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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.705 by gforget, Sat Jul 15 01:23:19 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 ecco, option to compute cost for total ssh (mean+anom)
8  o moved ptracer ctrl index 17 -> 32  o consistent with addition of ptracer and ssh in pkg/profiles
9    o profiles: adding ptracer and ssh
10    o testreport: change multi-test output-file name
11      (from output.txt.{name} to output.{name}.txt)
12    o profiles: now ok for mutli-threaded case
13    o seaice: add 4 parameters for different advection schemes for area,
14      (effective) seaice thickness, enthalphy, and snow height. Their default
15      is the standard parameter SEAICEadvScheme
16    o calc_gw:
17     - add cosFacU in zonal viscous flux (harmonic.visc.).
18     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
19       of tutorial_plume_on_slope.
20    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
21    o calc_gw: true flux-form, account for horizontal grid spacing.
22      update rotating_tank results, but not plume_on_slope (affected at
23      truncation level, 11 digits).
24    
25    checkpoint58l_post
26    o calc_gw:
27     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
28     - remove side-drag for now (need to fix it); update plume_on_slope results.
29     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
30    o commit code to make SST/SSS weights spatially variable
31      (based on either variable in-situ or variable initial T/S weights)
32    o pkg/ecco:
33      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
34        now based on horizontally varying weights wthetaLev, wsaltLev
35      * cost_averagesflags now returns year indices in addition to day, month
36      * sflux balance is performed on annual basis
37        (sflxumm, sfluxmm2, bal_sfluxmm)
38      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
39        including separate counting and multipliers
40    o pkg/rbcs
41      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
42    
43    checkpoint58k_post
44    o testreport:
45     - always build in dir. "build" (if not there, mkdir build instead of building
46       & running in input)
47     - run in dir run (if it exists), in build otherwise.
48     - call prepare_run (if input/prepare_run exists)
49     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
50    o pkg/exf modifications to interpolation and rotation routines for more
51       reasonable treatment of North Pole singularity: for tracers North Pole
52       value is set to northernmost zonal-mean value, for zonal velocity it is
53       set to zero, and for meridional velocity it is set to northernmost value.
54    o pkg/exf/exf_check_range.F
55     - add tile index to diagnostics and move stop statement to the very
56       end of the routine.
57    o pkg/diagnostics: (diagnostics_main_init.F)
58      define title of isomorphic variables according to the current config.
59    o pkg/thsice with pkg/seaice dynamics:
60    - fix domain of computation (interior only, required for exf) and do exchanges
61    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
62    o towards a standard way of dealing with multi-threading in MONITOR
63      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
64    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
65       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
66    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
67    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
68    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
69       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
70    o tracer advection:
71     - clean-up and simplify calc_common_factors.F
72     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
73       advection subroutine (but still not used within DST advection S/R)
74    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
75    
76    checkpoint58j_post
77    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
78      from file (collects calls previously in FORWARD_STEP)
79    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
80    o adjoint store dir. adjusted accordingly
81    o genmake2
82      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
83    
84    checkpoint58i_post
85    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
86      on wind stress (SEAICEstressFactor defaults to 1.)
87    o Total number of Timers is finite (<=40): comment out 2 non-essential one
88      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
89    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
90      on CS-grid: no longer loosing mass.
91    o exf & curvilinear-grid: no longer modify longitude xC & xG.
