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revision 1.465 by baylor, Thu Mar 24 14:51:34 2005 UTC revision 1.674 by jmc, Fri Jun 9 16:59:16 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    o exf & curvilinear-grid: no longer modify longitude xC & xG.
8    o pkg/ggl90: fix sloppy output and fix a bug
9    o pkg/seaice: added SEAICEuseEVPpickup parameter
10      - Set to false in order to start EVP solver with
11        non-EVP pickup files when using SEAICEuseEVP
12      - fix sign error in diffusion in seaice_calc_rhs
13    
14    checkpoint58h_post
15    * Modifications for bottom topography control
16      o replace hFacC by _hFacC at various places
17      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
18      o add non-self-adjoint cg2d_nsa
19      o update autodiff support routines
20      o re-initialise hfac after ctrl_depth_ini
21      o works for 5x5 box, doesnt work for global_ocean.90x40x15
22    * Adding verification for 5x5 box (4-layer) bottom topography control
23    
24    checkpoint58g_post
25    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
26       used for mean seasonal cycle, mean diurnal cycle); add an example
27       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
28    o pkg/ggl90:
29      - add parameter (minimum surface kinetic energy)
30      - fix bug (avoiding division by zero)
31    o couple pkg/thsice to pkg/seaice:
32      - modify advection in seaice to accomodate new scalar fields to be advected
33      - only muliDimAdection scheme work with seaice/thsice
34      - mapping of thsice-variables to seaice-variables, back and forth
35      - does not break the verification experiments, but does not give the
36        desired results either
37    o pkg/seaice
38      - make (default) second order advection a bit less confusing?
39    
40    checkpoint58f_post
41    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
42      to pkg/seaice):
43      - new routines thsice_map_exf and thsice_get_exf provide the interface
44      - add an additional formal parameter to thsice_solve4temp
45    o pkg/exf:
46      - add new fields wspeed, snowprecip (to be able to couple to thsice)
47      - correct Stefan-Boltzmann constant
48      - new parameter for longwave surface emittance
49      - separate some stuff from exf_bulkformulae into new routines  
50        exf_radiation, exf_wind
51      - add new parameters and constants: longwave emissivity for ocean, ice
52        and snow, evaporation parameters over ice
53      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
54        either wind from stress or stress from wind
55    o pkg/thSIce:
56    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
57    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
58       and THSICE_CALC_THICKN
59    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
60    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
61      to make debugging easier.
62    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
63    o pkg/bulk_force:
64      - clean-up comments and parameters ;
65      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
66    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
67      generate new output for test-experiment: aim.5l_cs.thSI
68    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
69      testreport accordingly
70    
71    checkpoint58e_post
72    o SEAICE_CGRID adjoint done
73    o R_STAR adjoint implemented.
74      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
75      * need to sort out init. of h0facc, etc.
76    o Make pkg/profile fully independent of ecco,cost, etc. stuff
77      to be able to use it in pure forward.
78    
79    checkpoint58d_post
80    o upgrade simple test-experiment to tutorial example:
81     step.1: duplicate the experiment and (step.2) will remove the old copy.
82      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
83      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
84      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
85      tutorial_global_oce_biogeo    <- copy of dic_example
86      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
87      tutorial_plume_on_slope       <- copy of plume_on_slope
88      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
89      tutorial_global_oce_optim     <- empty for now (David ?)
90      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
91     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
92    o correct a sign problem in cost_scat.F
93    o obcs and ptracers: fix boundary conditions for advections schemes
94      with larger stencil
95    o thsice adjoint: start
96    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
97      completeness
98    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
99      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
100    o ptracers adjoint:
101      * avoid extensive recomputatations
102      * fix missing re-init. of gptr (missed by TAF)
103    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
104      me to turn off the excessive output to STDOUT that this package produces
105    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
106      and add those terms in Vector-Invariant formulation.
107    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
108      if the control period (xx_hfluxperiod etc) is 0
109    o in profiles pkg, clean routines and fix details
110    o in ecco pkg, reading ssh data:
111      fix problem in case the model does not start at iter0=0
112    o fix mnc-pickup/restart for ptracers
113    o new package prifiles:
114      code to compute profile-based cost by Gael Forget
115      (modifs in ecco, ctrl, autodiff)
116    o Benign bug fix in initialization (spotted by M. Mazloff) of
117      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
118    
119    checkpoint58c_post
120    o adjoint: finish NLFS adjoint and provide reference output in
121      verification/global_ocean.90x40x15/results_ad_nlfs
122    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
123      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
124      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
125      with SEAICE_CGRID defined.
