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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.710 by jmc, Fri Aug 4 23:36:17 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 multi-threading and IO:
8  o moved ptracer ctrl index 17 -> 32    - all threads call READ_FLD S/R (needed if using SingleCpuIO):
9        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
10      - barrier before and after reading.
11      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
12      - avoid using MDS_WRITELOCAL for LAND pkg output.
13      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
14        common-block variables ; Allows multi-threading with master-thread IO.
15    o change default MAX_NO_THREADS from 32 to 4 ;
16      and stop cleanly when MAX_NO_THREADS is too small.
17    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
18    
19    checkpoint58m_post
20    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
21       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
22    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
23       keep global_ocean.90x40x15 (for AD testing) with former secondary test
24       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
25    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
26        add MITgcm_tutorials (= code + all the tutorials)
27    o ecco, option to compute cost for total ssh (mean+anom)
28    o consistent with addition of ptracer and ssh in pkg/profiles
29    o profiles: adding ptracer and ssh
30    o testreport: change multi-test output-file name
31      (from output.txt.{name} to output.{name}.txt)
32    o profiles: now ok for mutli-threaded case
33    o seaice: add 4 parameters for different advection schemes for area,
34      (effective) seaice thickness, enthalphy, and snow height. Their default
35      is the standard parameter SEAICEadvScheme
36    o calc_gw:
37     - add cosFacU in zonal viscous flux (harmonic.visc.).
38     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
39       of tutorial_plume_on_slope.
40    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
41    o calc_gw: true flux-form, account for horizontal grid spacing.
42      update rotating_tank results, but not plume_on_slope (affected at
43      truncation level, 11 digits).
44    
45    checkpoint58l_post
46    o calc_gw:
47     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
48     - remove side-drag for now (need to fix it); update plume_on_slope results.
49     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
50    o commit code to make SST/SSS weights spatially variable
51      (based on either variable in-situ or variable initial T/S weights)
52    o pkg/ecco:
53      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
54        now based on horizontally varying weights wthetaLev, wsaltLev
55      * cost_averagesflags now returns year indices in addition to day, month
56      * sflux balance is performed on annual basis
57        (sflxumm, sfluxmm2, bal_sfluxmm)
58      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
59        including separate counting and multipliers
60    o pkg/rbcs
61      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
62    
63    checkpoint58k_post
64    o testreport:
65     - always build in dir. "build" (if not there, mkdir build instead of building
66       & running in input)
67     - run in dir run (if it exists), in build otherwise.
68     - call prepare_run (if input/prepare_run exists)
69     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
70    o pkg/exf modifications to interpolation and rotation routines for more
71       reasonable treatment of North Pole singularity: for tracers North Pole
72       value is set to northernmost zonal-mean value, for zonal velocity it is
73       set to zero, and for meridional velocity it is set to northernmost value.
74    o pkg/exf/exf_check_range.F
75     - add tile index to diagnostics and move stop statement to the very
76       end of the routine.
77    o pkg/diagnostics: (diagnostics_main_init.F)
78      define title of isomorphic variables according to the current config.
79    o pkg/thsice with pkg/seaice dynamics:
80    - fix domain of computation (interior only, required for exf) and do exchanges
81    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
82    o towards a standard way of dealing with multi-threading in MONITOR
83      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
84    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
85       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
86    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
87    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
88    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
89       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
90    o tracer advection:
91     - clean-up and simplify calc_common_factors.F
92     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
93       advection subroutine (but still not used within DST advection S/R)
94    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
95    
96    checkpoint58j_post
97    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
98      from file (collects calls previously in FORWARD_STEP)
99    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
100    o adjoint store dir. adjusted accordingly
101    o genmake2
102      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
103    
104    checkpoint58i_post
105    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
106      on wind stress (SEAICEstressFactor defaults to 1.)
107    o Total number of Timers is finite (<=40): comment out 2 non-essential one
108      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
109    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
110      on CS-grid: no longer loosing mass.
111    o exf & curvilinear-grid: no longer modify longitude xC & xG.
