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revision 1.639 by heimbach, Thu Mar 23 23:08:09 2006 UTC revision 1.749 by mlosch, Thu Nov 23 10:03:44 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 new code to compute profile cost  o mom_common/vecinv/fluxform: fix a few initialisation isssues
8    by Gael Forget  o profiles: fix for multithreaded case
9    
10    o diagnostics: rename few diags:
11      s/'PRESSURE'/'RCENTER '/g
12      s/'TICE    '/'oceFreez'/g
13      s/'TAUX    '/'oceTAUX '/g
14      s/'TAUY    '/'oceTAUY '/g
15      s/'SWFLUX  '/'oceQsw  '/g
16      s/DIFx/DFxE/g
17      s/DIFy/DFyE/g
18      and add few ocean-forcing diagnostics:
19      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
20    o modifications to pkg/seaice/growth.F and budget.F, which change results of
21      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
22      as actual snow thickness.  It now refers everywhere to effective snow
23      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
24    
25    checkpoint58r_post
26    o modifications to pkg/seaice/growth.F, which change results of
27      lab_sea experiment: fixes pertain to melting snow over open water, to
28      masking EVAP under sea ice, and to using the correct AREA variable for
29      computations of EVAP, PRECIP, HSNOW, and GHEFF
30    o add ability to read bathy, salt, and theta using MNC (off by def)
31    o add flooding algorithm and advection of HSNOW for pkg/seaice;
32      both are turned off by default and do no change any results
33    o seaice advection with pkg/thsice: a step toward the use of non-linear
34      advection scheme, but #ifdef or commented out for now (requires more EXCH).
35    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
36      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
37      in natl_box (affects results @ truncation level: update output.txt)
38    o multi-threading and IO:
39      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
40      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
41        (needed to work with SingleCpuIO): tested in all verif. exp.
42    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
43      affects the results (but none of the verification test uses this scheme).
44    o Adding some pkg/diagnostics capability to pkg/seaice
45      (will certainly be subject to changes)
46    o ctrl: adding new control variables:
47      lwflux, lwdown, evap, snowprecip, apressure, runoff
48    
49    checkpoint58q_post
50    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
51      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
52      high_res_cube configuration by 4% on Columbia.
53    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
54      add (in global_with_exf/code) a version of EXF_INTERP_READ without
55      dynamical allocation (seems to work in multi-threaded).
56    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
57      single CPU io) so that TAF does not have to see EESUPPORT.h
58    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
59    
60    checkpoint58p_post
61    o obcs: stop if obcs is used with useCDscheme = .true.
62    o shelfice:
63     - fix a sign error so that no slip at shelfice interface works
64     - remove stop for combination non-hydrostatic code and shelfice. That does
65       not mean, that the results are correct, but at least they are numerically
66       stable
67    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
68    o added adjoint exch routined for all exch*3d* routines
69      and updated flow directives
70    
71    checkpoint58o_post
72    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
73      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
74    o change controling S/R for writing pickup file (new S/R do_write_pickup)
75      and clean-up reading/writing of pickup files.
76    o fix local version of read/write pickup (NH part) in rotating_tank/code
77    o simplify EXCH interface:
78     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
79     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
80    o added the regrid package
81    o shelfice:
82     - add a simple boundary layer scheme to reduce noise
83     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
84    
85    checkpoint58n_post
86    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
87       local variable (not in common block).
88    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
89      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
90      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
91        to work with SingleCpuIO.
92    o add "_d 0" to real constant of pkg/cfc subroutines ;
93       update exp. cfc_exemple & tutorial_cfc_offline output files.
94    o multi-threading and IO:
95      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
96        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
97      - barrier before and after reading.
98      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
99      - avoid using MDS_WRITELOCAL for LAND pkg output.
100      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
101        common-block variables ; Allows multi-threading with master-thread IO.
102    o change default MAX_NO_THREADS from 32 to 4 ;
103      and stop cleanly when MAX_NO_THREADS is too small.