126    o move calendarDumps from "data" to "data.cal" and clean-up the code
127      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
128    o add useEXF & useCAL flags (for now, set in hard-coded way)
129    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
130      (were missing in NH mode, and wrong in quasihydrostatic mode).
131      waiting for Chris updated version of calc_gw to add those CALLs.
132    o fix bug in quasihydrostatic S/R ;
133      add a test for this option: global_ocean.90x40x15.qshyd
134    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
135      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
136    o add on/off flag useOffLine for package OFFLINE
137    o seaice:
138      - modify advection so that it works also on the C-grid
139      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
140        problem in multi-tile runs with C-grid
141      - add flags for clipping ice velocities and/or masking solver forcing
142      - fix drag (ocean on ice) formulation and a bug that caused noise in the
143        C-grid solver
144      - added a few comments to seaice_diffusion.F
145      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
146        are now exclusive)
147      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
148        required re-ordering the code a little:
149       + make DAIRN global variable (defined in SEAICE)
150       + move computation of the viscosities eta and zeta into a new separate
151         routine (because I need to recompute them in seaice_ocean_stress.F)
152    
153    checkpoint58b_post
154    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
155      update output.txt of exp. aim.5l_cs.thSI
156    o various mnc cleanups and improvements:
157      + shrink lookup tables by factor of ~4
158      + better error reporting when running out of lookup space
159      + able to handle longer path/file names (up to 500 chars)
160    o adjoint:
161      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
162      - TBD: "hidden" mom_vecinv recomp. in dynamics
163    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
164     (allow to differentiate between forcing components using new integer flags:
165      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
166     and add new flag to put Dissipation tendency out of Adams-Bashforth.
167    o ecco
168      - enable trend removal from SSH anomaly obs.
169    o adjoint
170      - a fix for PmEpR when #undef EXACT_CONSERV
171      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
172      - try to fix "hidden" recomp. in forward_step for NLFS
173        (NLFS seems broken sometimes after I checked it in)
174    o seaice:
175     - add c-grid version of the dynamic solver:
176       + three new routines that are the c-grid substitute lsr, dynsolver
177         and ostres
178       + put a few fields that were local to dynsolver into global common
179         blocks, so that I can move the computation of stresses etc into
180         seaice_lsr (saves coding but may break the adjoint).
181     - replace more hardwired parameters by runtime parameters
182     - add ice masks that mask the rhs of the implicit solvers where there
183       is no ice (commented out in seaice_dynsolver, because i am not sure
184       if this works properly), eventually this should replace the clipping
185       of ice velocities in seaice_dynsolver to +/-40cm/s.
186    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
187      include it only where its needed
188    o move balancing of fluxes before the call of external_forcing_surf
189    o seaice:
190      - correct units of turning angles (now they are really in degrees)
191      - move computation of GWATX/Y out of main routine into dynsolver
192      - initialize GWATX/Y in seaice_init
193    o Apply mask on Fresh-Water flux (needed for SSH forcing).
194      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
195    o seaice: add runtime flags for turning angles (default to zero)
196    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
197      and trend from exf forcing and ctrl control adjustments
198    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
199      (since checkpoint57x_post)
200    o change the default rotation period to 86164.s = the Earth rotation
201    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
202      and based on a reference stratification. Tested within hs94.cs-32x32x5.
203    o seaice advection: add code for choosing between the default (2nd order
204      central differences) and multiDim advection schemes provided by
205      pkg/generic_advdiff
206    o seaice:
207      - removed all references to SEAICE_GRID.h fields from
208        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
209        (cubed-sphere configuration will change a little)
210      - grid computations in seaice_init are obsolete now.
211      - cleaned up code a little so that is easier to read (hopefully).
212      - added new (better?) discretizations of default advection and diffusion
213        (turn on with SEAICEuseFluxForm)
214      - replace 1 in 3d global fields by kSurface in growth.F
215      
216    checkpoint58a_post
217    o seaice:
218      - bug fix in advect.F
219    o shelfice:
220      - separate shelfice load anomaly from pload (breaks with time
221        dependent forcing), => introduce constant field shelficeLoadAnomaly.
222        Its default is 0., but it may be computed more cleverly from (unknown)
223        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
224        done offline. A good approximation of the pressure load anomaly is
225        necessary to avoid large initial adjustment processes underneath
226        deep-reaching shelfice.