112    o pkg/ggl90: fix sloppy output and fix a bug
113    o pkg/seaice: added SEAICEuseEVPpickup parameter
114      - Set to false in order to start EVP solver with
115        non-EVP pickup files when using SEAICEuseEVP
116      - fix sign error in diffusion in seaice_calc_rhs
117    
118    checkpoint58h_post
119    * Modifications for bottom topography control
120      o replace hFacC by _hFacC at various places
121      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
122      o add non-self-adjoint cg2d_nsa
123      o update autodiff support routines
124      o re-initialise hfac after ctrl_depth_ini
125      o works for 5x5 box, doesnt work for global_ocean.90x40x15
126    * Adding verification for 5x5 box (4-layer) bottom topography control
127    
128    checkpoint58g_post
129    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
130       used for mean seasonal cycle, mean diurnal cycle); add an example
131       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
132    o pkg/ggl90:
133      - add parameter (minimum surface kinetic energy)
134      - fix bug (avoiding division by zero)
135    o couple pkg/thsice to pkg/seaice:
136      - modify advection in seaice to accomodate new scalar fields to be advected
137      - only muliDimAdection scheme work with seaice/thsice
138      - mapping of thsice-variables to seaice-variables, back and forth
139      - does not break the verification experiments, but does not give the
140        desired results either
141    o pkg/seaice
142      - make (default) second order advection a bit less confusing?
143    
144    checkpoint58f_post
145    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
146      to pkg/seaice):
147      - new routines thsice_map_exf and thsice_get_exf provide the interface
148      - add an additional formal parameter to thsice_solve4temp
149    o pkg/exf:
150      - add new fields wspeed, snowprecip (to be able to couple to thsice)
151      - correct Stefan-Boltzmann constant
152      - new parameter for longwave surface emittance
153      - separate some stuff from exf_bulkformulae into new routines  
154        exf_radiation, exf_wind
155      - add new parameters and constants: longwave emissivity for ocean, ice
156        and snow, evaporation parameters over ice
157      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
158        either wind from stress or stress from wind
159    o pkg/thSIce:
160    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
161    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
162       and THSICE_CALC_THICKN
163    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
164    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
165      to make debugging easier.
166    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
167    o pkg/bulk_force:
168      - clean-up comments and parameters ;
169      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
170    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
171      generate new output for test-experiment: aim.5l_cs.thSI
172    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
173      testreport accordingly
174    
175    checkpoint58e_post
176    o SEAICE_CGRID adjoint done
177    o R_STAR adjoint implemented.
178      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
179      * need to sort out init. of h0facc, etc.
180    o Make pkg/profile fully independent of ecco,cost, etc. stuff
181      to be able to use it in pure forward.
182    
183    checkpoint58d_post
184    o upgrade simple test-experiment to tutorial example:
185     step.1: duplicate the experiment and (step.2) will remove the old copy.
186      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
187      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
188      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
189      tutorial_global_oce_biogeo    <- copy of dic_example
190      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
191      tutorial_plume_on_slope       <- copy of plume_on_slope
192      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
193      tutorial_global_oce_optim     <- empty for now (David ?)
194      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
195     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
196    o correct a sign problem in cost_scat.F
197    o obcs and ptracers: fix boundary conditions for advections schemes
198      with larger stencil
199    o thsice adjoint: start
200    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
201      completeness
202    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
203      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
204    o ptracers adjoint:
205      * avoid extensive recomputatations
206      * fix missing re-init. of gptr (missed by TAF)
207    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
208      me to turn off the excessive output to STDOUT that this package produces
209    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
210      and add those terms in Vector-Invariant formulation.
211    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
212      if the control period (xx_hfluxperiod etc) is 0
213    o in profiles pkg, clean routines and fix details
214    o in ecco pkg, reading ssh data:
215      fix problem in case the model does not start at iter0=0
216    o fix mnc-pickup/restart for ptracers
217    o new package prifiles:
218      code to compute profile-based cost by Gael Forget
219      (modifs in ecco, ctrl, autodiff)
220    o Benign bug fix in initialization (spotted by M. Mazloff) of
221      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
222    
223    checkpoint58c_post
224    o adjoint: finish NLFS adjoint and provide reference output in
225      verification/global_ocean.90x40x15/results_ad_nlfs
226    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
227      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
228      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
229      with SEAICE_CGRID defined.
