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revision 1.595 by heimbach, Thu Dec 22 21:16:17 2005 UTC revision 1.702 by jmc, Fri Jul 14 22:06:33 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 testreport: change multi-test output-file name
8      (from output.txt.{name} to output.{name}.txt)
9    o profiles: now ok for mutli-threaded case
10    o seaice: add 4 parameters for different advection schemes for area,
11      (effective) seaice thickness, enthalphy, and snow height. Their default
12      is the standard parameter SEAICEadvScheme
13    o calc_gw:
14     - add cosFacU in zonal viscous flux (harmonic.visc.).
15     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
16       of tutorial_plume_on_slope.
17    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
18    o calc_gw: true flux-form, account for horizontal grid spacing.
19      update rotating_tank results, but not plume_on_slope (affected at
20      truncation level, 11 digits).
21    
22    checkpoint58l_post
23    o calc_gw:
24     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
25     - remove side-drag for now (need to fix it); update plume_on_slope results.
26     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
27    o commit code to make SST/SSS weights spatially variable
28      (based on either variable in-situ or variable initial T/S weights)
29    o pkg/ecco:
30      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
31        now based on horizontally varying weights wthetaLev, wsaltLev
32      * cost_averagesflags now returns year indices in addition to day, month
33      * sflux balance is performed on annual basis
34        (sflxumm, sfluxmm2, bal_sfluxmm)
35      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
36        including separate counting and multipliers
37    o pkg/rbcs
38      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
39    
40    checkpoint58k_post
41    o testreport:
42     - always build in dir. "build" (if not there, mkdir build instead of building
43       & running in input)
44     - run in dir run (if it exists), in build otherwise.
45     - call prepare_run (if input/prepare_run exists)
46     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
47    o pkg/exf modifications to interpolation and rotation routines for more
48       reasonable treatment of North Pole singularity: for tracers North Pole
49       value is set to northernmost zonal-mean value, for zonal velocity it is
50       set to zero, and for meridional velocity it is set to northernmost value.
51    o pkg/exf/exf_check_range.F
52     - add tile index to diagnostics and move stop statement to the very
53       end of the routine.
54    o pkg/diagnostics: (diagnostics_main_init.F)
55      define title of isomorphic variables according to the current config.
56    o pkg/thsice with pkg/seaice dynamics:
57    - fix domain of computation (interior only, required for exf) and do exchanges
58    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
59    o towards a standard way of dealing with multi-threading in MONITOR
60      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
61    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
62       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
63    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
64    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
65    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
66       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
67    o tracer advection:
68     - clean-up and simplify calc_common_factors.F
69     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
70       advection subroutine (but still not used within DST advection S/R)
71    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
72    
73    checkpoint58j_post
74    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
75      from file (collects calls previously in FORWARD_STEP)
76    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
77    o adjoint store dir. adjusted accordingly
78    o genmake2
79      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
80    
81    checkpoint58i_post
82    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
83      on wind stress (SEAICEstressFactor defaults to 1.)
84    o Total number of Timers is finite (<=40): comment out 2 non-essential one
85      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
86    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
87      on CS-grid: no longer loosing mass.
88    o exf & curvilinear-grid: no longer modify longitude xC & xG.
89    o pkg/ggl90: fix sloppy output and fix a bug
90    o pkg/seaice: added SEAICEuseEVPpickup parameter
91      - Set to false in order to start EVP solver with
92        non-EVP pickup files when using SEAICEuseEVP
93      - fix sign error in diffusion in seaice_calc_rhs
94    
95    checkpoint58h_post
96    * Modifications for bottom topography control
97      o replace hFacC by _hFacC at various places
98      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
99      o add non-self-adjoint cg2d_nsa
100      o update autodiff support routines
101      o re-initialise hfac after ctrl_depth_ini
102      o works for 5x5 box, doesnt work for global_ocean.90x40x15
103    * Adding verification for 5x5 box (4-layer) bottom topography control
104    
105    checkpoint58g_post
106    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
107       used for mean seasonal cycle, mean diurnal cycle); add an example
108       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
109    o pkg/ggl90:
110      - add parameter (minimum surface kinetic energy)
111      - fix bug (avoiding division by zero)
112    o couple pkg/thsice to pkg/seaice:
113      - modify advection in seaice to accomodate new scalar fields to be advected
114      - only muliDimAdection scheme work with seaice/thsice
115      - mapping of thsice-variables to seaice-variables, back and forth
116      - does not break the verification experiments, but does not give the
117        desired results either
118    o pkg/seaice
119      - make (default) second order advection a bit less confusing?
