/[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 1.661 by heimbach, Thu May 25 18:37:35 2006 UTC revision 1.777 by jmc, Tue Mar 13 22:02:39 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint58w_post
8    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
9      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
10      (and replace horiVertRatio in NH code).
11      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
12                         and tutorial_plume_on_slope (sensitive to truncation)
13    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
14      directly to drive seaice model (C-grid only)
15    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
16     - reintroduce computation of wind from stress,
17     - compute tau (in exf_bulkformulae.F) from windstress averaged to
18       mass points to avoid tau = 0
19     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
20    o rdmnc.m: make it work with "global" files created with gluemnc
21    o rdmnc.m : some improvements in dealing with singleton dimension
22      (tested on all testreport mnc output files).
23    o genmake2: disable pkg/profiles if netcdf test fails.
24    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
25    o move call to cal_readparms up to make calendar parameters/variable available
26      to all packages
27    
28    checkpoint58v_post
29    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
30      useDynP_inEos_Zc tested.
31    o pkg/exf: changes to properly interpolate/mask/scale initial fields
32    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
33      and portions thereof.  See read_cs.txt for description and examples.
34    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
35      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
36      following the great-circle arc between those 2 points.
37    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
38      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
39    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
40     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
41     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
42     - still needs work (not working with some options ; efficiency to improve)
43       and serious testing.
44     - use this scheme for temperature & salinity in 2 advection test exp.:
45       advect_xy & advect_xz, respectively.
46    
47    checkpoint58u_post
48    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
49    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
50    o testreport: add option "-skipdir" to skip some test.
51    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
52      momentum calculation.
53    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
54    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
55      remove checkpoint.F and the_correction_step.F (no longer used);
56      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
57    o add option (linFSConserveTr) to correct for tracer source/sink due to
58      Linear Free surface
59    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
60    o pkg/thsice: fix reading mnc-pickups
61    
62    checkpoint58t_post
63    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
64    o pkg/mdsio:
65     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
66       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
67       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
68     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
69     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
70       either MDS_READ_FIELD or MDS_WRITE_FIELD )
71     - new S/R (to replace MDSWRITEMETA), which allows to write more
72       informations (variable names, time ...) to meta files.
73     - modify rdmds.m to give back the meta file content.
74    o pkg/diagnostics: change vertical interpolation to be safer, and more
75       flexible (define p-levels to interpolate to in data.diagnostics);
76      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
77       diagnostic pointer.
78    o pkg/seaice: more cleaning up of seaice_growth, added many comments
79    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
80    o fix multi-category seaice:
81     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
82       SEAICE_MULTICATEGORY
83     - fix short wave heat flux
84    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
85       and allow to use EVP solver. Change forward lab_sea: test both EVP
86       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
87    o Initial check-in of lab_sea adjoint
88      (very similar to natl_box_adjoint/code_seaice)
89      * used C-grid and EVP solver
90      * used KPP, GM/Redi
91      * uses inAdExact=.TRUE.
92      * gradient checks fail for both ADM and TLM
93        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
94        f.d. gradients actually seem more problematic than ADM, TLM gradients;
95        issue is related to forward mismatch between g77 an ifort
96    o pkg/seaice: overhaul of thermodynamics
97     - growth.F and groatb.F are replaced by new routine seaice_growth.F
98     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
99     - move a few global fields out of SEAICE.h into seaice_growth.F and
100       make them 2D (FICE/QNETO/ ...)
101     - remove FO (it is the same as QNETO)
102     - introduce a few local fields to avoid modifying external fields such
103       as atemp, etc.
104    
105    checkpoint58s_post
106    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
107      changed exf_set_gen.F so that
108        genperiod=0 means input file is one time-constant field and
109        genperiod=-12 means input file contains 12 monthly means
110    o CG2D: use pre-computed solver main-diagonal (stored in common block);
111      this affects truncation error ; generate new output file for exp. which
112      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
113        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
114        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
115        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
116        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
117        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
118    o start implementation of deep-atmosphere and anelastic formulation
119    o verification: remove 2nd copy of input files and use script "prepare_run"
120      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
121    o mom_common/vecinv/fluxform: fix a few initialisation isssues
122    o profiles: fix for multithreaded case
123    
124    o diagnostics: rename few diags:
125      s/'PRESSURE'/'RCENTER '/g
126      s/'TICE    '/'oceFreez'/g
127      s/'TAUX    '/'oceTAUX '/g
128      s/'TAUY    '/'oceTAUY '/g
129      s/'SWFLUX  '/'oceQsw  '/g
130      s/DIFx/DFxE/g
131      s/DIFy/DFyE/g
132      and add few ocean-forcing diagnostics:
133      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
134    o modifications to pkg/seaice/growth.F and budget.F, which change results of
135      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
136      as actual snow thickness.  It now refers everywhere to effective snow
137      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
138    
139    checkpoint58r_post
140    o modifications to pkg/seaice/growth.F, which change results of
141      lab_sea experiment: fixes pertain to melting snow over open water, to
142      masking EVAP under sea ice, and to using the correct AREA variable for
143      computations of EVAP, PRECIP, HSNOW, and GHEFF
144    o add ability to read bathy, salt, and theta using MNC (off by def)
145    o add flooding algorithm and advection of HSNOW for pkg/seaice;
146      both are turned off by default and do no change any results
147    o seaice advection with pkg/thsice: a step toward the use of non-linear
148      advection scheme, but #ifdef or commented out for now (requires more EXCH).
