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revision 1.222 by dimitri, Wed Dec 10 19:37:25 2003 UTC revision 1.1310 by mlosch, Tue Oct 12 16:03:58 2010 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/thsice:
8       - change a few routines for better vectorization: thsice_albedo.F,
9         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
10         not affected, but in particular the latter routine has changed
11         dramatically (not necessarily easier to read now).
12       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
13       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
14    o verification/lab_sea:
15      - overhaul of the forward model experiments. The main motivation
16        for this revision is that lab_sea has proven quite fragile (when
17        changing the sea-ice code, and switching platforms) to a point
18        when failures were very hard to attribute to specific code problems.
19      - the suspected reason for this fragility is noise amplification by evp so,
20        to start with, we decided to replace evp with lsr in the main experiment.
21      - the input.lsr experiment thus became obsolete and was removed.
22      - it was replaced with the input.fd experiment that uses an
23        analytical "free drift" solution as the ice velocity field.
24      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
25        will hopefully allow us to discriminate problems due to dynamic solvers
26        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
27        us to test additional options, along with the salt plume package.
28      - Finally a pickup was generated (at the end of a one year run) to
29        make the tests more representative of an actual model run. Previously
30        the tests starting point was a 1m thickness of ice everywhere.
31    o pkg/seaice:
32      - introducing S\R seaice_freedrift.F that compute the
33        analytical solution to an approximate ice momentum
34        equation (i.e. the simple stress/coriolis balance).
35      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
36        of the free drift velocity field, and enable its use.
37        To actually use the free drift solution as the model ice
38        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
39    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
40    
41    checkpoint62l (2010/10/04)
42    o pkg/seaice:
43      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
44      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
45       version (with USE_ORIGINAL_SBI undef);
46    o add hooks for new packages OASIS, the package will follow
47      (hooks exclude the seaice pkg for now)
48    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
49      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
50      rather than mdsio_readvector.F/mdsio_writevector.F, within
51      adread_adwrite.F to read/write adjoint-related tapes to disk.
52    o eesupp and pkg/mdsio: ALLOW_WHIO
53      Option to write/read 2D fields to files including tiles halos.
54      The main purpose is for adjoint related "tape I/O".
55      The secondary purpose is for debugging phases.
56      A word on those rather specifically intended purposes.
57      The code was meant to be stripped down to the bare minimum.
58      Typically, there is a unique and basic mapping to the global
59      buffer (tile by tile, then proc by proc, then level by level), and
60      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
61      meant to generate user friendly outputs of various shapes and forms.
62      Rather it is intended, for the knowledgeabale developers,
63      to be largely independent of the many mdsio options, to allow
64      outputs of tiles+halos in debugging phases and in adjoint runs,
65      and to allow some flexibility in tuning (adoint) I/O depending on each
66      file system behavior. With regard to tuning, most of the potential knobs
67      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
68      to specify directories, to specify the typical size of I/O calls, etc.)
69      are not yet included, and will be added if they prove useful.
70    o pkg/seaice:
71       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
72    o pkg/seaice:
73       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
74       code (seaice_budget_ice_if.F) which enable to recover old standard
75       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
76       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
77    o model/src (rStar):
78       use simple average (not area weighted) of rStarFac at U,V point when using
79       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
80       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
81    
82    checkpoint62k (2010/09/17)
83    o adjoint
84       * changed verification/global_ocean.cs32x15 ; adjoint now tests
85         Adams-Bashforth 3 + NLFS + RSTAR
86       * some more modifs required for ECCO-GODAE v4
87    o pkg/seaice
88       add SEAICE_AGE_VOL option to use volume instead of area for
89       integrating SEAICE_AGE
90    o model/src:
91       first check-in of sigma & hybrid-sigma coordinate code ; also includes
92       non-linear free-surface parts ; but pressure-gradient not yet coded.
93    o pkg/ptracers:
94       option for ptracer to convert Salt Relax into additional EmP.
95        tested in exp. global_ocean.90x40x15.dwnslp (update output)
96    
97    checkpoint62j (2010/08/25)
98    o pkg/ggl90:
99       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
100    o pkg/dic: car_flux.F, phos_flux.F
101      - reduce number of exp-calls in order to improve performance
102      - clean up a little (replace fields by their macros, etc., fix
103        typo in CPP-flag)
104    o pkg/ggl90: minor changes
105      - GGL90diffKrS was removed --> always use GGL90diffKr
106      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
107      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
108        (commented out for now)
109      - change in max/min operations to ensure that smoothing is ok
110      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
111      - always use diffKrNrT as background profile (i.e. never use diffKr field)
112    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
113    o pkg/dic:
114      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
115        vectorization
116      - small bug fix in insol for the unlikely case of a cartesian grid
117      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
118        + now vectorize, which also removes adjoint recomputations;
119        + replace integer maksp1 by _RL maskp1
120        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
121    
122    checkpoint62i (2010/07/21)
123    o pkg/flt:
124      - with OBCS: stop floats which enter the OB region
125    o model/src:
126      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
127        for implicit vertical advection.
128    o pkg/seaice:
129     - account for melting in seaice age evolution.
130     - remove double counting of seaice ridging effect on seaice age.
131    
132    checkpoint62h (2010/06/18)
133    o pkg/exch2:
134     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
135    o tools/genmake2
136      - remove "-pdefault" option: redundant with the use of "packages.conf";
137      - remove file pkg/pkg_default : set the default as a pkg group
138        ("default_pkg_list") defined in pkg/pkg_groups;
139      - fix for case pkg/pkg_depend is missing (was hanging before);
140      - add option "-pgroups" to specify a different pkg_groups than the default.
141    o verification/adjustment.cs-32x32x1:
142       add a "minimal" set-up test (code_min & input_min) which only compiles
143       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
144    o tools/genmake2
145      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
146      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
147    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
148      files are nearly the same anyway.
149      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
150       - redefinition of tau(i,i) (by a factor of ustar)
151       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
152       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
153       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
154       - replace
155         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
156         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
157         by
158         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
159         (changes results)
160       -> exf_bulkformulae v1.22,
161          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
162          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
163                    output.txt 1.63
164           offline_exf_seaice: output.seaicetd.txt 1.7
165           seaice_obcs: output.txt 1.10)
166      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
167       -> exf_bulkformulae v1.23,
168          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
169          and global_ocean.cs32x15.icedyn (only 11 matching digits)
170      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
171    o adjoint of exch-1:
172     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
173       (note: was already like this when using EXCH-2) and remove flow dir
174       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
175     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
176     - update pkg/exch2 diff list.
177    
178    checkpoint62g (2010/05/19)
179    o eesupp/src (exch-1):
180     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
181       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
182       (renamed to exch1_*rx_cube.F).
183     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
184       to call new exch1 S/R ; update Makefile and .cvsignore.
185     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
186       exch2_xy_rx later)
187      Note: after updating your code, need to run "make clean" in eesupp/src
188    o test experiment bottom_ctrl_5x5:
189       new output_adm.txt with fewer grdchk & less monitor output.
190    o model/src:
191      remove the call to ini_cori in initialise_varia.F (just keep the usual one
192       in initialise_fixed.F). More consistent with coriolis & horizontal grid
193       beeing treated in the same way (ini_grid is not called a 2nd time).
194    o pkg/exf:
195      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
196      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
197      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
198      - cosmetic changes to exf_bulkformulae.F to make it look more like
199        exf_bulk_largeyeager04.F
200    o eesupp/src (exch-1):
201      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
202      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
203        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
204        (even without using MPI).
205      - Message mode: move RecvAck setting (indicator of buffer being ready)
206        from send_put to recv_get S/R (was useless before, but not sure if
207        it's much more useful now);
208      - Switch the order of sync: MPI-proc 1rst and then threads;
209      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
210      - fix AD code for communication mode ='get' (but not used).
211    o model/src:
212      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
213      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
214    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
215    o pkg/ctrl: require a specific set of control variables and exf-flags for
216      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
217    o model/src:
218     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
219       1rst forward sweep, to avoid over-writing output files during recomputations
220       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
221     b) 2nd version:
222      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
223      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
224         writePickupAtEnd) + seaice & ptracers output;
225      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
226    o model/src:
227      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
228    o pkg/exch2:
229      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
230      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
231    o pkg/autodiff & exch2:
232      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
233      (for now, only if ALLOW_EXCH2 is defined).
234    o pkg/autodiff:
235      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
236        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
237       + clean-up comments (_RS is not always real*4)
238      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
239      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
240        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
241    o testreport (AD-tests):
242      no longer link files from dir "../input" (1rst link files from
243      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
244    
245    checkpoint62f (2010/04/29)
246    o model/src/the_main_loop.F:
247      adjust store directives for seaice evp and multicategory according to
248      pkg/ecco/the_main_loop.F
249    o adjoint:
250      global_sum_ad was incomplete (noted many times by many people ;)
251      nice description by Jean U. as follows:
252      * allreduce(var) in global_sum.F can be interpreted as
253        reduce(sum) followed by broadcast of sum.
254      * The adjoint of that is
255        sum(adjoint) followed by broadcast(summed adjoint value)
256        or in other words, allreduce(sum, adjoint vars)
257      We were missing the sum(adjoint)!
258      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
259      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
260      The fix should produce 16-digit accuracy between
261      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
262      multi-CPU single-tile (e.g. nSx=1, nPx-2)
263      We'll probably change this yet again shortly
264    o eesupp/src:
265      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
266    o pkg/icefront
267      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
268        specification of addmass array based on a 2D field, which is added
269        at bottommost wet level at each horizontal location.
270    o model/src:
271     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
272     layout; (not always compatible with delX,delY setting; commented out for now).
273    o pkg/exch2:
274     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
275     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
276    
277    checkpoint62e (2010/04/15)
278    o pkg/obcs:
279      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
280    o pkg/dic:
281      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
282        (note: not presently tested in any forward verification exp.)
283       update tutorial_global_oce_biogeo AD output file.
284    o pkg/exf:
285      - account for the variation of albedo as a function of zenith angle
286        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
287    o build_options:
288     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
289    o pkg/dic:
290      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
291      - use binary pickup file for restart;
292      - initialise atmos-CO2 box from dic_pCO2 parameter;
293      - fix multi-threaded.
294    o pkg/rbcs:
295     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
296       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
297     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
298       and update output.txt
299    o pkg/kpp:
300     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
301     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
302       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
303       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
304     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
305       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
306    o pkg/offline:
307      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
308      (bug was added in version 1.10 on 2007-08-23).
309    o pkg/offline:
310      - no need to specify periodicExternalForcing, etc ... to use offline pack
311      - offline input files no longer just single prec --> parameter offlineLoadPrec
312    o verification/lab_sea:
313      change AD test to multi-tile setup and update all 4 AD output.
314      NOTE: while cost function values remain very similar,
315      gradients are very different, although gradient checks are self-consistent
316      Should try to get to the bottom of this (cost function summation order?)
317    o pkg/dic:
318      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
319      a weakness of TAF that drops part of double precision in log10 derivative.
320      <= changes removed since problem has been fixed in current TAF version 1.9.71
321      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
322    o pkg/ecco:
323      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
324      update all 4 lab_sea AD output.
325    
326    checkpoint62d (2010/03/22)
327    o build_options:
328      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
329    o remove unbalanced quote (single or double) in commented line of source code
330      (may cause some warning with some preprocessor/makedepend versions).
331    o pkg/seaice:
332      fix seaice_model.F for adjoint (gael) and update AD results of experiments
333       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
334    o testreport:
335      add option '-runonly' (short: '-ro') to just do the run part (without make).
336    o eesupp: remove JAM communication code (obsolete).
337    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
338      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
339      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
340      (update also the output).
341    
342    checkpoint62c (2010/03/02)
343    o tools/build_options :
344       move (some) old optfiles from build_options/ to build_options/unsupported/
345    o model/src and pkg/exf
346       surface relaxation -- separating data and data.exf options
347       The point is to ensure that we specify the surface relaxation
348       either in data or in data.exf (but not half and half) and to
349       avoid an accidental relaxation to 0 (which happened if a time
350       scale was specified but the file name was left empty)
351    o model/src model/inc and pkg/mom_common
352       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
353       => addition to the viscosity field as computed by others schemes
354    o tools/build_options:
355      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
356        but keep the former optfile for few weeks for smooth transition
357    o pkg/ecco
358      - allow user defined cost function contributions
359            CPP: ALLOW_USERCOST_CONTRIBUTION
360            USAGE: compute contributions in cost_usercost_all.F
361      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
362          the two options are complementary.
363    o pkg/smooth
364      - migration from contrib to the main repository
365    
366    checkpoint62b (2010/01/26)
367    o pkg/monitor:
368      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
369        (in case someone forgot to update customized pieces of code)
370    o nonHydrostatic:
371      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
372      - add a simple 2-D experiment (short_surf_wave) to test it.
373    o pkg/icefront:
374       adding the shell of, and the hooks to, a new package that
375       will model melting and freezing of vertical glacier ice fronts
376    o momentum:
377      add diagnostics of momentum tendency from Hydrostatic pressure gradient
378       (without surf.pressure term: would need a 2nd filling since implicit term).
379    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
380      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
381      cannot deal with the former
382    o cleaning:
383      - remove all (except OpenAD) old TLM output from results_ad dirs.
