute cost for total ssh (mean+anom)
78    o consistent with addition of ptracer and ssh in pkg/profiles
79    o profiles: adding ptracer and ssh
80    o testreport: change multi-test output-file name
81      (from output.txt.{name} to output.{name}.txt)
82    o profiles: now ok for mutli-tiles case
83    o seaice: add 4 parameters for different advection schemes for area,
84      (effective) seaice thickness, enthalphy, and snow height. Their default
85      is the standard parameter SEAICEadvScheme
86    o calc_gw:
87     - add cosFacU in zonal viscous flux (harmonic.visc.).
88     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
89       of tutorial_plume_on_slope.
90    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
91    o calc_gw: true flux-form, account for horizontal grid spacing.
92      update rotating_tank results, but not plume_on_slope (affected at
93      truncation level, 11 digits).
94    
95    checkpoint58l_post
96    o calc_gw:
97     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
98     - remove side-drag for now (need to fix it); update plume_on_slope results.
99     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
100    o commit code to make SST/SSS weights spatially variable
101      (based on either variable in-situ or variable initial T/S weights)
102    o pkg/ecco:
103      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
104        now based on horizontally varying weights wthetaLev, wsaltLev
105      * cost_averagesflags now returns year indices in addition to day, month
106      * sflux balance is performed on annual basis
107        (sflxumm, sfluxmm2, bal_sfluxmm)
108      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
109        including separate counting and multipliers
110    o pkg/rbcs
111      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
112    
113    checkpoint58k_post
114    o testreport:
115     - always build in dir. "build" (if not there, mkdir build instead of building
116       & running in input)
117     - run in dir run (if it exists), in build otherwise.
118     - call prepare_run (if input/prepare_run exists)
119     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
120    o pkg/exf modifications to interpolation and rotation routines for more
121       reasonable treatment of North Pole singularity: for tracers North Pole
122       value is set to northernmost zonal-mean value, for zonal velocity it is
123       set to zero, and for meridional velocity it is set to northernmost value.
124    o pkg/exf/exf_check_range.F
125     - add tile index to diagnostics and move stop statement to the very
126       end of the routine.
127    o pkg/diagnostics: (diagnostics_main_init.F)
128      define title of isomorphic variables according to the current config.
129    o pkg/thsice with pkg/seaice dynamics:
130    - fix domain of computation (interior only, required for exf) and do exchanges
131    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
132    o towards a standard way of dealing with multi-threading in MONITOR
133      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
134    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
135       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
136    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
137    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
138    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
139       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
140    o tracer advection:
141     - clean-up and simplify calc_common_factors.F
142     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
143       advection subroutine (but still not used within DST advection S/R)
144    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
145    
146    checkpoint58j_post
147    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
148      from file (collects calls previously in FORWARD_STEP)
149    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
150    o adjoint store dir. adjusted accordingly
151    o genmake2
152      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
153    
154    checkpoint58i_post
155    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
156      on wind stress (SEAICEstressFactor defaults to 1.)
157    o Total number of Timers is finite (<=40): comment out 2 non-essential one
158      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
159    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
160      on CS-grid: no longer loosing mass.
161    o exf & curvilinear-grid: no longer modify longitude xC & xG.
162    o pkg/ggl90: fix sloppy output and fix a bug
163    o pkg/seaice: added SEAICEuseEVPpickup parameter
164      - Set to false in order to start EVP solver with
165        non-EVP pickup files when using SEAICEuseEVP
166      - fix sign error in diffusion in seaice_calc_rhs
167    
168    checkpoint58h_post
169    * Modifications for bottom topography control
170      o replace hFacC by _hFacC at various places
171      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
172      o add non-self-adjoint cg2d_nsa
173      o update autodiff support routines
174      o re-initialise hfac after ctrl_depth_ini
175      o works for 5x5 box, doesnt work for global_ocean.90x40x15
176    * Adding verification for 5x5 box (4-layer) bottom topography control
177    
178    checkpoint58g_post
179    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
180       used for mean seasonal cycle, mean diurnal cycle); add an example
181       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
182    o pkg/ggl90:
183      - add parameter (minimum surface kinetic energy)
184      - fix bug (avoiding division by zero)
185    o couple pkg/thsice to pkg/seaice:
186      - modify advection in seaice to accomodate new scalar fields to be advected
187      - only muliDimAdection scheme work with seaice/thsice
188      - mapping of thsice-variables to seaice-variables, back and forth
189      - does not break the verification experiments, but does not give the
190        desired results either
191    o pkg/seaice
192      - make (default) second order advection a bit less confusing?
193    
194    checkpoint58f_post
195    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
196      to pkg/seaice):
197      - new routines thsice_map_exf and thsice_get_exf provide the interface
198      - add an additional formal parameter to thsice_solve4temp
199    o pkg/exf:
200      - add new fields wspeed, snowprecip (to be able to couple to thsice)
201      - correct Stefan-Boltzmann constant
202      - new parameter for longwave surface emittance
203      - separate some stuff from exf_bulkformulae into new routines  
204        exf_radiation, exf_wind
205      - add new parameters and constants: longwave emissivity for ocean, ice
206        and snow, evaporation parameters over ice
207      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
208        either wind from stress or stress from wind
209    o pkg/thSIce:
210    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
211    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
212       and THSICE_CALC_THICKN
213    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
214    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
215      to make debugging easier.
