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revision 1.578 by jmc, Sat Nov 5 01:10:21 2005 UTC revision 1.680 by heimbach, Thu Jun 15 20:04:31 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint58j_post
8    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
9      from file (collects calls previously in FORWARD_STEP)
10    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
11    o adjoint store dir. adjusted accordingly
12    o genmake2
13      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
14    
15    checkpoint58i_post
16    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
17      on wind stress (SEAICEstressFactor defaults to 1.)
18    o Total number of Timers is finite (<=40): comment out 2 non-essential one
19      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
20    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
21      on CS-grid: no longer loosing mass.
22    o exf & curvilinear-grid: no longer modify longitude xC & xG.
23    o pkg/ggl90: fix sloppy output and fix a bug
24    o pkg/seaice: added SEAICEuseEVPpickup parameter
25      - Set to false in order to start EVP solver with
26        non-EVP pickup files when using SEAICEuseEVP
27      - fix sign error in diffusion in seaice_calc_rhs
28    
29    checkpoint58h_post
30    * Modifications for bottom topography control
31      o replace hFacC by _hFacC at various places
32      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
33      o add non-self-adjoint cg2d_nsa
34      o update autodiff support routines
35      o re-initialise hfac after ctrl_depth_ini
36      o works for 5x5 box, doesnt work for global_ocean.90x40x15
37    * Adding verification for 5x5 box (4-layer) bottom topography control
38    
39    checkpoint58g_post
40    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
41       used for mean seasonal cycle, mean diurnal cycle); add an example
42       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
43    o pkg/ggl90:
44      - add parameter (minimum surface kinetic energy)
45      - fix bug (avoiding division by zero)
46    o couple pkg/thsice to pkg/seaice:
47      - modify advection in seaice to accomodate new scalar fields to be advected
48      - only muliDimAdection scheme work with seaice/thsice
49      - mapping of thsice-variables to seaice-variables, back and forth
50      - does not break the verification experiments, but does not give the
51        desired results either
52    o pkg/seaice
53      - make (default) second order advection a bit less confusing?
54    
55    checkpoint58f_post
56    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
57      to pkg/seaice):
58      - new routines thsice_map_exf and thsice_get_exf provide the interface
59      - add an additional formal parameter to thsice_solve4temp
60    o pkg/exf:
61      - add new fields wspeed, snowprecip (to be able to couple to thsice)
62      - correct Stefan-Boltzmann constant
63      - new parameter for longwave surface emittance
64      - separate some stuff from exf_bulkformulae into new routines  
65        exf_radiation, exf_wind
66      - add new parameters and constants: longwave emissivity for ocean, ice
67        and snow, evaporation parameters over ice
68      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
69        either wind from stress or stress from wind
70    o pkg/thSIce:
71    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
72    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
73       and THSICE_CALC_THICKN
74    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
75    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
76      to make debugging easier.
77    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
78    o pkg/bulk_force:
79      - clean-up comments and parameters ;
80      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
81    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
82      generate new output for test-experiment: aim.5l_cs.thSI
83    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
84      testreport accordingly
85    
86    checkpoint58e_post
87    o SEAICE_CGRID adjoint done
88    o R_STAR adjoint implemented.
89      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
90      * need to sort out init. of h0facc, etc.
91    o Make pkg/profile fully independent of ecco,cost, etc. stuff
92      to be able to use it in pure forward.
93    
94    checkpoint58d_post
95    o upgrade simple test-experiment to tutorial example:
96     step.1: duplicate the experiment and (step.2) will remove the old copy.
97      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
98      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
99      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
100      tutorial_global_oce_biogeo    <- copy of dic_example
101      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
102      tutorial_plume_on_slope       <- copy of plume_on_slope
103      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
104      tutorial_global_oce_optim     <- empty for now (David ?)
105      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
106     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
107    o correct a sign problem in cost_scat.F
108    o obcs and ptracers: fix boundary conditions for advections schemes
109      with larger stencil
110    o thsice adjoint: start
111    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
112      completeness
113    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
114      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
115    o ptracers adjoint:
116      * avoid extensive recomputatations
117      * fix missing re-init. of gptr (missed by TAF)
118    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
119      me to turn off the excessive output to STDOUT that this package produces
120    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
121      and add those terms in Vector-Invariant formulation.
122    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
123      if the control period (xx_hfluxperiod etc) is 0
124    o in profiles pkg, clean routines and fix details
125    o in ecco pkg, reading ssh data:
126      fix problem in case the model does not start at iter0=0
127    o fix mnc-pickup/restart for ptracers
128    o new package prifiles:
129      code to compute profile-based cost by Gael Forget
130      (modifs in ecco, ctrl, autodiff)
131    o Benign bug fix in initialization (spotted by M. Mazloff) of
132      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
133    
134    checkpoint58c_post
135    o adjoint: finish NLFS adjoint and provide reference output in
136      verification/global_ocean.90x40x15/results_ad_nlfs
137    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
138      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
139      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
140      with SEAICE_CGRID defined.