92    o pkg/ggl90: fix sloppy output and fix a bug
93    o pkg/seaice: added SEAICEuseEVPpickup parameter
94      - Set to false in order to start EVP solver with
95        non-EVP pickup files when using SEAICEuseEVP
96      - fix sign error in diffusion in seaice_calc_rhs
97    
98    checkpoint58h_post
99    * Modifications for bottom topography control
100      o replace hFacC by _hFacC at various places
101      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
102      o add non-self-adjoint cg2d_nsa
103      o update autodiff support routines
104      o re-initialise hfac after ctrl_depth_ini
105      o works for 5x5 box, doesnt work for global_ocean.90x40x15
106    * Adding verification for 5x5 box (4-layer) bottom topography control
107    
108    checkpoint58g_post
109    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
110       used for mean seasonal cycle, mean diurnal cycle); add an example
111       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
112    o pkg/ggl90:
113      - add parameter (minimum surface kinetic energy)
114      - fix bug (avoiding division by zero)
115    o couple pkg/thsice to pkg/seaice:
116      - modify advection in seaice to accomodate new scalar fields to be advected
117      - only muliDimAdection scheme work with seaice/thsice
118      - mapping of thsice-variables to seaice-variables, back and forth
119      - does not break the verification experiments, but does not give the
120        desired results either
121    o pkg/seaice
122      - make (default) second order advection a bit less confusing?
123    
124    checkpoint58f_post
125    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
126      to pkg/seaice):
127      - new routines thsice_map_exf and thsice_get_exf provide the interface
128      - add an additional formal parameter to thsice_solve4temp
129    o pkg/exf:
130      - add new fields wspeed, snowprecip (to be able to couple to thsice)
131      - correct Stefan-Boltzmann constant
132      - new parameter for longwave surface emittance
133      - separate some stuff from exf_bulkformulae into new routines  
134        exf_radiation, exf_wind
135      - add new parameters and constants: longwave emissivity for ocean, ice
136        and snow, evaporation parameters over ice
137      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
138        either wind from stress or stress from wind
139    o pkg/thSIce:
140    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
141    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
142       and THSICE_CALC_THICKN
143    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
144    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
145      to make debugging easier.
146    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
147    o pkg/bulk_force:
148      - clean-up comments and parameters ;
149      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
150    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
151      generate new output for test-experiment: aim.5l_cs.thSI
152    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
153      testreport accordingly
154    
155    checkpoint58e_post
156    o SEAICE_CGRID adjoint done
157    o R_STAR adjoint implemented.
158      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
159      * need to sort out init. of h0facc, etc.
160    o Make pkg/profile fully independent of ecco,cost, etc. stuff
161      to be able to use it in pure forward.
162    
163    checkpoint58d_post
164    o upgrade simple test-experiment to tutorial example:
165     step.1: duplicate the experiment and (step.2) will remove the old copy.
166      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
167      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
168      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
169      tutorial_global_oce_biogeo    <- copy of dic_example
170      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
171      tutorial_plume_on_slope       <- copy of plume_on_slope
172      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
173      tutorial_global_oce_optim     <- empty for now (David ?)
174      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
175     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
176    o correct a sign problem in cost_scat.F
177    o obcs and ptracers: fix boundary conditions for advections schemes
178      with larger stencil
179    o thsice adjoint: start
180    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
181      completeness
182    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
183      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
184    o ptracers adjoint:
185      * avoid extensive recomputatations
186      * fix missing re-init. of gptr (missed by TAF)
187    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
188      me to turn off the excessive output to STDOUT that this package produces
189    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
190      and add those terms in Vector-Invariant formulation.
191    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
192      if the control period (xx_hfluxperiod etc) is 0
193    o in profiles pkg, clean routines and fix details
194    o in ecco pkg, reading ssh data:
195      fix problem in case the model does not start at iter0=0
196    o fix mnc-pickup/restart for ptracers
197    o new package prifiles:
198      code to compute profile-based cost by Gael Forget
199      (modifs in ecco, ctrl, autodiff)
200    o Benign bug fix in initialization (spotted by M. Mazloff) of
201      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
202    
203    checkpoint58c_post
204    o adjoint: finish NLFS adjoint and provide reference output in
205      verification/global_ocean.90x40x15/results_ad_nlfs
206    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
207      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
208      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
209      with SEAICE_CGRID defined.
210    o move calendarDumps from "data" to "data.cal" and clean-up the code
211      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
212    o add useEXF & useCAL flags (for now, set in hard-coded way)
213    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
214      (were missing in NH mode, and wrong in quasihydrostatic mode).