120    
121    checkpoint58f_post
122    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
123      to pkg/seaice):
124      - new routines thsice_map_exf and thsice_get_exf provide the interface
125      - add an additional formal parameter to thsice_solve4temp
126    o pkg/exf:
127      - add new fields wspeed, snowprecip (to be able to couple to thsice)
128      - correct Stefan-Boltzmann constant
129      - new parameter for longwave surface emittance
130      - separate some stuff from exf_bulkformulae into new routines  
131        exf_radiation, exf_wind
132      - add new parameters and constants: longwave emissivity for ocean, ice
133        and snow, evaporation parameters over ice
134      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
135        either wind from stress or stress from wind
136    o pkg/thSIce:
137    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
138    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
139       and THSICE_CALC_THICKN
140    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
141    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
142      to make debugging easier.
143    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
144    o pkg/bulk_force:
145      - clean-up comments and parameters ;
146      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
147    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
148      generate new output for test-experiment: aim.5l_cs.thSI
149    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
150      testreport accordingly
151    
152    checkpoint58e_post
153    o SEAICE_CGRID adjoint done
154    o R_STAR adjoint implemented.
155      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
156      * need to sort out init. of h0facc, etc.
157    o Make pkg/profile fully independent of ecco,cost, etc. stuff
158      to be able to use it in pure forward.
159    
160    checkpoint58d_post
161    o upgrade simple test-experiment to tutorial example:
162     step.1: duplicate the experiment and (step.2) will remove the old copy.
163      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
164      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
165      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
166      tutorial_global_oce_biogeo    <- copy of dic_example
167      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
168      tutorial_plume_on_slope       <- copy of plume_on_slope
169      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
170      tutorial_global_oce_optim     <- empty for now (David ?)
171      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
172     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
173    o correct a sign problem in cost_scat.F
174    o obcs and ptracers: fix boundary conditions for advections schemes
175      with larger stencil
176    o thsice adjoint: start
177    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
178      completeness
179    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
180      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
181    o ptracers adjoint:
182      * avoid extensive recomputatations
183      * fix missing re-init. of gptr (missed by TAF)
184    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
185      me to turn off the excessive output to STDOUT that this package produces
186    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
187      and add those terms in Vector-Invariant formulation.
188    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
189      if the control period (xx_hfluxperiod etc) is 0
190    o in profiles pkg, clean routines and fix details
191    o in ecco pkg, reading ssh data:
192      fix problem in case the model does not start at iter0=0
193    o fix mnc-pickup/restart for ptracers
194    o new package prifiles:
195      code to compute profile-based cost by Gael Forget
196      (modifs in ecco, ctrl, autodiff)
197    o Benign bug fix in initialization (spotted by M. Mazloff) of
198      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
199    
200    checkpoint58c_post
201    o adjoint: finish NLFS adjoint and provide reference output in
202      verification/global_ocean.90x40x15/results_ad_nlfs
203    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
204      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
205      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
206      with SEAICE_CGRID defined.
207    o move calendarDumps from "data" to "data.cal" and clean-up the code
208      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
209    o add useEXF & useCAL flags (for now, set in hard-coded way)
210    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
211      (were missing in NH mode, and wrong in quasihydrostatic mode).
212      waiting for Chris updated version of calc_gw to add those CALLs.
213    o fix bug in quasihydrostatic S/R ;
214      add a test for this option: global_ocean.90x40x15.qshyd
215    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
216      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
217    o add on/off flag useOffLine for package OFFLINE
218    o seaice:
219      - modify advection so that it works also on the C-grid
220      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
221        problem in multi-tile runs with C-grid
222      - add flags for clipping ice velocities and/or masking solver forcing
223      - fix drag (ocean on ice) formulation and a bug that caused noise in the
224        C-grid solver
225      - added a few comments to seaice_diffusion.F
226      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
227        are now exclusive)
228      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
229        required re-ordering the code a little:
230       + make DAIRN global variable (defined in SEAICE)
231       + move computation of the viscosities eta and zeta into a new separate
232         routine (because I need to recompute them in seaice_ocean_stress.F)
233    
234    checkpoint58b_post
235    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
236      update output.txt of exp. aim.5l_cs.thSI
237    o various mnc cleanups and improvements:
238      + shrink lookup tables by factor of ~4
239      + better error reporting when running out of lookup space
240      + able to handle longer path/file names (up to 500 chars)
241    o adjoint:
242      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
243      - TBD: "hidden" mom_vecinv recomp. in dynamics
244    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
245     (allow to differentiate between forcing components using new integer flags:
246      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
247     and add new flag to put Dissipation tendency out of Adams-Bashforth.
248    o ecco
249      - enable trend removal from SSH anomaly obs.
250    o adjoint
251      - a fix for PmEpR when #undef EXACT_CONSERV
252      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
253      - try to fix "hidden" recomp. in forward_step for NLFS
254        (NLFS seems broken sometimes after I checked it in)
255    o seaice:
256     - add c-grid version of the dynamic solver:
257       + three new routines that are the c-grid substitute lsr, dynsolver
258         and ostres
259       + put a few fields that were local to dynsolver into global common
260         blocks, so that I can move the computation of stresses etc into
261         seaice_lsr (saves coding but may break the adjoint).
