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revision 1.589 by jmc, Thu Dec 8 22:25:07 2005 UTC revision 1.686 by jmc, Fri Jun 23 04:36:25 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o towards a standard way of dealing with multi-threading in MONITOR
8      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
9    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
10       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
11    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
12    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
13    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
14       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
15    o tracer advection:
16     - clean-up and simplify calc_common_factors.F
17     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
18       advection subroutine (but still not used within DST advection S/R)
19    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
20    
21    checkpoint58j_post
22    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
23      from file (collects calls previously in FORWARD_STEP)
24    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
25    o adjoint store dir. adjusted accordingly
26    o genmake2
27      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
28    
29    checkpoint58i_post
30    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
31      on wind stress (SEAICEstressFactor defaults to 1.)
32    o Total number of Timers is finite (<=40): comment out 2 non-essential one
33      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
34    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
35      on CS-grid: no longer loosing mass.
36    o exf & curvilinear-grid: no longer modify longitude xC & xG.
37    o pkg/ggl90: fix sloppy output and fix a bug
38    o pkg/seaice: added SEAICEuseEVPpickup parameter
39      - Set to false in order to start EVP solver with
40        non-EVP pickup files when using SEAICEuseEVP
41      - fix sign error in diffusion in seaice_calc_rhs
42    
43    checkpoint58h_post
44    * Modifications for bottom topography control
45      o replace hFacC by _hFacC at various places
46      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
47      o add non-self-adjoint cg2d_nsa
48      o update autodiff support routines
49      o re-initialise hfac after ctrl_depth_ini
50      o works for 5x5 box, doesnt work for global_ocean.90x40x15
51    * Adding verification for 5x5 box (4-layer) bottom topography control
52    
53    checkpoint58g_post
54    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
55       used for mean seasonal cycle, mean diurnal cycle); add an example
56       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
57    o pkg/ggl90:
58      - add parameter (minimum surface kinetic energy)
59      - fix bug (avoiding division by zero)
60    o couple pkg/thsice to pkg/seaice:
61      - modify advection in seaice to accomodate new scalar fields to be advected
62      - only muliDimAdection scheme work with seaice/thsice
63      - mapping of thsice-variables to seaice-variables, back and forth
64      - does not break the verification experiments, but does not give the
65        desired results either
66    o pkg/seaice
67      - make (default) second order advection a bit less confusing?
68    
69    checkpoint58f_post
70    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
71      to pkg/seaice):
72      - new routines thsice_map_exf and thsice_get_exf provide the interface
73      - add an additional formal parameter to thsice_solve4temp
74    o pkg/exf:
75      - add new fields wspeed, snowprecip (to be able to couple to thsice)
76      - correct Stefan-Boltzmann constant
77      - new parameter for longwave surface emittance
78      - separate some stuff from exf_bulkformulae into new routines  
79        exf_radiation, exf_wind
80      - add new parameters and constants: longwave emissivity for ocean, ice
81        and snow, evaporation parameters over ice
82      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
83        either wind from stress or stress from wind
84    o pkg/thSIce:
85    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
86    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
87       and THSICE_CALC_THICKN
88    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
89    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
90      to make debugging easier.
91    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
92    o pkg/bulk_force:
93      - clean-up comments and parameters ;
94      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
95    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
96      generate new output for test-experiment: aim.5l_cs.thSI
97    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
98      testreport accordingly
99    
100    checkpoint58e_post
101    o SEAICE_CGRID adjoint done
102    o R_STAR adjoint implemented.
103      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
104      * need to sort out init. of h0facc, etc.
105    o Make pkg/profile fully independent of ecco,cost, etc. stuff
106      to be able to use it in pure forward.
107    
108    checkpoint58d_post
109    o upgrade simple test-experiment to tutorial example:
110     step.1: duplicate the experiment and (step.2) will remove the old copy.
111      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
112      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
113      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
114      tutorial_global_oce_biogeo    <- copy of dic_example
115      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
116      tutorial_plume_on_slope       <- copy of plume_on_slope
117      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
118      tutorial_global_oce_optim     <- empty for now (David ?)
119      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
120     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
121    o correct a sign problem in cost_scat.F
122    o obcs and ptracers: fix boundary conditions for advections schemes
123      with larger stencil
124    o thsice adjoint: start
125    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
126      completeness
127    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
128      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
129    o ptracers adjoint:
130      * avoid extensive recomputatations
131      * fix missing re-init. of gptr (missed by TAF)
132    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
133      me to turn off the excessive output to STDOUT that this package produces
134    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
135      and add those terms in Vector-Invariant formulation.
