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revision 1.322 by jmc, Tue Jul 6 02:44:27 2004 UTC revision 1.466 by heimbach, Fri Mar 25 00:30:46 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 S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
7    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
8      as well as grad(vort3).  Made it compatible with both approximate form
9      for the cubed sphere and full form of these gradients.  Added flag
10      useFullLeith to select between approximate and full form.  
11    o add "d0" in getcon.F to reduce differences between compilers/platforms
12      update output.txt of exp. fizhi-gridalt-hs
13    o change port_rand funtion to allow to set the seed.
14    o fix obscure MNC bug involving conversion between reals and integers
15      - it caused no problems with certain (eg. gcc, ifc) compilers but the
16        new version is now more standards-compliant
17    
18    checkpoint57e_post
19    o Adding eddy stress controls a la Ferreira et al.
20    checkpoint57e_pre
21    
22    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
23      update output.txt of exp. fizhi-gridalt-hs
24    o add more "Z" dimensions and associated coordinate vars to MNC
25    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
26    o parameter calendarDumps: when set, approximate months (30-31 days) and years
27      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
28      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
29      months and years.  Requires pkg/cal.
30    o diagnostics: add pickup functionality
31      - off by default for backwards compatibility
32      - current version only uses MDSIO -- MNC will be added
33    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
34    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
35    
36    checkpoint57d_post
37    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
38    o modify verification/ideal_2D_oce so that it tests the creation of mnc
39      output from the diagnostics package
40    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
41    o make genmake2 more portable by using ".$FS" instead of ".f" for more
42      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
43    o add coordinate variables to the MNC output from the diagnostics package
44    o change MNC-flags default value: true when useMNC=TRUE
45    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
46      the ability (off by default) to read the grid information using MNC
47    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
48    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
49    o do snap-shot diagnostics at the middle of the time-interval (instead of
50      at the end).
51    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
52      new test for AIM with thSIce + slab-ocean
53    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
54    o move state variable diagnostics to the beginning of the time step ;
55      (note: still needs some work specially for snap-shot diagnostics)
56      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
57    
58    checkpoint57c_post
59    o Change testing option (-ieee) to get closer agreement between g77 & ifort
60    o generate new output.txt files on faulks with g77 & the new -ieee option
61    checkpoint57c_pre
62    
63    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
64      update output.txt of exp. global_ocean.90x40x15
65    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
66      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
67    o add saltFlux(+File) forcing capability with periodicExternalForcing
68    o allow to use pkg diagnostics for GM-Redi & ThSIce output
69    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
70    o improvements for the MNC output from DIAGNOSTICS:
71      - correct handling of the unlimitied dimension
72      - all dims now have associated coordinate variables
73      - variables located at U, V, and Corner ("Z") points are now written
74        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
75        *all* data points are output
76    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
77    o added pkg/seaice/seaice_monitor.F
78    o mdsio_readfield.F can now read files visible only to master MPI process.
79    o pkg/seaice: some test code for ice-modified ocean stress
80    o exf_getffields interpolation defaults to bilinear for all scalar forcing
81      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
82      spurious negative numbers for precipitation and humidity.  Will cause
83      some small numerical differences for integrations using pkg/exf/exf_interp.F.
84    o pkg/ctrl/
85      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
86        May be enabled via doPackDiag
87      *  introduce z-scaling of
88         + gradient (doZscalePack) and
89         + control (doZscaleUnpack)
90    o pkg/mdsio/
91      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
92      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
93    
94    checkpoint57b_post
95    o simplify options in diagnostics_fill arguments (remove weird combinations)
96    o fix MNC coordinate variables so that they now contain per-face index
97      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
98      general, EXCH2 grids are only aligned to a "local" coordinate system
99    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
100    o Implement instantaneous output within pkg diagnostics:
101      setting a negative frequency in data.diagnostics produces
102     "snap-shot" output (as opposed to time-average if freq > 0)
103    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
104      NOTE: change ptracer diagnostics name: use 2 characters to work with
105            more than 9 tracers. Add also diagnostics of advect & diffus flux.
