/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.741 by jmc, Wed Nov 1 02:01:15 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o adding precip control xx_precip  o seaice advection with pkg/thsice: a step toward the use of non-linear
8  o moved ptracer ctrl index 17 -> 32    advection scheme, but #ifdef or commented out for now (requires more EXCH).
9    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
10      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
11      in natl_box (affects results @ truncation level: update output.txt)
12    o multi-threading and IO:
13      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
14      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
15        (needed to work with SingleCpuIO): tested in all verif. exp.
16    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
17      affects the results (but none of the verification test uses this scheme).
18    o Adding some pkg/diagnostics capability to pkg/seaice
19      (will certainly be subject to changes)
20    o ctrl: adding new control variables:
21      lwflux, lwdown, evap, snowprecip, apressure, runoff
22    
23    checkpoint58q_post
24    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
25      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
26      high_res_cube configuration by 4% on Columbia.
27    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
28      add (in global_with_exf/code) a version of EXF_INTERP_READ without
29      dynamical allocation (seems to work in multi-threaded).
30    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
31      single CPU io) so that TAF does not have to see EESUPPORT.h
32    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
33    
34    checkpoint58p_post
35    o obcs: stop if obcs is used with useCDscheme = .true.
36    o shelfice:
37     - fix a sign error so that no slip at shelfice interface works
38     - remove stop for combination non-hydrostatic code and shelfice. That does
39       not mean, that the results are correct, but at least they are numerically
40       stable
41    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
42    o added adjoint exch routined for all exch*3d* routines
43      and updated flow directives
44    
45    checkpoint58o_post
46    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
47      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
48    o change controling S/R for writing pickup file (new S/R do_write_pickup)
49      and clean-up reading/writing of pickup files.
50    o fix local version of read/write pickup (NH part) in rotating_tank/code
51    o simplify EXCH interface:
52     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
53     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
54    o added the regrid package
55    o shelfice:
56     - add a simple boundary layer scheme to reduce noise
57     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
58    
59    checkpoint58n_post
60    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
61       local variable (not in common block).
62    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
63      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
64      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
65        to work with SingleCpuIO.
66    o add "_d 0" to real constant of pkg/cfc subroutines ;
67       update exp. cfc_exemple & tutorial_cfc_offline output files.
68    o multi-threading and IO:
69      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
70        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
71      - barrier before and after reading.
72      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
73      - avoid using MDS_WRITELOCAL for LAND pkg output.
74      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
75        common-block variables ; Allows multi-threading with master-thread IO.
76    o change default MAX_NO_THREADS from 32 to 4 ;
77      and stop cleanly when MAX_NO_THREADS is too small.
78    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
79    
80    checkpoint58m_post
81    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
82       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
83    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
84       keep global_ocean.90x40x15 (for AD testing) with former secondary test
85       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
86    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
87        add MITgcm_tutorials (= code + all the tutorials)
88    o ecco, option to compute cost for total ssh (mean+anom)
89    o consistent with addition of ptracer and ssh in pkg/profiles
90    o profiles: adding ptracer and ssh
91    o testreport: change multi-test output-file name
92      (from output.txt.{name} to output.{name}.txt)
93    o profiles: now ok for mutli-tiles case
94    o seaice: add 4 parameters for different advection schemes for area,
95      (effective) seaice thickness, enthalphy, and snow height. Their default
96      is the standard parameter SEAICEadvScheme
97    o calc_gw:
98     - add cosFacU in zonal viscous flux (harmonic.visc.).
99     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
100       of tutorial_plume_on_slope.
101    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
102    o calc_gw: true flux-form, account for horizontal grid spacing.
103      update rotating_tank results, but not plume_on_slope (affected at
104      truncation level, 11 digits).
105    
106    checkpoint58l_post
107    o calc_gw:
108     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
109     - remove side-drag for now (need to fix it); update plume_on_slope results.
110     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
111    o commit code to make SST/SSS weights spatially variable
112      (based on either variable in-situ or variable initial T/S weights)
113    o pkg/ecco:
114      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
115        now based on horizontally varying weights wthetaLev, wsaltLev
116      * cost_averagesflags now returns year indices in addition to day, month
117      * sflux balance is performed on annual basis
118        (sflxumm, sfluxmm2, bal_sfluxmm)
119      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
120        including separate counting and multipliers
121    o pkg/rbcs
122      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
123    
124    checkpoint58k_post
125    o testreport:
126     - always build in dir. "build" (if not there, mkdir build instead of building
127       & running in input)
128     - run in dir run (if it exists), in build otherwise.