262     - replace more hardwired parameters by runtime parameters
263     - add ice masks that mask the rhs of the implicit solvers where there
264       is no ice (commented out in seaice_dynsolver, because i am not sure
265       if this works properly), eventually this should replace the clipping
266       of ice velocities in seaice_dynsolver to +/-40cm/s.
267    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
268      include it only where its needed
269    o move balancing of fluxes before the call of external_forcing_surf
270    o seaice:
271      - correct units of turning angles (now they are really in degrees)
272      - move computation of GWATX/Y out of main routine into dynsolver
273      - initialize GWATX/Y in seaice_init
274    o Apply mask on Fresh-Water flux (needed for SSH forcing).
275      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
276    o seaice: add runtime flags for turning angles (default to zero)
277    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
278      and trend from exf forcing and ctrl control adjustments
279    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
280      (since checkpoint57x_post)
281    o change the default rotation period to 86164.s = the Earth rotation
282    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
283      and based on a reference stratification. Tested within hs94.cs-32x32x5.
284    o seaice advection: add code for choosing between the default (2nd order
285      central differences) and multiDim advection schemes provided by
286      pkg/generic_advdiff
287    o seaice:
288      - removed all references to SEAICE_GRID.h fields from
289        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
290        (cubed-sphere configuration will change a little)
291      - grid computations in seaice_init are obsolete now.
292      - cleaned up code a little so that is easier to read (hopefully).
293      - added new (better?) discretizations of default advection and diffusion
294        (turn on with SEAICEuseFluxForm)
295      - replace 1 in 3d global fields by kSurface in growth.F
296      
297    checkpoint58a_post
298    o seaice:
299      - bug fix in advect.F
300    o shelfice:
301      - separate shelfice load anomaly from pload (breaks with time
302        dependent forcing), => introduce constant field shelficeLoadAnomaly.
303        Its default is 0., but it may be computed more cleverly from (unknown)
304        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
305        done offline. A good approximation of the pressure load anomaly is
306        necessary to avoid large initial adjustment processes underneath
307        deep-reaching shelfice.
308      - small fix in ISOMIP shelfice_thermodynamics
309      - add more sophisticated thermodynamics of Hellmer (1989), this is
310        now the default
311      - give a few constants more intuitive names
312    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
313      if bulk formulae are used in long integration (especially EmPmR). Turn
314      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
315      if balancePrintMean, the imbalance that is substracted is printed to
316      STDOUT.
317    o fix bug (typo) in obcs_apply_eta.F
318    o add a new package shelfice which enables us to model the circulation
319      underneath shelf-ice with draughts of hundreds of meters.
320     - works
321     - to do: + include improved thermodynamics
322              + check whether kSurfC (from model/inc/SURFACE.h) can be used
323                instead of new field kTopC
324              + can we use topoFile, Ro_surf and existing code in ini_depth.F
325                instead of new field R_shelfIce and new code in ini_depth.F
326                and ini_mask_etc.F?
327              + adjust vertical mixing schemes?
328    o seaice pkg:
329     - add a cpp-flag to include a simple formula for a salinity dependent
330       freezing point of sea water at the surface
331     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
332       meridional stresses are now different (and hopefully correct)
333    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
334       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
335       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
336    o pkg/diagnostics: add options and parameters for regional-statistics
337       diagnostics ; define regions by reading a region-mask from a file
338       (might add other options later)
339    o pkg/bulk_force:
340     - add option and parameters to use AIM surface-flux formulae.
341     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
342       others forcing fields (defined in PARM05, parameter file "data") are loaded
343       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
344     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
345     - use the right EXCH call for uwind,vwind (to work on CS-grid).
346     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
347       and parameters (note: calcWindStress replaces .NOT.readwindstress).
348     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
349    
350    checkpoint58
351    o add "--embed-source" option to genmake2 which, when the supporting
352      tools can be compiled (as determined by genmake2) will turn on the
353      embed_files package which then embeds the entire MITgcm source code
354      (*.[fFhc] + Makefile) used for the build within the executable
355      - requested by CNH but off by default
356      - adds a paltry <9MB to the mitgcmuv executable in most cases
357      - only writes the output when useEMBEDSRC in eedata is true
358    o clean up 3-dim. relaxation codes:
359      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
360      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
361      * Thanks to Tom Haine for testing!
362    
363    checkpoint57z_post
364  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
365    affects output (@ truncation level) of exp. plume_on_slope ; updated.    affects output (@ truncation level) of exp. plume_on_slope ; updated.
366  o fix the pickup behavior for obcs in combination with ptracers  o fix the pickup behavior for obcs in combination with ptracers

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