136    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
137      if the control period (xx_hfluxperiod etc) is 0
138    o in profiles pkg, clean routines and fix details
139    o in ecco pkg, reading ssh data:
140      fix problem in case the model does not start at iter0=0
141    o fix mnc-pickup/restart for ptracers
142    o new package prifiles:
143      code to compute profile-based cost by Gael Forget
144      (modifs in ecco, ctrl, autodiff)
145    o Benign bug fix in initialization (spotted by M. Mazloff) of
146      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
147    
148    checkpoint58c_post
149    o adjoint: finish NLFS adjoint and provide reference output in
150      verification/global_ocean.90x40x15/results_ad_nlfs
151    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
152      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
153      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
154      with SEAICE_CGRID defined.
155    o move calendarDumps from "data" to "data.cal" and clean-up the code
156      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
157    o add useEXF & useCAL flags (for now, set in hard-coded way)
158    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
159      (were missing in NH mode, and wrong in quasihydrostatic mode).
160      waiting for Chris updated version of calc_gw to add those CALLs.
161    o fix bug in quasihydrostatic S/R ;
162      add a test for this option: global_ocean.90x40x15.qshyd
163    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
164      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
165    o add on/off flag useOffLine for package OFFLINE
166    o seaice:
167      - modify advection so that it works also on the C-grid
168      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
169        problem in multi-tile runs with C-grid
170      - add flags for clipping ice velocities and/or masking solver forcing
171      - fix drag (ocean on ice) formulation and a bug that caused noise in the
172        C-grid solver
173      - added a few comments to seaice_diffusion.F
174      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
175        are now exclusive)
176      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
177        required re-ordering the code a little:
178       + make DAIRN global variable (defined in SEAICE)
179       + move computation of the viscosities eta and zeta into a new separate
180         routine (because I need to recompute them in seaice_ocean_stress.F)
181    
182    checkpoint58b_post
183    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
184      update output.txt of exp. aim.5l_cs.thSI
185    o various mnc cleanups and improvements:
186      + shrink lookup tables by factor of ~4
187      + better error reporting when running out of lookup space
188      + able to handle longer path/file names (up to 500 chars)
189    o adjoint:
190      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
191      - TBD: "hidden" mom_vecinv recomp. in dynamics
192    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
193     (allow to differentiate between forcing components using new integer flags:
194      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
195     and add new flag to put Dissipation tendency out of Adams-Bashforth.
196    o ecco
197      - enable trend removal from SSH anomaly obs.
198    o adjoint
199      - a fix for PmEpR when #undef EXACT_CONSERV
200      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
201      - try to fix "hidden" recomp. in forward_step for NLFS
202        (NLFS seems broken sometimes after I checked it in)
203    o seaice:
204     - add c-grid version of the dynamic solver:
205       + three new routines that are the c-grid substitute lsr, dynsolver
206         and ostres
207       + put a few fields that were local to dynsolver into global common
208         blocks, so that I can move the computation of stresses etc into
209         seaice_lsr (saves coding but may break the adjoint).
210     - replace more hardwired parameters by runtime parameters
211     - add ice masks that mask the rhs of the implicit solvers where there
212       is no ice (commented out in seaice_dynsolver, because i am not sure
213       if this works properly), eventually this should replace the clipping
214       of ice velocities in seaice_dynsolver to +/-40cm/s.
215    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
216      include it only where its needed
217    o move balancing of fluxes before the call of external_forcing_surf
218    o seaice:
219      - correct units of turning angles (now they are really in degrees)
220      - move computation of GWATX/Y out of main routine into dynsolver
221      - initialize GWATX/Y in seaice_init
222    o Apply mask on Fresh-Water flux (needed for SSH forcing).
223      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
224    o seaice: add runtime flags for turning angles (default to zero)
225    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
226      and trend from exf forcing and ctrl control adjustments
227    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
228      (since checkpoint57x_post)
229    o change the default rotation period to 86164.s = the Earth rotation
230    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
231      and based on a reference stratification. Tested within hs94.cs-32x32x5.
232    o seaice advection: add code for choosing between the default (2nd order
233      central differences) and multiDim advection schemes provided by
234      pkg/generic_advdiff
235    o seaice:
236      - removed all references to SEAICE_GRID.h fields from
237        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
238        (cubed-sphere configuration will change a little)
239      - grid computations in seaice_init are obsolete now.
