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revision 1.463 by jmc, Tue Mar 1 16:54:32 2005 UTC revision 1.669 by heimbach, Wed Jun 7 02:02:52 2006 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint58h_post
8    * Modifications for bottom topography control
9      o replace hFacC by _hFacC at various places
10      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
11      o add non-self-adjoint cg2d_nsa
12      o update autodiff support routines
13      o re-initialise hfac after ctrl_depth_ini
14      o works for 5x5 box, doesnt work for global_ocean.90x40x15
15    * Adding verification for 5x5 box (4-layer) bottom topography control
16    
17    checkpoint58g_post
18    o pkg/ggl90:
19      - add parameter (minimum surface kinetic energy)
20      - fix bug (avoiding division by zero)
21    o couple pkg/thsice to pkg/seaice:
22      - modify advection in seaice to accomodate new scalar fields to be advected
23      - only muliDimAdection scheme work with seaice/thsice
24      - mapping of thsice-variables to seaice-variables, back and forth
25      - does not break the verification experiments, but does not give the
26        desired results either
27    o pkg/seaice
28      - make (default) second order advection a bit less confusing?
29    
30    checkpoint58f_post
31    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
32      to pkg/seaice):
33      - new routines thsice_map_exf and thsice_get_exf provide the interface
34      - add an additional formal parameter to thsice_solve4temp
35    o pkg/exf:
36      - add new fields wspeed, snowprecip (to be able to couple to thsice)
37      - correct Stefan-Boltzmann constant
38      - new parameter for longwave surface emittance
39      - separate some stuff from exf_bulkformulae into new routines  
40        exf_radiation, exf_wind
41      - add new parameters and constants: longwave emissivity for ocean, ice
42        and snow, evaporation parameters over ice
43      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
44        either wind from stress or stress from wind
45    o pkg/thSIce:
46    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
47    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
48       and THSICE_CALC_THICKN
49    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
50    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
51      to make debugging easier.
52    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
53    o pkg/bulk_force:
54      - clean-up comments and parameters ;
55      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
56    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
57      generate new output for test-experiment: aim.5l_cs.thSI
58    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
59      testreport accordingly
60    
61    checkpoint58e_post
62    o SEAICE_CGRID adjoint done
63    o R_STAR adjoint implemented.
64      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
65      * need to sort out init. of h0facc, etc.
66    o Make pkg/profile fully independent of ecco,cost, etc. stuff
67      to be able to use it in pure forward.
68    
69    checkpoint58d_post
70    o upgrade simple test-experiment to tutorial example:
71     step.1: duplicate the experiment and (step.2) will remove the old copy.
72      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
73      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
74      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
75      tutorial_global_oce_biogeo    <- copy of dic_example
76      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
77      tutorial_plume_on_slope       <- copy of plume_on_slope
78      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
79      tutorial_global_oce_optim     <- empty for now (David ?)
80      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
81     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
82    o correct a sign problem in cost_scat.F
83    o obcs and ptracers: fix boundary conditions for advections schemes
84      with larger stencil
85    o thsice adjoint: start
86    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
87      completeness
88    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
89      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
90    o ptracers adjoint:
91      * avoid extensive recomputatations
92      * fix missing re-init. of gptr (missed by TAF)
93    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
94      me to turn off the excessive output to STDOUT that this package produces
95    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
96      and add those terms in Vector-Invariant formulation.
97    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
98      if the control period (xx_hfluxperiod etc) is 0
99    o in profiles pkg, clean routines and fix details
100    o in ecco pkg, reading ssh data:
101      fix problem in case the model does not start at iter0=0
102    o fix mnc-pickup/restart for ptracers
103    o new package prifiles:
104      code to compute profile-based cost by Gael Forget
105      (modifs in ecco, ctrl, autodiff)
106    o Benign bug fix in initialization (spotted by M. Mazloff) of
107      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
108    
109    checkpoint58c_post
110    o adjoint: finish NLFS adjoint and provide reference output in
111      verification/global_ocean.90x40x15/results_ad_nlfs
112    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
113      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
114      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
115      with SEAICE_CGRID defined.
116    o move calendarDumps from "data" to "data.cal" and clean-up the code
117      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
118    o add useEXF & useCAL flags (for now, set in hard-coded way)
119    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
120      (were missing in NH mode, and wrong in quasihydrostatic mode).