230    o move calendarDumps from "data" to "data.cal" and clean-up the code
231      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
232    o add useEXF & useCAL flags (for now, set in hard-coded way)
233    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
234      (were missing in NH mode, and wrong in quasihydrostatic mode).
235      waiting for Chris updated version of calc_gw to add those CALLs.
236    o fix bug in quasihydrostatic S/R ;
237      add a test for this option: global_ocean.90x40x15.qshyd
238    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
239      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
240    o add on/off flag useOffLine for package OFFLINE
241    o seaice:
242      - modify advection so that it works also on the C-grid
243      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
244        problem in multi-tile runs with C-grid
245      - add flags for clipping ice velocities and/or masking solver forcing
246      - fix drag (ocean on ice) formulation and a bug that caused noise in the
247        C-grid solver
248      - added a few comments to seaice_diffusion.F
249      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
250        are now exclusive)
251      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
252        required re-ordering the code a little:
253       + make DAIRN global variable (defined in SEAICE)
254       + move computation of the viscosities eta and zeta into a new separate
255         routine (because I need to recompute them in seaice_ocean_stress.F)
256    
257    checkpoint58b_post
258    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
259      update output.txt of exp. aim.5l_cs.thSI
260    o various mnc cleanups and improvements:
261      + shrink lookup tables by factor of ~4
262      + better error reporting when running out of lookup space
263      + able to handle longer path/file names (up to 500 chars)
264    o adjoint:
265      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
266      - TBD: "hidden" mom_vecinv recomp. in dynamics
267    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
268     (allow to differentiate between forcing components using new integer flags:
269      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
270     and add new flag to put Dissipation tendency out of Adams-Bashforth.
271    o ecco
272      - enable trend removal from SSH anomaly obs.
273    o adjoint
274      - a fix for PmEpR when #undef EXACT_CONSERV
275      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
276      - try to fix "hidden" recomp. in forward_step for NLFS
277        (NLFS seems broken sometimes after I checked it in)
278    o seaice:
279     - add c-grid version of the dynamic solver:
280       + three new routines that are the c-grid substitute lsr, dynsolver
281         and ostres
282       + put a few fields that were local to dynsolver into global common
283         blocks, so that I can move the computation of stresses etc into
284         seaice_lsr (saves coding but may break the adjoint).
285     - replace more hardwired parameters by runtime parameters
286     - add ice masks that mask the rhs of the implicit solvers where there
287       is no ice (commented out in seaice_dynsolver, because i am not sure
288       if this works properly), eventually this should replace the clipping
289       of ice velocities in seaice_dynsolver to +/-40cm/s.
290    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
291      include it only where its needed
292    o move balancing of fluxes before the call of external_forcing_surf
293    o seaice:
294      - correct units of turning angles (now they are really in degrees)
295      - move computation of GWATX/Y out of main routine into dynsolver
296      - initialize GWATX/Y in seaice_init
297    o Apply mask on Fresh-Water flux (needed for SSH forcing).
298      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
299    o seaice: add runtime flags for turning angles (default to zero)
300    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
301      and trend from exf forcing and ctrl control adjustments
302    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
303      (since checkpoint57x_post)
304    o change the default rotation period to 86164.s = the Earth rotation
305    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
306      and based on a reference stratification. Tested within hs94.cs-32x32x5.
307    o seaice advection: add code for choosing between the default (2nd order
308      central differences) and multiDim advection schemes provided by
309      pkg/generic_advdiff
310    o seaice:
311      - removed all references to SEAICE_GRID.h fields from
312        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
313        (cubed-sphere configuration will change a little)
314      - grid computations in seaice_init are obsolete now.
315      - cleaned up code a little so that is easier to read (hopefully).