215      waiting for Chris updated version of calc_gw to add those CALLs.
216    o fix bug in quasihydrostatic S/R ;
217      add a test for this option: global_ocean.90x40x15.qshyd
218    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
219      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
220    o add on/off flag useOffLine for package OFFLINE
221    o seaice:
222      - modify advection so that it works also on the C-grid
223      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
224        problem in multi-tile runs with C-grid
225      - add flags for clipping ice velocities and/or masking solver forcing
226      - fix drag (ocean on ice) formulation and a bug that caused noise in the
227        C-grid solver
228      - added a few comments to seaice_diffusion.F
229      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
230        are now exclusive)
231      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
232        required re-ordering the code a little:
233       + make DAIRN global variable (defined in SEAICE)
234       + move computation of the viscosities eta and zeta into a new separate
235         routine (because I need to recompute them in seaice_ocean_stress.F)
236    
237    checkpoint58b_post
238    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
239      update output.txt of exp. aim.5l_cs.thSI
240    o various mnc cleanups and improvements:
241      + shrink lookup tables by factor of ~4
242      + better error reporting when running out of lookup space
243      + able to handle longer path/file names (up to 500 chars)
244    o adjoint:
245      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
246      - TBD: "hidden" mom_vecinv recomp. in dynamics
247    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
248     (allow to differentiate between forcing components using new integer flags:
249      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
250     and add new flag to put Dissipation tendency out of Adams-Bashforth.
251    o ecco
252      - enable trend removal from SSH anomaly obs.
253    o adjoint
254      - a fix for PmEpR when #undef EXACT_CONSERV
255      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
256      - try to fix "hidden" recomp. in forward_step for NLFS
257        (NLFS seems broken sometimes after I checked it in)
258    o seaice:
259     - add c-grid version of the dynamic solver:
260       + three new routines that are the c-grid substitute lsr, dynsolver
261         and ostres
262       + put a few fields that were local to dynsolver into global common
263         blocks, so that I can move the computation of stresses etc into
264         seaice_lsr (saves coding but may break the adjoint).
265     - replace more hardwired parameters by runtime parameters
266     - add ice masks that mask the rhs of the implicit solvers where there
267       is no ice (commented out in seaice_dynsolver, because i am not sure
268       if this works properly), eventually this should replace the clipping
269       of ice velocities in seaice_dynsolver to +/-40cm/s.
270    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
271      include it only where its needed
272    o move balancing of fluxes before the call of external_forcing_surf
273    o seaice:
274      - correct units of turning angles (now they are really in degrees)
275      - move computation of GWATX/Y out of main routine into dynsolver
276      - initialize GWATX/Y in seaice_init
277    o Apply mask on Fresh-Water flux (needed for SSH forcing).
278      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
279    o seaice: add runtime flags for turning angles (default to zero)
280    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
281      and trend from exf forcing and ctrl control adjustments
282    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
283      (since checkpoint57x_post)
284    o change the default rotation period to 86164.s = the Earth rotation
285    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
286      and based on a reference stratification. Tested within hs94.cs-32x32x5.
287    o seaice advection: add code for choosing between the default (2nd order
288      central differences) and multiDim advection schemes provided by
289      pkg/generic_advdiff
290    o seaice:
291      - removed all references to SEAICE_GRID.h fields from
292        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
293        (cubed-sphere configuration will change a little)
294      - grid computations in seaice_init are obsolete now.
295      - cleaned up code a little so that is easier to read (hopefully).
296      - added new (better?) discretizations of default advection and diffusion
297        (turn on with SEAICEuseFluxForm)
298      - replace 1 in 3d global fields by kSurface in growth.F
299      
300    checkpoint58a_post
301    o seaice:
302      - bug fix in advect.F
303    o shelfice:
304      - separate shelfice load anomaly from pload (breaks with time
305        dependent forcing), => introduce constant field shelficeLoadAnomaly.