240      - cleaned up code a little so that is easier to read (hopefully).
241      - added new (better?) discretizations of default advection and diffusion
242        (turn on with SEAICEuseFluxForm)
243      - replace 1 in 3d global fields by kSurface in growth.F
244      
245    checkpoint58a_post
246    o seaice:
247      - bug fix in advect.F
248    o shelfice:
249      - separate shelfice load anomaly from pload (breaks with time
250        dependent forcing), => introduce constant field shelficeLoadAnomaly.
251        Its default is 0., but it may be computed more cleverly from (unknown)
252        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
253        done offline. A good approximation of the pressure load anomaly is
254        necessary to avoid large initial adjustment processes underneath
255        deep-reaching shelfice.
256      - small fix in ISOMIP shelfice_thermodynamics
257      - add more sophisticated thermodynamics of Hellmer (1989), this is
258        now the default
259      - give a few constants more intuitive names
260    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
261      if bulk formulae are used in long integration (especially EmPmR). Turn
262      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
263      if balancePrintMean, the imbalance that is substracted is printed to
264      STDOUT.
265    o fix bug (typo) in obcs_apply_eta.F
266    o add a new package shelfice which enables us to model the circulation
267      underneath shelf-ice with draughts of hundreds of meters.
268     - works
269     - to do: + include improved thermodynamics
270              + check whether kSurfC (from model/inc/SURFACE.h) can be used
271                instead of new field kTopC
272              + can we use topoFile, Ro_surf and existing code in ini_depth.F
273                instead of new field R_shelfIce and new code in ini_depth.F
274                and ini_mask_etc.F?
275              + adjust vertical mixing schemes?
276    o seaice pkg:
277     - add a cpp-flag to include a simple formula for a salinity dependent
278       freezing point of sea water at the surface
279     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
280       meridional stresses are now different (and hopefully correct)
281    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
282       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
283       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
284    o pkg/diagnostics: add options and parameters for regional-statistics
285       diagnostics ; define regions by reading a region-mask from a file
286       (might add other options later)
287    o pkg/bulk_force:
288     - add option and parameters to use AIM surface-flux formulae.
289     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
290       others forcing fields (defined in PARM05, parameter file "data") are loaded
291       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
292     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
293     - use the right EXCH call for uwind,vwind (to work on CS-grid).
294     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
295       and parameters (note: calcWindStress replaces .NOT.readwindstress).
296     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
297    
298    checkpoint58
299    o add "--embed-source" option to genmake2 which, when the supporting
300      tools can be compiled (as determined by genmake2) will turn on the
301      embed_files package which then embeds the entire MITgcm source code
302      (*.[fFhc] + Makefile) used for the build within the executable
303      - requested by CNH but off by default
304      - adds a paltry <9MB to the mitgcmuv executable in most cases
305      - only writes the output when useEMBEDSRC in eedata is true
306    o clean up 3-dim. relaxation codes:
307      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
308      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
309      * Thanks to Tom Haine for testing!
310    
311    checkpoint57z_post
312    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
313      affects output (@ truncation level) of exp. plume_on_slope ; updated.
314    o fix the pickup behavior for obcs in combination with ptracers
315    o fix a bug in ptracers_external_fields_load
316    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
317      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
318    o transfered surface NH pressure to eta field (if exactConserv).
319  o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)  o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
320       and update lab_sea output.txt file.       and update lab_sea output.txt file.
321    o completing 3-dim. relaxation code: additional term
322         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
323      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
324      * At compile time, in "EXF_OPTIONS.h" set
325          #define  ALLOW_CLIMTEMP_RELAXATION
326          #define  ALLOW_CLIMSALT_RELAXATION
327      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
328          tauThetaClimRelax3Dim = 15552000.0,
329          tauSaltClimRelax3Dim  = 15552000.0,
330      * 3 cases:
331          1) Use a constant-in-time 3-dim. field
332          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
333          3) Real-time relax. to time-evolving prescribed field
334    o Adding Laplacian-type smoothness constraint on
335      initial and boundary (forcing) controls (ic, bc)
336      * enable at compile-time via
337        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
338      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
339      * Absolute scale somewhat unclear so far
340      * no area weighting was included since no other cost term does so far
341    
342  checkpoint57y_post  checkpoint57y_post
343  First step for a NLFS adjoint  First step for a NLFS adjoint

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