149    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
150      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
151      in natl_box (affects results @ truncation level: update output.txt)
152    o multi-threading and IO:
153      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
154      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
155        (needed to work with SingleCpuIO): tested in all verif. exp.
156    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
157      affects the results (but none of the verification test uses this scheme).
158    o Adding some pkg/diagnostics capability to pkg/seaice
159      (will certainly be subject to changes)
160    o ctrl: adding new control variables:
161      lwflux, lwdown, evap, snowprecip, apressure, runoff
162    
163    checkpoint58q_post
164    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
165      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
166      high_res_cube configuration by 4% on Columbia.
167    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
168      add (in global_with_exf/code) a version of EXF_INTERP_READ without
169      dynamical allocation (seems to work in multi-threaded).
170    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
171      single CPU io) so that TAF does not have to see EESUPPORT.h
172    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
173    
174    checkpoint58p_post
175    o obcs: stop if obcs is used with useCDscheme = .true.
176    o shelfice:
177     - fix a sign error so that no slip at shelfice interface works
178     - remove stop for combination non-hydrostatic code and shelfice. That does
179       not mean, that the results are correct, but at least they are numerically
180       stable
181    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
182    o added adjoint exch routined for all exch*3d* routines
183      and updated flow directives
184    
185    checkpoint58o_post
186    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
187      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
188    o change controling S/R for writing pickup file (new S/R do_write_pickup)
189      and clean-up reading/writing of pickup files.
190    o fix local version of read/write pickup (NH part) in rotating_tank/code
191    o simplify EXCH interface:
192     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
193     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
194    o added the regrid package
195    o shelfice:
196     - add a simple boundary layer scheme to reduce noise
197     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
198    
199    checkpoint58n_post
200    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
201       local variable (not in common block).
202    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
203      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
204      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
205        to work with SingleCpuIO.
206    o add "_d 0" to real constant of pkg/cfc subroutines ;
207       update exp. cfc_exemple & tutorial_cfc_offline output files.
208    o multi-threading and IO:
209      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
210        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
211      - barrier before and after reading.
212      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
213      - avoid using MDS_WRITELOCAL for LAND pkg output.
214      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
215        common-block variables ; Allows multi-threading with master-thread IO.
216    o change default MAX_NO_THREADS from 32 to 4 ;
217      and stop cleanly when MAX_NO_THREADS is too small.
218    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
219    
220    checkpoint58m_post
221    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
222       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
223    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
224       keep global_ocean.90x40x15 (for AD testing) with former secondary test
225       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
226    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
227        add MITgcm_tutorials (= code + all the tutorials)
228    o ecco, option to compute cost for total ssh (mean+anom)
229    o consistent with addition of ptracer and ssh in pkg/profiles
230    o profiles: adding ptracer and ssh
231    o testreport: change multi-test output-file name
232      (from output.txt.{name} to output.{name}.txt)
233    o profiles: now ok for mutli-tiles case
234    o seaice: add 4 parameters for different advection schemes for area,
235      (effective) seaice thickness, enthalphy, and snow height. Their default
236      is the standard parameter SEAICEadvScheme
237    o calc_gw:
238     - add cosFacU in zonal viscous flux (harmonic.visc.).
239     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
240       of tutorial_plume_on_slope.
241    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
242    o calc_gw: true flux-form, account for horizontal grid spacing.
243      update rotating_tank results, but not plume_on_slope (affected at
244      truncation level, 11 digits).
245    
246    checkpoint58l_post
247    o calc_gw:
248     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
249     - remove side-drag for now (need to fix it); update plume_on_slope results.
