/[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 1.688 by jmc, Sun Jun 25 22:48:19 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 pkg/thsice with pkg/seaice dynamics:
8  o moved ptracer ctrl index 17 -> 32  - fix domain of computation (interior only, required for exf) and do exchanges
9    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
10    o towards a standard way of dealing with multi-threading in MONITOR
11      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
12    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
13       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
14    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
15    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
16    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
17       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
18    o tracer advection:
19     - clean-up and simplify calc_common_factors.F
20     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
21       advection subroutine (but still not used within DST advection S/R)
22    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
23    
24    checkpoint58j_post
25    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
26      from file (collects calls previously in FORWARD_STEP)
27    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
28    o adjoint store dir. adjusted accordingly
29    o genmake2
30      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
31    
32    checkpoint58i_post
33    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
34      on wind stress (SEAICEstressFactor defaults to 1.)
35    o Total number of Timers is finite (<=40): comment out 2 non-essential one
36      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
37    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
38      on CS-grid: no longer loosing mass.
39    o exf & curvilinear-grid: no longer modify longitude xC & xG.
40    o pkg/ggl90: fix sloppy output and fix a bug
41    o pkg/seaice: added SEAICEuseEVPpickup parameter
42      - Set to false in order to start EVP solver with
43        non-EVP pickup files when using SEAICEuseEVP
44      - fix sign error in diffusion in seaice_calc_rhs
45    
46    checkpoint58h_post
47    * Modifications for bottom topography control
48      o replace hFacC by _hFacC at various places
49      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
50      o add non-self-adjoint cg2d_nsa
51      o update autodiff support routines
52      o re-initialise hfac after ctrl_depth_ini
53      o works for 5x5 box, doesnt work for global_ocean.90x40x15
54    * Adding verification for 5x5 box (4-layer) bottom topography control
55    
56    checkpoint58g_post
57    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
58       used for mean seasonal cycle, mean diurnal cycle); add an example
59       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
60    o pkg/ggl90:
61      - add parameter (minimum surface kinetic energy)
62      - fix bug (avoiding division by zero)
63    o couple pkg/thsice to pkg/seaice:
64      - modify advection in seaice to accomodate new scalar fields to be advected
65      - only muliDimAdection scheme work with seaice/thsice
66      - mapping of thsice-variables to seaice-variables, back and forth
67      - does not break the verification experiments, but does not give the
68        desired results either
69    o pkg/seaice
70      - make (default) second order advection a bit less confusing?
71    
72    checkpoint58f_post
73    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
74      to pkg/seaice):
75      - new routines thsice_map_exf and thsice_get_exf provide the interface
76      - add an additional formal parameter to thsice_solve4temp
77    o pkg/exf:
78      - add new fields wspeed, snowprecip (to be able to couple to thsice)
79      - correct Stefan-Boltzmann constant
80      - new parameter for longwave surface emittance
81      - separate some stuff from exf_bulkformulae into new routines  
82        exf_radiation, exf_wind
83      - add new parameters and constants: longwave emissivity for ocean, ice
84        and snow, evaporation parameters over ice
85      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
86        either wind from stress or stress from wind
87    o pkg/thSIce:
88    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
89    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
90       and THSICE_CALC_THICKN
91    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
92    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
93      to make debugging easier.
94    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
95    o pkg/bulk_force:
96      - clean-up comments and parameters ;
97      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
98    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
99      generate new output for test-experiment: aim.5l_cs.thSI
100    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
101      testreport accordingly
102    
103    checkpoint58e_post
104    o SEAICE_CGRID adjoint done
105    o R_STAR adjoint implemented.
106      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
107      * need to sort out init. of h0facc, etc.
108    o Make pkg/profile fully independent of ecco,cost, etc. stuff
109      to be able to use it in pure forward.
110    
111    checkpoint58d_post
112    o upgrade simple test-experiment to tutorial example:
113     step.1: duplicate the experiment and (step.2) will remove the old copy.
114      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
115      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
116      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
117      tutorial_global_oce_biogeo    <- copy of dic_example
118      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
119      tutorial_plume_on_slope       <- copy of plume_on_slope
120      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
121      tutorial_global_oce_optim     <- empty for now (David ?)
