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Revision 1.486 - (hide annotations) (download)
Sun May 15 04:00:56 2005 UTC (19 years ago) by jmc
Branch: MAIN
Changes since 1.485: +4 -1 lines
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
  and rename it: DIFFERENT_MULTIPLE

1 jmc 1.486 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.485 2005/05/14 23:44:59 jmc Exp $
2 jmc 1.475 $Name: $
3 cnh 1.1
4     Notes on tags used in MITgcmUV
5     ==============================
6 edhill 1.458
7 jmc 1.486 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
8     and rename it: DIFFERENT_MULTIPLE
9    
10 jmc 1.485 checkpoint57h_post
11     o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
12 jmc 1.484 o pkg/diagnostics: change output frequency, now in seconds (instead
13     of Nb of iterations). This requires to change data.diagnostics.
14 jmc 1.483 checkpoint57h_pre
15    
16 edhill 1.482 o in mnc, let the user create the output dir if both mnc_outdir_date
17     and mnc_outdir_num are false
18 edhill 1.481 o add fflags() to pkg/diagnostics which allows one to specify, on a
19     per-file basis, the file precision [default behavior is unchanged]
20 dimitri 1.480 o added diagnostics to pkg/kpp, including computation of mixed layer
21     depth based on a temperature/density criterion
22     o updated verification/natl_box to test the new pkg/kpp diagnostics
23 jmc 1.479 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
24 jmc 1.478 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
25 edhill 1.477 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
26     not mnc -- this mistake was found by JMC and is now corrected
27    
28 jmc 1.476 checkpoint57g_post
29     o add Adams-Bashforth 3rd Order time stepping:
30     - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
31     - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
32 jmc 1.475 checkpoint57g_pre
33    
34 heimbach 1.472 o make lambda[Theta,Salt]ClimRelax spatially varying
35     (default remains spatially uniform constant based on tau)
36 heimbach 1.473 o added new control variables
37     * init. uVel, vVel, etanN
38     * lambda[Theta,Salt]ClimRelax
39     o separate masks used for ctrl_pack/unpack 'from write_grid' output
40     (suggested by G. Forget)
41 heimbach 1.472
42 jmc 1.471 checkpoint57f_post
43     o add parameter "baseTime" = model base time = time at iteration zero
44     new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
45     account for baseTime shift
46     o move Coriolis arrays from PARAMS.h to GRID.h
47 jmc 1.470 checkpoint57f_pre
48    
49 edhill 1.468 o mnc-ifying the seaice package
50 adcroft 1.467 o introduced an alternative length scale calculation for use in the limiting
51     maximum viscosity (off by default, see mom_vi_hdissip.F for details)
52 heimbach 1.466 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
53 baylor 1.465 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
54     as well as grad(vort3). Made it compatible with both approximate form
55     for the cubed sphere and full form of these gradients. Added flag
56     useFullLeith to select between approximate and full form.
57 jmc 1.464 o add "d0" in getcon.F to reduce differences between compilers/platforms
58     update output.txt of exp. fizhi-gridalt-hs
59 jmc 1.463 o change port_rand funtion to allow to set the seed.
60 edhill 1.462 o fix obscure MNC bug involving conversion between reals and integers
61     - it caused no problems with certain (eg. gcc, ifc) compilers but the
62     new version is now more standards-compliant
63 heimbach 1.469 o adjoint-related modifications
64     * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
65     * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
66     * mom_vi_hdissip: to be able to use Leith scheme in adjoint
67 edhill 1.462
68 heimbach 1.461 checkpoint57e_post
69     o Adding eddy stress controls a la Ferreira et al.
70 jmc 1.474 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
71 heimbach 1.460
72 jmc 1.459 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
73     update output.txt of exp. fizhi-gridalt-hs
74 edhill 1.458 o add more "Z" dimensions and associated coordinate vars to MNC
75 dimitri 1.457 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
76 dimitri 1.456 o parameter calendarDumps: when set, approximate months (30-31 days) and years
77     (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
78     KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
79     months and years. Requires pkg/cal.
80 edhill 1.455 o diagnostics: add pickup functionality
81     - off by default for backwards compatibility
82     - current version only uses MDSIO -- MNC will be added
83 jmc 1.454 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
84 jmc 1.452 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
85    
86 jmc 1.451 checkpoint57d_post
87     o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
88 edhill 1.450 o modify verification/ideal_2D_oce so that it tests the creation of mnc
89     output from the diagnostics package
90 jmc 1.449 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
91 edhill 1.448 o make genmake2 more portable by using ".$FS" instead of ".f" for more
92     of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
93 edhill 1.447 o add coordinate variables to the MNC output from the diagnostics package
94 jmc 1.446 o change MNC-flags default value: true when useMNC=TRUE
95 edhill 1.444 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
96     the ability (off by default) to read the grid information using MNC
97 jmc 1.445 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
98 jmc 1.443 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
99 jmc 1.442 o do snap-shot diagnostics at the middle of the time-interval (instead of
100     at the end).
101 jmc 1.441 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
102     new test for AIM with thSIce + slab-ocean
103 jmc 1.440 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
104 jmc 1.439 o move state variable diagnostics to the beginning of the time step ;
105     (note: still needs some work specially for snap-shot diagnostics)
106     duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
107    
108 jmc 1.438 checkpoint57c_post
109     o Change testing option (-ieee) to get closer agreement between g77 & ifort
110     o generate new output.txt files on faulks with g77 & the new -ieee option
111 jmc 1.437 checkpoint57c_pre
112    
113     o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
114 jmc 1.436 update output.txt of exp. global_ocean.90x40x15
115 jmc 1.435 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
116     results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
117 jmc 1.432 o add saltFlux(+File) forcing capability with periodicExternalForcing
118 jmc 1.431 o allow to use pkg diagnostics for GM-Redi & ThSIce output
119     o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
120 edhill 1.430 o improvements for the MNC output from DIAGNOSTICS:
121     - correct handling of the unlimitied dimension
122     - all dims now have associated coordinate variables
123     - variables located at U, V, and Corner ("Z") points are now written
124     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
125     *all* data points are output
126 dimitri 1.429 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
127 dimitri 1.428 o added pkg/seaice/seaice_monitor.F
128 dimitri 1.427 o mdsio_readfield.F can now read files visible only to master MPI process.
129 dimitri 1.426 o pkg/seaice: some test code for ice-modified ocean stress
130 dimitri 1.425 o exf_getffields interpolation defaults to bilinear for all scalar forcing
131     fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
132     spurious negative numbers for precipitation and humidity. Will cause
133     some small numerical differences for integrations using pkg/exf/exf_interp.F.
134 heimbach 1.434 o pkg/ctrl/
135     * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
136     May be enabled via doPackDiag
137     * introduce z-scaling of
138     + gradient (doZscalePack) and
139     + control (doZscaleUnpack)
140     o pkg/mdsio/
141     * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
142     * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
143 dimitri 1.425
144 jmc 1.424 checkpoint57b_post
145     o simplify options in diagnostics_fill arguments (remove weird combinations)
146 edhill 1.423 o fix MNC coordinate variables so that they now contain per-face index
147     values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
148     general, EXCH2 grids are only aligned to a "local" coordinate system
149 jmc 1.422 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
150     o Implement instantaneous output within pkg diagnostics:
151     setting a negative frequency in data.diagnostics produces
152     "snap-shot" output (as opposed to time-average if freq > 0)
153 jmc 1.421 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
154     NOTE: change ptracer diagnostics name: use 2 characters to work with
155     more than 9 tracers. Add also diagnostics of advect & diffus flux.
156 edhill 1.420 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
157     becomes the coordinate variable for the 'T' dimension
158 edhill 1.419 o add CF-style coordinate variables to MNC
159     - just a first cut: numbers are meaningless on the cubesphere and
160     missing along the T axis but otherwise it works!
161 dimitri 1.418 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
162 jmc 1.417 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
163 jmc 1.416 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
164     this is based directly on what the model compute, so that the content of
165     each diagnostics might be affected by switching options (e.g., implicitDiffusion)
166     o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
167 mlosch 1.415 o clean up build options files for SunOS, in particular
168     - remove -traditional from xmakedepend
169     - change -xarch=v9 to -xarch=native for f77
170     - restore use of make (not gmake)
171     - add CC=gcc if using g77
172 edhill 1.413 o changes per discussion of AM, JMC, & EH3 today:
173     - move redundant "grid" variables out of "state" -- in preparation of
174     creating proper CF-style coordinate variables and in recognition
175     that any/all grid variables can be easily copied (eg. w/NCO) from
176     the grid files into any of the other NetCDF files
177     - *always* output grid variables with MDSIO (this will eventually be
178     changed)
179     - output MNC grid file if useMNC is true
180 edhill 1.412 o every instance of _END_MASTER() has been found and replaced with
181     _END_MASTER( myThid ) in order to satisfy certain picky Sun
182     preprocessors
183 jmc 1.411 o re-arrange diagnostics pkg initialisation:
184     - allow each package to extend the available diagnostics list
185     - add some checking and fix small problems (multi-threaded, ...)
186     - new S/R diagnostics_fill (replace fill_diagnostics):
187     look through the short list of active diag. (instead of the long list)
188     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
189 edhill 1.381
190 heimbach 1.410 checkpoint57a_post
191     o this set of changes restores TAMC compatibility
192     tested for global_ocean.90x40x15 adjoint on trough
193     (what a pain)
194    
195 heimbach 1.409 checkpoint57a_pre
196     o some modifs in tools/build_options for sunos
197     o call ctrl_pack for ctrl at end for optimcycle=0
198    
199 jmc 1.408 checkpoint57
200 mlosch 1.406 o add horizontal bi-harmonic viscosity for vertical velocity
201     - new parameter viscA4W (defaults to viscA4)
202     - affects only non-hydrostatic code
203     - to be done: no-slip lateral boundary conditions
204 dimitri 1.405 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
205 jmc 1.404 o implement Implicit Vertical advection for pTracers
206 jmc 1.401 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
207 jmc 1.402 (implemented also for implicit vertical diffusion & advection)
208 mlosch 1.400 o OBCS: extend application of tracer open boundary conditions
209     to a strip beyond the boundary of width Olx/Oly
210 heimbach 1.403 o add call monitor to TAF set of required calls (flow directives)
211     and include in natl_box_adjoint
212     o untangle a few ifdefs related to cost, ctrl, autodiff
213     untangel a few ALLOW_ECCO_OPTIMIZATION
214 heimbach 1.407 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
215     (theta2, salt2 in ecco_cost_weights)
216 mlosch 1.400
217 mlosch 1.399 checkpoint56c_post
218     o OBCS as control variables
219     - update ctrl_ad_diff.list, obcs_ad_diff.list
220     - remove balance of obcs controls from default
221     - fix index bug nobcs in ctrl_init
222     - fix dummy fields filen in ctrl_pack
223     - add dummy weights for obcs
224     o lsopt: comment out fort.94 output
225     o optim:
226     - remove unnecessary header files
227     - adjusted namelists
228     - add xerbla.F to Makefile
229     o exf:
230     - multiple modifications of exf_check_range
231     - unit change in exf_init_runoff from [m/year] to [m/s]
232     o mdsio:
233     - i/o-vector change debugLevel from debLevA to debLevB
234    
235 mlosch 1.398 checkpoint56b_post
236 mlosch 1.397 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
237     is called from DO_THE_MODEL_IO
238     - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
239     - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
240     - clean up PTRACERS_WRITE_TIMEAVE a little
241 mlosch 1.396 o add another verification experiment that tests both the cfc-pkg and
242     the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
243     reactive tendencies treated inline with regular timestepping
244 mlosch 1.395 o testreport previously did a lousy job of comparing small numbers, so
245     we (Ed and Martin) changed the way the cut-off of 1.e-12 is
246     implemented in the little c-progam tmp_cmpnum.c which is embedded in
247     testreport.
248     o ptracers_monitor: bug fix for MPI
249    
250 mlosch 1.394 checkpoint56a_post
251     o GCHEM: finish reorganizating the package
252     - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
253     (introduces another 3D-array for each passive tracer, but only if
254     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
255     gchemTendency is not needed because the timestep is done separately)
256     - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
257     - GCHEM is now---more or less cleanly---separate from PTRACERS
258     - to bo done: handling of surfaceForcingPtr that is needed for KPP not
259     so clear to me how that should be done in a general way.
260     o CFC: improve formatting of output in CFC_ATMOS
261     o PTRACERS:
262     - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
263     that ALL experiments with ptracers enable can be checked. This makes
264     GCHEM_MONITOR obsolete.
265     - include a runtime parameter PTRACERS_monitorFreq that defaults to
266     monitorFreq
267     - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
268 edhill 1.393 o add PTRACERS (PTR0[1-5]) to testreport output
269 heimbach 1.391 o exf_check_range:
270     * default changed to .TRUE.
271     * will check values for niter0 if debLevA, every timestep if debLevB
272     * STOP in exf_check_range if 'out of range'
273     * range chosen generous to allow for potential extema
274     TBD: a version with stricter range
275     permitted range would be runtime parameters
276 jmc 1.390 o GMredi:
277     - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
278     - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
279     - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
280 mlosch 1.388 o GCHEM:
281     - move call to GCHEM_FORCING_SEP, so that it is now called before
282     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
283     - introduced a useGCHEM runtime flag and applied it everywhere.
