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revision 1.1135 by jmc, Sun Jun 28 16:55:11 2009 UTC revision 1.1355 by jmc, Wed Dec 22 00:41:46 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/mdsio+rw:
8      new S/R to read local (or tile independent) vector (read counterpart of
9       mds_writevec_loc, and front-end write_glvec_rl/rs).
10    o global_ocean.cs32x15: additional input_ad.seaice experiment
11        that uses pkg/seaice rather than pkg/thsice.
12        (using multidim advection for seaice)
13    o towards more F95 syntax for array specification in namelist:
14      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
15        of all verification experiments.
16           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
17          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
18      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
19    o global_ocean.cs32x15: additional input.seaice experiment
20        that uses pkg/seaice rather than pkg/thsice.
21    
22    checkpoint62p (2010/12/17)
23    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
24        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
25    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
26        allow for use of multim. advection in seaice adjoint.
27    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
28      - first attempt to close budgets by taking into account the freshwater
29        flux implied by the sublimation of snow and ice. So far only the
30        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
31        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
32    o eesupp/src:
33      new S/R with new option (NML_EXTENDED_F77) to change array specification
34      from F95 standard to commonly accepted extended F77 form.
35      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
36      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
37      for less tolerant f77 compiler (e.g., pgf77, g77).
38    o globalFiles:
39      commented out in parameter file "data" since it's not safe with MPI
40      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
41      in this case); no longer commented out in restart test (tst_2+2).
42    o add adTapeDir to specify a special directory where adjoint tapes are
43      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
44      and cannot be used together with mdsioLocalDir.
45    o nesting pkgs:
46      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
47      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
48      - add parameter files + utils dir + output from short run on beagle.
49    o pkg/seaice:
50        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
51    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
52      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
53    
54    checkpoint62o (2010/11/25)
55    o pkg/exf:
56      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
57    o pkg/seaice:
58      - seaice_ocean_stress: split a loop for better vectorization of the
59        adjoint code
60      - seaice_growth.F: fix bug in conservation of freshwater connected to
61        capping of heff, put contribution into d_HEFFbyNEG
62      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
63        by something more sensible (parameters that are what their name implies)
64      - change some defaults, so that by default exf-parameters are used for
65        things like rhoAir, cpAir,latent/sensible heat parameters, in order
66        to reproduce the old results, many data.seaice now contain funny values
67        for cpAir and latent heat of sublimation
68    o packages_readparms.F: move exf_readparms up in line so that
69        exf-parameters are visible for other packages (e.g. seaice)
70    o debugMode & debugLevel=2:
71      - differentiate between debugMode & debugLevel=2:
72        debugMode: controls printing of debug messages (sequence of S/R calls).
73        debugLevel: controls printing of algorithm intermediate results and stats.
74      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
75        => allows to print debug-stats without all sequence of call messages.
76      - switch control of debug print from debugLevel to debugMode in many S/R.
77    o pkg/obcs (obcs-sponge):
78        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
79        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
80    o pkg/generic_advdiff:
81      - record overlap minimum size for each advection scheme;
82      - refine criteria on overlap minimum size;
83      - check and stop (in gad_check) if overlap size is too small.
84    o pkg/obcs:
85      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
86        once, in ptracers_implicit.F)
87      - with seaice: remove test on empty file name in obcs_apply_seaice (always
88        apply OB values when tile has OB)
89    o model/src, coriolis setting:
90      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
91        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
92        files (selectCoriMap=3) with any grid.
93      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
94    o pkg/seaice/seaice_growth.F:
95        a few cosmetic changes that reduce the number of lines of code
96    o pkg/obcs: add boundary conditions following Stevens (1990)
97      - the code follows old MOM/NAOSIM code
98      - so far it is only implemented for the eastern and western boundaries
99        and NOT for pTracers
100    o pkg/rbcs:
101      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
102        beginning of the first rbcs forcing period.
103      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
104        offline package, i.e., one file per time, labeled by iteration number;
105        deltaTrbcs sets the timestep with which the data was generated;
106        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
107      - rbcsForcingCycle=0 makes forcing non-cyclic.
108      - make arithmetic safe for negative times and odd forcing periods.
109    
110    checkpoint62n (2010/11/09)
111    o pkg/seaice:
112        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
113    o pkg/obcs:
114       New S/R to copy tracer value from the OB location to narrow band region
115        (width = same as overlap) beyond the OB: preserve OB value (needed for
116        high-order scheme) which were overwritten by EXCH call if in overlap
117        region. Applied to theta, salt, ptracer and advected seaice variables.
118       With seaice: use maskInC in similar way as in gad_advection.F,
119        in seaice_advection.F and advect.F.
120       Update output of experiment seaice_obcs and change exp4 to test OBCS with
121        4th order Adv.Scheme. for pasive salt and ptracer.
122    o tools/genmake2:
123      - when looking for an optfile (not specified), only search for Fortran compiler
124        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
125      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
126        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
127      - set default for CPP to "cpp -traditional -P" (was the case without specifying
128        an optfile, but otherwise default was just "cpp".
129      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
130      - when "CC" is not set in the optfile, look for possible C compiler
131        (instead of just setting CC=cc)
132      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
133        => add a ".F" to ".o" rule for source files with no "#include" (such as
134           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
135      - move gfortran before g77 in list of possible Fortran compiler (consistent
136        with reference compiler switch from g77 to gfortran)
137    o pkg/seaice:
138      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
139        seaice_check that stops the model, when the CPP flag is used.
140      o seaice_growth.F: make capping of ice volume conserving by returning the
141        capped ice as freshwater to EmPmR. This does not change the verification
142        experiments but will change runs where the capping is acutally active
143    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
144      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
145         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
146         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
147    o tools/genmake2:
148      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
149      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
150      - clean previous genmake log files before anything else.
151      - change Makefile to remove testreport log files (*.tr_log) and genmake log
152        files only with "CLEAN" target (instead of "Clean");
153    o pkg/generic_advdiff:
154      Change OBCS in multiDim advection (gad_advection.F):
155       Use maskInC to prevent intermediate update of tracer-field in OB regions,
156       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
157       which were applying future time-step OB values.
158      This way, all explicit calculations use current-time-step OB values
159       (simpler and more consistent).
160      Affects results when set-up uses time-varying OBC and multi-dim advection;
161       update output of experiment seaice_obcs.
162    o pkg/seaice:
163      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
164       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
165         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
166      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
167       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
168       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
169    o pkg aim (2010/10/26):
170      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
171        formulation with obliquity, eccentricity, ... as run-time parameters,
172      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
173        upward shortwave radition at the surface (all-sky and clear-sky).
174    o pkg/obcs:
175      - writing sections with globalFiles=T does not work: switch to tiled-files
176        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
177      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
178      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
179    
180    checkpoint62m (2010/10/21)
181    o pkg/seaice: vectorize seaice_solve4temp.F
182      - move iterations loops outside of i/j-loops
183      - requires 2D arrays for TB and effConduct
184      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
185        modified in this routine
186      - a little bit of clean up, adjusting indentation, etc.
187      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
188        performance and '**TWO' by '**2' (because TWO is a float),
189        replaced ONE, ZERO
190    o eesupp/src:
191       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
192    o pkg/seaice/seaice_growth.F
193      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
194      merging process. The merged routine has two branches, and one activates the 'evolution'
195      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
196      In summary, here is what the '10/10 revision' did consist of
197        part 1: seaice_growth.F revisions 1.71 to 1.75
198          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
199            The emphasis here was on improving readability (e.g. by trying to use meaningful
200            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
201        part 1.5:
202          - revising the lab_sea experiment to make it a more useful (i.e. stable
203            and representative of an actual model run). This was done by generating a
204            (winter) pickup to start from, switching back the main experiment dynamic
205            solver from evp to lsr, having one of the experiments use the free drift solution.
206        part 2: seaice_growth.F revisions 1.76 to 1.85
207          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
208          - Sorting out the various fields units and sign (set early on and reset at the end)
209            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
210            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
211          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
212            and simplifying logical expressions to further improve readibility.
213        part 3: seaice_growth.F revisions 1.86 to 1.89
214          - Re-organize the blocks of code more logically.
215          - Merging the '_if.F' pieces that add something new.
216    o pkg/thsice:
217      - vectorize thsice_solve4temp and thsice_get_exf.
218        Problem: thsice_solve4temp has an unvectorizable statement that
219        might also be problematic for TAF
220      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
221        does not change the verifcation experiment, but will change all
222        experiments that have this flag undefined (not tested in verification);
223        a little reorganization to save a few 2D fields and recomputations
224      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
225      - 2nd step:  fix some store dirs
226        o seems to work somewhat, i.e. using ifort but not g77
227        o likely cause are incomplete init. or recomputation
228        o start verification/global_ocean.cs32x15/input_ad.thsice
229    o pkg/obcs: add support for exch2
230      - the position of the boundary and prescribed values are specified using
231        a global domain with exch2 facets stacked
232        - in x for N,S boundaries (like W2_mapIO=-1)
233        - in y for E,W boundaries (so E,W boundaries do not overlap)
234    o pkg/mdsio: add support for writing global sections with exch2
235        file layout is as for obcs described above:
236        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
237        - for y-z sections, facets are stacked in y
238    o pkg/thsice:
239       - change a few routines for better vectorization: thsice_albedo.F,
240         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
241         not affected, but in particular the latter routine has changed
242         dramatically (not necessarily easier to read now).
243       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
244       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
245    o verification/lab_sea:
246      - overhaul of the forward model experiments. The main motivation
247        for this revision is that lab_sea has proven quite fragile (when
248        changing the sea-ice code, and switching platforms) to a point
249        when failures were very hard to attribute to specific code problems.
250      - the suspected reason for this fragility is noise amplification by evp so,
251        to start with, we decided to replace evp with lsr in the main experiment.
252      - the input.lsr experiment thus became obsolete and was removed.
253      - it was replaced with the input.fd experiment that uses an
254        analytical "free drift" solution as the ice velocity field.
255      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
256        will hopefully allow us to discriminate problems due to dynamic solvers
257        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
258        us to test additional options, along with the salt plume package.
259      - Finally a pickup was generated (at the end of a one year run) to
260        make the tests more representative of an actual model run. Previously
261        the tests starting point was a 1m thickness of ice everywhere.
262    o pkg/seaice:
263      - introducing S\R seaice_freedrift.F that compute the
264        analytical solution to an approximate ice momentum
265        equation (i.e. the simple stress/coriolis balance).
266      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
267        of the free drift velocity field, and enable its use.
268        To actually use the free drift solution as the model ice
269        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
270    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
271    
272    checkpoint62l (2010/10/04)
273    o pkg/seaice:
274      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
275      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
276       version (with USE_ORIGINAL_SBI undef);
277    o add hooks for new packages OASIS, the package will follow
278      (hooks exclude the seaice pkg for now)
279    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
280      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
281      rather than mdsio_readvector.F/mdsio_writevector.F, within
282      adread_adwrite.F to read/write adjoint-related tapes to disk.
283    o eesupp and pkg/mdsio: ALLOW_WHIO
284      Option to write/read 2D fields to files including tiles halos.
285      The main purpose is for adjoint related "tape I/O".
286      The secondary purpose is for debugging phases.
287      A word on those rather specifically intended purposes.
288      The code was meant to be stripped down to the bare minimum.
289      Typically, there is a unique and basic mapping to the global
290      buffer (tile by tile, then proc by proc, then level by level), and
291      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
292      meant to generate user friendly outputs of various shapes and forms.
293      Rather it is intended, for the knowledgeabale developers,
294      to be largely independent of the many mdsio options, to allow
295      outputs of tiles+halos in debugging phases and in adjoint runs,
296      and to allow some flexibility in tuning (adoint) I/O depending on each
297      file system behavior. With regard to tuning, most of the potential knobs
298      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
299      to specify directories, to specify the typical size of I/O calls, etc.)
300      are not yet included, and will be added if they prove useful.
301    o pkg/seaice:
302       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
303    o pkg/seaice:
304       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
305       code (seaice_budget_ice_if.F) which enable to recover old standard
306       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
307       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
308    o model/src (rStar):
309       use simple average (not area weighted) of rStarFac at U,V point when using
310       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
311       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
312    
313    checkpoint62k (2010/09/17)
314    o adjoint
315       * changed verification/global_ocean.cs32x15 ; adjoint now tests
316         Adams-Bashforth 3 + NLFS + RSTAR
317       * some more modifs required for ECCO-GODAE v4
318    o pkg/seaice
319       add SEAICE_AGE_VOL option to use volume instead of area for
320       integrating SEAICE_AGE
321    o model/src:
322       first check-in of sigma & hybrid-sigma coordinate code ; also includes
323       non-linear free-surface parts ; but pressure-gradient not yet coded.
324    o pkg/ptracers:
325       option for ptracer to convert Salt Relax into additional EmP.
326        tested in exp. global_ocean.90x40x15.dwnslp (update output)
327    
328    checkpoint62j (2010/08/25)
329    o pkg/ggl90:
330       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
331    o pkg/dic: car_flux.F, phos_flux.F
332      - reduce number of exp-calls in order to improve performance
333      - clean up a little (replace fields by their macros, etc., fix
334        typo in CPP-flag)
335    o pkg/ggl90: minor changes
336      - GGL90diffKrS was removed --> always use GGL90diffKr
337      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
338      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
339        (commented out for now)
340      - change in max/min operations to ensure that smoothing is ok
341      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
342      - always use diffKrNrT as background profile (i.e. never use diffKr field)
343    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
344    o pkg/dic:
345      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
346        vectorization
347      - small bug fix in insol for the unlikely case of a cartesian grid
348      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
349        + now vectorize, which also removes adjoint recomputations;
350        + replace integer maksp1 by _RL maskp1
351        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
352    
353    checkpoint62i (2010/07/21)
354    o pkg/flt:
355      - with OBCS: stop floats which enter the OB region
356    o model/src:
357      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
358        for implicit vertical advection.
359    o pkg/seaice:
360     - account for melting in seaice age evolution.
361     - remove double counting of seaice ridging effect on seaice age.
362    
363    checkpoint62h (2010/06/18)
364    o pkg/exch2:
365     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
366    o tools/genmake2
367      - remove "-pdefault" option: redundant with the use of "packages.conf";
368      - remove file pkg/pkg_default : set the default as a pkg group
369        ("default_pkg_list") defined in pkg/pkg_groups;
370      - fix for case pkg/pkg_depend is missing (was hanging before);
371      - add option "-pgroups" to specify a different pkg_groups than the default.
372    o verification/adjustment.cs-32x32x1:
373       add a "minimal" set-up test (code_min & input_min) which only compiles
374       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
375    o tools/genmake2
376      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
377      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
378    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
379      files are nearly the same anyway.
380      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
381       - redefinition of tau(i,i) (by a factor of ustar)
382       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
383       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
384       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
385       - replace
386         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
387         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
388         by
389         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
390         (changes results)
391       -> exf_bulkformulae v1.22,
392          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
393          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
394                    output.txt 1.63
395           offline_exf_seaice: output.seaicetd.txt 1.7
396           seaice_obcs: output.txt 1.10)
397      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
398       -> exf_bulkformulae v1.23,
399          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
400          and global_ocean.cs32x15.icedyn (only 11 matching digits)
401      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
402    o adjoint of exch-1:
403     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
404       (note: was already like this when using EXCH-2) and remove flow dir
405       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
406     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
407     - update pkg/exch2 diff list.
408    
409    checkpoint62g (2010/05/19)
410    o eesupp/src (exch-1):
411     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
412       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
413       (renamed to exch1_*rx_cube.F).
414     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
415       to call new exch1 S/R ; update Makefile and .cvsignore.
416     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
417       exch2_xy_rx later)
418      Note: after updating your code, need to run "make clean" in eesupp/src
419    o test experiment bottom_ctrl_5x5:
420       new output_adm.txt with fewer grdchk & less monitor output.
421    o model/src:
422      remove the call to ini_cori in initialise_varia.F (just keep the usual one
423       in initialise_fixed.F). More consistent with coriolis & horizontal grid
424       beeing treated in the same way (ini_grid is not called a 2nd time).
425    o pkg/exf:
426      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
427      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
428      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
429      - cosmetic changes to exf_bulkformulae.F to make it look more like
430        exf_bulk_largeyeager04.F
431    o eesupp/src (exch-1):
432      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
433      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
434        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
435        (even without using MPI).
436      - Message mode: move RecvAck setting (indicator of buffer being ready)
437        from send_put to recv_get S/R (was useless before, but not sure if
438        it's much more useful now);
439      - Switch the order of sync: MPI-proc 1rst and then threads;
440      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
441      - fix AD code for communication mode ='get' (but not used).
442    o model/src:
443      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
444      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
445    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
446    o pkg/ctrl: require a specific set of control variables and exf-flags for
447      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
448    o model/src:
449     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
450       1rst forward sweep, to avoid over-writing output files during recomputations
451       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
452     b) 2nd version:
453      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
454      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
455         writePickupAtEnd) + seaice & ptracers output;
456      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
457    o model/src:
458      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
459    o pkg/exch2:
460      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
461      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
462    o pkg/autodiff & exch2:
463      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
464      (for now, only if ALLOW_EXCH2 is defined).
465    o pkg/autodiff:
466      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
467        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
468       + clean-up comments (_RS is not always real*4)
469      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
470      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
471        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
472    o testreport (AD-tests):
473      no longer link files from dir "../input" (1rst link files from
474      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
475    
476    checkpoint62f (2010/04/29)
477    o model/src/the_main_loop.F:
478      adjust store directives for seaice evp and multicategory according to
479      pkg/ecco/the_main_loop.F
480    o adjoint:
481      global_sum_ad was incomplete (noted many times by many people ;)
482      nice description by Jean U. as follows:
483      * allreduce(var) in global_sum.F can be interpreted as
484        reduce(sum) followed by broadcast of sum.