106    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
107      becomes the coordinate variable for the 'T' dimension
108    o add CF-style coordinate variables to MNC
109      - just a first cut:  numbers are meaningless on the cubesphere and
110        missing along the T axis but otherwise it works!
111    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
112    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
113    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
114      this is based directly on what the model compute, so that the content of
115      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
116    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
117    o clean up build options files for SunOS, in particular
118      - remove -traditional from xmakedepend
119      - change -xarch=v9 to -xarch=native for f77
120      - restore use of make (not gmake)
121      - add CC=gcc if using g77
122    o changes per discussion of AM, JMC, & EH3 today:
123      - move redundant "grid" variables out of "state" -- in preparation of
124        creating proper CF-style coordinate variables and in recognition
125        that any/all grid variables can be easily copied (eg. w/NCO) from
126        the grid files into any of the other NetCDF files
127      - *always* output grid variables with MDSIO (this will eventually be
128        changed)
129      - output MNC grid file if useMNC is true
130    o every instance of _END_MASTER() has been found and replaced with
131      _END_MASTER( myThid ) in order to satisfy certain picky Sun
132      preprocessors
133    o re-arrange diagnostics pkg initialisation:
134     - allow each package to extend the available diagnostics list
135     - add some checking and fix small problems (multi-threaded, ...)
136     - new S/R diagnostics_fill (replace fill_diagnostics):
137       look through the short list of active diag. (instead of the long list)
138       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
139    
140    checkpoint57a_post
141    o this set of changes restores TAMC compatibility
142      tested for global_ocean.90x40x15 adjoint on trough
143      (what a pain)
144    
145    checkpoint57a_pre
146    o some modifs in tools/build_options for sunos
147    o call ctrl_pack for ctrl at end for optimcycle=0
148    
149    checkpoint57
150    o add horizontal bi-harmonic viscosity for vertical velocity
151      - new parameter viscA4W (defaults to viscA4)
152      - affects only non-hydrostatic code
153      - to be done: no-slip lateral boundary conditions
154    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
155    o implement Implicit Vertical advection for pTracers
156    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
157      (implemented also for implicit vertical diffusion & advection)
158    o OBCS: extend application of tracer open boundary conditions
159      to a strip beyond the boundary of width Olx/Oly
160    o add call monitor to TAF set of required calls (flow directives)
161      and include in natl_box_adjoint
162    o untangle a few ifdefs related to cost, ctrl, autodiff
163      untangel a few ALLOW_ECCO_OPTIMIZATION
164    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
165      (theta2, salt2 in ecco_cost_weights)
166    
167    checkpoint56c_post
168    o OBCS as control variables
169      - update ctrl_ad_diff.list, obcs_ad_diff.list
170      - remove balance of obcs controls from default
171      - fix index bug nobcs in ctrl_init
172      - fix dummy fields filen in ctrl_pack
173      - add dummy weights for obcs
174    o lsopt: comment out fort.94 output
175    o optim:
176      - remove unnecessary header files
177      - adjusted namelists
178      - add xerbla.F to Makefile
179    o exf:
180      - multiple modifications of exf_check_range
181      - unit change in exf_init_runoff from [m/year] to [m/s]
182    o mdsio:
183      - i/o-vector change debugLevel from debLevA to debLevB
184    
185    checkpoint56b_post
186    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
187      is called from DO_THE_MODEL_IO
188      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
189      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
190      - clean up PTRACERS_WRITE_TIMEAVE a little
191    o add another verification experiment that tests both the cfc-pkg and
192      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
193      reactive tendencies treated inline with regular timestepping
194    o testreport previously did a lousy job of comparing small numbers, so
195      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
196      implemented in the little c-progam tmp_cmpnum.c which is embedded in
197      testreport.