227      - small fix in ISOMIP shelfice_thermodynamics
228      - add more sophisticated thermodynamics of Hellmer (1989), this is
229        now the default
230      - give a few constants more intuitive names
231    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
232      if bulk formulae are used in long integration (especially EmPmR). Turn
233      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
234      if balancePrintMean, the imbalance that is substracted is printed to
235      STDOUT.
236    o fix bug (typo) in obcs_apply_eta.F
237    o add a new package shelfice which enables us to model the circulation
238      underneath shelf-ice with draughts of hundreds of meters.
239     - works
240     - to do: + include improved thermodynamics
241              + check whether kSurfC (from model/inc/SURFACE.h) can be used
242                instead of new field kTopC
243              + can we use topoFile, Ro_surf and existing code in ini_depth.F
244                instead of new field R_shelfIce and new code in ini_depth.F
245                and ini_mask_etc.F?
246              + adjust vertical mixing schemes?
247    o seaice pkg:
248     - add a cpp-flag to include a simple formula for a salinity dependent
249       freezing point of sea water at the surface
250     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
251       meridional stresses are now different (and hopefully correct)
252    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
253       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
254       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
255    o pkg/diagnostics: add options and parameters for regional-statistics
256       diagnostics ; define regions by reading a region-mask from a file
257       (might add other options later)
258    o pkg/bulk_force:
259     - add option and parameters to use AIM surface-flux formulae.
260     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
261       others forcing fields (defined in PARM05, parameter file "data") are loaded
262       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
263     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
264     - use the right EXCH call for uwind,vwind (to work on CS-grid).
265     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
266       and parameters (note: calcWindStress replaces .NOT.readwindstress).
267     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
268    
269    checkpoint58
270    o add "--embed-source" option to genmake2 which, when the supporting
271      tools can be compiled (as determined by genmake2) will turn on the
272      embed_files package which then embeds the entire MITgcm source code
273      (*.[fFhc] + Makefile) used for the build within the executable
274      - requested by CNH but off by default
275      - adds a paltry <9MB to the mitgcmuv executable in most cases
276      - only writes the output when useEMBEDSRC in eedata is true
277    o clean up 3-dim. relaxation codes:
278      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
279      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
280      * Thanks to Tom Haine for testing!
281    
282    checkpoint57z_post
283    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
284      affects output (@ truncation level) of exp. plume_on_slope ; updated.
285    o fix the pickup behavior for obcs in combination with ptracers
286    o fix a bug in ptracers_external_fields_load
287    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
288      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
289    o transfered surface NH pressure to eta field (if exactConserv).
290    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
291         and update lab_sea output.txt file.
292    o completing 3-dim. relaxation code: additional term
293         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
294      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
295      * At compile time, in "EXF_OPTIONS.h" set
296          #define  ALLOW_CLIMTEMP_RELAXATION
297          #define  ALLOW_CLIMSALT_RELAXATION
298      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
299          tauThetaClimRelax3Dim = 15552000.0,
300          tauSaltClimRelax3Dim  = 15552000.0,
301      * 3 cases:
302          1) Use a constant-in-time 3-dim. field
303          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
304          3) Real-time relax. to time-evolving prescribed field
305    o Adding Laplacian-type smoothness constraint on
306      initial and boundary (forcing) controls (ic, bc)
307      * enable at compile-time via
308        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
309      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
310      * Absolute scale somewhat unclear so far
311      * no area weighting was included since no other cost term does so far
312    
313    checkpoint57y_post
314    First step for a NLFS adjoint
315    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
316    o new init. routines for calc_r_star, calc_surf_dr
317    o still need to deal with ini_masks_etc
318    o testreport seemed happy
319    checkpoint57y_pre
320    
321    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
322    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
323    o add new offset feature to offline pkg (plus minor cleanup)
324    o cfc fixes for final year of integration
325    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
326      be in GCHEM_OPTIONS).
327    
328    checkpoint57x_post
329    o fix testreport Pb in multiple test experiment.
