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revision 1.618 by jmc, Thu Mar 2 22:52:09 2006 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 seaice advection with pkg/thsice: a step toward the use of non-linear
8      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).  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)    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)  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  o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
362    and trend from exf forcing and ctrl control adjustments    and trend from exf forcing and ctrl control adjustments

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