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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.472 by heimbach, Wed Apr 6 20:19:34 2005 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o make lambda[Theta,Salt]ClimRelax spatially varying
7      (default remains spatially uniform constant based on tau)
8    
9    checkpoint57f_post
10    o add parameter "baseTime" = model base time = time at iteration zero
11      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
12      account for baseTime shift
13    o move Coriolis arrays from PARAMS.h to GRID.h
14    checkpoint57f_pre
15    
16    o mnc-ifying the seaice package
17    o introduced an alternative length scale calculation for use in the limiting
18      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
19    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
20    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
21      as well as grad(vort3).  Made it compatible with both approximate form
22      for the cubed sphere and full form of these gradients.  Added flag
23      useFullLeith to select between approximate and full form.  
24    o add "d0" in getcon.F to reduce differences between compilers/platforms
25      update output.txt of exp. fizhi-gridalt-hs
26    o change port_rand funtion to allow to set the seed.
27    o fix obscure MNC bug involving conversion between reals and integers
28      - it caused no problems with certain (eg. gcc, ifc) compilers but the
29        new version is now more standards-compliant
30    o adjoint-related modifications
31      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
32      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
33      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
34    
35    checkpoint57e_post
36    o Adding eddy stress controls a la Ferreira et al.
37    checkpoint57e_pre
38    
39    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
40      update output.txt of exp. fizhi-gridalt-hs
41    o add more "Z" dimensions and associated coordinate vars to MNC
42    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
43    o parameter calendarDumps: when set, approximate months (30-31 days) and years
44      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
45      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
46      months and years.  Requires pkg/cal.
47    o diagnostics: add pickup functionality
48      - off by default for backwards compatibility
49      - current version only uses MDSIO -- MNC will be added
50    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
51    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
52    
53    checkpoint57d_post
54    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
55    o modify verification/ideal_2D_oce so that it tests the creation of mnc
56      output from the diagnostics package
57    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
58    o make genmake2 more portable by using ".$FS" instead of ".f" for more
59      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
60    o add coordinate variables to the MNC output from the diagnostics package
61    o change MNC-flags default value: true when useMNC=TRUE
62    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
63      the ability (off by default) to read the grid information using MNC
64    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
65    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
66    o do snap-shot diagnostics at the middle of the time-interval (instead of
67      at the end).
68    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
69      new test for AIM with thSIce + slab-ocean
70    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
71    o move state variable diagnostics to the beginning of the time step ;
72      (note: still needs some work specially for snap-shot diagnostics)
73      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
74    
75    checkpoint57c_post
76    o Change testing option (-ieee) to get closer agreement between g77 & ifort
77    o generate new output.txt files on faulks with g77 & the new -ieee option
78    checkpoint57c_pre
79    
80    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
81      update output.txt of exp. global_ocean.90x40x15
82    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
83      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
84    o add saltFlux(+File) forcing capability with periodicExternalForcing
85    o allow to use pkg diagnostics for GM-Redi & ThSIce output
86    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
87    o improvements for the MNC output from DIAGNOSTICS:
88      - correct handling of the unlimitied dimension
89      - all dims now have associated coordinate variables
90      - variables located at U, V, and Corner ("Z") points are now written
91        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
92        *all* data points are output
93    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
94    o added pkg/seaice/seaice_monitor.F
95    o mdsio_readfield.F can now read files visible only to master MPI process.
96    o pkg/seaice: some test code for ice-modified ocean stress
97    o exf_getffields interpolation defaults to bilinear for all scalar forcing
98      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
99      spurious negative numbers for precipitation and humidity.  Will cause
100      some small numerical differences for integrations using pkg/exf/exf_interp.F.
101    o pkg/ctrl/
102      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
103        May be enabled via doPackDiag
104      *  introduce z-scaling of
105         + gradient (doZscalePack) and
106         + control (doZscaleUnpack)
107    o pkg/mdsio/
108      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
109      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
110    
111    checkpoint57b_post
112    o simplify options in diagnostics_fill arguments (remove weird combinations)
113    o fix MNC coordinate variables so that they now contain per-face index
114      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
115      general, EXCH2 grids are only aligned to a "local" coordinate system
116    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
117    o Implement instantaneous output within pkg diagnostics:
118      setting a negative frequency in data.diagnostics produces
119     "snap-shot" output (as opposed to time-average if freq > 0)
120    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
121      NOTE: change ptracer diagnostics name: use 2 characters to work with
122            more than 9 tracers. Add also diagnostics of advect & diffus flux.
123    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
124      becomes the coordinate variable for the 'T' dimension
125    o add CF-style coordinate variables to MNC
126      - just a first cut:  numbers are meaningless on the cubesphere and
127        missing along the T axis but otherwise it works!