198    o ptracers_monitor: bug fix for MPI
199    
200    checkpoint56a_post
201    o GCHEM: finish reorganizating the package
202      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
203        (introduces another 3D-array for each passive tracer, but only if
204        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
205        gchemTendency is not needed because the timestep is done separately)
206      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
207      - GCHEM is now---more or less cleanly---separate from PTRACERS
208      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
209        so clear to me how that should be done in a general way.
210    o CFC: improve formatting of output in CFC_ATMOS
211    o PTRACERS:
212      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
213        that ALL experiments with ptracers enable can be checked. This makes
214        GCHEM_MONITOR obsolete.
215      - include a runtime parameter PTRACERS_monitorFreq that defaults to
216        monitorFreq
217      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
218    o add PTRACERS (PTR0[1-5]) to testreport output
219    o exf_check_range:
220      * default changed to .TRUE.
221      * will check values for niter0 if debLevA, every timestep if debLevB
222      * STOP in exf_check_range if 'out of range'
223      * range chosen generous to allow for potential extema
224      TBD: a version with stricter range
225           permitted range would be runtime parameters
226    o GMredi:
227      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
228      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
229      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
230    o GCHEM:
231      - move call to GCHEM_FORCING_SEP, so that it is now called before
232        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
233      - introduced a useGCHEM runtime flag and applied it everywhere.
234      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
235        this flag is now only visible within GCHEM-pkg routines.
236      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
237        be replaced by a 3D array that is computed before thermodynamics; for
238        this, the tracer ID iTracer had to be included into the parameter list
239        of ptracers_forcing
240      - set up forward_step to call gchem_forcing, that will replace
241        gchem_forcing_int in ptracers_forcing
242      - cleaning up
243    o small cleaning of exch2: remove files that are also in eesupp/src
244    
245    checkpoint56
246    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
247    o mnc: cleanup "full" files--fixes out-of-memory problem
248    o ECCO-GODAE
249      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
250      * fully merged and updated from SIO code
251        windstress sign change affects
252        - exf_inscal_[u/v]stress
253        - sign of xx_tau[u/v] adjustments
254        - signs in cost_scat
255      * ctrl_get_gen: avoid update of tau[u/v] for first few days
256      * natl_box_adjoint updated and compressed
257      * 2-level checkpoint switch added
258        (tested in EXP. 1 of natl_box_adjoint)
259      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
260    o SVD
261      * first complete, non-hacked version for SVD calculations
262      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
263        performed via direct access files admtlm_vector.it????
264        (via ctrl_[un]pack)
265      * optimcycle is used for ARPACK iteration counter
266        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
267      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
268        and add linear transforms where necessary
269      * controls are initial/final SST, SSS (can be extended; need to check
270        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
271    o mdsio: filename info to both stderr, stdout
272    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
273      from sign change
274    
275    checkpoint55j_post
276    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
277      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
278    o add consistent build directories and .cvsignore files to verification
279    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
280    o make all subroutines 30 or less characters in length for certain older
281      compilers to work (a thorough search only turns up two routines in
282      pkg/ptracers)
283    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
284      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
285    
286    checkpoint55i_post
287    o change arrays for total vertical diffusivity (2.D if explicit,
288      3.D if implicit) ; each ptracer uses its own background value.