316      - added new (better?) discretizations of default advection and diffusion
317        (turn on with SEAICEuseFluxForm)
318      - replace 1 in 3d global fields by kSurface in growth.F
319      
320    checkpoint58a_post
321    o seaice:
322      - bug fix in advect.F
323    o shelfice:
324      - separate shelfice load anomaly from pload (breaks with time
325        dependent forcing), => introduce constant field shelficeLoadAnomaly.
326        Its default is 0., but it may be computed more cleverly from (unknown)
327        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
328        done offline. A good approximation of the pressure load anomaly is
329        necessary to avoid large initial adjustment processes underneath
330        deep-reaching shelfice.
331      - small fix in ISOMIP shelfice_thermodynamics
332      - add more sophisticated thermodynamics of Hellmer (1989), this is
333        now the default
334      - give a few constants more intuitive names
335    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
336      if bulk formulae are used in long integration (especially EmPmR). Turn
337      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
338      if balancePrintMean, the imbalance that is substracted is printed to
339      STDOUT.
340    o fix bug (typo) in obcs_apply_eta.F
341    o add a new package shelfice which enables us to model the circulation
342      underneath shelf-ice with draughts of hundreds of meters.
343     - works
344     - to do: + include improved thermodynamics
345              + check whether kSurfC (from model/inc/SURFACE.h) can be used
346                instead of new field kTopC
347              + can we use topoFile, Ro_surf and existing code in ini_depth.F
348                instead of new field R_shelfIce and new code in ini_depth.F
349                and ini_mask_etc.F?
350              + adjust vertical mixing schemes?
351    o seaice pkg:
352     - add a cpp-flag to include a simple formula for a salinity dependent
353       freezing point of sea water at the surface
354     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
355       meridional stresses are now different (and hopefully correct)
356    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
357       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
358       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
359    o pkg/diagnostics: add options and parameters for regional-statistics
360       diagnostics ; define regions by reading a region-mask from a file
361       (might add other options later)
362    o pkg/bulk_force:
363     - add option and parameters to use AIM surface-flux formulae.
364     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
365       others forcing fields (defined in PARM05, parameter file "data") are loaded
366       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
367     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
368     - use the right EXCH call for uwind,vwind (to work on CS-grid).
369     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
370       and parameters (note: calcWindStress replaces .NOT.readwindstress).
371     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
372    
373    checkpoint58
374    o add "--embed-source" option to genmake2 which, when the supporting
375      tools can be compiled (as determined by genmake2) will turn on the
376      embed_files package which then embeds the entire MITgcm source code
377      (*.[fFhc] + Makefile) used for the build within the executable
378      - requested by CNH but off by default
379      - adds a paltry <9MB to the mitgcmuv executable in most cases
380      - only writes the output when useEMBEDSRC in eedata is true
381    o clean up 3-dim. relaxation codes:
382      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
383      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
384      * Thanks to Tom Haine for testing!
385    
386    checkpoint57z_post
387    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
388      affects output (@ truncation level) of exp. plume_on_slope ; updated.
389    o fix the pickup behavior for obcs in combination with ptracers
390    o fix a bug in ptracers_external_fields_load
391    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
392      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
393    o transfered surface NH pressure to eta field (if exactConserv).
394    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
395         and update lab_sea output.txt file.
396    o completing 3-dim. relaxation code: additional term
397         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
398      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
399      * At compile time, in "EXF_OPTIONS.h" set
400          #define  ALLOW_CLIMTEMP_RELAXATION
401          #define  ALLOW_CLIMSALT_RELAXATION
402      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
403          tauThetaClimRelax3Dim = 15552000.0,
404          tauSaltClimRelax3Dim  = 15552000.0,
405      * 3 cases:
406          1) Use a constant-in-time 3-dim. field
407          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
408          3) Real-time relax. to time-evolving prescribed field
409    o Adding Laplacian-type smoothness constraint on
410      initial and boundary (forcing) controls (ic, bc)
411      * enable at compile-time via
412        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
413      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
414      * Absolute scale somewhat unclear so far
415      * no area weighting was included since no other cost term does so far
416    
417    checkpoint57y_post
418    First step for a NLFS adjoint
419    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
420    o new init. routines for calc_r_star, calc_surf_dr
421    o still need to deal with ini_masks_etc
422    o testreport seemed happy
423    checkpoint57y_pre
424    
425    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
426    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
427    o add new offset feature to offline pkg (plus minor cleanup)
428    o cfc fixes for final year of integration
429    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
430      be in GCHEM_OPTIONS).
