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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.422 by jmc, Mon Dec 20 02:42:42 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
7    o Implement instantaneous output within pkg diagnostics:
8      setting a negative frequency in data.diagnostics produces
9     "snap-shot" output (as opposed to time-average if freq > 0)
10    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
11      NOTE: change ptracer diagnostics name: use 2 characters to work with
12            more than 9 tracers. Add also diagnostics of advect & diffus flux.
13    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
14      becomes the coordinate variable for the 'T' dimension
15    o add CF-style coordinate variables to MNC
16      - just a first cut:  numbers are meaningless on the cubesphere and
17        missing along the T axis but otherwise it works!
18    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
19    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
20    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
21      this is based directly on what the model compute, so that the content of
22      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
23    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
24    o clean up build options files for SunOS, in particular
25      - remove -traditional from xmakedepend
26      - change -xarch=v9 to -xarch=native for f77
27      - restore use of make (not gmake)
28      - add CC=gcc if using g77
29    o changes per discussion of AM, JMC, & EH3 today:
30      - move redundant "grid" variables out of "state" -- in preparation of
31        creating proper CF-style coordinate variables and in recognition
32        that any/all grid variables can be easily copied (eg. w/NCO) from
33        the grid files into any of the other NetCDF files
34      - *always* output grid variables with MDSIO (this will eventually be
35        changed)
36      - output MNC grid file if useMNC is true
37    o every instance of _END_MASTER() has been found and replaced with
38      _END_MASTER( myThid ) in order to satisfy certain picky Sun
39      preprocessors
40    o re-arrange diagnostics pkg initialisation:
41     - allow each package to extend the available diagnostics list
42     - add some checking and fix small problems (multi-threaded, ...)
43     - new S/R diagnostics_fill (replace fill_diagnostics):
44       look through the short list of active diag. (instead of the long list)
45       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
46    
47    checkpoint57a_post
48    o this set of changes restores TAMC compatibility
49      tested for global_ocean.90x40x15 adjoint on trough
50      (what a pain)
51    
52    checkpoint57a_pre
53    o some modifs in tools/build_options for sunos
54    o call ctrl_pack for ctrl at end for optimcycle=0
55    
56    checkpoint57
57    o add horizontal bi-harmonic viscosity for vertical velocity
58      - new parameter viscA4W (defaults to viscA4)
59      - affects only non-hydrostatic code
60      - to be done: no-slip lateral boundary conditions
61    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
62    o implement Implicit Vertical advection for pTracers
63    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
64      (implemented also for implicit vertical diffusion & advection)
65    o OBCS: extend application of tracer open boundary conditions
66      to a strip beyond the boundary of width Olx/Oly
67    o add call monitor to TAF set of required calls (flow directives)
68      and include in natl_box_adjoint
69    o untangle a few ifdefs related to cost, ctrl, autodiff
70      untangel a few ALLOW_ECCO_OPTIMIZATION
71    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
72      (theta2, salt2 in ecco_cost_weights)
73    
74    checkpoint56c_post
75    o OBCS as control variables
76      - update ctrl_ad_diff.list, obcs_ad_diff.list
77      - remove balance of obcs controls from default
78      - fix index bug nobcs in ctrl_init
79      - fix dummy fields filen in ctrl_pack
80      - add dummy weights for obcs
81    o lsopt: comment out fort.94 output
82    o optim:
83      - remove unnecessary header files
84      - adjusted namelists
85      - add xerbla.F to Makefile
86    o exf:
87      - multiple modifications of exf_check_range
88      - unit change in exf_init_runoff from [m/year] to [m/s]
89    o mdsio:
90      - i/o-vector change debugLevel from debLevA to debLevB
91    
92    checkpoint56b_post
93    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
94      is called from DO_THE_MODEL_IO
95      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
96      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
97      - clean up PTRACERS_WRITE_TIMEAVE a little
98    o add another verification experiment that tests both the cfc-pkg and
99      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
100      reactive tendencies treated inline with regular timestepping
101    o testreport previously did a lousy job of comparing small numbers, so
102      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
103      implemented in the little c-progam tmp_cmpnum.c which is embedded in
104      testreport.
105    o ptracers_monitor: bug fix for MPI
106    
107    checkpoint56a_post
108    o GCHEM: finish reorganizating the package
109      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
110        (introduces another 3D-array for each passive tracer, but only if
111        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
112        gchemTendency is not needed because the timestep is done separately)
113      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
114      - GCHEM is now---more or less cleanly---separate from PTRACERS
115      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
116        so clear to me how that should be done in a general way.
117    o CFC: improve formatting of output in CFC_ATMOS
118    o PTRACERS:
119      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
120        that ALL experiments with ptracers enable can be checked. This makes
121        GCHEM_MONITOR obsolete.
122      - include a runtime parameter PTRACERS_monitorFreq that defaults to
123        monitorFreq
124      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
125    o add PTRACERS (PTR0[1-5]) to testreport output
126    o exf_check_range:
127      * default changed to .TRUE.
128      * will check values for niter0 if debLevA, every timestep if debLevB
129      * STOP in exf_check_range if 'out of range'
130      * range chosen generous to allow for potential extema
131      TBD: a version with stricter range
132           permitted range would be runtime parameters
133  o GMredi:  o GMredi:
134    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
135    - 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 138  o GCHEM:
138    - 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
139      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
140    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
141      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
142        this flag is now only visible within GCHEM-pkg routines.
143      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
144        be replaced by a 3D array that is computed before thermodynamics; for
145        this, the tracer ID iTracer had to be included into the parameter list
146        of ptracers_forcing
147      - set up forward_step to call gchem_forcing, that will replace
148        gchem_forcing_int in ptracers_forcing
149      - cleaning up
150  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
151    
152  checkpoint56  checkpoint56
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