485      * The adjoint of that is
486        sum(adjoint) followed by broadcast(summed adjoint value)
487        or in other words, allreduce(sum, adjoint vars)
488      We were missing the sum(adjoint)!
489      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
490      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
491      The fix should produce 16-digit accuracy between
492      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
493      multi-CPU single-tile (e.g. nSx=1, nPx-2)
494      We'll probably change this yet again shortly
495    o eesupp/src:
496      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
497    o pkg/icefront
498      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
499        specification of addmass array based on a 2D field, which is added
500        at bottommost wet level at each horizontal location.
501    o model/src:
502     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
503     layout; (not always compatible with delX,delY setting; commented out for now).
504    o pkg/exch2:
505     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
506     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
507    
508    checkpoint62e (2010/04/15)
509    o pkg/obcs:
510      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
511    o pkg/dic:
512      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
513        (note: not presently tested in any forward verification exp.)
514       update tutorial_global_oce_biogeo AD output file.
515    o pkg/exf:
516      - account for the variation of albedo as a function of zenith angle
517        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
518    o build_options:
519     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
520    o pkg/dic:
521      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
522      - use binary pickup file for restart;
523      - initialise atmos-CO2 box from dic_pCO2 parameter;
524      - fix multi-threaded.
525    o pkg/rbcs:
526     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
527       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
528     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
529       and update output.txt
530    o pkg/kpp:
531     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
532     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
533       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
534       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
535     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
536       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
537    o pkg/offline:
538      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
539      (bug was added in version 1.10 on 2007-08-23).
540    o pkg/offline:
541      - no need to specify periodicExternalForcing, etc ... to use offline pack
542      - offline input files no longer just single prec --> parameter offlineLoadPrec
543    o verification/lab_sea:
544      change AD test to multi-tile setup and update all 4 AD output.
545      NOTE: while cost function values remain very similar,
546      gradients are very different, although gradient checks are self-consistent
547      Should try to get to the bottom of this (cost function summation order?)
548    o pkg/dic:
549      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
550      a weakness of TAF that drops part of double precision in log10 derivative.
551      <= changes removed since problem has been fixed in current TAF version 1.9.71
552      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
553    o pkg/ecco:
554      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
555      update all 4 lab_sea AD output.
556    
557    checkpoint62d (2010/03/22)
558    o build_options:
559      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
560    o remove unbalanced quote (single or double) in commented line of source code
561      (may cause some warning with some preprocessor/makedepend versions).
562    o pkg/seaice:
563      fix seaice_model.F for adjoint (gael) and update AD results of experiments
564       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
565    o testreport:
566      add option '-runonly' (short: '-ro') to just do the run part (without make).
567    o eesupp: remove JAM communication code (obsolete).
568    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
569      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
570      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
571      (update also the output).
572    
573    checkpoint62c (2010/03/02)
574    o tools/build_options :
575       move (some) old optfiles from build_options/ to build_options/unsupported/
576    o model/src and pkg/exf
577       surface relaxation -- separating data and data.exf options
578       The point is to ensure that we specify the surface relaxation
579       either in data or in data.exf (but not half and half) and to
580       avoid an accidental relaxation to 0 (which happened if a time
581       scale was specified but the file name was left empty)
582    o model/src model/inc and pkg/mom_common
583       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
584       => addition to the viscosity field as computed by others schemes
585    o tools/build_options:
586      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
587        but keep the former optfile for few weeks for smooth transition
588    o pkg/ecco
589      - allow user defined cost function contributions
590         CPP: ALLOW_USERCOST_CONTRIBUTION
591         USAGE: compute contributions in cost_usercost_all.F
592      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
593          the two options are complementary.
594    o pkg/smooth
595      - migration from contrib to the main repository
596    
597    checkpoint62b (2010/01/26)
598    o pkg/monitor:
599      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
600        (in case someone forgot to update customized pieces of code)
601    o nonHydrostatic:
602      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
603      - add a simple 2-D experiment (short_surf_wave) to test it.
604    o pkg/icefront:
605       adding the shell of, and the hooks to, a new package that
606       will model melting and freezing of vertical glacier ice fronts
607    o momentum:
608      add diagnostics of momentum tendency from Hydrostatic pressure gradient
609       (without surf.pressure term: would need a 2nd filling since implicit term).
610    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
611      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
612      cannot deal with the former
613    o cleaning:
614      - remove all (except OpenAD) old TLM output from results_ad dirs.
615      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
616      - comment out maskH definition (replaced by maskInC)
617    o pkg/monitor:
618      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
619        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
620    
621    checkpoint62a (2010/01/15)
622    o model/src:
623      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
624    o pkg/diagnostics:
625      - add optional level number diagnostics (i.e., level number to be define
626        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
627      - strictly check for valid parser-code(10) ;
628      - check if adding diag to the list from the right place.
629    o pkg/longstep:
630      - change parameters and fix tracer conservation with rstar/nonlinear free surface
631    o diagnostics:
632     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
633       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
634    o pkg/diagnostics:
635     - Add option for writing vertical integral (sum of selected levels) of an output
636        field instead of writing output field levels. Activate this option on a per
637        output-file basis, by setting the 2nd character of fileflag to 'I'.
638     - Add field-specific information relative to level integral in 3rd postion
639        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
640        vertically (x level-thickness x hFac), "r"=same but without hFac.
641    o do_the_model_io:
642      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
643        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
644        writing pickups and stopping.
645    o pkg/diagnostics (for now, only with mdsio):
646      - write time information to meta file (and modify accordingly rdmds.m) :
647        time-averaged diagnostics output: write starting and ending time of the
648        time-averaging interval ; snap-shot diagnostics output remains unchanged;
649    o pkg/timeave:
650      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
651        always Nr), now assumed to be equal to number of levels of averaged field;
652        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
653    o pkg/sbo:
654      - fix ocean bottom pressure global-average & 2-D time-ave output (was
655        neither initialised nor filled).
656      - add starting iteration in suffix of global-average output file
657        (to avoid over-writing the file after a restart)
658      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
659    o time-average:
660      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
661        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
662         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
663        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
664      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
665      - fix missing accumulation for pkg/opps.
666      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
667         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
668      - fix initialisation of time-ave vars and do only full time-step increment
669        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
670    o pkg/layers:
671      - use standard RW pkg S/R to write the output
672        and remove local write_fld version (which had a problem).
673      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
674      - fix LAYERS_CALC argument list.
675    o pkg/timeave:
676      - store cumulative-time in a simple tiled array (drop the level index)
677      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
678    o pkg/ocn,aim_compon_interf
679      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
680    
681    checkpoint62  (2009/12/23)
682    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
683        (was not previously tested in any other exp.)
684    o pkg/monitor:
685      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
686        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
687        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
688      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
689      - change del2 calculation.
690      - use interior masks (instead of maskH, <- to be remove).
691      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
692    o mask & obcs:
693      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
694      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
695        (called after packages_init_fixed)
696    o pkg/obcs:
697      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
698        Fixes bug in obcs+exf with nSx*nSy.GT.1
699      - fix multi-tile handling in obcs balance code
700    o nonHydrostatic:
701      - Implement AB-3 for non-hydrostatic vertical momentum ;
702        (change ordering of var. stored in pickup file when using NH)
703      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
704      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
705        (in prep. for new NH free surface form).
706    o pkg/obcs:
707      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
708    o model/src:
709      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
710    
711    checkpoint61z (2009/12/01)
712    o nonHydrostatic:
713      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
714        a spurious source of energy in simple baroclinic adjusment test case.
715      Update all non-hydrostatic exp output.
716    o model/src (3-d solver):
717      Change again 3-D solver free-surface RHS term when exactConserv=T:
718        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
719        (which was not the case with previous formulation).
720      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
721      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
722    o nonHydrostatic:
723      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
724        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
725      - change 3-D solver to work with r* (for now, only with linear free-surf.)
726      - add few debug diagnostics (cg3d_x, residual)
727    o model/src:
728      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
729        update output of exp. global_ocean.cs32x15.viscA4
730    o update output of exp. global_ocean.cs32x15.icedyn after removing
731      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
732    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
733    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
734      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
735    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
736      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
737      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
738      to test this code
739    o pkg/cd_code:
740      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
741       C-grid momentum. D-grid velocity used to be stepped forward in time with
742       Adams-Bashforth only on surface pressure term. Tests show that using AB on
743       D-grid coriolis term improves stability (as expected from CD-scheme paper).
744      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
745      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
746       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
747       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
748      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
749           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
750    o pkg/obcs:
751     - fix bug in initialisation (broken since Oct 1rst modification)
752       for useOBCSprescribe without useEXF.
753    
754    checkpoint61y (2009/11/15)
755    o pkg/seaice
756     - change (once again) the discretization for the evp solver: rather than
757       squaring the averages of strain rates, average the squares to give
758       a better approximation to VP behavior (in simple test); this breaks
759       verification experiments that use EVP (lab_sea and lab_sea.hb87)
760        --> update outputs
761    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
762      to improve vectorization of adjoint code on TARGET_NEC_SX
763    o verification/vermix:
764      - change vermix to a more "classical" 1d column with high vertical
765        resolution, seasonal heat flux forcing and constant wind forcing
766        --> update outputs
767    o pkg/seaice
768     - fix diagnostics of principal stress components for EVP
769     - add optional diagnostics of non-linear convergence for LSOR solver
770     - make maximum zeta a runtime parameter
771    o model/src (3-d solver):
772      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
773       which consisted in removing the Surf. Non-Hydrostatic pressure from the
774       whole column and adding it to Eta (inspired from Casualli, 1999):
775       Only affects 3-D solver initial guess and only if using ExactConserv,
776       but tests did show a degradation of solver convergence. For this reason,
777       decide to disable this piece of code.
778       to recover previous version, just set zeroPsNH = exactConserv (line 78).
779      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
780    o pkg/ggl90:
781     - fix previous modif (unfortunatly has not been documented here).
782    o pkg/seaice/autodiff:
783     - add CPP flag to include clipping of zeta in EVP code;
784       although clipping of zeta is not necessary for EVP and not recommended
785       it was done by default, now clipping is disabled by default
786     - modify computation and store zetaC/Z in seaice_evp for TAF
787     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
788     - change seaice_calc_viscosities/strainrates for better
789       vectorization after AD by TAF
790     - rearrange common blocks in SEAICE.h once again for easier dumps of
791       adjoint output, adjust adcommon.h and g_common.h
792     - change flux form of default advection scheme for better vectorization
793       of adjoint code
794     - modify lab_sea/input.lsr to test the flux form of default advection
795       scheme
796    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
797      transition in checkpoint61r)
798    
799    checkpoint61x (2009/10/19)
800    o adjoint: adding two new verification experiments
801      * tutorial_global_biogeo: an online dic sensitivity experiment
802        (work with G. Forget)
803      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
804        (an update of the Dutkiewicz et al., 2006 paper)
805      Both use the same CO2FLUX cost function, but different controls
806      Gradient checks look good, but some recomp. could still be traightened out
807      Should add xx_dic control variable to test at some point
808    o model/src:
809      add run-time parameters to check and/or mask initial Temp & Salt
810    o pkg/ptracers:
811      apply zonal filter (if used) to all passive tracers
812    
813    checkpoint61w (2009/10/12)
814    o adjoint:
815      * update and finish work on adjoint of dic package (G. Forget)
816      * start adjoint of offline package
817      * bug fix for cube-sphere TLM code (active_file_g.F)
818    o tutorial_global_oce_optim:
819      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
820      and add SIZE.h_mpi for MPI testing
821    o pkg autodiff
822     - fix bug in autodiff_restore
823     - make genmake2 remove comments and empty lines from ad_input_code.f in
824       order to reduce file size (new script file remove_comments_sed)
825    o allows to specify vertical profile of vertical viscosity (viscArNr)
826    o pkg autodiff
827      autodiff_ini_model_io: comment out writing of grid information to netcdf
828      files, because at this time the grid fields are a bunch of zeros
829      (this is analogous to ini_mnc_vars.F)
830    o pkg seaice/autodiff:
831     left-over from removing the 3-time-level fields:
832     - small rearrangement of common blocks (SEAICE.h)
833     - fix field declaration in order to get meaningful output in
834       adseaice.*.nc (adcommon.h)
835    o pkg obcs:
836     - go through NH code only if nonHydrostatic=T
837     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
838     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
839       => Update output of experiment seaice_obcs
840     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
841     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
842     - fix restart for useOBCSprescribe + useEXF
843    o pkg ctrl
844     - make obcs as control parameter work also with useSingleCPUio
845     - replace a few sny and snx by Ny and Nx to be consistent with
846       ctrl_set_globfld_x/yz.F
847    o pkg seaice
848     - re-introduce global field frWtrAtm for the case of
849       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
850     - catch the case of an empty filename in seaice_cost_init_fixed.F
851    o pkg ecco:
852     - small bug fixes in the_main_loop
853      . fix order of monitor arguments
854      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
855      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
856        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
857     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
858       imbalance diagnostics for wmean_h/sflux = 0
859     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
860     - catch the case of empty filenames in ecco_cost_init_fixed.F
861       and ecco_readparms.F
862     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
863       to make this statement meaningfull in ecco_cost_weights.F
864    o pkg zonal_filt:
865      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
866      - when using rStar, filter uVel*hFacW instead of uVel
867       (tested without topography: fix a Pb of growing instability with NLFS)
868    o pkg/aim/thsice:
869     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
870      (works as SST restoring)
871    o pkg/thsice:
872     -add specific parameter for salt restoring in slab mixed-layer
873       (by default equal to the temperature restoring)
874    
875    checkpoint61v (2009/09/21)
876    o pkg/kpp:
877     -add double diffusive contributions as a hack, turned off by default
878      for now, and the code can be excluded with a CPP-flag
879      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
880     -add a verification experiments to "vermix" to test this code
881    o pkg/mom_common:
882      Move computation of length scales to mom_init_fixed.F (avoid recomputation
883      at each time-steps*levels).
884    o pkg/layers:
885      Created a new package for computing volume fluxes in temperature or
886      [not yet implemented] density layers, e.g. for calculating residual
887      overturning circulations.
888    o pkg/diagnostics:
889      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
890    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
891    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
892      To avoid mixing type (RS/RL) of input/output array argument,
893      replace single mixed-type array with a pair from each type (RS/RL).
894    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
895      is now implemented for all pkgs (previously only done for the main pickup)
896    
897    checkpoint61u (2009/08/25)
898    o pkg/obcs:
899      - change OB?eta from _RS to _RL and put them into a separate commen block
900      - add code to read OB?eta from a file via obcs_prescribe_read: the code
901        compiles and does not destroy any other experiments, the data is read
902        properly, but the code is not tested in actual applications
903    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
904      create a meaningful unit attribute for the time coordinate variable
905    o pkg/ebm: add plenty of missing "_d 0" ;
906       update results of experiment global_ocean_ebm (fwd + adjoint tests)
907      Notes: several pieces of code only works for (very) specific set up
908       (domain size, lat range, etc ...); should be documented & stop if one
909       of those assumptions is not meet.
910    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
911       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
912          and offline_exf_seaice (seaicetd + adjoint).
913    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
914       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
915        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
916    o few changes to pass when compiling with strick checking of arguments
917       across S/R (allow to find few bugs in S/R calls).
918    o pkg/seaice:
919     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
920       2d-fields, for slightly better performance
921    
922    checkpoint61t (2009/07/22)
923    o pkg/seaice:
924     - remove unused variables in seaice_evp
925     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
926    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
927       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
928       each processor opens a different file (a fix from Matt).
929    o cg2d:
930       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
931       this reduces number of EXCH calls by 2 when using exch2.
932       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
933       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
934    o pkg/thsice:
935       add code for Near Infra-Red albedo (from Jeff)
936       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
937    o ini_model_io:
938       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
939       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
940       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
941    
942    checkpoint61s (2009/06/30)
943    o pkg/exch2 (exch2_rxN_cube*):
944       remove last BARRIER (no need to synchronise after getting data from shared
945       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
946    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
947      and generate new output (for the 2 tests) using default rotationPeriod.
948  o pkg/exch2:  o pkg/exch2:
949    - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F    - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
950      (was already the case with AUTODIFF_EXCH2 defined)      (was already the case with AUTODIFF_EXCH2 defined)
951    - add bj in exch2 arrays and S/R.    - add bj in exch2 arrays and S/R.
952      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
953        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
954  o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep  o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
955    - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY    - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
956      GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT      GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
# Line 20  o build_options: ifort+mpi_aces optfile Line 963  o build_options: ifort+mpi_aces optfile
963  o pkg/seaice:  o pkg/seaice:
964    fix previous modif (3-level field removed) for old-pickup reading    fix previous modif (3-level field removed) for old-pickup reading
965    
966  checkpoint61r  checkpoint61r (2009/06/25)
967  o pkg/seaice:  o pkg/seaice:
968   - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:   - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
969    1. introduce fields for time step (N-1)    1. introduce fields for time step (N-1)
# Line 34  o pkg/seaice: Line 977  o pkg/seaice:
977   - adjusted adjoint accordingly;   - adjusted adjoint accordingly;
978     gradient checks have improved by an order of magnitude!     gradient checks have improved by an order of magnitude!
979    
980  checkpoint61q  checkpoint61q (2009/06/22)
981  o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver  o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
982   - the boundary conditions along open boundaries are unclear, because the   - the boundary conditions along open boundaries are unclear, because the
983     associated masks are set to zero and are thus treated as closed when     associated masks are set to zero and are thus treated as closed when
# Line 59  o pkg/seaice: Line 1002  o pkg/seaice:
1002   - add diagnostics for surface temperature, atmospheric and oceanic   - add diagnostics for surface temperature, atmospheric and oceanic
1003     heat flux, and atmospheric and oceanic ice growth     heat flux, and atmospheric and oceanic ice growth
1004    
1005  checkpoint61p  checkpoint61p (2009/06/10)
1006  o eesupp (global_max & global_sum):  o eesupp (global_max & global_sum):
1007   - add one more element to buffer (start at index 0) for GL_MAX/SUM output;   - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
1008   - remove starting & endding barrier (no longer needed)   - remove starting & endding barrier (no longer needed)
# Line 121  o eesupp: Line 1064  o eesupp:
1064    should be called before a "stop" if we know that all process are going    should be called before a "stop" if we know that all process are going
1065    to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.    to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
1066    
1067  checkpoint61o  checkpoint61o (2009/05/26)
1068  o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)  o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
1069  o model/src/ini_curvilinear_grid.F:  o model/src/ini_curvilinear_grid.F:
1070     compute angleSin/CosC when they are not read from a file     compute angleSin/CosC when they are not read from a file
# Line 162  o pkg/exch2: Line 1105  o pkg/exch2:
1105   - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"   - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
1106     in utils/exch2/input.     in utils/exch2/input.
