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revision 1.669 by heimbach, Wed Jun 7 02:02:52 2006 UTC revision 1.784 by jmc, Fri Apr 6 15:58:23 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 Added capability for 3D specification of background vertical diffusion
8      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
9      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
10      "data" file that contains the 3D vertical diffusivity coefficients.
11    o ice dynamics (pkg/seaice) with thsice thermodynamics:
12      - add code within pkg thsice to advect & diffuse sea-ice fields
13      similar to (and will replace) what has been added in  seaice_advdiff.F,
14      but: - conserving Mass, Heat & Salt.
15           - better when using non-linear advection scheme (not yet fully tested)
16           - can also be used in atmospheric set-up (for now, only the diffusion).
17    
18    checkpoint58x_post
19    o IO option for global-file compact format:
20      - add options when generating topology (utils/exch2/matlab-topology-generator)
21      - add I/O capability (pkg/mdsio).
22      - adapt utils/matlab/rdmds.m to read this format.
23      for now long-line format not yet supported by pkg/mdsio (& exch2).
24    o shelfice: add a few diagnostics
25    
26    checkpoint58w_post
27    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
28      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
29      (and replace horiVertRatio in NH code).
30      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
31                         and tutorial_plume_on_slope (sensitive to truncation)
32    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
33      directly to drive seaice model (C-grid only)
34    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
35     - reintroduce computation of wind from stress,
36     - compute tau (in exf_bulkformulae.F) from windstress averaged to
37       mass points to avoid tau = 0
38     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
39    o rdmnc.m: make it work with "global" files created with gluemnc
40    o rdmnc.m : some improvements in dealing with singleton dimension
41      (tested on all testreport mnc output files).
42    o genmake2: disable pkg/profiles if netcdf test fails.
43    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
44    o move call to cal_readparms up to make calendar parameters/variable available
45      to all packages
46    
47    checkpoint58v_post
48    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
49      useDynP_inEos_Zc tested.
50    o pkg/exf: changes to properly interpolate/mask/scale initial fields
51    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
52      and portions thereof.  See read_cs.txt for description and examples.
53    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
54      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
55      following the great-circle arc between those 2 points.
56    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
57      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
58    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
59     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
60     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
61     - still needs work (not working with some options ; efficiency to improve)
62       and serious testing.
63     - use this scheme for temperature & salinity in 2 advection test exp.:
64       advect_xy & advect_xz, respectively.
65    
66    checkpoint58u_post
67    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
68    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
69    o testreport: add option "-skipdir" to skip some test.
70    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
71      momentum calculation.
72    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
73    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
74      remove checkpoint.F and the_correction_step.F (no longer used);
75      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
76    o add option (linFSConserveTr) to correct for tracer source/sink due to
77      Linear Free surface
78    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
79    o pkg/thsice: fix reading mnc-pickups
80    
81    checkpoint58t_post
82    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
83    o pkg/mdsio:
84     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
85       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
86       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
87     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
88     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
89       either MDS_READ_FIELD or MDS_WRITE_FIELD )
90     - new S/R (to replace MDSWRITEMETA), which allows to write more
91       informations (variable names, time ...) to meta files.
92     - modify rdmds.m to give back the meta file content.
93    o pkg/diagnostics: change vertical interpolation to be safer, and more
94       flexible (define p-levels to interpolate to in data.diagnostics);
95      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
96       diagnostic pointer.
97    o pkg/seaice: more cleaning up of seaice_growth, added many comments
98    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
99    o fix multi-category seaice:
100     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
101       SEAICE_MULTICATEGORY
102     - fix short wave heat flux
103    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
104       and allow to use EVP solver. Change forward lab_sea: test both EVP
105       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
106    o Initial check-in of lab_sea adjoint
107      (very similar to natl_box_adjoint/code_seaice)
108      * used C-grid and EVP solver
109      * used KPP, GM/Redi
110      * uses inAdExact=.TRUE.
111      * gradient checks fail for both ADM and TLM
112        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
113        f.d. gradients actually seem more problematic than ADM, TLM gradients;
114        issue is related to forward mismatch between g77 an ifort
115    o pkg/seaice: overhaul of thermodynamics
116     - growth.F and groatb.F are replaced by new routine seaice_growth.F
117     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
118     - move a few global fields out of SEAICE.h into seaice_growth.F and
119       make them 2D (FICE/QNETO/ ...)
120     - remove FO (it is the same as QNETO)
121     - introduce a few local fields to avoid modifying external fields such
122       as atemp, etc.
