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revision 1.618 by jmc, Thu Mar 2 22:52:09 2006 UTC revision 1.727 by jmc, Thu Oct 5 18:44:20 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 pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
8    
9    checkpoint58p_post
10    o obcs: stop if obcs is used with useCDscheme = .true.
11    o shelfice:
12     - fix a sign error so that no slip at shelfice interface works
13     - remove stop for combination non-hydrostatic code and shelfice. That does
14       not mean, that the results are correct, but at least they are numerically
15       stable
16    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
17    o added adjoint exch routined for all exch*3d* routines
18      and updated flow directives
19    
20    checkpoint58o_post
21    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
22      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
23    o change controling S/R for writing pickup file (new S/R do_write_pickup)
24      and clean-up reading/writing of pickup files.
25    o fix local version of read/write pickup (NH part) in rotating_tank/code
26    o simplify EXCH interface:
27     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
28     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
29    o added the regrid package
30    o shelfice:
31     - add a simple boundary layer scheme to reduce noise
32     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
33    
34    checkpoint58n_post
35    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
36       local variable (not in common block).
37    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
38      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
39      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
40        to work with SingleCpuIO.
41    o add "_d 0" to real constant of pkg/cfc subroutines ;
42       update exp. cfc_exemple & tutorial_cfc_offline output files.
43    o multi-threading and IO:
44      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
45        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
46      - barrier before and after reading.
47      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
48      - avoid using MDS_WRITELOCAL for LAND pkg output.
49      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
50        common-block variables ; Allows multi-threading with master-thread IO.
51    o change default MAX_NO_THREADS from 32 to 4 ;
52      and stop cleanly when MAX_NO_THREADS is too small.
53    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
54    
55    checkpoint58m_post
56    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
57       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
58    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
59       keep global_ocean.90x40x15 (for AD testing) with former secondary test
60       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
61    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
62        add MITgcm_tutorials (= code + all the tutorials)
63    o ecco, option to compute cost for total ssh (mean+anom)
64    o consistent with addition of ptracer and ssh in pkg/profiles
65    o profiles: adding ptracer and ssh
66    o testreport: change multi-test output-file name
67      (from output.txt.{name} to output.{name}.txt)
68    o profiles: now ok for mutli-tiles case
69    o seaice: add 4 parameters for different advection schemes for area,
70      (effective) seaice thickness, enthalphy, and snow height. Their default
71      is the standard parameter SEAICEadvScheme
72    o calc_gw:
73     - add cosFacU in zonal viscous flux (harmonic.visc.).
74     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
75       of tutorial_plume_on_slope.
76    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
77    o calc_gw: true flux-form, account for horizontal grid spacing.
78      update rotating_tank results, but not plume_on_slope (affected at
79      truncation level, 11 digits).
80    
81    checkpoint58l_post
82    o calc_gw:
83     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
84     - remove side-drag for now (need to fix it); update plume_on_slope results.
85     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
86    o commit code to make SST/SSS weights spatially variable
87      (based on either variable in-situ or variable initial T/S weights)
88    o pkg/ecco:
89      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
90        now based on horizontally varying weights wthetaLev, wsaltLev
91      * cost_averagesflags now returns year indices in addition to day, month
92      * sflux balance is performed on annual basis
93        (sflxumm, sfluxmm2, bal_sfluxmm)
94      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
95        including separate counting and multipliers
96    o pkg/rbcs
97      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
98    
99    checkpoint58k_post
100    o testreport:
101     - always build in dir. "build" (if not there, mkdir build instead of building
102       & running in input)
103     - run in dir run (if it exists), in build otherwise.
104     - call prepare_run (if input/prepare_run exists)
105     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
106    o pkg/exf modifications to interpolation and rotation routines for more
107       reasonable treatment of North Pole singularity: for tracers North Pole
108       value is set to northernmost zonal-mean value, for zonal velocity it is
109       set to zero, and for meridional velocity it is set to northernmost value.
110    o pkg/exf/exf_check_range.F
111     - add tile index to diagnostics and move stop statement to the very
112       end of the routine.
113    o pkg/diagnostics: (diagnostics_main_init.F)
114      define title of isomorphic variables according to the current config.