330    o cleanup our namelist syntax in verification:
331      - make it more F95 standards compliant (some work still needed)
332      - allows the vast majority of our tests to work with gfortran
333    o Non-Hydrostatic:
334     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
335     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
336    o Allow to apply AB on T,S rather than on AB(gT,gS):
337     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
338     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
339       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
340     - need a "clever" read_pickup to restart from the other AB formulation
341    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
342    o remove some unused variables (reduces number of compiler warnings)
343    o adjoint
344      * Disable useVariableViscosity for adjoint for time being
345        (there are a number of extensive recomputations)
346      * Initialize certain variables needed for adjoint
347    
348    checkpoint57w_post
349    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
350                 fix the singleCpuIO RS version of MDSWRITEFIELD
351       and add a WARNING if using globalFiles=T with multi-processors.
352    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
353      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
354    o tracer advection scheme:
355      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
356       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
357       was not very convenient).
358      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
359       (further tests needed for the implicit DST & Flux-Limiter schemes).
360    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
361      and sRef for convenience, handy, when you want to initialize
362      ptracers in a large domain with a constant non-zero value. Also,
363      untangle ptracers_init.F a little.
364    
365    checkpoint57v_post
366    o change dome exp. to use variable viscosity in side-drag terms.
367    o remove all the files from the cfc_offline test since they are now
368      incorporated into tutorial_cfc_offline which has been producing
369      identical results for a few days of testing
370    o add new parameter: sideDragFactor to enable half-slip-side BC
371      and change side-drag S/R to use viscosity from mom_calc_visc
372      (can switch back by setting sideDragFactor=0.); affects results at
373      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
374       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
375    o vorticity & strain are now computed without masking, to account for
376      no-slip-side BC in variable viscosity calculation ; mask is applied
377      anyway later on, before computing advection/coriolis terms.
378    o modify exp4 to test new obcs support for reading from external files
379      and for passive tracers
380    o fix behavior of ptracers_monitor when monitor output is written to a
381      netcdf-file; still not independent of monitor.F (writes in the same
382      file).
383    o change default value of tRef (put a uniform, meaningful value for ocean
384      & atmos) and initialize sRef (was missing, as Martin mentioned).
385    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
386      to be proportional to enstrophy dissipation length.  Thus,
387       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
388      This is now consistent with Smagorinsky and with the manual.
389    
390    checkpoint57u_post
391    o OBCS and PTRACERS: add open boundary support for passive tracers
392      - either use homogenous (pseudo) v.Neumann conditions or prescribe
393        OB-values from file; this is not different from the way theta and salinity
394        are treated
395      - however, Orlanski-radiation conditions are not supported, and the model
396        will stop if you use pTracers and Orlanski at the same time.
397      - beefed up the rountine obcs_external_fields_load: now only those open
398        boundary values are overwritten with values from files for which there
399        are really files, otherwise the OB-fields remain untouched. This makes
400        it possible to use different OBs at different ends of the domain (as
401        with EXF)
402    o reduce number of exch calls in shap_filt (s2).
403    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
404      truncation level) 4/5 MLAdjust test results (11&12 digits match).
405    
406    checkpoint57t_post
407    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
408    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
409      same truncation, independent of the face number: affects affects several
410      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
411    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
412      note that biharmonic viscosity + no-slip was not tested in any experiment.
413    o fix bug in non-linear free-surf side-drag ; generate new output for
414      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
415    o make mnc honor the writeBinaryPrec flag for most kinds of output
416    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
417    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
418      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
419    o add brackets in multi-terms sum to get same truncation, independent of
420      the face number (manage to get exactly same value of gU,gV at the cs-edge)
421      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
422    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
423      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
424      a maximum grid-scale Reynolds number.  Also, changes all length calculations
425      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
426      Suggested values of viscosity parameters found in mom_calc_visc.
427      Many new viscosity diagnostics available.
428    
429    checkpoint57s_post
430    o Add clearing-house for viscosity calculations, mom_calc_visc and
431      correct numerous bugs in LeithD and Smagorinsky discretizations.  
432      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
433      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
434      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
435      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
436      The Strain-Tension form is now called with useStrainTensonVisc=.true.
437      ViscAhStrain and viscAhTension are now retired.
438    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
439    o In response to JMC's bug report, genmake2 now ignores any soft-links
440      that it finds in the *current* directory when searching for files.
441      Soft-links found in any other source directories will still work as
442      they did before.
443    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
444      a C routine to unlimit the stack size
445    o mnc-ify pkg/aim snapshot vars
446    o mnc-ify pkg/land as requested by Daniel
447    o various changes to mnc including:
448      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
449      - output can now be grouped so that all files within a group
450          change the ITER portion of their names in lock-step together
451      - can now read ("global") PER-FACE (in addition to PER-TILE) files
452          and works with both EXCH1 and EXCH2 (but needs more testing)
453      - writing works for all verification test cases w/ g77 on Linux
454    
455    checkpoint57r_post
456    o make MNC variable initialization happen earlier
457    o add diagnostics for (almost) each term of the momentum Eq.