1107    
1108  checkpoint61n  checkpoint61n (2009/05/12)
1109  o eesupp & mdsio (SingleCpuIO):  o eesupp & mdsio (SingleCpuIO):
1110    - move mapping to global io-buffer inside gather_2d/scater_2d: this save    - move mapping to global io-buffer inside gather_2d/scater_2d: this save
1111      memory (1 less 2D global RL array); skip 1 buffer copy; and only send/      memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
# Line 175  o pkg/mdsio: in preparation for topology Line 1118  o pkg/mdsio: in preparation for topology
1118      when using exch2. Add S/R to map global io-buffer to global model array.      when using exch2. Add S/R to map global io-buffer to global model array.
1119    - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.    - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
1120    
1121  checkpoint61m  checkpoint61m (2009/04/29)
1122  o write_utils : change WRITE_1D_R8 to WRITE_1D_RL  o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
1123    and add 3 other S/R for other types (R4,R8,RS).    and add 3 other S/R for other types (R4,R8,RS).
1124    Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.    Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
# Line 211  o pkg/exch2 (+ utils/exch2): ignore blan Line 1154  o pkg/exch2 (+ utils/exch2): ignore blan
1154    and keep the original tile numbering. Note: compatible with old    and keep the original tile numbering. Note: compatible with old
1155    W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.    W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
1156    
1157  checkpoint61l  checkpoint61l (2009/04/07)
1158  o Overlaps had been forgotten in calculating ijk keys : fixed  o Overlaps had been forgotten in calculating ijk keys : fixed
1159  o fix cyrus makedepend for gcc 4.4  o fix cyrus makedepend for gcc 4.4
1160  o experiment fizhi-cs-aqualev20:  o experiment fizhi-cs-aqualev20:
# Line 259  o pkg/seaice: Line 1202  o pkg/seaice:
1202      is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS      is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
1203    - seaice_growth: replace computation of UG by a simple copy from wspeed    - seaice_growth: replace computation of UG by a simple copy from wspeed
1204    
1205  checkpoint61k  checkpoint61k (2009/03/18)
1206  o pkg/seaice: a few bug fixes mostly concerning the metric terms:  o pkg/seaice: a few bug fixes mostly concerning the metric terms:
1207    seaice_lsr: fixed a few metric terms,    seaice_lsr: fixed a few metric terms,
1208                affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs                affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
# Line 276  o pkg/seaice: a few bug fixes mostly con Line 1219  o pkg/seaice: a few bug fixes mostly con
1219    updated all relevant verification experiments (except lab_sea//output_adm.txt    updated all relevant verification experiments (except lab_sea//output_adm.txt
1220      which was left over, but fails at level 7 & 6)      which was left over, but fails at level 7 & 6)
1221    
1222  checkpoint61j  checkpoint61j (2009/03/17)
1223  o pkg/seaice: turn a few hard wired parameters into run time parameters  o pkg/seaice: turn a few hard wired parameters into run time parameters
1224  o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model  o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
1225    time in seconds as promised by the usints in seaice_monitor and exf_monitor    time in seconds as promised by the usints in seaice_monitor and exf_monitor
# Line 304  o autodiff Line 1247  o autodiff
1247    TAF store directivs "byte" and "kind" seem equivalent;    TAF store directivs "byte" and "kind" seem equivalent;
1248    Most tamc.h have been updated correspondingly.    Most tamc.h have been updated correspondingly.
1249    
1250  checkpoint61i  checkpoint61i (2009/02/13)
1251  o autodiff:  o autodiff:
1252    fix autodiff_sore/_restore indices for obcs    fix autodiff_sore/_restore indices for obcs
1253    (spotted by I. Hoteit, M. Mazloff)    (spotted by I. Hoteit, M. Mazloff)
# Line 339  o pkg/ggl90: a few modifications: Line 1282  o pkg/ggl90: a few modifications:
1282  o rename thetaMin,phiMin -> xgOrigin,ygOrigin  o rename thetaMin,phiMin -> xgOrigin,ygOrigin
1283    (maintain temporary backward compatibility, until next checkpoint)    (maintain temporary backward compatibility, until next checkpoint)
1284    
1285  checkpoint61h  checkpoint61h (2009/01/27)
1286  o pkg/diagnostics with "periodic averaging diagnostics":  o pkg/diagnostics with "periodic averaging diagnostics":
1287    fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.    fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
1288  o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82  o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
# Line 363  o pkg/mdsio: read/write vector: Line 1306  o pkg/mdsio: read/write vector:
1306    (drop to 4 digits matching for grad). But this test does not look very    (drop to 4 digits matching for grad). But this test does not look very
1307    reliable (was already failling on eddy, fc5, at 6.digits). Update output.    reliable (was already failling on eddy, fc5, at 6.digits). Update output.
1308    
1309  checkpoint61g  checkpoint61g (2008/12/29)
1310  o pkg/flt:  o pkg/flt:
1311    - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)    - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
1312     + make OPTIONS file more standard.     + make OPTIONS file more standard.
# Line 376  o pkg/obcs: fix a CPP-flag, bug reported Line 1319  o pkg/obcs: fix a CPP-flag, bug reported
1319  o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to  o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
1320    a still unfixed compiler/optimization bug    a still unfixed compiler/optimization bug
1321    
1322  checkpoint61f  checkpoint61f (2008/11/21)
1323  o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;  o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
1324    update results of global_ocean.cs32x15.icedyn test.    update results of global_ocean.cs32x15.icedyn test.
1325  o move getcon.F from model/src to pkg/fizhi.  o move getcon.F from model/src to pkg/fizhi.
# Line 405  o fix CPP-flag REAL4_IS_SLOW, when _RS e Line 1348  o fix CPP-flag REAL4_IS_SLOW, when _RS e
1348   - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1   - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
1349     (generate new output).     (generate new output).
1350    
1351  checkpoint61e  checkpoint61e (2008/10/23)
1352  o gmredi (Visbeck-variable-K):  o gmredi (Visbeck-variable-K):
1353    - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h    - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
1354    - change computation of Visbeck-K where Slope > Smax :            - change computation of Visbeck-K where Slope > Smax :        
# Line 430  o pkg ggl90: Line 1373  o pkg ggl90:
1373          scale in ggl90_calc.F          scale in ggl90_calc.F
1374          (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)          (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
1375    
1376  checkpoint61d  checkpoint61d (2008/09/25)
1377  o adjoint modifs  o adjoint modifs
1378    - adapt to new field rhoInSitu    - adapt to new field rhoInSitu
1379    - allow to revert from StoreDynVars2D, StoreDynVars3D    - allow to revert from StoreDynVars2D, StoreDynVars3D
# Line 457  o add initialisation of deepFac if using Line 1400  o add initialisation of deepFac if using
1400    ini_reference_state.F --> load_ref_files.F (- set anelastic factors)    ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
1401  o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)  o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
1402    
1403  checkpoint61c  checkpoint61c (2008/08/30)
1404  o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"  o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
1405    to add mass source/sink of fluid in the interior (3-D generalisation    to add mass source/sink of fluid in the interior (3-D generalisation
1406    of oceanic real-fresh water flux).    of oceanic real-fresh water flux).
# Line 475  o change FIND_RHO to FIND_RHO_2D : Line 1418  o change FIND_RHO to FIND_RHO_2D :
1418    pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.    pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
1419  o new pkg: cheapaml  o new pkg: cheapaml
1420    
1421  checkpoint61b  checkpoint61b (2008/08/05)
1422  o exch2:  o exch2:
1423    change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)    change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
1424    - no longer depend on the order sequence (N,S,E,W).    - no longer depend on the order sequence (N,S,E,W).
# Line 490  o exch2: Line 1433  o exch2:
1433     more intuitive this way) ; rename/remove some variables.     more intuitive this way) ; rename/remove some variables.
1434   - change utils/exch2/matlab-topology-generator & code_mods accordingly.   - change utils/exch2/matlab-topology-generator & code_mods accordingly.
1435    
1436  checkpoint61a  checkpoint61a (2008/07/29)
1437  o exch2/matlab-topology-generator:  o exch2/matlab-topology-generator:
1438    fix bug in index bounds for N-S internal exchange (hard to tell if this    fix bug in index bounds for N-S internal exchange (hard to tell if this
1439    had any effect on the solution).    had any effect on the solution).
# Line 499  o pkg/mnc: small fix in mnc_handle_err: Line 1442  o pkg/mnc: small fix in mnc_handle_err:
1442  o testreport: modify syntax of awk, so that it works also with  o testreport: modify syntax of awk, so that it works also with
1443    awk, and not only with nawk and gawk    awk, and not only with nawk and gawk
1444    
1445  checkpoint61  checkpoint61 (2008/06/24)
1446  o autodiff  o autodiff
1447    Change default for TAF usage by removing argument '-nonew_arg'    Change default for TAF usage by removing argument '-nonew_arg'
1448    This changes TAF subroutine argument list (ordering of active var.)    This changes TAF subroutine argument list (ordering of active var.)
# Line 510  o autodiff Line 1453  o autodiff
1453    Tested TAF version is 1.9.22    Tested TAF version is 1.9.22
1454    N.B.: exch2 hand-written adjoint code currently not TAMC compatible    N.B.: exch2 hand-written adjoint code currently not TAMC compatible
1455    
1456  checkpoint60  checkpoint60 (2008/06/19)
1457  --->>> This is the last checkpoint for which generating the adjoint  --->>> This is the last checkpoint for which generating the adjoint
1458  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
1459  --->>> by default.  --->>> by default.
# Line 535  o bridging the gap between eddy stress a Line 1478  o bridging the gap between eddy stress a
1478    The key modifications are in model/src/taueddy_external_forcing.F    The key modifications are in model/src/taueddy_external_forcing.F
1479    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
1480    
1481  checkpoint59r  checkpoint59r (2008/05/29)
1482  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
1483    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
1484    fix option to read coriolis(@ cell-corner) from files with CS-grid.    fix option to read coriolis(@ cell-corner) from files with CS-grid.
# Line 566  o pkg/ptracers: add second-order moment Line 1509  o pkg/ptracers: add second-order moment
1509    (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)    (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
1510    and requires a fortran 90 compiler    and requires a fortran 90 compiler
1511    
1512  checkpoint59q  checkpoint59q (2008/05/06)
1513  o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)  o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
1514     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
1515  o Refresh tutorial_global_oce_biogeo, notably:  o Refresh tutorial_global_oce_biogeo, notably:
# Line 601  o thsice pkg: Line 1544  o thsice pkg:
1544    - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos    - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
1545    --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice    --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
1546    
1547  checkpoint59p  checkpoint59p (2008/04/10)
1548  o gchem / dic / cfc :  o gchem / dic / cfc :
1549    - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);    - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
1550    - add new parameter files: "data.dic" & "data.cfc" ;    - add new parameter files: "data.dic" & "data.cfc" ;
# Line 627  o in mom_calc_visc, fix average value of Line 1570  o in mom_calc_visc, fix average value of
1570    bottom ; only used with variable horizontal viscosity and non-hydrostatic.    bottom ; only used with variable horizontal viscosity and non-hydrostatic.
1571    also fix diagnostics VISCAHW & VISCA4W.    also fix diagnostics VISCAHW & VISCA4W.
1572    
1573  checkpoint59o  checkpoint59o (2008/03/07)
1574  o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).  o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
1575  o change the loop ordering in most gad_*_adv_x.F to improve vectorization:  o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
1576    move a few statemens out the main loop into separate loops    move a few statemens out the main loop into separate loops
# Line 668  o pkg/ctrl: Line 1611  o pkg/ctrl:
1611      introducing a generic routine (ctrl_map_ini_gen.F).      introducing a generic routine (ctrl_map_ini_gen.F).
1612    - Modification of ctrl_bound/adctrl_bound handling control vector bounds.    - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
1613    
1614  checkpoint59n  checkpoint59n (2008/02/09)
1615  o pkg/diagnostics: for large number of diagnostics, store diagnostic mate  o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
1616    number in dedicate array "hdiag":    number in dedicate array "hdiag":
1617    - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST    - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
# Line 722  o pkg/seaice: add a new flag SEAICEuseTE Line 1665  o pkg/seaice: add a new flag SEAICEuseTE
1665    for now this is only available for the C-grid code and also within    for now this is only available for the C-grid code and also within
1666    #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code    #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
1667    
1668  checkpoint59m  checkpoint59m (2008/01/14)
1669  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
1670    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
1671  o gad_som : fix flux output (& diagnostics) to have same units as other    o gad_som : fix flux output (& diagnostics) to have same units as other  
# Line 740  o pkg/obcs and pkg/seaice: Line 1683  o pkg/obcs and pkg/seaice:
1683  o pkg/salt_plume: added various options for salt plume depth  o pkg/salt_plume: added various options for salt plume depth
1684    criterion and for vertical distribution of the salt    criterion and for vertical distribution of the salt
1685    
1686  checkpoint59l  checkpoint59l (2007/12/18)
1687  o pkg/ptracers: new version of ptracers pickup:  o pkg/ptracers: new version of ptracers pickup:
1688    read meta file and write only fields which are needed to restart.    read meta file and write only fields which are needed to restart.
1689    ( same logic as main pickup file ; also using pickupStrictlyMatch )    ( same logic as main pickup file ; also using pickupStrictlyMatch )
# Line 762  o no longer write pickup from THE_MODEL_ Line 1705  o no longer write pickup from THE_MODEL_
1705  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
1706    or U/VICE from U/VWIND before computing U/VSTRESS    or U/VICE from U/VWIND before computing U/VSTRESS
1707    
1708  checkpoint59k  checkpoint59k (2007/11/30)
1709  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
1710    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
1711  o fix un-initialised variable problem (in mom_vecinv & shap_filt):  o fix un-initialised variable problem (in mom_vecinv & shap_filt):
# Line 784  o pkg/ptracers: Line 1727  o pkg/ptracers:
1727    use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).    use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
1728    to-do: fix pkg/diagnostics when large number of diagnostics are defined.    to-do: fix pkg/diagnostics when large number of diagnostics are defined.
1729    
1730  checkpoint59j  checkpoint59j (2007/11/09)
1731  o in pkgs: dic, obcs, offline, rbcs:  o in pkgs: dic, obcs, offline, rbcs:
1732    standard way to compute coeff. for time interpolation between 2 time reccords    standard way to compute coeff. for time interpolation between 2 time reccords
1733    which retains full precision (& make results less dependent on compiler).    which retains full precision (& make results less dependent on compiler).
# Line 827  o pkg/mdsio & pkg/rw: Line 1770  o pkg/mdsio & pkg/rw:
1770  o added open boundary conditions capability for seaice  o added open boundary conditions capability for seaice
1771      HSNOW, HSALT, UICE, and VICE      HSNOW, HSALT, UICE, and VICE
1772    
1773  checkpoint59i  checkpoint59i (2007/10/21)
1774  o adjoint:  o adjoint:
1775    * fix multiDimAdvection adjoint    * fix multiDimAdvection adjoint
1776      (partial recomputation problem by TAF for fVerT(:,:,kDown)      (partial recomputation problem by TAF for fVerT(:,:,kDown)
# Line 868  o change units of EmPmR (inside the code Line 1811  o change units of EmPmR (inside the code
1811    Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).    Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
1812    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
1813    
1814  checkpoint59h  checkpoint59h (2007/09/29)
1815  o pkg/exf:  o pkg/exf:
1816    - improve vectorization by moving if-statement out of loops in    - improve vectorization by moving if-statement out of loops in
1817      exf_mapfields, exf_radiation      exf_mapfields, exf_radiation
# Line 901  o pkg/thsice: Line 1844  o pkg/thsice:
1844  o testreport: change AD testing : check against results/output_adm.txt  o testreport: change AD testing : check against results/output_adm.txt
1845    using same scripts as for forward test.    using same scripts as for forward test.
1846    
1847  checkpoint59g  checkpoint59g (2007/09/17)
1848  o adjoint testing: in preparation for changing testreport:  o adjoint testing: in preparation for changing testreport:
1849    - output format: cost and grad written on separated lines    - output format: cost and grad written on separated lines
1850    - ad output results in directory "results" (instead of "results_ad")    - ad output results in directory "results" (instead of "results_ad")
# Line 946  o pkg/cd_code: add brackets in multiple Line 1889  o pkg/cd_code: add brackets in multiple
1889    global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,    global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1890    ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.    ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1891    
1892  checkpoint59f  checkpoint59f (2007/08/21)
1893  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1894  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1895    a bounded range (in forward mode)    a bounded range (in forward mode)
# Line 977  o pkg/seaice Line 1920  o pkg/seaice
1920  o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update  o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1921     output of global_ocean.cs32x15.thsice .     output of global_ocean.cs32x15.thsice .
1922    
1923  checkpoint59e  checkpoint59e (2007/07/26)
1924  o exch2: new S/R that only use the cube-tracer (center-position) exchange:  o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1925    for B-grid vector (not yet tested) and C-grid vector (<- only used    for B-grid vector (not yet tested) and C-grid vector (<- only used
1926    when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).    when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
# Line 1007  o pkg/seaice: Line 1950  o pkg/seaice:
1950    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1951    * applied OBCS T/S mask to HEFFM sea ice mask    * applied OBCS T/S mask to HEFFM sea ice mask
1952    
1953  checkpoint59d  checkpoint59d (2007/06/21)
1954  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1955   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1956   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
# Line 1053  o pkg/seaice: Line 1996  o pkg/seaice:
1996     It is turned off by default (=-1.), because it changes the results.     It is turned off by default (=-1.), because it changes the results.