129     - call prepare_run (if input/prepare_run exists)
130     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
131    o pkg/exf modifications to interpolation and rotation routines for more
132       reasonable treatment of North Pole singularity: for tracers North Pole
133       value is set to northernmost zonal-mean value, for zonal velocity it is
134       set to zero, and for meridional velocity it is set to northernmost value.
135    o pkg/exf/exf_check_range.F
136     - add tile index to diagnostics and move stop statement to the very
137       end of the routine.
138    o pkg/diagnostics: (diagnostics_main_init.F)
139      define title of isomorphic variables according to the current config.
140    o pkg/thsice with pkg/seaice dynamics:
141    - fix domain of computation (interior only, required for exf) and do exchanges
142    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
143    o towards a standard way of dealing with multi-threading in MONITOR
144      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
145    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
146       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
147    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
148    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
149    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
150       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
151    o tracer advection:
152     - clean-up and simplify calc_common_factors.F
153     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
154       advection subroutine (but still not used within DST advection S/R)
155    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
156    
157    checkpoint58j_post
158    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
159      from file (collects calls previously in FORWARD_STEP)
160    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
161    o adjoint store dir. adjusted accordingly
162    o genmake2
163      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
164    
165    checkpoint58i_post
166    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
167      on wind stress (SEAICEstressFactor defaults to 1.)
168    o Total number of Timers is finite (<=40): comment out 2 non-essential one
169      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
170    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
171      on CS-grid: no longer loosing mass.
172    o exf & curvilinear-grid: no longer modify longitude xC & xG.
173    o pkg/ggl90: fix sloppy output and fix a bug
174    o pkg/seaice: added SEAICEuseEVPpickup parameter
175      - Set to false in order to start EVP solver with
176        non-EVP pickup files when using SEAICEuseEVP
177      - fix sign error in diffusion in seaice_calc_rhs
178    
179    checkpoint58h_post
180    * Modifications for bottom topography control
181      o replace hFacC by _hFacC at various places
182      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
183      o add non-self-adjoint cg2d_nsa
184      o update autodiff support routines
185      o re-initialise hfac after ctrl_depth_ini
186      o works for 5x5 box, doesnt work for global_ocean.90x40x15
187    * Adding verification for 5x5 box (4-layer) bottom topography control
188    
189    checkpoint58g_post
190    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
191       used for mean seasonal cycle, mean diurnal cycle); add an example
192       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
193    o pkg/ggl90:
194      - add parameter (minimum surface kinetic energy)
195      - fix bug (avoiding division by zero)
196    o couple pkg/thsice to pkg/seaice:
197      - modify advection in seaice to accomodate new scalar fields to be advected
198      - only muliDimAdection scheme work with seaice/thsice
199      - mapping of thsice-variables to seaice-variables, back and forth
200      - does not break the verification experiments, but does not give the
201        desired results either
202    o pkg/seaice
203      - make (default) second order advection a bit less confusing?
204    
205    checkpoint58f_post
206    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
207      to pkg/seaice):
208      - new routines thsice_map_exf and thsice_get_exf provide the interface
209      - add an additional formal parameter to thsice_solve4temp
210    o pkg/exf:
211      - add new fields wspeed, snowprecip (to be able to couple to thsice)
212      - correct Stefan-Boltzmann constant
213      - new parameter for longwave surface emittance
214      - separate some stuff from exf_bulkformulae into new routines  
215        exf_radiation, exf_wind
216      - add new parameters and constants: longwave emissivity for ocean, ice
217        and snow, evaporation parameters over ice
218      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
219        either wind from stress or stress from wind
220    o pkg/thSIce:
221    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
222    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
223       and THSICE_CALC_THICKN
224    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
225    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
226      to make debugging easier.
227    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
228    o pkg/bulk_force:
229      - clean-up comments and parameters ;
230      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
231    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
232      generate new output for test-experiment: aim.5l_cs.thSI
233    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
234      testreport accordingly
235    
236    checkpoint58e_post
237    o SEAICE_CGRID adjoint done
238    o R_STAR adjoint implemented.
239      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
240      * need to sort out init. of h0facc, etc.
241    o Make pkg/profile fully independent of ecco,cost, etc. stuff
242      to be able to use it in pure forward.
243    
244    checkpoint58d_post
245    o upgrade simple test-experiment to tutorial example:
246     step.1: duplicate the experiment and (step.2) will remove the old copy.