306        Its default is 0., but it may be computed more cleverly from (unknown)
307        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
308        done offline. A good approximation of the pressure load anomaly is
309        necessary to avoid large initial adjustment processes underneath
310        deep-reaching shelfice.
311      - small fix in ISOMIP shelfice_thermodynamics
312      - add more sophisticated thermodynamics of Hellmer (1989), this is
313        now the default
314      - give a few constants more intuitive names
315    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
316      if bulk formulae are used in long integration (especially EmPmR). Turn
317      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
318      if balancePrintMean, the imbalance that is substracted is printed to
319      STDOUT.
320    o fix bug (typo) in obcs_apply_eta.F
321    o add a new package shelfice which enables us to model the circulation
322      underneath shelf-ice with draughts of hundreds of meters.
323     - works
324     - to do: + include improved thermodynamics
325              + check whether kSurfC (from model/inc/SURFACE.h) can be used
326                instead of new field kTopC
327              + can we use topoFile, Ro_surf and existing code in ini_depth.F
328                instead of new field R_shelfIce and new code in ini_depth.F
329                and ini_mask_etc.F?
330              + adjust vertical mixing schemes?
331    o seaice pkg:
332     - add a cpp-flag to include a simple formula for a salinity dependent
333       freezing point of sea water at the surface
334     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
335       meridional stresses are now different (and hopefully correct)
336    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
337       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
338       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
339    o pkg/diagnostics: add options and parameters for regional-statistics
340       diagnostics ; define regions by reading a region-mask from a file
341       (might add other options later)
342    o pkg/bulk_force:
343     - add option and parameters to use AIM surface-flux formulae.
344     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
345       others forcing fields (defined in PARM05, parameter file "data") are loaded
346       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
347     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
348     - use the right EXCH call for uwind,vwind (to work on CS-grid).
349     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
350       and parameters (note: calcWindStress replaces .NOT.readwindstress).
351     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
352    
353    checkpoint58
354    o add "--embed-source" option to genmake2 which, when the supporting
355      tools can be compiled (as determined by genmake2) will turn on the
356      embed_files package which then embeds the entire MITgcm source code
357      (*.[fFhc] + Makefile) used for the build within the executable
358      - requested by CNH but off by default
359      - adds a paltry <9MB to the mitgcmuv executable in most cases
360      - only writes the output when useEMBEDSRC in eedata is true
361    o clean up 3-dim. relaxation codes:
362      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
363      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
364      * Thanks to Tom Haine for testing!
365    
366    checkpoint57z_post
367    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
368      affects output (@ truncation level) of exp. plume_on_slope ; updated.
369    o fix the pickup behavior for obcs in combination with ptracers
370    o fix a bug in ptracers_external_fields_load
371    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
372      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
373    o transfered surface NH pressure to eta field (if exactConserv).
374    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
375         and update lab_sea output.txt file.
376    o completing 3-dim. relaxation code: additional term
377         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
378      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
379      * At compile time, in "EXF_OPTIONS.h" set
380          #define  ALLOW_CLIMTEMP_RELAXATION
381          #define  ALLOW_CLIMSALT_RELAXATION
382      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
383          tauThetaClimRelax3Dim = 15552000.0,
384          tauSaltClimRelax3Dim  = 15552000.0,
385      * 3 cases:
386          1) Use a constant-in-time 3-dim. field
387          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
388          3) Real-time relax. to time-evolving prescribed field
389    o Adding Laplacian-type smoothness constraint on
390      initial and boundary (forcing) controls (ic, bc)
391      * enable at compile-time via
392        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
393      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
394      * Absolute scale somewhat unclear so far
395      * no area weighting was included since no other cost term does so far
396    
397    checkpoint57y_post
398    First step for a NLFS adjoint
399    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
400    o new init. routines for calc_r_star, calc_surf_dr
401    o still need to deal with ini_masks_etc
402    o testreport seemed happy
403    checkpoint57y_pre
404    
405    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
406    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
407    o add new offset feature to offline pkg (plus minor cleanup)
408    o cfc fixes for final year of integration
409    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
410      be in GCHEM_OPTIONS).