121      waiting for Chris updated version of calc_gw to add those CALLs.
122    o fix bug in quasihydrostatic S/R ;
123      add a test for this option: global_ocean.90x40x15.qshyd
124    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
125      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
126    o add on/off flag useOffLine for package OFFLINE
127    o seaice:
128      - modify advection so that it works also on the C-grid
129      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
130        problem in multi-tile runs with C-grid
131      - add flags for clipping ice velocities and/or masking solver forcing
132      - fix drag (ocean on ice) formulation and a bug that caused noise in the
133        C-grid solver
134      - added a few comments to seaice_diffusion.F
135      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
136        are now exclusive)
137      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
138        required re-ordering the code a little:
139       + make DAIRN global variable (defined in SEAICE)
140       + move computation of the viscosities eta and zeta into a new separate
141         routine (because I need to recompute them in seaice_ocean_stress.F)
142    
143    checkpoint58b_post
144    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
145      update output.txt of exp. aim.5l_cs.thSI
146    o various mnc cleanups and improvements:
147      + shrink lookup tables by factor of ~4
148      + better error reporting when running out of lookup space
149      + able to handle longer path/file names (up to 500 chars)
150    o adjoint:
151      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
152      - TBD: "hidden" mom_vecinv recomp. in dynamics
153    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
154     (allow to differentiate between forcing components using new integer flags:
155      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
156     and add new flag to put Dissipation tendency out of Adams-Bashforth.
157    o ecco
158      - enable trend removal from SSH anomaly obs.
159    o adjoint
160      - a fix for PmEpR when #undef EXACT_CONSERV
161      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
162      - try to fix "hidden" recomp. in forward_step for NLFS
163        (NLFS seems broken sometimes after I checked it in)
164    o seaice:
165     - add c-grid version of the dynamic solver:
166       + three new routines that are the c-grid substitute lsr, dynsolver
167         and ostres
168       + put a few fields that were local to dynsolver into global common
169         blocks, so that I can move the computation of stresses etc into
170         seaice_lsr (saves coding but may break the adjoint).
171     - replace more hardwired parameters by runtime parameters
172     - add ice masks that mask the rhs of the implicit solvers where there
173       is no ice (commented out in seaice_dynsolver, because i am not sure
174       if this works properly), eventually this should replace the clipping
175       of ice velocities in seaice_dynsolver to +/-40cm/s.
176    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
177      include it only where its needed
178    o move balancing of fluxes before the call of external_forcing_surf
179    o seaice:
180      - correct units of turning angles (now they are really in degrees)
181      - move computation of GWATX/Y out of main routine into dynsolver
182      - initialize GWATX/Y in seaice_init
183    o Apply mask on Fresh-Water flux (needed for SSH forcing).
184      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
185    o seaice: add runtime flags for turning angles (default to zero)
186    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
187      and trend from exf forcing and ctrl control adjustments
188    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
189      (since checkpoint57x_post)
190    o change the default rotation period to 86164.s = the Earth rotation
191    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
192      and based on a reference stratification. Tested within hs94.cs-32x32x5.
193    o seaice advection: add code for choosing between the default (2nd order
194      central differences) and multiDim advection schemes provided by
195      pkg/generic_advdiff
196    o seaice:
197      - removed all references to SEAICE_GRID.h fields from
198        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
199        (cubed-sphere configuration will change a little)
200      - grid computations in seaice_init are obsolete now.
201      - cleaned up code a little so that is easier to read (hopefully).
202      - added new (better?) discretizations of default advection and diffusion
203        (turn on with SEAICEuseFluxForm)
204      - replace 1 in 3d global fields by kSurface in growth.F
205      
206    checkpoint58a_post
207    o seaice:
208      - bug fix in advect.F
209    o shelfice:
210      - separate shelfice load anomaly from pload (breaks with time
211        dependent forcing), => introduce constant field shelficeLoadAnomaly.
212        Its default is 0., but it may be computed more cleverly from (unknown)
213        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
214        done offline. A good approximation of the pressure load anomaly is
215        necessary to avoid large initial adjustment processes underneath
216        deep-reaching shelfice.
