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revision 1.615 by jmc, Thu Mar 2 02:03:39 2006 UTC revision 1.721 by dfer, Tue Aug 29 18:10:03 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 diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
8    
9    checkpoint58o_post
10    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
11      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
12    o change controling S/R for writing pickup file (new S/R do_write_pickup)
13      and clean-up reading/writing of pickup files.
14    o fix local version of read/write pickup (NH part) in rotating_tank/code
15    o simplify EXCH interface:
16     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
17     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
18    o added the regrid package
19    o shelfice:
20     - add a simple boundary layer scheme to reduce noise
21     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
22    
23    checkpoint58n_post
24    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
25       local variable (not in common block).
26    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
27      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
28      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
29        to work with SingleCpuIO.
30    o add "_d 0" to real constant of pkg/cfc subroutines ;
31       update exp. cfc_exemple & tutorial_cfc_offline output files.
32    o multi-threading and IO:
33      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
34        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
35      - barrier before and after reading.
36      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
37      - avoid using MDS_WRITELOCAL for LAND pkg output.
38      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
39        common-block variables ; Allows multi-threading with master-thread IO.
40    o change default MAX_NO_THREADS from 32 to 4 ;
41      and stop cleanly when MAX_NO_THREADS is too small.
42    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
43    
44    checkpoint58m_post
45    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
46       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
47    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
48       keep global_ocean.90x40x15 (for AD testing) with former secondary test
49       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
50    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
51        add MITgcm_tutorials (= code + all the tutorials)
52    o ecco, option to compute cost for total ssh (mean+anom)
53    o consistent with addition of ptracer and ssh in pkg/profiles
54    o profiles: adding ptracer and ssh
55    o testreport: change multi-test output-file name
56      (from output.txt.{name} to output.{name}.txt)
57    o profiles: now ok for mutli-tiles case
58    o seaice: add 4 parameters for different advection schemes for area,
59      (effective) seaice thickness, enthalphy, and snow height. Their default
60      is the standard parameter SEAICEadvScheme
61    o calc_gw:
62     - add cosFacU in zonal viscous flux (harmonic.visc.).
63     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
64       of tutorial_plume_on_slope.
65    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
66    o calc_gw: true flux-form, account for horizontal grid spacing.
67      update rotating_tank results, but not plume_on_slope (affected at
68      truncation level, 11 digits).
69    
70    checkpoint58l_post
71    o calc_gw:
72     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
73     - remove side-drag for now (need to fix it); update plume_on_slope results.
74     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
75    o commit code to make SST/SSS weights spatially variable
76      (based on either variable in-situ or variable initial T/S weights)
77    o pkg/ecco:
78      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
79        now based on horizontally varying weights wthetaLev, wsaltLev
80      * cost_averagesflags now returns year indices in addition to day, month
81      * sflux balance is performed on annual basis
82        (sflxumm, sfluxmm2, bal_sfluxmm)
83      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
84        including separate counting and multipliers
85    o pkg/rbcs
86      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
87    
88    checkpoint58k_post
89    o testreport:
90     - always build in dir. "build" (if not there, mkdir build instead of building
91       & running in input)
92     - run in dir run (if it exists), in build otherwise.
93     - call prepare_run (if input/prepare_run exists)
94     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
95    o pkg/exf modifications to interpolation and rotation routines for more
96       reasonable treatment of North Pole singularity: for tracers North Pole
97       value is set to northernmost zonal-mean value, for zonal velocity it is
98       set to zero, and for meridional velocity it is set to northernmost value.
99    o pkg/exf/exf_check_range.F
100     - add tile index to diagnostics and move stop statement to the very
101       end of the routine.
102    o pkg/diagnostics: (diagnostics_main_init.F)
103      define title of isomorphic variables according to the current config.
104    o pkg/thsice with pkg/seaice dynamics:
105    - fix domain of computation (interior only, required for exf) and do exchanges
106    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
107    o towards a standard way of dealing with multi-threading in MONITOR
108      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
109    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
110       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
111    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
112    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
113    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
114       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
115    o tracer advection:
116     - clean-up and simplify calc_common_factors.F
117     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
118       advection subroutine (but still not used within DST advection S/R)
119    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
120    
121    checkpoint58j_post
122    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
123      from file (collects calls previously in FORWARD_STEP)
124    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
125    o adjoint store dir. adjusted accordingly
126    o genmake2
127      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
128    
129    checkpoint58i_post
130    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
131      on wind stress (SEAICEstressFactor defaults to 1.)
