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revision 1.628 by jmc, Mon Mar 13 04:44:25 2006 UTC revision 1.752 by jmc, Tue Dec 5 22:15:47 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 CG2D: use pre-computed solver main-diagonal (stored in common block);
8      this affects truncation error ; generate new output file for exp. which
9      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
10        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
11        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
12        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
13        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
14        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
15    o start implementation of deep-atmosphere and anelastic formulation
16    o verification: remove 2nd copy of input files and use script "prepare_run"
17      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
18    o mom_common/vecinv/fluxform: fix a few initialisation isssues
19    o profiles: fix for multithreaded case
20    
21    o diagnostics: rename few diags:
22      s/'PRESSURE'/'RCENTER '/g
23      s/'TICE    '/'oceFreez'/g
24      s/'TAUX    '/'oceTAUX '/g
25      s/'TAUY    '/'oceTAUY '/g
26      s/'SWFLUX  '/'oceQsw  '/g
27      s/DIFx/DFxE/g
28      s/DIFy/DFyE/g
29      and add few ocean-forcing diagnostics:
30      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
31    o modifications to pkg/seaice/growth.F and budget.F, which change results of
32      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
33      as actual snow thickness.  It now refers everywhere to effective snow
34      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
35    
36    checkpoint58r_post
37    o modifications to pkg/seaice/growth.F, which change results of
38      lab_sea experiment: fixes pertain to melting snow over open water, to
39      masking EVAP under sea ice, and to using the correct AREA variable for
40      computations of EVAP, PRECIP, HSNOW, and GHEFF
41    o add ability to read bathy, salt, and theta using MNC (off by def)
42    o add flooding algorithm and advection of HSNOW for pkg/seaice;
43      both are turned off by default and do no change any results
44    o seaice advection with pkg/thsice: a step toward the use of non-linear
45      advection scheme, but #ifdef or commented out for now (requires more EXCH).
46    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
47      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
48      in natl_box (affects results @ truncation level: update output.txt)
49    o multi-threading and IO:
50      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
51      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
52        (needed to work with SingleCpuIO): tested in all verif. exp.
53    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
54      affects the results (but none of the verification test uses this scheme).
55    o Adding some pkg/diagnostics capability to pkg/seaice
56      (will certainly be subject to changes)
57    o ctrl: adding new control variables:
58      lwflux, lwdown, evap, snowprecip, apressure, runoff
59    
60    checkpoint58q_post
61    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
62      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
63      high_res_cube configuration by 4% on Columbia.
64    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
65      add (in global_with_exf/code) a version of EXF_INTERP_READ without
66      dynamical allocation (seems to work in multi-threaded).
67    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
68      single CPU io) so that TAF does not have to see EESUPPORT.h
69    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
70    
71    checkpoint58p_post
72    o obcs: stop if obcs is used with useCDscheme = .true.
73    o shelfice:
74     - fix a sign error so that no slip at shelfice interface works
75     - remove stop for combination non-hydrostatic code and shelfice. That does
76       not mean, that the results are correct, but at least they are numerically
77       stable
78    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
79    o added adjoint exch routined for all exch*3d* routines
80      and updated flow directives
81    
82    checkpoint58o_post
83    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
84      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
85    o change controling S/R for writing pickup file (new S/R do_write_pickup)
86      and clean-up reading/writing of pickup files.
87    o fix local version of read/write pickup (NH part) in rotating_tank/code
88    o simplify EXCH interface:
89     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
90     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
91    o added the regrid package
92    o shelfice:
93     - add a simple boundary layer scheme to reduce noise
94     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
95    
96    checkpoint58n_post
97    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
98       local variable (not in common block).
99    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
100      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
101      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
102        to work with SingleCpuIO.
103    o add "_d 0" to real constant of pkg/cfc subroutines ;
104       update exp. cfc_exemple & tutorial_cfc_offline output files.
105    o multi-threading and IO:
106      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
107        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
108      - barrier before and after reading.
109      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
110      - avoid using MDS_WRITELOCAL for LAND pkg output.
111      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
112        common-block variables ; Allows multi-threading with master-thread IO.
113    o change default MAX_NO_THREADS from 32 to 4 ;
114      and stop cleanly when MAX_NO_THREADS is too small.