122      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
123     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
124    o correct a sign problem in cost_scat.F
125    o obcs and ptracers: fix boundary conditions for advections schemes
126      with larger stencil
127    o thsice adjoint: start
128    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
129      completeness
130    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
131      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
132    o ptracers adjoint:
133      * avoid extensive recomputatations
134      * fix missing re-init. of gptr (missed by TAF)
135    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
136      me to turn off the excessive output to STDOUT that this package produces
137    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
138      and add those terms in Vector-Invariant formulation.
139    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
140      if the control period (xx_hfluxperiod etc) is 0
141    o in profiles pkg, clean routines and fix details
142    o in ecco pkg, reading ssh data:
143      fix problem in case the model does not start at iter0=0
144    o fix mnc-pickup/restart for ptracers
145    o new package prifiles:
146      code to compute profile-based cost by Gael Forget
147      (modifs in ecco, ctrl, autodiff)
148    o Benign bug fix in initialization (spotted by M. Mazloff) of
149      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
150    
151    checkpoint58c_post
152    o adjoint: finish NLFS adjoint and provide reference output in
153      verification/global_ocean.90x40x15/results_ad_nlfs
154    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
155      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
156      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
157      with SEAICE_CGRID defined.
158    o move calendarDumps from "data" to "data.cal" and clean-up the code
159      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
160    o add useEXF & useCAL flags (for now, set in hard-coded way)
161    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
162      (were missing in NH mode, and wrong in quasihydrostatic mode).
163      waiting for Chris updated version of calc_gw to add those CALLs.
164    o fix bug in quasihydrostatic S/R ;
165      add a test for this option: global_ocean.90x40x15.qshyd
166    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
167      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
168    o add on/off flag useOffLine for package OFFLINE
169    o seaice:
170      - modify advection so that it works also on the C-grid
171      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
172        problem in multi-tile runs with C-grid
173      - add flags for clipping ice velocities and/or masking solver forcing
174      - fix drag (ocean on ice) formulation and a bug that caused noise in the
175        C-grid solver
176      - added a few comments to seaice_diffusion.F
177      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
178        are now exclusive)
179      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
180        required re-ordering the code a little:
181       + make DAIRN global variable (defined in SEAICE)
182       + move computation of the viscosities eta and zeta into a new separate
183         routine (because I need to recompute them in seaice_ocean_stress.F)
184    
185    checkpoint58b_post
186    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
187      update output.txt of exp. aim.5l_cs.thSI
188    o various mnc cleanups and improvements:
189      + shrink lookup tables by factor of ~4
190      + better error reporting when running out of lookup space
191      + able to handle longer path/file names (up to 500 chars)
192    o adjoint:
193      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
194      - TBD: "hidden" mom_vecinv recomp. in dynamics
195    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
196     (allow to differentiate between forcing components using new integer flags:
197      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
198     and add new flag to put Dissipation tendency out of Adams-Bashforth.
199    o ecco
200      - enable trend removal from SSH anomaly obs.
201    o adjoint
202      - a fix for PmEpR when #undef EXACT_CONSERV
203      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
204      - try to fix "hidden" recomp. in forward_step for NLFS
205        (NLFS seems broken sometimes after I checked it in)
206    o seaice:
207     - add c-grid version of the dynamic solver:
208       + three new routines that are the c-grid substitute lsr, dynsolver
209         and ostres
210       + put a few fields that were local to dynsolver into global common
211         blocks, so that I can move the computation of stresses etc into
212         seaice_lsr (saves coding but may break the adjoint).
213     - replace more hardwired parameters by runtime parameters
214     - add ice masks that mask the rhs of the implicit solvers where there
215       is no ice (commented out in seaice_dynsolver, because i am not sure
216       if this works properly), eventually this should replace the clipping
217       of ice velocities in seaice_dynsolver to +/-40cm/s.
218    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
219      include it only where its needed
220    o move balancing of fluxes before the call of external_forcing_surf
221    o seaice:
222      - correct units of turning angles (now they are really in degrees)
223      - move computation of GWATX/Y out of main routine into dynsolver
224      - initialize GWATX/Y in seaice_init
225    o Apply mask on Fresh-Water flux (needed for SSH forcing).
226      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
227    o seaice: add runtime flags for turning angles (default to zero)
228    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
229      and trend from exf forcing and ctrl control adjustments
230    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
231      (since checkpoint57x_post)
232    o change the default rotation period to 86164.s = the Earth rotation
233    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
234      and based on a reference stratification. Tested within hs94.cs-32x32x5.
