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revision 1.669 by heimbach, Wed Jun 7 02:02:52 2006 UTC revision 1.789 by jmc, Mon Apr 16 23:48:40 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/exf:
8      move exf header files from lower_case.h to UPPER_CASE.h ;
9      add missing cvs Header & Name
10    o pkg/seaice:
11      - remove seaice_exch and seaice_exch_uv
12      - remove superfluous exchange of theta
13      - add myThid to seaice_budget_ocean/ice
14    
15    checkpoint58y_post
16    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
17      vertical diffusivity, similar to that in MOM4; turned on using
18      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
19      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
20    o Added capability for 3D specification of background vertical diffusion
21      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
22      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
23      "data" file that contains the 3D vertical diffusivity coefficients.
24    o ice dynamics (pkg/seaice) with thsice thermodynamics:
25      - add code within pkg thsice to advect & diffuse sea-ice fields
26      similar to (and will replace) what has been added in  seaice_advdiff.F,
27      but: - conserving Mass, Heat & Salt.
28           - better when using non-linear advection scheme (not yet fully tested)
29           - can also be used in atmospheric set-up (for now, only the diffusion).
30    
31    checkpoint58x_post
32    o IO option for global-file compact format:
33      - add options when generating topology (utils/exch2/matlab-topology-generator)
34      - add I/O capability (pkg/mdsio).
35      - adapt utils/matlab/rdmds.m to read this format.
36      for now long-line format not yet supported by pkg/mdsio (& exch2).
37    o shelfice: add a few diagnostics
38    
39    checkpoint58w_post
40    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
41      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
42      (and replace horiVertRatio in NH code).
43      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
44                         and tutorial_plume_on_slope (sensitive to truncation)
45    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
46      directly to drive seaice model (C-grid only)
47    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
48     - reintroduce computation of wind from stress,
49     - compute tau (in exf_bulkformulae.F) from windstress averaged to
50       mass points to avoid tau = 0
51     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
52    o rdmnc.m: make it work with "global" files created with gluemnc
53    o rdmnc.m : some improvements in dealing with singleton dimension
54      (tested on all testreport mnc output files).
55    o genmake2: disable pkg/profiles if netcdf test fails.
56    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
57    o move call to cal_readparms up to make calendar parameters/variable available
58      to all packages
59    
60    checkpoint58v_post
61    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
62      useDynP_inEos_Zc tested.
63    o pkg/exf: changes to properly interpolate/mask/scale initial fields
64    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
65      and portions thereof.  See read_cs.txt for description and examples.
66    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
67      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
68      following the great-circle arc between those 2 points.
69    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
70      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
71    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
72     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
73     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
74     - still needs work (not working with some options ; efficiency to improve)
75       and serious testing.
76     - use this scheme for temperature & salinity in 2 advection test exp.:
77       advect_xy & advect_xz, respectively.
78    
79    checkpoint58u_post
80    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
81    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
82    o testreport: add option "-skipdir" to skip some test.
83    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
84      momentum calculation.
85    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
86    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
87      remove checkpoint.F and the_correction_step.F (no longer used);
88      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
89    o add option (linFSConserveTr) to correct for tracer source/sink due to
90      Linear Free surface
91    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
92    o pkg/thsice: fix reading mnc-pickups
93    
94    checkpoint58t_post
95    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
96    o pkg/mdsio:
97     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
98       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
99       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
100     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
101     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
102       either MDS_READ_FIELD or MDS_WRITE_FIELD )
103     - new S/R (to replace MDSWRITEMETA), which allows to write more
104       informations (variable names, time ...) to meta files.
105     - modify rdmds.m to give back the meta file content.
106    o pkg/diagnostics: change vertical interpolation to be safer, and more
107       flexible (define p-levels to interpolate to in data.diagnostics);
108      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
109       diagnostic pointer.
110    o pkg/seaice: more cleaning up of seaice_growth, added many comments
111    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
112    o fix multi-category seaice:
113     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
114       SEAICE_MULTICATEGORY
115     - fix short wave heat flux
116    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
117       and allow to use EVP solver. Change forward lab_sea: test both EVP
118       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
119    o Initial check-in of lab_sea adjoint
120      (very similar to natl_box_adjoint/code_seaice)
121      * used C-grid and EVP solver
122      * used KPP, GM/Redi
123      * uses inAdExact=.TRUE.
124      * gradient checks fail for both ADM and TLM
125        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
126        f.d. gradients actually seem more problematic than ADM, TLM gradients;
127        issue is related to forward mismatch between g77 an ifort
128    o pkg/seaice: overhaul of thermodynamics
129     - growth.F and groatb.F are replaced by new routine seaice_growth.F
130     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
131     - move a few global fields out of SEAICE.h into seaice_growth.F and
132       make them 2D (FICE/QNETO/ ...)