384      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
385      - comment out maskH definition (replaced by maskInC)
386    o pkg/monitor:
387      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
388        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
389    
390    checkpoint62a (2010/01/15)
391    o model/src:
392      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
393    o pkg/diagnostics:
394      - add optional level number diagnostics (i.e., level number to be define
395        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
396      - strictly check for valid parser-code(10) ;
397      - check if adding diag to the list from the right place.
398    o pkg/longstep:
399      - change parameters and fix tracer conservation with rstar/nonlinear free surface
400    o diagnostics:
401     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
402       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
403    o pkg/diagnostics:
404     - Add option for writing vertical integral (sum of selected levels) of an output
405        field instead of writing output field levels. Activate this option on a per
406        output-file basis, by setting the 2nd character of fileflag to 'I'.
407     - Add field-specific information relative to level integral in 3rd postion
408        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
409        vertically (x level-thickness x hFac), "r"=same but without hFac.
410    o do_the_model_io:
411      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
412        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
413        writing pickups and stopping.
414    o pkg/diagnostics (for now, only with mdsio):
415      - write time information to meta file (and modify accordingly rdmds.m) :
416        time-averaged diagnostics output: write starting and ending time of the
417        time-averaging interval ; snap-shot diagnostics output remains unchanged;
418    o pkg/timeave:
419      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
420        always Nr), now assumed to be equal to number of levels of averaged field;
421        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
422    o pkg/sbo:
423      - fix ocean bottom pressure global-average & 2-D time-ave output (was
424        neither initialised nor filled).
425      - add starting iteration in suffix of global-average output file
426        (to avoid over-writing the file after a restart)
427      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
428    o time-average:
429      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
430        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
431         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
432        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
433      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
434      - fix missing accumulation for pkg/opps.
435      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
436         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
437      - fix initialisation of time-ave vars and do only full time-step increment
438        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
439    o pkg/layers:
440      - use standard RW pkg S/R to write the output
441        and remove local write_fld version (which had a problem).
442      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
443      - fix LAYERS_CALC argument list.
444    o pkg/timeave:
445      - store cumulative-time in a simple tiled array (drop the level index)
446      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
447    o pkg/ocn,aim_compon_interf
448      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
449    
450    checkpoint62  (2009/12/23)
451    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
452        (was not previously tested in any other exp.)
453    o pkg/monitor:
454      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
455        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
456        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
457      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
458      - change del2 calculation.
459      - use interior masks (instead of maskH, <- to be remove).
460      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
461    o mask & obcs:
462      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
463      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
464        (called after packages_init_fixed)
465    o pkg/obcs:
466      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
467        Fixes bug in obcs+exf with nSx*nSy.GT.1
468      - fix multi-tile handling in obcs balance code
469    o nonHydrostatic:
470      - Implement AB-3 for non-hydrostatic vertical momentum ;
471        (change ordering of var. stored in pickup file when using NH)
472      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
473      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
474        (in prep. for new NH free surface form).
475    o pkg/obcs:
476      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
477    o model/src:
478      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
479    
480    checkpoint61z (2009/12/01)
481    o nonHydrostatic:
482      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
483        a spurious source of energy in simple baroclinic adjusment test case.
484      Update all non-hydrostatic exp output.
485    o model/src (3-d solver):
486      Change again 3-D solver free-surface RHS term when exactConserv=T:
487        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
488        (which was not the case with previous formulation).
489      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
490      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
491    o nonHydrostatic:
492      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
493        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
494      - change 3-D solver to work with r* (for now, only with linear free-surf.)
495      - add few debug diagnostics (cg3d_x, residual)
496    o model/src:
497      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
498        update output of exp. global_ocean.cs32x15.viscA4
499    o update output of exp. global_ocean.cs32x15.icedyn after removing
500      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
501    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
502    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
503      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
504    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
505      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
506      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
507      to test this code
508    o pkg/cd_code:
509      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
510       C-grid momentum. D-grid velocity used to be stepped forward in time with
511       Adams-Bashforth only on surface pressure term. Tests show that using AB on
512       D-grid coriolis term improves stability (as expected from CD-scheme paper).
513      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
514      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
515       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
516       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
517      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
518           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
519    o pkg/obcs:
520     - fix bug in initialisation (broken since Oct 1rst modification)
521       for useOBCSprescribe without useEXF.
522    
523    checkpoint61y (2009/11/15)
524    o pkg/seaice
525     - change (once again) the discretization for the evp solver: rather than
526       squaring the averages of strain rates, average the squares to give
527       a better approximation to VP behavior (in simple test); this breaks
528       verification experiments that use EVP (lab_sea and lab_sea.hb87)
529        --> update outputs
530    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
531      to improve vectorization of adjoint code on TARGET_NEC_SX
532    o verification/vermix:
533      - change vermix to a more "classical" 1d column with high vertical
534        resolution, seasonal heat flux forcing and constant wind forcing
535        --> update outputs
536    o pkg/seaice
537     - fix diagnostics of principal stress components for EVP
538     - add optional diagnostics of non-linear convergence for LSOR solver
539     - make maximum zeta a runtime parameter
540    o model/src (3-d solver):
541      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
542       which consisted in removing the Surf. Non-Hydrostatic pressure from the
543       whole column and adding it to Eta (inspired from Casualli, 1999):
544       Only affects 3-D solver initial guess and only if using ExactConserv,
545       but tests did show a degradation of solver convergence. For this reason,
546       decide to disable this piece of code.
547       to recover previous version, just set zeroPsNH = exactConserv (line 78).
548      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
549    o pkg/ggl90:
550     - fix previous modif (unfortunatly has not been documented here).
551    o pkg/seaice/autodiff:
552     - add CPP flag to include clipping of zeta in EVP code;
553       although clipping of zeta is not necessary for EVP and not recommended
554       it was done by default, now clipping is disabled by default
555     - modify computation and store zetaC/Z in seaice_evp for TAF
556     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
557     - change seaice_calc_viscosities/strainrates for better
558       vectorization after AD by TAF
559     - rearrange common blocks in SEAICE.h once again for easier dumps of
560       adjoint output, adjust adcommon.h and g_common.h
561     - change flux form of default advection scheme for better vectorization
562       of adjoint code
563     - modify lab_sea/input.lsr to test the flux form of default advection
564       scheme
565    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
566      transition in checkpoint61r)
567    
568    checkpoint61x (2009/10/19)
569    o adjoint: adding two new verification experiments
570      * tutorial_global_biogeo: an online dic sensitivity experiment
571        (work with G. Forget)
572      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
573        (an update of the Dutkiewicz et al., 2006 paper)
574      Both use the same CO2FLUX cost function, but different controls
575      Gradient checks look good, but some recomp. could still be traightened out
576      Should add xx_dic control variable to test at some point
577    o model/src:
578      add run-time parameters to check and/or mask initial Temp & Salt
579    o pkg/ptracers:
580      apply zonal filter (if used) to all passive tracers
581    
582    checkpoint61w (2009/10/12)
583    o adjoint:
584      * update and finish work on adjoint of dic package (G. Forget)
585      * start adjoint of offline package
586      * bug fix for cube-sphere TLM code (active_file_g.F)
587    o tutorial_global_oce_optim:
588      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
589      and add SIZE.h_mpi for MPI testing
590    o pkg autodiff
591     - fix bug in autodiff_restore
592     - make genmake2 remove comments and empty lines from ad_input_code.f in
593       order to reduce file size (new script file remove_comments_sed)
594    o allows to specify vertical profile of vertical viscosity (viscArNr)
595    o pkg autodiff
596      autodiff_ini_model_io: comment out writing of grid information to netcdf
597      files, because at this time the grid fields are a bunch of zeros
598      (this is analogous to ini_mnc_vars.F)
599    o pkg seaice/autodiff:
600     left-over from removing the 3-time-level fields:
601     - small rearrangement of common blocks (SEAICE.h)
602     - fix field declaration in order to get meaningful output in
603       adseaice.*.nc (adcommon.h)
604    o pkg obcs:
605     - go through NH code only if nonHydrostatic=T
606     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
607     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
608       => Update output of experiment seaice_obcs
609     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
610     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
611     - fix restart for useOBCSprescribe + useEXF
612    o pkg ctrl
613     - make obcs as control parameter work also with useSingleCPUio
614     - replace a few sny and snx by Ny and Nx to be consistent with
615       ctrl_set_globfld_x/yz.F
616    o pkg seaice
617     - re-introduce global field frWtrAtm for the case of
618       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
619     - catch the case of an empty filename in seaice_cost_init_fixed.F
620    o pkg ecco:
621     - small bug fixes in the_main_loop
622      . fix order of monitor arguments
623      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
624      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
625        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
626     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
627       imbalance diagnostics for wmean_h/sflux = 0
628     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
629     - catch the case of empty filenames in ecco_cost_init_fixed.F
630       and ecco_readparms.F
631     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
632       to make this statement meaningfull in ecco_cost_weights.F
633    o pkg zonal_filt:
634      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
635      - when using rStar, filter uVel*hFacW instead of uVel
636       (tested without topography: fix a Pb of growing instability with NLFS)
637    o pkg/aim/thsice:
638     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
639      (works as SST restoring)
640    o pkg/thsice:
641     -add specific parameter for salt restoring in slab mixed-layer
642       (by default equal to the temperature restoring)
643    
644    checkpoint61v (2009/09/21)
645    o pkg/kpp:
646     -add double diffusive contributions as a hack, turned off by default
647      for now, and the code can be excluded with a CPP-flag
648      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
649     -add a verification experiments to "vermix" to test this code
650    o pkg/mom_common:
651      Move computation of length scales to mom_init_fixed.F (avoid recomputation
652      at each time-steps*levels).
653    o pkg/layers:
654      Created a new package for computing volume fluxes in temperature or
655      [not yet implemented] density layers, e.g. for calculating residual
656      overturning circulations.
657    o pkg/diagnostics:
658      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
659    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
660    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
661      To avoid mixing type (RS/RL) of input/output array argument,
662      replace single mixed-type array with a pair from each type (RS/RL).
663    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
664      is now implemented for all pkgs (previously only done for the main pickup)
665    
666    checkpoint61u (2009/08/25)
667    o pkg/obcs:
668      - change OB?eta from _RS to _RL and put them into a separate commen block
669      - add code to read OB?eta from a file via obcs_prescribe_read: the code
670        compiles and does not destroy any other experiments, the data is read
671        properly, but the code is not tested in actual applications
672    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
673      create a meaningful unit attribute for the time coordinate variable
674    o pkg/ebm: add plenty of missing "_d 0" ;
675       update results of experiment global_ocean_ebm (fwd + adjoint tests)
676      Notes: several pieces of code only works for (very) specific set up
677       (domain size, lat range, etc ...); should be documented & stop if one
678       of those assumptions is not meet.
679    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
680       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
681          and offline_exf_seaice (seaicetd + adjoint).
682    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
683       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
684        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
685    o few changes to pass when compiling with strick checking of arguments
686       across S/R (allow to find few bugs in S/R calls).
687    o pkg/seaice:
688     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
689       2d-fields, for slightly better performance
690    
691    checkpoint61t (2009/07/22)
692    o pkg/seaice:
693     - remove unused variables in seaice_evp
694     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
695    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
696       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
697       each processor opens a different file (a fix from Matt).
698    o cg2d:
699       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
700       this reduces number of EXCH calls by 2 when using exch2.
701       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
702       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
703    o pkg/thsice:
704       add code for Near Infra-Red albedo (from Jeff)
705       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
706    o ini_model_io:
707       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
708       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
709       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
710    
711    checkpoint61s (2009/06/30)
712    o pkg/exch2 (exch2_rxN_cube*):
713       remove last BARRIER (no need to synchronise after getting data from shared
714       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
715    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
716      and generate new output (for the 2 tests) using default rotationPeriod.
717    o pkg/exch2:
718      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
719        (was already the case with AUTODIFF_EXCH2 defined)
720      - add bj in exch2 arrays and S/R.
721      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
722        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
723    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
724      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
725        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
726      - verification experiment natl_box.longstep
727    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
728      allow different versions of ifort (8 or 9) and different versions
729       of mpi (mpich or mpich2) to be used with the same optfile.
730      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
731       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
732    o pkg/seaice:
733      fix previous modif (3-level field removed) for old-pickup reading
734    
735    checkpoint61r (2009/06/25)
736    o pkg/seaice:
737     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
738      1. introduce fields for time step (N-1)
739      2. do not use levels 2 and 3 anymore (but keep them)
740      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
741         includes changes to pkg/thsice/thsice_get_velocity.F,
742         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
743         pkg/obcs/obcs_apply_uvice.F.
744     - completely remove code for leap-frog time stepping for second order
745       advection
746     - adjusted adjoint accordingly;
747       gradient checks have improved by an order of magnitude!
748    
749    checkpoint61q (2009/06/22)
750    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
751     - the boundary conditions along open boundaries are unclear, because the
752       associated masks are set to zero and are thus treated as closed when
753       applying the slip-boundary conditions.
754     - move initialisation of grid variables from seaice_init_varia to _fixed
755    o adding doc/diags_changes.txt
756    o model/src:
757      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
758       to avoid "_diags" naming if no relation to pkg/diagnostics.
759      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
760       file and only call PLOT_FIELD_XYZ if debugMode=T.
761      remove few PLOT_FIELD_XY calls outside initialisation.
762      remove few unnecessary BARRIER.
