/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.695 by heimbach, Fri Jul 7 21:56:15 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 adding precip control xx_precip  o take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
8  o moved ptracer ctrl index 17 -> 32  o commit code to make SST/SSS weights spatially variable
9      (based on either variable in-situ or variable initial T/S weights)
10    o commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
11      now based on horizontally varying weights wthetaLev, wsaltLev
12    
13    checkpoint58k_post
14    o testreport:
15     - always build in dir. "build" (if not there, mkdir build instead of building
16       & running in input)
17     - run in dir run (if it exists), in build otherwise.
18     - call prepare_run (if input/prepare_run exists)
19     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
20    o pkg/exf modifications to interpolation and rotation routines for more
21       reasonable treatment of North Pole singularity: for tracers North Pole
22       value is set to northernmost zonal-mean value, for zonal velocity it is
23       set to zero, and for meridional velocity it is set to northernmost value.
24    o pkg/exf/exf_check_range.F
25     - add tile index to diagnostics and move stop statement to the very
26       end of the routine.
27    o pkg/diagnostics: (diagnostics_main_init.F)
28      define title of isomorphic variables according to the current config.
29    o pkg/thsice with pkg/seaice dynamics:
30    - fix domain of computation (interior only, required for exf) and do exchanges
31    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
32    o towards a standard way of dealing with multi-threading in MONITOR
33      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
34    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
35       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
36    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
37    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
38    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
39       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
40    o tracer advection:
41     - clean-up and simplify calc_common_factors.F
42     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
43       advection subroutine (but still not used within DST advection S/R)
44    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
45    
46    checkpoint58j_post
47    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
48      from file (collects calls previously in FORWARD_STEP)
49    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
50    o adjoint store dir. adjusted accordingly
51    o genmake2
52      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
53    
54    checkpoint58i_post
55    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
56      on wind stress (SEAICEstressFactor defaults to 1.)
57    o Total number of Timers is finite (<=40): comment out 2 non-essential one
58      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
59    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
60      on CS-grid: no longer loosing mass.
61    o exf & curvilinear-grid: no longer modify longitude xC & xG.
62    o pkg/ggl90: fix sloppy output and fix a bug
63    o pkg/seaice: added SEAICEuseEVPpickup parameter
64      - Set to false in order to start EVP solver with
65        non-EVP pickup files when using SEAICEuseEVP
66      - fix sign error in diffusion in seaice_calc_rhs
67    
68    checkpoint58h_post
69    * Modifications for bottom topography control
70      o replace hFacC by _hFacC at various places
71      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
72      o add non-self-adjoint cg2d_nsa
73      o update autodiff support routines
74      o re-initialise hfac after ctrl_depth_ini
75      o works for 5x5 box, doesnt work for global_ocean.90x40x15
76    * Adding verification for 5x5 box (4-layer) bottom topography control
77    
78    checkpoint58g_post
79    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
80       used for mean seasonal cycle, mean diurnal cycle); add an example
81       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
82    o pkg/ggl90:
83      - add parameter (minimum surface kinetic energy)
84      - fix bug (avoiding division by zero)
85    o couple pkg/thsice to pkg/seaice:
86      - modify advection in seaice to accomodate new scalar fields to be advected
87      - only muliDimAdection scheme work with seaice/thsice
88      - mapping of thsice-variables to seaice-variables, back and forth
89      - does not break the verification experiments, but does not give the
90        desired results either
91    o pkg/seaice
92      - make (default) second order advection a bit less confusing?
93    
94    checkpoint58f_post
95    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
96      to pkg/seaice):
97      - new routines thsice_map_exf and thsice_get_exf provide the interface
98      - add an additional formal parameter to thsice_solve4temp
99    o pkg/exf:
100      - add new fields wspeed, snowprecip (to be able to couple to thsice)
101      - correct Stefan-Boltzmann constant
102      - new parameter for longwave surface emittance
103      - separate some stuff from exf_bulkformulae into new routines  
104        exf_radiation, exf_wind
105      - add new parameters and constants: longwave emissivity for ocean, ice
106        and snow, evaporation parameters over ice
107      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
108        either wind from stress or stress from wind
109    o pkg/thSIce:
110    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
111    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
112       and THSICE_CALC_THICKN
113    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
114    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
115      to make debugging easier.
116    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
117    o pkg/bulk_force:
118      - clean-up comments and parameters ;
119      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
120    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
121      generate new output for test-experiment: aim.5l_cs.thSI
122    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
123      testreport accordingly
124    
125    checkpoint58e_post
126    o SEAICE_CGRID adjoint done
127    o R_STAR adjoint implemented.