458    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
459    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
460    o remove MINIMAL_TAVE_OUTPUT option ;
461      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
462    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
463      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
464    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
465    o add time-dependent SST, SSS control
466    o cost terms in ecco/ modularized (new cost_generic.F)
467    o cost_averages routines are modularized (new cost_averagesgeneric.F)
468    o new infrastructure for seaice model vs. obs misfits in seaice/
469      * driver from the_main_loop.F is seaice_cost_driver.F
470      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
471      * gradient check in Exp. 6a of natl_box_adjoint/
472    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
473      (see README file)
474    
475    checkpoint57q_post
476    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
477    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
478      - bug was reported by Jean-Michel and Ian Fenty
479    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
480      update exp. cpl_aim+ocn output.
481    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
482      Needed for high-res. runs with large global files
483      to be able to limit tapelev size
484    o Changed some tests for adjoint:
485      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
486      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
487      * global_ocean.90x40x15/ back to default 3-level checkpointing
488    o Modifications to enable scripted COMMON to MODULE conversion
489      * verification/OpenAD/code/ has necessary scripts and description;
490      * converts, compiles and runs successfully;
491    
492    checkpoint57p_post
493    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
494    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
495      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
496    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
497    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
498      (was already the case for dissipation with mom_vecinv,
499       and also the case for grad.PhiHyd when staggered-timeStep)
500      This will allow to put dissipation out-off the AB time-stepping.
501     Unfortunately, affects truncation error. Update output of exp. that "fails"
502      (cg2d matching number) and leave the others for later: front_relax(10),
503      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
504      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
505    
506    checkpoint57o_post
507    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
508      (2) its ready to be documented during the 20050801 DocFest
509    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
510      for ideal_2D_oce and lab_sea on linux_ia32_g77
511    o set to #undef CTRL_SET_OLD_MAXCVARS_30
512      in global1x1_tot/code_seaice_adj to access indices 32, 33
513      (worth another tag)
514    
515    checkpoint57n_post
516    o adding precip control xx_precip 32
517    o adding swflux control xx_swflux 33
518    o Replacing 10 forcing penalty cost routines by 1 generic.
519    o Implementing partitioning in time-mean and variable adjustment
520      for atmos. state.
521    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
522    o in natl_box_adjoint:
523      * updated exp 1 to 10
524        (but does not have time-mean vs. variable split results yet)
525    o updated global1x1/*_seaice_adj/
526      to incorporate latest changes
527    o enable useSingleCpuIO for mdsio vector routines
528      (applies in particular to tapelev I/O)
529    o removed inefficient K-loop in all active_file*control*.F
530    
531    checkpoint57m_post
532    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
533      and advect_cs (use EXCH-2 and standard cs-32 grid files).
534    o pkg/exch2: filling of face-corner halo regions is optional
535      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
536    
537    checkpoint57l_post
538     tag before updating tutorials (pre-release-2)
539    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
540       for output and interpolation of input fields onto model grid)
541    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
542       Affects results of exp. rotating_tank ; update output.txt.
543    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
544          and taking the square quantity and/or using a fraction-weight field.
545    o fix aim_diagnostics_init.F mate numbers.
546    o add mnc output capability to diagnostics/diagstat and update
547      our cvsignore files for the ACSII output generated
548    
549    checkpoint57k_post
550    o lab_sea now uses diagnostics package and provides a suite of
551      new EXF diagnostics output.
552    
553    checkpoint57j_post
554    o exf
555      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
556        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
557        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
558      * extended diagnostics output
559        - now includes all EXF variables
560        - hs, hl moved to common block
561        - separate S/R for diagnostics, called after ctrl vector is added
562        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
563        - EXFqnet contains true Qnet (i.e. includes qsw)
564      * updated verif. lab_sea, global_with_exf
565      * Rearranging hflux (exf_mapfields -> exf_getforcing)
566        to ensure that diagnostics sees a true EXFqnet
567    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
568    o diagnostics pkg: change pointers so that 1 diagnostic can be used
569      several times with different frequencies.