235    o seaice advection: add code for choosing between the default (2nd order
236      central differences) and multiDim advection schemes provided by
237      pkg/generic_advdiff
238    o seaice:
239      - removed all references to SEAICE_GRID.h fields from
240        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
241        (cubed-sphere configuration will change a little)
242      - grid computations in seaice_init are obsolete now.
243      - cleaned up code a little so that is easier to read (hopefully).
244      - added new (better?) discretizations of default advection and diffusion
245        (turn on with SEAICEuseFluxForm)
246      - replace 1 in 3d global fields by kSurface in growth.F
247      
248    checkpoint58a_post
249    o seaice:
250      - bug fix in advect.F
251    o shelfice:
252      - separate shelfice load anomaly from pload (breaks with time
253        dependent forcing), => introduce constant field shelficeLoadAnomaly.
254        Its default is 0., but it may be computed more cleverly from (unknown)
255        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
256        done offline. A good approximation of the pressure load anomaly is
257        necessary to avoid large initial adjustment processes underneath
258        deep-reaching shelfice.
259      - small fix in ISOMIP shelfice_thermodynamics
260      - add more sophisticated thermodynamics of Hellmer (1989), this is
261        now the default
262      - give a few constants more intuitive names
263    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
264      if bulk formulae are used in long integration (especially EmPmR). Turn
265      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
266      if balancePrintMean, the imbalance that is substracted is printed to
267      STDOUT.
268    o fix bug (typo) in obcs_apply_eta.F
269    o add a new package shelfice which enables us to model the circulation
270      underneath shelf-ice with draughts of hundreds of meters.
271     - works
272     - to do: + include improved thermodynamics
273              + check whether kSurfC (from model/inc/SURFACE.h) can be used
274                instead of new field kTopC
275              + can we use topoFile, Ro_surf and existing code in ini_depth.F
276                instead of new field R_shelfIce and new code in ini_depth.F
277                and ini_mask_etc.F?
278              + adjust vertical mixing schemes?
279    o seaice pkg:
280     - add a cpp-flag to include a simple formula for a salinity dependent
281       freezing point of sea water at the surface
282     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
283       meridional stresses are now different (and hopefully correct)
284    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
285       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
286       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
287    o pkg/diagnostics: add options and parameters for regional-statistics
288       diagnostics ; define regions by reading a region-mask from a file
289       (might add other options later)
290    o pkg/bulk_force:
291     - add option and parameters to use AIM surface-flux formulae.
292     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
293       others forcing fields (defined in PARM05, parameter file "data") are loaded
294       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
295     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
296     - use the right EXCH call for uwind,vwind (to work on CS-grid).
297     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
298       and parameters (note: calcWindStress replaces .NOT.readwindstress).
299     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
300    
301    checkpoint58
302    o add "--embed-source" option to genmake2 which, when the supporting
303      tools can be compiled (as determined by genmake2) will turn on the
304      embed_files package which then embeds the entire MITgcm source code
305      (*.[fFhc] + Makefile) used for the build within the executable
306      - requested by CNH but off by default
307      - adds a paltry <9MB to the mitgcmuv executable in most cases
308      - only writes the output when useEMBEDSRC in eedata is true
309    o clean up 3-dim. relaxation codes:
310      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
311      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
312      * Thanks to Tom Haine for testing!
313    
314    checkpoint57z_post
315    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
316      affects output (@ truncation level) of exp. plume_on_slope ; updated.
317    o fix the pickup behavior for obcs in combination with ptracers
318    o fix a bug in ptracers_external_fields_load
319    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
320      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
321    o transfered surface NH pressure to eta field (if exactConserv).
322    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
323         and update lab_sea output.txt file.