141    o move calendarDumps from "data" to "data.cal" and clean-up the code
142      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
143    o add useEXF & useCAL flags (for now, set in hard-coded way)
144    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
145      (were missing in NH mode, and wrong in quasihydrostatic mode).
146      waiting for Chris updated version of calc_gw to add those CALLs.
147    o fix bug in quasihydrostatic S/R ;
148      add a test for this option: global_ocean.90x40x15.qshyd
149    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
150      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
151    o add on/off flag useOffLine for package OFFLINE
152    o seaice:
153      - modify advection so that it works also on the C-grid
154      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
155        problem in multi-tile runs with C-grid
156      - add flags for clipping ice velocities and/or masking solver forcing
157      - fix drag (ocean on ice) formulation and a bug that caused noise in the
158        C-grid solver
159      - added a few comments to seaice_diffusion.F
160      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
161        are now exclusive)
162      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
163        required re-ordering the code a little:
164       + make DAIRN global variable (defined in SEAICE)
165       + move computation of the viscosities eta and zeta into a new separate
166         routine (because I need to recompute them in seaice_ocean_stress.F)
167    
168    checkpoint58b_post
169    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
170      update output.txt of exp. aim.5l_cs.thSI
171    o various mnc cleanups and improvements:
172      + shrink lookup tables by factor of ~4
173      + better error reporting when running out of lookup space
174      + able to handle longer path/file names (up to 500 chars)
175    o adjoint:
176      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
177      - TBD: "hidden" mom_vecinv recomp. in dynamics
178    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
179     (allow to differentiate between forcing components using new integer flags:
180      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
181     and add new flag to put Dissipation tendency out of Adams-Bashforth.
182    o ecco
183      - enable trend removal from SSH anomaly obs.
184    o adjoint
185      - a fix for PmEpR when #undef EXACT_CONSERV
186      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
187      - try to fix "hidden" recomp. in forward_step for NLFS
188        (NLFS seems broken sometimes after I checked it in)
189    o seaice:
190     - add c-grid version of the dynamic solver:
191       + three new routines that are the c-grid substitute lsr, dynsolver
192         and ostres
193       + put a few fields that were local to dynsolver into global common
194         blocks, so that I can move the computation of stresses etc into
195         seaice_lsr (saves coding but may break the adjoint).
196     - replace more hardwired parameters by runtime parameters
197     - add ice masks that mask the rhs of the implicit solvers where there
198       is no ice (commented out in seaice_dynsolver, because i am not sure
199       if this works properly), eventually this should replace the clipping
200       of ice velocities in seaice_dynsolver to +/-40cm/s.
201    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
202      include it only where its needed
203    o move balancing of fluxes before the call of external_forcing_surf
204    o seaice:
205      - correct units of turning angles (now they are really in degrees)
206      - move computation of GWATX/Y out of main routine into dynsolver
207      - initialize GWATX/Y in seaice_init
208    o Apply mask on Fresh-Water flux (needed for SSH forcing).
209      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
210    o seaice: add runtime flags for turning angles (default to zero)
211    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
212      and trend from exf forcing and ctrl control adjustments
213    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
214      (since checkpoint57x_post)
215    o change the default rotation period to 86164.s = the Earth rotation
216    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
217      and based on a reference stratification. Tested within hs94.cs-32x32x5.
218    o seaice advection: add code for choosing between the default (2nd order
219      central differences) and multiDim advection schemes provided by
220      pkg/generic_advdiff
221    o seaice:
222      - removed all references to SEAICE_GRID.h fields from
223        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
224        (cubed-sphere configuration will change a little)
225      - grid computations in seaice_init are obsolete now.
226      - cleaned up code a little so that is easier to read (hopefully).
227      - added new (better?) discretizations of default advection and diffusion
228        (turn on with SEAICEuseFluxForm)
229      - replace 1 in 3d global fields by kSurface in growth.F
230      
231    checkpoint58a_post
232    o seaice:
233      - bug fix in advect.F
234    o shelfice:
235      - separate shelfice load anomaly from pload (breaks with time
236        dependent forcing), => introduce constant field shelficeLoadAnomaly.
237        Its default is 0., but it may be computed more cleverly from (unknown)
238        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
239        done offline. A good approximation of the pressure load anomaly is
240        necessary to avoid large initial adjustment processes underneath
241        deep-reaching shelfice.
