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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.698 by jmc, Wed Jul 12 14:29:07 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 calc_gw: true flux-form, account for horizontal grid spacing.
8  o moved ptracer ctrl index 17 -> 32    update rotating_tank results, but not plume_on_slope (affected at
9      truncation level, 11 digits).
10    
11    checkpoint58l_post
12    o calc_gw:
13     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
14     - remove side-drag for now (need to fix it); update plume_on_slope results.
15     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
16    o commit code to make SST/SSS weights spatially variable
17      (based on either variable in-situ or variable initial T/S weights)
18    o pkg/ecco:
19      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
20        now based on horizontally varying weights wthetaLev, wsaltLev
21      * cost_averagesflags now returns year indices in addition to day, month
22      * sflux balance is performed on annual basis
23        (sflxumm, sfluxmm2, bal_sfluxmm)
24      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
25        including separate counting and multipliers
26    o pkg/rbcs
27      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
28    
29    checkpoint58k_post
30    o testreport:
31     - always build in dir. "build" (if not there, mkdir build instead of building
32       & running in input)
33     - run in dir run (if it exists), in build otherwise.
34     - call prepare_run (if input/prepare_run exists)
35     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
36    o pkg/exf modifications to interpolation and rotation routines for more
37       reasonable treatment of North Pole singularity: for tracers North Pole
38       value is set to northernmost zonal-mean value, for zonal velocity it is
39       set to zero, and for meridional velocity it is set to northernmost value.
40    o pkg/exf/exf_check_range.F
41     - add tile index to diagnostics and move stop statement to the very
42       end of the routine.
43    o pkg/diagnostics: (diagnostics_main_init.F)
44      define title of isomorphic variables according to the current config.
45    o pkg/thsice with pkg/seaice dynamics:
46    - fix domain of computation (interior only, required for exf) and do exchanges
47    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
48    o towards a standard way of dealing with multi-threading in MONITOR
49      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
50    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
51       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
52    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
53    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
54    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
55       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
56    o tracer advection:
57     - clean-up and simplify calc_common_factors.F
58     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
59       advection subroutine (but still not used within DST advection S/R)
60    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
61    
62    checkpoint58j_post
63    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
64      from file (collects calls previously in FORWARD_STEP)
65    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
66    o adjoint store dir. adjusted accordingly
67    o genmake2
68      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
69    
70    checkpoint58i_post
71    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
72      on wind stress (SEAICEstressFactor defaults to 1.)
73    o Total number of Timers is finite (<=40): comment out 2 non-essential one
74      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
75    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
76      on CS-grid: no longer loosing mass.
77    o exf & curvilinear-grid: no longer modify longitude xC & xG.
78    o pkg/ggl90: fix sloppy output and fix a bug
79    o pkg/seaice: added SEAICEuseEVPpickup parameter
80      - Set to false in order to start EVP solver with
81        non-EVP pickup files when using SEAICEuseEVP
82      - fix sign error in diffusion in seaice_calc_rhs
83    
84    checkpoint58h_post
85    * Modifications for bottom topography control
86      o replace hFacC by _hFacC at various places
87      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
88      o add non-self-adjoint cg2d_nsa
89      o update autodiff support routines
90      o re-initialise hfac after ctrl_depth_ini
91      o works for 5x5 box, doesnt work for global_ocean.90x40x15
92    * Adding verification for 5x5 box (4-layer) bottom topography control
93    
94    checkpoint58g_post
95    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
96       used for mean seasonal cycle, mean diurnal cycle); add an example
97       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
98    o pkg/ggl90:
99      - add parameter (minimum surface kinetic energy)
100      - fix bug (avoiding division by zero)
101    o couple pkg/thsice to pkg/seaice:
102      - modify advection in seaice to accomodate new scalar fields to be advected
103      - only muliDimAdection scheme work with seaice/thsice
104      - mapping of thsice-variables to seaice-variables, back and forth
105      - does not break the verification experiments, but does not give the
106        desired results either
107    o pkg/seaice
108      - make (default) second order advection a bit less confusing?
109    
110    checkpoint58f_post
111    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
112      to pkg/seaice):
113      - new routines thsice_map_exf and thsice_get_exf provide the interface
114      - add an additional formal parameter to thsice_solve4temp
115    o pkg/exf:
116      - add new fields wspeed, snowprecip (to be able to couple to thsice)
117      - correct Stefan-Boltzmann constant
118      - new parameter for longwave surface emittance
119      - separate some stuff from exf_bulkformulae into new routines  
120        exf_radiation, exf_wind
121      - add new parameters and constants: longwave emissivity for ocean, ice
122        and snow, evaporation parameters over ice
123      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
124        either wind from stress or stress from wind
125    o pkg/thSIce:
126    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
127    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
128       and THSICE_CALC_THICKN
129    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
130    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
131      to make debugging easier.