1997   - make it possible to read AREA from a file, too.   - make it possible to read AREA from a file, too.
1998    
1999  checkpoint59c  checkpoint59c (2007/06/04)
2000  o add S/R and diagnostics for oceanic mixed-layer depth  o add S/R and diagnostics for oceanic mixed-layer depth
2001  o move GMRedi call after all vertical mixing schemes (including KPP)  o move GMRedi call after all vertical mixing schemes (including KPP)
2002  o pkg/thsice:  o pkg/thsice:
# Line 1086  o adjoint: Line 2029  o adjoint:
2029    Storing is now bundled into large arrays to optimized I/O    Storing is now bundled into large arrays to optimized I/O
2030    (and second step in cleanup of the_main_loop)    (and second step in cleanup of the_main_loop)
2031    
2032  checkpoint59b  checkpoint59b (2007/05/16)
2033  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
2034    - export/import (between ocean & coupler) fields needed for ocean DIC.    - export/import (between ocean & coupler) fields needed for ocean DIC.
2035  o pkg/seaice:  o pkg/seaice:
# Line 1157  o pkg/seaice Line 2100  o pkg/seaice
2100  o OpenAD  o OpenAD
2101   - changed verification/OpenAD to full baroclinic setup (including GM/Redi)   - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
2102    
2103  checkpoint59a  checkpoint59a (2007/05/01)
2104  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
2105  o pkg/thsice: rename run-time parameters:  o pkg/thsice: rename run-time parameters:
2106     himin       -> hIceMin     himin       -> hIceMin
# Line 1199  o pkg/seaice: fix bug in evp solver, whi Line 2142  o pkg/seaice: fix bug in evp solver, whi
2142  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
2143    - add myThid to all kpp routines (long overdue)    - add myThid to all kpp routines (long overdue)
2144    
2145  checkpoint59  checkpoint59 (2007/04/19)
2146  o pkg/exf:  o pkg/exf:
2147    - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &    - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
2148      ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid      ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
# Line 1225  o pkg/thsise Line 2168  o pkg/thsise
2168    - 2nd set of modifs for thsice adjoint in conjunction with exf    - 2nd set of modifs for thsice adjoint in conjunction with exf
2169  o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)  o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
2170    
2171  checkpoint58y_post  checkpoint58y_post (2007/04/15)
2172  o Added capability for latitudinal dependence of Bryan and Lewis, 1979  o Added capability for latitudinal dependence of Bryan and Lewis, 1979
2173    vertical diffusivity, similar to that in MOM4; turned on using    vertical diffusivity, similar to that in MOM4; turned on using
2174    #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using    #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
# Line 1241  o ice dynamics (pkg/seaice) with thsice Line 2184  o ice dynamics (pkg/seaice) with thsice
2184         - better when using non-linear advection scheme (not yet fully tested)         - better when using non-linear advection scheme (not yet fully tested)
2185         - can also be used in atmospheric set-up (for now, only the diffusion).         - can also be used in atmospheric set-up (for now, only the diffusion).
2186    
2187  checkpoint58x_post  checkpoint58x_post (2007/04/04)
2188  o IO option for global-file compact format:  o IO option for global-file compact format:
2189    - add options when generating topology (utils/exch2/matlab-topology-generator)    - add options when generating topology (utils/exch2/matlab-topology-generator)
2190    - add I/O capability (pkg/mdsio).    - add I/O capability (pkg/mdsio).
# Line 1249  o IO option for global-file compact form Line 2192  o IO option for global-file compact form
2192    for now long-line format not yet supported by pkg/mdsio (& exch2).    for now long-line format not yet supported by pkg/mdsio (& exch2).
2193  o shelfice: add a few diagnostics  o shelfice: add a few diagnostics
2194    
2195  checkpoint58w_post  checkpoint58w_post (2007/03/13)
2196  o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:  o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
2197    rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref    rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
2198    (and replace horiVertRatio in NH code).    (and replace horiVertRatio in NH code).
# Line 1270  o cpl_aim+ocn exp.: use consistent rhoCo Line 2213  o cpl_aim+ocn exp.: use consistent rhoCo
2213  o move call to cal_readparms up to make calendar parameters/variable available  o move call to cal_readparms up to make calendar parameters/variable available
2214    to all packages    to all packages
2215    
2216  checkpoint58v_post  checkpoint58v_post (2007/02/08)
2217  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
2218    useDynP_inEos_Zc tested.    useDynP_inEos_Zc tested.
2219  o pkg/exf: changes to properly interpolate/mask/scale initial fields  o pkg/exf: changes to properly interpolate/mask/scale initial fields
# Line 1289  o 2nd-Order Moment Advection Scheme (Pra Line 2232  o 2nd-Order Moment Advection Scheme (Pra
2232   - use this scheme for temperature & salinity in 2 advection test exp.:   - use this scheme for temperature & salinity in 2 advection test exp.:
2233     advect_xy & advect_xz, respectively.     advect_xy & advect_xz, respectively.
2234    
2235  checkpoint58u_post  checkpoint58u_post (2007/01/12)
2236  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
2237  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
2238  o testreport: add option "-skipdir" to skip some test.  o testreport: add option "-skipdir" to skip some test.
# Line 1304  o add option (linFSConserveTr) to correc Line 2247  o add option (linFSConserveTr) to correc
2247  o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine  o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
2248  o pkg/thsice: fix reading mnc-pickups  o pkg/thsice: fix reading mnc-pickups
2249    
2250  checkpoint58t_post  checkpoint58t_post (2006/12/30)
2251  o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)  o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
2252  o pkg/mdsio:  o pkg/mdsio:
2253   - clean-up mdsio_readfield.F & mdsio_writefield_new.F and   - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
# Line 1347  o pkg/seaice: overhaul of thermodynamics Line 2290  o pkg/seaice: overhaul of thermodynamics
2290   - introduce a few local fields to avoid modifying external fields such   - introduce a few local fields to avoid modifying external fields such
2291     as atemp, etc.     as atemp, etc.
2292    
2293  checkpoint58s_post  checkpoint58s_post (2006/12/11)
2294  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
2295    changed exf_set_gen.F so that    changed exf_set_gen.F so that
2296      genperiod=0 means input file is one time-constant field and      genperiod=0 means input file is one time-constant field and
# Line 1381  o modifications to pkg/seaice/growth.F a Line 2324  o modifications to pkg/seaice/growth.F a
2324    as actual snow thickness.  It now refers everywhere to effective snow    as actual snow thickness.  It now refers everywhere to effective snow
2325    thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.    thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
2326    
2327  checkpoint58r_post  checkpoint58r_post (2006/11/17)
2328  o modifications to pkg/seaice/growth.F, which change results of  o modifications to pkg/seaice/growth.F, which change results of
2329    lab_sea experiment: fixes pertain to melting snow over open water, to    lab_sea experiment: fixes pertain to melting snow over open water, to
2330    masking EVAP under sea ice, and to using the correct AREA variable for    masking EVAP under sea ice, and to using the correct AREA variable for
# Line 1405  o Adding some pkg/diagnostics capability Line 2348  o Adding some pkg/diagnostics capability
2348  o ctrl: adding new control variables:  o ctrl: adding new control variables:
2349    lwflux, lwdown, evap, snowprecip, apressure, runoff    lwflux, lwdown, evap, snowprecip, apressure, runoff
2350    
2351  checkpoint58q_post  checkpoint58q_post (2006/10/20)
2352  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
2353    1/6-deg Southern Ocean configuration by 8% on IBM Datastar and    1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
2354    high_res_cube configuration by 4% on Columbia.    high_res_cube configuration by 4% on Columbia.
# Line 1416  o new function "MASTER_CPU_IO" (=T if ma Line 2359  o new function "MASTER_CPU_IO" (=T if ma
2359    single CPU io) so that TAF does not have to see EESUPPORT.h    single CPU io) so that TAF does not have to see EESUPPORT.h
2360  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
2361    
2362  checkpoint58p_post  checkpoint58p_post (2006/09/08)
2363  o obcs: stop if obcs is used with useCDscheme = .true.  o obcs: stop if obcs is used with useCDscheme = .true.
2364  o shelfice:  o shelfice:
2365   - fix a sign error so that no slip at shelfice interface works   - fix a sign error so that no slip at shelfice interface works
# Line 1427  o diagnoctics: modify UVELPHI and VVELPH Line 2370  o diagnoctics: modify UVELPHI and VVELPH
2370  o added adjoint exch routined for all exch*3d* routines  o added adjoint exch routined for all exch*3d* routines
2371    and updated flow directives    and updated flow directives
2372    
2373  checkpoint58o_post  checkpoint58o_post (2006/08/28)
2374  o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;  o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
2375    remove old subroutines (_XY_ & _XYZ_); update the adjoint version.    remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
2376  o change controling S/R for writing pickup file (new S/R do_write_pickup)  o change controling S/R for writing pickup file (new S/R do_write_pickup)
# Line 1441  o shelfice: Line 2384  o shelfice:
2384   - add a simple boundary layer scheme to reduce noise   - add a simple boundary layer scheme to reduce noise
2385   - fix the indexing in shelfice_u/v_drag so that there will be actually drag   - fix the indexing in shelfice_u/v_drag so that there will be actually drag
2386    
2387  checkpoint58n_post  checkpoint58n_post (2006/08/14)
2388  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
2389     local variable (not in common block).     local variable (not in common block).
2390  o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.  o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
# Line 1462  o change default MAX_NO_THREADS from 32 Line 2405  o change default MAX_NO_THREADS from 32
2405    and stop cleanly when MAX_NO_THREADS is too small.    and stop cleanly when MAX_NO_THREADS is too small.
2406  o add S/R BAR_CHECK to check multi-threaded barrier synchronization  o add S/R BAR_CHECK to check multi-threaded barrier synchronization
2407    
2408  checkpoint58m_post  checkpoint58m_post (2006/07/17)
2409  o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.  o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
2410     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
2411  o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.  o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
# Line 1488  o calc_gw: true flux-form, account for h Line 2431  o calc_gw: true flux-form, account for h
2431    update rotating_tank results, but not plume_on_slope (affected at    update rotating_tank results, but not plume_on_slope (affected at
2432    truncation level, 11 digits).    truncation level, 11 digits).
2433    
2434  checkpoint58l_post  checkpoint58l_post (2006/07/12)
2435  o calc_gw:  o calc_gw:
2436   - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V   - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
2437   - remove side-drag for now (need to fix it); update plume_on_slope results.   - remove side-drag for now (need to fix it); update plume_on_slope results.
# Line 1506  o pkg/ecco: Line 2449  o pkg/ecco:
2449  o pkg/rbcs  o pkg/rbcs
2450    * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing    * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
2451    
2452  checkpoint58k_post  checkpoint58k_post (2006/07/06)
2453  o testreport:  o testreport:
2454   - always build in dir. "build" (if not there, mkdir build instead of building   - always build in dir. "build" (if not there, mkdir build instead of building
2455     & running in input)     & running in input)
# Line 1539  o tracer advection: Line 2482  o tracer advection:
2482     advection subroutine (but still not used within DST advection S/R)     advection subroutine (but still not used within DST advection S/R)
2483  o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)  o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
2484    
2485  checkpoint58j_post  checkpoint58j_post (2006/06/15)
2486  o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields  o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
2487    from file (collects calls previously in FORWARD_STEP)    from file (collects calls previously in FORWARD_STEP)
2488  o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS  o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
# Line 1547  o adjoint store dir. adjusted accordingl Line 2490  o adjoint store dir. adjusted accordingl
2490  o genmake2  o genmake2
2491    replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.    replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
2492    
2493  checkpoint58i_post  checkpoint58i_post (2006/06/14)
2494  o pkg/seaice: add parameter that allows to scale/turn off effect of seaice  o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
2495    on wind stress (SEAICEstressFactor defaults to 1.)    on wind stress (SEAICEstressFactor defaults to 1.)
2496  o Total number of Timers is finite (<=40): comment out 2 non-essential one  o Total number of Timers is finite (<=40): comment out 2 non-essential one
# Line 1561  o pkg/seaice: added SEAICEuseEVPpickup p Line 2504  o pkg/seaice: added SEAICEuseEVPpickup p
2504      non-EVP pickup files when using SEAICEuseEVP      non-EVP pickup files when using SEAICEuseEVP
2505    - fix sign error in diffusion in seaice_calc_rhs    - fix sign error in diffusion in seaice_calc_rhs
2506    
2507  checkpoint58h_post  checkpoint58h_post (2006/06/07)
2508  * Modifications for bottom topography control  * Modifications for bottom topography control
2509    o replace hFacC by _hFacC at various places    o replace hFacC by _hFacC at various places
2510    o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL    o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
# Line 1571  checkpoint58h_post Line 2514  checkpoint58h_post
2514    o works for 5x5 box, doesnt work for global_ocean.90x40x15    o works for 5x5 box, doesnt work for global_ocean.90x40x15
2515  * Adding verification for 5x5 box (4-layer) bottom topography control  * Adding verification for 5x5 box (4-layer) bottom topography control
2516    
2517  checkpoint58g_post  checkpoint58g_post (2006/06/07)
2518  o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,  o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
2519     used for mean seasonal cycle, mean diurnal cycle); add an example     used for mean seasonal cycle, mean diurnal cycle); add an example
2520     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
# Line 1587  o couple pkg/thsice to pkg/seaice: Line 2530  o couple pkg/thsice to pkg/seaice:
2530  o pkg/seaice  o pkg/seaice
2531    - make (default) second order advection a bit less confusing?    - make (default) second order advection a bit less confusing?
2532    
2533  checkpoint58f_post  checkpoint58f_post (2006/06/05)
2534  o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice  o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
2535    to pkg/seaice):    to pkg/seaice):
2536    - new routines thsice_map_exf and thsice_get_exf provide the interface    - new routines thsice_map_exf and thsice_get_exf provide the interface
# Line 1618  o fix bug in aim+thsice albedo: snow & i Line 2561  o fix bug in aim+thsice albedo: snow & i
2561  o results_ad : rename "output.txt_adm" to "output_adm.txt" and change  o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
2562    testreport accordingly    testreport accordingly
2563    
2564  checkpoint58e_post  checkpoint58e_post (2006/05/17)
2565  o SEAICE_CGRID adjoint done  o SEAICE_CGRID adjoint done
2566  o R_STAR adjoint implemented.  o R_STAR adjoint implemented.
2567    * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )    * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
# Line 1626  o R_STAR adjoint implemented. Line 2569  o R_STAR adjoint implemented.
2569  o Make pkg/profile fully independent of ecco,cost, etc. stuff  o Make pkg/profile fully independent of ecco,cost, etc. stuff
2570    to be able to use it in pure forward.    to be able to use it in pure forward.
2571    
2572  checkpoint58d_post  checkpoint58d_post (2006/04/21)
2573  o upgrade simple test-experiment to tutorial example:  o upgrade simple test-experiment to tutorial example:
2574   step.1: duplicate the experiment and (step.2) will remove the old copy.   step.1: duplicate the experiment and (step.2) will remove the old copy.
2575    tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)    tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
# Line 1666  o new package prifiles: Line 2609  o new package prifiles:
2609  o Benign bug fix in initialization (spotted by M. Mazloff) of  o Benign bug fix in initialization (spotted by M. Mazloff) of
2610    ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F    ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
2611    
2612  checkpoint58c_post  checkpoint58c_post (2006/03/23)
2613  o adjoint: finish NLFS adjoint and provide reference output in  o adjoint: finish NLFS adjoint and provide reference output in
2614    verification/global_ocean.90x40x15/results_ad_nlfs    verification/global_ocean.90x40x15/results_ad_nlfs
2615  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
# Line 1700  o seaice: Line 2643  o seaice:
2643     + move computation of the viscosities eta and zeta into a new separate     + move computation of the viscosities eta and zeta into a new separate
2644       routine (because I need to recompute them in seaice_ocean_stress.F)       routine (because I need to recompute them in seaice_ocean_stress.F)
2645    
2646  checkpoint58b_post  checkpoint58b_post (2006/03/13)
2647  o AIM+thSIce: fix sign of Short-Wave through the Ice ;  o AIM+thSIce: fix sign of Short-Wave through the Ice ;
2648    update output.txt of exp. aim.5l_cs.thSI    update output.txt of exp. aim.5l_cs.thSI
2649  o various mnc cleanups and improvements:  o various mnc cleanups and improvements:
# Line 1763  o seaice: Line 2706  o seaice:
2706      (turn on with SEAICEuseFluxForm)      (turn on with SEAICEuseFluxForm)
2707    - replace 1 in 3d global fields by kSurface in growth.F    - replace 1 in 3d global fields by kSurface in growth.F
2708        
2709  checkpoint58a_post  checkpoint58a_post (2006/02/13)
2710  o seaice:  o seaice:
2711    - bug fix in advect.F    - bug fix in advect.F
2712  o shelfice:  o shelfice:
# Line 1816  o pkg/bulk_force: Line 2759  o pkg/bulk_force:
2759     and parameters (note: calcWindStress replaces .NOT.readwindstress).     and parameters (note: calcWindStress replaces .NOT.readwindstress).
2760   - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).   - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
2761    
2762  checkpoint58  checkpoint58 (2006/01/12)
2763  o add "--embed-source" option to genmake2 which, when the supporting  o add "--embed-source" option to genmake2 which, when the supporting
2764    tools can be compiled (as determined by genmake2) will turn on the    tools can be compiled (as determined by genmake2) will turn on the
2765    embed_files package which then embeds the entire MITgcm source code    embed_files package which then embeds the entire MITgcm source code
# Line 1829  o clean up 3-dim. relaxation codes: Line 2772  o clean up 3-dim. relaxation codes:
2772    * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)    * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
2773    * Thanks to Tom Haine for testing!    * Thanks to Tom Haine for testing!