763    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
764      of salt_plume package in Southern Ocean
765    o pkg/thsice:
766     - fix hOceMxL in overlap (needed for sea-ice advection);
767       update output of experiment global_ocean.cs32x15.icedyn.
768    o pkg/seaice:
769     - make the (placeholder-)tracer IceAge a little more meaningful
770      by avoiding ridging of age due to convergent ice flow
771     - add diagnostics for surface temperature, atmospheric and oceanic
772       heat flux, and atmospheric and oceanic ice growth
773    
774    checkpoint61p (2009/06/10)
775    o eesupp (global_max & global_sum):
776     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
777     - remove starting & endding barrier (no longer needed)
778    o pkg/mdsio, writelocal:
779       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
780       (remove the STOP): uses shared buffer IO to store data from all threads
781       and then let master-thread write nThreads tiles.
782    o pkg/mdsio (read/write field):
783     - tiled IO done in 1 piece (all levels at a time);
784     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
785     - multi-threaded: allow to read/write local (non-shared) array
786       (was already working with singleCpuIO ; now works also without);
787       => no longer needs barrier call after reading a file (added inside
788       mds_read/write field).
789     - move barrier calls outside gather/scatter_2d to mds_read/write_field
790    o pkg/obcs/exf
791      - exf_getffieldrec.F: add a few ". _d 0" and
792                            add code to catch the case fldperiod = 0.  
793      - obcs_precribe_read.F: change if statements so that they match
794                              the variable type (_RL)
795      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
796        exf_iprec) as part of namelist EXF_NML_01
797    o pkg/mdsio:
798      - read/write tiled (local) files: read/write 1-level tile chunk at a time
799        (instead of segment of length sNx); expected to speed up tiled IO.
800    o pkg/exch2:
801      - take buffer copy from/to array out of S/R exch2_send/recv into new
802        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
803        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
804      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
805      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
806        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
807        including Topology header file (and common blocks).
808      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
809        remove 2nd exch call in exch2_s3d_rx (no longer needed).
810      - document S/R arg. list (+ update some comments)
811    o pkg/seaice:
812      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
813        temperature and humidity over sea ice based on climatological values.
814      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
815        of LSR (this change is expected to change the results slightly because now
816        it uses slightly difference moduli from the second last LSR solution, but
817        that is more consistent with the stress computations; this part of the code
818        is not tested in the verification experiments)
819      - fix diagnostics for flux of ice in case of B-grid
820      - turn strain rates eij and press into global fields within global
821        common block in SEAICE.h for more straighforward diagnostics
822      - fix diagnostics for principal stress components, press, zeta, eta
823        to give something meaning full
824    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
825      new output (all 4 tests) using default rotationPeriod.
826    o pkg KPP:
827      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
828      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
829        and normal grid from 1 to Nr)
830    o Fix computations of L4rdt in mom_calc_visc.F
831    o eesupp:
832      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
833      should be called before a "stop" if we know that all process are going
834      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
835    
836    checkpoint61o (2009/05/26)
837    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
838    o model/src/ini_curvilinear_grid.F:
839       compute angleSin/CosC when they are not read from a file
840    o pkg/seaice:
841       add pseudo time stepping for LSOR
842    o pkg/exch2:
843       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
844    o pkg/seaice:
845       Adding separate sea ice albedo, drag coefficients, and HO in Southern
846       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
847    o SingleCpuIO:
848       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
849    o pkg/seaice:
850       put exchanged variable in (local) common block for MPI+Multi-Threads
851       to work (necessary with exch1, and for now with exch2 too).
852    o verification: to get more experiments tested with mpi, mth and mpi+mth,
853      change tiling of:
854       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
855       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
856      update output of exp:
857       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
858       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
859      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
860                       (note: output.txt generated on faulks using only 1 tile)
861    o eesupp & mdsio (SingleCpuIO):
862     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
863       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
864       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
865     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
866     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
867       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
868    o pkg/exch2:
869     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
870       read parameter file "data.exch2" if it exists; otherwise try default regular
871       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
872     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
873       with new code (not to be used, just as a backup solution).
874     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
875       in utils/exch2/input.
876    
877    checkpoint61n (2009/05/12)
878    o eesupp & mdsio (SingleCpuIO):
879      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
880        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
881        receive real*4 array (instead of real*8) to read/write 32.bit files.
882        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
883         and remove new mapping S/R)
884    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
885      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
886        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
887        when using exch2. Add S/R to map global io-buffer to global model array.
888      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
889    
890    checkpoint61m (2009/04/29)
891    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
892      and add 3 other S/R for other types (R4,R8,RS).
893      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
894    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
895     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
896     - reduce number of macro definitions (keep only those which are used);
897       can always call directly the corrresponding S/R if needed.
898     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
899       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
900     Fixed wrong type of arg in:
901       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
902       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
903     To fix: global_sum of var in common block is wrong (multi-threaded) in:
904       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
905     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
906    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
907      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
908    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
909    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
910      edges are closed (zero depth); might happen with "blank tiles";
911      for now, disabled if using OBCS.
912    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
913      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
914    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
915      to reduce length of 1.D array print in STDOUT.
916    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
917      + use 48 tiles (16x8): this will allow to test "blank tiles".
918    o start to test MPI + multi-threaded (change testreport to skip tests
919      where number of tiles do not match).
920    o genmake2: add option "-omp" to turn on Open-MP ;
921      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
922    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
923      and keep the original tile numbering. Note: compatible with old
924      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
925    
926    checkpoint61l (2009/04/07)
927    o Overlaps had been forgotten in calculating ijk keys : fixed
928    o fix cyrus makedepend for gcc 4.4
929    o experiment fizhi-cs-aqualev20:
930      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
931      and generate new output. Note: new output is much closer to the old
932      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
933      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
934    o pkg/fizhi:
935     - change to avoid indices going deliberately over array-bounds
936     - remove unnecessary MPI stuff
937     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
938     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
939       does not go over array-bounds and therefore returns reliable output.
940     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
941       this S/R has 4 output arguments, which are used inside "get_alarm";
942       when it is called with the same variable "ndum" in place of several
943       output arguments, this produces weird side effect inside "get_alarm"
944      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
945       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
946       address) and produces error.
947    o tools/gemake2: (March 27-29 2009)
948      with option "-mpi": link *_mpi files from "MODS" dir (this is what
949      testreport does).
950    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
951    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
952       update lab_sea.lsr & lab_sea.salt_plume results
953    o pkg/seaice:
954      Major overhaul of the LSOR solver: change discretization from original
955      finite differences to finite volume. The old routine is still in the
956      file seaice_lsr.F and can be turned on with the CPP-flag
957      SEAICE_OLD_AND_BAD_DISCRETIZATION
958      Along with this change, the discretization of the strain rates is changed.
959      The same flag turns on the old discretization in seaice_calc_strainrates.F
960      All verification experiments with seaice are affected (except for
961      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
962      results by setting the above flag.
963      Further changes involve changes in defaults:
964      - ALLOW_FLOODING is defined and turned on by default
965      - SEAICEadvSnow = .true. is now the default
966      - SEAICEadvSalt = .true. is now the default
967      - SEAICEadvAge  = .true. is now the default
968      - SEAICE_clipVelocities  = .false. is now the default
969                                         (as per J. Zhang's recommendation)
970      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
971        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
972      - seaice_growth: replace computation of UG by a simple copy from wspeed
973    
974    checkpoint61k (2009/03/18)
975    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
976      seaice_lsr: fixed a few metric terms,
977                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
978                  add more debugging diagnostics
979      seaice_evp: removed superfluous many metric terms of FV discretization
980                  of stress divergence
981                  affects lab_sea, lab_sea.hb87
982      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
983                  of stress divergence for non-evp solver
984                  (this part is not tested anywhere)
985      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
986                  they were effectively only half slip
987                  affects lab_sea.hb87
988      updated all relevant verification experiments (except lab_sea//output_adm.txt
989        which was left over, but fails at level 7 & 6)
990    
991    checkpoint61j (2009/03/17)
992    o pkg/seaice: turn a few hard wired parameters into run time parameters
993    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
994      time in seconds as promised by the usints in seaice_monitor and exf_monitor
995    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
996      that are not cubed-sphere grids
997    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
998    o pkg/ctrl:
999      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
1000    o non-hydrostatic (calc_gw.F):
1001      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
1002      update output of exp. global_ocean.cs32x15.viscA4
1003    o remove backward compatibility for thetaMin,phiMin
1004      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
1005    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
1006      interpolated wind field not only for curvilineargrid=.true., but also
1007      for a rotated grid (rotateGrid=.true.)
1008    o pkg/exf: add capability to bypass interpolation for runoff
1009      by setting yet another CPP-flag
1010    o eesupp/src, B-grid exchange:
1011      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
1012    o autodiff
1013      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
1014      allows to switch to single-prec common blocks;
1015      corresponding switch occurs in tamc.h, integer isbyte
1016      TAF store directivs "byte" and "kind" seem equivalent;
1017      Most tamc.h have been updated correspondingly.
1018    
1019    checkpoint61i (2009/02/13)
1020    o autodiff:
1021      fix autodiff_sore/_restore indices for obcs
1022      (spotted by I. Hoteit, M. Mazloff)
1023    o pkg/autodiff, pkg/ctrl:
1024      Add flag to reduce all tapelev I/O to single-prec.
1025      In data.ctrl set
1026        doSinglePrecTapelev = .TRUE.
1027    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
1028      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
1029    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
1030      real fresh water flux (not yet)
1031    o pkg/mdsio & rw:
1032     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
1033     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
1034    o pkg/flt:
1035     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
1036       init_fixed & ini_varia.
1037     - clean-up & simplify linear interpolation S/R:
1038       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
1039     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
1040     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
1041     - add vert. coordinate & horiz. indices to output files.
1042     - change vertical position in initial condition, from index to depth [m].
1043     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
1044       (easier to get to a curvilinear grid) ; delX,delY no longer used.
1045    o pkg/ggl90: a few modifications:
1046     - fix bottom boundary condition, and interpolation of KappaE
1047       near top and bottom
1048     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
1049     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
1050     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
1051    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
1052      (maintain temporary backward compatibility, until next checkpoint)
1053    
1054    checkpoint61h (2009/01/27)
1055    o pkg/diagnostics with "periodic averaging diagnostics":
1056      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
1057    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
1058    o pkg/obcs: fix loop ranges for balancing code
1059    o pkg/flt:
1060     - improve criteria for finding which tile owns a float.
1061     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
1062    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
1063      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
1064      with ocean biogeo)
1065    o pkg/flt:
1066     - do some cleaning and fix the restart ;
1067     - add output.txt in flt_example/results to get this pkg tested.
1068    o genmake2: add an EXTENDED_SRC option and flag.
1069       for now, cannot be turned on on command line (only through genmake_local)
1070    o pkg/mdsio: read/write vector:
1071     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
1072     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
1073       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
1074     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
1075      (drop to 4 digits matching for grad). But this test does not look very
1076      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
1077    
1078    checkpoint61g (2008/12/29)
1079    o pkg/flt:
1080      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
1081       + make OPTIONS file more standard.
1082      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
1083      - fix _BYTESWAPIO CPP-Flag
1084      - standard reading of file-parameter "data.flt"
1085      - fix argument list of S/R FLT_RESTART
1086      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
1087    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
1088    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
1089      a still unfixed compiler/optimization bug
1090    
1091    checkpoint61f (2008/11/21)
1092    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
1093      update results of global_ocean.cs32x15.icedyn test.
1094    o move getcon.F from model/src to pkg/fizhi.
1095    o pkg/exf: add parameter for extrapolation of temp up to the surface
1096       and option to prevent negative evap (in bulk_largeyeager04 only).
1097    o Prather Advection scheme: fix tracer conservation for divergent flow
1098      (e.g., when using NonLin Free-Surface).
1099    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
1100    o gmredi (Visbeck-variable-K):
1101     - add more parameters to Visbeck-variable-K.
1102     - use a 5 points average for dSigmaR in Visbeck-K calculation
1103       (more "homogenous": same stencil and same weights as in dSigmaH)
1104     - update output of ideal_2D_oce experiment.
1105    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
1106      (#undef REAL4_IS_SLOW)
1107     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
1108       coordinate variable
1109     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
1110       (surface forcing fields), removes some of the functionality
1111     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
1112     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
1113       probably not all: copy _RS surface flux fields to RL field before
1114       calling DIAGNOSTICS_FILL
1115     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
1116       real*4 (CALL EXCH_*_RS) versions.
1117     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
1118       (generate new output).
1119    
1120    checkpoint61e (2008/10/23)
1121    o gmredi (Visbeck-variable-K):
1122      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
1123      - change computation of Visbeck-K where Slope > Smax :        
1124        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
1125        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
1126    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
1127      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
1128    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
1129    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
1130      does not become too large (to avoid precision problems in implicit-diffusion
1131      solver); update ideal_2D_oce output.