411    
412    checkpoint57x_post
413    o fix testreport Pb in multiple test experiment.
414    o cleanup our namelist syntax in verification:
415      - make it more F95 standards compliant (some work still needed)
416      - allows the vast majority of our tests to work with gfortran
417    o Non-Hydrostatic:
418     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
419     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
420    o Allow to apply AB on T,S rather than on AB(gT,gS):
421     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
422     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
423       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
424     - need a "clever" read_pickup to restart from the other AB formulation
425    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
426    o remove some unused variables (reduces number of compiler warnings)
427    o adjoint
428      * Disable useVariableViscosity for adjoint for time being
429        (there are a number of extensive recomputations)
430      * Initialize certain variables needed for adjoint
431    
432    checkpoint57w_post
433    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
434                 fix the singleCpuIO RS version of MDSWRITEFIELD
435       and add a WARNING if using globalFiles=T with multi-processors.
436    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
437      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
438    o tracer advection scheme:
439      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
440       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
441       was not very convenient).
442      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
443       (further tests needed for the implicit DST & Flux-Limiter schemes).
444    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
445      and sRef for convenience, handy, when you want to initialize
446      ptracers in a large domain with a constant non-zero value. Also,
447      untangle ptracers_init.F a little.
448    
449    checkpoint57v_post
450    o change dome exp. to use variable viscosity in side-drag terms.
451    o remove all the files from the cfc_offline test since they are now
452      incorporated into tutorial_cfc_offline which has been producing
453      identical results for a few days of testing
454    o add new parameter: sideDragFactor to enable half-slip-side BC
455      and change side-drag S/R to use viscosity from mom_calc_visc
456      (can switch back by setting sideDragFactor=0.); affects results at
457      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
458       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
459    o vorticity & strain are now computed without masking, to account for
460      no-slip-side BC in variable viscosity calculation ; mask is applied
461      anyway later on, before computing advection/coriolis terms.
462    o modify exp4 to test new obcs support for reading from external files
463      and for passive tracers
464    o fix behavior of ptracers_monitor when monitor output is written to a
465      netcdf-file; still not independent of monitor.F (writes in the same
466      file).
467    o change default value of tRef (put a uniform, meaningful value for ocean
468      & atmos) and initialize sRef (was missing, as Martin mentioned).
469    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
470      to be proportional to enstrophy dissipation length.  Thus,
471       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
472      This is now consistent with Smagorinsky and with the manual.
473    
474    checkpoint57u_post
475    o OBCS and PTRACERS: add open boundary support for passive tracers
476      - either use homogenous (pseudo) v.Neumann conditions or prescribe
477        OB-values from file; this is not different from the way theta and salinity
478        are treated
479      - however, Orlanski-radiation conditions are not supported, and the model
480        will stop if you use pTracers and Orlanski at the same time.
481      - beefed up the rountine obcs_external_fields_load: now only those open
482        boundary values are overwritten with values from files for which there
483        are really files, otherwise the OB-fields remain untouched. This makes
484        it possible to use different OBs at different ends of the domain (as
485        with EXF)
486    o reduce number of exch calls in shap_filt (s2).
487    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
488      truncation level) 4/5 MLAdjust test results (11&12 digits match).
489    
490    checkpoint57t_post
491    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
492    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
493      same truncation, independent of the face number: affects affects several
494      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
495    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
496      note that biharmonic viscosity + no-slip was not tested in any experiment.
497    o fix bug in non-linear free-surf side-drag ; generate new output for
498      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
499    o make mnc honor the writeBinaryPrec flag for most kinds of output
500    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
501    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
502      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
503    o add brackets in multi-terms sum to get same truncation, independent of
504      the face number (manage to get exactly same value of gU,gV at the cs-edge)
505      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
506    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
507      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
508      a maximum grid-scale Reynolds number.  Also, changes all length calculations
509      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
510      Suggested values of viscosity parameters found in mom_calc_visc.
511      Many new viscosity diagnostics available.
512    
513    checkpoint57s_post
514    o Add clearing-house for viscosity calculations, mom_calc_visc and
515      correct numerous bugs in LeithD and Smagorinsky discretizations.  