284 mlosch 1.392 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
285     this flag is now only visible within GCHEM-pkg routines.
286     - moved gchem_forcing_int temporarily into ptracers_forcing, this will
287     be replaced by a 3D array that is computed before thermodynamics; for
288     this, the tracer ID iTracer had to be included into the parameter list
289     of ptracers_forcing
290 mlosch 1.394 - set up forward_step to call gchem_forcing, that will replace
291 mlosch 1.392 gchem_forcing_int in ptracers_forcing
292     - cleaning up
293 jmc 1.389 o small cleaning of exch2: remove files that are also in eesupp/src
294 mlosch 1.387
295 heimbach 1.386 checkpoint56
296 jmc 1.385 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
297 edhill 1.384 o mnc: cleanup "full" files--fixes out-of-memory problem
298 heimbach 1.386 o ECCO-GODAE
299     * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
300     * fully merged and updated from SIO code
301     windstress sign change affects
302     - exf_inscal_[u/v]stress
303     - sign of xx_tau[u/v] adjustments
304     - signs in cost_scat
305     * ctrl_get_gen: avoid update of tau[u/v] for first few days
306     * natl_box_adjoint updated and compressed
307     * 2-level checkpoint switch added
308     (tested in EXP. 1 of natl_box_adjoint)
309     * new switch doInitXX to avoid init. of xx_... in optimcycle=0
310     o SVD
311     * first complete, non-hacked version for SVD calculations
312     * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
313     performed via direct access files admtlm_vector.it????
314     (via ctrl_[un]pack)
315     * optimcycle is used for ARPACK iteration counter
316     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
317     * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
318     and add linear transforms where necessary
319     * controls are initial/final SST, SSS (can be extended; need to check
320     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
321     o mdsio: filename info to both stderr, stdout
322     o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
323     from sign change
324 edhill 1.384
325 jmc 1.383 checkpoint55j_post
326 jmc 1.382 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
327     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
328 edhill 1.381 o add consistent build directories and .cvsignore files to verification
329 dimitri 1.380 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
330 edhill 1.379 o make all subroutines 30 or less characters in length for certain older
331     compilers to work (a thorough search only turns up two routines in
332     pkg/ptracers)
333 jmc 1.378 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
334     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
335    
336 jmc 1.377 checkpoint55i_post
337 jmc 1.376 o change arrays for total vertical diffusivity (2.D if explicit,
338     3.D if implicit) ; each ptracer uses its own background value.
339 edhill 1.375 o added mnc/NetCDF output capability to ocn_compon_interf
340     - added bits to verification/cpl_aim+ocn so that it can run on
341     ITRDA and other clusters without the mpirun "-wd" option
342 afe 1.374 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
343     configuration
344 edhill 1.373 o give MNC the ability to create additional files rather than
345     exceeding a specified file size limit "MNC_MAX_FILESIZE"
346     - the default is just less than 2GB which is a practical limit
347     on many systems
348 jmc 1.372 o Compute the non-local term using either KPP vertical diffusivity (=default)
349     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
350 jmc 1.349
351 jmc 1.371 checkpoint55h_post
352     o add verification test "vermix"
353 edhill 1.370 o remove all the *_ioinc flags and replace with the single global
354     outputTypesInclusive flag
355 jmc 1.369 o allow to set a vertical profile of vertical diffusivity for T & S
356 jmc 1.371 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
357     o useMNC moved from data.mnc to data.pkg
358 jmc 1.369
359 heimbach 1.368 checkpoint55g_post
360     o Renaming carbon AD experiments to comply with testreport conventions
361     o Updating adjoint of Held-Suarez hs94.1x64x5
362     o Fixing directives for non-ECCO forward_step, after ECCO directives
363     have been fixed to avoid recomp. of do_oceanic_phys
364     Works well for global_ocean.90x40x15,
365     but recomp. issue remains for carbon
366     o Updating adjoint output for natl_box_adjoint after
367     pkg/ecco has been modified (see taga c55d_post)
368    
369 edhill 1.367 checkpoint55f_post
370     o rename to timeave_init_fixed
371    
372 heimbach 1.366 checkpoint55e_post
373     o some delicate re-shuffle of store directives to avoid one
374     extra call of do_oceanic_physics
375     affects ecco_the_main_loop.F, do_oceanic_physics.F
376     checkpoint_lev1_directives.h
377     o NB: this may break global_ocean adjoint temporarily,
378     but it is clear how to fix it. Will do later, need this now.
379    
380 heimbach 1.365 checkpoint55d_post
381     o ECCO specific cost function terms (up-to-date with 1x1 runs)
382     o ecco_cost_weights is modified to 1x1 runs
383     o modifs to allow observations to be read in as
384     single file or yearly files
385     o enable to read exf forcing fields as either
386     single file or yearly files (flag useExfYearlyFields)
387     checkpoint55d_pre
388    
389     o switch between 2-level and 3-level checkpointing
390 edhill 1.364 o add ability of MNC to write local and "partial" (eg. 2D slices where
391     the full 3D field is never actually stored) arrays to NetCDF files
392     with the correct (that is, the complete multi-dimensional) set of
393     array indicies
394     - used in mom_vecinv() to write the diagFreq output
395     - tested (demonstrated) in verification/aim.5l_cs
396 edhill 1.363 o further mnc-ification
397     - add verification/lab_sea to the list with mnc setups
398     - fix undefined mnc v-names in cd_code
399     - add kpp to mnc output (both snapshot and timeave)
400 mlosch 1.362 o non-hydrostatic code
401     - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
402     in calc_gw.F
403     - defaults to viscAh
404     - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
405     friction or Leith) in non-hydrostatic mode, as long as there is
406     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
407 heimbach 1.360 o pkg/cost
408     extend simple cost functions to treat time mean quantities
409     (T,U,V) via cost_accumulate_state from cost_tile
410 jmc 1.358 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
411     be 2 times larger than the minimum size the advection scheme requires.
412     now get a perfect conservation of salt in advect_cs test-exp (updated)
413 mlosch 1.356 o GGL90 (Gaspar's TKE mixed layer)
414     - add horizontal diffusion of TKE, requires exchanges in
415     do_fields_blocking_exchanges, horizontal diffusivity is zero by
416     default. In OPA there is no horizontal diffusion of TKE but the
417     mixing coefficients are computed from a horizontal average of TKE of
418     6 points or so. I think that diffusion has a little more physical
419     justification.
420     - clean up ggl90_calc in the hope of reducing memory usage (this hope
421     was in vain)
422     - mask tke-variable in ggl90_init
423 jmc 1.355 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
424     o fix biharmonic diffusion on CS-grid.
425 mlosch 1.354 o more obcs stuff
426     - added obcs_external_fields_load as an alternative to the EXF-pkg option
427     for reading boundary values. This routine is called from
428     obcs_prescribe_read
429     - updated obcs_check
430 mlosch 1.357 - changed sponge layer relaxation parameter units for days to seconds
431     - turned off sponge layer by default
432 heimbach 1.359 - changed argument list of OBCS_CALC to myTime+deltaTclock
433 mlosch 1.361 - fixed about 35 bugs in obcs_external_fields_load
434 mlosch 1.354
435 heimbach 1.353 checkpoint55c_post
436 heimbach 1.352 o obcs stuff
437     - new runtime flags useOBCSprescribe, useOBCSbalance
438     - re-arranged obcs_calc
439     - moved exf_getobcs to obcs_prescibe_read
440     obcs_prescibe_read is called after ORLANSKI stuff
441     and independent of it (executable can contain all).
442     - updated obcs_check
443 heimbach 1.353 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
444     These may be necessary only if tangential velocities are
445     prescribed at OB, not sure, needs testing.
446 edhill 1.351 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
447     which simplifies the calls and passes the ifc check-bounds test
448    
449 jmc 1.350 checkpoint55b_post
450     o add a 2D scalar, Z location, exchange_2 routine.
451 jmc 1.349 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
452     to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
453     affects advect_cs results (for the wrong reason): update output.txt
454 jmc 1.348 o use a more standard discretization for biharmonic viscosity ;
455     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
456     affects results of dome set-up: update output.txt
457     o fix gad_advection.F (CubedSphere part), back to version 1.23
458     o fix bug in mom_vi_del2uv.F (CubedSphere part).
459 mlosch 1.341
460 heimbach 1.347 checkpoint55a_post
461     o merged code to
462     * prescribe/read time-dependent open boundaries
463     (works in conjunction with exf, cal)
464     * sponge layer code for open boundaries
465     * each boundary N/S/E/W now has its own CPP option
466     (healthy for the adjoint)
467    
468 heimbach 1.346 checkpoint55
469     o up-to-date adjoint of previous breaks
470     - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
471     - global_ocean_ebm: adjoint still needs fix (TLM ok)
472     - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
473     - carbon: * remove tr1-related adjoint verification
474     * add ptracer as control variable
475     o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
476     (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
477    
478 heimbach 1.345 checkpoint54f_post
479     o in verification/carbin/ remove experiment related to
480     ALLOW_PASSIVE_TRACER (array tr1 etc)
481     code_ad/ input_ad/ results_ad
482    
483 mlosch 1.344 o add two new packages
484     - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
485     + subject to optimization (memory)
486     - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
487     + subject to reordering (many GOTOs in the original code)
488     + so far opps is called for every (i,j) point, and then operates in
489     the vertical; one may want to reorder the scheme in order operate in
490     horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
491     fields)
492 edhill 1.343 o overhaul of IO so that we now have flags for MDSIO and/or MNC
493     - all verification tests compile and run with linux_ia32_g77
494     - defaults are compatible with current input files--nothing
495     should change if you were not previously using MNC
496     - MNC output has been added in numerous places (eg. timeave)
497     but there are still a few writes not yet do-able with MNC
498     (this is in progress)
499     - flags now allow for either/or/both use of MDSIO and MNC and
500     documentation will soon follow
501     - numerous small formatting cleanups for ProTeX
502 edhill 1.342 o add version info (via BUILD_INFO.h) to MNC and stdout
503    
504 mlosch 1.341 checkpoint54e_post
505     o add two new packages
506     - pp81 (Packanowski and Philander, 1981), Richardson number and
507     stratification dependent mixing
508     - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
509     - these scheme operate in a similar manner as KPP (without ghat, of
510     course), however there is only one diffusivity that is used for both
511     temperature and salinity (and passive tracers)ç
512 stephd 1.340 o add offline package
513 edhill 1.339 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
514     provided by Stephanie Dutkiewicz
515 edhill 1.338 o genmake2: add ability to search for C compilers and cleanup test output
516     - fixes recent SX-6 problems and should help with others (eg. HP-UX)
517    
518 jmc 1.337 checkpoint54d_post
519 adcroft 1.336 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
520 jmc 1.337 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
521     leading to additional shift by 5 days each year of integration
522     (i.e. leading to considerable offset over the years)
523 jmc 1.335 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
524     o start with no AB and no initial filtering (staggerTimeStep):
525     change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
526     o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
527     (external loading & cpl import/export stay in forward_step.F)
528     o update coupling interface to work with new staggerTimeStep
529     o change MDSIO ptracers_pickup.
530 jmc 1.334 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
531 edhill 1.333 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
532 jmc 1.334 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
533 edhill 1.333
534 jmc 1.332 checkpoint54c_post
535 jmc 1.331 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
536     this affects (truncation error) output.txt of test-exp:
537     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
538     o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
539 jmc 1.330 o change Qnet to always be the net heat flux, (+upward).
540     affects (truncation error) output of natl_box exp.: updated
541 jmc 1.329 o define the max number of passive tracers in PTRACERS_SIZE.h
542     o start to test mnc routinely in exp0
543     o add sea-ice loading (sIceLoad) as a new forcing field.