1132    o pkg ggl90:
1133      - in ggl90_cal.F: compute only one set of visc/diff, used to
1134        step forward TKE/T/S/momentum
1135      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
1136        have Prandlt =1)
1137    o gmredi (fm07):
1138      - add lower limit on Transition layer thickness + lower limit on 1/lambda
1139      - allow to set few more params from data.gmredi
1140    o pkg ggl90:
1141          - add missing sqrt(2) factor in computation of mixing length
1142            scale in ggl90_calc.F
1143            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
1144    
1145    checkpoint61d (2008/09/25)
1146    o adjoint modifs
1147      - adapt to new field rhoInSitu
1148      - allow to revert from StoreDynVars2D, StoreDynVars3D
1149        to individual fields
1150        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
1151    o store 3-D (in-situ) density in commom block (DYNVARS.h)
1152     - save 1 rho computation.
1153     - no longer modify T & S inland when using down_slope pkg.
1154    o gad_som : allow to switch to SOM advection for T & S without corresponding
1155      pickup files (using new S/R: MDS_CHECK4FILE).
1156    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
1157      (for useSingleCpuIO to work in multi-threaded)
1158    o pkg/shelfice:
1159     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
1160       with SHELFICEtopoFile in data.shelfice
1161     - move code for reading ice shelf topography and modifying hFacC into separate
1162       subroutines of the shelfice package
1163     - separate initialisation of "fixed" and "variable" variables
1164     - kTopC is not (yet) replaced by kSurfC, although this is possible
1165    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
1166    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
1167      and rename:
1168      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
1169      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
1170    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
1171    
1172    checkpoint61c (2008/08/30)
1173    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
1174      to add mass source/sink of fluid in the interior (3-D generalisation
1175      of oceanic real-fresh water flux).
1176    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
1177    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
1178    o new pkg: down_slope
1179      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
1180      - presently, modify T & S inland (dwnslp_calc_rho.F).
1181        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
1182      - implementation for ocean in P-coords not tested.
1183      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
1184    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
1185      (to facilitate conversion of oceanic pkg to p-coordinate).
1186    o change FIND_RHO to FIND_RHO_2D :
1187      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
1188    o new pkg: cheapaml
1189    
1190    checkpoint61b (2008/08/05)
1191    o exch2:
1192      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
1193      - no longer depend on the order sequence (N,S,E,W).
1194      - 3rd exchange no longer needed (tested with 24 tiles).
1195      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
1196      - exch_UV_A-grid readily available (but not yet tested).
1197      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
1198      (both are no longer needed) in exch_uv: no effect in forward run; but
1199       get truncation error differences with adjoint exch.
1200    o exch2:
1201     - change index-bounds storage (moved from target to local tile,
1202       more intuitive this way) ; rename/remove some variables.
1203     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
1204    
1205    checkpoint61a (2008/07/29)
1206    o exch2/matlab-topology-generator:
1207      fix bug in index bounds for N-S internal exchange (hard to tell if this
1208      had any effect on the solution).
1209    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
1210      is exceeded
1211    o testreport: modify syntax of awk, so that it works also with
1212      awk, and not only with nawk and gawk
1213    
1214    checkpoint61 (2008/06/24)
1215    o autodiff
1216      Change default for TAF usage by removing argument '-nonew_arg'
1217      This changes TAF subroutine argument list (ordering of active var.)
1218      Omission of this flag leads to incompatibility w.r.t. TAMC
1219      To restore TAMC-compatibility, need following modifs:
1220      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
1221      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
1222      Tested TAF version is 1.9.22
1223      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
1224    
1225    checkpoint60 (2008/06/19)
1226    --->>> This is the last checkpoint for which generating the adjoint
1227    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
1228    --->>> by default.
1229    --->>> Future checkpoints will ommit this flag by default.
1230    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
1231    o pkg/grdchk: Add gradient check to etan0 perturbations.
1232    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
1233    o pkg/autodiff: more flexibility in zeroadj.
1234      model/src: modifying do_oceanic_phys.F accordingly.
1235    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
1236    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
1237      special setup of gmredi for which the adjoint is stable
1238      enough for parameter optimization.
1239    o bridging the gap between eddy stress and GM.
1240      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
1241          along with a change in CPP option (now ALLOW_EDDYPSI).
1242      -> when using GM w/ GM_AdvForm:
1243          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
1244          is applied either in the tracer Eq. or in momentum Eq.
1245          depending on data.gmredi (intro. GM_InMomAsStress).
1246      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
1247      The key modifications are in model/src/taueddy_external_forcing.F
1248      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
1249    
1250    checkpoint59r (2008/05/29)
1251    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
1252      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
1253      fix option to read coriolis(@ cell-corner) from files with CS-grid.
1254    o pkg/mnc: add some attributes to standard 1D-coordinate variables
1255    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
1256      mass points, when using mnc for output
1257      - add runtime parameter (missing_value, missing_value_int) to override
1258        default (which is the value of getcon('UNDEF'))
1259    o pkg/mnc: prepare mnc for the actual use of missing values with the
1260      diagnostics package: small fix in mnc_cw_readwrite.template and more
1261      initialisation of never used fields
1262      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
1263      versions
1264    o pkg/thsice/thsice_ini_vars.F added default initial values so that
1265      thermodynamics sea ice solver does not blow up when some initial fields
1266      are missing.
1267    o move from external_forcing_surf.F to ini_forcing.F
1268      the p-coord. hack consisting in using pLoad to set phi0surf ;
1269      update output of tutorial_global_oce_in_p (affected @ truncation level).
1270    o Freshen up a bit hs94.1x64x5, notably:
1271      remove rotationPeriod and tRef=5*0. (adjoint only), and add
1272      exactConserv=.TRUE.
1273    o pkg/generic_advdiff:
1274      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
1275      applies to files where Temperature & Salinity 2nd Order moments are used.
1276    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
1277      this uses a dynamically allocated internal state data structure
1278      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
1279      and requires a fortran 90 compiler
1280    
1281    checkpoint59q (2008/05/06)
1282    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
1283       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
1284    o Refresh tutorial_global_oce_biogeo, notably:
1285      - change bathymetry (put back seamounts in ACC, use hFacs)
1286      - change EOS (POLY3 --> JMD95Z)
1287      - use Bryan-Lewis vertical diffusivity
1288      - use multidimensional advection
1289      - remove old virtual virtual in dic pkg, now done through ptracer pkg
1290      - change a couple of parameters in dic pkg
1291    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
1292    o pkg/obcs: change default to OBCSfixTopo = .true.,
1293      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
1294      - replace "debugMode" with "debugLevel .GE. debLevB"
1295    o implementation of TAF directives for gchem,cfc,dic
1296    o remove "exp5" (replaced by tutorial_deep_convection).
1297    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
1298      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
1299      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
1300      --> changes results in exp4, seaice_obcs
1301    o tutorial_deep_convection :
1302      update the set-up and increase resolution and domain size ; start
1303      from pseudo initial conditions = output at t=120mn in order to see
1304      something happening when running testreport.
1305    o pkg/seaice: add os7mp as an advection scheme
1306                  add check for advection schemes
1307                  add a flag for restoring T and S underneath sea ice
1308    o pkg/my82: add netcdf-support and diagnostics
1309    o thsice pkg:
1310      - Now hsMax limits snow height by turning it into ice following
1311        flooding scheme (and now conserving energy)
1312      - Slight rewriting of the formula in thsice_calc_thick.F
1313      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
1314      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
1315    
1316    checkpoint59p (2008/04/10)
1317    o gchem / dic / cfc :
1318      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
1319      - add new parameter files: "data.dic" & "data.cfc" ;
1320      - various re-arrangement in initialisation & header file ;
1321      - fix tutorial_global_oce_biogeo for multi-threaded test.
1322    o pkg/dic: test for "pickup_dic" file when restarting ;
1323      if no pickup-file, can restart with a re-initialised pH (same as it did
1324      before) providing pickupStrictlyMatch is set to False.
1325    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
1326      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
1327    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
1328      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
1329    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
1330     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
1331       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
1332    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
1333       scheme to use for vorticty-term ;
1334     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
1335       (with default selectVortScheme, return to original discretisation)
1336     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
1337    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
1338    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
1339      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
1340      also fix diagnostics VISCAHW & VISCA4W.
1341    
1342    checkpoint59o (2008/03/07)
1343    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
1344    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
1345      move a few statemens out the main loop into separate loops
1346    o pkg/shelfice:
1347      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
1348        (kg/m^2/s), does not break tests, because in verification/isomip,
1349        rhoConstFresh=rhoConst (by accident)
1350      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
1351      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
1352        new file model/src/seawater.F, so that they are available for all pkgs.
1353      - convert potential temperature into in-situ temperature. This changes the
1354        isomip tests => update tests
1355    o add a flag writePickupAtEnd (default=true) to be able to suppress
1356      writing a pickup at the last timestep
1357    o tools/mpack-1.6 :
1358      - disable automake (not working) and autoconf (not needed).
1359      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
1360        also cleaner with much less compilation warnings.
1361    o pkg/profiles:
1362      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
1363      (for "less than 32 characters name" compiler requirement)
1364    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
1365      conditions that have a different sampling frequency than S/T/U/V obcs
1366    o pkg/diagnostics (stats-diags):
1367      - fix global Min/Max in case 1 processor get only empty tiles
1368    o genmake2: replace (4 times)
1369         make genmake_tc_1.o >> genmake_warnings 2>&1
1370      with
1371         COMM="$CC $CFLAGS -c genmake_tc_1.c"
1372         echo $COMM >> genmake_warnings
1373         $COMM >> genmake_warnings 2>&1
1374      to make genmake2 always see the value of CC as specified in the optfile.
1375    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
1376      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
1377      - modify verification advect_cs test to test SOM-advection on CS-grid.
1378    o pkg/ctrl:
1379      - Rewrite of ctrl_map_ini_ecco.F,
1380        introducing a generic routine (ctrl_map_ini_gen.F).
1381      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
1382    
1383    checkpoint59n (2008/02/09)
1384    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
1385      number in dedicate array "hdiag":
1386      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
1387        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
1388      - many small changes (integer format) for large number of diagnostics
1389      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
1390        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
1391    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
1392      usingSphericalGrid, this allows to define the rotated grid coordinates
1393      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
1394      geographical coordinates according to the inverse of the rotation defined
1395      by the Euler angles, so that Coriolis parameter and online-interpolation by
1396      exf works with the geographical coordinates on XC/YC/XG/YG.
1397      Naturally, this feature does not work with all packages, so some
1398      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
1399      profiles), because there the coordinates are assumed to be regular
1400      spherical grid coordinates.
1401    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
1402      - introduce isopycnal diffusion coefficient control.
1403    o tools/adjoint_options:
1404      - additional control vector components.
1405    o pkg/mnc: have mnc create marginally meaning full coordinate variables
1406      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
1407    o pkg/mypackage:
1408      - add example of read/write pickup for state-var ;
1409      - add entry points to the main code for state-vars diags & write-pickup.
1410    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
1411      transitions for useExfYearlyFields
1412      - add new subroutine that determines the file to read from for
1413        use*YearlyFields = .TRUE. and .FALSE.
1414      - add a verification experiment to global_with_exf that tests
1415        useExfYearlyFields with USE_EXF_INTERPOLATION defined
1416    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
1417      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
1418      subroutines (which could be generated from a template, because they are
1419      almost identical), for now they are included in obcs_prescribe_read.F for
1420      simplicity
1421    o pkg/exf:
1422      - add a little more diagnostic to exf_interp_read (in analogy to
1423        mds_read_field, can be turned off with debugLevel < debugLevA=1)
1424      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
1425        ugly but fast by unrolling short inner loops, inserting a unroll=8
1426        directive in routine lagran, and splitting a loop and making do while the
1427        outermost loop (the latter requires the intoduction of index arrays)
1428    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
1429    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
1430      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
1431    o verification/seaice_obcs: updated for restart test and latest options
1432    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
1433      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
1434      for now this is only available for the C-grid code and also within
1435      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
1436    
1437    checkpoint59m (2008/01/14)
1438    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
1439      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
1440    o gad_som : fix flux output (& diagnostics) to have same units as other  
1441      advection scheme fluxes (was previously multiplied by deltaT).  
1442    o added verification/seaice_obcs both to test seaice open boundaries
1443      and to provide an example matlab scrpt for generating them
1444    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
1445    o pkg/salt_plume: clean up salt_plume_frac.F to
1446      remove redundancy in PlumeMethod 1 and 4
1447    o pkg/kpp: added saltplume diagnostics
1448    o pkg/obcs and pkg/seaice:
1449      - do not set uice and vice to zero when OB*icefile are unspecified
1450      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
1451      - moved seaice tracer obcs after call to seaice_growth
1452    o pkg/salt_plume: added various options for salt plume depth
1453      criterion and for vertical distribution of the salt
1454    
1455    checkpoint59l (2007/12/18)
1456    o pkg/ptracers: new version of ptracers pickup:
1457      read meta file and write only fields which are needed to restart.
1458      ( same logic as main pickup file ; also using pickupStrictlyMatch )
1459    o pkg/seaice:
1460      - add timescale for melting due to warm mixed layer as a means of
1461        setting SEAICE_availHeatFrac more conveniently
1462      - add a CPP-flag/runtime parameter check for flooding algorithm
1463      - reformulated availHeat in seaice_growth.F to be independent of AREA
1464    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
1465      unit changes
1466    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
1467    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
1468      SX vector computer.
1469    o pkg/seaice:
1470      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
1471        seaice forcing fields can now be read only through pkg/exf
1472      - removed some unused halos
1473    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
1474    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
1475      or U/VICE from U/VWIND before computing U/VSTRESS
1476    
1477    checkpoint59k (2007/11/30)
1478    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
1479      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
1480    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
1481      all experiments pass when compile with un-initialised var. checking option.