128      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
129      * need to sort out init. of h0facc, etc.
130    o Make pkg/profile fully independent of ecco,cost, etc. stuff
131      to be able to use it in pure forward.
132    
133    checkpoint58d_post
134    o upgrade simple test-experiment to tutorial example:
135     step.1: duplicate the experiment and (step.2) will remove the old copy.
136      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
137      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
138      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
139      tutorial_global_oce_biogeo    <- copy of dic_example
140      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
141      tutorial_plume_on_slope       <- copy of plume_on_slope
142      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
143      tutorial_global_oce_optim     <- empty for now (David ?)
144      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
145     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
146    o correct a sign problem in cost_scat.F
147    o obcs and ptracers: fix boundary conditions for advections schemes
148      with larger stencil
149    o thsice adjoint: start
150    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
151      completeness
152    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
153      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
154    o ptracers adjoint:
155      * avoid extensive recomputatations
156      * fix missing re-init. of gptr (missed by TAF)
157    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
158      me to turn off the excessive output to STDOUT that this package produces
159    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
160      and add those terms in Vector-Invariant formulation.
161    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
162      if the control period (xx_hfluxperiod etc) is 0
163    o in profiles pkg, clean routines and fix details
164    o in ecco pkg, reading ssh data:
165      fix problem in case the model does not start at iter0=0
166    o fix mnc-pickup/restart for ptracers
167    o new package prifiles:
168      code to compute profile-based cost by Gael Forget
169      (modifs in ecco, ctrl, autodiff)
170    o Benign bug fix in initialization (spotted by M. Mazloff) of
171      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
172    
173    checkpoint58c_post
174    o adjoint: finish NLFS adjoint and provide reference output in
175      verification/global_ocean.90x40x15/results_ad_nlfs
176    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
177      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
178      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
179      with SEAICE_CGRID defined.
180    o move calendarDumps from "data" to "data.cal" and clean-up the code
181      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
182    o add useEXF & useCAL flags (for now, set in hard-coded way)
183    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
184      (were missing in NH mode, and wrong in quasihydrostatic mode).
185      waiting for Chris updated version of calc_gw to add those CALLs.
186    o fix bug in quasihydrostatic S/R ;
187      add a test for this option: global_ocean.90x40x15.qshyd
188    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
189      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
190    o add on/off flag useOffLine for package OFFLINE
191    o seaice:
192      - modify advection so that it works also on the C-grid
193      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
194        problem in multi-tile runs with C-grid
195      - add flags for clipping ice velocities and/or masking solver forcing
196      - fix drag (ocean on ice) formulation and a bug that caused noise in the
197        C-grid solver
198      - added a few comments to seaice_diffusion.F
199      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
200        are now exclusive)
201      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
202        required re-ordering the code a little:
203       + make DAIRN global variable (defined in SEAICE)
204       + move computation of the viscosities eta and zeta into a new separate
205         routine (because I need to recompute them in seaice_ocean_stress.F)
206    
207    checkpoint58b_post
208    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
209      update output.txt of exp. aim.5l_cs.thSI
210    o various mnc cleanups and improvements:
211      + shrink lookup tables by factor of ~4
212      + better error reporting when running out of lookup space
213      + able to handle longer path/file names (up to 500 chars)
214    o adjoint:
215      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
216      - TBD: "hidden" mom_vecinv recomp. in dynamics
217    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
218     (allow to differentiate between forcing components using new integer flags:
219      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
220     and add new flag to put Dissipation tendency out of Adams-Bashforth.
221    o ecco
222      - enable trend removal from SSH anomaly obs.
223    o adjoint
224      - a fix for PmEpR when #undef EXACT_CONSERV
225      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
226      - try to fix "hidden" recomp. in forward_step for NLFS
227        (NLFS seems broken sometimes after I checked it in)
228    o seaice:
229     - add c-grid version of the dynamic solver:
230       + three new routines that are the c-grid substitute lsr, dynsolver
231         and ostres
232       + put a few fields that were local to dynsolver into global common
233         blocks, so that I can move the computation of stresses etc into
234         seaice_lsr (saves coding but may break the adjoint).
235     - replace more hardwired parameters by runtime parameters
236     - add ice masks that mask the rhs of the implicit solvers where there
237       is no ice (commented out in seaice_dynsolver, because i am not sure
238       if this works properly), eventually this should replace the clipping
239       of ice velocities in seaice_dynsolver to +/-40cm/s.