132    o Total number of Timers is finite (<=40): comment out 2 non-essential one
133      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
134    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
135      on CS-grid: no longer loosing mass.
136    o exf & curvilinear-grid: no longer modify longitude xC & xG.
137    o pkg/ggl90: fix sloppy output and fix a bug
138    o pkg/seaice: added SEAICEuseEVPpickup parameter
139      - Set to false in order to start EVP solver with
140        non-EVP pickup files when using SEAICEuseEVP
141      - fix sign error in diffusion in seaice_calc_rhs
142    
143    checkpoint58h_post
144    * Modifications for bottom topography control
145      o replace hFacC by _hFacC at various places
146      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
147      o add non-self-adjoint cg2d_nsa
148      o update autodiff support routines
149      o re-initialise hfac after ctrl_depth_ini
150      o works for 5x5 box, doesnt work for global_ocean.90x40x15
151    * Adding verification for 5x5 box (4-layer) bottom topography control
152    
153    checkpoint58g_post
154    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
155       used for mean seasonal cycle, mean diurnal cycle); add an example
156       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
157    o pkg/ggl90:
158      - add parameter (minimum surface kinetic energy)
159      - fix bug (avoiding division by zero)
160    o couple pkg/thsice to pkg/seaice:
161      - modify advection in seaice to accomodate new scalar fields to be advected
162      - only muliDimAdection scheme work with seaice/thsice
163      - mapping of thsice-variables to seaice-variables, back and forth
164      - does not break the verification experiments, but does not give the
165        desired results either
166    o pkg/seaice
167      - make (default) second order advection a bit less confusing?
168    
169    checkpoint58f_post
170    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
171      to pkg/seaice):
172      - new routines thsice_map_exf and thsice_get_exf provide the interface
173      - add an additional formal parameter to thsice_solve4temp
174    o pkg/exf:
175      - add new fields wspeed, snowprecip (to be able to couple to thsice)
176      - correct Stefan-Boltzmann constant
177      - new parameter for longwave surface emittance
178      - separate some stuff from exf_bulkformulae into new routines  
179        exf_radiation, exf_wind
180      - add new parameters and constants: longwave emissivity for ocean, ice
181        and snow, evaporation parameters over ice
182      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
183        either wind from stress or stress from wind
184    o pkg/thSIce:
185    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
186    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
187       and THSICE_CALC_THICKN
188    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
189    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
190      to make debugging easier.
191    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
192    o pkg/bulk_force:
193      - clean-up comments and parameters ;
194      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
195    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
196      generate new output for test-experiment: aim.5l_cs.thSI
197    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
198      testreport accordingly
199    
200    checkpoint58e_post
201    o SEAICE_CGRID adjoint done
202    o R_STAR adjoint implemented.
203      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
204      * need to sort out init. of h0facc, etc.
205    o Make pkg/profile fully independent of ecco,cost, etc. stuff
206      to be able to use it in pure forward.
207    
208    checkpoint58d_post
209    o upgrade simple test-experiment to tutorial example:
210     step.1: duplicate the experiment and (step.2) will remove the old copy.
211      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
212      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
213      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
214      tutorial_global_oce_biogeo    <- copy of dic_example
215      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
216      tutorial_plume_on_slope       <- copy of plume_on_slope
217      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
218      tutorial_global_oce_optim     <- empty for now (David ?)
219      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
220     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
221    o correct a sign problem in cost_scat.F
222    o obcs and ptracers: fix boundary conditions for advections schemes
223      with larger stencil
224    o thsice adjoint: start
225    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
226      completeness
227    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
228      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
229    o ptracers adjoint:
230      * avoid extensive recomputatations
231      * fix missing re-init. of gptr (missed by TAF)
232    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
233      me to turn off the excessive output to STDOUT that this package produces
234    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
235      and add those terms in Vector-Invariant formulation.