1482    o added pkg/salt_plume
1483    o script to test restart (for now, in MITgcm_contrib/jmc_script)
1484    o pkg/seaice: new read/write pickup version.
1485      read meta file and write only fields which are needed to restart.
1486      ( same logic as main pickup file ; also using pickupStrictlyMatch )
1487    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
1488    o lab_sea.hb87: modify the domain & update output.hb87.txt :
1489      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
1490      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
1491      process. Fixed here by closing the domain at the Northern boundary.
1492    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
1493    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
1494      a set of consecutive levels in/from a 3-D array.
1495    o pkg/ptracers:
1496      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
1497      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
1498    
1499    checkpoint59j (2007/11/09)
1500    o in pkgs: dic, obcs, offline, rbcs:
1501      standard way to compute coeff. for time interpolation between 2 time reccords
1502      which retains full precision (& make results less dependent on compiler).
1503      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
1504    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
1505      packages instead of reading ice cover and wind speed separately
1506    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
1507     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
1508      to allow to compile customized code before the update)
1509    o cleaning-up:
1510      - fix CPP instruction syntax in pkg/obcs
1511      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
1512        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
1513      - fix some threads issue in IO parts.
1514    o pkg/dic:
1515      - add tons of "_d 0" (--> much better testreports !)
1516       and then update outputs of tutorial_global_oce_biogeo
1517    o pkg/mom_fluxform:
1518      add a special version of momentum advection intended to conserve momentum
1519      next to a bathymetry step or a coastline edge. (default = off = #undef)
1520    o new read/write pickup version:
1521      - for now, only implemented for main (mdsio) pickup file.
1522      - write out only what is needed to restart; merge pickup_nh , pickup_ph
1523        and main pickup together.
1524      - read meta file; read only what is needed to restart; stop if a field
1525        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
1526        if it make sense (even if the restart is not perfect).
1527      - if no meta file, assume that pickup to read corresponds exactly to
1528        a pickup that would currently be written.
1529      - read pickup written in the old format (until checkpoint59i) if it
1530        recognizes an old meta file (no field-list).
1531      - add a meta file in exp. which starts from a pickup: 2 cases:
1532        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
1533         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
1534        b) a meta file describing the content of the associated pickup file
1535         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
1536    o pkg/mdsio & pkg/rw:
1537      - new routine to read a meta file ; new set of routine to read
1538        Multiple-fields file (with meta file).
1539    o added open boundary conditions capability for seaice
1540        HSNOW, HSALT, UICE, and VICE
1541    
1542    checkpoint59i (2007/10/21)
1543    o adjoint:
1544      * fix multiDimAdvection adjoint
1545        (partial recomputation problem by TAF for fVerT(:,:,kDown)
1546        and comlev1 size definition (maxpass vs. max. number of tracers)
1547      * verification/global_ocean.90x45x15 adjoint now tests
1548        NLFS and multiDimAdvection using DST3 (=30)
1549      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
1550    o pkg/kpp: add "_d 0" to real constant (if missing);
1551      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
1552      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
1553    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
1554      for internal parameters related to restart process (formerly from PARAMS.h)
1555      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
1556    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
1557      as argument. (only atm2d & obcs write_pickup have not yet been updated)
1558    o pkg/monitor:
1559      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
1560      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
1561      - account for deep Atmosphere factor and density factor (anelastic)
1562    o added open boundary conditions capability for seaice HEFF and AREA
1563    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
1564      thermodynamics
1565      - requires a little reorganization, which affects the testreport results
1566        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
1567        so that now the conservative form is tested
1568      - add a few comments
1569    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
1570    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
1571    o add new diagnostics to seaice: advective, diffusive fluxes (only for
1572      multidim-advection, for scheme 2 they are not filled) and transports,
1573      thermodynamic growth rates
1574    o change units of EmPmR (inside the code, + within coupling interface)
1575      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
1576      Affects results @ truncation level (cg2d match) and update output of
1577       experiments: lab_sea(6), global_ocean.90x40x15(10),
1578      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
1579      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
1580      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
1581      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
1582    
1583    checkpoint59h (2007/09/29)
1584    o pkg/exf:
1585      - improve vectorization by moving if-statement out of loops in
1586        exf_mapfields, exf_radiation
1587      - exf_bulkformulae.F: introduce 2D fields and vectorize code
1588    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
1589    o testreport:
1590      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
1591        monitor & update offline_exf_seaice exp. output.
1592      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
1593    o pkg/seaice:
1594      - bug fix in the evp solver: boundary conditions were affected be
1595        masking of zMax/zMin (changes results)
1596      - minor bug fix in boundary conditions in seaice_calc_strainrates
1597        (changes results for no_slip)
1598      - seaice_lsr.F: make interpolation of eta dependent on boundaries
1599      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
1600      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
1601        stress formulation and no-slip boundary conditions
1602    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
1603      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
1604    o pkg/seaice: a first HSALT time stepping equation has been checked in
1605    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
1606      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
1607      without requiring DO-IF statements
1608    o pkg/thsice:
1609      use continuous power-law function for partition of energy between lateral
1610      melting/freezing and thinning/thickening ; old code using step function
1611      still available with #undef THSICE_FRACEN_POWERLAW
1612      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
1613    o testreport: change AD testing : check against results/output_adm.txt
1614      using same scripts as for forward test.
1615    
1616    checkpoint59g (2007/09/17)
1617    o adjoint testing: in preparation for changing testreport:
1618      - output format: cost and grad written on separated lines
1619      - ad output results in directory "results" (instead of "results_ad")
1620    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
1621    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
1622    o pkg/ecco: allow user defined cost function contributions
1623    o testreport:
1624      Allow to choose (per experiment) the list of tested output variables
1625       and the main variable (used to issue a pass/FAIL ) ;
1626      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
1627      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
1628      Also modify printing of summary:
1629       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
1630       b) echo the list of tested variables in the individual summary.txt of
1631          each experiment.
1632    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
1633      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
1634      (but still depend on the tile decompostion of the domain).
1635    o pkg/seaice: change a discretization detail to make the B-grid code
1636      "more symmetric". This change is likely to remove all "ridges/leads" that
1637      where quasi-aligned with the grid in B-grid solutions. It may also be
1638      the solution to the stress coupling issues with the B-grid.
1639    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1640      remove .cvsignore from input dir. (since testreport no longer run here).
1641    o pkg/thsice:
1642     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1643     - fix reshaping of sea-ice just after advection:
1644       melt all the ice only if ice-volume is too small.
1645     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1646       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1647     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1648    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1649      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1650    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1651      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1652      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1653      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1654      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1655      -> update output.txt
1656    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1657     this affects truncation error: -> update output.txt of exp:
1658      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1659      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1660    
1661    checkpoint59f (2007/08/21)
1662    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1663    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1664      a bounded range (in forward mode)
1665    o pkg/ecco, ctrl, autodiff and mom_common:
1666     internal parameter controls, completements of implementations
1667    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1668    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1669      (not seem any difference in testing results).
1670    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1671       at face corners.
1672    o pkg/generic_advdiff:
1673     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1674      loop range indices for computing vertical advection tendency
1675      and do the calculation in the interior only (no overlap) ;
1676      for now, only implemented for SOM advection (to save CPU time).
1677     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1678    o exch2 adjoint
1679      First set of changes:
1680      - add exch2 hand-written adjoint templates
1681      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1682        This will require cleanup in pkg/autodiff/*.F
1683        (changed routines currently kept separate in verif. code/)
1684      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1685        that used to hide exch2 or cubed-sphere specific code
1686        (commented via 'cph-exch2')
1687    o pkg/seaice
1688      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1689    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1690       output of global_ocean.cs32x15.thsice .
1691    
1692    checkpoint59e (2007/07/26)
1693    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1694      for B-grid vector (not yet tested) and C-grid vector (<- only used
1695      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1696    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1697      (#ifdef ALLOW_SALT_PLUME)
1698    o gather_2d/scatter_2d: removed halo regions
1699    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1700      scheme and the corresponding test case (under front_relax dir). For now,
1701      only available with Skew-flux form and not yet tested in realistic set-up.
1702      adjoint: store directives updated, but gradient checks deteriorated,
1703      so maybe GM/Redi adjoint is now broken.
1704    o seaice adjoint
1705      * add AREA, HEFF, HSNOW as control variable
1706        (should not change lab_sea results)
1707      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1708    o pkg/seaice:
1709      * added computation of saltFlux in seaice_growth;
1710        For time being, sea ice salinity is assumed constant
1711        contribution of snow flooding to freshening of sea ice is neglected.
1712        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1713        defaults to 0.0 in order to maintain backward compatibility.
1714        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1715      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1716      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1717        heat content used to melt or grow ice
1718      * commented out cap of HICE: it helps keep ice thinner
1719      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1720      * applied OBCS T/S mask to HEFFM sea ice mask
1721    
1722    checkpoint59d (2007/06/21)
1723    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1724     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1725     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1726    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1727     and change default value of parameter "GM_Small_Number";
1728     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1729       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1730       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1731    o pkg/ecco: cost function when applying pkg/smooth to controls
1732    o pkg/ctrl: add forcingPrecond run time parameter
1733    o pkg/seaice:
1734     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1735     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1736       changes verification/lab_sea
1737     - rearrange implicit part of u-equation in LSR solver to make it easier to
1738       read, understand, and debug. This causes changes at the truncation level.
1739     - fix (serious) bug in the boundary conditions (sign error in the implicit
1740       part) of the LSR solver. Changes all LSR results.
1741     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1742       is initilized with small values - does not change lab_sea results.
1743     - added HsnowFile initialization capability
1744    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1745     initialization of pkg/smooth and application to control vector
1746    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1747    o dependencies: pkg/profiles requires pkg/cal
1748    o pkg/profiles:
1749     - added option ALLOW_PROFILES_GENERICGRID
1750         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1751         that interpolation information (grid points and coefficients) is provided
1752         within the netcdf input files.
1753         -> sample matlab scripts can be found in MITgcm_contrib/gael
1754         that allow you to prepare netcdf input files.
1755     - also modified: cleaner include statements, cleaner error print statements,
1756       cleaner stops when error, and more tests of the netcdf input files consistency.
1757    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1758    o pkg/seaice:
1759     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1760       requires a new routine: seaice_diagnostics_fill.F
1761     - make sure that seaice does not move if not forced (pressure replacement
1762       method, Hibler and Ip, 1995), changes results
1763     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1764     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1765       It is turned off by default (=-1.), because it changes the results.
1766     - make it possible to read AREA from a file, too.
1767    
1768    checkpoint59c (2007/06/04)
1769    o add S/R and diagnostics for oceanic mixed-layer depth
1770    o move GMRedi call after all vertical mixing schemes (including KPP)
1771    o pkg/thsice:
1772     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1773      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1774    o pkg/obcs:
1775     - bug fix for balance code
1776    o pkg/seaice:
1777      - allow values of SEAICE_elasticParm > 1
1778      - add new parameter SEAICE_evpTauRelax as an alternative
1779        to SEAICE_elasticParm
1780      - make lsr boundary conditions free slip (by default), changes result
1781      - add code for no slip boundary conditions for lsr
1782      - set minimum of zeta to zero (and not 4e8) (changes results)
1783      - add a cap on AREA after advecting AREA if seaice_growth is not called
1784    o change calculation of Visbeck K:
1785      - no longer depend on tapering scheme; instead, compute slope (limited
1786        by GM_maxSlope). this is equivalent to what was comuted before with
1787        clipping or linear tappering.
1788      - fix vertical averaging (wrong by 1/2 level)
1789      - leave the old version (but will not be maintained) within
1790        #ifdef OLD_VISBECK_CALC / #endif
1791      - update output of exp. ideal_2D_oce
1792    o change error catch in calc_r_star to improve vectorization
1793    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1794      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1795    o adjoint:
1796      Re-organized adjoint checkpointing according to Matt Mazloff
1797      (but with modifs/completions/cleanups)
1798      Storing is now bundled into large arrays to optimized I/O
1799      (and second step in cleanup of the_main_loop)
1800    
1801    checkpoint59b (2007/05/16)
1802    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1803      - export/import (between ocean & coupler) fields needed for ocean DIC.
1804    o pkg/seaice:
1805      - get rid of three more exchanges seaice_calc_viscosities (required
1806        different loop boundaries in seaice_lsr and seaice_ocean_stress)
1807      - bug fix in seaice_ocean_stress (update of lab_sea required)
1808      - reduce loop boundaries to necessary minimum also in seaice_evp
1809      - go back to the old way of computing deltaC/Z as the adjoint likes that
1810        better
1811    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
1812      passive tracer to an Age Tracer) + update output.txt
1813    o pkg/exf:
1814      - implement A-grid / C-grid selection for wind-stress input files.
1815      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
1816      for now, in exf_bulk_largeyeager04.F only :
1817      - change implementation for case where windspeed + 2. components wind-stress
1818        are read-in. AND use rhoConstFresh to convert evap.
1819    o pkg/seaice:
1820      - use correct EXCH_UV for wind-forcing (on A-grid).
1821      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
1822        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1823    o pkg/exf:
1824      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1825      EXF_INTERPOLATION:
1826      - merge global_with_exf/code version of exf_interp_read.F
1827        to the main code ;
1828      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1829        reading the file ; Important: This options needs to be defined to recover
1830        previous code.