128    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
129    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
130    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
131      this is based directly on what the model compute, so that the content of
132      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
133    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
134    o clean up build options files for SunOS, in particular
135      - remove -traditional from xmakedepend
136      - change -xarch=v9 to -xarch=native for f77
137      - restore use of make (not gmake)
138      - add CC=gcc if using g77
139    o changes per discussion of AM, JMC, & EH3 today:
140      - move redundant "grid" variables out of "state" -- in preparation of
141        creating proper CF-style coordinate variables and in recognition
142        that any/all grid variables can be easily copied (eg. w/NCO) from
143        the grid files into any of the other NetCDF files
144      - *always* output grid variables with MDSIO (this will eventually be
145        changed)
146      - output MNC grid file if useMNC is true
147    o every instance of _END_MASTER() has been found and replaced with
148      _END_MASTER( myThid ) in order to satisfy certain picky Sun
149      preprocessors
150    o re-arrange diagnostics pkg initialisation:
151     - allow each package to extend the available diagnostics list
152     - add some checking and fix small problems (multi-threaded, ...)
153     - new S/R diagnostics_fill (replace fill_diagnostics):
154       look through the short list of active diag. (instead of the long list)
155       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
156    
157    checkpoint57a_post
158    o this set of changes restores TAMC compatibility
159      tested for global_ocean.90x40x15 adjoint on trough
160      (what a pain)
161    
162    checkpoint57a_pre
163    o some modifs in tools/build_options for sunos
164    o call ctrl_pack for ctrl at end for optimcycle=0
165    
166    checkpoint57
167    o add horizontal bi-harmonic viscosity for vertical velocity
168      - new parameter viscA4W (defaults to viscA4)
169      - affects only non-hydrostatic code
170      - to be done: no-slip lateral boundary conditions
171    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
172    o implement Implicit Vertical advection for pTracers
173    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
174      (implemented also for implicit vertical diffusion & advection)
175    o OBCS: extend application of tracer open boundary conditions
176      to a strip beyond the boundary of width Olx/Oly
177    o add call monitor to TAF set of required calls (flow directives)
178      and include in natl_box_adjoint
179    o untangle a few ifdefs related to cost, ctrl, autodiff
180      untangel a few ALLOW_ECCO_OPTIMIZATION
181    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
182      (theta2, salt2 in ecco_cost_weights)
183    
184    checkpoint56c_post
185    o OBCS as control variables
186      - update ctrl_ad_diff.list, obcs_ad_diff.list
187      - remove balance of obcs controls from default
188      - fix index bug nobcs in ctrl_init
189      - fix dummy fields filen in ctrl_pack
190      - add dummy weights for obcs
191    o lsopt: comment out fort.94 output
192    o optim:
193      - remove unnecessary header files
194      - adjusted namelists
195      - add xerbla.F to Makefile
196    o exf:
197      - multiple modifications of exf_check_range
198      - unit change in exf_init_runoff from [m/year] to [m/s]
199    o mdsio:
200      - i/o-vector change debugLevel from debLevA to debLevB
201    
202    checkpoint56b_post
203    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
204      is called from DO_THE_MODEL_IO
205      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
206      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
207      - clean up PTRACERS_WRITE_TIMEAVE a little
208    o add another verification experiment that tests both the cfc-pkg and
209      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
210      reactive tendencies treated inline with regular timestepping
211    o testreport previously did a lousy job of comparing small numbers, so
212      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
213      implemented in the little c-progam tmp_cmpnum.c which is embedded in
214      testreport.
215    o ptracers_monitor: bug fix for MPI
216    
217    checkpoint56a_post
218    o GCHEM: finish reorganizating the package
219      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
220        (introduces another 3D-array for each passive tracer, but only if
221        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
222        gchemTendency is not needed because the timestep is done separately)
223      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
224      - GCHEM is now---more or less cleanly---separate from PTRACERS
225      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
226        so clear to me how that should be done in a general way.
227    o CFC: improve formatting of output in CFC_ATMOS
228    o PTRACERS:
229      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
230        that ALL experiments with ptracers enable can be checked. This makes
231        GCHEM_MONITOR obsolete.
232      - include a runtime parameter PTRACERS_monitorFreq that defaults to
233        monitorFreq
234      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
235    o add PTRACERS (PTR0[1-5]) to testreport output
236    o exf_check_range:
237      * default changed to .TRUE.
238      * will check values for niter0 if debLevA, every timestep if debLevB
239      * STOP in exf_check_range if 'out of range'
240      * range chosen generous to allow for potential extema
241      TBD: a version with stricter range
242           permitted range would be runtime parameters
243  o GMredi:  o GMredi:
244    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
245    - 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 248  o GCHEM:
248    - 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
249      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
250    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
251      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
252        this flag is now only visible within GCHEM-pkg routines.
253      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
254        be replaced by a 3D array that is computed before thermodynamics; for
255        this, the tracer ID iTracer had to be included into the parameter list
256        of ptracers_forcing
257      - set up forward_step to call gchem_forcing, that will replace
258        gchem_forcing_int in ptracers_forcing
259      - cleaning up
260  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
261    
262  checkpoint56  checkpoint56

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