115    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
116    
117    checkpoint58m_post
118    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
119       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
120    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
121       keep global_ocean.90x40x15 (for AD testing) with former secondary test
122       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
123    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
124        add MITgcm_tutorials (= code + all the tutorials)
125    o ecco, option to compute cost for total ssh (mean+anom)
126    o consistent with addition of ptracer and ssh in pkg/profiles
127    o profiles: adding ptracer and ssh
128    o testreport: change multi-test output-file name
129      (from output.txt.{name} to output.{name}.txt)
130    o profiles: now ok for mutli-tiles case
131    o seaice: add 4 parameters for different advection schemes for area,
132      (effective) seaice thickness, enthalphy, and snow height. Their default
133      is the standard parameter SEAICEadvScheme
134    o calc_gw:
135     - add cosFacU in zonal viscous flux (harmonic.visc.).
136     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
137       of tutorial_plume_on_slope.
138    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
139    o calc_gw: true flux-form, account for horizontal grid spacing.
140      update rotating_tank results, but not plume_on_slope (affected at
141      truncation level, 11 digits).
142    
143    checkpoint58l_post
144    o calc_gw:
145     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
146     - remove side-drag for now (need to fix it); update plume_on_slope results.
147     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
148    o commit code to make SST/SSS weights spatially variable
149      (based on either variable in-situ or variable initial T/S weights)
150    o pkg/ecco:
151      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
152        now based on horizontally varying weights wthetaLev, wsaltLev
153      * cost_averagesflags now returns year indices in addition to day, month
154      * sflux balance is performed on annual basis
155        (sflxumm, sfluxmm2, bal_sfluxmm)
156      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
157        including separate counting and multipliers
158    o pkg/rbcs
159      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
160    
161    checkpoint58k_post
162    o testreport:
163     - always build in dir. "build" (if not there, mkdir build instead of building
164       & running in input)
165     - run in dir run (if it exists), in build otherwise.
166     - call prepare_run (if input/prepare_run exists)
167     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
168    o pkg/exf modifications to interpolation and rotation routines for more
169       reasonable treatment of North Pole singularity: for tracers North Pole
170       value is set to northernmost zonal-mean value, for zonal velocity it is
171       set to zero, and for meridional velocity it is set to northernmost value.
172    o pkg/exf/exf_check_range.F
173     - add tile index to diagnostics and move stop statement to the very
174       end of the routine.
175    o pkg/diagnostics: (diagnostics_main_init.F)
176      define title of isomorphic variables according to the current config.
177    o pkg/thsice with pkg/seaice dynamics:
178    - fix domain of computation (interior only, required for exf) and do exchanges
179    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
180    o towards a standard way of dealing with multi-threading in MONITOR
181      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
182    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
183       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
184    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
185    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
186    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
187       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
188    o tracer advection:
189     - clean-up and simplify calc_common_factors.F
190     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
191       advection subroutine (but still not used within DST advection S/R)
192    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
193    
194    checkpoint58j_post
195    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
196      from file (collects calls previously in FORWARD_STEP)
197    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
198    o adjoint store dir. adjusted accordingly
199    o genmake2
200      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
201    
202    checkpoint58i_post
203    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
204      on wind stress (SEAICEstressFactor defaults to 1.)
205    o Total number of Timers is finite (<=40): comment out 2 non-essential one
206      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
207    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
208      on CS-grid: no longer loosing mass.
209    o exf & curvilinear-grid: no longer modify longitude xC & xG.
210    o pkg/ggl90: fix sloppy output and fix a bug
211    o pkg/seaice: added SEAICEuseEVPpickup parameter
212      - Set to false in order to start EVP solver with
213        non-EVP pickup files when using SEAICEuseEVP
214      - fix sign error in diffusion in seaice_calc_rhs
215    
216    checkpoint58h_post
217    * Modifications for bottom topography control
218      o replace hFacC by _hFacC at various places
219      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
220      o add non-self-adjoint cg2d_nsa
221      o update autodiff support routines
222      o re-initialise hfac after ctrl_depth_ini
223      o works for 5x5 box, doesnt work for global_ocean.90x40x15
224    * Adding verification for 5x5 box (4-layer) bottom topography control
225    
226    checkpoint58g_post
227    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
228       used for mean seasonal cycle, mean diurnal cycle); add an example
229       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
230    o pkg/ggl90:
231      - add parameter (minimum surface kinetic energy)
232      - fix bug (avoiding division by zero)
233    o couple pkg/thsice to pkg/seaice:
234      - modify advection in seaice to accomodate new scalar fields to be advected
235      - only muliDimAdection scheme work with seaice/thsice
236      - mapping of thsice-variables to seaice-variables, back and forth
237      - does not break the verification experiments, but does not give the
238        desired results either
239    o pkg/seaice
240      - make (default) second order advection a bit less confusing?