544    
545 jmc 1.328 checkpoint54b_post
546 edhill 1.327 o add testreport "-j JOBS" option for parallel builds (tested and pretty
547     impressive on Altix and Opteron systems)
548 edhill 1.326 o diagnostics can now write NetCDF files through the mnc package
549 jmc 1.325 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
550 jmc 1.324 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
551 jmc 1.323 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
552     affects (truncation error) output of lab_sea & natl_box exp.: updated
553     o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
554    
555 jmc 1.322 checkpoint54a_post
556     o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
557     o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
558     o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
559     o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
560     + internal_wave (shift in writing cg2d_ini_res)
561 jmc 1.321 checkpoint54a_pre
562    
563 dimitri 1.320 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
564     - modified verification/lab_sea and natl_box_adjoint accordingly
565    
566 heimbach 1.319 checkpoint54
567 heimbach 1.318 checkpoint53g_post
568 jmc 1.317 o prepare splitting of thermodynamics: store convect.counter in common block
569 jmc 1.316 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
570     output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
571 dimitri 1.315 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
572 jmc 1.314 o new parameter "nShapS": allow to treat differently S from T (nShapT)
573     o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
574 heimbach 1.318 o restore adjointability
575 jmc 1.314
576 jmc 1.313 checkpoint53f_post
577     o modifications that affect AIM experiment results (update output.txt):
578     - no advection of S at top interface Nr (pkg/generic_advdiff)
579     - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
580 jmc 1.312 o AIM pkg:
581     - include stability function into surf.Flux derivative relative to Tsurf
582     - calculate clear-sky radiation & surface temp. change (for diagnostics)
583 jmc 1.313
584 afe 1.311 checkpoint53e_post
585     o merged cylindrical coord configuration
586     o added rotating_tank experiment
587 afe 1.310 checkpoint53e_pre
588    
589 jmc 1.309 checkpoint53d_post
590 jmc 1.308 o faulks upgraded: re-generate output.txt that have changed:
591     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
592 adcroft 1.307 o Added Bryan and Lewis, 1979, vertical diffusivity profile
593 jmc 1.306 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
594 adcroft 1.305 o added Sadourny discretization of Coriolis
595     - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
596     - re-enabled use of omega3 (useAbsVorticity)
597 adcroft 1.304 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
598 jmc 1.309 vector-invariant equations
599 adcroft 1.304 - note: does *NOT* yet use same variable visc. for no-slip BC's.
600 mlosch 1.303 o recoded the lateral boundary conditions for non-hydrostatic w, this time
601     hopefully without new bugs
602     - still to do: biharmonic friction for non-hydrostatic w
603 adcroft 1.302 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
604     o regenerated output for global_ocean_ebm (using -ieee)
605 adcroft 1.301 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
606     of mom_common/
607     - simple re-arrangement of instructions within computing loop
608     checkpoint53d_pre
609 mlosch 1.297
610 heimbach 1.300 checkpoint53c_post
611 jmc 1.299 o new version of coupler for AIM+thSIce and Ocean models
612     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
613     - land: change Evaporation of snow
614     - aim with thSIce: fix bug in snow-precip.
615 mlosch 1.297 o changes to calc_gw.F
616     - bug fix for w^2 term near the bottom boundary
617     - (hopefully) improve the lateral slip boundary condtions for use with
618     partial/looped cells
619     - because the bug fix changes two verification experiments anyway (exp5
620     and plume on slope), change the lateral boundary condition from half slip
621     to the value of no_slip_sides
622 heimbach 1.298 o ebm package wasnt quite up to the parallel task. Fixed that.
623 heimbach 1.300 o Adjoint of EBM package + verification
624     * TLM OK
625     * ADM not sufficient accuracy yet (needs further testing)
626 heimbach 1.295
627 heimbach 1.296 checkpoint53b_post
628     o Commiting new energy balance model to repository
629     * package is pkg/ebm
630     * verif. is verification/global_ocean_ebm
631     * references are in ebm_driver.F
632     C * X. Wang, P. Stone and J. Marotzke, 1999:
633     C Global thermohaline circulation. Part I:
634     C Sensitivity to atmospheric moisture transport.
635     C J. Climate 12(1), 71-82
636     C * X. Wang, P. Stone and J. Marotzke, 1999:
637     C Global thermohaline circulation. Part II:
638     C Sensitivity with interactive transport.
639     C J. Climate 12(1), 83-91
640     C * M. Nakamura, P. Stone and J. Marotzke, 1994:
641     C Destabilization of the thermohaline circulation
642     C by atmospheric eddy transports.
643     C J. Climate 7(12), 1870-1882
644     o Will need long integration testing.
645 heimbach 1.295 checkpoint53b_pre
646 dimitri 1.292
647 adcroft 1.294 o created pkg/mom_common in preparation for variable viscosity code
648     o renamed and split ini_mnc_io
649 jmc 1.293 o pkg/land: only liquid water can diffuse or run-off
650     o AIM using land: soil wetness availability account for snow
651 dimitri 1.292 o added printMapIncludesZeros to EEPARMS namelist
652 heimbach 1.290
653     checkpoint53a_post
654     o restore TAMC compatiility for exf_constants.h
655     (no usage of _d in .h)
656     o Additional storing in KPP in an attempt to fix
657     TAMC problem with adjoint of KPP code.
658     (no success...)
659     Identical code works fine with TAF.
660 dimitri 1.291 o Fixed verification/natl_box_adjoint experiments.
661     Initial conditions for Experiments 4 and 5 are now
662     set to "SEAICE_initialHEFF=0", which is more reasonable,
663     and hence gives results closer to that of Experiment 2.
664     Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
665 cnh 1.289
666     checkpoint53
667     o stable checkpoint with up to date adjoint
668     TLM tests only run for 1st grdchk at the moment. Its unclear if
669     this is a code problem or a problem with resetting code for g_
670     variables that is being autogenerated wrong.
671     Otherwise:
672     o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
673     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
674     are both still in chaos following their security messes.
675 jmc 1.279
676 edhill 1.288 checkpoint52n_post
677     o various build (mostly genmake2) changes including:
678     - ability to build/run more easily within Cygwin and MacOS X
679     - more complicated Makefiles with a stronger dependence on Gnu Make
680 dimitri 1.285 o pkg/seaice modifications
681 dimitri 1.287 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
682     of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
683     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
684 dimitri 1.285 - changed proxy for geostrophic velocity and updated
685 dimitri 1.286 verification/lab_sea/results/* accordingly
686 dimitri 1.285 - removed ADI dynamic solver from pkg/seaice
687     - replaced all occurrences of 1/CSTICE or 1/CSUICE
688     they caused a segmentation fault under certain circumstances
689 mlosch 1.283 - removed unused field WATR
690 mlosch 1.282 o bug fix in exf-package:
691     - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
692     now reflect that.
693 mlosch 1.281 o small fixes in the cal-package:
694     - set reference date to first of January for the 'model'-calendar
695     - failing of cal_CheckDate in cal_FullDate now actually results in a
696     warning
697 mlosch 1.280 o small modifications in exf-package to increase flexibility:
698     - change climtempfreeze from a constant to a runtime parameter that
699     is specified in data.exf_clim (default = -1.9)
700     - introduce runtime parameter windstressmax (default = 2.0) that is
701     specified in data.exf
702 jmc 1.279 o fix in pkg/thsice:
703     - update Evap (Tsf changes) to be consistent with Latent heat flux
704     - maintain snow precipitation unchanged (even if Tsf >=0).
705     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
706 edhill 1.272
707 jmc 1.278 checkpoint52m_post
708 mlosch 1.277 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
709     this does not change any of the results, because myIter=0 in swfrac always
710     lead to jwtype=2 (the default anyway), but the call makes little sense
711     as a default
712 jmc 1.276 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
713 jmc 1.275 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
714     atmospheric model (AIM) to use it ; add a "slab ocean" component.
715     o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
716     o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
717 dimitri 1.274 o extending useSingleCpuIO option to work with new exch2 I/O format
718     - old-style, missing-tile I/O is still accessible by defining CPP
719     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
720 edhill 1.273 o monitor package can write to NetCDF files and/or STDOUT
721     o fix re-definition bug in MNC_GRID_INIT_ALL()
722 edhill 1.272 o doc/api_reference added
723     - a framework for building an API Reference Manual using all
724     the "protex" comments embedded in the code
725     - see pkg/generic_advdiff, pkg/mnc for examples
726 edhill 1.269 o MNC:
727     - make myThid the last argument for all subroutines
728     - new default for the grid files: NO halos
729 edhill 1.270 - add useMNC and other run-time flags
730     - separate per-file-group handling of the unlimited dimension
731     - early initialization of MNC w/ flags read at the eeboot stage
732     and lookup tables set in initialize_fixed
733     - write all MNC output to a freshly-created directory
734 jmc 1.268 o thermodynamics sea-ice (thsice) is now tested with testreport.
735     o test exp. advect_cs: use the standard cs32 grid ; update output.
736 heimbach 1.271 o Added functionality to grdchk:
737     pick global i,j,k position (or nearest wet) where to perform check.
738 jmc 1.266
739 jmc 1.267 checkpoint52l_post
740     o new land formulation:
741     a) use ground enthalpy as prognostic variable to ensure exact
742     energy conservation.
743     b) account for water temperature and for latent heat of freezing
744     in all processes (rain, run-off, ground storage)
745     c) compute surface and ground temperature implicitly.
746     o aim_v23 modification for new land model:
747     a) Treat separately land / ocean / sea-ice surface fluxes
748     to allow implicit computation of land & sea-ice surface temp.
749     b) add snow precipitation.
750 jmc 1.266 checkpoint52l_pre
751    
752 jmc 1.265 o fix problem (when 1 tile is empty) in min/max monitor.
753     o fix bug in timeAve (u,vZetatave in common block)
754 dimitri 1.264 o no restoring terms under ice for pkg/seaice
755 dimitri 1.263 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
756     o bug fix for pkg/seaice pickups
757 edhill 1.262 o change MNC call locations and add coordinate attributes
758 jmc 1.260 o mask vorticity at the corner ; affects global_ocean.cs output
759     o fix ini_curvilinear_grid ; test CS experiments with mpi
760 jmc 1.259 o aim.5l_cs: modify sea-ice fraction input file ; update output
761 heimbach 1.261 o exf: Adding simple range check routine for exf fields after read
762 adcroft 1.256
763 heimbach 1.257 checkpoint52k_post
764 adcroft 1.256 o removed top-level directory "diags"
765     - we migrated these functions to pkg/timeave a long time ago
766     o fixed bug introduced in pkg/monitor
767 heimbach 1.257 o accuracy ctrlprec = 32 insuffient for gradient checks using
768     averaged fields (I/O via cost_averages)
769     -> use ctrl.h in active_file*.F to control I/O precision.
770     o paramter list of CALL ADTHE_MAIN_LOOP
771     o added initial do_the_model_io to ecco
772     o set all ...Freq to zero after cost_final
773     taveFreq, dumpFreq, pChkptFreq
774 heimbach 1.258 o MAIN and ECCO differentiability restored
775 heimbach 1.255
776     checkpoint52j_post
777     o fix nchklev in tamc.h for global_ocean...
778     o Bringing flow and store directives up-to-date
779     o Really weird thing!
780     call do_the_model_io from the_main_loop with parameters
781     starttime, niter0, instead of mytime, myiter, screws up the adjoint:
782     TAF places a faulty re-call of initialise_varia
783     after cost_final call which should not be there!
784     checkpoint52j_pre
785 jmc 1.253
786 afe 1.254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
787     error messages
788 jmc 1.253 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
789 afe 1.252 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
790     debug output
791 afe 1.251 o modfied mdsio_writefield.F to handle non-global files under exch2
792 jmc 1.250 o update AIM Cubed-Sphere exp (aim.5l_cs):
793     use land, p*, and Franco.M forcing fields with fractional land-sea mask.
794     o update AIM Equatorial Channel exp:
795     use standard aim_v23 pkg and change the SST fields to be more realistic.
796 afe 1.248 o globalFile now works with exch2
797 afe 1.247 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
798 jmc 1.253 mon_vort3.F to make exch2 friendly with >1 tile per cube face
799 dimitri 1.249 o limit timeave output for hi-res integrations
800 adcroft 1.245
801     checkpoint52i_post
802     o removed CPP_EEOPTIONS.h from verification/*/code
803     o updated the tiling for global_ocean_pressure
804     checkpoint52i_pre
805 jmc 1.246
806     o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
807     the old pkg/aim).
808 afe 1.239
809 dimitri 1.244 checkpoint52h_pre
810 afe 1.243 o shortened offending lines in exch2_send_rx?.template
811 afe 1.242 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
812 edhill 1.240 o genmake2: add build & execute test for NetCDF code
813 afe 1.239 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
814     old grid files, moved CPP_EEMACROS.h to pkg/exch2
815 dimitri 1.238 o added useSingleCPUIO flag to monitor.F and mon_out.F
816 dimitri 1.241 o added temporary hack for sea-ice dynamics on the cube:
817     metric terms are ignored and it is assumed that
818     there is no sea-ice on cube faces 1, 2, 4, and 5.
819 dimitri 1.238
820     checkpoint52f_post
821 afe 1.236 o added exch2 cube routines to pkg/exch2
822     o modified hs94.cs-32x32x5 to use it
823     o added new grid files to hs94.cs-32x32x5
824 dimitri 1.238 checkpoint52f_pre
825 dimitri 1.228
826 jmc 1.235 checkpoint52e_post
827 jmc 1.234 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
828     for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
829 jmc 1.235 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
830     to work with implicit vertical advection and AB ;
831     o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
832     o update output (gad_calc_rhs.F changes affect truncation error) of exp:
833     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
834 jmc 1.233 checkpoint52e_pre
835    
836     o fix bug in impldiff when Nr=1 or Nr=2.