115    o pkg/thsice with pkg/seaice dynamics:
116    - fix domain of computation (interior only, required for exf) and do exchanges
117    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
118    o towards a standard way of dealing with multi-threading in MONITOR
119      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
120    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
121       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
122    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
123    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
124    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
125       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
126    o tracer advection:
127     - clean-up and simplify calc_common_factors.F
128     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
129       advection subroutine (but still not used within DST advection S/R)
130    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
131    
132    checkpoint58j_post
133    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
134      from file (collects calls previously in FORWARD_STEP)
135    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
136    o adjoint store dir. adjusted accordingly
137    o genmake2
138      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
139    
140    checkpoint58i_post
141    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
142      on wind stress (SEAICEstressFactor defaults to 1.)
143    o Total number of Timers is finite (<=40): comment out 2 non-essential one
144      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
145    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
146      on CS-grid: no longer loosing mass.
147    o exf & curvilinear-grid: no longer modify longitude xC & xG.
148    o pkg/ggl90: fix sloppy output and fix a bug
149    o pkg/seaice: added SEAICEuseEVPpickup parameter
150      - Set to false in order to start EVP solver with
151        non-EVP pickup files when using SEAICEuseEVP
152      - fix sign error in diffusion in seaice_calc_rhs
153    
154    checkpoint58h_post
155    * Modifications for bottom topography control
156      o replace hFacC by _hFacC at various places
157      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
158      o add non-self-adjoint cg2d_nsa
159      o update autodiff support routines
160      o re-initialise hfac after ctrl_depth_ini
161      o works for 5x5 box, doesnt work for global_ocean.90x40x15
162    * Adding verification for 5x5 box (4-layer) bottom topography control
163    
164    checkpoint58g_post
165    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
166       used for mean seasonal cycle, mean diurnal cycle); add an example
167       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
168    o pkg/ggl90:
169      - add parameter (minimum surface kinetic energy)
170      - fix bug (avoiding division by zero)
171    o couple pkg/thsice to pkg/seaice:
172      - modify advection in seaice to accomodate new scalar fields to be advected
173      - only muliDimAdection scheme work with seaice/thsice
174      - mapping of thsice-variables to seaice-variables, back and forth
175      - does not break the verification experiments, but does not give the
176        desired results either
177    o pkg/seaice
178      - make (default) second order advection a bit less confusing?
179    
180    checkpoint58f_post
181    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
182      to pkg/seaice):
183      - new routines thsice_map_exf and thsice_get_exf provide the interface
184      - add an additional formal parameter to thsice_solve4temp
185    o pkg/exf:
186      - add new fields wspeed, snowprecip (to be able to couple to thsice)
187      - correct Stefan-Boltzmann constant
188      - new parameter for longwave surface emittance
189      - separate some stuff from exf_bulkformulae into new routines  
190        exf_radiation, exf_wind
191      - add new parameters and constants: longwave emissivity for ocean, ice
192        and snow, evaporation parameters over ice
193      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
194        either wind from stress or stress from wind
195    o pkg/thSIce:
196    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
197    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
198       and THSICE_CALC_THICKN
199    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
200    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
201      to make debugging easier.
202    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
203    o pkg/bulk_force:
204      - clean-up comments and parameters ;
205      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
206    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
207      generate new output for test-experiment: aim.5l_cs.thSI
208    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
209      testreport accordingly
210    
211    checkpoint58e_post
212    o SEAICE_CGRID adjoint done
213    o R_STAR adjoint implemented.
214      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
215      * need to sort out init. of h0facc, etc.
216    o Make pkg/profile fully independent of ecco,cost, etc. stuff
217      to be able to use it in pure forward.
218    
219    checkpoint58d_post
220    o upgrade simple test-experiment to tutorial example:
221     step.1: duplicate the experiment and (step.2) will remove the old copy.
222      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
223      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
224      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
225      tutorial_global_oce_biogeo    <- copy of dic_example
226      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
227      tutorial_plume_on_slope       <- copy of plume_on_slope
228      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
229      tutorial_global_oce_optim     <- empty for now (David ?)
230      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
231     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
232    o correct a sign problem in cost_scat.F
233    o obcs and ptracers: fix boundary conditions for advections schemes
234      with larger stencil
235    o thsice adjoint: start
236    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
237      completeness
238    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
239      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
240    o ptracers adjoint:
241      * avoid extensive recomputatations
242      * fix missing re-init. of gptr (missed by TAF)
243    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
244      me to turn off the excessive output to STDOUT that this package produces
245    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
246      and add those terms in Vector-Invariant formulation.