240    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
241      include it only where its needed
242    o move balancing of fluxes before the call of external_forcing_surf
243    o seaice:
244      - correct units of turning angles (now they are really in degrees)
245      - move computation of GWATX/Y out of main routine into dynsolver
246      - initialize GWATX/Y in seaice_init
247    o Apply mask on Fresh-Water flux (needed for SSH forcing).
248      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
249    o seaice: add runtime flags for turning angles (default to zero)
250    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
251      and trend from exf forcing and ctrl control adjustments
252    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
253      (since checkpoint57x_post)
254    o change the default rotation period to 86164.s = the Earth rotation
255    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
256      and based on a reference stratification. Tested within hs94.cs-32x32x5.
257    o seaice advection: add code for choosing between the default (2nd order
258      central differences) and multiDim advection schemes provided by
259      pkg/generic_advdiff
260    o seaice:
261      - removed all references to SEAICE_GRID.h fields from
262        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
263        (cubed-sphere configuration will change a little)
264      - grid computations in seaice_init are obsolete now.
265      - cleaned up code a little so that is easier to read (hopefully).
266      - added new (better?) discretizations of default advection and diffusion
267        (turn on with SEAICEuseFluxForm)
268      - replace 1 in 3d global fields by kSurface in growth.F
269      
270    checkpoint58a_post
271    o seaice:
272      - bug fix in advect.F
273    o shelfice:
274      - separate shelfice load anomaly from pload (breaks with time
275        dependent forcing), => introduce constant field shelficeLoadAnomaly.
276        Its default is 0., but it may be computed more cleverly from (unknown)
277        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
278        done offline. A good approximation of the pressure load anomaly is
279        necessary to avoid large initial adjustment processes underneath
280        deep-reaching shelfice.
281      - small fix in ISOMIP shelfice_thermodynamics
282      - add more sophisticated thermodynamics of Hellmer (1989), this is
283        now the default
284      - give a few constants more intuitive names
285    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
286      if bulk formulae are used in long integration (especially EmPmR). Turn
287      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
288      if balancePrintMean, the imbalance that is substracted is printed to
289      STDOUT.
290    o fix bug (typo) in obcs_apply_eta.F
291    o add a new package shelfice which enables us to model the circulation
292      underneath shelf-ice with draughts of hundreds of meters.
293     - works
294     - to do: + include improved thermodynamics
295              + check whether kSurfC (from model/inc/SURFACE.h) can be used
296                instead of new field kTopC
297              + can we use topoFile, Ro_surf and existing code in ini_depth.F
298                instead of new field R_shelfIce and new code in ini_depth.F
299                and ini_mask_etc.F?
300              + adjust vertical mixing schemes?
301    o seaice pkg:
302     - add a cpp-flag to include a simple formula for a salinity dependent
303       freezing point of sea water at the surface
304     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
305       meridional stresses are now different (and hopefully correct)
306    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
307       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
308       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
309    o pkg/diagnostics: add options and parameters for regional-statistics
310       diagnostics ; define regions by reading a region-mask from a file
311       (might add other options later)
312    o pkg/bulk_force:
313     - add option and parameters to use AIM surface-flux formulae.
314     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
315       others forcing fields (defined in PARM05, parameter file "data") are loaded
316       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
317     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
318     - use the right EXCH call for uwind,vwind (to work on CS-grid).
319     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
320       and parameters (note: calcWindStress replaces .NOT.readwindstress).
321     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
322    
323    checkpoint58
324    o add "--embed-source" option to genmake2 which, when the supporting
325      tools can be compiled (as determined by genmake2) will turn on the
326      embed_files package which then embeds the entire MITgcm source code
327      (*.[fFhc] + Makefile) used for the build within the executable
328      - requested by CNH but off by default
329      - adds a paltry <9MB to the mitgcmuv executable in most cases
330      - only writes the output when useEMBEDSRC in eedata is true
331    o clean up 3-dim. relaxation codes:
332      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
333      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
334      * Thanks to Tom Haine for testing!
335    
336    checkpoint57z_post
337    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
338      affects output (@ truncation level) of exp. plume_on_slope ; updated.
339    o fix the pickup behavior for obcs in combination with ptracers
340    o fix a bug in ptracers_external_fields_load
341    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
342      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
343    o transfered surface NH pressure to eta field (if exactConserv).
344    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
345         and update lab_sea output.txt file.