837 jmc 1.232 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
838     o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
839 jmc 1.229 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
840     ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
841 dimitri 1.228 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
842 dimitri 1.231 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
843     o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
844 jmc 1.220
845 jmc 1.226 checkpoint52d_post
846 adcroft 1.230 o re-tiled many expts to allow comparison in multi-processor mode
847     - updated output accordingly
848     - changed hs94.128x64x5 to use intial T from file rather than use the
849     random number generator
850 molod 1.227 o add infrastructure in model routines for fizhi and gridalt packages
851 jmc 1.220 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
852 dimitri 1.222 o changes to permit hi-res, cubed-sphere, configuration
853     - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
854     - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
855     - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
856     of surface winds for the cube
857     (A verification experiment, based on global_ocean.cs32x15, but with
858     pkg/seaice turned on and with on-the-fly interpolation from the NCEP
859     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
860     complete with example surface forcing files and matlab scripts to look
861     at the output and compare it with that of global_ocean.cs32x15.)
862 jmc 1.223 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
863     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
864     to conform to the common rule.
865 jmc 1.224 o check-in the first version of the coupler + interfaces for multi-components
866     set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
867     - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
868     - atmosphere: use pkg aim_v23 ; no sea-ice for now.
869     - ocean and atmos. share the same horizontal grid (no interpolation).
870     - exchanges between component and coupler is done in forward_step
871 jmc 1.225 o new verification experiment, cpl_aim+ocn:
872     coupled ocean - AIM atmosphere on cs32 grid.
873 jmc 1.217
874 dimitri 1.219 checkpoint52d_pre
875 jmc 1.217 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
876 jmc 1.218 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
877 heimbach 1.213
878 heimbach 1.216 checkpoint52c_post
879 heimbach 1.213 o Fixing OPTIONS files for use of exf:
880     - ALLOW_ECCO not needed
881     - ECCO_CPPOPTIONS.h should not be included from
882     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
883     as has been the case in the past
884     - All cal/exf related options are currently set in
885     single header file. Should remain so until we
886     agree on a consistent new policy.
887 heimbach 1.214 o Removed all CPP options for cal package.
888     cal has no more CPP options.
889 heimbach 1.215 o modified STOREs in GAD_ADVECTION
890     o corrected key comp. for passkey
891 heimbach 1.210
892 jmc 1.212 checkpoint52b_post
893     o new version: "thsice" of thermodynamic sea-ice pkg:
894     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
895     - modify fluxes but do not change theta directly;
896     - light cleaning of bulk_force pkg (still needed with thsice).
897     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
898     + output_thsice.txt to test thsice & bulk_force pkgs.
899     o put back grid & coriolis monitor output.
900 jmc 1.211 checkpoint52b_pre
901    
902     o call "do_the_model_io" at the beginning (=> dump initial state)
903     o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
904 heimbach 1.210 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
905     (need info on NUMBER_OF_PTRACERS)
906     o missing PTRACERS headers in some routines
907     o default tamc.h in pkg/autodiff supposed to crash
908     to ensure proper customization
909 dimitri 1.206
910 heimbach 1.209 checkpoint52a_post
911 jmc 1.208 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
912 dimitri 1.207 - moved surfaceTendencyTice from pkg/seaice to main code
913 jmc 1.208 - subroutine FREEZE_SURFACE now limits only surface temperature
914     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
915     => new output.txt for global_ocean.cs32x15 & global_with_exf
916     - keep the old version of FREEZE for backward compatibility;
917     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
918 heimbach 1.209 - corresponding modifs for TAF directives
919 dimitri 1.207 o added surface flux output variables to TIMEAVE_STATVARS
920     o time-averaged output for pkg/ptracers
921 heimbach 1.209 o fix problem with ECCO-related divided adjoint
922     snapshot file was missing some ad-variables,
923     but no warning issued by TAF
924 dimitri 1.206
925 dimitri 1.207 checkpoint52a_pre
926 dimitri 1.206 o some bug fixes for #undef REAL4_IS_SLOW
927 heimbach 1.205
928     checkpoint52 = ecco_c52_e35
929     o after testing adjoints of checkpoint51u_post
930 edhill 1.203
931 heimbach 1.204 checkpoint51u_post
932     o this is the post-merge tag of the ecco-branch
933     (needs another clean checkout and re-testing)
934     o various natl_box_adjoint configs and results
935     but no input fields
936     o obcs adjoint not yet merged!
937     o adding ECCO global 1x1 and 2x2 degree configs
938     o updated/extended some store directives for seaice
939     o pkg/ecco now containes ecco-specific part of cost function
940     o top level routines the_main_loop, forward_step
941     supersede those in model/src/
942     previous input data.cost now in data.ecco
943     (new namelist ecco_cost_nml)
944     o in ctrl/ cleaned some cross-dependencies and updated CPP options
945    
946     checkpoint51t_post
947     o this is the pre-merge tag of the ecco-branch
948    
949 edhill 1.203 checkpoint51s_post
950     o cleanup: removed various obsolete #define-s
951 heimbach 1.204 o pkg/grdchk
952     - renamed 'ph-grd 3' to 'grad-res'
953     - merged from ecco-branch
954     (remaining bug fixes for obcs gradient checks)
955     - additional high-precision output for testreport
956     (grep for 'precision_grdchk_result')
957 edhill 1.202
958     checkpoint51r_post
959     o cleaned up or removed CPP_OPTIONS.h files
960     o updated results for some of the tests to reflect the new
961     optfiles (-ieee: -O0 instead of -O3)
962 heimbach 1.201
963     checkpoint51q_post
964     o cd_code:
965     - moved cd_scheme.F -> cd_code_scheme.F
966     - separate read_checkpoint from cd_code_ini_vars.F
967     - separated cd_code part from write_checkpoint
968     - updated AD_SOURCE, generated .flow
969     - added CD_CODE_VARS.h to the_main_loop
970     - Moving cd_code specific store dir.s to pkg/cd_code
971     o ctrl package totally restructured
972     - pack/unpack now optional and decoupled from
973     xx_/adxx_ I/O
974     - ctrl_pack/unpack cleaned
975     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
976     - confined inclusion of AD_CONFIG.h to where necessary.
977     o genmake2: changed AD dependencies from SRCFILES to AD_FILES
978 edhill 1.198
979 edhill 1.200 checkpoint51p_post
980 edhill 1.198 o create initial cd_code package
981 edhill 1.199 - WARNING: the initialization of fields within packages
982     is broken because INI_FIELDS (where READ_CHECKPOINT is
983     called) is called *before* PACKAGES_INIT_VARIABLES.
984     This seems to be backwards since
985     1) its important to initially zero the entire field including
986     the "halo" region
987     2) zeroing needs to be done *before* reading pickup info
988     and the pickup call might or might not happen in any
989     particular run
990     - this needs an overhaul for R2
991 edhill 1.198 o cleanup verification/*/code/GMREDI_OPTIONS.h
992     o cleanup testreport
993 heimbach 1.196
994     checkpoint51o_post
995     o bringing AD-related verif's up to date with genmake2
996     - carbon/
997     - global_ocean.90x40x15/
998     - hs.94.1x64x5/
999     - (front_relax/ )
1000     o (more) consistent directory structure for AD-related verif.'s
1001     o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
1002     o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
1003     o bug fix in find_alpha.F for MDJWF:
1004     - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
1005     change rho -> rho-rhoConst
1006     - replace call find_rho to find_rhonum
1007     o initialisation of rFlx extended to full array (required by TAF)
1008     and shifted to thermodynamics
1009     o removed PTRACERS.h in ptracers routine
1010     o added surfacetendencyPtr to S/R parameter list pracers_forcing
1011     o Correcting initialisations for fVerU, fVerV.
1012     o helping TAF to recognize dependency on kUp for
1013     fVerU, fVerV
1014     o Replacing delZ by delR in pkg/ctrl/
1015     checkpoint51o_pre
1016 dimitri 1.192
1017 edhill 1.195 o undid all of cp51 pending some cleanups and discussion
1018 heimbach 1.197 o added the [#include "AD_CONFIG.h"] statement to all files that need
1019     it for adjoint/tl #defines
1020     o re-worked the build logic in genmake2 to support AD_CONFIG.h
1021     o removed tools/genmake since it no longer works
1022 dimitri 1.194
1023     checkpoint51n_post
1024     o modifications to make FREEZE flux visible to pkg/kpp
1025     - moved surfaceTendencyTice from pkg/seaice to main code
1026     - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
1027     - subroutine FREEZE now limits only surface temperature
1028     (this means new output.txt for global_ocean.90x40x15,
1029     global_ocean.cs32x15, and global_with_exf)
1030     o added surface flux output variables to TIMEAVE_STATVARS
1031    
1032     checkpoint51n_pre
1033 dimitri 1.192 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
1034 edhill 1.193 o added [#include "AD_CONFIG.h"] to all files that use the following
1035     defines:
1036     - ALLOW_ADJOINT_RUN
1037     - ALLOW_TANGENTLINEAR_RUN
1038     - ALLOW_ECCO_OPTIMIZATION
1039 edhill 1.190
1040 edhill 1.191 checkpoint51m_post
1041 edhill 1.190 o incorporating changes to get TAMC/TAF working in genmake2
1042     - added new TAMC/TAF targets to the Makefile
1043     - various cleanups related to package handling
1044 edhill 1.191 - these changes should have no impact on the forward model
1045 dimitri 1.189
1046     checkpoint51l_post
1047     o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
1048     - faster algorithm for cal_addtime.F
1049     - higher precision arithmetic, where needed
1050     - pkg/exf *startdate variables changed from calendar date to
1051     model integration time
1052    
1053     checkpoint51l_pre
1054 jmc 1.188 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
1055     o enable to apply restoring on S & T only in a latitude band.
1056     o update output (external_forcing_surf modif. change truncation errors)
1057     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
1058 edhill 1.186
1059 jmc 1.187 checkpoint51k_post
1060     o change default to: useNHMTerms=.FALSE.
1061     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
1062     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
1063     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
1064     exp1, ideal_2D_oce
1065     - change data file of oceanic exp (leave the results unchanged for now)
1066     exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
1067     o set gravitySign automatically according to the vertical coordinate used
1068     (and change sign: back to "logical" value: +1 when R increases downward)
1069 edhill 1.186 o added an include barrier to the default CPP_OPTIONS.h and
1070     removed the #include "PACKAGES_CONFIG.h" from it
1071 jmc 1.187 o fix a bug in mom_fluxform (from chk51j_post)
1072 heimbach 1.185
1073     checkpoint51j_post
1074     o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
1075     o adjusted some flow directives (dynamics, thermodynamics)
1076     o added cubed-sphere case to test cost function
1077     o heckpoint_lev?_directives.h now include
1078     pkg-specific directives, whenever those are enabled.
1079     o Moving pkg-specific flow directives to corresponding pkg
1080     Moving pkg-specific differentiation list to corresponding pkg
1081     Moving pkg-specific checkpoint-lev storing to corresponding pkg
1082     ---> conventions are
1083     - pkg_ad.flow
1084     - pkg_ad_diff.list
1085     - pkg_ad_check_lev?_dir.h
1086 stephd 1.181
1087 edhill 1.184 checkpoint51i_post
1088     o merge of the branch-genmake2
1089     - knowingly breaks the older genmake
1090     - automatic generation of all ALLOW_${PKG_NAME} defines
1091     - new testreport supersedes older testscript
1092     o large number of package inclusion and header cleanups
1093     checkpoint51i_pre
1094    
1095 edhill 1.183 o new output for adjoin of global ocean vector invariant
1096     o fix for checkpoint of thermodynamic seaice and bulk_force
1097     o Steph gchem various cleanups
1098    
1099 stephd 1.181 checkpoint 51h_pre
1100 edhill 1.183 o fixed some single quotes
1101 stephd 1.181 o modify gchem pkg to be more versatile
1102     o modifications to clean up dic pkg
1103     o add pkg/cfc
1104 heimbach 1.182
1105     checkpoint51g_post
1106     o provide links for ARPACK and ADM*TLM
1107     o start removing verification/vero/
1108     o update AD-related stuff
1109     (in particular some IF-statements in model/src/ routines)
1110     o adding to verification/global_ocean.90x40x15/ adjoint of
1111     vector invariant setup
1112 dimitri 1.177
1113 heimbach 1.180 checkpoint51f_post
1114 jmc 1.179 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
1115 dimitri 1.178 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
1116 dimitri 1.177 of tracer Green's fucntions for ocean inversion project.
1117 dimitri 1.175
1118 dimitri 1.176 checkpoint51f_pre
1119 dimitri 1.175 o Added on-the-fly spatial interpolation capability
1120     "USE_EXF_INTERPOLATION" to pkg/exf.
1121 dimitri 1.176 - This is a temporary Cartesian-grid hack until
1122 dimitri 1.175 the super-duper ESMF coupler becomes available.
1123 dimitri 1.176 - See verification/global_with_exf/README for usage example.
1124     - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
1125     flags and modified pkg/seaice accordingly.
1126 dimitri 1.175 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
1127     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
1128     non-local transport term.
1129 heimbach 1.172
1130 jmc 1.174 checkpoint51e_post
1131     o pkg/mom_vecinv:
1132     - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
1133     - add time-ave diagnostic of vorticity advection.
1134     o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
1135     o atmospheric geopotential: - include water vapor effect;
1136     - use p^kappa in p* scaling.
1137 jmc 1.173 o land pkg: read initial state from files.