1831        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1832      - no longer loose real*8 precision along the way when using exf_iprec=64.
1833    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1834      - change discretisation of evp-solver in order to avoid another exchange
1835        (changes lab_sea) and clean up a little
1836      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1837        help the adjoint (this also changes the results slightly)
1838      - add a few "_d 0" where they had been missing in seaice_evp.F
1839      - cleaning up: remove unused seaice_calc_rhs.F
1840    o pkg/exf: some cleaning-up:
1841      - change various "constants" into runtime parameters
1842      - cleaned-up Large&Yeager04 routine which should eventually
1843        replace exf_bulkformulae.F (changed names of S/R and CPP)
1844        and merged various ALLOW_ATM_WIND options
1845     only used with thsice pkg (in thsice_get_exf.F):
1846      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1847        which are used when useStabilityFct_overIce=TRUE (= the default)
1848      - change default values of ice & snow emissivity and scale downward LW
1849        by ice & snow emissivity.
1850    o pkg/thsice:
1851     fix few little problems, in thsice_calc_thickn.F:
1852      - growth vertically (and not laterally) if iceFrac == iceMaskMax
1853      - melt only laterally if hIce < hThinIce (as the comments say)
1854      and in thsice_extend.F:
1855      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1856      - start to form ice as soon as the minimum ice-volume is reachable.
1857     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1858      and cpl_aim+ocn
1859    o pkg/kpp
1860     - move computation of surface related input fields to KPP into a new
1861       subroutine kpp_forcing_surf.F
1862     - remove wrong (within bi,bj loops) EXCH calls.
1863     - little cleaning (add argument myThid in last position, cvs header ...)
1864     - for now, fix conservation problem by exchanging KPPviscAz (may not
1865       be the best fix)
1866    o pkg/seaice
1867     - check for inconsistent evp parameter/cpp-flag combination
1868     - remove leftover errIO flat for obsolete name list error handling
1869    o OpenAD
1870     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1871    
1872    checkpoint59a (2007/05/01)
1873    o pkg/seaice: some parameter clarifications and a little bit of clean up
1874    o pkg/thsice: rename run-time parameters:
1875       himin       -> hIceMin
1876       himin0      -> hThinIce
1877       hihig       -> hThickIce
1878       i0          -> i0swFrac
1879       transCoef   -> bMeltCoef
1880       frac_energy -> fracMelting
1881      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
1882       with default values (for now) that do not change the results.
1883      remove old version of thsice vars advection in pkg/seaice.
1884    o in FFIELDS.h:
1885      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
1886      - make pLoad & sIceLoad always available (but still only used if
1887         ATMOSPHERIC_LOADING is #define).
1888    o pkg/kpp: replaced _KPP_RL with _RL
1889    o bug fixes for vertical diffusivity computations when both KPP and
1890        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1891        are no longer updating the vertical diffusivity array
1892        (passed as argument) but are (re-) setting those arrays.
1893    o pkg/seaice: fix bug in evp solver, while doing that
1894      - change (improve?) discretization of stress computations for both
1895        cgrid-lsr and evp solver
1896      - add a new routine to compute strain rates
1897      - the above changes lab_sea results
1898      - add no slip conditions for evp solver (off by default), lsr-version
1899        may follow
1900      - fix exchange for shear at Z-points (does not change lab_sea)
1901      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
1902        (to force the user to pick a time step since there is not "safe" way
1903        of choosing it)
1904      - add principal stress diagnostics
1905      - rearrange fields for evp a little to avoid having to call a: too many
1906        exchanges and b: exchanges for stress trensor components which we do
1907        not have.
1908      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
1909        of evp, complete rewrite for lsr case (latter is does not yet work
1910        in all cases)
1911    o pkg/kpp: add code to have mixing in shelf ice caverns
1912      - add myThid to all kpp routines (long overdue)
1913    
1914    checkpoint59 (2007/04/19)
1915    o pkg/exf:
1916      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1917        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
1918      - move exf header files from lower_case.h to UPPER_CASE.h ;
1919        add missing cvs Header & Name
1920      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
1921      - add namelist param. selectStressGridPosition, exf_monFreq
1922      - retire many _CLIM routines, and remove data.exf_clim
1923        + params moved to data.exf
1924        + climsst, climsss now handled by exf_set_gen, i.e.
1925          climss?period=0 refers to constant field,
1926          climss?period=-12 to monthly forcing
1927      - split up namelists in data.exf
1928    o pkg/seaice:
1929      - remove seaice_exch and seaice_exch_uv
1930      - remove superfluous exchange of theta
1931      - add myThid to seaice_budget_ocean/ice
1932      - add new interface for atmospheric wind forcing (C-grid only)
1933        + new routine
1934        + two new field (taux, tauy for stress over ice)
1935        + removed one global field (DAIRN) for C-grid case only
1936    o pkg/thsise
1937      - 2nd set of modifs for thsice adjoint in conjunction with exf
1938    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
1939    
1940    checkpoint58y_post (2007/04/15)
1941    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
1942      vertical diffusivity, similar to that in MOM4; turned on using
1943      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
1944      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
1945    o Added capability for 3D specification of background vertical diffusion
1946      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
1947      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
1948      "data" file that contains the 3D vertical diffusivity coefficients.
1949    o ice dynamics (pkg/seaice) with thsice thermodynamics:
1950      - add code within pkg thsice to advect & diffuse sea-ice fields
1951      similar to (and will replace) what has been added in  seaice_advdiff.F,
1952      but: - conserving Mass, Heat & Salt.
1953           - better when using non-linear advection scheme (not yet fully tested)
1954           - can also be used in atmospheric set-up (for now, only the diffusion).
1955    
1956    checkpoint58x_post (2007/04/04)
1957    o IO option for global-file compact format:
1958      - add options when generating topology (utils/exch2/matlab-topology-generator)
1959      - add I/O capability (pkg/mdsio).
1960      - adapt utils/matlab/rdmds.m to read this format.
1961      for now long-line format not yet supported by pkg/mdsio (& exch2).
1962    o shelfice: add a few diagnostics
1963    
1964    checkpoint58w_post (2007/03/13)
1965    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
1966      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
1967      (and replace horiVertRatio in NH code).
1968      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
1969                         and tutorial_plume_on_slope (sensitive to truncation)
1970    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
1971      directly to drive seaice model (C-grid only)
1972    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
1973     - reintroduce computation of wind from stress,
1974     - compute tau (in exf_bulkformulae.F) from windstress averaged to
1975       mass points to avoid tau = 0
1976     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
1977    o rdmnc.m: make it work with "global" files created with gluemnc
1978    o rdmnc.m : some improvements in dealing with singleton dimension
1979      (tested on all testreport mnc output files).
1980    o genmake2: disable pkg/profiles if netcdf test fails.
1981    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
1982    o move call to cal_readparms up to make calendar parameters/variable available
1983      to all packages
1984    
1985    checkpoint58v_post (2007/02/08)
1986    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
1987      useDynP_inEos_Zc tested.
1988    o pkg/exf: changes to properly interpolate/mask/scale initial fields
1989    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1990      and portions thereof.  See read_cs.txt for description and examples.
1991    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1992      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1993      following the great-circle arc between those 2 points.
1994    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1995      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1996    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1997     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1998     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1999     - still needs work (not working with some options ; efficiency to improve)
2000       and serious testing.
2001     - use this scheme for temperature & salinity in 2 advection test exp.:
2002       advect_xy & advect_xz, respectively.
2003    
2004    checkpoint58u_post (2007/01/12)
2005    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
2006    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
2007    o testreport: add option "-skipdir" to skip some test.
2008    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
2009      momentum calculation.
2010    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
2011    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
2012      remove checkpoint.F and the_correction_step.F (no longer used);
2013      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
2014    o add option (linFSConserveTr) to correct for tracer source/sink due to
2015      Linear Free surface
2016    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
2017    o pkg/thsice: fix reading mnc-pickups
2018    
2019    checkpoint58t_post (2006/12/30)
2020    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
2021    o pkg/mdsio:
2022     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
2023       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
2024       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
2025     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
2026     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
2027       either MDS_READ_FIELD or MDS_WRITE_FIELD )
2028     - new S/R (to replace MDSWRITEMETA), which allows to write more
2029       informations (variable names, time ...) to meta files.
2030     - modify rdmds.m to give back the meta file content.
2031    o pkg/diagnostics: change vertical interpolation to be safer, and more
2032       flexible (define p-levels to interpolate to in data.diagnostics);
2033      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
2034       diagnostic pointer.
2035    o pkg/seaice: more cleaning up of seaice_growth, added many comments
2036    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
2037    o fix multi-category seaice:
2038     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
2039       SEAICE_MULTICATEGORY
2040     - fix short wave heat flux
2041    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
2042       and allow to use EVP solver. Change forward lab_sea: test both EVP
2043       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
2044    o Initial check-in of lab_sea adjoint
2045      (very similar to natl_box_adjoint/code_seaice)
2046      * used C-grid and EVP solver
2047      * used KPP, GM/Redi
2048      * uses inAdExact=.TRUE.
2049      * gradient checks fail for both ADM and TLM
2050        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
2051        f.d. gradients actually seem more problematic than ADM, TLM gradients;
2052        issue is related to forward mismatch between g77 an ifort
2053    o pkg/seaice: overhaul of thermodynamics
2054     - growth.F and groatb.F are replaced by new routine seaice_growth.F
2055     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
2056     - move a few global fields out of SEAICE.h into seaice_growth.F and
2057       make them 2D (FICE/QNETO/ ...)
2058     - remove FO (it is the same as QNETO)
2059     - introduce a few local fields to avoid modifying external fields such
2060       as atemp, etc.
2061    
2062    checkpoint58s_post (2006/12/11)
2063    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
2064      changed exf_set_gen.F so that
2065        genperiod=0 means input file is one time-constant field and
2066        genperiod=-12 means input file contains 12 monthly means
2067    o CG2D: use pre-computed solver main-diagonal (stored in common block);
2068      this affects truncation error ; generate new output file for exp. which
2069      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
2070        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
2071        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
2072        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
2073        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
2074        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
2075    o start implementation of deep-atmosphere and anelastic formulation
2076    o verification: remove 2nd copy of input files and use script "prepare_run"
2077      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
2078    o mom_common/vecinv/fluxform: fix a few initialisation isssues
2079    o profiles: fix for multithreaded case
2080    
2081    o diagnostics: rename few diags:
2082      s/'PRESSURE'/'RCENTER '/g
2083      s/'TICE    '/'oceFreez'/g
2084      s/'TAUX    '/'oceTAUX '/g
2085      s/'TAUY    '/'oceTAUY '/g
2086      s/'SWFLUX  '/'oceQsw  '/g
2087      s/DIFx/DFxE/g
2088      s/DIFy/DFyE/g
2089      and add few ocean-forcing diagnostics:
2090      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
2091    o modifications to pkg/seaice/growth.F and budget.F, which change results of
2092      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
2093      as actual snow thickness.  It now refers everywhere to effective snow
2094      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
2095    
2096    checkpoint58r_post (2006/11/17)
2097    o modifications to pkg/seaice/growth.F, which change results of
2098      lab_sea experiment: fixes pertain to melting snow over open water, to
2099      masking EVAP under sea ice, and to using the correct AREA variable for
2100      computations of EVAP, PRECIP, HSNOW, and GHEFF
2101    o add ability to read bathy, salt, and theta using MNC (off by def)
2102    o add flooding algorithm and advection of HSNOW for pkg/seaice;
2103      both are turned off by default and do no change any results
2104    o seaice advection with pkg/thsice: a step toward the use of non-linear
2105      advection scheme, but #ifdef or commented out for now (requires more EXCH).
2106    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
2107      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
2108      in natl_box (affects results @ truncation level: update output.txt)
2109    o multi-threading and IO:
2110      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
2111      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
2112        (needed to work with SingleCpuIO): tested in all verif. exp.
2113    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
2114      affects the results (but none of the verification test uses this scheme).
2115    o Adding some pkg/diagnostics capability to pkg/seaice
2116      (will certainly be subject to changes)
2117    o ctrl: adding new control variables:
2118      lwflux, lwdown, evap, snowprecip, apressure, runoff
2119    
2120    checkpoint58q_post (2006/10/20)
2121    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
2122      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
2123      high_res_cube configuration by 4% on Columbia.
2124    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
2125      add (in global_with_exf/code) a version of EXF_INTERP_READ without
2126      dynamical allocation (seems to work in multi-threaded).
2127    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
2128      single CPU io) so that TAF does not have to see EESUPPORT.h
2129    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
2130    
2131    checkpoint58p_post (2006/09/08)
2132    o obcs: stop if obcs is used with useCDscheme = .true.
2133    o shelfice:
2134     - fix a sign error so that no slip at shelfice interface works
2135     - remove stop for combination non-hydrostatic code and shelfice. That does
2136       not mean, that the results are correct, but at least they are numerically
2137       stable
2138    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
2139    o added adjoint exch routined for all exch*3d* routines
2140      and updated flow directives
2141    
2142    checkpoint58o_post (2006/08/28)
2143    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
2144      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
2145    o change controling S/R for writing pickup file (new S/R do_write_pickup)
2146      and clean-up reading/writing of pickup files.