242      - small fix in ISOMIP shelfice_thermodynamics
243      - add more sophisticated thermodynamics of Hellmer (1989), this is
244        now the default
245      - give a few constants more intuitive names
246    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
247      if bulk formulae are used in long integration (especially EmPmR). Turn
248      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
249      if balancePrintMean, the imbalance that is substracted is printed to
250      STDOUT.
251    o fix bug (typo) in obcs_apply_eta.F
252    o add a new package shelfice which enables us to model the circulation
253      underneath shelf-ice with draughts of hundreds of meters.
254     - works
255     - to do: + include improved thermodynamics
256              + check whether kSurfC (from model/inc/SURFACE.h) can be used
257                instead of new field kTopC
258              + can we use topoFile, Ro_surf and existing code in ini_depth.F
259                instead of new field R_shelfIce and new code in ini_depth.F
260                and ini_mask_etc.F?
261              + adjust vertical mixing schemes?
262    o seaice pkg:
263     - add a cpp-flag to include a simple formula for a salinity dependent
264       freezing point of sea water at the surface
265     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
266       meridional stresses are now different (and hopefully correct)
267    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
268       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
269       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
270    o pkg/diagnostics: add options and parameters for regional-statistics
271       diagnostics ; define regions by reading a region-mask from a file
272       (might add other options later)
273    o pkg/bulk_force:
274     - add option and parameters to use AIM surface-flux formulae.
275     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
276       others forcing fields (defined in PARM05, parameter file "data") are loaded
277       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
278     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
279     - use the right EXCH call for uwind,vwind (to work on CS-grid).
280     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
281       and parameters (note: calcWindStress replaces .NOT.readwindstress).
282     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
283    
284    checkpoint58
285    o add "--embed-source" option to genmake2 which, when the supporting
286      tools can be compiled (as determined by genmake2) will turn on the
287      embed_files package which then embeds the entire MITgcm source code
288      (*.[fFhc] + Makefile) used for the build within the executable
289      - requested by CNH but off by default
290      - adds a paltry <9MB to the mitgcmuv executable in most cases
291      - only writes the output when useEMBEDSRC in eedata is true
292    o clean up 3-dim. relaxation codes:
293      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
294      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
295      * Thanks to Tom Haine for testing!
296    
297    checkpoint57z_post
298    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
299      affects output (@ truncation level) of exp. plume_on_slope ; updated.
300    o fix the pickup behavior for obcs in combination with ptracers
301    o fix a bug in ptracers_external_fields_load
302    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
303      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
304    o transfered surface NH pressure to eta field (if exactConserv).
305    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
306         and update lab_sea output.txt file.
307    o completing 3-dim. relaxation code: additional term
308         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
309      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
310      * At compile time, in "EXF_OPTIONS.h" set
311          #define  ALLOW_CLIMTEMP_RELAXATION
312          #define  ALLOW_CLIMSALT_RELAXATION
313      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
314          tauThetaClimRelax3Dim = 15552000.0,
315          tauSaltClimRelax3Dim  = 15552000.0,
316      * 3 cases:
317          1) Use a constant-in-time 3-dim. field
318          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
319          3) Real-time relax. to time-evolving prescribed field
320    o Adding Laplacian-type smoothness constraint on
321      initial and boundary (forcing) controls (ic, bc)
322      * enable at compile-time via
323        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
324      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
325      * Absolute scale somewhat unclear so far
326      * no area weighting was included since no other cost term does so far
327    
328    checkpoint57y_post
329    First step for a NLFS adjoint
330    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
331    o new init. routines for calc_r_star, calc_surf_dr
332    o still need to deal with ini_masks_etc
333    o testreport seemed happy
334    checkpoint57y_pre
335    
336    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
337    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
338    o add new offset feature to offline pkg (plus minor cleanup)
339    o cfc fixes for final year of integration
340    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
341      be in GCHEM_OPTIONS).
342    
343    checkpoint57x_post
344    o fix testreport Pb in multiple test experiment.
345    o cleanup our namelist syntax in verification:
346      - make it more F95 standards compliant (some work still needed)
347      - allows the vast majority of our tests to work with gfortran
348    o Non-Hydrostatic:
349     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
350     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
351    o Allow to apply AB on T,S rather than on AB(gT,gS):
352     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
353     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
354       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
355     - need a "clever" read_pickup to restart from the other AB formulation
356  o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h  o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
357  o remove some unused variables (reduces number of compiler warnings)  o remove some unused variables (reduces number of compiler warnings)
358    o adjoint
359      * Disable useVariableViscosity for adjoint for time being
360        (there are a number of extensive recomputations)
361      * Initialize certain variables needed for adjoint
362    
363  checkpoint57w_post  checkpoint57w_post
364  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names

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