289    o added mnc/NetCDF output capability to ocn_compon_interf
290      - added bits to verification/cpl_aim+ocn so that it can run on
291        ITRDA and other clusters without the mpirun "-wd" option
292    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
293      configuration
294    o give MNC the ability to create additional files rather than
295      exceeding a specified file size limit "MNC_MAX_FILESIZE"
296      - the default is just less than 2GB which is a practical limit
297        on many systems
298    o Compute the non-local term using either KPP vertical diffusivity (=default)
299       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
300    
301    checkpoint55h_post
302    o add verification test "vermix"
303    o remove all the *_ioinc flags and replace with the single global
304      outputTypesInclusive flag
305    o allow to set a vertical profile of vertical diffusivity for T & S
306    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
307    o useMNC moved from data.mnc to data.pkg
308    
309    checkpoint55g_post
310    o Renaming carbon AD experiments to comply with testreport conventions
311    o Updating adjoint of Held-Suarez hs94.1x64x5
312    o Fixing directives for non-ECCO forward_step, after ECCO directives
313      have been fixed to avoid recomp. of do_oceanic_phys
314      Works well for global_ocean.90x40x15,
315      but recomp. issue remains for carbon
316    o Updating adjoint output for natl_box_adjoint after
317      pkg/ecco has been modified (see taga c55d_post)
318    
319    checkpoint55f_post
320    o rename to timeave_init_fixed
321    
322    checkpoint55e_post
323    o some delicate re-shuffle of store directives to avoid one
324      extra call of do_oceanic_physics
325      affects ecco_the_main_loop.F, do_oceanic_physics.F
326      checkpoint_lev1_directives.h
327    o NB: this may break global_ocean adjoint temporarily,
328      but it is clear how to fix it. Will do later, need this now.
329    
330    checkpoint55d_post
331    o ECCO specific cost function terms (up-to-date with 1x1 runs)
332    o ecco_cost_weights is modified to 1x1 runs
333    o modifs to allow observations to be read in as
334      single file or yearly files
335    o enable to read exf forcing fields as either
336      single file or yearly files (flag useExfYearlyFields)
337    checkpoint55d_pre
338    
339    o switch between 2-level and 3-level checkpointing
340    o add ability of MNC to write local and "partial" (eg. 2D slices where
341      the full 3D field is never actually stored) arrays to NetCDF files
342      with the correct (that is, the complete multi-dimensional) set of
343      array indicies
344      - used in mom_vecinv() to write the diagFreq output
345      - tested (demonstrated) in verification/aim.5l_cs
346    o further mnc-ification
347      - add verification/lab_sea to the list with mnc setups
348      - fix undefined mnc v-names in cd_code
349      - add kpp to mnc output (both snapshot and timeave)
350    o non-hydrostatic code
351      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
352        in calc_gw.F
353      - defaults to viscAh
354      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
355        friction or Leith) in non-hydrostatic mode, as long as there is
356        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
357    o pkg/cost
358      extend simple cost functions to treat time mean quantities
359      (T,U,V) via cost_accumulate_state from cost_tile
360    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
361        be 2 times larger than the minimum size the advection scheme requires.
362        now get a perfect conservation of salt in advect_cs test-exp (updated)
363    o GGL90 (Gaspar's TKE mixed layer)
364      - add horizontal diffusion of TKE, requires exchanges in
365        do_fields_blocking_exchanges, horizontal diffusivity is zero by
366        default. In OPA there is no horizontal diffusion of TKE but the
367        mixing coefficients are computed from a horizontal average of TKE of
368        6 points or so. I think that diffusion has a little more physical
369        justification.
370      - clean up ggl90_calc in the hope of reducing memory usage (this hope
371        was in vain)
372      - mask tke-variable in ggl90_init
373    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
374    o fix biharmonic diffusion on CS-grid.
375    o more obcs stuff
376      - added obcs_external_fields_load as an alternative to the EXF-pkg option
377        for reading boundary values. This routine is called from
378        obcs_prescribe_read
379      - updated obcs_check
380      - changed sponge layer relaxation parameter units for days to seconds
381      - turned off sponge layer by default
382      - changed argument list of OBCS_CALC to myTime+deltaTclock
383      - fixed about 35 bugs in obcs_external_fields_load
384    
385    checkpoint55c_post
386    o obcs stuff
387      - new runtime flags useOBCSprescribe, useOBCSbalance
388      - re-arranged obcs_calc
389      - moved exf_getobcs to obcs_prescibe_read
390        obcs_prescibe_read is called after ORLANSKI stuff
391        and independent of it (executable can contain all).
392      - updated obcs_check
393      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
394        These may be necessary only if tangential velocities are
395        prescribed at OB, not sure, needs testing.
