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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.513 by jmc, Wed Jul 13 00:50:58 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 cos & sin of grid-direction orientation angle (curvilinear grid only,
8       for output and interpolation of input fields onto model grid)
9    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
10       Affects results of exp. rotating_tank ; update output.txt.
11    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
12          and taking the square quantity and/or using a fraction-weight field.
13    o fix aim_diagnostics_init.F mate numbers.
14    o add mnc output capability to diagnostics/diagstat and update
15      our cvsignore files for the ACSII output generated
16    
17    checkpoint57k_post
18    o lab_sea now uses diagnostics package and provides a suite of
19      new EXF diagnostics output.
20    
21    checkpoint57j_post
22    o exf
23      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
24        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
25        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
26      * extended diagnostics output
27        - now includes all EXF variables
28        - hs, hl moved to common block
29        - separate S/R for diagnostics, called after ctrl vector is added
30        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
31        - EXFqnet contains true Qnet (i.e. includes qsw)
32      * updated verif. lab_sea, global_with_exf
33      * Rearranging hflux (exf_mapfields -> exf_getforcing)
34        to ensure that diagnostics sees a true EXFqnet
35    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
36    o diagnostics pkg: change pointers so that 1 diagnostic can be used
37      several times with different frequencies.
38    o mnc-ify the thsice package as requested by Daniel Enderton
39      - the monitor--MNC output needs work
40      - many attributes need to be added (most are currently blank)
41    o mnc-ify theaim_v23 package as requested by Daniel Enderton
42      - many attributes need to be added (most are currently blank)
43    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
44    o add Sadourny like discretization to the 4th.O vorticity advection scheme
45    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
46      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
47         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
48    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
49     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
50    
51    checkpoint57i_post
52    o Diagnostics package was changed: diagnostic allocation is now deactivated
53      by setting an empty file name in the namelist (used to be by setting 0 frequency)
54    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
55      add 1rst Order upwind vertical Shear.
56    o add a quick fix for A/B checkpointing in OFFLINE mode
57    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
58      end-run around the C/Fortran linking horror in eesup/src/timers.F
59    o added pkg/runclock: allows user to terminate run based on wall clock
60    o added non-hydrostatic scaling parameter: nh_am2
61    o pkg/my82: futile attempt to make results compiler-independent by adding
62      some "_d 0", etc. no effect.
63    o for mnc output, fill the 'T' coordinate var with myTime and create a
64      separate 'iter' variable for iteration count
65    o pkg/diagnostics:
66      add new capability: output of Global/Regional & per-level statistics ;
67      tested against monitor output (including land & thSIce) on various exp.
68    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
69    
70    checkpoint57h_done
71      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
72      data.diagnostics, data.gchem, data.ptracers) is done.
73    
74    o pkg/diagnostics: prepare for Global/Regional statistics.
75      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
76    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
77      and rename it: DIFFERENT_MULTIPLE
78    
79    checkpoint57h_post
80    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
81    o pkg/diagnostics: change output frequency, now in seconds (instead
82      of Nb of iterations). This requires to change data.diagnostics.
83    checkpoint57h_pre
84    
85    o in mnc, let the user create the output dir if both mnc_outdir_date
86      and mnc_outdir_num are false
87    o add fflags() to pkg/diagnostics which allows one to specify, on a
88      per-file basis, the file precision [default behavior is unchanged]
89    o added diagnostics to pkg/kpp, including computation of mixed layer
90      depth based on a temperature/density criterion
91    o updated verification/natl_box to test the new pkg/kpp diagnostics
92    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
93    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
94    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
95      not mnc -- this mistake was found by JMC and is now corrected
96    
97    checkpoint57g_post
98    o add Adams-Bashforth 3rd Order time stepping:
99      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
100      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
101    checkpoint57g_pre
102    
103    o make lambda[Theta,Salt]ClimRelax spatially varying
104      (default remains spatially uniform constant based on tau)
105    o added new control variables
106      * init. uVel, vVel, etanN
107      * lambda[Theta,Salt]ClimRelax
108    o separate masks used for ctrl_pack/unpack 'from write_grid' output
109      (suggested by G. Forget)
110    
111    checkpoint57f_post
112    o add parameter "baseTime" = model base time = time at iteration zero
113      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
114      account for baseTime shift
115    o move Coriolis arrays from PARAMS.h to GRID.h
116    checkpoint57f_pre
117    
118    o mnc-ifying the seaice package
119    o introduced an alternative length scale calculation for use in the limiting
120      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
121    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
122    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
123      as well as grad(vort3).  Made it compatible with both approximate form
124      for the cubed sphere and full form of these gradients.  Added flag
125      useFullLeith to select between approximate and full form.  