104    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
105    
106    checkpoint58m_post
107    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
108       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
109    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
110       keep global_ocean.90x40x15 (for AD testing) with former secondary test
111       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
112    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
113        add MITgcm_tutorials (= code + all the tutorials)
114    o ecco, option to compute cost for total ssh (mean+anom)
115    o consistent with addition of ptracer and ssh in pkg/profiles
116    o profiles: adding ptracer and ssh
117    o testreport: change multi-test output-file name
118      (from output.txt.{name} to output.{name}.txt)
119    o profiles: now ok for mutli-tiles case
120    o seaice: add 4 parameters for different advection schemes for area,
121      (effective) seaice thickness, enthalphy, and snow height. Their default
122      is the standard parameter SEAICEadvScheme
123    o calc_gw:
124     - add cosFacU in zonal viscous flux (harmonic.visc.).
125     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
126       of tutorial_plume_on_slope.
127    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
128    o calc_gw: true flux-form, account for horizontal grid spacing.
129      update rotating_tank results, but not plume_on_slope (affected at
130      truncation level, 11 digits).
131    
132    checkpoint58l_post
133    o calc_gw:
134     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
135     - remove side-drag for now (need to fix it); update plume_on_slope results.
136     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
137    o commit code to make SST/SSS weights spatially variable
138      (based on either variable in-situ or variable initial T/S weights)
139    o pkg/ecco:
140      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
141        now based on horizontally varying weights wthetaLev, wsaltLev
142      * cost_averagesflags now returns year indices in addition to day, month
143      * sflux balance is performed on annual basis
144        (sflxumm, sfluxmm2, bal_sfluxmm)
145      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
146        including separate counting and multipliers
147    o pkg/rbcs
148      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
149    
150    checkpoint58k_post
151    o testreport:
152     - always build in dir. "build" (if not there, mkdir build instead of building
153       & running in input)
154     - run in dir run (if it exists), in build otherwise.
155     - call prepare_run (if input/prepare_run exists)
156     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
157    o pkg/exf modifications to interpolation and rotation routines for more
158       reasonable treatment of North Pole singularity: for tracers North Pole
159       value is set to northernmost zonal-mean value, for zonal velocity it is
160       set to zero, and for meridional velocity it is set to northernmost value.
161    o pkg/exf/exf_check_range.F
162     - add tile index to diagnostics and move stop statement to the very
163       end of the routine.
164    o pkg/diagnostics: (diagnostics_main_init.F)
165      define title of isomorphic variables according to the current config.
166    o pkg/thsice with pkg/seaice dynamics:
167    - fix domain of computation (interior only, required for exf) and do exchanges
168    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
169    o towards a standard way of dealing with multi-threading in MONITOR
170      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
171    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
172       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
173    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
174    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
175    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
176       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
177    o tracer advection:
178     - clean-up and simplify calc_common_factors.F
179     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
180       advection subroutine (but still not used within DST advection S/R)
181    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
182    
183    checkpoint58j_post
184    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
185      from file (collects calls previously in FORWARD_STEP)
186    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
187    o adjoint store dir. adjusted accordingly
188    o genmake2
189      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
190    
191    checkpoint58i_post
192    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
193      on wind stress (SEAICEstressFactor defaults to 1.)
194    o Total number of Timers is finite (<=40): comment out 2 non-essential one
195      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
196    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
197      on CS-grid: no longer loosing mass.
198    o exf & curvilinear-grid: no longer modify longitude xC & xG.