2147    o fix local version of read/write pickup (NH part) in rotating_tank/code
2148    o simplify EXCH interface:
2149     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
2150     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
2151    o added the regrid package
2152    o shelfice:
2153     - add a simple boundary layer scheme to reduce noise
2154     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
2155    
2156    checkpoint58n_post (2006/08/14)
2157    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
2158       local variable (not in common block).
2159    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
2160      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
2161      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
2162        to work with SingleCpuIO.
2163    o add "_d 0" to real constant of pkg/cfc subroutines ;
2164       update exp. cfc_exemple & tutorial_cfc_offline output files.
2165    o multi-threading and IO:
2166      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
2167        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
2168      - barrier before and after reading.
2169      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
2170      - avoid using MDS_WRITELOCAL for LAND pkg output.
2171      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
2172        common-block variables ; Allows multi-threading with master-thread IO.
2173    o change default MAX_NO_THREADS from 32 to 4 ;
2174      and stop cleanly when MAX_NO_THREADS is too small.
2175    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
2176    
2177    checkpoint58m_post (2006/07/17)
2178    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
2179       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
2180    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
2181       keep global_ocean.90x40x15 (for AD testing) with former secondary test
2182       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
2183    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
2184        add MITgcm_tutorials (= code + all the tutorials)
2185    o ecco, option to compute cost for total ssh (mean+anom)
2186    o consistent with addition of ptracer and ssh in pkg/profiles
2187    o profiles: adding ptracer and ssh
2188    o testreport: change multi-test output-file name
2189      (from output.txt.{name} to output.{name}.txt)
2190    o profiles: now ok for mutli-tiles case
2191    o seaice: add 4 parameters for different advection schemes for area,
2192      (effective) seaice thickness, enthalphy, and snow height. Their default
2193      is the standard parameter SEAICEadvScheme
2194    o calc_gw:
2195     - add cosFacU in zonal viscous flux (harmonic.visc.).
2196     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
2197       of tutorial_plume_on_slope.
2198    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
2199    o calc_gw: true flux-form, account for horizontal grid spacing.
2200      update rotating_tank results, but not plume_on_slope (affected at
2201      truncation level, 11 digits).
2202    
2203    checkpoint58l_post (2006/07/12)
2204    o calc_gw:
2205     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
2206     - remove side-drag for now (need to fix it); update plume_on_slope results.
2207     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
2208    o commit code to make SST/SSS weights spatially variable
2209      (based on either variable in-situ or variable initial T/S weights)
2210    o pkg/ecco:
2211      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
2212        now based on horizontally varying weights wthetaLev, wsaltLev
2213      * cost_averagesflags now returns year indices in addition to day, month
2214      * sflux balance is performed on annual basis
2215        (sflxumm, sfluxmm2, bal_sfluxmm)
2216      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
2217        including separate counting and multipliers
2218    o pkg/rbcs
2219      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
2220    
2221    checkpoint58k_post (2006/07/06)
2222    o testreport:
2223     - always build in dir. "build" (if not there, mkdir build instead of building
2224       & running in input)
2225     - run in dir run (if it exists), in build otherwise.
2226     - call prepare_run (if input/prepare_run exists)
2227     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
2228    o pkg/exf modifications to interpolation and rotation routines for more
2229       reasonable treatment of North Pole singularity: for tracers North Pole
2230       value is set to northernmost zonal-mean value, for zonal velocity it is
2231       set to zero, and for meridional velocity it is set to northernmost value.
2232    o pkg/exf/exf_check_range.F
2233     - add tile index to diagnostics and move stop statement to the very
2234       end of the routine.
2235    o pkg/diagnostics: (diagnostics_main_init.F)
2236      define title of isomorphic variables according to the current config.
2237    o pkg/thsice with pkg/seaice dynamics:
2238    - fix domain of computation (interior only, required for exf) and do exchanges
2239    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
2240    o towards a standard way of dealing with multi-threading in MONITOR
2241      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
2242    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
2243       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
2244    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
2245    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
2246    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
2247       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
2248    o tracer advection:
2249     - clean-up and simplify calc_common_factors.F
2250     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
2251       advection subroutine (but still not used within DST advection S/R)
2252    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
2253    
2254    checkpoint58j_post (2006/06/15)
2255    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
2256      from file (collects calls previously in FORWARD_STEP)
2257    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
2258    o adjoint store dir. adjusted accordingly
2259    o genmake2
2260      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
2261    
2262    checkpoint58i_post (2006/06/14)
2263    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
2264      on wind stress (SEAICEstressFactor defaults to 1.)
2265    o Total number of Timers is finite (<=40): comment out 2 non-essential one
2266      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
2267    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
2268      on CS-grid: no longer loosing mass.
2269    o exf & curvilinear-grid: no longer modify longitude xC & xG.
2270    o pkg/ggl90: fix sloppy output and fix a bug
2271    o pkg/seaice: added SEAICEuseEVPpickup parameter
2272      - Set to false in order to start EVP solver with
2273        non-EVP pickup files when using SEAICEuseEVP
2274      - fix sign error in diffusion in seaice_calc_rhs
2275    
2276    checkpoint58h_post (2006/06/07)
2277    * Modifications for bottom topography control
2278      o replace hFacC by _hFacC at various places
2279      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
2280      o add non-self-adjoint cg2d_nsa
2281      o update autodiff support routines
2282      o re-initialise hfac after ctrl_depth_ini
2283      o works for 5x5 box, doesnt work for global_ocean.90x40x15
2284    * Adding verification for 5x5 box (4-layer) bottom topography control
2285    
2286    checkpoint58g_post (2006/06/07)
2287    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
2288       used for mean seasonal cycle, mean diurnal cycle); add an example
2289       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
2290    o pkg/ggl90:
2291      - add parameter (minimum surface kinetic energy)
2292      - fix bug (avoiding division by zero)
2293    o couple pkg/thsice to pkg/seaice:
2294      - modify advection in seaice to accomodate new scalar fields to be advected
2295      - only muliDimAdection scheme work with seaice/thsice
2296      - mapping of thsice-variables to seaice-variables, back and forth
2297      - does not break the verification experiments, but does not give the
2298        desired results either
2299    o pkg/seaice
2300      - make (default) second order advection a bit less confusing?
2301    
2302    checkpoint58f_post (2006/06/05)
2303    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
2304      to pkg/seaice):
2305      - new routines thsice_map_exf and thsice_get_exf provide the interface
2306      - add an additional formal parameter to thsice_solve4temp
2307    o pkg/exf:
2308      - add new fields wspeed, snowprecip (to be able to couple to thsice)
2309      - correct Stefan-Boltzmann constant
2310      - new parameter for longwave surface emittance
2311      - separate some stuff from exf_bulkformulae into new routines  
2312        exf_radiation, exf_wind
2313      - add new parameters and constants: longwave emissivity for ocean, ice
2314        and snow, evaporation parameters over ice
2315      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
2316        either wind from stress or stress from wind
2317    o pkg/thSIce:
2318    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
2319    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
2320       and THSICE_CALC_THICKN
2321    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
2322    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
2323      to make debugging easier.
2324    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
2325    o pkg/bulk_force:
2326      - clean-up comments and parameters ;
2327      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
2328    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
2329      generate new output for test-experiment: aim.5l_cs.thSI
2330    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
2331      testreport accordingly
2332    
2333    checkpoint58e_post (2006/05/17)
2334    o SEAICE_CGRID adjoint done
2335    o R_STAR adjoint implemented.
2336      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
2337      * need to sort out init. of h0facc, etc.
2338    o Make pkg/profile fully independent of ecco,cost, etc. stuff
2339      to be able to use it in pure forward.
2340    
2341    checkpoint58d_post (2006/04/21)
2342    o upgrade simple test-experiment to tutorial example:
2343     step.1: duplicate the experiment and (step.2) will remove the old copy.
2344      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
2345      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
2346      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
2347      tutorial_global_oce_biogeo    <- copy of dic_example
2348      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
2349      tutorial_plume_on_slope       <- copy of plume_on_slope
2350      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
2351      tutorial_global_oce_optim     <- empty for now (David ?)
2352      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
2353     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
2354    o correct a sign problem in cost_scat.F
2355    o obcs and ptracers: fix boundary conditions for advections schemes
2356      with larger stencil
2357    o thsice adjoint: start
2358    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
2359      completeness
2360    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
2361      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
2362    o ptracers adjoint:
2363      * avoid extensive recomputatations
2364      * fix missing re-init. of gptr (missed by TAF)
2365    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
2366      me to turn off the excessive output to STDOUT that this package produces
2367    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
2368      and add those terms in Vector-Invariant formulation.
2369    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
2370      if the control period (xx_hfluxperiod etc) is 0
2371    o in profiles pkg, clean routines and fix details
2372    o in ecco pkg, reading ssh data:
2373      fix problem in case the model does not start at iter0=0
2374    o fix mnc-pickup/restart for ptracers
2375    o new package prifiles:
2376      code to compute profile-based cost by Gael Forget
2377      (modifs in ecco, ctrl, autodiff)
2378    o Benign bug fix in initialization (spotted by M. Mazloff) of
2379      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
2380    
2381    checkpoint58c_post (2006/03/23)
2382    o adjoint: finish NLFS adjoint and provide reference output in
2383      verification/global_ocean.90x40x15/results_ad_nlfs
2384    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
2385      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
2386      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
2387      with SEAICE_CGRID defined.
2388    o move calendarDumps from "data" to "data.cal" and clean-up the code
2389      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
2390    o add useEXF & useCAL flags (for now, set in hard-coded way)
2391    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
2392      (were missing in NH mode, and wrong in quasihydrostatic mode).
2393      waiting for Chris updated version of calc_gw to add those CALLs.
2394    o fix bug in quasihydrostatic S/R ;
2395      add a test for this option: global_ocean.90x40x15.qshyd
2396    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
2397      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
2398    o add on/off flag useOffLine for package OFFLINE
2399    o seaice:
2400      - modify advection so that it works also on the C-grid
2401      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
2402        problem in multi-tile runs with C-grid
2403      - add flags for clipping ice velocities and/or masking solver forcing
2404      - fix drag (ocean on ice) formulation and a bug that caused noise in the
2405        C-grid solver
2406      - added a few comments to seaice_diffusion.F
2407      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
2408        are now exclusive)
2409      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
2410        required re-ordering the code a little:
2411       + make DAIRN global variable (defined in SEAICE)
2412       + move computation of the viscosities eta and zeta into a new separate
2413         routine (because I need to recompute them in seaice_ocean_stress.F)
2414    
2415    checkpoint58b_post (2006/03/13)
2416    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
2417      update output.txt of exp. aim.5l_cs.thSI
2418    o various mnc cleanups and improvements:
2419      + shrink lookup tables by factor of ~4
2420      + better error reporting when running out of lookup space
2421      + able to handle longer path/file names (up to 500 chars)
2422    o adjoint:
2423      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
2424      - TBD: "hidden" mom_vecinv recomp. in dynamics
2425    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
2426     (allow to differentiate between forcing components using new integer flags:
2427      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
2428     and add new flag to put Dissipation tendency out of Adams-Bashforth.
2429    o ecco
2430      - enable trend removal from SSH anomaly obs.
2431    o adjoint
2432      - a fix for PmEpR when #undef EXACT_CONSERV
2433      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
2434      - try to fix "hidden" recomp. in forward_step for NLFS
2435        (NLFS seems broken sometimes after I checked it in)
2436    o seaice:
2437     - add c-grid version of the dynamic solver:
2438       + three new routines that are the c-grid substitute lsr, dynsolver
2439         and ostres
2440       + put a few fields that were local to dynsolver into global common
2441         blocks, so that I can move the computation of stresses etc into
2442         seaice_lsr (saves coding but may break the adjoint).
2443     - replace more hardwired parameters by runtime parameters
2444     - add ice masks that mask the rhs of the implicit solvers where there
2445       is no ice (commented out in seaice_dynsolver, because i am not sure
2446       if this works properly), eventually this should replace the clipping
2447       of ice velocities in seaice_dynsolver to +/-40cm/s.
2448    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
2449      include it only where its needed
2450    o move balancing of fluxes before the call of external_forcing_surf
2451    o seaice:
2452      - correct units of turning angles (now they are really in degrees)
2453      - move computation of GWATX/Y out of main routine into dynsolver
2454      - initialize GWATX/Y in seaice_init
2455    o Apply mask on Fresh-Water flux (needed for SSH forcing).
2456      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
2457    o seaice: add runtime flags for turning angles (default to zero)
2458    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
2459      and trend from exf forcing and ctrl control adjustments
2460    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
2461      (since checkpoint57x_post)
2462    o change the default rotation period to 86164.s = the Earth rotation
2463    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
2464      and based on a reference stratification. Tested within hs94.cs-32x32x5.
2465    o seaice advection: add code for choosing between the default (2nd order
2466      central differences) and multiDim advection schemes provided by
2467      pkg/generic_advdiff
2468    o seaice:
2469      - removed all references to SEAICE_GRID.h fields from
2470        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
2471        (cubed-sphere configuration will change a little)
2472      - grid computations in seaice_init are obsolete now.
2473      - cleaned up code a little so that is easier to read (hopefully).