324    o completing 3-dim. relaxation code: additional term
325         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
326      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
327      * At compile time, in "EXF_OPTIONS.h" set
328          #define  ALLOW_CLIMTEMP_RELAXATION
329          #define  ALLOW_CLIMSALT_RELAXATION
330      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
331          tauThetaClimRelax3Dim = 15552000.0,
332          tauSaltClimRelax3Dim  = 15552000.0,
333      * 3 cases:
334          1) Use a constant-in-time 3-dim. field
335          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
336          3) Real-time relax. to time-evolving prescribed field
337    o Adding Laplacian-type smoothness constraint on
338      initial and boundary (forcing) controls (ic, bc)
339      * enable at compile-time via
340        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
341      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
342      * Absolute scale somewhat unclear so far
343      * no area weighting was included since no other cost term does so far
344    
345    checkpoint57y_post
346    First step for a NLFS adjoint
347    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
348    o new init. routines for calc_r_star, calc_surf_dr
349    o still need to deal with ini_masks_etc
350    o testreport seemed happy
351    checkpoint57y_pre
352    
353    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
354    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
355    o add new offset feature to offline pkg (plus minor cleanup)
356    o cfc fixes for final year of integration
357    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
358      be in GCHEM_OPTIONS).
359    
360    checkpoint57x_post
361    o fix testreport Pb in multiple test experiment.
362    o cleanup our namelist syntax in verification:
363      - make it more F95 standards compliant (some work still needed)
364      - allows the vast majority of our tests to work with gfortran
365    o Non-Hydrostatic:
366     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
367     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
368    o Allow to apply AB on T,S rather than on AB(gT,gS):
369     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
370     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
371       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
372     - need a "clever" read_pickup to restart from the other AB formulation
373    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
374    o remove some unused variables (reduces number of compiler warnings)
375    o adjoint
376      * Disable useVariableViscosity for adjoint for time being
377        (there are a number of extensive recomputations)
378      * Initialize certain variables needed for adjoint
379    
380    checkpoint57w_post
381    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
382                 fix the singleCpuIO RS version of MDSWRITEFIELD
383       and add a WARNING if using globalFiles=T with multi-processors.
384    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
385      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
386    o tracer advection scheme:
387      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
388       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
389       was not very convenient).
390      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
391       (further tests needed for the implicit DST & Flux-Limiter schemes).
392    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
393      and sRef for convenience, handy, when you want to initialize
394      ptracers in a large domain with a constant non-zero value. Also,
395      untangle ptracers_init.F a little.
396    
397    checkpoint57v_post
398    o change dome exp. to use variable viscosity in side-drag terms.
399    o remove all the files from the cfc_offline test since they are now
400      incorporated into tutorial_cfc_offline which has been producing
401      identical results for a few days of testing
402    o add new parameter: sideDragFactor to enable half-slip-side BC
403      and change side-drag S/R to use viscosity from mom_calc_visc
404      (can switch back by setting sideDragFactor=0.); affects results at
405      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
406       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
407    o vorticity & strain are now computed without masking, to account for
408      no-slip-side BC in variable viscosity calculation ; mask is applied
409      anyway later on, before computing advection/coriolis terms.
410    o modify exp4 to test new obcs support for reading from external files
411      and for passive tracers
412    o fix behavior of ptracers_monitor when monitor output is written to a
413      netcdf-file; still not independent of monitor.F (writes in the same
414      file).
415    o change default value of tRef (put a uniform, meaningful value for ocean
416      & atmos) and initialize sRef (was missing, as Martin mentioned).
417    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
418      to be proportional to enstrophy dissipation length.  Thus,
419       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
420      This is now consistent with Smagorinsky and with the manual.
421    
422    checkpoint57u_post
423    o OBCS and PTRACERS: add open boundary support for passive tracers
424      - either use homogenous (pseudo) v.Neumann conditions or prescribe
425        OB-values from file; this is not different from the way theta and salinity
426        are treated
427      - however, Orlanski-radiation conditions are not supported, and the model
428        will stop if you use pTracers and Orlanski at the same time.
429      - beefed up the rountine obcs_external_fields_load: now only those open
430        boundary values are overwritten with values from files for which there
431        are really files, otherwise the OB-fields remain untouched. This makes
432        it possible to use different OBs at different ends of the domain (as
433        with EXF)
434    o reduce number of exch calls in shap_filt (s2).
435    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
436      truncation level) 4/5 MLAdjust test results (11&12 digits match).
437    
438    checkpoint57t_post
439    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
440    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
441      same truncation, independent of the face number: affects affects several
442      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
443    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
444      note that biharmonic viscosity + no-slip was not tested in any experiment.