199    o pkg/ggl90: fix sloppy output and fix a bug
200    o pkg/seaice: added SEAICEuseEVPpickup parameter
201      - Set to false in order to start EVP solver with
202        non-EVP pickup files when using SEAICEuseEVP
203      - fix sign error in diffusion in seaice_calc_rhs
204    
205    checkpoint58h_post
206    * Modifications for bottom topography control
207      o replace hFacC by _hFacC at various places
208      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
209      o add non-self-adjoint cg2d_nsa
210      o update autodiff support routines
211      o re-initialise hfac after ctrl_depth_ini
212      o works for 5x5 box, doesnt work for global_ocean.90x40x15
213    * Adding verification for 5x5 box (4-layer) bottom topography control
214    
215    checkpoint58g_post
216    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
217       used for mean seasonal cycle, mean diurnal cycle); add an example
218       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
219    o pkg/ggl90:
220      - add parameter (minimum surface kinetic energy)
221      - fix bug (avoiding division by zero)
222    o couple pkg/thsice to pkg/seaice:
223      - modify advection in seaice to accomodate new scalar fields to be advected
224      - only muliDimAdection scheme work with seaice/thsice
225      - mapping of thsice-variables to seaice-variables, back and forth
226      - does not break the verification experiments, but does not give the
227        desired results either
228    o pkg/seaice
229      - make (default) second order advection a bit less confusing?
230    
231    checkpoint58f_post
232    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
233      to pkg/seaice):
234      - new routines thsice_map_exf and thsice_get_exf provide the interface
235      - add an additional formal parameter to thsice_solve4temp
236    o pkg/exf:
237      - add new fields wspeed, snowprecip (to be able to couple to thsice)
238      - correct Stefan-Boltzmann constant
239      - new parameter for longwave surface emittance
240      - separate some stuff from exf_bulkformulae into new routines  
241        exf_radiation, exf_wind
242      - add new parameters and constants: longwave emissivity for ocean, ice
243        and snow, evaporation parameters over ice
244      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
245        either wind from stress or stress from wind
246    o pkg/thSIce:
247    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
248    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
249       and THSICE_CALC_THICKN
250    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
251    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
252      to make debugging easier.
253    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
254    o pkg/bulk_force:
255      - clean-up comments and parameters ;
256      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
257    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
258      generate new output for test-experiment: aim.5l_cs.thSI
259    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
260      testreport accordingly
261    
262    checkpoint58e_post
263    o SEAICE_CGRID adjoint done
264    o R_STAR adjoint implemented.
265      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
266      * need to sort out init. of h0facc, etc.
267    o Make pkg/profile fully independent of ecco,cost, etc. stuff
268      to be able to use it in pure forward.
269    
270    checkpoint58d_post
271    o upgrade simple test-experiment to tutorial example:
272     step.1: duplicate the experiment and (step.2) will remove the old copy.
273      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
274      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
275      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
276      tutorial_global_oce_biogeo    <- copy of dic_example
277      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
278      tutorial_plume_on_slope       <- copy of plume_on_slope
279      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
280      tutorial_global_oce_optim     <- empty for now (David ?)
281      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
282     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
283    o correct a sign problem in cost_scat.F
284    o obcs and ptracers: fix boundary conditions for advections schemes
285      with larger stencil
286    o thsice adjoint: start
287    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
288      completeness
289    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
290      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
291    o ptracers adjoint:
292      * avoid extensive recomputatations
293      * fix missing re-init. of gptr (missed by TAF)
294    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
295      me to turn off the excessive output to STDOUT that this package produces
296    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
297      and add those terms in Vector-Invariant formulation.
298    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
299      if the control period (xx_hfluxperiod etc) is 0
300    o in profiles pkg, clean routines and fix details
301    o in ecco pkg, reading ssh data:
302      fix problem in case the model does not start at iter0=0
303    o fix mnc-pickup/restart for ptracers
304    o new package prifiles:
305      code to compute profile-based cost by Gael Forget
306    (modifs in ecco, ctrl, autodiff)    (modifs in ecco, ctrl, autodiff)
307    o Benign bug fix in initialization (spotted by M. Mazloff) of
308      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
309    
310  checkpoint58c_post  checkpoint58c_post
311  o adjoint: finish NLFS adjoint and provide reference output in  o adjoint: finish NLFS adjoint and provide reference output in

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