570    o mnc-ify the thsice package as requested by Daniel Enderton
571      - the monitor--MNC output needs work
572      - many attributes need to be added (most are currently blank)
573    o mnc-ify theaim_v23 package as requested by Daniel Enderton
574      - many attributes need to be added (most are currently blank)
575    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
576    o add Sadourny like discretization to the 4th.O vorticity advection scheme
577    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
578      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
579         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
580    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
581     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
582    
583    checkpoint57i_post
584    o Diagnostics package was changed: diagnostic allocation is now deactivated
585      by setting an empty file name in the namelist (used to be by setting 0 frequency)
586    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
587      add 1rst Order upwind vertical Shear.
588    o add a quick fix for A/B checkpointing in OFFLINE mode
589    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
590      end-run around the C/Fortran linking horror in eesup/src/timers.F
591    o added pkg/runclock: allows user to terminate run based on wall clock
592    o added non-hydrostatic scaling parameter: nh_am2
593    o pkg/my82: futile attempt to make results compiler-independent by adding
594      some "_d 0", etc. no effect.
595    o for mnc output, fill the 'T' coordinate var with myTime and create a
596      separate 'iter' variable for iteration count
597    o pkg/diagnostics:
598      add new capability: output of Global/Regional & per-level statistics ;
599      tested against monitor output (including land & thSIce) on various exp.
600    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
601    
602    checkpoint57h_done
603      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
604      data.diagnostics, data.gchem, data.ptracers) is done.
605    
606    o pkg/diagnostics: prepare for Global/Regional statistics.
607      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
608    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
609      and rename it: DIFFERENT_MULTIPLE
610    
611    checkpoint57h_post
612    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
613    o pkg/diagnostics: change output frequency, now in seconds (instead
614      of Nb of iterations). This requires to change data.diagnostics.
615    checkpoint57h_pre
616    
617    o in mnc, let the user create the output dir if both mnc_outdir_date
618      and mnc_outdir_num are false
619    o add fflags() to pkg/diagnostics which allows one to specify, on a
620      per-file basis, the file precision [default behavior is unchanged]
621    o added diagnostics to pkg/kpp, including computation of mixed layer
622      depth based on a temperature/density criterion
623    o updated verification/natl_box to test the new pkg/kpp diagnostics
624    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
625    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
626    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
627      not mnc -- this mistake was found by JMC and is now corrected
628    
629    checkpoint57g_post
630    o add Adams-Bashforth 3rd Order time stepping:
631      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
632      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
633    checkpoint57g_pre
634    
635    o make lambda[Theta,Salt]ClimRelax spatially varying
636      (default remains spatially uniform constant based on tau)
637    o added new control variables
638      * init. uVel, vVel, etanN
639      * lambda[Theta,Salt]ClimRelax
640    o separate masks used for ctrl_pack/unpack 'from write_grid' output
641      (suggested by G. Forget)
642    
643    checkpoint57f_post
644    o add parameter "baseTime" = model base time = time at iteration zero
645      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
646      account for baseTime shift
647    o move Coriolis arrays from PARAMS.h to GRID.h
648    checkpoint57f_pre
649    
650    o mnc-ifying the seaice package
651    o introduced an alternative length scale calculation for use in the limiting
652      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
653    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
654  o added modified Leith scheme with viscosity proportional to grad(Hdiv)  o added modified Leith scheme with viscosity proportional to grad(Hdiv)
655    as well as grad(vort3).  Made it compatible with both approximate form    as well as grad(vort3).  Made it compatible with both approximate form
656    for the cubed sphere and full form of these gradients.  Added flag    for the cubed sphere and full form of these gradients.  Added flag
# Line 13  o change port_rand funtion to allow to s Line 661  o change port_rand funtion to allow to s
661  o fix obscure MNC bug involving conversion between reals and integers  o fix obscure MNC bug involving conversion between reals and integers
662    - it caused no problems with certain (eg. gcc, ifc) compilers but the    - it caused no problems with certain (eg. gcc, ifc) compilers but the
663      new version is now more standards-compliant      new version is now more standards-compliant
664    o adjoint-related modifications
665      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
666      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
667      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
668    
669  checkpoint57e_post  checkpoint57e_post
670  o Adding eddy stress controls a la Ferreira et al.  o Adding eddy stress controls a la Ferreira et al.
671  checkpoint57e_pre  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
672    
673  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
674    update output.txt of exp. fizhi-gridalt-hs    update output.txt of exp. fizhi-gridalt-hs

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