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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.418 by dimitri, Fri Dec 17 19:17:56 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 add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
7    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
8    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
9      this is based directly on what the model compute, so that the content of
10      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
11    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
12    o clean up build options files for SunOS, in particular
13      - remove -traditional from xmakedepend
14      - change -xarch=v9 to -xarch=native for f77
15      - restore use of make (not gmake)
16      - add CC=gcc if using g77
17    o changes per discussion of AM, JMC, & EH3 today:
18      - move redundant "grid" variables out of "state" -- in preparation of
19        creating proper CF-style coordinate variables and in recognition
20        that any/all grid variables can be easily copied (eg. w/NCO) from
21        the grid files into any of the other NetCDF files
22      - *always* output grid variables with MDSIO (this will eventually be
23        changed)
24      - output MNC grid file if useMNC is true
25    o every instance of _END_MASTER() has been found and replaced with
26      _END_MASTER( myThid ) in order to satisfy certain picky Sun
27      preprocessors
28    o re-arrange diagnostics pkg initialisation:
29     - allow each package to extend the available diagnostics list
30     - add some checking and fix small problems (multi-threaded, ...)
31     - new S/R diagnostics_fill (replace fill_diagnostics):
32       look through the short list of active diag. (instead of the long list)
33       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
34    
35    checkpoint57a_post
36    o this set of changes restores TAMC compatibility
37      tested for global_ocean.90x40x15 adjoint on trough
38      (what a pain)
39    
40    checkpoint57a_pre
41    o some modifs in tools/build_options for sunos
42    o call ctrl_pack for ctrl at end for optimcycle=0
43    
44    checkpoint57
45    o add horizontal bi-harmonic viscosity for vertical velocity
46      - new parameter viscA4W (defaults to viscA4)
47      - affects only non-hydrostatic code
48      - to be done: no-slip lateral boundary conditions
49    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
50    o implement Implicit Vertical advection for pTracers
51    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
52      (implemented also for implicit vertical diffusion & advection)
53    o OBCS: extend application of tracer open boundary conditions
54      to a strip beyond the boundary of width Olx/Oly
55    o add call monitor to TAF set of required calls (flow directives)
56      and include in natl_box_adjoint
57    o untangle a few ifdefs related to cost, ctrl, autodiff
58      untangel a few ALLOW_ECCO_OPTIMIZATION
59    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
60      (theta2, salt2 in ecco_cost_weights)
61    
62    checkpoint56c_post
63    o OBCS as control variables
64      - update ctrl_ad_diff.list, obcs_ad_diff.list
65      - remove balance of obcs controls from default
66      - fix index bug nobcs in ctrl_init
67      - fix dummy fields filen in ctrl_pack
68      - add dummy weights for obcs
69    o lsopt: comment out fort.94 output
70    o optim:
71      - remove unnecessary header files
72      - adjusted namelists
73      - add xerbla.F to Makefile
74    o exf:
75      - multiple modifications of exf_check_range
76      - unit change in exf_init_runoff from [m/year] to [m/s]
77    o mdsio:
78      - i/o-vector change debugLevel from debLevA to debLevB
79    
80    checkpoint56b_post
81    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
82      is called from DO_THE_MODEL_IO
83      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
84      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
85      - clean up PTRACERS_WRITE_TIMEAVE a little
86    o add another verification experiment that tests both the cfc-pkg and
87      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
88      reactive tendencies treated inline with regular timestepping
89    o testreport previously did a lousy job of comparing small numbers, so
90      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
91      implemented in the little c-progam tmp_cmpnum.c which is embedded in
92      testreport.
93    o ptracers_monitor: bug fix for MPI
94    
95    checkpoint56a_post
96    o GCHEM: finish reorganizating the package
97      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
98        (introduces another 3D-array for each passive tracer, but only if
99        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
100        gchemTendency is not needed because the timestep is done separately)
101      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
102      - GCHEM is now---more or less cleanly---separate from PTRACERS
103      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
104        so clear to me how that should be done in a general way.
105    o CFC: improve formatting of output in CFC_ATMOS
106    o PTRACERS:
107      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
108        that ALL experiments with ptracers enable can be checked. This makes
109        GCHEM_MONITOR obsolete.
110      - include a runtime parameter PTRACERS_monitorFreq that defaults to
111        monitorFreq
112      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
113    o add PTRACERS (PTR0[1-5]) to testreport output
114    o exf_check_range:
115      * default changed to .TRUE.
116      * will check values for niter0 if debLevA, every timestep if debLevB
117      * STOP in exf_check_range if 'out of range'
118      * range chosen generous to allow for potential extema
119      TBD: a version with stricter range
120           permitted range would be runtime parameters
121  o GMredi:  o GMredi:
122    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
123    - 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 126  o GCHEM:
126    - 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
127      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
128    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
129      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
130        this flag is now only visible within GCHEM-pkg routines.
131      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
132        be replaced by a 3D array that is computed before thermodynamics; for
133        this, the tracer ID iTracer had to be included into the parameter list
134        of ptracers_forcing
135      - set up forward_step to call gchem_forcing, that will replace
136        gchem_forcing_int in ptracers_forcing
137      - cleaning up
138  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
139    
140  checkpoint56  checkpoint56
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