132    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
133    o pkg/bulk_force:
134      - clean-up comments and parameters ;
135      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
136    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
137      generate new output for test-experiment: aim.5l_cs.thSI
138    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
139      testreport accordingly
140    
141    checkpoint58e_post
142    o SEAICE_CGRID adjoint done
143    o R_STAR adjoint implemented.
144      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
145      * need to sort out init. of h0facc, etc.
146    o Make pkg/profile fully independent of ecco,cost, etc. stuff
147      to be able to use it in pure forward.
148    
149    checkpoint58d_post
150    o upgrade simple test-experiment to tutorial example:
151     step.1: duplicate the experiment and (step.2) will remove the old copy.
152      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
153      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
154      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
155      tutorial_global_oce_biogeo    <- copy of dic_example
156      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
157      tutorial_plume_on_slope       <- copy of plume_on_slope
158      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
159      tutorial_global_oce_optim     <- empty for now (David ?)
160      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
161     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
162    o correct a sign problem in cost_scat.F
163    o obcs and ptracers: fix boundary conditions for advections schemes
164      with larger stencil
165    o thsice adjoint: start
166    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
167      completeness
168    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
169      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
170    o ptracers adjoint:
171      * avoid extensive recomputatations
172      * fix missing re-init. of gptr (missed by TAF)
173    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
174      me to turn off the excessive output to STDOUT that this package produces
175    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
176      and add those terms in Vector-Invariant formulation.
177    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
178      if the control period (xx_hfluxperiod etc) is 0
179    o in profiles pkg, clean routines and fix details
180    o in ecco pkg, reading ssh data:
181      fix problem in case the model does not start at iter0=0
182    o fix mnc-pickup/restart for ptracers
183    o new package prifiles:
184      code to compute profile-based cost by Gael Forget
185      (modifs in ecco, ctrl, autodiff)
186    o Benign bug fix in initialization (spotted by M. Mazloff) of
187      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
188    
189    checkpoint58c_post
190    o adjoint: finish NLFS adjoint and provide reference output in
191      verification/global_ocean.90x40x15/results_ad_nlfs
192    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
193      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
194      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
195      with SEAICE_CGRID defined.
196    o move calendarDumps from "data" to "data.cal" and clean-up the code
197      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
198    o add useEXF & useCAL flags (for now, set in hard-coded way)
199    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
200      (were missing in NH mode, and wrong in quasihydrostatic mode).
201      waiting for Chris updated version of calc_gw to add those CALLs.
202    o fix bug in quasihydrostatic S/R ;
203      add a test for this option: global_ocean.90x40x15.qshyd
204    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
205      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
206    o add on/off flag useOffLine for package OFFLINE
207    o seaice:
208      - modify advection so that it works also on the C-grid
209      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
210        problem in multi-tile runs with C-grid
211      - add flags for clipping ice velocities and/or masking solver forcing
212      - fix drag (ocean on ice) formulation and a bug that caused noise in the
213        C-grid solver
214      - added a few comments to seaice_diffusion.F
215      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
216        are now exclusive)
217      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
218        required re-ordering the code a little:
219       + make DAIRN global variable (defined in SEAICE)
220       + move computation of the viscosities eta and zeta into a new separate
221         routine (because I need to recompute them in seaice_ocean_stress.F)
222    
223    checkpoint58b_post
224    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
225      update output.txt of exp. aim.5l_cs.thSI
226    o various mnc cleanups and improvements:
227      + shrink lookup tables by factor of ~4
228      + better error reporting when running out of lookup space
229      + able to handle longer path/file names (up to 500 chars)
230    o adjoint:
231      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
232      - TBD: "hidden" mom_vecinv recomp. in dynamics
233    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
234     (allow to differentiate between forcing components using new integer flags:
235      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
236     and add new flag to put Dissipation tendency out of Adams-Bashforth.
237    o ecco
238      - enable trend removal from SSH anomaly obs.
239    o adjoint
240      - a fix for PmEpR when #undef EXACT_CONSERV
241      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
242      - try to fix "hidden" recomp. in forward_step for NLFS
243        (NLFS seems broken sometimes after I checked it in)
244    o seaice:
245     - add c-grid version of the dynamic solver:
246       + three new routines that are the c-grid substitute lsr, dynsolver
247         and ostres
248       + put a few fields that were local to dynsolver into global common
249         blocks, so that I can move the computation of stresses etc into
250         seaice_lsr (saves coding but may break the adjoint).