250     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
251    o commit code to make SST/SSS weights spatially variable
252      (based on either variable in-situ or variable initial T/S weights)
253    o pkg/ecco:
254      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
255        now based on horizontally varying weights wthetaLev, wsaltLev
256      * cost_averagesflags now returns year indices in addition to day, month
257      * sflux balance is performed on annual basis
258        (sflxumm, sfluxmm2, bal_sfluxmm)
259      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
260        including separate counting and multipliers
261    o pkg/rbcs
262      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
263    
264    checkpoint58k_post
265    o testreport:
266     - always build in dir. "build" (if not there, mkdir build instead of building
267       & running in input)
268     - run in dir run (if it exists), in build otherwise.
269     - call prepare_run (if input/prepare_run exists)
270     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
271    o pkg/exf modifications to interpolation and rotation routines for more
272       reasonable treatment of North Pole singularity: for tracers North Pole
273       value is set to northernmost zonal-mean value, for zonal velocity it is
274       set to zero, and for meridional velocity it is set to northernmost value.
275    o pkg/exf/exf_check_range.F
276     - add tile index to diagnostics and move stop statement to the very
277       end of the routine.
278    o pkg/diagnostics: (diagnostics_main_init.F)
279      define title of isomorphic variables according to the current config.
280    o pkg/thsice with pkg/seaice dynamics:
281    - fix domain of computation (interior only, required for exf) and do exchanges
282    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
283    o towards a standard way of dealing with multi-threading in MONITOR
284      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
285    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
286       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
287    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
288    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
289    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
290       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
291    o tracer advection:
292     - clean-up and simplify calc_common_factors.F
293     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
294       advection subroutine (but still not used within DST advection S/R)
295    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
296    
297    checkpoint58j_post
298    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
299      from file (collects calls previously in FORWARD_STEP)
300    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
301    o adjoint store dir. adjusted accordingly
302    o genmake2
303      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
304    
305    checkpoint58i_post
306    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
307      on wind stress (SEAICEstressFactor defaults to 1.)
308    o Total number of Timers is finite (<=40): comment out 2 non-essential one
309      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
310    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
311      on CS-grid: no longer loosing mass.
312    o exf & curvilinear-grid: no longer modify longitude xC & xG.
313    o pkg/ggl90: fix sloppy output and fix a bug
314    o pkg/seaice: added SEAICEuseEVPpickup parameter
315      - Set to false in order to start EVP solver with
316        non-EVP pickup files when using SEAICEuseEVP
317      - fix sign error in diffusion in seaice_calc_rhs
318    
319    checkpoint58h_post
320    * Modifications for bottom topography control
321      o replace hFacC by _hFacC at various places
322      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
323      o add non-self-adjoint cg2d_nsa
324      o update autodiff support routines
325      o re-initialise hfac after ctrl_depth_ini
326      o works for 5x5 box, doesnt work for global_ocean.90x40x15
327    * Adding verification for 5x5 box (4-layer) bottom topography control
328    
329    checkpoint58g_post
330    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
331       used for mean seasonal cycle, mean diurnal cycle); add an example
332       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
333    o pkg/ggl90:
334      - add parameter (minimum surface kinetic energy)
335      - fix bug (avoiding division by zero)
336    o couple pkg/thsice to pkg/seaice:
337      - modify advection in seaice to accomodate new scalar fields to be advected
338      - only muliDimAdection scheme work with seaice/thsice
339      - mapping of thsice-variables to seaice-variables, back and forth
340      - does not break the verification experiments, but does not give the
341        desired results either
342    o pkg/seaice
343      - make (default) second order advection a bit less confusing?
344    
345    checkpoint58f_post
346    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
347      to pkg/seaice):
348      - new routines thsice_map_exf and thsice_get_exf provide the interface
349      - add an additional formal parameter to thsice_solve4temp
350  o pkg/exf:  o pkg/exf:
351    - add new fields wspeed, snowprecip (to be able to couple to thsice)    - add new fields wspeed, snowprecip (to be able to couple to thsice)
352    - correct Stefan-Boltzmann constant    - correct Stefan-Boltzmann constant
353    - new parameter for longwave surface emittance    - new parameter for longwave surface emittance
354    - separate some stuff from exf_bulkformulae into new routines      - separate some stuff from exf_bulkformulae into new routines  
355      exf_radiation, exf_wind      exf_radiation, exf_wind
356      - add new parameters and constants: longwave emissivity for ocean, ice
357        and snow, evaporation parameters over ice
358      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
359        either wind from stress or stress from wind
360  o pkg/thSIce:  o pkg/thSIce:
361  - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F  - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
362  - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND  - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND

Legend:
Removed from v.1.661  
changed lines
  Added in v.1.777

  ViewVC Help
Powered by ViewVC 1.1.22