1138     o AIM : add stratospheric drag in the upper level
1139    
1140 heimbach 1.172 checkpoint51d_post
1141 jmc 1.173 o change function ILNBLNK (=> last non-blank char.) to return zero
1142     (instead of the string length) when the string. char is empty
1143 jmc 1.171 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
1144 heimbach 1.172 o modif's to restore TAMC compatibility
1145     - avoid "_d" constructs in PARAMETER declarations
1146     - avoid interrupting lines by comment lines
1147     o Use cluster local disks for purely local I/O
1148     vs. globally visible disks needed for ctrl stuff
1149     (merged from ecco-branch)
1150     - new active_file_loc... and mdsio_..._loc routines
1151     - affected packages: autodiff, ctrl, grdchk, mdsio
1152 heimbach 1.169
1153 heimbach 1.170 checkpoint51c_post
1154     o introducing integer flag debugLevel
1155     - debLevZero: suppress all output
1156     - debLevA: standard
1157     - debLevB: equivalent to current debugMode=.TRUE.
1158     o introducing pathname variable mdsioLocalDir for mdsio
1159     that can be specified at runtime
1160     (relevant for cluster I/O to local disk)
1161     `
1162 heimbach 1.169 >>>checkpoint51b_post
1163     adjoint of ptracers
1164     o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
1165     o extended state in checkpoint_lev?, etc.
1166     o alternative ctrl/cost with tr1 or ptracer
1167     o new comlev1_bibj_ptracers
1168     o new ptracers.flow
1169     o made ptracers_forcing same as external_forcing_s
1170     o added verification for adjoint with ptracers
1171     - adm. grdchk fail so far
1172     - tlm. grdchk OK
1173     - checked tapelev/comlev recomputations: OK
1174     <<<checkpoint51b_pre
1175 stephd 1.168
1176     checkpoint51a_post
1177     o added code for biogeochemistry package
1178     - new pkgs: dic, gchem
1179     - new subroutine in ptracers
1180     o modify code for biogeo packages
1181     - in model/src and pkg/ptracers
1182 heimbach 1.166
1183     checkpoint51
1184     o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
1185     - autodiff, ctrl, exf, grdchk, seaice
1186     kept separate packages
1187     - cost, ecco, obcs
1188 heimbach 1.167 o updating verification/internal_wave, verification/lab_sea
1189     (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
1190 heimbach 1.165
1191     checkpoint50i_post
1192     o Preparing next differentiable checkpoint and sync
1193     of MAIN vs. ecco-branch
1194     - 1st step: this one is differentiable
1195     - 2nd step: next(! not this) checkpoint will have updated packages
1196     from ecco-branch)
1197 jmc 1.161
1198 heimbach 1.164 checkpoint50h_post
1199 jmc 1.163 o new package "land": provide surface BC for AIM.
1200     o pkg/ptracers: apply exchange to all tracers after reading a pickup.
1201 jmc 1.161 o AIM: use true log-P extrapolation for near surface temp (= as in
1202     F.Molteni paper) ; update aim.5l_cs output.
1203 adcroft 1.162 o New variable in PARM03 for more flexible pickups
1204 heimbach 1.164 o somewhat cleaned package initialisation sequence for
1205     ctrl/ cost/ ecco/ in packages_... routines
1206 dimitri 1.160
1207     checkpoint50g_post
1208     o merged with release1_p17 (pkg/seaice and verification/lab_sea)
1209     - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
1210     - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
1211     made the default because of faster convergence than ADI
1212 heimbach 1.159
1213     checkpoint50f_post
1214     o exf totally restructured
1215     - replaced all exf_set_ routines by one generic exf_set_gen.F
1216     and made sure it's still differentiable
1217     - split exf_getffields.F into new exf_bulkformulae.F
1218     - exf_inscal_/exf_outscal_ suffixes consistent with field names
1219     - updated adjoint/makefile and relevant verif. accordingly
1220 adcroft 1.156
1221 heimbach 1.158 checkpoint50f_pre
1222 jmc 1.157 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
1223     + change Evap over land. (update aim.5l_cs output)
1224 adcroft 1.156 o added missing .cvsignores and made uniform across expts
1225     o changed configuration of tidal_basin_2d expt
1226     o added pkg/debug functions for tracing code in fatal crashes
1227     o tidied pkg/monitor to use MONITOR_OPTIONS.h
1228     o new fn in pkg/monitor to stop model if solution grows too big
1229     o removed lots of single quotes from comments
1230    
1231 mlosch 1.155 checkpoint50e_post
1232     o make KPP work with PTRACERS
1233     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
1234     nearly a copy of kpp_transport_s
1235     - there is no analogue to SurfaceTendencyS, so I have to use
1236     gPtr(of the surface layer) instead
1237     o add a new platform SunFire+mpi (SunFire 15000) to genmake
1238     checkpoint50e_pre
1239    
1240     checkpoint50d_post
1241 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
1242     files analogous to write_state.F
1243     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
1244     analogous to the cg2d-related output.
1245 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
1246     so that writing to internal file fn (with length 512) fails.
1247 mlosch 1.154 checkpoint50d_pre
1248 jmc 1.151
1249 jmc 1.153 checkpoint50c_post
1250     o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
1251 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
1252 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
1253     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
1254     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
1255 dimitri 1.150
1256     checkpoint50c_pre
1257     Merging from release1_p13:
1258     o bug fix for pkg/seaice dynamic solver
1259     o Added SEAICE_initialHEFF to pkg/seaice
1260 jmc 1.149
1261     checkpoint50b_post
1262     o store u*,v* in gU,V instead of in guNm1,gvNm1
1263     o in order to put the momForcing out of the Adams-Bashforth:
1264     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
1265     to timestep.F
1266     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
1267     o re-generate output for highly sensitive test-exp:
1268     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
1269 heimbach 1.146
1270 jmc 1.148 checkpoint50b_pre
1271 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
1272 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
1273     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
1274 heimbach 1.145
1275     checkpoint50a_post
1276     o Bug fix for merging between c50 and KPP.
1277     ikey was passed from thermodynamics to kpp_calc via
1278     common block rather than being recomputed in kpp_calc,
1279     in contradiction with new key itdkey.
1280     New key ikppkey created, and tamc.h headers updated.
1281 heimbach 1.143
1282 heimbach 1.144 checkpoint50
1283     - 2nd step of merge with ecco-branch:
1284     merge changes in ecco-branch back into main trunk
1285     - bug fix in find_alpha
1286     - more storing in gmredi_calc_tensor.F, kpp_routines.F
1287     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
1288     - merged some sliced AD support routines
1289    
1290 heimbach 1.143 checkpoint49
1291     merged from ecco-branch:
1292     o exf:
1293     - Enable initialisation of forcing fields to constant
1294     (runtime) values.
1295     - in exf_getffields.F
1296     Reduce i-/j-loop to interior domain, discarding overlaps.
1297     That also fixes wrong TAF-key computations for key_1, key_2
1298     with bulf formulae.
1299     - exf_init.F modify #ifdef for exf_init_evap
1300     - exf_getffieldrec.F, ctrl_getrec.F
1301     The following INT-usages are not safe:
1302     fldsecs = int(fldsecs/fldperiod)*fldperiod
1303     fldcount = int(fldsecs/fldperiod) + 1
1304     and were modified.
1305     o autodiff: checkpoint_lev...
1306     - updated storing for bulk formulae (some arrays were missing)
1307     - added state for seaice package
1308     - synchronized with main branch
1309     o DIVA:
1310     Modif.s in
1311 heimbach 1.144 - the_main_loop.F
1312     - the_model_main.F
1313 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
1314     o With these changes, it is possible to fully separate
1315     the first forward run to compute the cost function (mdthe_main_loop)
1316     and adjoint runs over individual DIVA intervals (adthe_main_loop)
1317     into separate model executions.
1318     This enables better tuning of DIVA to given queue sizes.
1319     o Loss of cost function value in consecutive DIVA runs is
1320     fixed by storing to 'costfinal' file.
1321     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
1322     beginning/end of adjoint integration is accounted for.
1323     The current changes apply to TAF-1.4.26.
1324     TAF has one remaining bug, requiring one manual change
1325     (see MITgcm manual).
1326     o cal: synchronized between MAIN and ecco-branch
1327 heimbach 1.141
1328 heimbach 1.142 checkpoint48i_post
1329 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
1330     (mostly adding new routines to make list and replacing
1331     pressure by totPhiHyd).
1332     o Updated and merged grdchk package
1333     - has both ADM and TLM checks
1334     - works for single- and multi-proc.
1335     - output cleaned
1336     - worked successfully for parallel DIVA
1337     o genmake:
1338     - Adding -platform=SP4
1339     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
1340     o Modif. for DIVA:
1341     ctrl_unpack should not be called in intermediate DIVA interval.
1342     (similar thing would apply for active files such as
1343     tbar, sbar, psbar, which should not be reinitialised;
1344     only relevant for ecco-branch)
1345 dimitri 1.136
1346 heimbach 1.140 checkpoint48h_post
1347 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
1348 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
1349     o Added SEAICE_initialHEFF to pkg/seaice
1350 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
1351 jmc 1.135
1352     checkpoint48g_post
1353     --- EOS:
1354     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
1355     store total Potential in totPhyHyd for diagnostics & EOS.
1356     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
1357     --- Pressure/geopotential gradient:
1358     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
1359     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
1360     ( changes results of global_ocean_pressure )
1361     o NLFS + z-coord.: add eta*Rho' contribution.
1362     o accurate phiHyd when using interface-W at the middle between 2 centers
1363     ( changes results of ideal_2D_oce )
1364     o includes r* 2nd term in potential gradient.
1365 dimitri 1.134
1366     checkpoint48f_post
1367     Merging from release1_p12:
1368     o Modifications for using pkg/exf with pkg/seaice
1369     - improved description of the various forcing configurations
1370     - added basic radiation bulk formulae to pkg/exf
1371     - units/sign fix for evap computation in exf_getffields.F
1372     - updated verification/global_with_exf/results/output.txt
1373     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
1374     (SBO) core products, including oceanic mass, center-of-mass,
1375     angular, and bottom pressure (see pkg/sbo/README.sbo).
1376     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
1377     to avoid negative values in shallow regions.
1378     - updated verification/natl_box/results/output.txt
1379     - updated verification/lab_sea/results/output.txt
1380     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
1381     o Added useSingleCpuIO option (see PARAMS.h).
1382     o Updated useSingleCpuIO option in mdsio_writefield.F to
1383     work with multi-field files, e.g., for single-file pickup.
1384     o pkg/seaice:
1385     - bug fix in growth.F: QNET for no shortwave case
1386     - added HeffFile for specifying initial sea-ice thickness
1387     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
1388     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
1389     kpp_transport_t.F, forward_step.F, and the_main_loop.F
1390     o pkg/seaice:
1391     - adjoint-friendly modifications
1392     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
1393 jmc 1.131
1394 jmc 1.133 checkpoint48e_post
1395 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
1396 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
1397     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
1398     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
1399     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
1400 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
1401 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
1402     inverted_barometer solid-body.cs-32x32x1
1403     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
1404 jmc 1.130
1405     checkpoint48d_post
1406     o in preparation for r*:
1407     a) use pre-computed gradient of hydrostatic potential:
1408     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
1409     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
1410     => affects results of glob_oce_pressure (different truncation error)
1411     update output.txt of ideal_2D_oce & global_ocean_pressure
1412 jmc 1.129
1413     checkpoint48d_pre
1414     o in preparation for r*:
1415     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
1416     pass the 2 comp. of the grad. as arguments to momentum S/R.
1417     but for the moment, only used if it does not change the results.
1418     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
1419 jmc 1.126
1420 heimbach 1.128 checkpoint48c_post
1421     Modifications in treatment of initial flux forcing controls
1422     to avoid extra storing of flux fields.
1423    
1424     checkpoint48c_pre
1425 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
1426 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
1427 jmc 1.124
1428 jmc 1.125 checkpoint48b_post
1429 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
1430     (modification to pressure gradient not yet implemented)
1431     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
1432     (for U & V) that are used for vertical advection of momentum.
1433 jmc 1.123
1434     checkpoint48a_post
1435     o In preparation for r*, use temp. array to compute vertical transport
1436     in flux-form momentum pkg. => change results of few test-exp.
1437     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
1438     lab_sea, natl_box & plume_on_slope
1439 jmc 1.122
1440     checkpoint48
1441     o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
1442 heimbach 1.121
1443     checkpoint47j_post
1444 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
1445 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
1446     o added exch in ctrl_map_...
1447     o aveFreq.=0. at end of cost_final to avoid overwrite in
1448     reverse checkpointing loop
1449     o Yet more changes in gmredi:
1450     * adgmredi_calc_tensor
1451     avoiding all recomputation of gmredi_slope_limit
1452     * adgmredi_x/y/rtransport
1453     added flag for excessive storing to avoid recomp. of
1454     u/v/rtans, dTdx/y/z
1455     -> this is not really necessary and very memory-consuming
1456     * adgmredi_slope_psi:
1457     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
1458     * gmredi_slope_limit
1459     re-activated full calculation of taperfct for case 'ac02'
1460     o updating verification/ adjoints of carbon, global_ocean.90x40x15
1461 heimbach 1.116
1462 jmc 1.119 checkpoint47i_post
1463     o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
1464     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
1465     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
1466     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
1467     o gmredi: fix few bugs.