123    
124    checkpoint58s_post
125    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
126      changed exf_set_gen.F so that
127        genperiod=0 means input file is one time-constant field and
128        genperiod=-12 means input file contains 12 monthly means
129    o CG2D: use pre-computed solver main-diagonal (stored in common block);
130      this affects truncation error ; generate new output file for exp. which
131      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
132        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
133        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
134        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
135        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
136        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
137    o start implementation of deep-atmosphere and anelastic formulation
138    o verification: remove 2nd copy of input files and use script "prepare_run"
139      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
140    o mom_common/vecinv/fluxform: fix a few initialisation isssues
141    o profiles: fix for multithreaded case
142    
143    o diagnostics: rename few diags:
144      s/'PRESSURE'/'RCENTER '/g
145      s/'TICE    '/'oceFreez'/g
146      s/'TAUX    '/'oceTAUX '/g
147      s/'TAUY    '/'oceTAUY '/g
148      s/'SWFLUX  '/'oceQsw  '/g
149      s/DIFx/DFxE/g
150      s/DIFy/DFyE/g
151      and add few ocean-forcing diagnostics:
152      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
153    o modifications to pkg/seaice/growth.F and budget.F, which change results of
154      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
155      as actual snow thickness.  It now refers everywhere to effective snow
156      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
157    
158    checkpoint58r_post
159    o modifications to pkg/seaice/growth.F, which change results of
160      lab_sea experiment: fixes pertain to melting snow over open water, to
161      masking EVAP under sea ice, and to using the correct AREA variable for
162      computations of EVAP, PRECIP, HSNOW, and GHEFF
163    o add ability to read bathy, salt, and theta using MNC (off by def)
164    o add flooding algorithm and advection of HSNOW for pkg/seaice;
165      both are turned off by default and do no change any results
166    o seaice advection with pkg/thsice: a step toward the use of non-linear
167      advection scheme, but #ifdef or commented out for now (requires more EXCH).
168    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
169      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
170      in natl_box (affects results @ truncation level: update output.txt)
171    o multi-threading and IO:
172      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
173      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
174        (needed to work with SingleCpuIO): tested in all verif. exp.
175    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
176      affects the results (but none of the verification test uses this scheme).
177    o Adding some pkg/diagnostics capability to pkg/seaice
178      (will certainly be subject to changes)
179    o ctrl: adding new control variables:
180      lwflux, lwdown, evap, snowprecip, apressure, runoff
181    
182    checkpoint58q_post
183    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
184      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
185      high_res_cube configuration by 4% on Columbia.
186    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
187      add (in global_with_exf/code) a version of EXF_INTERP_READ without
188      dynamical allocation (seems to work in multi-threaded).
189    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
190      single CPU io) so that TAF does not have to see EESUPPORT.h
191    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
192    
193    checkpoint58p_post
194    o obcs: stop if obcs is used with useCDscheme = .true.
195    o shelfice:
196     - fix a sign error so that no slip at shelfice interface works
197     - remove stop for combination non-hydrostatic code and shelfice. That does
198       not mean, that the results are correct, but at least they are numerically
199       stable
200    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
201    o added adjoint exch routined for all exch*3d* routines
202      and updated flow directives
203    
204    checkpoint58o_post
205    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
206      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
207    o change controling S/R for writing pickup file (new S/R do_write_pickup)
208      and clean-up reading/writing of pickup files.
209    o fix local version of read/write pickup (NH part) in rotating_tank/code
210    o simplify EXCH interface:
211     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
212     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
213    o added the regrid package
214    o shelfice:
215     - add a simple boundary layer scheme to reduce noise
216     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
217    
218    checkpoint58n_post
219    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
220       local variable (not in common block).
221    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
222      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
223      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
224        to work with SingleCpuIO.
225    o add "_d 0" to real constant of pkg/cfc subroutines ;
226       update exp. cfc_exemple & tutorial_cfc_offline output files.
227    o multi-threading and IO:
228      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
229        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
230      - barrier before and after reading.
231      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
232      - avoid using MDS_WRITELOCAL for LAND pkg output.
233      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
234        common-block variables ; Allows multi-threading with master-thread IO.
235    o change default MAX_NO_THREADS from 32 to 4 ;
236      and stop cleanly when MAX_NO_THREADS is too small.
