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revision 1.598 by edhill, Wed Jan 11 06:04:11 2006 UTC revision 1.713 by jmc, Mon Aug 14 00:43:23 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 fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
8       local variable (not in common block).
9    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
10      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
11      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
12        to work with SingleCpuIO.
13    o add "_d 0" to real constant of pkg/cfc subroutines ;
14       update exp. cfc_exemple & tutorial_cfc_offline output files.
15    o multi-threading and IO:
16      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
17        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
18      - barrier before and after reading.
19      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
20      - avoid using MDS_WRITELOCAL for LAND pkg output.
21      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
22        common-block variables ; Allows multi-threading with master-thread IO.
23    o change default MAX_NO_THREADS from 32 to 4 ;
24      and stop cleanly when MAX_NO_THREADS is too small.
25    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
26    
27    checkpoint58m_post
28    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
29       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
30    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
31       keep global_ocean.90x40x15 (for AD testing) with former secondary test
32       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
33    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
34        add MITgcm_tutorials (= code + all the tutorials)
35    o ecco, option to compute cost for total ssh (mean+anom)
36    o consistent with addition of ptracer and ssh in pkg/profiles
37    o profiles: adding ptracer and ssh
38    o testreport: change multi-test output-file name
39      (from output.txt.{name} to output.{name}.txt)
40    o profiles: now ok for mutli-tiles case
41    o seaice: add 4 parameters for different advection schemes for area,
42      (effective) seaice thickness, enthalphy, and snow height. Their default
43      is the standard parameter SEAICEadvScheme
44    o calc_gw:
45     - add cosFacU in zonal viscous flux (harmonic.visc.).
46     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
47       of tutorial_plume_on_slope.
48    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
49    o calc_gw: true flux-form, account for horizontal grid spacing.
50      update rotating_tank results, but not plume_on_slope (affected at
51      truncation level, 11 digits).
52    
53    checkpoint58l_post
54    o calc_gw:
55     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
56     - remove side-drag for now (need to fix it); update plume_on_slope results.
57     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
58    o commit code to make SST/SSS weights spatially variable
59      (based on either variable in-situ or variable initial T/S weights)
60    o pkg/ecco:
61      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
62        now based on horizontally varying weights wthetaLev, wsaltLev
63      * cost_averagesflags now returns year indices in addition to day, month
64      * sflux balance is performed on annual basis
65        (sflxumm, sfluxmm2, bal_sfluxmm)
66      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
67        including separate counting and multipliers
68    o pkg/rbcs
69      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
70    
71    checkpoint58k_post
72    o testreport:
73     - always build in dir. "build" (if not there, mkdir build instead of building
74       & running in input)
75     - run in dir run (if it exists), in build otherwise.
76     - call prepare_run (if input/prepare_run exists)
77     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
78    o pkg/exf modifications to interpolation and rotation routines for more
79       reasonable treatment of North Pole singularity: for tracers North Pole
80       value is set to northernmost zonal-mean value, for zonal velocity it is
81       set to zero, and for meridional velocity it is set to northernmost value.
82    o pkg/exf/exf_check_range.F
83     - add tile index to diagnostics and move stop statement to the very
84       end of the routine.
85    o pkg/diagnostics: (diagnostics_main_init.F)
86      define title of isomorphic variables according to the current config.
87    o pkg/thsice with pkg/seaice dynamics:
88    - fix domain of computation (interior only, required for exf) and do exchanges
89    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
90    o towards a standard way of dealing with multi-threading in MONITOR
91      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
92    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
93       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
94    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
95    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
96    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
97       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
98    o tracer advection:
99     - clean-up and simplify calc_common_factors.F
100     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
101       advection subroutine (but still not used within DST advection S/R)
102    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
103    
104    checkpoint58j_post
105    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
106      from file (collects calls previously in FORWARD_STEP)
107    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
108    o adjoint store dir. adjusted accordingly
109    o genmake2
110      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
111    
112    checkpoint58i_post
113    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
114      on wind stress (SEAICEstressFactor defaults to 1.)
115    o Total number of Timers is finite (<=40): comment out 2 non-essential one
116      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
117    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
118      on CS-grid: no longer loosing mass.
119    o exf & curvilinear-grid: no longer modify longitude xC & xG.
120    o pkg/ggl90: fix sloppy output and fix a bug
121    o pkg/seaice: added SEAICEuseEVPpickup parameter
122      - Set to false in order to start EVP solver with
123        non-EVP pickup files when using SEAICEuseEVP
124      - fix sign error in diffusion in seaice_calc_rhs
125    
126    checkpoint58h_post
127    * Modifications for bottom topography control
128      o replace hFacC by _hFacC at various places
129      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
130      o add non-self-adjoint cg2d_nsa
131      o update autodiff support routines
132      o re-initialise hfac after ctrl_depth_ini
133      o works for 5x5 box, doesnt work for global_ocean.90x40x15
134    * Adding verification for 5x5 box (4-layer) bottom topography control
135    
136    checkpoint58g_post
137    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
138       used for mean seasonal cycle, mean diurnal cycle); add an example
139       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
140    o pkg/ggl90:
141      - add parameter (minimum surface kinetic energy)
142      - fix bug (avoiding division by zero)
143    o couple pkg/thsice to pkg/seaice:
144      - modify advection in seaice to accomodate new scalar fields to be advected
145      - only muliDimAdection scheme work with seaice/thsice
146      - mapping of thsice-variables to seaice-variables, back and forth
147      - does not break the verification experiments, but does not give the
148        desired results either
149    o pkg/seaice
150      - make (default) second order advection a bit less confusing?