2774    
2775  checkpoint57z_post  checkpoint57z_post (2005/12/31)
2776  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
2777    affects output (@ truncation level) of exp. plume_on_slope ; updated.    affects output (@ truncation level) of exp. plume_on_slope ; updated.
2778  o fix the pickup behavior for obcs in combination with ptracers  o fix the pickup behavior for obcs in combination with ptracers
# Line 1860  o Adding Laplacian-type smoothness const Line 2803  o Adding Laplacian-type smoothness const
2803    * Absolute scale somewhat unclear so far    * Absolute scale somewhat unclear so far
2804    * no area weighting was included since no other cost term does so far    * no area weighting was included since no other cost term does so far
2805    
2806  checkpoint57y_post  checkpoint57y_post (2005/12/08)
2807  First step for a NLFS adjoint  First step for a NLFS adjoint
2808  o initially suppress rStar (new flag DISABLE_RSTAR_CODE)  o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
2809  o new init. routines for calc_r_star, calc_surf_dr  o new init. routines for calc_r_star, calc_surf_dr
2810  o still need to deal with ini_masks_etc  o still need to deal with ini_masks_etc
2811  o testreport seemed happy  o testreport seemed happy
2812  checkpoint57y_pre  checkpoint57y_pre (2005/12/08)
2813    
2814  o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.  o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
2815  o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)  o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
# Line 1875  o cfc fixes for final year of integratio Line 2818  o cfc fixes for final year of integratio
2818  o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should  o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
2819    be in GCHEM_OPTIONS).    be in GCHEM_OPTIONS).
2820    
2821  checkpoint57x_post  checkpoint57x_post (2005/12/04)
2822  o fix testreport Pb in multiple test experiment.  o fix testreport Pb in multiple test experiment.
2823  o cleanup our namelist syntax in verification:  o cleanup our namelist syntax in verification:
2824    - make it more F95 standards compliant (some work still needed)    - make it more F95 standards compliant (some work still needed)
# Line 1895  o adjoint Line 2838  o adjoint
2838      (there are a number of extensive recomputations)      (there are a number of extensive recomputations)
2839    * Initialize certain variables needed for adjoint    * Initialize certain variables needed for adjoint
2840    
2841  checkpoint57w_post  checkpoint57w_post (2005/11/03)
2842  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
2843               fix the singleCpuIO RS version of MDSWRITEFIELD               fix the singleCpuIO RS version of MDSWRITEFIELD
2844     and add a WARNING if using globalFiles=T with multi-processors.     and add a WARNING if using globalFiles=T with multi-processors.
# Line 1912  o PTRACERS: added namelist parameter PTR Line 2855  o PTRACERS: added namelist parameter PTR
2855    ptracers in a large domain with a constant non-zero value. Also,    ptracers in a large domain with a constant non-zero value. Also,
2856    untangle ptracers_init.F a little.    untangle ptracers_init.F a little.
2857    
2858  checkpoint57v_post  checkpoint57v_post (2005/10/13)
2859  o change dome exp. to use variable viscosity in side-drag terms.  o change dome exp. to use variable viscosity in side-drag terms.
2860  o remove all the files from the cfc_offline test since they are now  o remove all the files from the cfc_offline test since they are now
2861    incorporated into tutorial_cfc_offline which has been producing    incorporated into tutorial_cfc_offline which has been producing
# Line 1953  o reduce number of exch calls in shap_fi Line 2896  o reduce number of exch calls in shap_fi
2896  o CS-grid: fix divergence contribution to Leith viscosity. Affects (@  o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
2897    truncation level) 4/5 MLAdjust test results (11&12 digits match).    truncation level) 4/5 MLAdjust test results (11&12 digits match).
2898    
2899  checkpoint57t_post  checkpoint57t_post (2005/10/03)
2900  o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4  o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
2901  o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get  o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
2902    same truncation, independent of the face number: affects affects several    same truncation, independent of the face number: affects affects several
# Line 1976  o Clean, new version of mom_calc_visc. Line 2919  o Clean, new version of mom_calc_visc.
2919    Suggested values of viscosity parameters found in mom_calc_visc.    Suggested values of viscosity parameters found in mom_calc_visc.
2920    Many new viscosity diagnostics available.    Many new viscosity diagnostics available.
2921    
2922  checkpoint57s_post  checkpoint57s_post (2005/09/20)
2923  o Add clearing-house for viscosity calculations, mom_calc_visc and  o Add clearing-house for viscosity calculations, mom_calc_visc and
2924    correct numerous bugs in LeithD and Smagorinsky discretizations.      correct numerous bugs in LeithD and Smagorinsky discretizations.  
2925    mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be    mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
# Line 2002  o various changes to mnc including: Line 2945  o various changes to mnc including:
2945        and works with both EXCH1 and EXCH2 (but needs more testing)        and works with both EXCH1 and EXCH2 (but needs more testing)
2946    - writing works for all verification test cases w/ g77 on Linux    - writing works for all verification test cases w/ g77 on Linux
2947    
2948  checkpoint57r_post  checkpoint57r_post (2005/09/07)
2949  o make MNC variable initialization happen earlier  o make MNC variable initialization happen earlier
2950  o add diagnostics for (almost) each term of the momentum Eq.  o add diagnostics for (almost) each term of the momentum Eq.
2951  o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.  o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
# Line 2022  o new infrastructure for seaice model vs Line 2965  o new infrastructure for seaice model vs
2965  o natl_box_adjoint input_seaice for Lab. Sea now available online via wget  o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2966    (see README file)    (see README file)
2967    
2968  checkpoint57q_post  checkpoint57q_post (2005/08/19)
2969  o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)  o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2970  o fix annoying months-old bug in mnc/mdsio output for seaice pkg  o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2971    - bug was reported by Jean-Michel and Ian Fenty    - bug was reported by Jean-Michel and Ian Fenty
# Line 2039  o Modifications to enable scripted COMMO Line 2982  o Modifications to enable scripted COMMO
2982    * verification/OpenAD/code/ has necessary scripts and description;    * verification/OpenAD/code/ has necessary scripts and description;
2983    * converts, compiles and runs successfully;    * converts, compiles and runs successfully;
2984    
2985  checkpoint57p_post  checkpoint57p_post (2005/08/01)
2986  o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F  o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2987  o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED  o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2988    (already the case for some pkgs, including recent MNC_init, e.g. thsice)    (already the case for some pkgs, including recent MNC_init, e.g. thsice)
# Line 2053  o Dissipation & phiHyd gradient are alwa Line 2996  o Dissipation & phiHyd gradient are alwa
2996    global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),    global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2997    matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).    matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2998    
2999  checkpoint57o_post  checkpoint57o_post (2005/07/30)
3000  o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and  o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
3001    (2) its ready to be documented during the 20050801 DocFest    (2) its ready to be documented during the 20050801 DocFest
3002  o MNC-ify the gmredi package -- tested and works w/ and w/o mnc  o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
# Line 2062  o set to #undef CTRL_SET_OLD_MAXCVARS_30 Line 3005  o set to #undef CTRL_SET_OLD_MAXCVARS_30
3005    in global1x1_tot/code_seaice_adj to access indices 32, 33    in global1x1_tot/code_seaice_adj to access indices 32, 33
3006    (worth another tag)    (worth another tag)
3007    
3008  checkpoint57n_post  checkpoint57n_post (2005/07/29)
3009  o adding precip control xx_precip 32  o adding precip control xx_precip 32
3010  o adding swflux control xx_swflux 33  o adding swflux control xx_swflux 33
3011  o Replacing 10 forcing penalty cost routines by 1 generic.  o Replacing 10 forcing penalty cost routines by 1 generic.
# Line 2078  o enable useSingleCpuIO for mdsio vector Line 3021  o enable useSingleCpuIO for mdsio vector
3021    (applies in particular to tapelev I/O)    (applies in particular to tapelev I/O)
3022  o removed inefficient K-loop in all active_file*control*.F  o removed inefficient K-loop in all active_file*control*.F
3023    
3024  checkpoint57m_post  checkpoint57m_post (2005/07/28)
3025  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
3026    and advect_cs (use EXCH-2 and standard cs-32 grid files).    and advect_cs (use EXCH-2 and standard cs-32 grid files).
3027  o pkg/exch2: filling of face-corner halo regions is optional  o pkg/exch2: filling of face-corner halo regions is optional
3028    (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.    (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
3029    
3030  checkpoint57l_post  checkpoint57l_post (2005/07/14)
3031   tag before updating tutorials (pre-release-2)   tag before updating tutorials (pre-release-2)
3032  o add cos & sin of grid-direction orientation angle (curvilinear grid only,  o add cos & sin of grid-direction orientation angle (curvilinear grid only,
3033     for output and interpolation of input fields onto model grid)     for output and interpolation of input fields onto model grid)
# Line 2096  o fix aim_diagnostics_init.F mate number Line 3039  o fix aim_diagnostics_init.F mate number
3039  o add mnc output capability to diagnostics/diagstat and update  o add mnc output capability to diagnostics/diagstat and update
3040    our cvsignore files for the ACSII output generated    our cvsignore files for the ACSII output generated
3041    
3042  checkpoint57k_post  checkpoint57k_post (2005/07/02)
3043  o lab_sea now uses diagnostics package and provides a suite of  o lab_sea now uses diagnostics package and provides a suite of
3044    new EXF diagnostics output.    new EXF diagnostics output.
3045    
3046  checkpoint57j_post  checkpoint57j_post (2005/06/30)
3047  o exf  o exf
3048    * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):    * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
3049      Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);      Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
# Line 2130  o fix bug in rStar code (calc_r_star.F) Line 3073  o fix bug in rStar code (calc_r_star.F)
3073  o fix few little things to avoid floating error with -ftrapuv (ifort v9)  o fix few little things to avoid floating error with -ftrapuv (ifort v9)
3074   (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)   (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
3075    
3076  checkpoint57i_post  checkpoint57i_post (2005/06/19)
3077  o Diagnostics package was changed: diagnostic allocation is now deactivated  o Diagnostics package was changed: diagnostic allocation is now deactivated
3078    by setting an empty file name in the namelist (used to be by setting 0 frequency)    by setting an empty file name in the namelist (used to be by setting 0 frequency)
3079  o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;  o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
# Line 2149  o pkg/diagnostics: Line 3092  o pkg/diagnostics:
3092    tested against monitor output (including land & thSIce) on various exp.    tested against monitor output (including land & thSIce) on various exp.
3093  o make seaice-pkg I/O type flags (MNC/MDS) more standard.  o make seaice-pkg I/O type flags (MNC/MDS) more standard.
3094    
3095  checkpoint57h_done  checkpoint57h_done (2005/05/19)
3096    tag after changing user customized files (DIAGNOSTICS_SIZE.h,    tag after changing user customized files (DIAGNOSTICS_SIZE.h,
3097    data.diagnostics, data.gchem, data.ptracers) is done.    data.diagnostics, data.gchem, data.ptracers) is done.
3098    
# Line 2158  o pkg/diagnostics: prepare for Global/Re Line 3101  o pkg/diagnostics: prepare for Global/Re
3101  o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE  o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
3102    and rename it: DIFFERENT_MULTIPLE    and rename it: DIFFERENT_MULTIPLE
3103    
3104  checkpoint57h_post  checkpoint57h_post (2005/05/14)
3105  o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers  o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
3106  o pkg/diagnostics: change output frequency, now in seconds (instead  o pkg/diagnostics: change output frequency, now in seconds (instead
3107    of Nb of iterations). This requires to change data.diagnostics.    of Nb of iterations). This requires to change data.diagnostics.
3108  checkpoint57h_pre  checkpoint57h_pre (2005/05/12)
3109    
3110  o in mnc, let the user create the output dir if both mnc_outdir_date  o in mnc, let the user create the output dir if both mnc_outdir_date
3111    and mnc_outdir_num are false    and mnc_outdir_num are false
# Line 2176  o test AB-3 code with 4th.Order advectio Line 3119  o test AB-3 code with 4th.Order advectio
3119  o fix mnc flags in pkg/seaice so that they are "owned" by seaice,  o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
3120    not mnc -- this mistake was found by JMC and is now corrected    not mnc -- this mistake was found by JMC and is now corrected
3121    
3122  checkpoint57g_post  checkpoint57g_post (2005/04/15)
3123  o add Adams-Bashforth 3rd Order time stepping:  o add Adams-Bashforth 3rd Order time stepping:
3124    - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)    - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
3125    - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...    - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
3126  checkpoint57g_pre  checkpoint57g_pre (2005/04/15)
3127    
3128  o make lambda[Theta,Salt]ClimRelax spatially varying  o make lambda[Theta,Salt]ClimRelax spatially varying
3129    (default remains spatially uniform constant based on tau)    (default remains spatially uniform constant based on tau)
# Line 2190  o added new control variables Line 3133  o added new control variables
3133  o separate masks used for ctrl_pack/unpack 'from write_grid' output  o separate masks used for ctrl_pack/unpack 'from write_grid' output
3134    (suggested by G. Forget)    (suggested by G. Forget)
3135    
3136  checkpoint57f_post  checkpoint57f_post (2005/04/06)
3137  o add parameter "baseTime" = model base time = time at iteration zero  o add parameter "baseTime" = model base time = time at iteration zero
3138    new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to    new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
3139    account for baseTime shift    account for baseTime shift
3140  o move Coriolis arrays from PARAMS.h to GRID.h  o move Coriolis arrays from PARAMS.h to GRID.h
3141  checkpoint57f_pre  checkpoint57f_pre (2005/04/06)
3142    
3143  o mnc-ifying the seaice package  o mnc-ifying the seaice package
3144  o introduced an alternative length scale calculation for use in the limiting  o introduced an alternative length scale calculation for use in the limiting
# Line 2216  o adjoint-related modifications Line 3159  o adjoint-related modifications
3159    * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33    * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
3160    * mom_vi_hdissip: to be able to use Leith scheme in adjoint    * mom_vi_hdissip: to be able to use Leith scheme in adjoint
3161    
3162  checkpoint57e_post  checkpoint57e_post (2005/02/28)
3163  o Adding eddy stress controls a la Ferreira et al.  o Adding eddy stress controls a la Ferreira et al.
3164  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
3165    
# Line 2234  o diagnostics: add pickup functionality Line 3177  o diagnostics: add pickup functionality
3177  o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.  o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
3178  o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)  o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
3179    
3180  checkpoint57d_post  checkpoint57d_post (2005/02/11)
3181  o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing  o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
3182  o modify verification/ideal_2D_oce so that it tests the creation of mnc  o modify verification/ideal_2D_oce so that it tests the creation of mnc
3183    output from the diagnostics package    output from the diagnostics package
# Line 2256  o move state variable diagnostics to the Line 3199  o move state variable diagnostics to the
3199    (note: still needs some work specially for snap-shot diagnostics)    (note: still needs some work specially for snap-shot diagnostics)
3200    duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z    duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
3201    
3202  checkpoint57c_post  checkpoint57c_post (2005/01/27)
3203  o Change testing option (-ieee) to get closer agreement between g77 & ifort  o Change testing option (-ieee) to get closer agreement between g77 & ifort
3204  o generate new output.txt files on faulks with g77 & the new -ieee option  o generate new output.txt files on faulks with g77 & the new -ieee option
3205  checkpoint57c_pre  checkpoint57c_pre (2005/01/27)
3206    
3207  o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);  o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
3208    update output.txt of exp. global_ocean.90x40x15    update output.txt of exp. global_ocean.90x40x15
# Line 2292  o pkg/mdsio/ Line 3235  o pkg/mdsio/
3235    * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F    * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
3236    * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)    * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
3237    
3238  checkpoint57b_post  checkpoint57b_post (2004/12/20)
3239  o simplify options in diagnostics_fill arguments (remove weird combinations)  o simplify options in diagnostics_fill arguments (remove weird combinations)
3240  o fix MNC coordinate variables so that they now contain per-face index  o fix MNC coordinate variables so that they now contain per-face index
3241    values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in    values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
# Line 2338  o re-arrange diagnostics pkg initialisat Line 3281  o re-arrange diagnostics pkg initialisat
3281     look through the short list of active diag. (instead of the long list)     look through the short list of active diag. (instead of the long list)
3282     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
3283    
3284  checkpoint57a_post  checkpoint57a_post (2004/12/10)
3285  o this set of changes restores TAMC compatibility  o this set of changes restores TAMC compatibility
3286    tested for global_ocean.90x40x15 adjoint on trough    tested for global_ocean.90x40x15 adjoint on trough
3287    (what a pain)    (what a pain)
3288    
3289  checkpoint57a_pre  checkpoint57a_pre (2004/12/10)
3290  o some modifs in tools/build_options for sunos  o some modifs in tools/build_options for sunos
3291  o call ctrl_pack for ctrl at end for optimcycle=0  o call ctrl_pack for ctrl at end for optimcycle=0
3292    
3293  checkpoint57  checkpoint57 (2004/12/09)
3294  o add horizontal bi-harmonic viscosity for vertical velocity  o add horizontal bi-harmonic viscosity for vertical velocity
3295    - new parameter viscA4W (defaults to viscA4)    - new parameter viscA4W (defaults to viscA4)
3296    - affects only non-hydrostatic code    - affects only non-hydrostatic code
# Line 2365  o untangle a few ifdefs related to cost, Line 3308  o untangle a few ifdefs related to cost,
3308  o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)  o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
3309    (theta2, salt2 in ecco_cost_weights)    (theta2, salt2 in ecco_cost_weights)
3310    
3311  checkpoint56c_post  checkpoint56c_post (2004/12/03)
3312  o OBCS as control variables  o OBCS as control variables
3313    - update ctrl_ad_diff.list, obcs_ad_diff.list    - update ctrl_ad_diff.list, obcs_ad_diff.list
3314    - remove balance of obcs controls from default    - remove balance of obcs controls from default
# Line 2383  o exf: Line 3326  o exf:
3326  o mdsio:  o mdsio:
3327    - i/o-vector change debugLevel from debLevA to debLevB    - i/o-vector change debugLevel from debLevA to debLevB
3328    
3329  checkpoint56b_post  checkpoint56b_post (2004/12/01)
3330  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
3331    is called from DO_THE_MODEL_IO    is called from DO_THE_MODEL_IO
3332    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
# Line 2398  o testreport previously did a lousy job Line 3341  o testreport previously did a lousy job
3341    testreport.    testreport.