247    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
248      if the control period (xx_hfluxperiod etc) is 0
249    o in profiles pkg, clean routines and fix details
250    o in ecco pkg, reading ssh data:
251      fix problem in case the model does not start at iter0=0
252    o fix mnc-pickup/restart for ptracers
253    o new package prifiles:
254      code to compute profile-based cost by Gael Forget
255      (modifs in ecco, ctrl, autodiff)
256    o Benign bug fix in initialization (spotted by M. Mazloff) of
257      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
258    
259    checkpoint58c_post
260    o adjoint: finish NLFS adjoint and provide reference output in
261      verification/global_ocean.90x40x15/results_ad_nlfs
262    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
263      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
264      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
265      with SEAICE_CGRID defined.
266    o move calendarDumps from "data" to "data.cal" and clean-up the code
267      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
268    o add useEXF & useCAL flags (for now, set in hard-coded way)
269    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
270      (were missing in NH mode, and wrong in quasihydrostatic mode).
271      waiting for Chris updated version of calc_gw to add those CALLs.
272    o fix bug in quasihydrostatic S/R ;
273      add a test for this option: global_ocean.90x40x15.qshyd
274    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
275      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
276    o add on/off flag useOffLine for package OFFLINE
277    o seaice:
278      - modify advection so that it works also on the C-grid
279      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
280        problem in multi-tile runs with C-grid
281      - add flags for clipping ice velocities and/or masking solver forcing
282      - fix drag (ocean on ice) formulation and a bug that caused noise in the
283        C-grid solver
284      - added a few comments to seaice_diffusion.F
285      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
286        are now exclusive)
287      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
288        required re-ordering the code a little:
289       + make DAIRN global variable (defined in SEAICE)
290       + move computation of the viscosities eta and zeta into a new separate
291         routine (because I need to recompute them in seaice_ocean_stress.F)
292    
293    checkpoint58b_post
294    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
295      update output.txt of exp. aim.5l_cs.thSI
296    o various mnc cleanups and improvements:
297      + shrink lookup tables by factor of ~4
298      + better error reporting when running out of lookup space
299      + able to handle longer path/file names (up to 500 chars)
300    o adjoint:
301      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
302      - TBD: "hidden" mom_vecinv recomp. in dynamics
303    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
304     (allow to differentiate between forcing components using new integer flags:
305      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
306     and add new flag to put Dissipation tendency out of Adams-Bashforth.
307    o ecco
308      - enable trend removal from SSH anomaly obs.
309    o adjoint
310      - a fix for PmEpR when #undef EXACT_CONSERV
311      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
312      - try to fix "hidden" recomp. in forward_step for NLFS
313        (NLFS seems broken sometimes after I checked it in)
314    o seaice:
315     - add c-grid version of the dynamic solver:
316       + three new routines that are the c-grid substitute lsr, dynsolver
317         and ostres
318       + put a few fields that were local to dynsolver into global common
319         blocks, so that I can move the computation of stresses etc into
320         seaice_lsr (saves coding but may break the adjoint).
321     - replace more hardwired parameters by runtime parameters
322     - add ice masks that mask the rhs of the implicit solvers where there
323       is no ice (commented out in seaice_dynsolver, because i am not sure
324       if this works properly), eventually this should replace the clipping
325       of ice velocities in seaice_dynsolver to +/-40cm/s.
326    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
327      include it only where its needed
328    o move balancing of fluxes before the call of external_forcing_surf
329    o seaice:
330      - correct units of turning angles (now they are really in degrees)
331      - move computation of GWATX/Y out of main routine into dynsolver
332      - initialize GWATX/Y in seaice_init
333  o Apply mask on Fresh-Water flux (needed for SSH forcing).  o Apply mask on Fresh-Water flux (needed for SSH forcing).
334    update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)    update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
335  o seaice: add runtime flags for turning angles (default to zero)  o seaice: add runtime flags for turning angles (default to zero)
336  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
337    and trend from exf forcing and ctrl control adjustments    and trend from exf forcing and ctrl control adjustments

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