236    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
237      if the control period (xx_hfluxperiod etc) is 0
238    o in profiles pkg, clean routines and fix details
239    o in ecco pkg, reading ssh data:
240      fix problem in case the model does not start at iter0=0
241    o fix mnc-pickup/restart for ptracers
242    o new package prifiles:
243      code to compute profile-based cost by Gael Forget
244      (modifs in ecco, ctrl, autodiff)
245    o Benign bug fix in initialization (spotted by M. Mazloff) of
246      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
247    
248    checkpoint58c_post
249    o adjoint: finish NLFS adjoint and provide reference output in
250      verification/global_ocean.90x40x15/results_ad_nlfs
251    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
252      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
253      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
254      with SEAICE_CGRID defined.
255    o move calendarDumps from "data" to "data.cal" and clean-up the code
256      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
257    o add useEXF & useCAL flags (for now, set in hard-coded way)
258    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
259      (were missing in NH mode, and wrong in quasihydrostatic mode).
260      waiting for Chris updated version of calc_gw to add those CALLs.
261    o fix bug in quasihydrostatic S/R ;
262      add a test for this option: global_ocean.90x40x15.qshyd
263    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
264      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
265    o add on/off flag useOffLine for package OFFLINE
266    o seaice:
267      - modify advection so that it works also on the C-grid
268      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
269        problem in multi-tile runs with C-grid
270      - add flags for clipping ice velocities and/or masking solver forcing
271      - fix drag (ocean on ice) formulation and a bug that caused noise in the
272        C-grid solver
273      - added a few comments to seaice_diffusion.F
274      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
275        are now exclusive)
276      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
277        required re-ordering the code a little:
278       + make DAIRN global variable (defined in SEAICE)
279       + move computation of the viscosities eta and zeta into a new separate
280         routine (because I need to recompute them in seaice_ocean_stress.F)
281    
282    checkpoint58b_post
283    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
284      update output.txt of exp. aim.5l_cs.thSI
285    o various mnc cleanups and improvements:
286      + shrink lookup tables by factor of ~4
287      + better error reporting when running out of lookup space
288      + able to handle longer path/file names (up to 500 chars)
289    o adjoint:
290      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
291      - TBD: "hidden" mom_vecinv recomp. in dynamics
292    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
293     (allow to differentiate between forcing components using new integer flags:
294      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
295     and add new flag to put Dissipation tendency out of Adams-Bashforth.
296    o ecco
297      - enable trend removal from SSH anomaly obs.
298    o adjoint
299      - a fix for PmEpR when #undef EXACT_CONSERV
300      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
301      - try to fix "hidden" recomp. in forward_step for NLFS
302        (NLFS seems broken sometimes after I checked it in)
303    o seaice:
304     - add c-grid version of the dynamic solver:
305       + three new routines that are the c-grid substitute lsr, dynsolver
306         and ostres
307       + put a few fields that were local to dynsolver into global common
308         blocks, so that I can move the computation of stresses etc into
309         seaice_lsr (saves coding but may break the adjoint).
310     - replace more hardwired parameters by runtime parameters
311     - add ice masks that mask the rhs of the implicit solvers where there
312       is no ice (commented out in seaice_dynsolver, because i am not sure
313       if this works properly), eventually this should replace the clipping
314       of ice velocities in seaice_dynsolver to +/-40cm/s.
315    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
316      include it only where its needed
317    o move balancing of fluxes before the call of external_forcing_surf
318    o seaice:
319      - correct units of turning angles (now they are really in degrees)
320      - move computation of GWATX/Y out of main routine into dynsolver
321      - initialize GWATX/Y in seaice_init
322    o Apply mask on Fresh-Water flux (needed for SSH forcing).
323      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
324    o seaice: add runtime flags for turning angles (default to zero)
325    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
326      and trend from exf forcing and ctrl control adjustments
327    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
328      (since checkpoint57x_post)
329  o change the default rotation period to 86164.s = the Earth rotation  o change the default rotation period to 86164.s = the Earth rotation
330  o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)  o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
331    and based on a reference stratification. Tested within hs94.cs-32x32x5.    and based on a reference stratification. Tested within hs94.cs-32x32x5.

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