3342  o ptracers_monitor: bug fix for MPI  o ptracers_monitor: bug fix for MPI
3343    
3344  checkpoint56a_post  checkpoint56a_post (2004/11/28)
3345  o GCHEM: finish reorganizating the package  o GCHEM: finish reorganizating the package
3346    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
3347      (introduces another 3D-array for each passive tracer, but only if      (introduces another 3D-array for each passive tracer, but only if
# Line 2443  o GCHEM: Line 3386  o GCHEM:
3386    - cleaning up    - cleaning up
3387  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
3388    
3389  checkpoint56  checkpoint56 (2004/11/17)
3390  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
3391  o mnc: cleanup "full" files--fixes out-of-memory problem  o mnc: cleanup "full" files--fixes out-of-memory problem
3392  o ECCO-GODAE  o ECCO-GODAE
# Line 2473  o mdsio: filename info to both stderr, s Line 3416  o mdsio: filename info to both stderr, s
3416  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
3417    from sign change    from sign change
3418    
3419  checkpoint55j_post  checkpoint55j_post (2004/11/10)
3420  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
3421    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3422  o add consistent build directories and .cvsignore files to verification  o add consistent build directories and .cvsignore files to verification
# Line 2484  o make all subroutines 30 or less charac Line 3427  o make all subroutines 30 or less charac
3427  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
3428    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3429    
3430  checkpoint55i_post  checkpoint55i_post (2004/10/28)
3431  o change arrays for total vertical diffusivity (2.D if explicit,  o change arrays for total vertical diffusivity (2.D if explicit,
3432    3.D if implicit) ; each ptracer uses its own background value.    3.D if implicit) ; each ptracer uses its own background value.
3433  o added mnc/NetCDF output capability to ocn_compon_interf  o added mnc/NetCDF output capability to ocn_compon_interf
# Line 2499  o give MNC the ability to create additio Line 3442  o give MNC the ability to create additio
3442  o Compute the non-local term using either KPP vertical diffusivity (=default)  o Compute the non-local term using either KPP vertical diffusivity (=default)
3443     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
3444    
3445  checkpoint55h_post  checkpoint55h_post (2004/10/20)
3446  o add verification test "vermix"  o add verification test "vermix"
3447  o remove all the *_ioinc flags and replace with the single global  o remove all the *_ioinc flags and replace with the single global
3448    outputTypesInclusive flag    outputTypesInclusive flag
# Line 2507  o allow to set a vertical profile of ver Line 3450  o allow to set a vertical profile of ver
3450  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
3451  o useMNC moved from data.mnc to data.pkg  o useMNC moved from data.mnc to data.pkg
3452    
3453  checkpoint55g_post  checkpoint55g_post (2004/10/14)
3454  o Renaming carbon AD experiments to comply with testreport conventions  o Renaming carbon AD experiments to comply with testreport conventions
3455  o Updating adjoint of Held-Suarez hs94.1x64x5  o Updating adjoint of Held-Suarez hs94.1x64x5
3456  o Fixing directives for non-ECCO forward_step, after ECCO directives  o Fixing directives for non-ECCO forward_step, after ECCO directives
# Line 2517  o Fixing directives for non-ECCO forward Line 3460  o Fixing directives for non-ECCO forward
3460  o Updating adjoint output for natl_box_adjoint after  o Updating adjoint output for natl_box_adjoint after
3461    pkg/ecco has been modified (see taga c55d_post)    pkg/ecco has been modified (see taga c55d_post)
3462    
3463  checkpoint55f_post  checkpoint55f_post (2004/10/13)
3464  o rename to timeave_init_fixed  o rename to timeave_init_fixed
3465    
3466  checkpoint55e_post  checkpoint55e_post (2004/10/13)
3467  o some delicate re-shuffle of store directives to avoid one  o some delicate re-shuffle of store directives to avoid one
3468    extra call of do_oceanic_physics    extra call of do_oceanic_physics
3469    affects ecco_the_main_loop.F, do_oceanic_physics.F    affects ecco_the_main_loop.F, do_oceanic_physics.F
# Line 2528  o some delicate re-shuffle of store dire Line 3471  o some delicate re-shuffle of store dire
3471  o NB: this may break global_ocean adjoint temporarily,  o NB: this may break global_ocean adjoint temporarily,
3472    but it is clear how to fix it. Will do later, need this now.    but it is clear how to fix it. Will do later, need this now.
3473    
3474  checkpoint55d_post  checkpoint55d_post (2004/10/11)
3475  o ECCO specific cost function terms (up-to-date with 1x1 runs)  o ECCO specific cost function terms (up-to-date with 1x1 runs)
3476  o ecco_cost_weights is modified to 1x1 runs  o ecco_cost_weights is modified to 1x1 runs
3477  o modifs to allow observations to be read in as  o modifs to allow observations to be read in as
3478    single file or yearly files    single file or yearly files
3479  o enable to read exf forcing fields as either  o enable to read exf forcing fields as either
3480    single file or yearly files (flag useExfYearlyFields)    single file or yearly files (flag useExfYearlyFields)
3481  checkpoint55d_pre  checkpoint55d_pre (2004/10/08)
3482    
3483  o switch between 2-level and 3-level checkpointing  o switch between 2-level and 3-level checkpointing
3484  o add ability of MNC to write local and "partial" (eg. 2D slices where  o add ability of MNC to write local and "partial" (eg. 2D slices where
# Line 2583  o more obcs stuff Line 3526  o more obcs stuff
3526    - changed argument list of OBCS_CALC to myTime+deltaTclock    - changed argument list of OBCS_CALC to myTime+deltaTclock
3527    - fixed about 35 bugs in obcs_external_fields_load    - fixed about 35 bugs in obcs_external_fields_load
3528    
3529  checkpoint55c_post  checkpoint55c_post (2004/09/23)
3530  o obcs stuff  o obcs stuff
3531    - new runtime flags useOBCSprescribe, useOBCSbalance    - new runtime flags useOBCSprescribe, useOBCSbalance
3532    - re-arranged obcs_calc    - re-arranged obcs_calc
# Line 2597  o obcs stuff Line 3540  o obcs stuff
3540  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
3541    which simplifies the calls and passes the ifc check-bounds test    which simplifies the calls and passes the ifc check-bounds test
3542    
3543  checkpoint55b_post  checkpoint55b_post (2004/09/22)
3544  o add a 2D scalar, Z location, exchange_2 routine.  o add a 2D scalar, Z location, exchange_2 routine.
3545  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
3546    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
# Line 2608  o use a more standard discretization for Line 3551  o use a more standard discretization for
3551  o fix gad_advection.F (CubedSphere part), back to version 1.23  o fix gad_advection.F (CubedSphere part), back to version 1.23
3552  o fix bug in mom_vi_del2uv.F (CubedSphere part).  o fix bug in mom_vi_del2uv.F (CubedSphere part).
3553    
3554  checkpoint55a_post  checkpoint55a_post (2004/09/20)
3555  o merged code to  o merged code to
3556    * prescribe/read time-dependent open boundaries    * prescribe/read time-dependent open boundaries
3557      (works in conjunction with exf, cal)      (works in conjunction with exf, cal)
# Line 2616  o merged code to Line 3559  o merged code to
3559    * each boundary N/S/E/W now has its own CPP option    * each boundary N/S/E/W now has its own CPP option
3560      (healthy for the adjoint)      (healthy for the adjoint)
3561    
3562  checkpoint55  checkpoint55 (2004/09/17)
3563  o up-to-date adjoint of previous breaks  o up-to-date adjoint of previous breaks
3564    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
3565    - global_ocean_ebm: adjoint still needs fix (TLM ok)    - global_ocean_ebm: adjoint still needs fix (TLM ok)
# Line 2626  o up-to-date adjoint of previous breaks Line 3569  o up-to-date adjoint of previous breaks
3569  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
3570    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
3571    
3572  checkpoint54f_post  checkpoint54f_post (2004/09/16)
3573  o in verification/carbin/ remove experiment related to  o in verification/carbin/ remove experiment related to
3574    ALLOW_PASSIVE_TRACER (array tr1 etc)    ALLOW_PASSIVE_TRACER (array tr1 etc)
3575    code_ad/ input_ad/ results_ad    code_ad/ input_ad/ results_ad
# Line 2652  o overhaul of IO so that we now have fla Line 3595  o overhaul of IO so that we now have fla
3595    - numerous small formatting cleanups for ProTeX    - numerous small formatting cleanups for ProTeX
3596  o add version info (via BUILD_INFO.h) to MNC and stdout  o add version info (via BUILD_INFO.h) to MNC and stdout
3597    
3598  checkpoint54e_post  checkpoint54e_post (2004/09/02)
3599  o add two new packages  o add two new packages
3600    - pp81 (Packanowski and Philander, 1981), Richardson number and    - pp81 (Packanowski and Philander, 1981), Richardson number and
3601      stratification dependent mixing      stratification dependent mixing
# Line 2666  o add "verification/dic_example" which c Line 3609  o add "verification/dic_example" which c
3609  o genmake2: add ability to search for C compilers and cleanup test output  o genmake2: add ability to search for C compilers and cleanup test output
3610    - fixes recent SX-6 problems and should help with others (eg. HP-UX)    - fixes recent SX-6 problems and should help with others (eg. HP-UX)
3611    
3612  checkpoint54d_post  checkpoint54d_post (2004/07/27)
3613  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
3614  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
3615    leading to additional shift by 5 days each year of integration    leading to additional shift by 5 days each year of integration
# Line 2682  o fix a bug in Flux deriv. vs Ts (pkg/ai Line 3625  o fix a bug in Flux deriv. vs Ts (pkg/ai
3625  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
3626  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
3627    
3628  checkpoint54c_post  checkpoint54c_post (2004/07/18)
3629  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
3630    this affects (truncation error) output.txt of test-exp:    this affects (truncation error) output.txt of test-exp:
3631     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
# Line 2693  o define the max number of passive trace Line 3636  o define the max number of passive trace
3636  o start to test mnc routinely in exp0  o start to test mnc routinely in exp0
3637  o add sea-ice loading (sIceLoad) as a new forcing field.  o add sea-ice loading (sIceLoad) as a new forcing field.
3638    
3639  checkpoint54b_post  checkpoint54b_post (2004/07/08)
3640  o add testreport "-j JOBS" option for parallel builds (tested and pretty  o add testreport "-j JOBS" option for parallel builds (tested and pretty
3641     impressive on Altix and Opteron systems)     impressive on Altix and Opteron systems)
3642  o diagnostics can now write NetCDF files through the mnc package  o diagnostics can now write NetCDF files through the mnc package
# Line 2703  o staggerTimeStep & NLFS: rescale T & S Line 3646  o staggerTimeStep & NLFS: rescale T & S
3646    affects (truncation error) output of lab_sea & natl_box exp.: updated    affects (truncation error) output of lab_sea & natl_box exp.: updated
3647  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
3648    
3649  checkpoint54a_post  checkpoint54a_post (2004/07/06)
3650  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
3651  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
3652  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
3653  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
3654    + internal_wave (shift in writing cg2d_ini_res)    + internal_wave (shift in writing cg2d_ini_res)
3655  checkpoint54a_pre  checkpoint54a_pre (2004/07/05)
3656    
3657  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
3658    - modified verification/lab_sea and natl_box_adjoint accordingly    - modified verification/lab_sea and natl_box_adjoint accordingly
3659    
3660  checkpoint54  checkpoint54 (2004/07/02)
3661  checkpoint53g_post  checkpoint53g_post (2004/07/02)
3662  o prepare splitting of thermodynamics: store convect.counter in common block  o prepare splitting of thermodynamics: store convect.counter in common block
3663  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
3664    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
# Line 2724  o new parameter "nShapS": allow to treat Line 3667  o new parameter "nShapS": allow to treat
3667  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
3668  o restore adjointability  o restore adjointability
3669    
3670  checkpoint53f_post  checkpoint53f_post (2004/06/25)
3671  o modifications that affect AIM experiment results (update output.txt):  o modifications that affect AIM experiment results (update output.txt):
3672    - no advection of S at top interface Nr (pkg/generic_advdiff)    - no advection of S at top interface Nr (pkg/generic_advdiff)
3673    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
# Line 2737  o merged cylindrical coord configuration Line 3680  o merged cylindrical coord configuration
3680  o added rotating_tank experiment  o added rotating_tank experiment
3681  checkpoint53e_pre  checkpoint53e_pre
3682    
3683  checkpoint53d_post  checkpoint53d_post (2004/06/14)
3684  o faulks upgraded: re-generate output.txt that have changed:  o faulks upgraded: re-generate output.txt that have changed:
3685     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
3686  o Added Bryan and Lewis, 1979, vertical diffusivity profile  o Added Bryan and Lewis, 1979, vertical diffusivity profile
# Line 2756  o regenerated output for global_ocean_eb Line 3699  o regenerated output for global_ocean_eb
3699  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
3700    of mom_common/    of mom_common/
3701    - simple re-arrangement of instructions within computing loop    - simple re-arrangement of instructions within computing loop
3702  checkpoint53d_pre  checkpoint53d_pre (2004/05/21)
3703    
3704  checkpoint53c_post  checkpoint53c_post (2004/05/21)
3705  o new version of coupler for AIM+thSIce and Ocean models  o new version of coupler for AIM+thSIce and Ocean models
3706   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
3707   - land: change Evaporation of snow   - land: change Evaporation of snow
# Line 2775  o Adjoint of EBM package + verification Line 3718  o Adjoint of EBM package + verification
3718    * TLM OK    * TLM OK
3719    * ADM not sufficient accuracy yet (needs further testing)    * ADM not sufficient accuracy yet (needs further testing)
3720    
3721  checkpoint53b_post  checkpoint53b_post (2004/05/14)
3722  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository
3723    * package is pkg/ebm    * package is pkg/ebm
3724    * verif. is verification/global_ocean_ebm    * verif. is verification/global_ocean_ebm
# Line 2793  C        Destabilization of the thermoha Line 3736  C        Destabilization of the thermoha
3736  C        by atmospheric eddy transports.  C        by atmospheric eddy transports.
3737  C        J. Climate 7(12), 1870-1882  C        J. Climate 7(12), 1870-1882
3738  o Will need long integration testing.  o Will need long integration testing.
3739  checkpoint53b_pre  checkpoint53b_pre (2004/05/14)
3740    
3741  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code
3742  o renamed and split ini_mnc_io  o renamed and split ini_mnc_io
# Line 2801  o pkg/land: only liquid water can diffus Line 3744  o pkg/land: only liquid water can diffus
3744  o AIM using land: soil wetness availability account for snow  o AIM using land: soil wetness availability account for snow
3745  o added printMapIncludesZeros to EEPARMS namelist  o added printMapIncludesZeros to EEPARMS namelist
3746    
3747  checkpoint53a_post  checkpoint53a_post (2004/05/11)
3748  o restore TAMC compatiility for exf_constants.h  o restore TAMC compatiility for exf_constants.h
3749    (no usage of _d in .h)    (no usage of _d in .h)
3750  o Additional storing in KPP in an attempt to fix  o Additional storing in KPP in an attempt to fix
# Line 2814  o Fixed verification/natl_box_adjoint ex Line 3757  o Fixed verification/natl_box_adjoint ex
3757    and hence gives results closer to that of Experiment 2.    and hence gives results closer to that of Experiment 2.
3758    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
3759    
3760  checkpoint53  checkpoint53 (2004/05/06)
3761  o stable checkpoint with up to date adjoint  o stable checkpoint with up to date adjoint
3762    TLM tests only run for 1st grdchk at the moment. Its unclear if    TLM tests only run for 1st grdchk at the moment. Its unclear if
3763    this is a code problem or a problem with resetting code for g_    this is a code problem or a problem with resetting code for g_
# Line 2824  o stable checkpoint with up to date adjo Line 3767  o stable checkpoint with up to date adjo
3767     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
3768       are both still in chaos following their security messes.       are both still in chaos following their security messes.
3769    
3770  checkpoint52n_post  checkpoint52n_post (2004/05/06)
3771  o various build (mostly genmake2) changes including:  o various build (mostly genmake2) changes including:
3772    - ability to build/run more easily within Cygwin and MacOS X    - ability to build/run more easily within Cygwin and MacOS X
3773    - more complicated Makefiles with a stronger dependence on Gnu Make    - more complicated Makefiles with a stronger dependence on Gnu Make
# Line 2855  o fix in pkg/thsice: Line 3798  o fix in pkg/thsice:
3798    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
3799   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
3800    
3801  checkpoint52m_post  checkpoint52m_post (2004/04/18)
3802  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
3803    this does not change any of the results, because myIter=0 in swfrac always    this does not change any of the results, because myIter=0 in swfrac always
3804    lead to jwtype=2 (the default anyway), but the call makes little sense    lead to jwtype=2 (the default anyway), but the call makes little sense
# Line 2887  o test exp. advect_cs: use the standard Line 3830  o test exp. advect_cs: use the standard
3830  o Added functionality to grdchk:  o Added functionality to grdchk:
3831    pick global i,j,k position (or nearest wet) where to perform check.    pick global i,j,k position (or nearest wet) where to perform check.
3832    
3833  checkpoint52l_post  checkpoint52l_post (2004/03/11)
3834  o new land formulation:  o new land formulation:
3835    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
3836       energy conservation.       energy conservation.
# Line 2898  o aim_v23 modification for new land mode Line 3841  o aim_v23 modification for new land mode
3841    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
3842       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
3843    b) add snow precipitation.    b) add snow precipitation.
