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revision 1.601 by jmc, Tue Jan 24 03:17:38 2006 UTC revision 1.722 by jmc, Thu Aug 31 15:33:43 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    
8    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
9    
10    checkpoint58o_post
11    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
12      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
13    o change controling S/R for writing pickup file (new S/R do_write_pickup)
14      and clean-up reading/writing of pickup files.
15    o fix local version of read/write pickup (NH part) in rotating_tank/code
16    o simplify EXCH interface:
17     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
18     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
19    o added the regrid package
20    o shelfice:
21     - add a simple boundary layer scheme to reduce noise
22     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
23    
24    checkpoint58n_post
25    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
26       local variable (not in common block).
27    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
28      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
29      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
30        to work with SingleCpuIO.
31    o add "_d 0" to real constant of pkg/cfc subroutines ;
32       update exp. cfc_exemple & tutorial_cfc_offline output files.
33    o multi-threading and IO:
34      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
35        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
36      - barrier before and after reading.
37      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
38      - avoid using MDS_WRITELOCAL for LAND pkg output.
39      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
40        common-block variables ; Allows multi-threading with master-thread IO.
41    o change default MAX_NO_THREADS from 32 to 4 ;
42      and stop cleanly when MAX_NO_THREADS is too small.
43    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
44    
45    checkpoint58m_post
46    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
47       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
48    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
49       keep global_ocean.90x40x15 (for AD testing) with former secondary test
50       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
51    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
52        add MITgcm_tutorials (= code + all the tutorials)
53    o ecco, option to compute cost for total ssh (mean+anom)
54    o consistent with addition of ptracer and ssh in pkg/profiles
55    o profiles: adding ptracer and ssh
56    o testreport: change multi-test output-file name
57      (from output.txt.{name} to output.{name}.txt)
58    o profiles: now ok for mutli-tiles case
59    o seaice: add 4 parameters for different advection schemes for area,
60      (effective) seaice thickness, enthalphy, and snow height. Their default
61      is the standard parameter SEAICEadvScheme
62    o calc_gw:
63     - add cosFacU in zonal viscous flux (harmonic.visc.).
64     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
65       of tutorial_plume_on_slope.
66    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
67    o calc_gw: true flux-form, account for horizontal grid spacing.
68      update rotating_tank results, but not plume_on_slope (affected at
69      truncation level, 11 digits).
70    
71    checkpoint58l_post
72    o calc_gw:
73     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
74     - remove side-drag for now (need to fix it); update plume_on_slope results.
75     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
76    o commit code to make SST/SSS weights spatially variable
77      (based on either variable in-situ or variable initial T/S weights)
78    o pkg/ecco:
79      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
80        now based on horizontally varying weights wthetaLev, wsaltLev
81      * cost_averagesflags now returns year indices in addition to day, month
82      * sflux balance is performed on annual basis
83        (sflxumm, sfluxmm2, bal_sfluxmm)
84      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
85        including separate counting and multipliers
86    o pkg/rbcs
87      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
88    
89    checkpoint58k_post
90    o testreport:
91     - always build in dir. "build" (if not there, mkdir build instead of building
92       & running in input)
93     - run in dir run (if it exists), in build otherwise.
94     - call prepare_run (if input/prepare_run exists)
95     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
96    o pkg/exf modifications to interpolation and rotation routines for more
97       reasonable treatment of North Pole singularity: for tracers North Pole
98       value is set to northernmost zonal-mean value, for zonal velocity it is
99       set to zero, and for meridional velocity it is set to northernmost value.
100    o pkg/exf/exf_check_range.F
101     - add tile index to diagnostics and move stop statement to the very
102       end of the routine.
103    o pkg/diagnostics: (diagnostics_main_init.F)
104      define title of isomorphic variables according to the current config.
105    o pkg/thsice with pkg/seaice dynamics:
106    - fix domain of computation (interior only, required for exf) and do exchanges
107    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
108    o towards a standard way of dealing with multi-threading in MONITOR
109      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
110    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
111       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
112    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
113    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
114    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
115       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
116    o tracer advection:
117     - clean-up and simplify calc_common_factors.F
118     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
119       advection subroutine (but still not used within DST advection S/R)
120    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
121    
122    checkpoint58j_post
123    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
124      from file (collects calls previously in FORWARD_STEP)
125    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
126    o adjoint store dir. adjusted accordingly
127    o genmake2
128      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
129    
130    checkpoint58i_post
131    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
132      on wind stress (SEAICEstressFactor defaults to 1.)
133    o Total number of Timers is finite (<=40): comment out 2 non-essential one
134      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
135    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
136      on CS-grid: no longer loosing mass.
137    o exf & curvilinear-grid: no longer modify longitude xC & xG.