217      - small fix in ISOMIP shelfice_thermodynamics
218      - add more sophisticated thermodynamics of Hellmer (1989), this is
219        now the default
220      - give a few constants more intuitive names
221    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
222      if bulk formulae are used in long integration (especially EmPmR). Turn
223      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
224      if balancePrintMean, the imbalance that is substracted is printed to
225      STDOUT.
226    o fix bug (typo) in obcs_apply_eta.F
227    o add a new package shelfice which enables us to model the circulation
228      underneath shelf-ice with draughts of hundreds of meters.
229     - works
230     - to do: + include improved thermodynamics
231              + check whether kSurfC (from model/inc/SURFACE.h) can be used
232                instead of new field kTopC
233              + can we use topoFile, Ro_surf and existing code in ini_depth.F
234                instead of new field R_shelfIce and new code in ini_depth.F
235                and ini_mask_etc.F?
236              + adjust vertical mixing schemes?
237    o seaice pkg:
238     - add a cpp-flag to include a simple formula for a salinity dependent
239       freezing point of sea water at the surface
240     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
241       meridional stresses are now different (and hopefully correct)
242    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
243       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
244       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
245    o pkg/diagnostics: add options and parameters for regional-statistics
246       diagnostics ; define regions by reading a region-mask from a file
247       (might add other options later)
248    o pkg/bulk_force:
249     - add option and parameters to use AIM surface-flux formulae.
250     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
251       others forcing fields (defined in PARM05, parameter file "data") are loaded
252       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
253     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
254     - use the right EXCH call for uwind,vwind (to work on CS-grid).
255     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
256       and parameters (note: calcWindStress replaces .NOT.readwindstress).
257     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
258    
259    checkpoint58
260    o add "--embed-source" option to genmake2 which, when the supporting
261      tools can be compiled (as determined by genmake2) will turn on the
262      embed_files package which then embeds the entire MITgcm source code
263      (*.[fFhc] + Makefile) used for the build within the executable
264      - requested by CNH but off by default
265      - adds a paltry <9MB to the mitgcmuv executable in most cases
266      - only writes the output when useEMBEDSRC in eedata is true
267    o clean up 3-dim. relaxation codes:
268      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
269      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
270      * Thanks to Tom Haine for testing!
271    
272    checkpoint57z_post
273    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
274      affects output (@ truncation level) of exp. plume_on_slope ; updated.
275    o fix the pickup behavior for obcs in combination with ptracers
276    o fix a bug in ptracers_external_fields_load
277    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
278      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
279    o transfered surface NH pressure to eta field (if exactConserv).
280    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
281         and update lab_sea output.txt file.
282    o completing 3-dim. relaxation code: additional term
283         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
284      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
285      * At compile time, in "EXF_OPTIONS.h" set
286          #define  ALLOW_CLIMTEMP_RELAXATION
287          #define  ALLOW_CLIMSALT_RELAXATION
288      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
289          tauThetaClimRelax3Dim = 15552000.0,
290          tauSaltClimRelax3Dim  = 15552000.0,
291      * 3 cases:
292          1) Use a constant-in-time 3-dim. field
293          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
294          3) Real-time relax. to time-evolving prescribed field
295    o Adding Laplacian-type smoothness constraint on
296      initial and boundary (forcing) controls (ic, bc)
297      * enable at compile-time via
298        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
299      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
300      * Absolute scale somewhat unclear so far
301      * no area weighting was included since no other cost term does so far
302    
303    checkpoint57y_post
304    First step for a NLFS adjoint
305    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
306    o new init. routines for calc_r_star, calc_surf_dr
307    o still need to deal with ini_masks_etc
308    o testreport seemed happy
309    checkpoint57y_pre
310    
311    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
312    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
313    o add new offset feature to offline pkg (plus minor cleanup)
314    o cfc fixes for final year of integration
315    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
316      be in GCHEM_OPTIONS).
317    
318    checkpoint57x_post
319    o fix testreport Pb in multiple test experiment.
320    o cleanup our namelist syntax in verification:
321      - make it more F95 standards compliant (some work still needed)
322      - allows the vast majority of our tests to work with gfortran
323    o Non-Hydrostatic:
324     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
325     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
326    o Allow to apply AB on T,S rather than on AB(gT,gS):
327     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
328     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
329       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
330     - need a "clever" read_pickup to restart from the other AB formulation
331    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
332    o remove some unused variables (reduces number of compiler warnings)
333    o adjoint
334      * Disable useVariableViscosity for adjoint for time being
335        (there are a number of extensive recomputations)
336      * Initialize certain variables needed for adjoint
337    
338    checkpoint57w_post
339    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
340                 fix the singleCpuIO RS version of MDSWRITEFIELD
341       and add a WARNING if using globalFiles=T with multi-processors.
