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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.510 by edhill, Wed Jul 6 02:13:52 2005 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o add mnc output capability to diagnostics/diagstat and update
8      our cvsignore files for the ACSII output generated
9    
10    checkpoint57k_post
11    o lab_sea now uses diagnostics package and provides a suite of
12      new EXF diagnostics output.
13    
14    checkpoint57j_post
15    o exf
16      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
17        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
18        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
19      * extended diagnostics output
20        - now includes all EXF variables
21        - hs, hl moved to common block
22        - separate S/R for diagnostics, called after ctrl vector is added
23        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
24        - EXFqnet contains true Qnet (i.e. includes qsw)
25      * updated verif. lab_sea, global_with_exf
26      * Rearranging hflux (exf_mapfields -> exf_getforcing)
27        to ensure that diagnostics sees a true EXFqnet
28    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
29    o diagnostics pkg: change pointers so that 1 diagnostic can be used
30      several times with different frequencies.
31    o mnc-ify the thsice package as requested by Daniel Enderton
32      - the monitor--MNC output needs work
33      - many attributes need to be added (most are currently blank)
34    o mnc-ify theaim_v23 package as requested by Daniel Enderton
35      - many attributes need to be added (most are currently blank)
36    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
37    o add Sadourny like discretization to the 4th.O vorticity advection scheme
38    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
39      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
40         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
41    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
42     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
43    
44    checkpoint57i_post
45    o Diagnostics package was changed: diagnostic allocation is now deactivated
46      by setting an empty file name in the namelist (used to be by setting 0 frequency)
47    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
48      add 1rst Order upwind vertical Shear.
49    o add a quick fix for A/B checkpointing in OFFLINE mode
50    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
51      end-run around the C/Fortran linking horror in eesup/src/timers.F
52    o added pkg/runclock: allows user to terminate run based on wall clock
53    o added non-hydrostatic scaling parameter: nh_am2
54    o pkg/my82: futile attempt to make results compiler-independent by adding
55      some "_d 0", etc. no effect.
56    o for mnc output, fill the 'T' coordinate var with myTime and create a
57      separate 'iter' variable for iteration count
58    o pkg/diagnostics:
59      add new capability: output of Global/Regional & per-level statistics ;
60      tested against monitor output (including land & thSIce) on various exp.
61    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
62    
63    checkpoint57h_done
64      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
65      data.diagnostics, data.gchem, data.ptracers) is done.
66    
67    o pkg/diagnostics: prepare for Global/Regional statistics.
68      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
69    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
70      and rename it: DIFFERENT_MULTIPLE
71    
72    checkpoint57h_post
73    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
74    o pkg/diagnostics: change output frequency, now in seconds (instead
75      of Nb of iterations). This requires to change data.diagnostics.
76    checkpoint57h_pre
77    
78    o in mnc, let the user create the output dir if both mnc_outdir_date
79      and mnc_outdir_num are false
80    o add fflags() to pkg/diagnostics which allows one to specify, on a
81      per-file basis, the file precision [default behavior is unchanged]
82    o added diagnostics to pkg/kpp, including computation of mixed layer
83      depth based on a temperature/density criterion
84    o updated verification/natl_box to test the new pkg/kpp diagnostics
85    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
86    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
87    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
88      not mnc -- this mistake was found by JMC and is now corrected
89    
90    checkpoint57g_post
91    o add Adams-Bashforth 3rd Order time stepping:
92      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
93      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
94    checkpoint57g_pre
95    
96    o make lambda[Theta,Salt]ClimRelax spatially varying
97      (default remains spatially uniform constant based on tau)
98    o added new control variables
99      * init. uVel, vVel, etanN
100      * lambda[Theta,Salt]ClimRelax
101    o separate masks used for ctrl_pack/unpack 'from write_grid' output
102      (suggested by G. Forget)
103    
104    checkpoint57f_post
105    o add parameter "baseTime" = model base time = time at iteration zero
106      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
107      account for baseTime shift
108    o move Coriolis arrays from PARAMS.h to GRID.h
109    checkpoint57f_pre
110    
111    o mnc-ifying the seaice package
112    o introduced an alternative length scale calculation for use in the limiting
113      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
114    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
115    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
116      as well as grad(vort3).  Made it compatible with both approximate form
117      for the cubed sphere and full form of these gradients.  Added flag
118      useFullLeith to select between approximate and full form.  
119    o add "d0" in getcon.F to reduce differences between compilers/platforms
120      update output.txt of exp. fizhi-gridalt-hs
121    o change port_rand funtion to allow to set the seed.