3844  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
3845    
3846  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
3847  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 2911  o fix ini_curvilinear_grid ; test CS exp Line 3854  o fix ini_curvilinear_grid ; test CS exp
3854  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
3855  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
3856    
3857  checkpoint52k_post  checkpoint52k_post (2004/02/23)
3858  o removed top-level directory "diags"  o removed top-level directory "diags"
3859    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
3860  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 2924  o set all ...Freq to zero after cost_fin Line 3867  o set all ...Freq to zero after cost_fin
3867    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
3868  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
3869    
3870  checkpoint52j_post  checkpoint52j_post (2004/02/18)
3871  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
3872  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
3873  o Really weird thing!  o Really weird thing!
# Line 2932  o Really weird thing! Line 3875  o Really weird thing!
3875    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
3876    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
3877    after cost_final call which should not be there!    after cost_final call which should not be there!
3878  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
3879    
3880  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
3881    error messages    error messages
# Line 2949  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 3892  o merged mom_vi_calc_relvort3.F, mom_vi_
3892    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
3893  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
3894    
3895  checkpoint52i_post  checkpoint52i_post (2004/01/21)
3896  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
3897  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
3898  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
3899    
3900  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
3901    the old pkg/aim).    the old pkg/aim).
3902    
3903  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
3904  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
3905  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
3906  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 2968  o added temporary hack for sea-ice dynam Line 3911  o added temporary hack for sea-ice dynam
3911    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
3912    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
3913    
3914  checkpoint52f_post  checkpoint52f_post (2004/01/09)
3915  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
3916  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
3917  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
3918  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
3919    
3920  checkpoint52e_post  checkpoint52e_post (2004/01/07)
3921  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
3922    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
3923  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 2982  o step.1 : rewrite (as in MultiDimAdvec) Line 3925  o step.1 : rewrite (as in MultiDimAdvec)
3925  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
3926  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
3927   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
3928  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
3929    
3930  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
3931  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 2993  o added exf_offset_atemp for Celsius to Line 3936  o added exf_offset_atemp for Celsius to
3936  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
3937  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
3938    
3939  checkpoint52d_post  checkpoint52d_post (2003/12/16)
3940  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
3941    - updated output accordingly    - updated output accordingly
3942    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 3022  o check-in the first version of the coup Line 3965  o check-in the first version of the coup
3965  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
3966     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
3967    
3968  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
3969  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
3970  o add call to AIM pendant S/R in external_forcing & external_fields_load.F  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
3971    
3972  checkpoint52c_post  checkpoint52c_post (2003/11/25)
3973  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
3974    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
3975    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 3040  o Removed all CPP options for cal packag Line 3983  o Removed all CPP options for cal packag
3983  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
3984  o corrected key comp. for passkey  o corrected key comp. for passkey
3985    
3986  checkpoint52b_post  checkpoint52b_post (2003/11/23)
3987  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
3988   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
3989   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 3048  o new version: "thsice" of thermodynamic Line 3991  o new version: "thsice" of thermodynamic
3991   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
3992     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
3993  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
3994  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
3995    
3996  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
3997  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
# Line 3058  o missing PTRACERS headers in some routi Line 4001  o missing PTRACERS headers in some routi
4001  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
4002    to ensure proper customization    to ensure proper customization
4003    
4004  checkpoint52a_post  checkpoint52a_post (2003/11/17)
4005  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
4006    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
4007    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 3073  o fix problem with ECCO-related divided Line 4016  o fix problem with ECCO-related divided
4016    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
4017    but no warning issued by TAF    but no warning issued by TAF
4018    
4019  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
4020  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
4021    
4022  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
4023  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
4024    
4025  checkpoint51u_post  checkpoint51u_post (2003/11/06)
4026  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
4027    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
4028  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 3094  o top level routines the_main_loop, forw Line 4037  o top level routines the_main_loop, forw
4037    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
4038  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
4039    
4040  checkpoint51t_post  checkpoint51t_post (2003/11/04)
4041  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
4042    
4043  checkpoint51s_post  checkpoint51s_post (2003/11/04)
4044  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
4045  o pkg/grdchk  o pkg/grdchk
4046    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 3106  o pkg/grdchk Line 4049  o pkg/grdchk
4049    - additional high-precision output for testreport    - additional high-precision output for testreport
4050      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
4051    
4052  checkpoint51r_post  checkpoint51r_post (2003/11/03)
4053  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
4054  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
4055    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
4056    
4057  checkpoint51q_post  checkpoint51q_post (2003/10/30)
4058  o cd_code:  o cd_code:
4059    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
4060    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 3127  o ctrl package totally restructured Line 4070  o ctrl package totally restructured
4070    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
4071  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
4072    
4073  checkpoint51p_post  checkpoint51p_post (2003/10/30)
4074  o create initial cd_code package  o create initial cd_code package
4075    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
4076      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 3142  o create initial cd_code package Line 4085  o create initial cd_code package
4085  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
4086  o cleanup testreport  o cleanup testreport
4087    
4088  checkpoint51o_post  checkpoint51o_post (2003/10/27)
4089  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
4090    - carbon/    - carbon/
4091    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 3163  o Correcting initialisations for fVerU, Line 4106  o Correcting initialisations for fVerU,
4106  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
4107    fVerU, fVerV    fVerU, fVerV
4108  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
4109  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
4110    
4111  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
4112  o added the [#include "AD_CONFIG.h"] statement to all files that need  o added the [#include "AD_CONFIG.h"] statement to all files that need
# Line 3171  o added the [#include "AD_CONFIG.h"] sta Line 4114  o added the [#include "AD_CONFIG.h"] sta
4114   o re-worked the build logic in genmake2 to support AD_CONFIG.h   o re-worked the build logic in genmake2 to support AD_CONFIG.h
4115   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
4116    
4117  checkpoint51n_post  checkpoint51n_post (2003/10/23)
4118  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
4119    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
4120    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 3180  o modifications to make FREEZE flux visi Line 4123  o modifications to make FREEZE flux visi
4123       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
4124  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
4125    
4126  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
4127  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
4128  o added [#include "AD_CONFIG.h"] to all files that use the following  o added [#include "AD_CONFIG.h"] to all files that use the following
4129    defines:    defines:
# Line 3188  o added [#include "AD_CONFIG.h"] to all Line 4131  o added [#include "AD_CONFIG.h"] to all
4131    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
4132    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
4133    
4134  checkpoint51m_post  checkpoint51m_post (2003/10/21)
4135  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
4136    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
4137    - various cleanups related to package handling    - various cleanups related to package handling
4138    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
4139    
4140  checkpoint51l_post  checkpoint51l_post (2003/10/20)
4141  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
4142   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
4143   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
4144   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
4145     model integration time     model integration time
4146    
4147  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
4148  o add salt flux to forcing fields (used when salty sea-ice forms or melts)  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
4149  o enable to apply restoring on S & T only in a latitude band.  o enable to apply restoring on S & T only in a latitude band.
4150  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
4151     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
4152    
4153  checkpoint51k_post  checkpoint51k_post (2003/10/16)
4154  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
4155   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
4156     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
# Line 3221  o added an include barrier to the defaul Line 4164  o added an include barrier to the defaul
4164    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
4165  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
4166    
4167  checkpoint51j_post  checkpoint51j_post (2003/10/10)
4168  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
4169  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
4170  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 3235  o Moving pkg-specific flow directives to Line 4178  o Moving pkg-specific flow directives to
4178         - pkg_ad_diff.list         - pkg_ad_diff.list
4179         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
4180    
4181  checkpoint51i_post  checkpoint51i_post (2003/10/09)
4182  o merge of the branch-genmake2  o merge of the branch-genmake2
4183    - knowingly breaks the older genmake    - knowingly breaks the older genmake
4184    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
4185    - new testreport supersedes older testscript    - new testreport supersedes older testscript
4186  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
4187  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
4188    
4189  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
4190  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 3253  o modify gchem pkg to be more versatile Line 4196  o modify gchem pkg to be more versatile
4196  o modifications to clean up dic pkg  o modifications to clean up dic pkg
4197  o add pkg/cfc  o add pkg/cfc
4198    
4199  checkpoint51g_post  checkpoint51g_post (2003/10/02)
4200  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
4201  o start removing verification/vero/  o start removing verification/vero/
4202  o update AD-related stuff  o update AD-related stuff
# Line 3261  o update AD-related stuff Line 4204  o update AD-related stuff
4204  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
4205    vector invariant setup    vector invariant setup
4206    
4207  checkpoint51f_post  checkpoint51f_post (2003/10/02)
4208  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
4209  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
4210    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
4211    
4212  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
4213  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
4214      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
4215    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 3278  o Bug fix to pkg/ptracers, pkg/generic_a Line 4221  o Bug fix to pkg/ptracers, pkg/generic_a
4221      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
4222      non-local transport term.      non-local transport term.
4223    
4224  checkpoint51e_post  checkpoint51e_post (2003/08/03)
4225  o pkg/mom_vecinv:  o pkg/mom_vecinv:
4226    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
4227    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 3288  o atmospheric geopotential: - include wa Line 4231  o atmospheric geopotential: - include wa
4231  o land pkg: read initial state from files.  o land pkg: read initial state from files.
4232  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
4233    
4234  checkpoint51d_post  checkpoint51d_post (2003/07/18)
4235  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
4236    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
4237  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
# Line 3301  o Use cluster local disks for purely loc Line 4244  o Use cluster local disks for purely loc
4244    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
4245    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
4246    
4247  checkpoint51c_post  checkpoint51c_post (2003/07/08)
4248  o introducing integer flag debugLevel  o introducing integer flag debugLevel
4249    - debLevZero: suppress all output    - debLevZero: suppress all output
4250    - debLevA: standard    - debLevA: standard
# Line 3324  o added verification for adjoint with pt Line 4267  o added verification for adjoint with pt
4267    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
4268  <<<checkpoint51b_pre  <<<checkpoint51b_pre
4269    
4270  checkpoint51a_post  checkpoint51a_post (2003/06/25)
4271  o added code for biogeochemistry package  o added code for biogeochemistry package
4272    - new pkgs: dic, gchem    - new pkgs: dic, gchem
4273    - new subroutine in ptracers    - new subroutine in ptracers
4274  o modify code for biogeo packages  o modify code for biogeo packages
4275    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
4276    
4277  checkpoint51  checkpoint51 (2003/06/24)
4278  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
4279    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
4280    kept separate packages    kept separate packages
# Line 3339  o merged improved packages from ecco-bra Line 4282  o merged improved packages from ecco-bra
4282  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
4283    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
4284    
4285  checkpoint50i_post  checkpoint50i_post (2003/06/23)
4286  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
4287    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
4288    - 1st step: this one is differentiable    - 1st step: this one is differentiable
4289    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
4290                from ecco-branch)                from ecco-branch)
4291    
4292  checkpoint50h_post  checkpoint50h_post (2003/06/20)
4293  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
4294  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
4295  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
# Line 3355  o New variable in PARM03 for more flexib Line 4298  o New variable in PARM03 for more flexib
4298  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
4299    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
4300    
4301  checkpoint50g_post  checkpoint50g_post (2003/05/23)
4302  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
4303    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
4304    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
4305      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
4306    
4307  checkpoint50f_post  checkpoint50f_post (2003/05/23)
4308  o exf totally restructured  o exf totally restructured
4309    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
4310      and made sure it's still differentiable      and made sure it's still differentiable
# Line 3369  o exf totally restructured Line 4312  o exf totally restructured
4312    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
4313    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
4314    
4315  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
4316   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
4317        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
4318   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 3379  checkpoint50f_pre Line 4322  checkpoint50f_pre
4322   o new fn in pkg/monitor to stop model if solution grows too big   o new fn in pkg/monitor to stop model if solution grows too big
4323   o removed lots of single quotes from comments   o removed lots of single quotes from comments
4324    
4325  checkpoint50e_post  checkpoint50e_post (2003/05/14)
4326  o make KPP work with PTRACERS  o make KPP work with PTRACERS
4327   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
4328     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
4329   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
4330     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
4331  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
4332  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
4333    
4334  checkpoint50d_post  checkpoint50d_post (2003/05/13)
4335  o change kpp output from multiple-record state files to single-record state  o change kpp output from multiple-record state files to single-record state
4336    files analogous to write_state.F    files analogous to write_state.F
4337  o reduce the output frequency of cg3d-related stuff to the monitor frequency,  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
4338    analogous to the cg2d-related output.    analogous to the cg2d-related output.
4339  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
4340    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
4341  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
4342    
4343  checkpoint50c_post  checkpoint50c_post (2003/05/12)
4344  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
4345  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
4346  o add time-average diagnostic of U*V and vertical diffusive flux for theta.  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
4347  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
4348  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
4349    
4350  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
4351  Merging from release1_p13:  Merging from release1_p13:
4352  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
4353  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4354    
4355  checkpoint50b_post  checkpoint50b_post (2003/04/17)
4356  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
4357  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
4358    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 3418  o new flag "useCDscheme" (default=F); re Line 4361  o new flag "useCDscheme" (default=F); re
4361  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
4362     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
4363    
4364  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
4365  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
4366  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
4367    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
4368    
4369  checkpoint50a_post  checkpoint50a_post (2003/03/21)
4370  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
4371    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
4372    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
4373    in contradiction with new key itdkey.    in contradiction with new key itdkey.
4374    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
4375    
4376  checkpoint50  checkpoint50 (2003/03/08)
4377  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
4378    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
4379  - bug fix in find_alpha  - bug fix in find_alpha
# Line 3438  checkpoint50 Line 4381  checkpoint50
4381  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
4382  - merged some sliced AD support routines  - merged some sliced AD support routines
4383    
4384  checkpoint49  checkpoint49 (2003/03/06)
4385  merged from ecco-branch:  merged from ecco-branch:
4386  o exf:  o exf:
4387    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 3476  o DIVA: Line 4419  o DIVA:
4419    (see MITgcm manual).    (see MITgcm manual).
4420  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
4421    
4422  checkpoint48i_post  checkpoint48i_post (2003/03/05)
4423  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
4424    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
4425    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 3494  o Modif. for DIVA: Line 4437  o Modif. for DIVA:
4437    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
4438    only relevant for ecco-branch)    only relevant for ecco-branch)
4439    
4440  checkpoint48h_post  checkpoint48h_post (2003/02/28)
4441  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
4442  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
4443  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4444  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
4445    
4446  checkpoint48g_post  checkpoint48g_post (2003/02/18)
4447  --- EOS:  --- EOS:
4448  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
4449    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 3514  o accurate phiHyd when using interface-W Line 4457  o accurate phiHyd when using interface-W
4457   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
4458  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
4459    
4460  checkpoint48f_post  checkpoint48f_post (2003/02/18)
4461  Merging from release1_p12:  Merging from release1_p12:
4462  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
4463    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 3542  o pkg/seaice: Line 4485  o pkg/seaice:
4485    - adjoint-friendly modifications    - adjoint-friendly modifications
4486    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
4487    
4488  checkpoint48e_post  checkpoint48e_post (2003/02/12)
4489  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
4490  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
4491    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
# Line 3553  o following exp works with Olx=Oly=2 (an Line 4496  o following exp works with Olx=Oly=2 (an
4496      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
4497    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
4498    
4499  checkpoint48d_post  checkpoint48d_post (2003/02/09)
4500  o in preparation for r*:  o in preparation for r*:
4501   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
4502      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
# Line 3561  o in preparation for r*: Line 4504  o in preparation for r*:
4504      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
4505    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
4506    
4507  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
4508  o in preparation for r*:  o in preparation for r*:
4509    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
4510    pass the 2 comp. of the grad. as arguments to momentum S/R.    pass the 2 comp. of the grad. as arguments to momentum S/R.
4511    but for the moment, only used if it does not change the results.    but for the moment, only used if it does not change the results.