251     - replace more hardwired parameters by runtime parameters
252     - add ice masks that mask the rhs of the implicit solvers where there
253       is no ice (commented out in seaice_dynsolver, because i am not sure
254       if this works properly), eventually this should replace the clipping
255       of ice velocities in seaice_dynsolver to +/-40cm/s.
256    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
257      include it only where its needed
258    o move balancing of fluxes before the call of external_forcing_surf
259    o seaice:
260      - correct units of turning angles (now they are really in degrees)
261      - move computation of GWATX/Y out of main routine into dynsolver
262      - initialize GWATX/Y in seaice_init
263    o Apply mask on Fresh-Water flux (needed for SSH forcing).
264      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
265    o seaice: add runtime flags for turning angles (default to zero)
266    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
267      and trend from exf forcing and ctrl control adjustments
268    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
269      (since checkpoint57x_post)
270    o change the default rotation period to 86164.s = the Earth rotation
271    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
272      and based on a reference stratification. Tested within hs94.cs-32x32x5.
273    o seaice advection: add code for choosing between the default (2nd order
274      central differences) and multiDim advection schemes provided by
275      pkg/generic_advdiff
276    o seaice:
277      - removed all references to SEAICE_GRID.h fields from
278        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
279        (cubed-sphere configuration will change a little)
280      - grid computations in seaice_init are obsolete now.
281      - cleaned up code a little so that is easier to read (hopefully).
282      - added new (better?) discretizations of default advection and diffusion
283        (turn on with SEAICEuseFluxForm)
284      - replace 1 in 3d global fields by kSurface in growth.F
285      
286    checkpoint58a_post
287    o seaice:
288      - bug fix in advect.F
289    o shelfice:
290      - separate shelfice load anomaly from pload (breaks with time
291        dependent forcing), => introduce constant field shelficeLoadAnomaly.
292        Its default is 0., but it may be computed more cleverly from (unknown)
293        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
294        done offline. A good approximation of the pressure load anomaly is
295        necessary to avoid large initial adjustment processes underneath
296        deep-reaching shelfice.
297      - small fix in ISOMIP shelfice_thermodynamics
298      - add more sophisticated thermodynamics of Hellmer (1989), this is
299        now the default
300      - give a few constants more intuitive names
301    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
302      if bulk formulae are used in long integration (especially EmPmR). Turn
303      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
304      if balancePrintMean, the imbalance that is substracted is printed to
305      STDOUT.
306    o fix bug (typo) in obcs_apply_eta.F
307    o add a new package shelfice which enables us to model the circulation
308      underneath shelf-ice with draughts of hundreds of meters.
309     - works
310     - to do: + include improved thermodynamics
311              + check whether kSurfC (from model/inc/SURFACE.h) can be used
312                instead of new field kTopC
313              + can we use topoFile, Ro_surf and existing code in ini_depth.F
314                instead of new field R_shelfIce and new code in ini_depth.F
315                and ini_mask_etc.F?
316              + adjust vertical mixing schemes?
317    o seaice pkg:
318     - add a cpp-flag to include a simple formula for a salinity dependent
319       freezing point of sea water at the surface
320     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
321       meridional stresses are now different (and hopefully correct)
322    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
323       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
324       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
325    o pkg/diagnostics: add options and parameters for regional-statistics
326       diagnostics ; define regions by reading a region-mask from a file
327       (might add other options later)
328    o pkg/bulk_force:
329     - add option and parameters to use AIM surface-flux formulae.
330     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
331       others forcing fields (defined in PARM05, parameter file "data") are loaded
332       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
333     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
334     - use the right EXCH call for uwind,vwind (to work on CS-grid).
335     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
336       and parameters (note: calcWindStress replaces .NOT.readwindstress).
337     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
338    
339    checkpoint58
340    o add "--embed-source" option to genmake2 which, when the supporting
341      tools can be compiled (as determined by genmake2) will turn on the
342      embed_files package which then embeds the entire MITgcm source code
343      (*.[fFhc] + Makefile) used for the build within the executable
344      - requested by CNH but off by default
345      - adds a paltry <9MB to the mitgcmuv executable in most cases
346      - only writes the output when useEMBEDSRC in eedata is true
347    o clean up 3-dim. relaxation codes:
348      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
349      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
350      * Thanks to Tom Haine for testing!
351    
352    checkpoint57z_post
353    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
354      affects output (@ truncation level) of exp. plume_on_slope ; updated.
355    o fix the pickup behavior for obcs in combination with ptracers
356    o fix a bug in ptracers_external_fields_load
357    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
358      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
359    o transfered surface NH pressure to eta field (if exactConserv).