431    
432    checkpoint57x_post
433    o fix testreport Pb in multiple test experiment.
434    o cleanup our namelist syntax in verification:
435      - make it more F95 standards compliant (some work still needed)
436      - allows the vast majority of our tests to work with gfortran
437    o Non-Hydrostatic:
438     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
439     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
440    o Allow to apply AB on T,S rather than on AB(gT,gS):
441     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
442     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
443       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
444     - need a "clever" read_pickup to restart from the other AB formulation
445    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
446    o remove some unused variables (reduces number of compiler warnings)
447    o adjoint
448      * Disable useVariableViscosity for adjoint for time being
449        (there are a number of extensive recomputations)
450      * Initialize certain variables needed for adjoint
451    
452    checkpoint57w_post
453    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
454                 fix the singleCpuIO RS version of MDSWRITEFIELD
455       and add a WARNING if using globalFiles=T with multi-processors.
456    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
457      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
458    o tracer advection scheme:
459      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
460       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
461       was not very convenient).
462      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
463       (further tests needed for the implicit DST & Flux-Limiter schemes).
464    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
465      and sRef for convenience, handy, when you want to initialize
466      ptracers in a large domain with a constant non-zero value. Also,
467      untangle ptracers_init.F a little.
468    
469    checkpoint57v_post
470    o change dome exp. to use variable viscosity in side-drag terms.
471    o remove all the files from the cfc_offline test since they are now
472      incorporated into tutorial_cfc_offline which has been producing
473      identical results for a few days of testing
474    o add new parameter: sideDragFactor to enable half-slip-side BC
475      and change side-drag S/R to use viscosity from mom_calc_visc
476      (can switch back by setting sideDragFactor=0.); affects results at
477      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
478       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
479    o vorticity & strain are now computed without masking, to account for
480      no-slip-side BC in variable viscosity calculation ; mask is applied
481      anyway later on, before computing advection/coriolis terms.
482    o modify exp4 to test new obcs support for reading from external files
483      and for passive tracers
484    o fix behavior of ptracers_monitor when monitor output is written to a
485      netcdf-file; still not independent of monitor.F (writes in the same
486      file).
487    o change default value of tRef (put a uniform, meaningful value for ocean
488      & atmos) and initialize sRef (was missing, as Martin mentioned).
489    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
490      to be proportional to enstrophy dissipation length.  Thus,
491       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
492      This is now consistent with Smagorinsky and with the manual.
493    
494    checkpoint57u_post
495    o OBCS and PTRACERS: add open boundary support for passive tracers
496      - either use homogenous (pseudo) v.Neumann conditions or prescribe
497        OB-values from file; this is not different from the way theta and salinity
498        are treated
499      - however, Orlanski-radiation conditions are not supported, and the model
500        will stop if you use pTracers and Orlanski at the same time.
501      - beefed up the rountine obcs_external_fields_load: now only those open
502        boundary values are overwritten with values from files for which there
503        are really files, otherwise the OB-fields remain untouched. This makes
504        it possible to use different OBs at different ends of the domain (as
505        with EXF)
506    o reduce number of exch calls in shap_filt (s2).
507    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
508      truncation level) 4/5 MLAdjust test results (11&12 digits match).
509    
510    checkpoint57t_post
511    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
512    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
513      same truncation, independent of the face number: affects affects several
514      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
515    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
516      note that biharmonic viscosity + no-slip was not tested in any experiment.
517    o fix bug in non-linear free-surf side-drag ; generate new output for
518      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
519    o make mnc honor the writeBinaryPrec flag for most kinds of output
520    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
521    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
522      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
523    o add brackets in multi-terms sum to get same truncation, independent of
524      the face number (manage to get exactly same value of gU,gV at the cs-edge)
525      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
526    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
527      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
528      a maximum grid-scale Reynolds number.  Also, changes all length calculations
529      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
530      Suggested values of viscosity parameters found in mom_calc_visc.
531      Many new viscosity diagnostics available.
532    
533    checkpoint57s_post
534    o Add clearing-house for viscosity calculations, mom_calc_visc and
535      correct numerous bugs in LeithD and Smagorinsky discretizations.  