216    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
217    o pkg/bulk_force:
218      - clean-up comments and parameters ;
219      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
220    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
221      generate new output for test-experiment: aim.5l_cs.thSI
222    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
223      testreport accordingly
224    
225    checkpoint58e_post
226    o SEAICE_CGRID adjoint done
227    o R_STAR adjoint implemented.
228      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
229      * need to sort out init. of h0facc, etc.
230    o Make pkg/profile fully independent of ecco,cost, etc. stuff
231      to be able to use it in pure forward.
232    
233    checkpoint58d_post
234    o upgrade simple test-experiment to tutorial example:
235     step.1: duplicate the experiment and (step.2) will remove the old copy.
236      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
237      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
238      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
239      tutorial_global_oce_biogeo    <- copy of dic_example
240      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
241      tutorial_plume_on_slope       <- copy of plume_on_slope
242      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
243      tutorial_global_oce_optim     <- empty for now (David ?)
244      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
245     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
246    o correct a sign problem in cost_scat.F
247    o obcs and ptracers: fix boundary conditions for advections schemes
248      with larger stencil
249    o thsice adjoint: start
250    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
251      completeness
252    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
253      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
254    o ptracers adjoint:
255      * avoid extensive recomputatations
256      * fix missing re-init. of gptr (missed by TAF)
257    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
258      me to turn off the excessive output to STDOUT that this package produces
259    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
260      and add those terms in Vector-Invariant formulation.
261    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
262      if the control period (xx_hfluxperiod etc) is 0
263    o in profiles pkg, clean routines and fix details
264    o in ecco pkg, reading ssh data:
265      fix problem in case the model does not start at iter0=0
266    o fix mnc-pickup/restart for ptracers
267    o new package prifiles:
268      code to compute profile-based cost by Gael Forget
269      (modifs in ecco, ctrl, autodiff)
270    o Benign bug fix in initialization (spotted by M. Mazloff) of
271      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
272    
273    checkpoint58c_post
274    o adjoint: finish NLFS adjoint and provide reference output in
275      verification/global_ocean.90x40x15/results_ad_nlfs
276    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
277      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
278      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
279      with SEAICE_CGRID defined.
280    o move calendarDumps from "data" to "data.cal" and clean-up the code
281      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
282    o add useEXF & useCAL flags (for now, set in hard-coded way)
283    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
284      (were missing in NH mode, and wrong in quasihydrostatic mode).
285      waiting for Chris updated version of calc_gw to add those CALLs.
286    o fix bug in quasihydrostatic S/R ;
287      add a test for this option: global_ocean.90x40x15.qshyd
288    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
289      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
290    o add on/off flag useOffLine for package OFFLINE
291    o seaice:
292      - modify advection so that it works also on the C-grid
293      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
294        problem in multi-tile runs with C-grid
295      - add flags for clipping ice velocities and/or masking solver forcing
296      - fix drag (ocean on ice) formulation and a bug that caused noise in the
297        C-grid solver
298      - added a few comments to seaice_diffusion.F
299      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
300        are now exclusive)
301      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
302        required re-ordering the code a little:
303       + make DAIRN global variable (defined in SEAICE)
304       + move computation of the viscosities eta and zeta into a new separate
305         routine (because I need to recompute them in seaice_ocean_stress.F)
306    
307    checkpoint58b_post
308    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
309      update output.txt of exp. aim.5l_cs.thSI
310    o various mnc cleanups and improvements:
311      + shrink lookup tables by factor of ~4
312      + better error reporting when running out of lookup space
313      + able to handle longer path/file names (up to 500 chars)
314    o adjoint:
315      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
316      - TBD: "hidden" mom_vecinv recomp. in dynamics
317    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
318     (allow to differentiate between forcing components using new integer flags:
319      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
320     and add new flag to put Dissipation tendency out of Adams-Bashforth.
321    o ecco
322      - enable trend removal from SSH anomaly obs.
323    o adjoint
324      - a fix for PmEpR when #undef EXACT_CONSERV
325      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
326      - try to fix "hidden" recomp. in forward_step for NLFS
327        (NLFS seems broken sometimes after I checked it in)
328    o seaice:
329     - add c-grid version of the dynamic solver:
330       + three new routines that are the c-grid substitute lsr, dynsolver
331         and ostres
332       + put a few fields that were local to dynsolver into global common
333         blocks, so that I can move the computation of stresses etc into
334         seaice_lsr (saves coding but may break the adjoint).
335     - replace more hardwired parameters by runtime parameters
336     - add ice masks that mask the rhs of the implicit solvers where there
337       is no ice (commented out in seaice_dynsolver, because i am not sure
338       if this works properly), eventually this should replace the clipping
339       of ice velocities in seaice_dynsolver to +/-40cm/s.
340    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
341      include it only where its needed
342    o move balancing of fluxes before the call of external_forcing_surf
343    o seaice:
344      - correct units of turning angles (now they are really in degrees)
345      - move computation of GWATX/Y out of main routine into dynsolver
346      - initialize GWATX/Y in seaice_init
347    o Apply mask on Fresh-Water flux (needed for SSH forcing).
348      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
349  o seaice: add runtime flags for turning angles (default to zero)  o seaice: add runtime flags for turning angles (default to zero)
350  o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean  o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
351    and trend from exf forcing and ctrl control adjustments    and trend from exf forcing and ctrl control adjustments

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