396    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
397      which simplifies the calls and passes the ifc check-bounds test
398    
399    checkpoint55b_post
400    o add a 2D scalar, Z location, exchange_2 routine.
401    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
402      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
403      affects advect_cs results (for the wrong reason): update output.txt
404    o use a more standard discretization for biharmonic viscosity ;
405     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
406      affects results of dome set-up: update output.txt
407    o fix gad_advection.F (CubedSphere part), back to version 1.23
408    o fix bug in mom_vi_del2uv.F (CubedSphere part).
409    
410    checkpoint55a_post
411    o merged code to
412      * prescribe/read time-dependent open boundaries
413        (works in conjunction with exf, cal)
414      * sponge layer code for open boundaries
415      * each boundary N/S/E/W now has its own CPP option
416        (healthy for the adjoint)
417    
418    checkpoint55
419    o up-to-date adjoint of previous breaks
420      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
421      - global_ocean_ebm: adjoint still needs fix (TLM ok)
422      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
423      - carbon: * remove tr1-related adjoint verification
424                * add ptracer as control variable
425    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
426      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
427    
428    checkpoint54f_post
429    o in verification/carbin/ remove experiment related to
430      ALLOW_PASSIVE_TRACER (array tr1 etc)
431      code_ad/ input_ad/ results_ad
432    
433    o add two new packages
434      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
435        + subject to optimization (memory)
436      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
437        + subject to reordering (many GOTOs in the original code)
438        + so far opps is called for every (i,j) point, and then operates in
439          the vertical; one may want to reorder the scheme in order operate in
440          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
441          fields)
442    o overhaul of IO so that we now have flags for MDSIO and/or MNC
443      - all verification tests compile and run with linux_ia32_g77
444      - defaults are compatible with current input files--nothing
445        should change if you were not previously using MNC
446      - MNC output has been added in numerous places (eg. timeave)
447        but there are still a few writes not yet do-able with MNC
448        (this is in progress)
449      - flags now allow for either/or/both use of MDSIO and MNC and
450        documentation will soon follow
451      - numerous small formatting cleanups for ProTeX
452    o add version info (via BUILD_INFO.h) to MNC and stdout
453    
454    checkpoint54e_post
455    o add two new packages
456      - pp81 (Packanowski and Philander, 1981), Richardson number and
457        stratification dependent mixing
458      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
459      - these scheme operate in a similar manner as KPP (without ghat, of
460        course), however there is only one diffusivity that is used for both
461        temperature and salinity (and passive tracers)ç
462    o add offline package
463    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
464      provided by Stephanie Dutkiewicz
465    o genmake2: add ability to search for C compilers and cleanup test output
466      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
467    
468    checkpoint54d_post
469    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
470    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
471      leading to additional shift by 5 days each year of integration
472       (i.e. leading to considerable offset over the years)
473    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
474    o start with no AB and no initial filtering (staggerTimeStep):
475      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
476    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
477      (external loading & cpl import/export stay in forward_step.F)
478    o update coupling interface to work with new staggerTimeStep
479    o change MDSIO ptracers_pickup.
480    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
481    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
482    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
483    
484    checkpoint54c_post
485    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
486      this affects (truncation error) output.txt of test-exp:
487       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
488    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
489    o change Qnet to always be the net heat flux, (+upward).
490      affects (truncation error) output of natl_box exp.: updated
491    o define the max number of passive tracers in PTRACERS_SIZE.h
492    o start to test mnc routinely in exp0
493    o add sea-ice loading (sIceLoad) as a new forcing field.
494    
495    checkpoint54b_post
496    o add testreport "-j JOBS" option for parallel builds (tested and pretty
497       impressive on Altix and Opteron systems)
498    o diagnostics can now write NetCDF files through the mnc package
499    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
500    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
501    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
502      affects (truncation error) output of lab_sea & natl_box exp.: updated
503    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
504    
505  checkpoint54a_post  checkpoint54a_post
506  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
507  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
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