126    o add "d0" in getcon.F to reduce differences between compilers/platforms
127      update output.txt of exp. fizhi-gridalt-hs
128    o change port_rand funtion to allow to set the seed.
129    o fix obscure MNC bug involving conversion between reals and integers
130      - it caused no problems with certain (eg. gcc, ifc) compilers but the
131        new version is now more standards-compliant
132    o adjoint-related modifications
133      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
134      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
135      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
136    
137    checkpoint57e_post
138    o Adding eddy stress controls a la Ferreira et al.
139    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
140    
141    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
142      update output.txt of exp. fizhi-gridalt-hs
143    o add more "Z" dimensions and associated coordinate vars to MNC
144    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
145    o parameter calendarDumps: when set, approximate months (30-31 days) and years
146      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
147      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
148      months and years.  Requires pkg/cal.
149    o diagnostics: add pickup functionality
150      - off by default for backwards compatibility
151      - current version only uses MDSIO -- MNC will be added
152    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
153    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
154    
155    checkpoint57d_post
156    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
157    o modify verification/ideal_2D_oce so that it tests the creation of mnc
158      output from the diagnostics package
159    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
160    o make genmake2 more portable by using ".$FS" instead of ".f" for more
161      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
162    o add coordinate variables to the MNC output from the diagnostics package
163    o change MNC-flags default value: true when useMNC=TRUE
164    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
165      the ability (off by default) to read the grid information using MNC
166    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
167    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
168    o do snap-shot diagnostics at the middle of the time-interval (instead of
169      at the end).
170    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
171      new test for AIM with thSIce + slab-ocean
172    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
173    o move state variable diagnostics to the beginning of the time step ;
174      (note: still needs some work specially for snap-shot diagnostics)
175      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
176    
177    checkpoint57c_post
178    o Change testing option (-ieee) to get closer agreement between g77 & ifort
179    o generate new output.txt files on faulks with g77 & the new -ieee option
180    checkpoint57c_pre
181    
182    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
183      update output.txt of exp. global_ocean.90x40x15
184    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
185      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
186    o add saltFlux(+File) forcing capability with periodicExternalForcing
187    o allow to use pkg diagnostics for GM-Redi & ThSIce output
188    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
189    o improvements for the MNC output from DIAGNOSTICS:
190      - correct handling of the unlimitied dimension
191      - all dims now have associated coordinate variables
192      - variables located at U, V, and Corner ("Z") points are now written
193        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
194        *all* data points are output
195    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
196    o added pkg/seaice/seaice_monitor.F
197    o mdsio_readfield.F can now read files visible only to master MPI process.
198    o pkg/seaice: some test code for ice-modified ocean stress
199    o exf_getffields interpolation defaults to bilinear for all scalar forcing
200      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
201      spurious negative numbers for precipitation and humidity.  Will cause
202      some small numerical differences for integrations using pkg/exf/exf_interp.F.
203    o pkg/ctrl/
204      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
205        May be enabled via doPackDiag
206      *  introduce z-scaling of
207         + gradient (doZscalePack) and
208         + control (doZscaleUnpack)
209    o pkg/mdsio/
210      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
211      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
212    
213    checkpoint57b_post
214    o simplify options in diagnostics_fill arguments (remove weird combinations)
215    o fix MNC coordinate variables so that they now contain per-face index
216      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
217      general, EXCH2 grids are only aligned to a "local" coordinate system
218    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
219    o Implement instantaneous output within pkg diagnostics:
220      setting a negative frequency in data.diagnostics produces
221     "snap-shot" output (as opposed to time-average if freq > 0)
222    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
223      NOTE: change ptracer diagnostics name: use 2 characters to work with
224            more than 9 tracers. Add also diagnostics of advect & diffus flux.
225    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
226      becomes the coordinate variable for the 'T' dimension
227    o add CF-style coordinate variables to MNC
228      - just a first cut:  numbers are meaningless on the cubesphere and
229        missing along the T axis but otherwise it works!
230    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
231    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
232    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
233      this is based directly on what the model compute, so that the content of
234      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
235    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
236    o clean up build options files for SunOS, in particular
237      - remove -traditional from xmakedepend
238      - change -xarch=v9 to -xarch=native for f77
239      - restore use of make (not gmake)
240      - add CC=gcc if using g77
241    o changes per discussion of AM, JMC, & EH3 today:
242      - move redundant "grid" variables out of "state" -- in preparation of
243        creating proper CF-style coordinate variables and in recognition
244        that any/all grid variables can be easily copied (eg. w/NCO) from
245        the grid files into any of the other NetCDF files
246      - *always* output grid variables with MDSIO (this will eventually be
247        changed)
248      - output MNC grid file if useMNC is true
249    o every instance of _END_MASTER() has been found and replaced with
250      _END_MASTER( myThid ) in order to satisfy certain picky Sun
251      preprocessors
252    o re-arrange diagnostics pkg initialisation:
253     - allow each package to extend the available diagnostics list
254     - add some checking and fix small problems (multi-threaded, ...)