122    o fix obscure MNC bug involving conversion between reals and integers
123      - it caused no problems with certain (eg. gcc, ifc) compilers but the
124        new version is now more standards-compliant
125    o adjoint-related modifications
126      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
127      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
128      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
129    
130    checkpoint57e_post
131    o Adding eddy stress controls a la Ferreira et al.
132    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
133    
134    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
135      update output.txt of exp. fizhi-gridalt-hs
136    o add more "Z" dimensions and associated coordinate vars to MNC
137    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
138    o parameter calendarDumps: when set, approximate months (30-31 days) and years
139      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
140      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
141      months and years.  Requires pkg/cal.
142    o diagnostics: add pickup functionality
143      - off by default for backwards compatibility
144      - current version only uses MDSIO -- MNC will be added
145    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
146    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
147    
148    checkpoint57d_post
149    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
150    o modify verification/ideal_2D_oce so that it tests the creation of mnc
151      output from the diagnostics package
152    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
153    o make genmake2 more portable by using ".$FS" instead of ".f" for more
154      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
155    o add coordinate variables to the MNC output from the diagnostics package
156    o change MNC-flags default value: true when useMNC=TRUE
157    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
158      the ability (off by default) to read the grid information using MNC
159    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
160    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
161    o do snap-shot diagnostics at the middle of the time-interval (instead of
162      at the end).
163    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
164      new test for AIM with thSIce + slab-ocean
165    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
166    o move state variable diagnostics to the beginning of the time step ;
167      (note: still needs some work specially for snap-shot diagnostics)
168      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
169    
170    checkpoint57c_post
171    o Change testing option (-ieee) to get closer agreement between g77 & ifort
172    o generate new output.txt files on faulks with g77 & the new -ieee option
173    checkpoint57c_pre
174    
175    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
176      update output.txt of exp. global_ocean.90x40x15
177    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
178      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
179    o add saltFlux(+File) forcing capability with periodicExternalForcing
180    o allow to use pkg diagnostics for GM-Redi & ThSIce output
181    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
182    o improvements for the MNC output from DIAGNOSTICS:
183      - correct handling of the unlimitied dimension
184      - all dims now have associated coordinate variables
185      - variables located at U, V, and Corner ("Z") points are now written
186        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
187        *all* data points are output
188    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
189    o added pkg/seaice/seaice_monitor.F
190    o mdsio_readfield.F can now read files visible only to master MPI process.
191    o pkg/seaice: some test code for ice-modified ocean stress
192    o exf_getffields interpolation defaults to bilinear for all scalar forcing
193      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
194      spurious negative numbers for precipitation and humidity.  Will cause
195      some small numerical differences for integrations using pkg/exf/exf_interp.F.
196    o pkg/ctrl/
197      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
198        May be enabled via doPackDiag
199      *  introduce z-scaling of
200         + gradient (doZscalePack) and
201         + control (doZscaleUnpack)
202    o pkg/mdsio/
203      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
204      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
205    
206    checkpoint57b_post
207    o simplify options in diagnostics_fill arguments (remove weird combinations)
208    o fix MNC coordinate variables so that they now contain per-face index
209      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
210      general, EXCH2 grids are only aligned to a "local" coordinate system
211    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
212    o Implement instantaneous output within pkg diagnostics:
213      setting a negative frequency in data.diagnostics produces
214     "snap-shot" output (as opposed to time-average if freq > 0)
215    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
216      NOTE: change ptracer diagnostics name: use 2 characters to work with
217            more than 9 tracers. Add also diagnostics of advect & diffus flux.
218    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
219      becomes the coordinate variable for the 'T' dimension
220    o add CF-style coordinate variables to MNC
221      - just a first cut:  numbers are meaningless on the cubesphere and
222        missing along the T axis but otherwise it works!
223    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
224    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
225    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
226      this is based directly on what the model compute, so that the content of
227      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
228    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
229    o clean up build options files for SunOS, in particular
230      - remove -traditional from xmakedepend
231      - change -xarch=v9 to -xarch=native for f77
232      - restore use of make (not gmake)
233      - add CC=gcc if using g77
234    o changes per discussion of AM, JMC, & EH3 today:
235      - move redundant "grid" variables out of "state" -- in preparation of
236        creating proper CF-style coordinate variables and in recognition
237        that any/all grid variables can be easily copied (eg. w/NCO) from
238        the grid files into any of the other NetCDF files
239      - *always* output grid variables with MDSIO (this will eventually be
240        changed)
241      - output MNC grid file if useMNC is true
242    o every instance of _END_MASTER() has been found and replaced with
243      _END_MASTER( myThid ) in order to satisfy certain picky Sun
244      preprocessors
245    o re-arrange diagnostics pkg initialisation:
246     - allow each package to extend the available diagnostics list
247     - add some checking and fix small problems (multi-threaded, ...)