241    
242    checkpoint58f_post
243    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
244      to pkg/seaice):
245      - new routines thsice_map_exf and thsice_get_exf provide the interface
246      - add an additional formal parameter to thsice_solve4temp
247    o pkg/exf:
248      - add new fields wspeed, snowprecip (to be able to couple to thsice)
249      - correct Stefan-Boltzmann constant
250      - new parameter for longwave surface emittance
251      - separate some stuff from exf_bulkformulae into new routines  
252        exf_radiation, exf_wind
253      - add new parameters and constants: longwave emissivity for ocean, ice
254        and snow, evaporation parameters over ice
255      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
256        either wind from stress or stress from wind
257    o pkg/thSIce:
258    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
259    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
260       and THSICE_CALC_THICKN
261    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
262    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
263      to make debugging easier.
264    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
265    o pkg/bulk_force:
266      - clean-up comments and parameters ;
267      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
268    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
269      generate new output for test-experiment: aim.5l_cs.thSI
270    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
271      testreport accordingly
272    
273    checkpoint58e_post
274    o SEAICE_CGRID adjoint done
275    o R_STAR adjoint implemented.
276      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
277      * need to sort out init. of h0facc, etc.
278    o Make pkg/profile fully independent of ecco,cost, etc. stuff
279      to be able to use it in pure forward.
280    
281    checkpoint58d_post
282    o upgrade simple test-experiment to tutorial example:
283     step.1: duplicate the experiment and (step.2) will remove the old copy.
284      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
285      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
286      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
287      tutorial_global_oce_biogeo    <- copy of dic_example
288      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
289      tutorial_plume_on_slope       <- copy of plume_on_slope
290      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
291      tutorial_global_oce_optim     <- empty for now (David ?)
292      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
293     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
294    o correct a sign problem in cost_scat.F
295    o obcs and ptracers: fix boundary conditions for advections schemes
296      with larger stencil
297    o thsice adjoint: start
298    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
299      completeness
300    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
301      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
302    o ptracers adjoint:
303      * avoid extensive recomputatations
304      * fix missing re-init. of gptr (missed by TAF)
305    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
306      me to turn off the excessive output to STDOUT that this package produces
307    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
308      and add those terms in Vector-Invariant formulation.
309    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
310      if the control period (xx_hfluxperiod etc) is 0
311    o in profiles pkg, clean routines and fix details
312    o in ecco pkg, reading ssh data:
313      fix problem in case the model does not start at iter0=0
314    o fix mnc-pickup/restart for ptracers
315    o new package prifiles:
316      code to compute profile-based cost by Gael Forget
317      (modifs in ecco, ctrl, autodiff)
318    o Benign bug fix in initialization (spotted by M. Mazloff) of
319      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
320    
321    checkpoint58c_post
322    o adjoint: finish NLFS adjoint and provide reference output in
323      verification/global_ocean.90x40x15/results_ad_nlfs
324    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
325      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
326      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
327      with SEAICE_CGRID defined.
328    o move calendarDumps from "data" to "data.cal" and clean-up the code
329      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
330    o add useEXF & useCAL flags (for now, set in hard-coded way)
331    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
332      (were missing in NH mode, and wrong in quasihydrostatic mode).
333      waiting for Chris updated version of calc_gw to add those CALLs.
334    o fix bug in quasihydrostatic S/R ;
335      add a test for this option: global_ocean.90x40x15.qshyd
336    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
337      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
338    o add on/off flag useOffLine for package OFFLINE
339    o seaice:
340      - modify advection so that it works also on the C-grid
341      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
342        problem in multi-tile runs with C-grid
343      - add flags for clipping ice velocities and/or masking solver forcing
344      - fix drag (ocean on ice) formulation and a bug that caused noise in the
345        C-grid solver
346      - added a few comments to seaice_diffusion.F
347      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
348        are now exclusive)
349      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
350        required re-ordering the code a little:
351       + make DAIRN global variable (defined in SEAICE)
352       + move computation of the viscosities eta and zeta into a new separate
353         routine (because I need to recompute them in seaice_ocean_stress.F)
354    
355  checkpoint58b_post  checkpoint58b_post
356  o AIM+thSIce: fix sign of Short-Wave through the Ice ;  o AIM+thSIce: fix sign of Short-Wave through the Ice ;
357    update output.txt of exp. aim.5l_cs.thSI    update output.txt of exp. aim.5l_cs.thSI

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