360    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
361         and update lab_sea output.txt file.
362    o completing 3-dim. relaxation code: additional term
363         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
364      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
365      * At compile time, in "EXF_OPTIONS.h" set
366          #define  ALLOW_CLIMTEMP_RELAXATION
367          #define  ALLOW_CLIMSALT_RELAXATION
368      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
369          tauThetaClimRelax3Dim = 15552000.0,
370          tauSaltClimRelax3Dim  = 15552000.0,
371      * 3 cases:
372          1) Use a constant-in-time 3-dim. field
373          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
374          3) Real-time relax. to time-evolving prescribed field
375    o Adding Laplacian-type smoothness constraint on
376      initial and boundary (forcing) controls (ic, bc)
377      * enable at compile-time via
378        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
379      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
380      * Absolute scale somewhat unclear so far
381      * no area weighting was included since no other cost term does so far
382    
383    checkpoint57y_post
384    First step for a NLFS adjoint
385    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
386    o new init. routines for calc_r_star, calc_surf_dr
387    o still need to deal with ini_masks_etc
388    o testreport seemed happy
389    checkpoint57y_pre
390    
391    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
392    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
393    o add new offset feature to offline pkg (plus minor cleanup)
394    o cfc fixes for final year of integration
395    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
396      be in GCHEM_OPTIONS).
397    
398    checkpoint57x_post
399    o fix testreport Pb in multiple test experiment.
400    o cleanup our namelist syntax in verification:
401      - make it more F95 standards compliant (some work still needed)
402      - allows the vast majority of our tests to work with gfortran
403    o Non-Hydrostatic:
404     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
405     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
406    o Allow to apply AB on T,S rather than on AB(gT,gS):
407     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
408     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
409       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
410     - need a "clever" read_pickup to restart from the other AB formulation
411    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
412    o remove some unused variables (reduces number of compiler warnings)
413    o adjoint
414      * Disable useVariableViscosity for adjoint for time being
415        (there are a number of extensive recomputations)
416      * Initialize certain variables needed for adjoint
417    
418    checkpoint57w_post
419    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
420                 fix the singleCpuIO RS version of MDSWRITEFIELD
421       and add a WARNING if using globalFiles=T with multi-processors.
422    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
423      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
424    o tracer advection scheme:
425      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
426       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
427       was not very convenient).
428      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
429       (further tests needed for the implicit DST & Flux-Limiter schemes).
430    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
431      and sRef for convenience, handy, when you want to initialize
432      ptracers in a large domain with a constant non-zero value. Also,
433      untangle ptracers_init.F a little.
434    
435    checkpoint57v_post
436    o change dome exp. to use variable viscosity in side-drag terms.
437    o remove all the files from the cfc_offline test since they are now
438      incorporated into tutorial_cfc_offline which has been producing
439      identical results for a few days of testing
440    o add new parameter: sideDragFactor to enable half-slip-side BC
441      and change side-drag S/R to use viscosity from mom_calc_visc
442      (can switch back by setting sideDragFactor=0.); affects results at
443      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
444       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
445    o vorticity & strain are now computed without masking, to account for
446      no-slip-side BC in variable viscosity calculation ; mask is applied
447      anyway later on, before computing advection/coriolis terms.
448    o modify exp4 to test new obcs support for reading from external files
449      and for passive tracers
450    o fix behavior of ptracers_monitor when monitor output is written to a
451      netcdf-file; still not independent of monitor.F (writes in the same
452      file).
453    o change default value of tRef (put a uniform, meaningful value for ocean
454      & atmos) and initialize sRef (was missing, as Martin mentioned).
455    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
456      to be proportional to enstrophy dissipation length.  Thus,
457       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
458      This is now consistent with Smagorinsky and with the manual.
459    
460    checkpoint57u_post
461    o OBCS and PTRACERS: add open boundary support for passive tracers
462      - either use homogenous (pseudo) v.Neumann conditions or prescribe
463        OB-values from file; this is not different from the way theta and salinity
464        are treated
465      - however, Orlanski-radiation conditions are not supported, and the model
466        will stop if you use pTracers and Orlanski at the same time.
467      - beefed up the rountine obcs_external_fields_load: now only those open
468        boundary values are overwritten with values from files for which there
469        are really files, otherwise the OB-fields remain untouched. This makes
470        it possible to use different OBs at different ends of the domain (as
471        with EXF)
472    o reduce number of exch calls in shap_filt (s2).
473    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
474      truncation level) 4/5 MLAdjust test results (11&12 digits match).