133     - remove FO (it is the same as QNETO)
134     - introduce a few local fields to avoid modifying external fields such
135       as atemp, etc.
136    
137    checkpoint58s_post
138    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
139      changed exf_set_gen.F so that
140        genperiod=0 means input file is one time-constant field and
141        genperiod=-12 means input file contains 12 monthly means
142    o CG2D: use pre-computed solver main-diagonal (stored in common block);
143      this affects truncation error ; generate new output file for exp. which
144      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
145        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
146        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
147        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
148        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
149        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
150    o start implementation of deep-atmosphere and anelastic formulation
151    o verification: remove 2nd copy of input files and use script "prepare_run"
152      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
153    o mom_common/vecinv/fluxform: fix a few initialisation isssues
154    o profiles: fix for multithreaded case
155    
156    o diagnostics: rename few diags:
157      s/'PRESSURE'/'RCENTER '/g
158      s/'TICE    '/'oceFreez'/g
159      s/'TAUX    '/'oceTAUX '/g
160      s/'TAUY    '/'oceTAUY '/g
161      s/'SWFLUX  '/'oceQsw  '/g
162      s/DIFx/DFxE/g
163      s/DIFy/DFyE/g
164      and add few ocean-forcing diagnostics:
165      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
166    o modifications to pkg/seaice/growth.F and budget.F, which change results of
167      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
168      as actual snow thickness.  It now refers everywhere to effective snow
169      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
170    
171    checkpoint58r_post
172    o modifications to pkg/seaice/growth.F, which change results of
173      lab_sea experiment: fixes pertain to melting snow over open water, to
174      masking EVAP under sea ice, and to using the correct AREA variable for
175      computations of EVAP, PRECIP, HSNOW, and GHEFF
176    o add ability to read bathy, salt, and theta using MNC (off by def)
177    o add flooding algorithm and advection of HSNOW for pkg/seaice;
178      both are turned off by default and do no change any results
179    o seaice advection with pkg/thsice: a step toward the use of non-linear
180      advection scheme, but #ifdef or commented out for now (requires more EXCH).
181    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
182      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
183      in natl_box (affects results @ truncation level: update output.txt)
184    o multi-threading and IO:
185      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
186      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
187        (needed to work with SingleCpuIO): tested in all verif. exp.
188    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
189      affects the results (but none of the verification test uses this scheme).
190    o Adding some pkg/diagnostics capability to pkg/seaice
191      (will certainly be subject to changes)
192    o ctrl: adding new control variables:
193      lwflux, lwdown, evap, snowprecip, apressure, runoff
194    
195    checkpoint58q_post
196    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
197      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
198      high_res_cube configuration by 4% on Columbia.
199    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
200      add (in global_with_exf/code) a version of EXF_INTERP_READ without
201      dynamical allocation (seems to work in multi-threaded).
202    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
203      single CPU io) so that TAF does not have to see EESUPPORT.h
204    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
205    
206    checkpoint58p_post
207    o obcs: stop if obcs is used with useCDscheme = .true.
208    o shelfice:
209     - fix a sign error so that no slip at shelfice interface works
210     - remove stop for combination non-hydrostatic code and shelfice. That does
211       not mean, that the results are correct, but at least they are numerically
212       stable
213    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
214    o added adjoint exch routined for all exch*3d* routines
215      and updated flow directives
216    
217    checkpoint58o_post
218    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
219      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
220    o change controling S/R for writing pickup file (new S/R do_write_pickup)
221      and clean-up reading/writing of pickup files.
222    o fix local version of read/write pickup (NH part) in rotating_tank/code
223    o simplify EXCH interface:
224     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
225     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
226    o added the regrid package
227    o shelfice:
228     - add a simple boundary layer scheme to reduce noise
229     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
230    
231    checkpoint58n_post
232    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
233       local variable (not in common block).
234    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
235      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
236      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
237        to work with SingleCpuIO.
238    o add "_d 0" to real constant of pkg/cfc subroutines ;
239       update exp. cfc_exemple & tutorial_cfc_offline output files.
240    o multi-threading and IO:
241      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
242        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
243      - barrier before and after reading.
244      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
245      - avoid using MDS_WRITELOCAL for LAND pkg output.
246      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
247        common-block variables ; Allows multi-threading with master-thread IO.
248    o change default MAX_NO_THREADS from 32 to 4 ;
249      and stop cleanly when MAX_NO_THREADS is too small.