255     - new S/R diagnostics_fill (replace fill_diagnostics):
256       look through the short list of active diag. (instead of the long list)
257       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
258    
259    checkpoint57a_post
260    o this set of changes restores TAMC compatibility
261      tested for global_ocean.90x40x15 adjoint on trough
262      (what a pain)
263    
264    checkpoint57a_pre
265    o some modifs in tools/build_options for sunos
266    o call ctrl_pack for ctrl at end for optimcycle=0
267    
268    checkpoint57
269    o add horizontal bi-harmonic viscosity for vertical velocity
270      - new parameter viscA4W (defaults to viscA4)
271      - affects only non-hydrostatic code
272      - to be done: no-slip lateral boundary conditions
273    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
274    o implement Implicit Vertical advection for pTracers
275    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
276      (implemented also for implicit vertical diffusion & advection)
277    o OBCS: extend application of tracer open boundary conditions
278      to a strip beyond the boundary of width Olx/Oly
279    o add call monitor to TAF set of required calls (flow directives)
280      and include in natl_box_adjoint
281    o untangle a few ifdefs related to cost, ctrl, autodiff
282      untangel a few ALLOW_ECCO_OPTIMIZATION
283    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
284      (theta2, salt2 in ecco_cost_weights)
285    
286    checkpoint56c_post
287    o OBCS as control variables
288      - update ctrl_ad_diff.list, obcs_ad_diff.list
289      - remove balance of obcs controls from default
290      - fix index bug nobcs in ctrl_init
291      - fix dummy fields filen in ctrl_pack
292      - add dummy weights for obcs
293    o lsopt: comment out fort.94 output
294    o optim:
295      - remove unnecessary header files
296      - adjusted namelists
297      - add xerbla.F to Makefile
298    o exf:
299      - multiple modifications of exf_check_range
300      - unit change in exf_init_runoff from [m/year] to [m/s]
301    o mdsio:
302      - i/o-vector change debugLevel from debLevA to debLevB
303    
304    checkpoint56b_post
305    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
306      is called from DO_THE_MODEL_IO
307      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
308      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
309      - clean up PTRACERS_WRITE_TIMEAVE a little
310    o add another verification experiment that tests both the cfc-pkg and
311      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
312      reactive tendencies treated inline with regular timestepping
313    o testreport previously did a lousy job of comparing small numbers, so
314      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
315      implemented in the little c-progam tmp_cmpnum.c which is embedded in
316      testreport.
317    o ptracers_monitor: bug fix for MPI
318    
319    checkpoint56a_post
320    o GCHEM: finish reorganizating the package
321      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
322        (introduces another 3D-array for each passive tracer, but only if
323        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
324        gchemTendency is not needed because the timestep is done separately)
325      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
326      - GCHEM is now---more or less cleanly---separate from PTRACERS
327      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
328        so clear to me how that should be done in a general way.
329    o CFC: improve formatting of output in CFC_ATMOS
330    o PTRACERS:
331      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
332        that ALL experiments with ptracers enable can be checked. This makes
333        GCHEM_MONITOR obsolete.
334      - include a runtime parameter PTRACERS_monitorFreq that defaults to
335        monitorFreq
336      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
337    o add PTRACERS (PTR0[1-5]) to testreport output
338    o exf_check_range:
339      * default changed to .TRUE.
340      * will check values for niter0 if debLevA, every timestep if debLevB
341      * STOP in exf_check_range if 'out of range'
342      * range chosen generous to allow for potential extema
343      TBD: a version with stricter range
344           permitted range would be runtime parameters
345  o GMredi:  o GMredi:
346    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
347    - 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 350  o GCHEM:
350    - 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
351      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
352    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
353      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
354        this flag is now only visible within GCHEM-pkg routines.
355      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
356        be replaced by a 3D array that is computed before thermodynamics; for
357        this, the tracer ID iTracer had to be included into the parameter list
358        of ptracers_forcing
359      - set up forward_step to call gchem_forcing, that will replace
360        gchem_forcing_int in ptracers_forcing
361      - cleaning up
362  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
363    
364  checkpoint56  checkpoint56

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