248     - new S/R diagnostics_fill (replace fill_diagnostics):
249       look through the short list of active diag. (instead of the long list)
250       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
251    
252    checkpoint57a_post
253    o this set of changes restores TAMC compatibility
254      tested for global_ocean.90x40x15 adjoint on trough
255      (what a pain)
256    
257    checkpoint57a_pre
258    o some modifs in tools/build_options for sunos
259    o call ctrl_pack for ctrl at end for optimcycle=0
260    
261    checkpoint57
262    o add horizontal bi-harmonic viscosity for vertical velocity
263      - new parameter viscA4W (defaults to viscA4)
264      - affects only non-hydrostatic code
265      - to be done: no-slip lateral boundary conditions
266    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
267    o implement Implicit Vertical advection for pTracers
268    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
269      (implemented also for implicit vertical diffusion & advection)
270    o OBCS: extend application of tracer open boundary conditions
271      to a strip beyond the boundary of width Olx/Oly
272    o add call monitor to TAF set of required calls (flow directives)
273      and include in natl_box_adjoint
274    o untangle a few ifdefs related to cost, ctrl, autodiff
275      untangel a few ALLOW_ECCO_OPTIMIZATION
276    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
277      (theta2, salt2 in ecco_cost_weights)
278    
279    checkpoint56c_post
280    o OBCS as control variables
281      - update ctrl_ad_diff.list, obcs_ad_diff.list
282      - remove balance of obcs controls from default
283      - fix index bug nobcs in ctrl_init
284      - fix dummy fields filen in ctrl_pack
285      - add dummy weights for obcs
286    o lsopt: comment out fort.94 output
287    o optim:
288      - remove unnecessary header files
289      - adjusted namelists
290      - add xerbla.F to Makefile
291    o exf:
292      - multiple modifications of exf_check_range
293      - unit change in exf_init_runoff from [m/year] to [m/s]
294    o mdsio:
295      - i/o-vector change debugLevel from debLevA to debLevB
296    
297    checkpoint56b_post
298    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
299      is called from DO_THE_MODEL_IO
300      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
301      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
302      - clean up PTRACERS_WRITE_TIMEAVE a little
303    o add another verification experiment that tests both the cfc-pkg and
304      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
305      reactive tendencies treated inline with regular timestepping
306    o testreport previously did a lousy job of comparing small numbers, so
307      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
308      implemented in the little c-progam tmp_cmpnum.c which is embedded in
309      testreport.
310    o ptracers_monitor: bug fix for MPI
311    
312    checkpoint56a_post
313    o GCHEM: finish reorganizating the package
314      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
315        (introduces another 3D-array for each passive tracer, but only if
316        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
317        gchemTendency is not needed because the timestep is done separately)
318      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
319      - GCHEM is now---more or less cleanly---separate from PTRACERS
320      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
321        so clear to me how that should be done in a general way.
322    o CFC: improve formatting of output in CFC_ATMOS
323    o PTRACERS:
324      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
325        that ALL experiments with ptracers enable can be checked. This makes
326        GCHEM_MONITOR obsolete.
327      - include a runtime parameter PTRACERS_monitorFreq that defaults to
328        monitorFreq
329      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
330    o add PTRACERS (PTR0[1-5]) to testreport output
331    o exf_check_range:
332      * default changed to .TRUE.
333      * will check values for niter0 if debLevA, every timestep if debLevB
334      * STOP in exf_check_range if 'out of range'
335      * range chosen generous to allow for potential extema
336      TBD: a version with stricter range
337           permitted range would be runtime parameters
338  o GMredi:  o GMredi:
339    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
340    - 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 343  o GCHEM:
343    - 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
344      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
345    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
346      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
347        this flag is now only visible within GCHEM-pkg routines.
348      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
349        be replaced by a 3D array that is computed before thermodynamics; for
350        this, the tracer ID iTracer had to be included into the parameter list
351        of ptracers_forcing
352      - set up forward_step to call gchem_forcing, that will replace
353        gchem_forcing_int in ptracers_forcing
354      - cleaning up
355  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
356    
357  checkpoint56  checkpoint56

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