138    o pkg/ggl90: fix sloppy output and fix a bug
139    o pkg/seaice: added SEAICEuseEVPpickup parameter
140      - Set to false in order to start EVP solver with
141        non-EVP pickup files when using SEAICEuseEVP
142      - fix sign error in diffusion in seaice_calc_rhs
143    
144    checkpoint58h_post
145    * Modifications for bottom topography control
146      o replace hFacC by _hFacC at various places
147      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
148      o add non-self-adjoint cg2d_nsa
149      o update autodiff support routines
150      o re-initialise hfac after ctrl_depth_ini
151      o works for 5x5 box, doesnt work for global_ocean.90x40x15
152    * Adding verification for 5x5 box (4-layer) bottom topography control
153    
154    checkpoint58g_post
155    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
156       used for mean seasonal cycle, mean diurnal cycle); add an example
157       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
158    o pkg/ggl90:
159      - add parameter (minimum surface kinetic energy)
160      - fix bug (avoiding division by zero)
161    o couple pkg/thsice to pkg/seaice:
162      - modify advection in seaice to accomodate new scalar fields to be advected
163      - only muliDimAdection scheme work with seaice/thsice
164      - mapping of thsice-variables to seaice-variables, back and forth
165      - does not break the verification experiments, but does not give the
166        desired results either
167    o pkg/seaice
168      - make (default) second order advection a bit less confusing?
169    
170    checkpoint58f_post
171    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
172      to pkg/seaice):
173      - new routines thsice_map_exf and thsice_get_exf provide the interface
174      - add an additional formal parameter to thsice_solve4temp
175    o pkg/exf:
176      - add new fields wspeed, snowprecip (to be able to couple to thsice)
177      - correct Stefan-Boltzmann constant
178      - new parameter for longwave surface emittance
179      - separate some stuff from exf_bulkformulae into new routines  
180        exf_radiation, exf_wind
181      - add new parameters and constants: longwave emissivity for ocean, ice
182        and snow, evaporation parameters over ice
183      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
184        either wind from stress or stress from wind
185    o pkg/thSIce:
186    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
187    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
188       and THSICE_CALC_THICKN
189    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
190    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
191      to make debugging easier.
192    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
193    o pkg/bulk_force:
194      - clean-up comments and parameters ;
195      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
196    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
197      generate new output for test-experiment: aim.5l_cs.thSI
198    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
199      testreport accordingly
200    
201    checkpoint58e_post
202    o SEAICE_CGRID adjoint done
203    o R_STAR adjoint implemented.
204      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
205      * need to sort out init. of h0facc, etc.
206    o Make pkg/profile fully independent of ecco,cost, etc. stuff
207      to be able to use it in pure forward.
208    
209    checkpoint58d_post
210    o upgrade simple test-experiment to tutorial example:
211     step.1: duplicate the experiment and (step.2) will remove the old copy.
212      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
213      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
214      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
215      tutorial_global_oce_biogeo    <- copy of dic_example
216      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
217      tutorial_plume_on_slope       <- copy of plume_on_slope
218      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
219      tutorial_global_oce_optim     <- empty for now (David ?)
220      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
221     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
222    o correct a sign problem in cost_scat.F
223    o obcs and ptracers: fix boundary conditions for advections schemes
224      with larger stencil
225    o thsice adjoint: start
226    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
227      completeness
228    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
229      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
230    o ptracers adjoint:
231      * avoid extensive recomputatations
232      * fix missing re-init. of gptr (missed by TAF)
233    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
234      me to turn off the excessive output to STDOUT that this package produces
235    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
236      and add those terms in Vector-Invariant formulation.
237    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
238      if the control period (xx_hfluxperiod etc) is 0
239    o in profiles pkg, clean routines and fix details
240    o in ecco pkg, reading ssh data:
241      fix problem in case the model does not start at iter0=0
242    o fix mnc-pickup/restart for ptracers
243    o new package prifiles:
244      code to compute profile-based cost by Gael Forget
245      (modifs in ecco, ctrl, autodiff)
246    o Benign bug fix in initialization (spotted by M. Mazloff) of
247      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
248    
249    checkpoint58c_post
250    o adjoint: finish NLFS adjoint and provide reference output in
251      verification/global_ocean.90x40x15/results_ad_nlfs
252    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
253      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
254      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
255      with SEAICE_CGRID defined.
256    o move calendarDumps from "data" to "data.cal" and clean-up the code
257      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
258    o add useEXF & useCAL flags (for now, set in hard-coded way)
259    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
260      (were missing in NH mode, and wrong in quasihydrostatic mode).
261      waiting for Chris updated version of calc_gw to add those CALLs.