342    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
343      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
344    o tracer advection scheme:
345      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
346       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
347       was not very convenient).
348      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
349       (further tests needed for the implicit DST & Flux-Limiter schemes).
350    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
351      and sRef for convenience, handy, when you want to initialize
352      ptracers in a large domain with a constant non-zero value. Also,
353      untangle ptracers_init.F a little.
354    
355    checkpoint57v_post
356    o change dome exp. to use variable viscosity in side-drag terms.
357    o remove all the files from the cfc_offline test since they are now
358      incorporated into tutorial_cfc_offline which has been producing
359      identical results for a few days of testing
360    o add new parameter: sideDragFactor to enable half-slip-side BC
361      and change side-drag S/R to use viscosity from mom_calc_visc
362      (can switch back by setting sideDragFactor=0.); affects results at
363      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
364       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
365    o vorticity & strain are now computed without masking, to account for
366      no-slip-side BC in variable viscosity calculation ; mask is applied
367      anyway later on, before computing advection/coriolis terms.
368    o modify exp4 to test new obcs support for reading from external files
369      and for passive tracers
370    o fix behavior of ptracers_monitor when monitor output is written to a
371      netcdf-file; still not independent of monitor.F (writes in the same
372      file).
373    o change default value of tRef (put a uniform, meaningful value for ocean
374      & atmos) and initialize sRef (was missing, as Martin mentioned).
375    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
376      to be proportional to enstrophy dissipation length.  Thus,
377       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
378      This is now consistent with Smagorinsky and with the manual.
379    
380    checkpoint57u_post
381    o OBCS and PTRACERS: add open boundary support for passive tracers
382      - either use homogenous (pseudo) v.Neumann conditions or prescribe
383        OB-values from file; this is not different from the way theta and salinity
384        are treated
385      - however, Orlanski-radiation conditions are not supported, and the model
386        will stop if you use pTracers and Orlanski at the same time.
387      - beefed up the rountine obcs_external_fields_load: now only those open
388        boundary values are overwritten with values from files for which there
389        are really files, otherwise the OB-fields remain untouched. This makes
390        it possible to use different OBs at different ends of the domain (as
391        with EXF)
392    o reduce number of exch calls in shap_filt (s2).
393    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
394      truncation level) 4/5 MLAdjust test results (11&12 digits match).
395    
396    checkpoint57t_post
397    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
398    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
399      same truncation, independent of the face number: affects affects several
400      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
401    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
402      note that biharmonic viscosity + no-slip was not tested in any experiment.
403    o fix bug in non-linear free-surf side-drag ; generate new output for
404      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
405    o make mnc honor the writeBinaryPrec flag for most kinds of output
406    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
407    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
408      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
409    o add brackets in multi-terms sum to get same truncation, independent of
410      the face number (manage to get exactly same value of gU,gV at the cs-edge)
411      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
412    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
413      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
414      a maximum grid-scale Reynolds number.  Also, changes all length calculations
415      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
416      Suggested values of viscosity parameters found in mom_calc_visc.
417      Many new viscosity diagnostics available.
418    
419    checkpoint57s_post
420    o Add clearing-house for viscosity calculations, mom_calc_visc and
421      correct numerous bugs in LeithD and Smagorinsky discretizations.  
422      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
423      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
424      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
425      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
426      The Strain-Tension form is now called with useStrainTensonVisc=.true.
427      ViscAhStrain and viscAhTension are now retired.
428    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
429    o In response to JMC's bug report, genmake2 now ignores any soft-links
430      that it finds in the *current* directory when searching for files.
431      Soft-links found in any other source directories will still work as
432      they did before.
433    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
434      a C routine to unlimit the stack size
435    o mnc-ify pkg/aim snapshot vars
436    o mnc-ify pkg/land as requested by Daniel
437    o various changes to mnc including:
438      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
439      - output can now be grouped so that all files within a group
440          change the ITER portion of their names in lock-step together
441      - can now read ("global") PER-FACE (in addition to PER-TILE) files
442          and works with both EXCH1 and EXCH2 (but needs more testing)
443      - writing works for all verification test cases w/ g77 on Linux
444    
445    checkpoint57r_post
446    o make MNC variable initialization happen earlier
447    o add diagnostics for (almost) each term of the momentum Eq.