151    
152    checkpoint58f_post
153    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
154      to pkg/seaice):
155      - new routines thsice_map_exf and thsice_get_exf provide the interface
156      - add an additional formal parameter to thsice_solve4temp
157    o pkg/exf:
158      - add new fields wspeed, snowprecip (to be able to couple to thsice)
159      - correct Stefan-Boltzmann constant
160      - new parameter for longwave surface emittance
161      - separate some stuff from exf_bulkformulae into new routines  
162        exf_radiation, exf_wind
163      - add new parameters and constants: longwave emissivity for ocean, ice
164        and snow, evaporation parameters over ice
165      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
166        either wind from stress or stress from wind
167    o pkg/thSIce:
168    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
169    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
170       and THSICE_CALC_THICKN
171    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
172    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
173      to make debugging easier.
174    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
175    o pkg/bulk_force:
176      - clean-up comments and parameters ;
177      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
178    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
179      generate new output for test-experiment: aim.5l_cs.thSI
180    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
181      testreport accordingly
182    
183    checkpoint58e_post
184    o SEAICE_CGRID adjoint done
185    o R_STAR adjoint implemented.
186      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
187      * need to sort out init. of h0facc, etc.
188    o Make pkg/profile fully independent of ecco,cost, etc. stuff
189      to be able to use it in pure forward.
190    
191    checkpoint58d_post
192    o upgrade simple test-experiment to tutorial example:
193     step.1: duplicate the experiment and (step.2) will remove the old copy.
194      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
195      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
196      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
197      tutorial_global_oce_biogeo    <- copy of dic_example
198      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
199      tutorial_plume_on_slope       <- copy of plume_on_slope
200      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
201      tutorial_global_oce_optim     <- empty for now (David ?)
202      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
203     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
204    o correct a sign problem in cost_scat.F
205    o obcs and ptracers: fix boundary conditions for advections schemes
206      with larger stencil
207    o thsice adjoint: start
208    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
209      completeness
210    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
211      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
212    o ptracers adjoint:
213      * avoid extensive recomputatations
214      * fix missing re-init. of gptr (missed by TAF)
215    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
216      me to turn off the excessive output to STDOUT that this package produces
217    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
218      and add those terms in Vector-Invariant formulation.
219    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
220      if the control period (xx_hfluxperiod etc) is 0
221    o in profiles pkg, clean routines and fix details
222    o in ecco pkg, reading ssh data:
223      fix problem in case the model does not start at iter0=0
224    o fix mnc-pickup/restart for ptracers
225    o new package prifiles:
226      code to compute profile-based cost by Gael Forget
227      (modifs in ecco, ctrl, autodiff)
228    o Benign bug fix in initialization (spotted by M. Mazloff) of
229      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
230    
231    checkpoint58c_post
232    o adjoint: finish NLFS adjoint and provide reference output in
233      verification/global_ocean.90x40x15/results_ad_nlfs
234    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
235      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
236      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
237      with SEAICE_CGRID defined.
238    o move calendarDumps from "data" to "data.cal" and clean-up the code
239      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
240    o add useEXF & useCAL flags (for now, set in hard-coded way)
241    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
242      (were missing in NH mode, and wrong in quasihydrostatic mode).
243      waiting for Chris updated version of calc_gw to add those CALLs.
244    o fix bug in quasihydrostatic S/R ;
245      add a test for this option: global_ocean.90x40x15.qshyd
246    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
247      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
248    o add on/off flag useOffLine for package OFFLINE
249    o seaice:
250      - modify advection so that it works also on the C-grid
251      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
252        problem in multi-tile runs with C-grid
253      - add flags for clipping ice velocities and/or masking solver forcing
254      - fix drag (ocean on ice) formulation and a bug that caused noise in the
255        C-grid solver
256      - added a few comments to seaice_diffusion.F
257      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
258        are now exclusive)
259      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
260        required re-ordering the code a little:
261       + make DAIRN global variable (defined in SEAICE)
262       + move computation of the viscosities eta and zeta into a new separate
263         routine (because I need to recompute them in seaice_ocean_stress.F)
264    
265    checkpoint58b_post
266    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
267      update output.txt of exp. aim.5l_cs.thSI
268    o various mnc cleanups and improvements:
269      + shrink lookup tables by factor of ~4
270      + better error reporting when running out of lookup space
271      + able to handle longer path/file names (up to 500 chars)
272    o adjoint:
273      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
274      - TBD: "hidden" mom_vecinv recomp. in dynamics
275    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
276     (allow to differentiate between forcing components using new integer flags:
277      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
278     and add new flag to put Dissipation tendency out of Adams-Bashforth.