262    o fix bug in quasihydrostatic S/R ;
263      add a test for this option: global_ocean.90x40x15.qshyd
264    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
265      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
266    o add on/off flag useOffLine for package OFFLINE
267    o seaice:
268      - modify advection so that it works also on the C-grid
269      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
270        problem in multi-tile runs with C-grid
271      - add flags for clipping ice velocities and/or masking solver forcing
272      - fix drag (ocean on ice) formulation and a bug that caused noise in the
273        C-grid solver
274      - added a few comments to seaice_diffusion.F
275      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
276        are now exclusive)
277      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
278        required re-ordering the code a little:
279       + make DAIRN global variable (defined in SEAICE)
280       + move computation of the viscosities eta and zeta into a new separate
281         routine (because I need to recompute them in seaice_ocean_stress.F)
282    
283    checkpoint58b_post
284    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
285      update output.txt of exp. aim.5l_cs.thSI
286    o various mnc cleanups and improvements:
287      + shrink lookup tables by factor of ~4
288      + better error reporting when running out of lookup space
289      + able to handle longer path/file names (up to 500 chars)
290    o adjoint:
291      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
292      - TBD: "hidden" mom_vecinv recomp. in dynamics
293    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
294     (allow to differentiate between forcing components using new integer flags:
295      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
296     and add new flag to put Dissipation tendency out of Adams-Bashforth.
297    o ecco
298      - enable trend removal from SSH anomaly obs.
299    o adjoint
300      - a fix for PmEpR when #undef EXACT_CONSERV
301      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
302      - try to fix "hidden" recomp. in forward_step for NLFS
303        (NLFS seems broken sometimes after I checked it in)
304    o seaice:
305     - add c-grid version of the dynamic solver:
306       + three new routines that are the c-grid substitute lsr, dynsolver
307         and ostres
308       + put a few fields that were local to dynsolver into global common
309         blocks, so that I can move the computation of stresses etc into
310         seaice_lsr (saves coding but may break the adjoint).
311     - replace more hardwired parameters by runtime parameters
312     - add ice masks that mask the rhs of the implicit solvers where there
313       is no ice (commented out in seaice_dynsolver, because i am not sure
314       if this works properly), eventually this should replace the clipping
315       of ice velocities in seaice_dynsolver to +/-40cm/s.
316    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
317      include it only where its needed
318    o move balancing of fluxes before the call of external_forcing_surf
319    o seaice:
320      - correct units of turning angles (now they are really in degrees)
321      - move computation of GWATX/Y out of main routine into dynsolver
322      - initialize GWATX/Y in seaice_init
323    o Apply mask on Fresh-Water flux (needed for SSH forcing).
324      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
325    o seaice: add runtime flags for turning angles (default to zero)
326    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
327      and trend from exf forcing and ctrl control adjustments
328    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
329      (since checkpoint57x_post)
330    o change the default rotation period to 86164.s = the Earth rotation
331    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
332      and based on a reference stratification. Tested within hs94.cs-32x32x5.
333    o seaice advection: add code for choosing between the default (2nd order
334      central differences) and multiDim advection schemes provided by
335      pkg/generic_advdiff
336    o seaice:
337      - removed all references to SEAICE_GRID.h fields from
338        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
339        (cubed-sphere configuration will change a little)
340      - grid computations in seaice_init are obsolete now.
341      - cleaned up code a little so that is easier to read (hopefully).
342      - added new (better?) discretizations of default advection and diffusion
343        (turn on with SEAICEuseFluxForm)
344      - replace 1 in 3d global fields by kSurface in growth.F
345      
346    checkpoint58a_post
347    o seaice:
348      - bug fix in advect.F
349    o shelfice:
350      - separate shelfice load anomaly from pload (breaks with time
351        dependent forcing), => introduce constant field shelficeLoadAnomaly.
352        Its default is 0., but it may be computed more cleverly from (unknown)
353        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
354        done offline. A good approximation of the pressure load anomaly is
355        necessary to avoid large initial adjustment processes underneath
356        deep-reaching shelfice.
357      - small fix in ISOMIP shelfice_thermodynamics
358      - add more sophisticated thermodynamics of Hellmer (1989), this is
359        now the default
360      - give a few constants more intuitive names
361    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
362      if bulk formulae are used in long integration (especially EmPmR). Turn
363      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
364      if balancePrintMean, the imbalance that is substracted is printed to
365      STDOUT.
366    o fix bug (typo) in obcs_apply_eta.F
367    o add a new package shelfice which enables us to model the circulation
368      underneath shelf-ice with draughts of hundreds of meters.
369     - works
370     - to do: + include improved thermodynamics
371              + check whether kSurfC (from model/inc/SURFACE.h) can be used
372                instead of new field kTopC
373              + can we use topoFile, Ro_surf and existing code in ini_depth.F
374                instead of new field R_shelfIce and new code in ini_depth.F
375                and ini_mask_etc.F?
376              + adjust vertical mixing schemes?
377    o seaice pkg:
378     - add a cpp-flag to include a simple formula for a salinity dependent
379       freezing point of sea water at the surface
380     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
381       meridional stresses are now different (and hopefully correct)
382    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
383       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
384       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
385  o pkg/diagnostics: add options and parameters for regional-statistics  o pkg/diagnostics: add options and parameters for regional-statistics
386     diagnostics ; define regions by reading a region-mask from a file     diagnostics ; define regions by reading a region-mask from a file
387     (might add other options later)     (might add other options later)

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