448    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
449    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
450    o remove MINIMAL_TAVE_OUTPUT option ;
451      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
452    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
453      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
454    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
455    o add time-dependent SST, SSS control
456    o cost terms in ecco/ modularized (new cost_generic.F)
457    o cost_averages routines are modularized (new cost_averagesgeneric.F)
458    o new infrastructure for seaice model vs. obs misfits in seaice/
459      * driver from the_main_loop.F is seaice_cost_driver.F
460      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
461      * gradient check in Exp. 6a of natl_box_adjoint/
462    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
463      (see README file)
464    
465    checkpoint57q_post
466    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
467    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
468      - bug was reported by Jean-Michel and Ian Fenty
469    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
470      update exp. cpl_aim+ocn output.
471    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
472      Needed for high-res. runs with large global files
473      to be able to limit tapelev size
474    o Changed some tests for adjoint:
475      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
476      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
477      * global_ocean.90x40x15/ back to default 3-level checkpointing
478    o Modifications to enable scripted COMMON to MODULE conversion
479      * verification/OpenAD/code/ has necessary scripts and description;
480      * converts, compiles and runs successfully;
481    
482    checkpoint57p_post
483    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
484    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
485      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
486    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
487    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
488      (was already the case for dissipation with mom_vecinv,
489       and also the case for grad.PhiHyd when staggered-timeStep)
490      This will allow to put dissipation out-off the AB time-stepping.
491     Unfortunately, affects truncation error. Update output of exp. that "fails"
492      (cg2d matching number) and leave the others for later: front_relax(10),
493      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
494      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
495    
496    checkpoint57o_post
497    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
498      (2) its ready to be documented during the 20050801 DocFest
499    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
500      for ideal_2D_oce and lab_sea on linux_ia32_g77
501    o set to #undef CTRL_SET_OLD_MAXCVARS_30
502      in global1x1_tot/code_seaice_adj to access indices 32, 33
503      (worth another tag)
504    
505    checkpoint57n_post
506    o adding precip control xx_precip 32
507    o adding swflux control xx_swflux 33
508    o Replacing 10 forcing penalty cost routines by 1 generic.
509    o Implementing partitioning in time-mean and variable adjustment
510      for atmos. state.
511    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
512    o in natl_box_adjoint:
513      * updated exp 1 to 10
514        (but does not have time-mean vs. variable split results yet)
515    o updated global1x1/*_seaice_adj/
516      to incorporate latest changes
517    o enable useSingleCpuIO for mdsio vector routines
518      (applies in particular to tapelev I/O)
519    o removed inefficient K-loop in all active_file*control*.F
520    
521    checkpoint57m_post
522    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
523      and advect_cs (use EXCH-2 and standard cs-32 grid files).
524    o pkg/exch2: filling of face-corner halo regions is optional
525      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
526    
527    checkpoint57l_post
528     tag before updating tutorials (pre-release-2)
529    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
530       for output and interpolation of input fields onto model grid)
531    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
532       Affects results of exp. rotating_tank ; update output.txt.
533    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
534          and taking the square quantity and/or using a fraction-weight field.
535    o fix aim_diagnostics_init.F mate numbers.
536    o add mnc output capability to diagnostics/diagstat and update
537      our cvsignore files for the ACSII output generated
538    
539    checkpoint57k_post
540    o lab_sea now uses diagnostics package and provides a suite of
541      new EXF diagnostics output.
542    
543    checkpoint57j_post
544    o exf
545      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
546        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
547        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
548      * extended diagnostics output
549        - now includes all EXF variables
550        - hs, hl moved to common block
551        - separate S/R for diagnostics, called after ctrl vector is added
552        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
553        - EXFqnet contains true Qnet (i.e. includes qsw)
554      * updated verif. lab_sea, global_with_exf
555      * Rearranging hflux (exf_mapfields -> exf_getforcing)
556        to ensure that diagnostics sees a true EXFqnet
557    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
558    o diagnostics pkg: change pointers so that 1 diagnostic can be used
559      several times with different frequencies.