237    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
238    
239    checkpoint58m_post
240    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
241       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
242    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
243       keep global_ocean.90x40x15 (for AD testing) with former secondary test
244       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
245    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
246        add MITgcm_tutorials (= code + all the tutorials)
247    o ecco, option to compute cost for total ssh (mean+anom)
248    o consistent with addition of ptracer and ssh in pkg/profiles
249    o profiles: adding ptracer and ssh
250    o testreport: change multi-test output-file name
251      (from output.txt.{name} to output.{name}.txt)
252    o profiles: now ok for mutli-tiles case
253    o seaice: add 4 parameters for different advection schemes for area,
254      (effective) seaice thickness, enthalphy, and snow height. Their default
255      is the standard parameter SEAICEadvScheme
256    o calc_gw:
257     - add cosFacU in zonal viscous flux (harmonic.visc.).
258     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
259       of tutorial_plume_on_slope.
260    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
261    o calc_gw: true flux-form, account for horizontal grid spacing.
262      update rotating_tank results, but not plume_on_slope (affected at
263      truncation level, 11 digits).
264    
265    checkpoint58l_post
266    o calc_gw:
267     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
268     - remove side-drag for now (need to fix it); update plume_on_slope results.
269     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
270    o commit code to make SST/SSS weights spatially variable
271      (based on either variable in-situ or variable initial T/S weights)
272    o pkg/ecco:
273      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
274        now based on horizontally varying weights wthetaLev, wsaltLev
275      * cost_averagesflags now returns year indices in addition to day, month
276      * sflux balance is performed on annual basis
277        (sflxumm, sfluxmm2, bal_sfluxmm)
278      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
279        including separate counting and multipliers
280    o pkg/rbcs
281      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
282    
283    checkpoint58k_post
284    o testreport:
285     - always build in dir. "build" (if not there, mkdir build instead of building
286       & running in input)
287     - run in dir run (if it exists), in build otherwise.
288     - call prepare_run (if input/prepare_run exists)
289     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
290    o pkg/exf modifications to interpolation and rotation routines for more
291       reasonable treatment of North Pole singularity: for tracers North Pole
292       value is set to northernmost zonal-mean value, for zonal velocity it is
293       set to zero, and for meridional velocity it is set to northernmost value.
294    o pkg/exf/exf_check_range.F
295     - add tile index to diagnostics and move stop statement to the very
296       end of the routine.
297    o pkg/diagnostics: (diagnostics_main_init.F)
298      define title of isomorphic variables according to the current config.
299    o pkg/thsice with pkg/seaice dynamics:
300    - fix domain of computation (interior only, required for exf) and do exchanges
301    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
302    o towards a standard way of dealing with multi-threading in MONITOR
303      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
304    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
305       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
306    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
307    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
308    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
309       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
310    o tracer advection:
311     - clean-up and simplify calc_common_factors.F
312     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
313       advection subroutine (but still not used within DST advection S/R)
314    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
315    
316    checkpoint58j_post
317    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
318      from file (collects calls previously in FORWARD_STEP)
319    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
320    o adjoint store dir. adjusted accordingly
321    o genmake2
322      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
323    
324    checkpoint58i_post
325    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
326      on wind stress (SEAICEstressFactor defaults to 1.)
327    o Total number of Timers is finite (<=40): comment out 2 non-essential one
328      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
329    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
330      on CS-grid: no longer loosing mass.
331    o exf & curvilinear-grid: no longer modify longitude xC & xG.
332    o pkg/ggl90: fix sloppy output and fix a bug
333    o pkg/seaice: added SEAICEuseEVPpickup parameter
334      - Set to false in order to start EVP solver with
335        non-EVP pickup files when using SEAICEuseEVP
336      - fix sign error in diffusion in seaice_calc_rhs
337    
338  checkpoint58h_post  checkpoint58h_post
339  * Modifications for bottom topography control  * Modifications for bottom topography control
340    o replace hFacC by _hFacC at various places    o replace hFacC by _hFacC at various places
# Line 15  checkpoint58h_post Line 346  checkpoint58h_post
346  * Adding verification for 5x5 box (4-layer) bottom topography control  * Adding verification for 5x5 box (4-layer) bottom topography control
347    
348  checkpoint58g_post  checkpoint58g_post
349    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
350       used for mean seasonal cycle, mean diurnal cycle); add an example
351       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
352  o pkg/ggl90:  o pkg/ggl90:
353    - add parameter (minimum surface kinetic energy)    - add parameter (minimum surface kinetic energy)
354    - fix bug (avoiding division by zero)    - fix bug (avoiding division by zero)

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