536      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
537      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
538      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
539      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
540      The Strain-Tension form is now called with useStrainTensonVisc=.true.
541      ViscAhStrain and viscAhTension are now retired.
542    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
543    o In response to JMC's bug report, genmake2 now ignores any soft-links
544      that it finds in the *current* directory when searching for files.
545      Soft-links found in any other source directories will still work as
546      they did before.
547    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
548      a C routine to unlimit the stack size
549    o mnc-ify pkg/aim snapshot vars
550    o mnc-ify pkg/land as requested by Daniel
551    o various changes to mnc including:
552      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
553      - output can now be grouped so that all files within a group
554          change the ITER portion of their names in lock-step together
555      - can now read ("global") PER-FACE (in addition to PER-TILE) files
556          and works with both EXCH1 and EXCH2 (but needs more testing)
557      - writing works for all verification test cases w/ g77 on Linux
558    
559    checkpoint57r_post
560    o make MNC variable initialization happen earlier
561    o add diagnostics for (almost) each term of the momentum Eq.
562    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
563    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
564    o remove MINIMAL_TAVE_OUTPUT option ;
565      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
566    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
567      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
568    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
569    o add time-dependent SST, SSS control
570    o cost terms in ecco/ modularized (new cost_generic.F)
571    o cost_averages routines are modularized (new cost_averagesgeneric.F)
572    o new infrastructure for seaice model vs. obs misfits in seaice/
573      * driver from the_main_loop.F is seaice_cost_driver.F
574      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
575      * gradient check in Exp. 6a of natl_box_adjoint/
576    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
577      (see README file)
578    
579    checkpoint57q_post
580    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
581    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
582      - bug was reported by Jean-Michel and Ian Fenty
583    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
584      update exp. cpl_aim+ocn output.
585    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
586      Needed for high-res. runs with large global files
587      to be able to limit tapelev size
588    o Changed some tests for adjoint:
589      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
590      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
591      * global_ocean.90x40x15/ back to default 3-level checkpointing
592    o Modifications to enable scripted COMMON to MODULE conversion
593      * verification/OpenAD/code/ has necessary scripts and description;
594      * converts, compiles and runs successfully;
595    
596    checkpoint57p_post
597    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
598    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
599      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
600    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
601    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
602      (was already the case for dissipation with mom_vecinv,
603       and also the case for grad.PhiHyd when staggered-timeStep)
604      This will allow to put dissipation out-off the AB time-stepping.
605     Unfortunately, affects truncation error. Update output of exp. that "fails"
606      (cg2d matching number) and leave the others for later: front_relax(10),
607      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
608      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
609    
610    checkpoint57o_post
611    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
612      (2) its ready to be documented during the 20050801 DocFest
613    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
614      for ideal_2D_oce and lab_sea on linux_ia32_g77
615    o set to #undef CTRL_SET_OLD_MAXCVARS_30
616      in global1x1_tot/code_seaice_adj to access indices 32, 33
617      (worth another tag)
618    
619    checkpoint57n_post
620    o adding precip control xx_precip 32
621    o adding swflux control xx_swflux 33
622    o Replacing 10 forcing penalty cost routines by 1 generic.
623    o Implementing partitioning in time-mean and variable adjustment
624      for atmos. state.
625    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
626  o in natl_box_adjoint:  o in natl_box_adjoint:
627    * updated: results_bulk/    * updated exp 1 to 10
628    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
629    o updated global1x1/*_seaice_adj/
630      to incorporate latest changes
631    o enable useSingleCpuIO for mdsio vector routines
632      (applies in particular to tapelev I/O)
633    o removed inefficient K-loop in all active_file*control*.F
634    
635  checkpoint57m_post  checkpoint57m_post
636  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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