4512  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
4513    
4514  checkpoint48c_post  checkpoint48c_post (2003/02/06)
4515  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
4516  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
4517    
4518  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
4519  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
4520  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
4521    
4522  checkpoint48b_post  checkpoint48b_post (2003/01/27)
4523  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
4524   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
4525  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
4526    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
4527    
4528  checkpoint48a_post  checkpoint48a_post (2003/01/24)
4529  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
4530     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
4531    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
4532                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
4533    
4534  checkpoint48  checkpoint48 (2003/01/23)
4535  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
4536    
4537  checkpoint47j_post  checkpoint47j_post (2003/01/21)
4538  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
4539  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
4540  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 3610  o Yet more changes in gmredi: Line 4553  o Yet more changes in gmredi:
4553      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
4554  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
4555    
4556  checkpoint47i_post  checkpoint47i_post (2003/01/13)
4557  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
4558  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
4559    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
# Line 3626  o case GM_BOLUS_ADVEC should be cleaned Line 4569  o case GM_BOLUS_ADVEC should be cleaned
4569    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
4570  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
4571    
4572  checkpoint47g_post  checkpoint47g_post (2003/01/10)
4573  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
4574    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
4575  o After TAF bug fix:  o After TAF bug fix:
# Line 3652  Gradient checks OK for Line 4595  Gradient checks OK for
4595  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
4596  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
4597    
4598  checkpoint47f_post  checkpoint47f_post (2002/12/28)
4599  Merging from release1_p10:  Merging from release1_p10:
4600  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
4601    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 3664  o modifications for using pkg/exf with p Line 4607  o modifications for using pkg/exf with p
4607    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
4608      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
4609    
4610  checkpoint47e_post  checkpoint47e_post (2002/12/27)
4611  o created a tag prior to creating a branch  o created a tag prior to creating a branch
4612    
4613  checkpoint47d_post  checkpoint47d_post (2002/12/16)
4614  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
4615    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
4616  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
4617    oceanic pressure coordinates code    oceanic pressure coordinates code
4618  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
4619    also described in the tutorial section of the manual    also described in the tutorial section of the manual
4620  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
4621    
4622  checkpoint47c_post  checkpoint47c_post (2002/12/16)
4623  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
4624    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
4625    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 3688  o OCEANICP & realFreshWater: include P-E Line 4631  o OCEANICP & realFreshWater: include P-E
4631    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
4632  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
4633    
4634  checkpoint47b_post  checkpoint47b_post (2002/12/05)
4635  Merging from release1_p9:  Merging from release1_p9:
4636  o pkg/seaice  o pkg/seaice
4637    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 3705  o verification/lab_sea Line 4648  o verification/lab_sea
4648    - added missing matlab routines    - added missing matlab routines
4649    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
4650    
4651  checkpoint47a_post  checkpoint47a_post (2002/11/23)
4652  o new pkg: aim_v23  o new pkg: aim_v23
4653   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
4654     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 3722  o bulk_force and therm_seaice Line 4665  o bulk_force and therm_seaice
4665  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
4666     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
4667    
4668  checkpoint47  checkpoint47 (2002/11/15)
4669  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
4670  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
4671  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 3751  o Updated verification/carbon/ Line 4694  o Updated verification/carbon/
4694    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
4695    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
4696    
4697  checkpoint46n_post  checkpoint46n_post (2002/11/12)
4698  Merging from release1_p8:  Merging from release1_p8:
4699  o verification/natl_box:  o verification/natl_box:
4700    updating new external_fields_load routine    updating new external_fields_load routine
# Line 3805  o Adding new verification experiment glo Line 4748  o Adding new verification experiment glo
4748    the exf (and cal) package instead of the    the exf (and cal) package instead of the
4749    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
4750    
4751  checkpoint46m_post  checkpoint46m_post (2002/11/07)
4752  o modified testscript to return -- when there are no lines of "%MON" output  o modified testscript to return -- when there are no lines of "%MON" output
4753  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
4754    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 3818  o introduced flag for controllin non-hyd Line 4761  o introduced flag for controllin non-hyd
4761  o removed gravitySign from PARM04  o removed gravitySign from PARM04
4762  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
4763    
4764  checkpoint46l_post  checkpoint46l_post (2002/11/01)
4765  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
4766   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
4767     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 3831  o made convective adjustment work with p Line 4774  o made convective adjustment work with p
4774     at the beginning of find_rho, find_alpha, and find_beta, does a     at the beginning of find_rho, find_alpha, and find_beta, does a
4775     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
4776     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
4777  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
4778    
4779  checkpoint46k_post  checkpoint46k_post (2002/10/23)
4780  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
4781   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
4782   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 3847  o S/R aim_initialise.F replace S/R aim_i Line 4790  o S/R aim_initialise.F replace S/R aim_i
4790   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
4791   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
4792    
4793  checkpoint46j_post  checkpoint46j_post (2002/10/07)
4794  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
4795  o move wVel computation at the end of the time step, in S/R integr_continuity  o move wVel computation at the end of the time step, in S/R integr_continuity
4796  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
4797  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
4798  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
4799    
4800  checkpoint46i_post  checkpoint46i_post (2002/09/25)
4801  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
4802    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
4803    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
4804    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
4805    
4806  checkpoint46h_post  checkpoint46h_post (2002/09/25)
4807  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
4808    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
4809      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
# Line 3870  o introduced new parameter rhoConstFresh Line 4813  o introduced new parameter rhoConstFresh
4813    value is 999.8 kg/m^3    value is 999.8 kg/m^3
4814  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
4815    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
4816  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
4817    
4818   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
4819   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
4820   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
4821    
4822  checkpoint46g_post  checkpoint46g_post (2002/09/18)
4823  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
4824    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
4825    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 3894  o cleaned up find_rho Line 4837  o cleaned up find_rho
4837    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
4838  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
4839    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
4840  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
4841    
4842  checkpoint46f_post  checkpoint46f_post (2002/09/16)
4843  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
4844    - extended active file handling to g_... files    - extended active file handling to g_... files
4845    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 3904  o Enable tangent linear (forward mode) g Line 4847  o Enable tangent linear (forward mode) g
4847  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
4848  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
4849    
4850  checkpoint46e_post  checkpoint46e_post (2002/09/05)
4851  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
4852    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
4853    - caveat: the equation of state is only valid for a smaller (more    - caveat: the equation of state is only valid for a smaller (more
# Line 3913  o Added new equation of state -> MDJWF Line 4856  o Added new equation of state -> MDJWF
4856    - added more check values for density in check_eos (ini_eos.F), some of    - added more check values for density in check_eos (ini_eos.F), some of
4857      the old check values are out of the range of the MDJWF-eos, so don't      the old check values are out of the range of the MDJWF-eos, so don't
4858      expect perfect matches for those      expect perfect matches for those
4859  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
4860    
4861  checkpoint46d_post  checkpoint46d_post (2002/08/19)
4862  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
4863    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
4864    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
4865    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
4866  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
4867    in find_alpha/beta.    in find_alpha/beta.
4868  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
4869    
4870  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
4871    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
4872    
4873  checkpoint46c_post  checkpoint46c_post (2002/08/15)
4874  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
4875   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
4876   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
4877      the factor dRdZ which I added when we first switched to R coordinates).      the factor dRdZ which I added when we first switched to R coordinates).
4878   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
4879   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
4880  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
4881    
4882  checkpoint46b_post  checkpoint46b_post (2002/08/07)
4883  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
4884    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
4885    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 3945  o Added UNESCO EOS, but not recommended Line 4888  o Added UNESCO EOS, but not recommended
4888    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
4889  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
4890    unesco.f to be used with POLY3    unesco.f to be used with POLY3
4891  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
4892    
4893  checkpoint46a_post  checkpoint46a_post (2002/07/31)
4894  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
4895    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
4896    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
4897  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
4898  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
4899  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
4900    
4901  checkpoint46  checkpoint46 (2002/07/13)
4902  further merges from release1_p5  further merges from release1_p5
4903  o new ctrl package  o new ctrl package
4904    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 3982  o added hooks for Eliassen Palm fluxes ( Line 4925  o added hooks for Eliassen Palm fluxes (
4925  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
4926  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
4927    
4928  checkpoint45d_post  checkpoint45d_post (2002/07/12)
4929  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
4930  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
4931    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 3996  o add new flags: Line 4939  o add new flags:
4939   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
4940  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
4941    
4942  checkpoint45c_post  checkpoint45c_post (2002/05/30)
4943  o Removed f90 comments ("!")  o Removed f90 comments ("!")
4944  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
4945    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 4004  o modifications to gradient check packag Line 4947  o modifications to gradient check packag
4947    - enable centered differences    - enable centered differences
4948    - modified format of standard output    - modified format of standard output
4949    
4950  checkpoint45b_post  checkpoint45b_post (2002/05/30)
4951  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
4952  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
4953  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 4016  o in initialise_varia, moved call packag Line 4959  o in initialise_varia, moved call packag
4959    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
4960  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
4961    
4962  checkpoint45a_post  checkpoint45a_post (2002/05/01)
4963  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
4964  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
4965  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
# Line 4036  o errorMessageUnit set non-equal zero in Line 4979  o errorMessageUnit set non-equal zero in
4979    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
4980  o modified carbon verif.  o modified carbon verif.
4981    
4982  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
4983  o vertical grid option: allow to put the Interface at the middle between  o vertical grid option: allow to put the Interface at the middle between
4984    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
4985  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
4986    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
4987    
4988  checkpoint44g_post  checkpoint44g_post (2002/03/05)
4989  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
4990    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
4991    
# Line 4107  o merge of relevant stuff from the ecco- Line 5050  o merge of relevant stuff from the ecco-
5050  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
5051  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
5052    
5053  checkpoint44  checkpoint44 (2002/01/18)
5054  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
5055  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
5056  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 4115  o update AIM experiments (NCEP input fil Line 5058  o update AIM experiments (NCEP input fil
5058  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
5059  o added some stuff for AD  o added some stuff for AD
5060    
5061  checkpoint43  checkpoint43 (2001/09/28)
5062  o added two new advection tests  o added two new advection tests
5063  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
5064  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
5065  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
5066    
5067  checkpoint42  checkpoint42 (2001/09/27)
5068    Fixed AD-related problems:    Fixed AD-related problems:
5069  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
5070    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 4133  o Modified store directives for split of Line 5076  o Modified store directives for split of
5076    for the case ALLOW_KPP    for the case ALLOW_KPP
5077  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
5078    
5079  checkpoint41  checkpoint41 (2001/09/27)
5080  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
5081    to work with protex    to work with protex
5082    
5083  checkpoint40  checkpoint40 (2001/09/27)
5084  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
5085  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
5086  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 4146  o more mods for non-linear free-surface Line 5089  o more mods for non-linear free-surface
5089  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
5090  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
5091    
5092  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
5093  o added DST advection schemes  o added DST advection schemes
5094  o fix MPI bug on SGI's  o fix MPI bug on SGI's
5095  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 4156  o changes to commenting of arguments for Line 5099  o changes to commenting of arguments for
5099  o added/updated many matlab scripts  o added/updated many matlab scripts
5100  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
5101        
5102  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
5103  o new package rw/  o new package rw/
5104    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
5105    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 4175  o TAMC-related update to cope with mom_f Line 5118  o TAMC-related update to cope with mom_f
5118    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
5119    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
5120    
5121  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
5122  o bug fix in dynamics.F  o bug fix in dynamics.F
5123    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
5124  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
5125  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
5126    related to TAF    related to TAF
5127    
5128  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
5129  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
5130  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
5131    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 4190  o corresponding split of calc_diffusivit Line 5133  o corresponding split of calc_diffusivit
5133  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
5134  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
5135    
5136  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
5137  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
5138    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
5139  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 4204  o added new expt "solid-body.cs-32x32x1" Line 5147  o added new expt "solid-body.cs-32x32x1"
5147    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
5148      is not necessarily any better than the current one...      is not necessarily any better than the current one...
5149    
5150  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
5151  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
5152    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
5153  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 4212  o extended iMin,jMin range for calc_comm Line 5155  o extended iMin,jMin range for calc_comm
5155  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
5156  o a few minor updates and fixes  o a few minor updates and fixes
5157    
5158  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
5159  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
5160  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
5161  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
5162    
5163  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
5164  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
5165  o Added gradient check package  o Added gradient check package
5166  o Added routines for passive tracer handling  o Added routines for passive tracer handling
5167  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
5168    
5169  checkpoint39  checkpoint39 (2001/05/14)
5170   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
5171     (mainly missing or wrong directives)     (mainly missing or wrong directives)
5172   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 4237  checkpoint39 Line 5180  checkpoint39
5180           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
5181   o disabled some packages by default in genmake   o disabled some packages by default in genmake
5182    
5183  checkpoint38  checkpoint38 (2001/04/10)
5184   o see notes_c37_adj.txt   o see notes_c37_adj.txt
5185   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
5186   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 4245  checkpoint38 Line 5188  checkpoint38
5188     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
5189   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
5190    
5191  checkpoint37  checkpoint37 (2001/03/13)
5192   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
5193     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
5194      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 4262  checkpoint37 Line 5205  checkpoint37
5205   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
5206   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
5207    
5208  checkpoint36  checkpoint36 (2001/02/20)
5209   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
5210   o recover Time-Average diagnostics   o recover Time-Average diagnostics
5211   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
5212   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
5213    
5214  checkpoint35  checkpoint35 (2001/02/08)
5215   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
5216   o allows staggered time-stepping   o allows staggered time-stepping
5217   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
5218   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
5219    
5220  checkpoint34  checkpoint34 (2001/01/30)
5221   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
5222   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
5223     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 4285  checkpoint34 Line 5228  checkpoint34
5228   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
5229   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
5230    
5231  checkpoint33  checkpoint33 (2000/11/30)
5232   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
5233   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
5234     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 4303  checkpoint33 Line 5246  checkpoint33
5246       possibly use them.       possibly use them.
5247   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
5248    
5249  checkpoint32  checkpoint32 (2000/11/13)
5250   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
5251     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
5252   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 4314  checkpoint32 Line 5257  checkpoint32
5257   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
5258   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
5259    
5260  checkpoint31  checkpoint31 (2000/09/11)
5261   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
5262     -> new routines packages_...F     -> new routines packages_...F
5263     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 4331  checkpoint31 Line 5274  checkpoint31
5274     - not yet tested for GMRedi.     - not yet tested for GMRedi.
5275     - not yet tested for KPP.     - not yet tested for KPP.
5276    
5277  checkpoint30  checkpoint30 (2000/07/13)
5278   o Updates for OBCs   o Updates for OBCs
5279   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
5280   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 4340  checkpoint30 Line 5283  checkpoint30
5283   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
5284     and entry for T90 in genmake     and entry for T90 in genmake
5285    
5286  checkpoint29  checkpoint29 (2000/06/21)
5287   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
5288    
5289  checkpoint28  checkpoint28 (2000/06/09)
5290   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
5291   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
5292   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 4356  checkpoint28 Line 5299  checkpoint28
5299     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
5300   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
5301    
5302  checkpoint27  checkpoint27 (2000/04/10)
5303   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
5304     formulation works properly with variable resolution.     formulation works properly with variable resolution.
5305   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 4364  checkpoint27 Line 5307  checkpoint27
5307   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
5308     in new routine ini_psurf()     in new routine ini_psurf()
5309    
5310  checkpoint26  checkpoint26 (2000/04/05)
5311   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
5312     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
5313   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 4374  checkpoint26 Line 5317  checkpoint26
5317     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
5318   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
5319    
5320  checkpoint25  checkpoint25 (2000/03/15)
5321   o updates for OBCs and NH   o updates for OBCs and NH
5322   o dramatically reduced memory usage   o dramatically reduced memory usage
5323   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 4385  checkpoint25 Line 5328  checkpoint25
5328      an explicit free-surface option)      an explicit free-surface option)
5329   o initial state input files for U and V   o initial state input files for U and V
5330    
5331  checkpoint24  checkpoint24 (1999/08/02)
5332   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
5333   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
5334   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
5335    
5336  checkpoint23  checkpoint23 (1999/05/26)
5337   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
5338   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
5339    
5340  checkpoint22  checkpoint22 (1999/05/18)
5341   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
5342   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
5343    
5344  checkpoint21  checkpoint21 (1999/05/18)
5345   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
5346   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
5347   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
5348   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
5349    
5350  checkpoint20  checkpoint20 (1999/03/22)
5351   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
5352   o Added non-hydrostatic code   o Added non-hydrostatic code
5353   o Fixed some input data   o Fixed some input data
5354   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
5355    
5356  checkpoint19  checkpoint19 (1998/12/15)
5357   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
5358   o Added new code for open boundaries.   o Added new code for open boundaries.
5359   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 4418  checkpoint19 Line 5361  checkpoint19
5361   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
5362   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
5363    
5364  checkpoint18  checkpoint18 (1998/11/30)
5365   o Further changes for optional code generation with   o Further changes for optional code generation with
5366     CPP - ugh!     CPP - ugh!
5367    
5368  checkpoint17  checkpoint17 (1998/11/03)
5369   o Beginning to incorporating modularity   o Beginning to incorporating modularity
5370     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
5371   o Small changes for TAMC complinace   o Small changes for TAMC complinace
5372   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
5373     configuration "exp0".     configuration "exp0".
5374    
5375  checkpoint16  checkpoint16 (1998/10/28)
5376   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
5377     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
5378     assignment is an addition.     assignment is an addition.
# Line 4437  checkpoint16 Line 5380  checkpoint16
5380     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
5381     limit ).     limit ).
5382    
5383  checkpoint15  checkpoint15 (1998/09/29)
5384   Rewrote exchange routines to allow   Rewrote exchange routines to allow
5385   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
5386   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 4446  checkpoint15 Line 5389  checkpoint15
5389     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
5390     communication method.     communication method.
5391    
5392  checkpoint14  checkpoint14 (1998/09/09)
5393   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
5394   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
5395    
5396  checkpoint13  checkpoint13 (1998/07/17)
5397   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
5398   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
5399   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 4465  branch-point-rdot Line 5408  branch-point-rdot
5408   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
5409   we've actually tested it...   we've actually tested it...
5410    
5411  checkpoint12  checkpoint12 (1998/07/08)
5412   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
5413   configure script).   configure script).
5414   Released to testers.   Released to testers.
5415    
5416  checkpoint11  checkpoint11 (1998/07/02)
5417   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
5418   and ini_masks_etc().   and ini_masks_etc().
5419    
5420  checkpoint10  checkpoint10 (1998/07/01)
5421   Introduced the configure script.   Introduced the configure script.
5422   Separated out the diags package.   Separated out the diags package.
5423   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
5424   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
5425    
5426  checkpoint9  checkpoint9 (1998/06/22)
5427   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
5428   General tidy-up.   General tidy-up.
5429   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
5430    
5431  checkpoint8  checkpoint8 (1998/06/22)
5432   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
5433   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
5434    
# Line 4495  checkpoint7-4degree-ref Line 5438  checkpoint7-4degree-ref
5438   model etc..   model etc..
5439   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
5440    
5441  checkpoint7  checkpoint7 (1998/06/15)
5442   Created by cnh   Created by cnh
5443   Simple 4 degree global simulation   Simple 4 degree global simulation
5444   configuration.   configuration.
# Line 4503  checkpoint7 Line 5446  checkpoint7
5446   hydrography, bathymetry etc   hydrography, bathymetry etc
5447   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
5448    
5449  checkpoint6  checkpoint6 (1998/06/08)
5450   Created by cnh   Created by cnh
5451   merged checkpoint5 with CD and   merged checkpoint5 with CD and
5452   spherical polar code.   spherical polar code.
5453   Still some problems with GM Redi   Still some problems with GM Redi
5454   abd full topography.   abd full topography.
5455    
5456  checkpoint5  checkpoint5 (1998/06/08)
5457   Created by AJA   Created by AJA
5458   contains updates to GM Redi   contains updates to GM Redi
5459   and reordered timestepping loop   and reordered timestepping loop
5460   for Implicit Diffusion.   for Implicit Diffusion.
5461    
5462  checkpoint4  checkpoint4 (1998/05/30)
5463   Created by cnh   Created by cnh
5464   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
5465   grid variations are limited.   grid variations are limited.
5466   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
5467   for generation.   for generation.
5468    
5469  checkpoint3  checkpoint3 (1998/05/26)
5470   Created by cnh   Created by cnh
5471   Added extra flags for runtime options   Added extra flags for runtime options
5472   Added this file   Added this file

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