516      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
517      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
518      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
519      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
520      The Strain-Tension form is now called with useStrainTensonVisc=.true.
521      ViscAhStrain and viscAhTension are now retired.
522    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
523    o In response to JMC's bug report, genmake2 now ignores any soft-links
524      that it finds in the *current* directory when searching for files.
525      Soft-links found in any other source directories will still work as
526      they did before.
527    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
528      a C routine to unlimit the stack size
529    o mnc-ify pkg/aim snapshot vars
530    o mnc-ify pkg/land as requested by Daniel
531    o various changes to mnc including:
532      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
533      - output can now be grouped so that all files within a group
534          change the ITER portion of their names in lock-step together
535      - can now read ("global") PER-FACE (in addition to PER-TILE) files
536          and works with both EXCH1 and EXCH2 (but needs more testing)
537      - writing works for all verification test cases w/ g77 on Linux
538    
539    checkpoint57r_post
540    o make MNC variable initialization happen earlier
541    o add diagnostics for (almost) each term of the momentum Eq.
542    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
543    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
544    o remove MINIMAL_TAVE_OUTPUT option ;
545      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
546    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
547      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
548    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
549    o add time-dependent SST, SSS control
550    o cost terms in ecco/ modularized (new cost_generic.F)
551    o cost_averages routines are modularized (new cost_averagesgeneric.F)
552    o new infrastructure for seaice model vs. obs misfits in seaice/
553      * driver from the_main_loop.F is seaice_cost_driver.F
554      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
555      * gradient check in Exp. 6a of natl_box_adjoint/
556    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
557      (see README file)
558    
559    checkpoint57q_post
560    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
561    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
562      - bug was reported by Jean-Michel and Ian Fenty
563    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
564      update exp. cpl_aim+ocn output.
565    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
566      Needed for high-res. runs with large global files
567      to be able to limit tapelev size
568    o Changed some tests for adjoint:
569      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
570      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
571      * global_ocean.90x40x15/ back to default 3-level checkpointing
572    o Modifications to enable scripted COMMON to MODULE conversion
573      * verification/OpenAD/code/ has necessary scripts and description;
574      * converts, compiles and runs successfully;
575    
576    checkpoint57p_post
577    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
578    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
579      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
580    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
581    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
582      (was already the case for dissipation with mom_vecinv,
583       and also the case for grad.PhiHyd when staggered-timeStep)
584      This will allow to put dissipation out-off the AB time-stepping.
585     Unfortunately, affects truncation error. Update output of exp. that "fails"
586      (cg2d matching number) and leave the others for later: front_relax(10),
587      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
588      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
589    
590    checkpoint57o_post
591    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
592      (2) its ready to be documented during the 20050801 DocFest
593    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
594      for ideal_2D_oce and lab_sea on linux_ia32_g77
595    o set to #undef CTRL_SET_OLD_MAXCVARS_30
596      in global1x1_tot/code_seaice_adj to access indices 32, 33
597      (worth another tag)
598    
599    checkpoint57n_post
600    o adding precip control xx_precip 32
601    o adding swflux control xx_swflux 33
602    o Replacing 10 forcing penalty cost routines by 1 generic.
603    o Implementing partitioning in time-mean and variable adjustment
604      for atmos. state.
605    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
606  o in natl_box_adjoint:  o in natl_box_adjoint:
607    * updated: results_bulk/    * updated exp 1 to 10
608    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
609    o updated global1x1/*_seaice_adj/
610      to incorporate latest changes
611    o enable useSingleCpuIO for mdsio vector routines
612      (applies in particular to tapelev I/O)
613    o removed inefficient K-loop in all active_file*control*.F
614    
615  checkpoint57m_post  checkpoint57m_post
616  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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