445    o fix bug in non-linear free-surf side-drag ; generate new output for
446      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
447    o make mnc honor the writeBinaryPrec flag for most kinds of output
448    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
449    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
450      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
451    o add brackets in multi-terms sum to get same truncation, independent of
452      the face number (manage to get exactly same value of gU,gV at the cs-edge)
453      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
454    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
455      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
456      a maximum grid-scale Reynolds number.  Also, changes all length calculations
457      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
458      Suggested values of viscosity parameters found in mom_calc_visc.
459      Many new viscosity diagnostics available.
460    
461    checkpoint57s_post
462    o Add clearing-house for viscosity calculations, mom_calc_visc and
463      correct numerous bugs in LeithD and Smagorinsky discretizations.  
464      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
465      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
466      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
467      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
468      The Strain-Tension form is now called with useStrainTensonVisc=.true.
469      ViscAhStrain and viscAhTension are now retired.
470    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
471    o In response to JMC's bug report, genmake2 now ignores any soft-links
472      that it finds in the *current* directory when searching for files.
473      Soft-links found in any other source directories will still work as
474      they did before.
475    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
476      a C routine to unlimit the stack size
477    o mnc-ify pkg/aim snapshot vars
478    o mnc-ify pkg/land as requested by Daniel
479    o various changes to mnc including:
480      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
481      - output can now be grouped so that all files within a group
482          change the ITER portion of their names in lock-step together
483      - can now read ("global") PER-FACE (in addition to PER-TILE) files
484          and works with both EXCH1 and EXCH2 (but needs more testing)
485      - writing works for all verification test cases w/ g77 on Linux
486    
487    checkpoint57r_post
488    o make MNC variable initialization happen earlier
489    o add diagnostics for (almost) each term of the momentum Eq.
490    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
491    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
492    o remove MINIMAL_TAVE_OUTPUT option ;
493      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
494    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
495      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
496    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
497    o add time-dependent SST, SSS control
498    o cost terms in ecco/ modularized (new cost_generic.F)
499    o cost_averages routines are modularized (new cost_averagesgeneric.F)
500    o new infrastructure for seaice model vs. obs misfits in seaice/
501      * driver from the_main_loop.F is seaice_cost_driver.F
502      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
503      * gradient check in Exp. 6a of natl_box_adjoint/
504    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
505      (see README file)
506    
507    checkpoint57q_post
508    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
509    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
510      - bug was reported by Jean-Michel and Ian Fenty
511    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
512      update exp. cpl_aim+ocn output.
513    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
514      Needed for high-res. runs with large global files
515      to be able to limit tapelev size
516    o Changed some tests for adjoint:
517      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
518      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
519      * global_ocean.90x40x15/ back to default 3-level checkpointing
520    o Modifications to enable scripted COMMON to MODULE conversion
521      * verification/OpenAD/code/ has necessary scripts and description;
522      * converts, compiles and runs successfully;
523    
524    checkpoint57p_post
525    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
526    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
527      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
528    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
529    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
530      (was already the case for dissipation with mom_vecinv,
531       and also the case for grad.PhiHyd when staggered-timeStep)
532      This will allow to put dissipation out-off the AB time-stepping.
533     Unfortunately, affects truncation error. Update output of exp. that "fails"
534      (cg2d matching number) and leave the others for later: front_relax(10),
535      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
536      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
537    
538    checkpoint57o_post
539    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
540      (2) its ready to be documented during the 20050801 DocFest
541    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
542      for ideal_2D_oce and lab_sea on linux_ia32_g77
543    o set to #undef CTRL_SET_OLD_MAXCVARS_30
544      in global1x1_tot/code_seaice_adj to access indices 32, 33
545      (worth another tag)
546    
547    checkpoint57n_post
548    o adding precip control xx_precip 32
549    o adding swflux control xx_swflux 33
550    o Replacing 10 forcing penalty cost routines by 1 generic.
551    o Implementing partitioning in time-mean and variable adjustment
552      for atmos. state.
553    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
554  o in natl_box_adjoint:  o in natl_box_adjoint:
555    * updated: results_bulk/    * updated exp 1 to 10
556    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
557    o updated global1x1/*_seaice_adj/
558      to incorporate latest changes
559    o enable useSingleCpuIO for mdsio vector routines
560      (applies in particular to tapelev I/O)
561    o removed inefficient K-loop in all active_file*control*.F
562    
563  checkpoint57m_post  checkpoint57m_post
564  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.1.688
  ViewVC Help
Powered by ViewVC 1.1.22