560    o mnc-ify the thsice package as requested by Daniel Enderton
561      - the monitor--MNC output needs work
562      - many attributes need to be added (most are currently blank)
563    o mnc-ify theaim_v23 package as requested by Daniel Enderton
564      - many attributes need to be added (most are currently blank)
565    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
566    o add Sadourny like discretization to the 4th.O vorticity advection scheme
567    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
568      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
569         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
570    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
571     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
572    
573    checkpoint57i_post
574    o Diagnostics package was changed: diagnostic allocation is now deactivated
575      by setting an empty file name in the namelist (used to be by setting 0 frequency)
576    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
577      add 1rst Order upwind vertical Shear.
578    o add a quick fix for A/B checkpointing in OFFLINE mode
579    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
580      end-run around the C/Fortran linking horror in eesup/src/timers.F
581    o added pkg/runclock: allows user to terminate run based on wall clock
582    o added non-hydrostatic scaling parameter: nh_am2
583    o pkg/my82: futile attempt to make results compiler-independent by adding
584      some "_d 0", etc. no effect.
585    o for mnc output, fill the 'T' coordinate var with myTime and create a
586      separate 'iter' variable for iteration count
587    o pkg/diagnostics:
588      add new capability: output of Global/Regional & per-level statistics ;
589      tested against monitor output (including land & thSIce) on various exp.
590    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
591    
592    checkpoint57h_done
593      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
594      data.diagnostics, data.gchem, data.ptracers) is done.
595    
596    o pkg/diagnostics: prepare for Global/Regional statistics.
597      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
598    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
599      and rename it: DIFFERENT_MULTIPLE
600    
601    checkpoint57h_post
602    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
603    o pkg/diagnostics: change output frequency, now in seconds (instead
604      of Nb of iterations). This requires to change data.diagnostics.
605    checkpoint57h_pre
606    
607    o in mnc, let the user create the output dir if both mnc_outdir_date
608      and mnc_outdir_num are false
609    o add fflags() to pkg/diagnostics which allows one to specify, on a
610      per-file basis, the file precision [default behavior is unchanged]
611    o added diagnostics to pkg/kpp, including computation of mixed layer
612      depth based on a temperature/density criterion
613    o updated verification/natl_box to test the new pkg/kpp diagnostics
614    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
615    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
616    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
617      not mnc -- this mistake was found by JMC and is now corrected
618    
619    checkpoint57g_post
620    o add Adams-Bashforth 3rd Order time stepping:
621      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
622      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
623    checkpoint57g_pre
624    
625    o make lambda[Theta,Salt]ClimRelax spatially varying
626      (default remains spatially uniform constant based on tau)
627    o added new control variables
628      * init. uVel, vVel, etanN
629      * lambda[Theta,Salt]ClimRelax
630    o separate masks used for ctrl_pack/unpack 'from write_grid' output
631      (suggested by G. Forget)
632    
633    checkpoint57f_post
634    o add parameter "baseTime" = model base time = time at iteration zero
635      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
636      account for baseTime shift
637    o move Coriolis arrays from PARAMS.h to GRID.h
638    checkpoint57f_pre
639    
640    o mnc-ifying the seaice package
641    o introduced an alternative length scale calculation for use in the limiting
642      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
643    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
644    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
645      as well as grad(vort3).  Made it compatible with both approximate form
646      for the cubed sphere and full form of these gradients.  Added flag
647      useFullLeith to select between approximate and full form.  
648    o add "d0" in getcon.F to reduce differences between compilers/platforms
649      update output.txt of exp. fizhi-gridalt-hs
650  o change port_rand funtion to allow to set the seed.  o change port_rand funtion to allow to set the seed.
651  o fix obscure MNC bug involving conversion between reals and integers  o fix obscure MNC bug involving conversion between reals and integers
652    - it caused no problems with certain (eg. gcc, ifc) compilers but the    - it caused no problems with certain (eg. gcc, ifc) compilers but the
653      new version is now more standards-compliant      new version is now more standards-compliant
654    o adjoint-related modifications
655      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
656      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
657      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
658    
659  checkpoint57e_post  checkpoint57e_post
660  o Adding eddy stress controls a la Ferreira et al.  o Adding eddy stress controls a la Ferreira et al.
661  checkpoint57e_pre  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
662    
663  o fizhi pkg: fix AtoC and CtoA when called with same input & output array  o fizhi pkg: fix AtoC and CtoA when called with same input & output array
664    update output.txt of exp. fizhi-gridalt-hs    update output.txt of exp. fizhi-gridalt-hs

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