247      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
248      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
249      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
250      tutorial_global_oce_biogeo    <- copy of dic_example
251      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
252      tutorial_plume_on_slope       <- copy of plume_on_slope
253      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
254      tutorial_global_oce_optim     <- empty for now (David ?)
255      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
256     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
257    o correct a sign problem in cost_scat.F
258    o obcs and ptracers: fix boundary conditions for advections schemes
259      with larger stencil
260    o thsice adjoint: start
261    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
262      completeness
263    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
264      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
265    o ptracers adjoint:
266      * avoid extensive recomputatations
267      * fix missing re-init. of gptr (missed by TAF)
268    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
269      me to turn off the excessive output to STDOUT that this package produces
270    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
271      and add those terms in Vector-Invariant formulation.
272    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
273      if the control period (xx_hfluxperiod etc) is 0
274    o in profiles pkg, clean routines and fix details
275    o in ecco pkg, reading ssh data:
276      fix problem in case the model does not start at iter0=0
277    o fix mnc-pickup/restart for ptracers
278    o new package prifiles:
279      code to compute profile-based cost by Gael Forget
280      (modifs in ecco, ctrl, autodiff)
281    o Benign bug fix in initialization (spotted by M. Mazloff) of
282      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
283    
284    checkpoint58c_post
285    o adjoint: finish NLFS adjoint and provide reference output in
286      verification/global_ocean.90x40x15/results_ad_nlfs
287    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
288      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
289      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
290      with SEAICE_CGRID defined.
291    o move calendarDumps from "data" to "data.cal" and clean-up the code
292      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
293    o add useEXF & useCAL flags (for now, set in hard-coded way)
294    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
295      (were missing in NH mode, and wrong in quasihydrostatic mode).
296      waiting for Chris updated version of calc_gw to add those CALLs.
297    o fix bug in quasihydrostatic S/R ;
298      add a test for this option: global_ocean.90x40x15.qshyd
299    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
300      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
301    o add on/off flag useOffLine for package OFFLINE
302    o seaice:
303      - modify advection so that it works also on the C-grid
304      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
305        problem in multi-tile runs with C-grid
306      - add flags for clipping ice velocities and/or masking solver forcing
307      - fix drag (ocean on ice) formulation and a bug that caused noise in the
308        C-grid solver
309      - added a few comments to seaice_diffusion.F
310      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
311        are now exclusive)
312      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
313        required re-ordering the code a little:
314       + make DAIRN global variable (defined in SEAICE)
315       + move computation of the viscosities eta and zeta into a new separate
316         routine (because I need to recompute them in seaice_ocean_stress.F)
317    
318    checkpoint58b_post
319    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
320      update output.txt of exp. aim.5l_cs.thSI
321    o various mnc cleanups and improvements:
322      + shrink lookup tables by factor of ~4
323      + better error reporting when running out of lookup space
324      + able to handle longer path/file names (up to 500 chars)
325    o adjoint:
326      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
327      - TBD: "hidden" mom_vecinv recomp. in dynamics
328    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
329     (allow to differentiate between forcing components using new integer flags:
330      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
331     and add new flag to put Dissipation tendency out of Adams-Bashforth.
332    o ecco
333      - enable trend removal from SSH anomaly obs.
334    o adjoint
335      - a fix for PmEpR when #undef EXACT_CONSERV
336      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
337      - try to fix "hidden" recomp. in forward_step for NLFS
338        (NLFS seems broken sometimes after I checked it in)
339    o seaice:
340     - add c-grid version of the dynamic solver:
341       + three new routines that are the c-grid substitute lsr, dynsolver
342         and ostres
343       + put a few fields that were local to dynsolver into global common
344         blocks, so that I can move the computation of stresses etc into
345         seaice_lsr (saves coding but may break the adjoint).
346     - replace more hardwired parameters by runtime parameters
347     - add ice masks that mask the rhs of the implicit solvers where there
348       is no ice (commented out in seaice_dynsolver, because i am not sure
349       if this works properly), eventually this should replace the clipping
350       of ice velocities in seaice_dynsolver to +/-40cm/s.
351    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
352      include it only where its needed
353    o move balancing of fluxes before the call of external_forcing_surf
354    o seaice:
355      - correct units of turning angles (now they are really in degrees)
356      - move computation of GWATX/Y out of main routine into dynsolver
357      - initialize GWATX/Y in seaice_init
358    o Apply mask on Fresh-Water flux (needed for SSH forcing).