346    o completing 3-dim. relaxation code: additional term
347         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
348      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
349      * At compile time, in "EXF_OPTIONS.h" set
350          #define  ALLOW_CLIMTEMP_RELAXATION
351          #define  ALLOW_CLIMSALT_RELAXATION
352      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
353          tauThetaClimRelax3Dim = 15552000.0,
354          tauSaltClimRelax3Dim  = 15552000.0,
355      * 3 cases:
356          1) Use a constant-in-time 3-dim. field
357          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
358          3) Real-time relax. to time-evolving prescribed field
359    o Adding Laplacian-type smoothness constraint on
360      initial and boundary (forcing) controls (ic, bc)
361      * enable at compile-time via
362        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
363      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
364      * Absolute scale somewhat unclear so far
365      * no area weighting was included since no other cost term does so far
366    
367    checkpoint57y_post
368    First step for a NLFS adjoint
369    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
370    o new init. routines for calc_r_star, calc_surf_dr
371    o still need to deal with ini_masks_etc
372    o testreport seemed happy
373    checkpoint57y_pre
374    
375    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
376    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
377    o add new offset feature to offline pkg (plus minor cleanup)
378    o cfc fixes for final year of integration
379    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
380      be in GCHEM_OPTIONS).
381    
382    checkpoint57x_post
383    o fix testreport Pb in multiple test experiment.
384    o cleanup our namelist syntax in verification:
385      - make it more F95 standards compliant (some work still needed)
386      - allows the vast majority of our tests to work with gfortran
387    o Non-Hydrostatic:
388     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
389     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
390    o Allow to apply AB on T,S rather than on AB(gT,gS):
391     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
392     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
393       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
394     - need a "clever" read_pickup to restart from the other AB formulation
395    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
396    o remove some unused variables (reduces number of compiler warnings)
397    o adjoint
398      * Disable useVariableViscosity for adjoint for time being
399        (there are a number of extensive recomputations)
400      * Initialize certain variables needed for adjoint
401    
402    checkpoint57w_post
403    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
404                 fix the singleCpuIO RS version of MDSWRITEFIELD
405       and add a WARNING if using globalFiles=T with multi-processors.
406    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
407      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
408    o tracer advection scheme:
409      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
410       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
411       was not very convenient).
412      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
413       (further tests needed for the implicit DST & Flux-Limiter schemes).
414    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
415      and sRef for convenience, handy, when you want to initialize
416      ptracers in a large domain with a constant non-zero value. Also,
417      untangle ptracers_init.F a little.
418    
419    checkpoint57v_post
420    o change dome exp. to use variable viscosity in side-drag terms.
421    o remove all the files from the cfc_offline test since they are now
422      incorporated into tutorial_cfc_offline which has been producing
423      identical results for a few days of testing
424    o add new parameter: sideDragFactor to enable half-slip-side BC
425      and change side-drag S/R to use viscosity from mom_calc_visc
426      (can switch back by setting sideDragFactor=0.); affects results at
427      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
428       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
429    o vorticity & strain are now computed without masking, to account for
430      no-slip-side BC in variable viscosity calculation ; mask is applied
431      anyway later on, before computing advection/coriolis terms.
432    o modify exp4 to test new obcs support for reading from external files
433      and for passive tracers
434    o fix behavior of ptracers_monitor when monitor output is written to a
435      netcdf-file; still not independent of monitor.F (writes in the same
436      file).
437    o change default value of tRef (put a uniform, meaningful value for ocean
438      & atmos) and initialize sRef (was missing, as Martin mentioned).
439    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
440      to be proportional to enstrophy dissipation length.  Thus,
441       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
442      This is now consistent with Smagorinsky and with the manual.
443    
444    checkpoint57u_post
445    o OBCS and PTRACERS: add open boundary support for passive tracers
446      - either use homogenous (pseudo) v.Neumann conditions or prescribe
447        OB-values from file; this is not different from the way theta and salinity
448        are treated
449      - however, Orlanski-radiation conditions are not supported, and the model
450        will stop if you use pTracers and Orlanski at the same time.
451      - beefed up the rountine obcs_external_fields_load: now only those open
452        boundary values are overwritten with values from files for which there
453        are really files, otherwise the OB-fields remain untouched. This makes
454        it possible to use different OBs at different ends of the domain (as
455        with EXF)
456    o reduce number of exch calls in shap_filt (s2).
457    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
458      truncation level) 4/5 MLAdjust test results (11&12 digits match).
459    
460    checkpoint57t_post
461    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
462    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
463      same truncation, independent of the face number: affects affects several
464      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
465    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
466      note that biharmonic viscosity + no-slip was not tested in any experiment.