1468    
1469 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
1470 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
1471     o few modif.'s to get latest version adjointed
1472     (mainly kick out code in ini_linear_phisurf)
1473     o modif's to run adjoint with exactConserv
1474     o case GM_BOLUS_ADVEC should be cleaned
1475     S/R gmredi_slope_psi should be cleaned
1476     o verification/carbon now has exactConserv=.TRUE.
1477 jmc 1.114
1478 heimbach 1.115 checkpoint47g_post
1479 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
1480     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
1481 heimbach 1.115 o After TAF bug fix:
1482     Tested adjoint of gmredi package.
1483     Tests were done with checkpoint47 rather than with latest
1484     checkpoint47f_post since the latter is broken for the adjoint
1485     verification/carbon/ contains both ADM and TLM gradient checks.
1486     Here they are, before they get changed/lost/stolen.
1487     Mostly modif.'s to fix numerical sensitivities.
1488     Gradient checks OK for
1489     - GM_taper_scheme:
1490     * clipping
1491     * ac02
1492     * linear
1493     * glw91
1494     * dm95
1495     * ldd97
1496     - GMREDI_OPTIONS:
1497     * GM_VISBECK_VARIABLE_K
1498     * GM_NON_UNITY_DIAGONAL
1499     * GM_EXTRA_DIAGONAL
1500     * GM_BOLUS_ADVEC
1501     in conjunction with data.gmredi parameters to be checked in
1502     in a few minutes under verification/carbon/code/
1503 cheisey 1.112
1504 dimitri 1.113 checkpoint47f_post
1505     Merging from release1_p10:
1506     o modifications for using pkg/exf with pkg/seaice
1507     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
1508     and SEAICE_EXTERNAL_FLUXES
1509     - pkg/exf CPP options EXF_READ_EVAP and
1510     EXF_NO_BULK_COMPUTATIONS
1511     - usage examples are Experiments 8 and 9 in
1512     verification/lab_sea/README
1513     - verification/lab_sea default experiment now uses
1514     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
1515    
1516 cheisey 1.112 checkpoint47e_post
1517     o created a tag prior to creating a branch
1518    
1519 mlosch 1.111 checkpoint47d_post
1520     o fixed bug in the oceanic pressure coordinates code: vertical viscosity
1521     at the bottom boundary had an erroneous half slip boundary condition
1522     o added bottom drag and no slip boundary condition capabilities to
1523     oceanic pressure coordinates code
1524     o added new verification experiment global_ocean_pressure, this experiment is
1525     also described in the tutorial section of the manual
1526     checkpoint47d_pre
1527 cheisey 1.110
1528     checkpoint47c_post
1529     o Added a verification experiment for a global cubed-sphere ocean run
1530     - verification/global_ocean.cubed32x32x30
1531     - uses pkg/therm_seaice and pkg/bulk_forcing
1532 jmc 1.109
1533     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
1534     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
1535     when using P-coordinate; only implemented for atmospheric config.
1536     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
1537     NOTES: requires option NONLIN_FRSURF to be "#define".
1538     o update advect_xz/results/output.txt (left from checkpoint44g_post)
1539 dimitri 1.108
1540     checkpoint47b_post
1541     Merging from release1_p9:
1542     o pkg/seaice
1543     - removed GOTO's and added taf directives
1544     - double precision constants to reduce the g77 (Linux)
1545     to F77 (SGI) differences reported in release1_p8
1546     o tools/genmake
1547     - added SGI options
1548     o verification/testscript
1549     - updated to that of checkpoint47a_post
1550     o verification/global_ocean.90x40x15/input/eedata
1551     - modified for SGI f77 compatibility
1552     o verification/lab_sea
1553     - added description of sea-ice model
1554     - added missing matlab routines
1555     - added test of thermodynamics parallelization
1556 jmc 1.105
1557 jmc 1.106 checkpoint47a_post
1558 jmc 1.105 o new pkg: aim_v23
1559     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
1560     for now, keep the same surface forcing as before.
1561     - Part-Cell implemented into AIM; check that Heat & Water are conserved
1562     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
1563     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
1564     o add diagnostic of surface correction term in monitor output
1565 jmc 1.106
1566     o bulk_force and therm_seaice
1567 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
1568     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
1569     - Earlier integration from Stephaine Dutkiewicz
1570     and Patrick Heimbach.
1571     - Two ifdef statements for compile time,
1572     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
1573 heimbach 1.104
1574     checkpoint47
1575     differentiable version of checkpoint46n_post
1576     o bug fix in quasihydrostaticterms
1577     o * "clean" adjoint code (in terms of extensive recomputations)
1578     can now be obtained for all GMREDI options (i.e. for
1579     - GM_VISBECK_VARIABLE_K
1580     - GM_NON_UNITY_DIAGONAL
1581     - GM_EXTRA_DIAGONAL
1582     - GM_BOLUS_ADVEC )
1583     * However, wrong gradient check problem remains unsolved.
1584     * New CPP options have been introduced for different
1585     tapering schemes
1586     o external_fields_load now part of differentiation list
1587     o pressure needs multiple storing;
1588     would be nice to have store_pressure at beginning or
1589     end of forward_step, e.g. by having phiHyd global (5-dim.)
1590     (NB: pressure is needed for certain cases in find_rho,
1591     which is also invoked through convective_adjustment).
1592     o recomputations in find_rho for cases
1593     'JMD95'/'UNESCO' or 'MDJWF' are OK.
1594     o #define ATMOSPHERIC_LOADING should be differentiable
1595     o ini_forcing shifted to begining of initialise_varia
1596     o Incorporating QNVS line search routines into MITgcm
1597     (this is separate code, and therefore not under pkg)
1598     lsopt/, optim/
1599     o Updated verification/carbon/
1600     - #define GM_VISBECK_VARIABLE_K
1601     - GM_taper_scheme = 'ldd97'
1602 heimbach 1.103
1603     checkpoint46n_post
1604     Merging from release1_p8:
1605     o verification/natl_box:
1606     updating new external_fields_load routine
1607     o New package: pkg/seaice
1608     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
1609     The sea-ice code is based on Hibler (1979-1980).
1610     Two sea-ice dynamic solvers, ADI and LSR, are included.
1611     In addition to computing prognostic sea-ice variables and diagnosing
1612     the forcing/external data fields that drive the ocean model,
1613     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
1614     The implied surface heat flux is then stored in variable
1615     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
1616     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
1617     non-local transport term. Because this call precedes model
1618     thermodynamics, temperature under sea-ice may not be "exactly" at
1619     the freezing point by the time theta is dumped or time-averaged.
1620     N.B.: fairly large differences in accuracy occur across
1621     different platforms/compilers; comparison between
1622     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
1623     generated output gives:
1624     T S U V
1625     C D M c m s m s m s m s
1626     n p a R g m m e . m m e . m m e . m m e .
1627     f n k u 2 i a a d i a a d i a a d i a a d
1628     g d e n d n x n . n x n . n x n . n x n .
1629    
1630     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
1631     o GAD:
1632     - generated new common blocks to account for call of
1633     same gad routines with differing traceridentities
1634     (needed to modify tracerIdentity indices in GAD.h)
1635     - generated separate common blocks for case useCubedSphereExchange
1636     (Department of Futurology)
1637     - parameter lists to gmredi_?transport: added tracerIdentity
1638     - added new key indices to tamc.h
1639     o external_fields_load:
1640     - added this routine to TAF list
1641     - needed to make some common blocks global and additional storing
1642     along the same lines as exf package (checkpoint_lev?_directives.h)
1643     o exf:
1644     updated external forcing package
1645     - bug fixes carried over from ecco-branch
1646     (missing OBCS_OPTIONS.h in two routines)
1647     - enable easy to use "no forcing".
1648     - added exf I/O for atmospheric loading
1649     - added exf I/O for runoff data
1650     - transfered scaling between exf <-> MITgcm to exf namelist
1651     o Adding new verification experiment global_with_exf.
1652     This verification experiment is almost identical to the
1653     global_ocean.90x40x15 experiment, except that it uses
1654     the exf (and cal) package instead of the
1655     external_fields_load routine (cf README file).
1656 adcroft 1.94
1657 adcroft 1.102 checkpoint46m_post
1658 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
1659 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
1660     and new routine quasihydrostaticterms()
1661 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
1662     New routine: mom_u_coriolis_nh()
1663 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
1664     Depend on correct sign of gravitySign.
1665 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
1666 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
1667 adcroft 1.95 o removed gravitySign from PARM04
1668 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
1669 mlosch 1.93
1670     checkpoint46l_post
1671     o made convective adjustment work with pressure coordinates:
1672     - changed the direction of k-loop in convective_adjustment.F for the
1673     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
1674     - adjusted the reference pressure k-index in convective_adjustment.F
1675     - adjusted the convection condition in convect.F (in analogy to
1676     calc_ivdc.F)
1677     - convective_adjustment no longer computes anything on the halos
1678     - removed the warnings about negative salinity from find_rho.F and
1679     find_alpha.F; instead the new routine look_for_neg_salinity, called
1680     at the beginning of find_rho, find_alpha, and find_beta, does a
1681     check of the entire slice, if CPP-option
1682     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
1683     checkpoint46l_pre
1684 mlosch 1.91
1685 mlosch 1.92 checkpoint46k_post
1686 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
1687     - new bathymetry (the world according to A., JMC, and M.)
1688     - new initial fields and forcing fields (*.bin files)
1689     - new POLY3.COEFFS (for the next release one should switch to a full
1690     equation of state: JMD95P or MDJWF)
1691     - fixed several errors and redundancies in the data file
1692     - experiment uses looped cells
1693     - added matlab directory with diagnostic scripts for plotting of output
1694 jmc 1.90
1695     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
1696     - read AIM physics parameters from a file (data.aimphys)
1697     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
1698 jmc 1.89
1699     checkpoint46j_post
1700     o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
1701     o move wVel computation at the end of the time step, in S/R integr_continuity
1702     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
1703     o update timeave pkg for wVel diagnostic.
1704     checkpoint46j_pre
1705 mlosch 1.87
1706 jmc 1.88 checkpoint46i_post
1707     o Clean up AIM package (and keep the results unchanged):
1708     include CPP_OPTION and use IMPLICT NONE in all routines ;
1709     declare all the variables _RL ; use _d 0 for all numerical constants.
1710     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
1711 mlosch 1.87
1712     checkpoint46h_post
1713     o cleaned up the use of rhoNil and rhoConst.
1714     - rhoNil should only appear in the LINEAR equation of state, everywhere
1715     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
1716     and the dynamical equations are all divided by rhoConst
1717     o introduced new parameter rhoConstFresh, a reference density of fresh
1718     water, to remove the fresh water flux's dependence on rhoNil. The default
1719     value is 999.8 kg/m^3
1720     o cleanup up external_forcing.F and external_forcing_surf.F
1721     - can now be used by both OCEANIC and OCEANICP
1722     checkpoint46h_pre
1723    
1724     Added code to convert surface volume flux (fresh water) into
1725     a mass flux when using P coordinates in the ocean (OCEANICP).
1726     Note: It assumes you have set rho0=rhoConst=density of fresh water.
1727 mlosch 1.86
1728     checkpoint46g_post
1729     o Include a new diagnostic variable phiHydLow for the ocean model
1730     - in z-coordinates, it is the bottom pressure anomaly
1731     - in p-coordinates, it is the sea surface elevation
1732     - in both cases, these variable have global drift, reflecting the mass
1733     drift in z-coordinates and the volume drift in p-coordinates
1734     - included time averaging for phiHydLow, be aware of the drift!
1735     o depth-dependent computation of Bo_surf for pressure coordinates
1736     in the ocean (buoyancyRelation='OCEANICP')
1737     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
1738     Theta, Salinity, and Pressure in the parameter list. This routine is
1739     presently contained in find_rho.F. This routine does not give the
1740     correct density for 'POLY3', which would be a z-dependent reference
1741     density.
1742     o cleaned up find_rho
1743     - removed obsolete 'eqn' from the parameter list.
1744     o added two new verification experiments: gop and goz
1745     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
1746     checkpoint46g_pre
1747 heimbach 1.85
1748     checkpoint46f_post
1749     o Enable tangent linear (forward mode) gradient checks:
1750     - extended active file handling to g_... files
1751     - added TANGENT_SIMULATION to theSimulationMode
1752     - extended grdchk package accordingly
1753     o added tangent linear setup in verification/carbon/code_ftl
1754     o added adjoint setup in verification/front_relax/code_ad
1755 mlosch 1.82
1756 cnh 1.84 checkpoint46e_post
1757 mlosch 1.83 o Added new equation of state -> MDJWF
1758     - EOS of McDougall et al., 2002, JAOT, submitted
1759     - caveat: the equation of state is only valid for a smaller (more
1760     realistic?) range of values than JMD95P/Z and UNESCO
1761     - added masks to the calculation of pressure in store_pressure
1762     - added more check values for density in check_eos (ini_eos.F), some of
1763     the old check values are out of the range of the MDJWF-eos, so don't
1764     expect perfect matches for those
1765 cnh 1.84 checkpoint46e_pre
1766 mlosch 1.83
1767 mlosch 1.82 checkpoint46d_post
1768     o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
1769     'OCEANICP', also initialised field pressure correctly in ini_eos in the
1770     case of pressure coordinates. eosType='JMD95Z' in
1771     combination with buoyancyRelation='OCEANICP' now causes an error.