359      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
360    o seaice: add runtime flags for turning angles (default to zero)
361    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
362      and trend from exf forcing and ctrl control adjustments
363    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
364      (since checkpoint57x_post)
365    o change the default rotation period to 86164.s = the Earth rotation
366    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
367      and based on a reference stratification. Tested within hs94.cs-32x32x5.
368    o seaice advection: add code for choosing between the default (2nd order
369      central differences) and multiDim advection schemes provided by
370      pkg/generic_advdiff
371    o seaice:
372      - removed all references to SEAICE_GRID.h fields from
373        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
374        (cubed-sphere configuration will change a little)
375      - grid computations in seaice_init are obsolete now.
376      - cleaned up code a little so that is easier to read (hopefully).
377      - added new (better?) discretizations of default advection and diffusion
378        (turn on with SEAICEuseFluxForm)
379      - replace 1 in 3d global fields by kSurface in growth.F
380      
381    checkpoint58a_post
382    o seaice:
383      - bug fix in advect.F
384    o shelfice:
385      - separate shelfice load anomaly from pload (breaks with time
386        dependent forcing), => introduce constant field shelficeLoadAnomaly.
387        Its default is 0., but it may be computed more cleverly from (unknown)
388        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
389        done offline. A good approximation of the pressure load anomaly is
390        necessary to avoid large initial adjustment processes underneath
391        deep-reaching shelfice.
392      - small fix in ISOMIP shelfice_thermodynamics
393      - add more sophisticated thermodynamics of Hellmer (1989), this is
394        now the default
395      - give a few constants more intuitive names
396    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
397      if bulk formulae are used in long integration (especially EmPmR). Turn
398      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
399      if balancePrintMean, the imbalance that is substracted is printed to
400      STDOUT.
401    o fix bug (typo) in obcs_apply_eta.F
402    o add a new package shelfice which enables us to model the circulation
403      underneath shelf-ice with draughts of hundreds of meters.
404     - works
405     - to do: + include improved thermodynamics
406              + check whether kSurfC (from model/inc/SURFACE.h) can be used
407                instead of new field kTopC
408              + can we use topoFile, Ro_surf and existing code in ini_depth.F
409                instead of new field R_shelfIce and new code in ini_depth.F
410                and ini_mask_etc.F?
411              + adjust vertical mixing schemes?
412    o seaice pkg:
413     - add a cpp-flag to include a simple formula for a salinity dependent
414       freezing point of sea water at the surface
415     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
416       meridional stresses are now different (and hopefully correct)
417    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
418       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
419       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
420    o pkg/diagnostics: add options and parameters for regional-statistics
421       diagnostics ; define regions by reading a region-mask from a file
422       (might add other options later)
423    o pkg/bulk_force:
424     - add option and parameters to use AIM surface-flux formulae.
425     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
426       others forcing fields (defined in PARM05, parameter file "data") are loaded
427       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
428     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
429     - use the right EXCH call for uwind,vwind (to work on CS-grid).
430     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
431       and parameters (note: calcWindStress replaces .NOT.readwindstress).
432     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
433    
434    checkpoint58
435    o add "--embed-source" option to genmake2 which, when the supporting
436      tools can be compiled (as determined by genmake2) will turn on the
437      embed_files package which then embeds the entire MITgcm source code
438      (*.[fFhc] + Makefile) used for the build within the executable
439      - requested by CNH but off by default
440      - adds a paltry <9MB to the mitgcmuv executable in most cases
441      - only writes the output when useEMBEDSRC in eedata is true
442    o clean up 3-dim. relaxation codes:
443      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
444      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
445      * Thanks to Tom Haine for testing!
446    
447    checkpoint57z_post
448    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
449      affects output (@ truncation level) of exp. plume_on_slope ; updated.
450    o fix the pickup behavior for obcs in combination with ptracers
451    o fix a bug in ptracers_external_fields_load
452    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
453      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
454    o transfered surface NH pressure to eta field (if exactConserv).
455    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
456         and update lab_sea output.txt file.