250    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
251    
252    checkpoint58m_post
253    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
254       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
255    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
256       keep global_ocean.90x40x15 (for AD testing) with former secondary test
257       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
258    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
259        add MITgcm_tutorials (= code + all the tutorials)
260    o ecco, option to compute cost for total ssh (mean+anom)
261    o consistent with addition of ptracer and ssh in pkg/profiles
262    o profiles: adding ptracer and ssh
263    o testreport: change multi-test output-file name
264      (from output.txt.{name} to output.{name}.txt)
265    o profiles: now ok for mutli-tiles case
266    o seaice: add 4 parameters for different advection schemes for area,
267      (effective) seaice thickness, enthalphy, and snow height. Their default
268      is the standard parameter SEAICEadvScheme
269    o calc_gw:
270     - add cosFacU in zonal viscous flux (harmonic.visc.).
271     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
272       of tutorial_plume_on_slope.
273    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
274    o calc_gw: true flux-form, account for horizontal grid spacing.
275      update rotating_tank results, but not plume_on_slope (affected at
276      truncation level, 11 digits).
277    
278    checkpoint58l_post
279    o calc_gw:
280     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
281     - remove side-drag for now (need to fix it); update plume_on_slope results.
282     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
283    o commit code to make SST/SSS weights spatially variable
284      (based on either variable in-situ or variable initial T/S weights)
285    o pkg/ecco:
286      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
287        now based on horizontally varying weights wthetaLev, wsaltLev
288      * cost_averagesflags now returns year indices in addition to day, month
289      * sflux balance is performed on annual basis
290        (sflxumm, sfluxmm2, bal_sfluxmm)
291      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
292        including separate counting and multipliers
293    o pkg/rbcs
294      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
295    
296    checkpoint58k_post
297    o testreport:
298     - always build in dir. "build" (if not there, mkdir build instead of building
299       & running in input)
300     - run in dir run (if it exists), in build otherwise.
301     - call prepare_run (if input/prepare_run exists)
302     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
303    o pkg/exf modifications to interpolation and rotation routines for more
304       reasonable treatment of North Pole singularity: for tracers North Pole
305       value is set to northernmost zonal-mean value, for zonal velocity it is
306       set to zero, and for meridional velocity it is set to northernmost value.
307    o pkg/exf/exf_check_range.F
308     - add tile index to diagnostics and move stop statement to the very
309       end of the routine.
310    o pkg/diagnostics: (diagnostics_main_init.F)
311      define title of isomorphic variables according to the current config.
312    o pkg/thsice with pkg/seaice dynamics:
313    - fix domain of computation (interior only, required for exf) and do exchanges
314    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
315    o towards a standard way of dealing with multi-threading in MONITOR
316      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
317    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
318       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
319    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
320    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
321    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
322       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
323    o tracer advection:
324     - clean-up and simplify calc_common_factors.F
325     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
326       advection subroutine (but still not used within DST advection S/R)
327    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
328    
329    checkpoint58j_post
330    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
331      from file (collects calls previously in FORWARD_STEP)
332    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
333    o adjoint store dir. adjusted accordingly
334    o genmake2
335      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
336    
337    checkpoint58i_post
338    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
339      on wind stress (SEAICEstressFactor defaults to 1.)
340    o Total number of Timers is finite (<=40): comment out 2 non-essential one
341      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
342    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
343      on CS-grid: no longer loosing mass.
344    o exf & curvilinear-grid: no longer modify longitude xC & xG.
345    o pkg/ggl90: fix sloppy output and fix a bug
346    o pkg/seaice: added SEAICEuseEVPpickup parameter
347      - Set to false in order to start EVP solver with
348        non-EVP pickup files when using SEAICEuseEVP
349      - fix sign error in diffusion in seaice_calc_rhs
350    
351  checkpoint58h_post  checkpoint58h_post
352  * Modifications for bottom topography control  * Modifications for bottom topography control
353    o replace hFacC by _hFacC at various places    o replace hFacC by _hFacC at various places
# Line 15  checkpoint58h_post Line 359  checkpoint58h_post
359  * Adding verification for 5x5 box (4-layer) bottom topography control  * Adding verification for 5x5 box (4-layer) bottom topography control
360    
361  checkpoint58g_post  checkpoint58g_post
362    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
363       used for mean seasonal cycle, mean diurnal cycle); add an example
364       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
365  o pkg/ggl90:  o pkg/ggl90:
366    - add parameter (minimum surface kinetic energy)    - add parameter (minimum surface kinetic energy)
367    - fix bug (avoiding division by zero)    - fix bug (avoiding division by zero)

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