1772     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
1773     in find_alpha/beta.
1774     checkpoint46d_pre
1775    
1776     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
1777     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
1778 adcroft 1.81
1779     checkpoint46c_post
1780     o Changes necessary for ocean in p-coordinates
1781     - Added new buoyancy relation = 'OCEANICP'
1782     - Added new parameters = gravitySign (this used to be contained inside
1783     the factor dRdZ which I added when we first switched to R coordinates).
1784     X GM/Redi is not compatible (yet)
1785     X bottom drag and no-slip need to be debugged.
1786     checkpoint46c_pre
1787 mlosch 1.80
1788     checkpoint46b_post
1789     o Added new equation of state -> JMD95Z and JMD95P
1790 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
1791 mlosch 1.80 - moved all EOS parameters into EOS.h
1792     - new routines ini_eos.F, store_pressure.F
1793     o Added UNESCO EOS, but not recommended because it requires
1794     in-situ temperature (see JMD95)
1795     o Modified formatting for knudsen2.f in utils/knudsen2 and added
1796     unesco.f to be used with POLY3
1797     checkpoint46b_pre
1798 mlosch 1.79
1799     checkpoint46a_post
1800     o Added (atmospheric) pressure loading
1801     - new field in FFIELDS.h, etc...
1802     - new cpp flag ATMOSPHERIC_LOADING
1803     o Changed hFacC to _hFacC in calc_phi_hyd.F
1804     o Added SHORTWAVE_HEATING to some files for consistency
1805     checkpoint46a_pre
1806 heimbach 1.78
1807     checkpoint46
1808     further merges from release1_p5
1809     o new ctrl package
1810     - adopted from ECCO environment to enable optimization
1811     - added Eliassen Palm fluxes to controls
1812     o added Eliassen Palm flux controls to gradient check package
1813     o cost package
1814     - Compatible with new ctrl package
1815     - added Eliassen Palm cost hooks
1816     - modif's of existing cost functions
1817     o Adjoint-related bug fixes in kpp:
1818     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
1819     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
1820     o autodiff package
1821     - flow directives:
1822     + new for S/R do_the_model_io
1823     + enhanced for S/R checkpoint
1824     + new gmredi.flow
1825     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
1826     disable adcommon.h/g_common.h by default.
1827     - fixed problem for adjoint of global_max
1828     o modified verification/carbon/
1829     o New setup for adjoint of global_ocean
1830     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
1831     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
1832     o incorporated hooks for sponge layer code (external_forcing.F)
1833    
1834 jmc 1.77 checkpoint45d_post
1835     o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
1836 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
1837     (affects plume_on_slope "cg2d" output)
1838 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
1839     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
1840 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
1841 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
1842     o add new flags:
1843     - T,S forcing inside/outside Adams-Bashforth
1844     - turn off temp,salt advection and/or forcing
1845     - for each tracer, define internal flag for multiDimAdvection & A-B
1846     o monitor: change definition of KE to check conservation of Energy
1847 heimbach 1.73
1848     checkpoint45c_post
1849     o Removed f90 comments ("!")
1850     o Modified initialisations to enable exf package for MITgcm
1851     (without invoking ECCO_PACKAGE).
1852     o modifications to gradient check package (Martin Losch)
1853     - enable centered differences
1854     - modified format of standard output
1855 heimbach 1.72
1856     checkpoint45b_post
1857     o cleaned exchange calls in cg2d
1858     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
1859     o included CPP option SINGLE_LAYER_MODE in thermodynamics
1860     to configure barotropic setup (Martin Losch)
1861     o moved some initialisations within bi,bj loop in dynamics
1862     (TAF flow dependency)
1863     o in initialise_varia, moved call packages_init_variables
1864     before convective_adjustment_init
1865     (corresponding adjustment of TAF tape initialisation).
1866     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
1867 jmc 1.70
1868 jmc 1.71 checkpoint45a_post
1869     o compute Rho over the whole domain (extend iMin,jMin indices)
1870     o specific exchange for X-slice domain (case Ny=1)
1871 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
1872     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
1873 jmc 1.67
1874 heimbach 1.69 checkpoint44h_post = checkpoint45
1875     o Fix to restore differentiability:
1876     place at which packages_init_variables is called in
1877     initialise_varia is crucial for reverse control flow.
1878     o modifications in GMRedi to enable stable adjoint
1879     (corresponding modif's in thermodynamics, dynamics)
1880     o added missing hook for sponge layer code in external_forcing
1881     o modified test cost functions
1882     o storing in gad_advection (plus removal of write(0,*)!
1883     o missing headers TR1.h added in convective_adjustment routines
1884     o errorMessageUnit set non-equal zero in eeboot
1885     (conflict on some platforms, e.g. IBM SP3)
1886     o modified carbon verif.
1887    
1888     checkpoint44h_pre
1889 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
1890     2 cell-centers ; replace delZ in pkg/kpp by drF.
1891 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
1892     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
1893 jmc 1.66
1894     checkpoint44g_post
1895     o fix surface correction term in multiDimAdvection (affects plume_on_slope
1896     results) ; ifdef missing in thermodynamics.F
1897 adcroft 1.65
1898     checkpoint44f_pre,checkpoint44f_post
1899     o added PTRACERS package
1900     This allows an arbitrary number of passive tracers to be integrated
1901     forward simultaneously with the dynamicaly model.
1902     + Implemented so far:
1903     - basic forward algorithm (time-stepping, advection, diffusion, convection)
1904     - I/O and checkpointing
1905     - GM/Redi *but* using the GM/Redi coefficient of Salt
1906     + Not implemented so far:
1907     - KPP
1908     - OBCS
1909     + No specific example supplied (yet) but global_ocean.90x40x15 has the
1910     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
1911     line in data.pkg.
1912     + This package is disabled by default since it increases storage.
1913    
1914 jmc 1.60
1915 adcroft 1.64 o testscript: added -cleanup option
1916 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
1917     b) enable to filter 2D fields.
1918 adcroft 1.62
1919     checkpoint44e_pre,post
1920     o re-wrote convective adjustment to use pre-calculated weights
1921     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
1922     Adds: model/src/convective_weights.F, convectively_mixtracer.F
1923     Original calls to convect() still in place.
1924 heimbach 1.61
1925     chkpt44d_pre,post
1926     o added missing EXCLUDE_MONITOR flags
1927     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
1928     (incompatible typ in MIN/MAX expressions caused problems
1929     on IBM SP3)
1930     o in genmake added variable MAKEDEPEND
1931     plus resetting for case SunOS
1932     o added timer_stats.c routine for IBM SP3
1933     o removed variables in dynamics
1934     !!! I forgot to create tag chkpt44d_pre !!!
1935     !!! But chkpt44d_pre = chkpt44c_post !!!
1936 jmc 1.63
1937     o real fresh water flux implemented with non-linear free-surface.
1938 heimbach 1.58
1939 jmc 1.59 chkpt44c_pre,post
1940     o few fix (mask in shap_s2, EmPmR in external_field_load,
1941     USE_NATURAL_BCS in solve_for_P);
1942     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
1943    
1944 heimbach 1.58 checkpoint44b_pre/_post
1945     o merge of relevant stuff from the ecco-branch:
1946     - genmake: removed $S64 overwrite for case SunOS
1947     - pkg/exf: update and corrections for field swapping and obcs
1948     - pkg/ecco: parameter lists for the_model_main, the_main_loop
1949     harmonized between ECCO and MITgcm
1950     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
1951     updated checkpointing_lev... lists for obcs
1952     - model/src: minor changes in forward_step, plot_field
1953     added directive for divided adjoint in the_main_loop
1954     - pkg/mdsio: added mdsio_gl_slice
1955 jmc 1.57
1956     o check parameters & config (chkpt44a_pre,post)
1957 jmc 1.56 o OBC and NonLin_FrSurf.
1958    
1959 heimbach 1.55 checkpoint44
1960 jmc 1.54 o fix bug in mom_vi_del2uv
1961 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
1962     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
1963     o update AIM experiments (NCEP input files)
1964     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
1965 heimbach 1.55 o added some stuff for AD
1966 adcroft 1.53
1967     checkpoint43
1968     o added two new advection tests
1969     o added global 4x4 degree ocean test
1970     o added test of H&S94 with free surface on cube
1971     o some final mods for gradient check, adjoint,...
1972 heimbach 1.52
1973     checkpoint42
1974     Fixed AD-related problems:
1975     o Store directives up-to-date with re-arranged Adams-Bashforth
1976     (mainly thermodynamics.F)
1977     o New store directives for multi-dim. advection schemes
1978     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
1979     * new common block and key passkey
1980     (mainly gad_advection.F)
1981     o Modified store directives for split of dynamics/thermodynamics
1982     for the case ALLOW_KPP
1983     o Cleaned argument list for timestep_tracer.F
1984 adcroft 1.51
1985     checkpoint41
1986     o re-formatted/added comments in prologues of key subroutines
1987     to work with protex
1988 heimbach 1.47
1989 adcroft 1.50 checkpoint40
1990     o moved calc_gs, calc_gt and calc_tr1 back to model/src
1991     o added FLT (floats) package from Arne along with demo. experiment
1992     o re-arranged Adams-Bashforth scheme for tracers to allow easier
1993     implementation of forward-in-time forcing terms
1994     o more mods for non-linear free-surface including new variable
1995     o modified multi-dim method to work on cube
1996     o bug fix in KPP (from DM)
1997    
1998 adcroft 1.49 checkpoint40pre9
1999     o added DST advection schemes
2000     o fix MPI bug on SGI's
2001     o modifications for non-linear free-surface
2002     o fixed conditionals for fixed flow/passive tracer only mode
2003     o added tension/strain form of stress tensor
2004     o changes to commenting of arguments for TAF/TAMC
2005     o added/updated many matlab scripts
2006 adcroft 1.50 o added multi-dimensional advection method for tracers
2007 adcroft 1.49
2008 adcroft 1.48 checkpoint40pre8
2009 heimbach 1.47 o new package rw/
2010     Added method for dumping intermediate local arrays:
2011     mdsio_writetile - same as mdsio_writefield except works from inside
2012     bi,bj loop
2013     mdsio_writelocal - same as mdsio_writetile except works for local
2014     arrays
2015     write_local_r? - higher-level wrapper for mdsio_writelocal
2016     Controlled by diagFreq. Defaults to zero (ie. no dumps)
2017     Example given at end of mom_vecinv.F that dumps some local arrays.
2018     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
2019     control flux-form versus vector invariant code.
2020     Switch is runtime flag vectorInvariantMomentum (defaults to false)
2021     or genmake -DISABLE ...
2022     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
2023     (additional storing is now needed for case vecinv;
2024     currently nothing implemented to switch this storing off
2025     in case fluxform is used since no CPP flag available).
2026 heimbach 1.46
2027     checkpoint40pre7
2028     o bug fix in dynamics.F
2029     calc_viscosity called before k=1,Nr loop.
2030     o added some #ifdef's ALLOW_PASSIVE_TRACER
2031     o cleaned initialisations in ctrl_map_ini
2032     related to TAF
2033 heimbach 1.45
2034     checkpoint40pre6
2035     o split dynamics into thermodynamics & dynamics
2036     o corresponding split of calc_diffusivity into
2037     calc_diffusivity, calc_viscosity
2038     (kpp_calc_diff, kpp_calc_visc).
2039     o Added diffkr, kapgm to control variables
2040     o bug fix in gmredi_slope_limit for ldd97
2041 adcroft 1.44
2042     checkpoint40pre5
2043     o proper initialization of Adams-Bashforth time stepping
2044     + uses forward step for very first step of model (iter=0)
2045     o re-generated *all* output since almost all output is modified by this
2046     change (sorry but we've been putting this one off for about 2 years)
2047     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
2048     *not* regenerated since they are already out of date and I don't
2049     want to create the impression that they are suddenly working.
2050     o removed KAP stuff for DEC's
2051     o modified/added many .cvsignore files in */code and */input
2052     o added new expt "solid-body.cs-32x32x1"
2053     + this uses an alternative form of ini_curvilinear_grid.F which
2054     is not necessarily any better than the current one...
2055 heimbach 1.43
2056     checkpoint40pre4
2057     o added re-initialisations of utrans,vtrans,rtrans in
2058     calc_common_factors which are crucial for TAF.