457    o completing 3-dim. relaxation code: additional term
458         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
459      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
460      * At compile time, in "EXF_OPTIONS.h" set
461          #define  ALLOW_CLIMTEMP_RELAXATION
462          #define  ALLOW_CLIMSALT_RELAXATION
463      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
464          tauThetaClimRelax3Dim = 15552000.0,
465          tauSaltClimRelax3Dim  = 15552000.0,
466      * 3 cases:
467          1) Use a constant-in-time 3-dim. field
468          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
469          3) Real-time relax. to time-evolving prescribed field
470    o Adding Laplacian-type smoothness constraint on
471      initial and boundary (forcing) controls (ic, bc)
472      * enable at compile-time via
473        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
474      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
475      * Absolute scale somewhat unclear so far
476      * no area weighting was included since no other cost term does so far
477    
478    checkpoint57y_post
479    First step for a NLFS adjoint
480    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
481    o new init. routines for calc_r_star, calc_surf_dr
482    o still need to deal with ini_masks_etc
483    o testreport seemed happy
484    checkpoint57y_pre
485    
486    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
487    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
488    o add new offset feature to offline pkg (plus minor cleanup)
489    o cfc fixes for final year of integration
490    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
491      be in GCHEM_OPTIONS).
492    
493    checkpoint57x_post
494    o fix testreport Pb in multiple test experiment.
495    o cleanup our namelist syntax in verification:
496      - make it more F95 standards compliant (some work still needed)
497      - allows the vast majority of our tests to work with gfortran
498    o Non-Hydrostatic:
499     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
500     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
501    o Allow to apply AB on T,S rather than on AB(gT,gS):
502     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
503     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
504       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
505     - need a "clever" read_pickup to restart from the other AB formulation
506    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
507    o remove some unused variables (reduces number of compiler warnings)
508    o adjoint
509      * Disable useVariableViscosity for adjoint for time being
510        (there are a number of extensive recomputations)
511      * Initialize certain variables needed for adjoint
512    
513    checkpoint57w_post
514    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
515                 fix the singleCpuIO RS version of MDSWRITEFIELD
516       and add a WARNING if using globalFiles=T with multi-processors.
517    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
518      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
519    o tracer advection scheme:
520      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
521       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
522       was not very convenient).
523      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
524       (further tests needed for the implicit DST & Flux-Limiter schemes).
525    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
526      and sRef for convenience, handy, when you want to initialize
527      ptracers in a large domain with a constant non-zero value. Also,
528      untangle ptracers_init.F a little.
529    
530    checkpoint57v_post
531    o change dome exp. to use variable viscosity in side-drag terms.
532    o remove all the files from the cfc_offline test since they are now
533      incorporated into tutorial_cfc_offline which has been producing
534      identical results for a few days of testing
535    o add new parameter: sideDragFactor to enable half-slip-side BC
536      and change side-drag S/R to use viscosity from mom_calc_visc
537      (can switch back by setting sideDragFactor=0.); affects results at
538      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
539       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
540    o vorticity & strain are now computed without masking, to account for
541      no-slip-side BC in variable viscosity calculation ; mask is applied
542      anyway later on, before computing advection/coriolis terms.
543    o modify exp4 to test new obcs support for reading from external files
544      and for passive tracers
545    o fix behavior of ptracers_monitor when monitor output is written to a
546      netcdf-file; still not independent of monitor.F (writes in the same
547      file).
548    o change default value of tRef (put a uniform, meaningful value for ocean
549      & atmos) and initialize sRef (was missing, as Martin mentioned).
550    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
551      to be proportional to enstrophy dissipation length.  Thus,
552       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
553      This is now consistent with Smagorinsky and with the manual.
554    
555    checkpoint57u_post
556    o OBCS and PTRACERS: add open boundary support for passive tracers
557      - either use homogenous (pseudo) v.Neumann conditions or prescribe
558        OB-values from file; this is not different from the way theta and salinity
559        are treated
560      - however, Orlanski-radiation conditions are not supported, and the model
561        will stop if you use pTracers and Orlanski at the same time.
562      - beefed up the rountine obcs_external_fields_load: now only those open
563        boundary values are overwritten with values from files for which there
564        are really files, otherwise the OB-fields remain untouched. This makes
565        it possible to use different OBs at different ends of the domain (as
566        with EXF)
567    o reduce number of exch calls in shap_filt (s2).
568    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
569      truncation level) 4/5 MLAdjust test results (11&12 digits match).
570    
571    checkpoint57t_post
572    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
573    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
574      same truncation, independent of the face number: affects affects several
575      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
576    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
577      note that biharmonic viscosity + no-slip was not tested in any experiment.
