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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.424 by jmc, Mon Dec 20 19:56:15 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint57b_post
7    o simplify options in diagnostics_fill arguments (remove weird combinations)
8    o fix MNC coordinate variables so that they now contain per-face index
9      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
10      general, EXCH2 grids are only aligned to a "local" coordinate system
11    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
12    o Implement instantaneous output within pkg diagnostics:
13      setting a negative frequency in data.diagnostics produces
14     "snap-shot" output (as opposed to time-average if freq > 0)
15    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
16      NOTE: change ptracer diagnostics name: use 2 characters to work with
17            more than 9 tracers. Add also diagnostics of advect & diffus flux.
18    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
19      becomes the coordinate variable for the 'T' dimension
20    o add CF-style coordinate variables to MNC
21      - just a first cut:  numbers are meaningless on the cubesphere and
22        missing along the T axis but otherwise it works!
23    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
24    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
25    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
26      this is based directly on what the model compute, so that the content of
27      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
28    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
29    o clean up build options files for SunOS, in particular
30      - remove -traditional from xmakedepend
31      - change -xarch=v9 to -xarch=native for f77
32      - restore use of make (not gmake)
33      - add CC=gcc if using g77
34    o changes per discussion of AM, JMC, & EH3 today:
35      - move redundant "grid" variables out of "state" -- in preparation of
36        creating proper CF-style coordinate variables and in recognition
37        that any/all grid variables can be easily copied (eg. w/NCO) from
38        the grid files into any of the other NetCDF files
39      - *always* output grid variables with MDSIO (this will eventually be
40        changed)
41      - output MNC grid file if useMNC is true
42    o every instance of _END_MASTER() has been found and replaced with
43      _END_MASTER( myThid ) in order to satisfy certain picky Sun
44      preprocessors
45    o re-arrange diagnostics pkg initialisation:
46     - allow each package to extend the available diagnostics list
47     - add some checking and fix small problems (multi-threaded, ...)
48     - new S/R diagnostics_fill (replace fill_diagnostics):
49       look through the short list of active diag. (instead of the long list)
50       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
51    
52    checkpoint57a_post
53    o this set of changes restores TAMC compatibility
54      tested for global_ocean.90x40x15 adjoint on trough
55      (what a pain)
56    
57    checkpoint57a_pre
58    o some modifs in tools/build_options for sunos
59    o call ctrl_pack for ctrl at end for optimcycle=0
60    
61    checkpoint57
62    o add horizontal bi-harmonic viscosity for vertical velocity
63      - new parameter viscA4W (defaults to viscA4)
64      - affects only non-hydrostatic code
65      - to be done: no-slip lateral boundary conditions
66    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
67    o implement Implicit Vertical advection for pTracers
68    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
69      (implemented also for implicit vertical diffusion & advection)
70    o OBCS: extend application of tracer open boundary conditions
71      to a strip beyond the boundary of width Olx/Oly
72    o add call monitor to TAF set of required calls (flow directives)
73      and include in natl_box_adjoint
74    o untangle a few ifdefs related to cost, ctrl, autodiff
75      untangel a few ALLOW_ECCO_OPTIMIZATION
76    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
77      (theta2, salt2 in ecco_cost_weights)
78    
79    checkpoint56c_post
80    o OBCS as control variables
81      - update ctrl_ad_diff.list, obcs_ad_diff.list
82      - remove balance of obcs controls from default
83      - fix index bug nobcs in ctrl_init
84      - fix dummy fields filen in ctrl_pack
85      - add dummy weights for obcs
86    o lsopt: comment out fort.94 output
87    o optim:
88      - remove unnecessary header files
89      - adjusted namelists
90      - add xerbla.F to Makefile
91    o exf:
92      - multiple modifications of exf_check_range
93      - unit change in exf_init_runoff from [m/year] to [m/s]
94    o mdsio:
95      - i/o-vector change debugLevel from debLevA to debLevB
96    
97    checkpoint56b_post
98    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
99      is called from DO_THE_MODEL_IO
100      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
101      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
102      - clean up PTRACERS_WRITE_TIMEAVE a little
103    o add another verification experiment that tests both the cfc-pkg and
104      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
105      reactive tendencies treated inline with regular timestepping
106    o testreport previously did a lousy job of comparing small numbers, so
107      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
108      implemented in the little c-progam tmp_cmpnum.c which is embedded in
109      testreport.
110    o ptracers_monitor: bug fix for MPI
111    
112    checkpoint56a_post
113    o GCHEM: finish reorganizating the package
114      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
115        (introduces another 3D-array for each passive tracer, but only if
116        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
117        gchemTendency is not needed because the timestep is done separately)
118      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
119      - GCHEM is now---more or less cleanly---separate from PTRACERS
120      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
121        so clear to me how that should be done in a general way.
122    o CFC: improve formatting of output in CFC_ATMOS
123    o PTRACERS:
124      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
125        that ALL experiments with ptracers enable can be checked. This makes
126        GCHEM_MONITOR obsolete.
127      - include a runtime parameter PTRACERS_monitorFreq that defaults to
128        monitorFreq
129      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
130    o add PTRACERS (PTR0[1-5]) to testreport output
131    o exf_check_range:
132      * default changed to .TRUE.
133      * will check values for niter0 if debLevA, every timestep if debLevB
134      * STOP in exf_check_range if 'out of range'
135      * range chosen generous to allow for potential extema
136      TBD: a version with stricter range
137           permitted range would be runtime parameters
138  o GMredi:  o GMredi:
139    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
140    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
# Line 11  o GCHEM: Line 143  o GCHEM:
143    - move call to GCHEM_FORCING_SEP, so that it is now called before    - move call to GCHEM_FORCING_SEP, so that it is now called before
144      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
145    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
146      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
147        this flag is now only visible within GCHEM-pkg routines.
148      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
149        be replaced by a 3D array that is computed before thermodynamics; for
150        this, the tracer ID iTracer had to be included into the parameter list
151        of ptracers_forcing
152      - set up forward_step to call gchem_forcing, that will replace
153        gchem_forcing_int in ptracers_forcing
154      - cleaning up
155  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
156    
157  checkpoint56  checkpoint56
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