2059     o extended iMin,jMin range for calc_common_factors,
2060     calc_diffusivity
2061     o added option ALLOW_PASSIVE_TRACER
2062     o a few minor updates and fixes
2063    
2064 heimbach 1.42 checkpoint40pre3
2065     o created calc_gtr1.F for gad package
2066     o split the_main_loop and re-introduced forward_step
2067     o some recomputations of nIter0 for TAMC
2068    
2069 heimbach 1.41 checkpoint40pre2
2070     o Updated to latest branch of AJA, JMC
2071     o Added gradient check package
2072     o Added routines for passive tracer handling
2073     o Added carbon sequestration sensitivity experiment
2074    
2075 heimbach 1.39 checkpoint39
2076     o Modifications and fixes to support TAMC
2077     (mainly missing or wrong directives)
2078     o Corrected common blocks when fooling TAMC to produce adjoint I/O
2079     in addummy_in_stepping
2080     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
2081     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
2082     o Included following packages:
2083     cal: calendar
2084     exf: external forcing
2085     ecco: essential routines to control use of cal, exf
2086     (NB: this is not the full ECCO environment)
2087 heimbach 1.40 o disabled some packages by default in genmake
2088 heimbach 1.39
2089 heimbach 1.38 checkpoint38
2090     o see notes_c37_adj.txt
2091     o corrected wrong layer index in external_forcing_t
2092     o replaced the_main_loop/forward_step by the_main_loop
2093     o removed forceoutput from write_state
2094     (replaced criteria for initial/final state)
2095     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
2096 jmc 1.36
2097 jmc 1.37 checkpoint37
2098     o mdsio.F routine split and packaged in pkg/mdsio
2099     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
2100     used unless genmake -disable=mdsio)
2101     o allow a more precise surface-geopotential gradient for the atmosphere
2102     taking into account the change in space of Alpha (=1/rho) at the surface.
2103     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
2104     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
2105     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
2106     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
2107     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
2108     o Time-Average diagnostics defined as a pseudo package "timeave".
2109     o pickup files : old pickup (before c35) did not work with new code (c35
2110     and after) unless activating 2 commented lines in initialise-varia.
2111     o Non-Hydrostatic pickup file Pb fixed.
2112     o bug with Rigid-lid version (since c35) fixed.
2113    
2114 jmc 1.36 checkpoint36
2115 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
2116 jmc 1.36 o recover Time-Average diagnostics
2117     o fix Pb in checkpoint (PR#19)
2118     o AIM become a standard package ; clean unused CPP_kees
2119 jmc 1.35
2120     checkpoint35
2121     o subtantial rewrite of dynamics.f
2122     o allows staggered time-stepping
2123     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
2124     o added bottom drag (linear + quadratic)
2125 heimbach 1.33
2126     checkpoint34
2127     o Modified exchange routines for correct reverse simulation.
2128     o Added verification output to comply with bug fix in impldiff.F
2129     as of c33 (exp2, natl_box).
2130     o Corrected store directives in dynamics.F
2131     o Corrected array boundaries in impldiff.F
2132     o Corrected array dimensions in gmredi.
2133     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
2134 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
2135 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
2136 adcroft 1.32
2137     checkpoint33
2138     o Fixed bug in lower BC in impldiff.F
2139     o Fixed confusion about units of forcing arrays in FFIELDS.h
2140     namely Fu,Fv,Qnet,Qsw,EmPmR:
2141     - Removed verification/natl_box/code/external_fields_scale.F
2142     (did not differ from that in model/src)
2143     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
2144     (see FFIELDS.h for description)
2145     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
2146     kpp_calc.F and kpp_transport_t.F
2147     - Removed model/src/external_fields_scale.F and calls to it
2148     - verification/natl_box uses flux data with "atmospheric" sign so
2149     a special version of external_fields_load.F is used to
2150     change the data as it's read in. This way, the arrays
2151     have the right units and signs at all times tha a user could
2152     possibly use them.
2153     o Corrected genmake to delete a temporary file during configuration
2154 heimbach 1.31
2155     checkpoint32
2156     o Scaling of forcing fields moved from external_forcing.F to
2157     external_fields_scale.F, called directly after loading fields.
2158     o Surface relaxation terms added to surface tendency fields in
2159     extra subroutine.
2160     o impldiff.F changed to avoid storing by TAMC of huge intermediate
2161     fields.
2162     o Changes in GMRedi to comply with packaging structure.
2163     o Modifications and bug fixes in KPP package.
2164     o Verification experiment for KPP added (verification/nat_box/)
2165 heimbach 1.30
2166     checkpoint31
2167     o Packages interface brought in line with defined standard
2168     -> new routines packages_...F
2169     -> changes in initialise_fixed.F, initialise_varia.F
2170     -> enables initialisation interface for ECCO package
2171     o Rescaling of external forcing fields immediately after read
2172     (removed from external_forcing.F)
2173     -> new: surface_fields_scale.F
2174     -> affects ini_foorcing.F, external_fields_load.F
2175     o Computation of surface tendencies before tendency updates.
2176     -> new: external_forcing_surf.F
2177     o Change of variable names useGMRedi, useKPP, useECCO
2178     o Further changes in dynamics.F, impldiff.F for TAMC
2179     o Tested for experiments 0, 2, 4.
2180     - not yet tested for GMRedi.
2181     - not yet tested for KPP.
2182 adcroft 1.29
2183     checkpoint30
2184     o Updates for OBCs
2185     o New experiment for test OBCs (internal_wave)
2186     o New output.txt in verification/exp4/results/
2187     o Updates for KPP: calculation of viscosity corrected, new variables
2188     kpp_dumpFreq and kpp_taveFreq
2189     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
2190     and entry for T90 in genmake
2191 adcroft 1.28
2192     checkpoint29
2193     o packaged KPP and GM/Redi
2194 heimbach 1.27
2195     checkpoint28
2196     o Corrected initialization of hFacMin for difference vertical coordinates
2197     o Modified calculation of partial cell thickness to more robust algorithm
2198     o config_summary.F: replaced write_1D_... by write_0D_...
2199     read_write.F: added subroutines write_0D_...
2200     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
2201     included some initialisations required for TAMC.
2202     o routine calc_isoslopes: modified sqrt computation to make it
2203     differentiable for zero argument.
2204     o routines dynamics, impldiff:
2205     included store directives and tape key computations required for TAMC.
2206     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
2207 adcroft 1.26
2208     checkpoint27
2209     o fixed calc_isoslopes() to so that cancellation of terms in tensor
2210     formulation works properly with variable resolution.
2211     o restructured the calling tree between the_model_main() and dynamics()
2212     o split initialise() into initialise_fixed() and initialise_varia()
2213     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
2214     in new routine ini_psurf()
2215 adcroft 1.25
2216     checkpoint26
2217     o moved some #ifdef in optional routines to encompass everything
2218     except the argument declarations. This was using up some memory.
2219     o fixed macros like _ADT to work with both versions of Linux cpp
2220     o cleaned up some unused and uninitialized variables
2221     (helps when debugging with strict compile options)
2222     o split up CPP_EEOPTIONS.h into options and macros
2223     (macros are now in eesupp/inc/CPP_EEMACROS.h)
2224     o patch for 2 processor JAM mode
2225 adcroft 1.24
2226     checkpoint25
2227     o updates for OBCs and NH
2228     o dramatically reduced memory usage
2229     o added "JAM" routines for use on Artic network
2230     o parameterization of convection by implicit vertical diffusion
2231     o added a diagnostic of convective index
2232     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
2233     (this is was partly for OBCs and NH but also in anticipation of
2234     an explicit free-surface option)
2235     o initial state input files for U and V
2236 adcroft 1.23
2237     checkpoint24
2238     o Removed some spurious "REAL"s
2239     o Updated KPP to latest version from JPL
2240     o Added a COS(latitude) in horizontal viscosity
2241 adcroft 1.22
2242     checkpoint23
2243     o Added del^4 diffusion for salt and temperature
2244     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
2245 adcroft 1.21
2246     checkpoint22
2247     o Made many small changes: implicit none, format(i5), etc...
2248     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
2249 adcroft 1.20
2250     checkpoint21
2251     o Introduced new I/O package that supports direct-access records (mdsio.F)
2252     o Split-up mid-level I/O routines
2253     o Updated input data for experiments 0,1,2,4 and 5
2254     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
2255 adcroft 1.18
2256 adcroft 1.19 checkpoint20
2257     o Tidied up open-boundaries some more
2258     o Added non-hydrostatic code
2259     o Fixed some input data
2260     o Modified MPI start-up to work in "coupled" context.
2261    
2262 adcroft 1.18 checkpoint19
2263     o Tidied up directory structure for verification experiments.
2264     o Added new code for open boundaries.
2265     o Corrected advective terms near boundaries.
2266     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
2267     o Implemented free-slip/no-slip BCs and del^4 dissipation.
2268 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
2269 cnh 1.17
2270     checkpoint18
2271     o Further changes for optional code generation with
2272     CPP - ugh!
2273 cnh 1.16
2274     checkpoint17
2275     o Beginning to incorporating modularity
2276     for supporting atmos. and ocean configs.
2277     o Small changes for TAMC complinace
2278     o New ultra simple test case. Barotropic box
2279     configuration "exp0".
2280 cnh 1.15
2281     checkpoint16
2282     o Minor changes to exchange routines to support
2283     accumulation in reverse mode. Adjoint of an
2284     assignment is an addition.
2285     o Changes to support compilation by TAMC (LR(1)
2286     syntax) and by g77 under Linux ( 72 character
2287     limit ).
2288 cnh 1.14
2289     checkpoint15
2290     Rewrote exchange routines to allow
2291     o General tile <-> tile connectivity.
2292     o TAMC reverse mode flag ( is this really needed? )
2293     o Variable width overlap and exchange region widths.
2294     o Hooks for sharing data via DMA, Arctic, Memory Channel,
2295     shmput/shmget, VIA, SYSV shmem and every other cool
2296     communication method.
2297 cnh 1.13
2298     checkpoint14
2299     Consistent isomorphism chages made. These allow dynamical core
2300     to support both pressure and meters as a vertical coordinate.
2301 cnh 1.12
2302     checkpoint13
2303     Release which corrects global_max problem and a couple
2304     of KGM time-averaging diagnostic errors. Also contains
2305     a double-gyre experiment setup as well as the baseline
2306     4 degree global template. The double gyre template is
2307     organised to allow it to be applied automatically to
2308     the baseline configuration.
2309 adcroft 1.11
2310     branch-point-rdot
2311     A few tidy-ups have been made bt the real point of this
2312     check-point (excuse the pun) is to allow a branch to be
2313     made for the purposes of adding the rDot alterations.
2314     I don't want to commit the rDot to the main-trunk until
2315     we've actually tested it...
2316 cnh 1.10
2317     checkpoint12
2318     Tidy up and added generic genmake script (formerly
2319     configure script).
2320     Released to testers.
2321 adcroft 1.9
2322     checkpoint11
2323     Re-arranged initialise() and introduced ini_vertical_grid()
2324     and ini_masks_etc().
2325 adcroft 1.8
2326     checkpoint10
2327     Introduced the configure script.
2328     Separated out the diags package.
2329     Added template for writing time-averages of tile/intermediate quantities.
2330     Updated SIZE.h in exp2 and made the data big-endian.
2331 adcroft 1.7
2332     checkpoint9
2333     MPI fix. Filename changes (meta/data). salbin*y stuff.
2334     General tidy-up.
2335     SST.bin SSS.bin added to verification/exp2
2336 adcroft 1.6
2337     checkpoint8
2338     Inludes time-dependant forcing and time-averaging.
2339     Works at 4x4 and 2.8125x2.8125 global
2340    
2341     checkpoint7-4degree-ref
2342     Branch from checkpoint7. Released for application to
2343     global modeling and general modeling - process studies, regional
2344     model etc..
2345     Configured for verification/exp2 - 4 degree global, two process.
2346 cnh 1.5
2347     checkpoint7
2348     Created by cnh
2349     Simple 4 degree global simulation
2350     configuration.
2351     Includes climatological wind,
2352     hydrography, bathymetry etc
2353     Does not include Heat Flux and E-P
2354 cnh 1.4
2355     checkpoint6
2356     Created by cnh
2357     merged checkpoint5 with CD and
2358     spherical polar code.
2359     Still some problems with GM Redi
2360     abd full topography.
2361 cnh 1.3
2362     checkpoint5
2363     Created by AJA
2364     contains updates to GM Redi
2365     and reordered timestepping loop
2366     for Implicit Diffusion.
2367 cnh 1.2
2368     checkpoint4
2369     Created by cnh
2370     Contains memory saving macros ( _rdxc etc..) for when
2371     grid variations are limited.
2372     Contains polynomial coeffs for EOS and knudsen program
2373     for generation.
2374    
2375 cnh 1.1 checkpoint3
2376     Created by cnh
2377     Added extra flags for runtime options
2378     Added this file
2379     Added implicit free-surface
2380     Added pre-conditioner
2381     Put compare01 into repository ( compare01/... )
2382     Put data and eedata into repository ( verification/exp1 )
2383    
2384     checkpoint2
2385     Created by AJA
2386     Added GM/Redi
2387    
2388     checkpoint1
2389     Created by AJA
2390     Restructured kloop in dynamics.F
2391     Added non-linear EOS
2392    
2393 cnh 1.2 baseline
2394     Original checked in code
2395 cnh 1.1

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