467    o fix bug in non-linear free-surf side-drag ; generate new output for
468      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
469    o make mnc honor the writeBinaryPrec flag for most kinds of output
470    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
471    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
472      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
473    o add brackets in multi-terms sum to get same truncation, independent of
474      the face number (manage to get exactly same value of gU,gV at the cs-edge)
475      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
476    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
477      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
478      a maximum grid-scale Reynolds number.  Also, changes all length calculations
479      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
480      Suggested values of viscosity parameters found in mom_calc_visc.
481      Many new viscosity diagnostics available.
482    
483    checkpoint57s_post
484    o Add clearing-house for viscosity calculations, mom_calc_visc and
485      correct numerous bugs in LeithD and Smagorinsky discretizations.  
486      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
487      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
488      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
489      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
490      The Strain-Tension form is now called with useStrainTensonVisc=.true.
491      ViscAhStrain and viscAhTension are now retired.
492    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
493    o In response to JMC's bug report, genmake2 now ignores any soft-links
494      that it finds in the *current* directory when searching for files.
495      Soft-links found in any other source directories will still work as
496      they did before.
497    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
498      a C routine to unlimit the stack size
499    o mnc-ify pkg/aim snapshot vars
500    o mnc-ify pkg/land as requested by Daniel
501    o various changes to mnc including:
502      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
503      - output can now be grouped so that all files within a group
504          change the ITER portion of their names in lock-step together
505      - can now read ("global") PER-FACE (in addition to PER-TILE) files
506          and works with both EXCH1 and EXCH2 (but needs more testing)
507      - writing works for all verification test cases w/ g77 on Linux
508    
509    checkpoint57r_post
510    o make MNC variable initialization happen earlier
511    o add diagnostics for (almost) each term of the momentum Eq.
512    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
513    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
514    o remove MINIMAL_TAVE_OUTPUT option ;
515      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
516    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
517      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
518    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
519    o add time-dependent SST, SSS control
520    o cost terms in ecco/ modularized (new cost_generic.F)
521    o cost_averages routines are modularized (new cost_averagesgeneric.F)
522    o new infrastructure for seaice model vs. obs misfits in seaice/
523      * driver from the_main_loop.F is seaice_cost_driver.F
524      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
525      * gradient check in Exp. 6a of natl_box_adjoint/
526    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
527      (see README file)
528    
529    checkpoint57q_post
530    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
531    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
532      - bug was reported by Jean-Michel and Ian Fenty
533    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
534      update exp. cpl_aim+ocn output.
535    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
536      Needed for high-res. runs with large global files
537      to be able to limit tapelev size
538    o Changed some tests for adjoint:
539      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
540      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
541      * global_ocean.90x40x15/ back to default 3-level checkpointing
542    o Modifications to enable scripted COMMON to MODULE conversion
543      * verification/OpenAD/code/ has necessary scripts and description;
544      * converts, compiles and runs successfully;
545    
546    checkpoint57p_post
547    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
548    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
549      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
550    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
551    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
552      (was already the case for dissipation with mom_vecinv,
553       and also the case for grad.PhiHyd when staggered-timeStep)
554      This will allow to put dissipation out-off the AB time-stepping.
555     Unfortunately, affects truncation error. Update output of exp. that "fails"
556      (cg2d matching number) and leave the others for later: front_relax(10),
557      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
558      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
559    
560    checkpoint57o_post
561    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
562      (2) its ready to be documented during the 20050801 DocFest
563    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
564      for ideal_2D_oce and lab_sea on linux_ia32_g77
565    o set to #undef CTRL_SET_OLD_MAXCVARS_30
566      in global1x1_tot/code_seaice_adj to access indices 32, 33
567      (worth another tag)
568    
569    checkpoint57n_post
570    o adding precip control xx_precip 32
571    o adding swflux control xx_swflux 33
572    o Replacing 10 forcing penalty cost routines by 1 generic.
573    o Implementing partitioning in time-mean and variable adjustment
574      for atmos. state.
575    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
576  o in natl_box_adjoint:  o in natl_box_adjoint:
577    * updated: results_bulk/    * updated exp 1 to 10
578    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
579    o updated global1x1/*_seaice_adj/
580      to incorporate latest changes
581    o enable useSingleCpuIO for mdsio vector routines
582      (applies in particular to tapelev I/O)
583    o removed inefficient K-loop in all active_file*control*.F
584    
585  checkpoint57m_post  checkpoint57m_post
586  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
Legend:
Removed from v.1.519  
changed lines
  Added in v.1.695
  ViewVC Help
Powered by ViewVC 1.1.22