578    o fix bug in non-linear free-surf side-drag ; generate new output for
579      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
580    o make mnc honor the writeBinaryPrec flag for most kinds of output
581    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
582    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
583      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
584    o add brackets in multi-terms sum to get same truncation, independent of
585      the face number (manage to get exactly same value of gU,gV at the cs-edge)
586      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
587    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
588      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
589      a maximum grid-scale Reynolds number.  Also, changes all length calculations
590      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
591      Suggested values of viscosity parameters found in mom_calc_visc.
592      Many new viscosity diagnostics available.
593    
594    checkpoint57s_post
595    o Add clearing-house for viscosity calculations, mom_calc_visc and
596      correct numerous bugs in LeithD and Smagorinsky discretizations.  
597      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
598      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
599      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
600      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
601      The Strain-Tension form is now called with useStrainTensonVisc=.true.
602      ViscAhStrain and viscAhTension are now retired.
603    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
604    o In response to JMC's bug report, genmake2 now ignores any soft-links
605      that it finds in the *current* directory when searching for files.
606      Soft-links found in any other source directories will still work as
607      they did before.
608    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
609      a C routine to unlimit the stack size
610    o mnc-ify pkg/aim snapshot vars
611    o mnc-ify pkg/land as requested by Daniel
612    o various changes to mnc including:
613      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
614      - output can now be grouped so that all files within a group
615          change the ITER portion of their names in lock-step together
616      - can now read ("global") PER-FACE (in addition to PER-TILE) files
617          and works with both EXCH1 and EXCH2 (but needs more testing)
618      - writing works for all verification test cases w/ g77 on Linux
619    
620    checkpoint57r_post
621    o make MNC variable initialization happen earlier
622    o add diagnostics for (almost) each term of the momentum Eq.
623    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
624    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
625    o remove MINIMAL_TAVE_OUTPUT option ;
626      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
627    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
628      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
629    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
630    o add time-dependent SST, SSS control
631    o cost terms in ecco/ modularized (new cost_generic.F)
632    o cost_averages routines are modularized (new cost_averagesgeneric.F)
633    o new infrastructure for seaice model vs. obs misfits in seaice/
634      * driver from the_main_loop.F is seaice_cost_driver.F
635      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
636      * gradient check in Exp. 6a of natl_box_adjoint/
637    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
638      (see README file)
639    
640    checkpoint57q_post
641    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
642    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
643      - bug was reported by Jean-Michel and Ian Fenty
644    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
645      update exp. cpl_aim+ocn output.
646    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
647      Needed for high-res. runs with large global files
648      to be able to limit tapelev size
649    o Changed some tests for adjoint:
650      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
651      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
652      * global_ocean.90x40x15/ back to default 3-level checkpointing
653    o Modifications to enable scripted COMMON to MODULE conversion
654      * verification/OpenAD/code/ has necessary scripts and description;
655      * converts, compiles and runs successfully;
656    
657    checkpoint57p_post
658    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
659    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
660      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
661    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
662    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
663      (was already the case for dissipation with mom_vecinv,
664       and also the case for grad.PhiHyd when staggered-timeStep)
665      This will allow to put dissipation out-off the AB time-stepping.
666     Unfortunately, affects truncation error. Update output of exp. that "fails"
667      (cg2d matching number) and leave the others for later: front_relax(10),
668      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
669      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
670    
671    checkpoint57o_post
672    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
673      (2) its ready to be documented during the 20050801 DocFest
674    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
675      for ideal_2D_oce and lab_sea on linux_ia32_g77
676    o set to #undef CTRL_SET_OLD_MAXCVARS_30
677      in global1x1_tot/code_seaice_adj to access indices 32, 33
678      (worth another tag)
679    
680    checkpoint57n_post
681    o adding precip control xx_precip 32
682    o adding swflux control xx_swflux 33
683    o Replacing 10 forcing penalty cost routines by 1 generic.
684    o Implementing partitioning in time-mean and variable adjustment
685      for atmos. state.
686    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
687  o in natl_box_adjoint:  o in natl_box_adjoint:
688    * updated: results_bulk/    * updated exp 1 to 10
689    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
690    o updated global1x1/*_seaice_adj/
691      to incorporate latest changes
692    o enable useSingleCpuIO for mdsio vector routines
693      (applies in particular to tapelev I/O)
694    o removed inefficient K-loop in all active_file*control*.F
695    
696  checkpoint57m_post  checkpoint57m_post
697  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
Legend:
Removed from v.1.519  
changed lines
  Added in v.1.741
  ViewVC Help
Powered by ViewVC 1.1.22