475    
476    checkpoint57t_post
477    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
478    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
479      same truncation, independent of the face number: affects affects several
480      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
481    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
482      note that biharmonic viscosity + no-slip was not tested in any experiment.
483    o fix bug in non-linear free-surf side-drag ; generate new output for
484      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
485    o make mnc honor the writeBinaryPrec flag for most kinds of output
486    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
487    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
488      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
489    o add brackets in multi-terms sum to get same truncation, independent of
490      the face number (manage to get exactly same value of gU,gV at the cs-edge)
491      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
492    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
493      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
494      a maximum grid-scale Reynolds number.  Also, changes all length calculations
495      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
496      Suggested values of viscosity parameters found in mom_calc_visc.
497      Many new viscosity diagnostics available.
498    
499    checkpoint57s_post
500    o Add clearing-house for viscosity calculations, mom_calc_visc and
501      correct numerous bugs in LeithD and Smagorinsky discretizations.  
502      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
503      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
504      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
505      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
506      The Strain-Tension form is now called with useStrainTensonVisc=.true.
507      ViscAhStrain and viscAhTension are now retired.
508    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
509    o In response to JMC's bug report, genmake2 now ignores any soft-links
510      that it finds in the *current* directory when searching for files.
511      Soft-links found in any other source directories will still work as
512      they did before.
513    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
514      a C routine to unlimit the stack size
515    o mnc-ify pkg/aim snapshot vars
516    o mnc-ify pkg/land as requested by Daniel
517    o various changes to mnc including:
518      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
519      - output can now be grouped so that all files within a group
520          change the ITER portion of their names in lock-step together
521      - can now read ("global") PER-FACE (in addition to PER-TILE) files
522          and works with both EXCH1 and EXCH2 (but needs more testing)
523      - writing works for all verification test cases w/ g77 on Linux
524    
525    checkpoint57r_post
526    o make MNC variable initialization happen earlier
527    o add diagnostics for (almost) each term of the momentum Eq.
528    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
529    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
530    o remove MINIMAL_TAVE_OUTPUT option ;
531      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
532    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
533      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
534    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
535    o add time-dependent SST, SSS control
536    o cost terms in ecco/ modularized (new cost_generic.F)
537    o cost_averages routines are modularized (new cost_averagesgeneric.F)
538    o new infrastructure for seaice model vs. obs misfits in seaice/
539      * driver from the_main_loop.F is seaice_cost_driver.F
540      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
541      * gradient check in Exp. 6a of natl_box_adjoint/
542    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
543      (see README file)
544    
545    checkpoint57q_post
546    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
547    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
548      - bug was reported by Jean-Michel and Ian Fenty
549    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
550      update exp. cpl_aim+ocn output.
551    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
552      Needed for high-res. runs with large global files
553      to be able to limit tapelev size
554    o Changed some tests for adjoint:
555      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
556      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
557      * global_ocean.90x40x15/ back to default 3-level checkpointing
558    o Modifications to enable scripted COMMON to MODULE conversion
559      * verification/OpenAD/code/ has necessary scripts and description;
560      * converts, compiles and runs successfully;
561    
562    checkpoint57p_post
563    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
564    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
565      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
566    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
567    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
568      (was already the case for dissipation with mom_vecinv,
569       and also the case for grad.PhiHyd when staggered-timeStep)
570      This will allow to put dissipation out-off the AB time-stepping.
571     Unfortunately, affects truncation error. Update output of exp. that "fails"
572      (cg2d matching number) and leave the others for later: front_relax(10),
573      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
574      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
575    
576    checkpoint57o_post
577    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
578      (2) its ready to be documented during the 20050801 DocFest
579    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
580      for ideal_2D_oce and lab_sea on linux_ia32_g77
581    o set to #undef CTRL_SET_OLD_MAXCVARS_30
582      in global1x1_tot/code_seaice_adj to access indices 32, 33
583      (worth another tag)
584    
585    checkpoint57n_post
586    o adding precip control xx_precip 32
587    o adding swflux control xx_swflux 33
588    o Replacing 10 forcing penalty cost routines by 1 generic.
589    o Implementing partitioning in time-mean and variable adjustment
590      for atmos. state.
591    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
592  o in natl_box_adjoint:  o in natl_box_adjoint:
593    * updated: results_bulk/    * updated exp 1 to 10
594    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
595    o updated global1x1/*_seaice_adj/
596      to incorporate latest changes
597    o enable useSingleCpuIO for mdsio vector routines
598      (applies in particular to tapelev I/O)
599    o removed inefficient K-loop in all active_file*control*.F
600    
601  checkpoint57m_post  checkpoint57m_post
602  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)
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