279    o ecco
280      - enable trend removal from SSH anomaly obs.
281    o adjoint
282      - a fix for PmEpR when #undef EXACT_CONSERV
283      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
284      - try to fix "hidden" recomp. in forward_step for NLFS
285        (NLFS seems broken sometimes after I checked it in)
286    o seaice:
287     - add c-grid version of the dynamic solver:
288       + three new routines that are the c-grid substitute lsr, dynsolver
289         and ostres
290       + put a few fields that were local to dynsolver into global common
291         blocks, so that I can move the computation of stresses etc into
292         seaice_lsr (saves coding but may break the adjoint).
293     - replace more hardwired parameters by runtime parameters
294     - add ice masks that mask the rhs of the implicit solvers where there
295       is no ice (commented out in seaice_dynsolver, because i am not sure
296       if this works properly), eventually this should replace the clipping
297       of ice velocities in seaice_dynsolver to +/-40cm/s.
298    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
299      include it only where its needed
300    o move balancing of fluxes before the call of external_forcing_surf
301    o seaice:
302      - correct units of turning angles (now they are really in degrees)
303      - move computation of GWATX/Y out of main routine into dynsolver
304      - initialize GWATX/Y in seaice_init
305    o Apply mask on Fresh-Water flux (needed for SSH forcing).
306      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
307    o seaice: add runtime flags for turning angles (default to zero)
308    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
309      and trend from exf forcing and ctrl control adjustments
310    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
311      (since checkpoint57x_post)
312    o change the default rotation period to 86164.s = the Earth rotation
313    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
314      and based on a reference stratification. Tested within hs94.cs-32x32x5.
315    o seaice advection: add code for choosing between the default (2nd order
316      central differences) and multiDim advection schemes provided by
317      pkg/generic_advdiff
318    o seaice:
319      - removed all references to SEAICE_GRID.h fields from
320        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
321        (cubed-sphere configuration will change a little)
322      - grid computations in seaice_init are obsolete now.
323      - cleaned up code a little so that is easier to read (hopefully).
324      - added new (better?) discretizations of default advection and diffusion
325        (turn on with SEAICEuseFluxForm)
326      - replace 1 in 3d global fields by kSurface in growth.F
327      
328    checkpoint58a_post
329    o seaice:
330      - bug fix in advect.F
331    o shelfice:
332      - separate shelfice load anomaly from pload (breaks with time
333        dependent forcing), => introduce constant field shelficeLoadAnomaly.
334        Its default is 0., but it may be computed more cleverly from (unknown)
335        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
336        done offline. A good approximation of the pressure load anomaly is
337        necessary to avoid large initial adjustment processes underneath
338        deep-reaching shelfice.
339      - small fix in ISOMIP shelfice_thermodynamics
340      - add more sophisticated thermodynamics of Hellmer (1989), this is
341        now the default
342      - give a few constants more intuitive names
343    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
344      if bulk formulae are used in long integration (especially EmPmR). Turn
345      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
346      if balancePrintMean, the imbalance that is substracted is printed to
347      STDOUT.
348    o fix bug (typo) in obcs_apply_eta.F
349    o add a new package shelfice which enables us to model the circulation
350      underneath shelf-ice with draughts of hundreds of meters.
351     - works
352     - to do: + include improved thermodynamics
353              + check whether kSurfC (from model/inc/SURFACE.h) can be used
354                instead of new field kTopC
355              + can we use topoFile, Ro_surf and existing code in ini_depth.F
356                instead of new field R_shelfIce and new code in ini_depth.F
357                and ini_mask_etc.F?
358              + adjust vertical mixing schemes?
359    o seaice pkg:
360     - add a cpp-flag to include a simple formula for a salinity dependent
361       freezing point of sea water at the surface
362     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
363       meridional stresses are now different (and hopefully correct)
364    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
365       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
366       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
367    o pkg/diagnostics: add options and parameters for regional-statistics
368       diagnostics ; define regions by reading a region-mask from a file
369       (might add other options later)
370    o pkg/bulk_force:
371     - add option and parameters to use AIM surface-flux formulae.
372     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
373       others forcing fields (defined in PARM05, parameter file "data") are loaded
374       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
375     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
376     - use the right EXCH call for uwind,vwind (to work on CS-grid).
377     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
378       and parameters (note: calcWindStress replaces .NOT.readwindstress).
379     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
380    
381    checkpoint58
382  o add "--embed-source" option to genmake2 which, when the supporting  o add "--embed-source" option to genmake2 which, when the supporting
383    tools can be compiled (as determined by genmake2) will turn on the    tools can be compiled (as determined by genmake2) will turn on the
384    embed_files package which then embeds the entire MITgcm source code    embed_files package which then embeds the entire MITgcm source code

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