2474      - added new (better?) discretizations of default advection and diffusion
2475        (turn on with SEAICEuseFluxForm)
2476      - replace 1 in 3d global fields by kSurface in growth.F
2477      
2478    checkpoint58a_post (2006/02/13)
2479    o seaice:
2480      - bug fix in advect.F
2481    o shelfice:
2482      - separate shelfice load anomaly from pload (breaks with time
2483        dependent forcing), => introduce constant field shelficeLoadAnomaly.
2484        Its default is 0., but it may be computed more cleverly from (unknown)
2485        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
2486        done offline. A good approximation of the pressure load anomaly is
2487        necessary to avoid large initial adjustment processes underneath
2488        deep-reaching shelfice.
2489      - small fix in ISOMIP shelfice_thermodynamics
2490      - add more sophisticated thermodynamics of Hellmer (1989), this is
2491        now the default
2492      - give a few constants more intuitive names
2493    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
2494      if bulk formulae are used in long integration (especially EmPmR). Turn
2495      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
2496      if balancePrintMean, the imbalance that is substracted is printed to
2497      STDOUT.
2498    o fix bug (typo) in obcs_apply_eta.F
2499    o add a new package shelfice which enables us to model the circulation
2500      underneath shelf-ice with draughts of hundreds of meters.
2501     - works
2502     - to do: + include improved thermodynamics
2503              + check whether kSurfC (from model/inc/SURFACE.h) can be used
2504                instead of new field kTopC
2505              + can we use topoFile, Ro_surf and existing code in ini_depth.F
2506                instead of new field R_shelfIce and new code in ini_depth.F
2507                and ini_mask_etc.F?
2508              + adjust vertical mixing schemes?
2509    o seaice pkg:
2510     - add a cpp-flag to include a simple formula for a salinity dependent
2511       freezing point of sea water at the surface
2512     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
2513       meridional stresses are now different (and hopefully correct)
2514    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
2515       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
2516       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
2517    o pkg/diagnostics: add options and parameters for regional-statistics
2518       diagnostics ; define regions by reading a region-mask from a file
2519       (might add other options later)
2520    o pkg/bulk_force:
2521     - add option and parameters to use AIM surface-flux formulae.
2522     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
2523       others forcing fields (defined in PARM05, parameter file "data") are loaded
2524       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
2525     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
2526     - use the right EXCH call for uwind,vwind (to work on CS-grid).
2527     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
2528       and parameters (note: calcWindStress replaces .NOT.readwindstress).
2529     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
2530    
2531    checkpoint58 (2006/01/12)
2532    o add "--embed-source" option to genmake2 which, when the supporting
2533      tools can be compiled (as determined by genmake2) will turn on the
2534      embed_files package which then embeds the entire MITgcm source code
2535      (*.[fFhc] + Makefile) used for the build within the executable
2536      - requested by CNH but off by default
2537      - adds a paltry <9MB to the mitgcmuv executable in most cases
2538      - only writes the output when useEMBEDSRC in eedata is true
2539    o clean up 3-dim. relaxation codes:
2540      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
2541      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
2542      * Thanks to Tom Haine for testing!
2543    
2544    checkpoint57z_post (2005/12/31)
2545    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
2546      affects output (@ truncation level) of exp. plume_on_slope ; updated.
2547    o fix the pickup behavior for obcs in combination with ptracers
2548    o fix a bug in ptracers_external_fields_load
2549    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
2550      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
2551    o transfered surface NH pressure to eta field (if exactConserv).
2552    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
2553         and update lab_sea output.txt file.
2554    o completing 3-dim. relaxation code: additional term
2555         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
2556      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
2557      * At compile time, in "EXF_OPTIONS.h" set
2558          #define  ALLOW_CLIMTEMP_RELAXATION
2559          #define  ALLOW_CLIMSALT_RELAXATION
2560      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
2561          tauThetaClimRelax3Dim = 15552000.0,
2562          tauSaltClimRelax3Dim  = 15552000.0,
2563      * 3 cases:
2564          1) Use a constant-in-time 3-dim. field
2565          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
2566          3) Real-time relax. to time-evolving prescribed field
2567    o Adding Laplacian-type smoothness constraint on
2568      initial and boundary (forcing) controls (ic, bc)
2569      * enable at compile-time via
2570        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
2571      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
2572      * Absolute scale somewhat unclear so far
2573      * no area weighting was included since no other cost term does so far
2574    
2575    checkpoint57y_post (2005/12/08)
2576    First step for a NLFS adjoint
2577    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
2578    o new init. routines for calc_r_star, calc_surf_dr
2579    o still need to deal with ini_masks_etc
2580    o testreport seemed happy
2581    checkpoint57y_pre (2005/12/08)
2582    
2583    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
2584    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
2585    o add new offset feature to offline pkg (plus minor cleanup)
2586    o cfc fixes for final year of integration
2587    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
2588      be in GCHEM_OPTIONS).
2589    
2590    checkpoint57x_post (2005/12/04)
2591    o fix testreport Pb in multiple test experiment.
2592    o cleanup our namelist syntax in verification:
2593      - make it more F95 standards compliant (some work still needed)
2594      - allows the vast majority of our tests to work with gfortran
2595    o Non-Hydrostatic:
2596     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
2597     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
2598    o Allow to apply AB on T,S rather than on AB(gT,gS):
2599     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
2600     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
2601       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
2602     - need a "clever" read_pickup to restart from the other AB formulation
2603    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
2604    o remove some unused variables (reduces number of compiler warnings)
2605    o adjoint
2606      * Disable useVariableViscosity for adjoint for time being
2607        (there are a number of extensive recomputations)
2608      * Initialize certain variables needed for adjoint
2609    
2610    checkpoint57w_post (2005/11/03)
2611    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
2612                 fix the singleCpuIO RS version of MDSWRITEFIELD
2613       and add a WARNING if using globalFiles=T with multi-processors.
2614    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
2615      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
2616    o tracer advection scheme:
2617      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
2618       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
2619       was not very convenient).
2620      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
2621       (further tests needed for the implicit DST & Flux-Limiter schemes).
2622    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
2623      and sRef for convenience, handy, when you want to initialize
2624      ptracers in a large domain with a constant non-zero value. Also,
2625      untangle ptracers_init.F a little.
2626    
2627    checkpoint57v_post (2005/10/13)
2628    o change dome exp. to use variable viscosity in side-drag terms.
2629    o remove all the files from the cfc_offline test since they are now
2630      incorporated into tutorial_cfc_offline which has been producing
2631      identical results for a few days of testing
2632    o add new parameter: sideDragFactor to enable half-slip-side BC
2633      and change side-drag S/R to use viscosity from mom_calc_visc
2634      (can switch back by setting sideDragFactor=0.); affects results at
2635      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
2636       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
2637    o vorticity & strain are now computed without masking, to account for
2638      no-slip-side BC in variable viscosity calculation ; mask is applied
2639      anyway later on, before computing advection/coriolis terms.
2640    o modify exp4 to test new obcs support for reading from external files
2641      and for passive tracers
2642    o fix behavior of ptracers_monitor when monitor output is written to a
2643      netcdf-file; still not independent of monitor.F (writes in the same
2644      file).
2645    o change default value of tRef (put a uniform, meaningful value for ocean
2646      & atmos) and initialize sRef (was missing, as Martin mentioned).
2647    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
2648      to be proportional to enstrophy dissipation length.  Thus,
2649       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
2650      This is now consistent with Smagorinsky and with the manual.
2651    
2652    checkpoint57u_post
2653    o OBCS and PTRACERS: add open boundary support for passive tracers
2654      - either use homogenous (pseudo) v.Neumann conditions or prescribe
2655        OB-values from file; this is not different from the way theta and salinity
2656        are treated
2657      - however, Orlanski-radiation conditions are not supported, and the model
2658        will stop if you use pTracers and Orlanski at the same time.
2659      - beefed up the rountine obcs_external_fields_load: now only those open
2660        boundary values are overwritten with values from files for which there
2661        are really files, otherwise the OB-fields remain untouched. This makes
2662        it possible to use different OBs at different ends of the domain (as
2663        with EXF)
2664    o reduce number of exch calls in shap_filt (s2).
2665    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
2666      truncation level) 4/5 MLAdjust test results (11&12 digits match).
2667    
2668    checkpoint57t_post (2005/10/03)
2669    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
2670    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
2671      same truncation, independent of the face number: affects affects several
2672      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
2673    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
2674      note that biharmonic viscosity + no-slip was not tested in any experiment.
2675    o fix bug in non-linear free-surf side-drag ; generate new output for
2676      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
2677    o make mnc honor the writeBinaryPrec flag for most kinds of output
2678    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
2679    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
2680      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
2681    o add brackets in multi-terms sum to get same truncation, independent of
2682      the face number (manage to get exactly same value of gU,gV at the cs-edge)
2683      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
2684    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
2685      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
2686      a maximum grid-scale Reynolds number.  Also, changes all length calculations
2687      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
2688      Suggested values of viscosity parameters found in mom_calc_visc.
2689      Many new viscosity diagnostics available.
2690    
2691    checkpoint57s_post (2005/09/20)
2692    o Add clearing-house for viscosity calculations, mom_calc_visc and
2693      correct numerous bugs in LeithD and Smagorinsky discretizations.  
2694      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
2695      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
2696      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
2697      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
2698      The Strain-Tension form is now called with useStrainTensonVisc=.true.
2699      ViscAhStrain and viscAhTension are now retired.
2700    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
2701    o In response to JMC's bug report, genmake2 now ignores any soft-links
2702      that it finds in the *current* directory when searching for files.
2703      Soft-links found in any other source directories will still work as
2704      they did before.
2705    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
2706      a C routine to unlimit the stack size
2707    o mnc-ify pkg/aim snapshot vars
2708    o mnc-ify pkg/land as requested by Daniel
2709    o various changes to mnc including:
2710      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
2711      - output can now be grouped so that all files within a group
2712          change the ITER portion of their names in lock-step together
2713      - can now read ("global") PER-FACE (in addition to PER-TILE) files
2714          and works with both EXCH1 and EXCH2 (but needs more testing)
2715      - writing works for all verification test cases w/ g77 on Linux
2716    
2717    checkpoint57r_post (2005/09/07)
2718    o make MNC variable initialization happen earlier
2719    o add diagnostics for (almost) each term of the momentum Eq.
2720    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2721    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
2722    o remove MINIMAL_TAVE_OUTPUT option ;
2723      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
2724    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
2725      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
2726    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
2727    o add time-dependent SST, SSS control
2728    o cost terms in ecco/ modularized (new cost_generic.F)
2729    o cost_averages routines are modularized (new cost_averagesgeneric.F)
2730    o new infrastructure for seaice model vs. obs misfits in seaice/
2731      * driver from the_main_loop.F is seaice_cost_driver.F
2732      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
2733      * gradient check in Exp. 6a of natl_box_adjoint/
2734    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2735      (see README file)
2736    
2737    checkpoint57q_post (2005/08/19)
2738    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2739    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2740      - bug was reported by Jean-Michel and Ian Fenty
2741    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
2742      update exp. cpl_aim+ocn output.
2743    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
2744      Needed for high-res. runs with large global files
2745      to be able to limit tapelev size
2746    o Changed some tests for adjoint:
2747      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
2748      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
2749      * global_ocean.90x40x15/ back to default 3-level checkpointing
2750    o Modifications to enable scripted COMMON to MODULE conversion
2751      * verification/OpenAD/code/ has necessary scripts and description;
2752      * converts, compiles and runs successfully;
2753    
2754    checkpoint57p_post (2005/08/01)
2755    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2756    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2757      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
2758    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
2759    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
2760      (was already the case for dissipation with mom_vecinv,
2761       and also the case for grad.PhiHyd when staggered-timeStep)
2762      This will allow to put dissipation out-off the AB time-stepping.
2763     Unfortunately, affects truncation error. Update output of exp. that "fails"
2764      (cg2d matching number) and leave the others for later: front_relax(10),
2765      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2766      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2767    
2768    checkpoint57o_post (2005/07/30)
2769    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
2770      (2) its ready to be documented during the 20050801 DocFest
2771    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
2772      for ideal_2D_oce and lab_sea on linux_ia32_g77
2773    o set to #undef CTRL_SET_OLD_MAXCVARS_30
2774      in global1x1_tot/code_seaice_adj to access indices 32, 33
2775      (worth another tag)
2776    
2777    checkpoint57n_post (2005/07/29)
2778    o adding precip control xx_precip 32
2779    o adding swflux control xx_swflux 33
2780    o Replacing 10 forcing penalty cost routines by 1 generic.
2781    o Implementing partitioning in time-mean and variable adjustment
2782      for atmos. state.
2783    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
2784    o in natl_box_adjoint:
2785      * updated exp 1 to 10
2786        (but does not have time-mean vs. variable split results yet)
2787    o updated global1x1/*_seaice_adj/
2788      to incorporate latest changes
2789    o enable useSingleCpuIO for mdsio vector routines
2790      (applies in particular to tapelev I/O)
2791    o removed inefficient K-loop in all active_file*control*.F
2792    
2793    checkpoint57m_post (2005/07/28)
2794    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
2795      and advect_cs (use EXCH-2 and standard cs-32 grid files).
2796    o pkg/exch2: filling of face-corner halo regions is optional
2797      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
2798    
2799    checkpoint57l_post (2005/07/14)
2800     tag before updating tutorials (pre-release-2)
2801    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
2802       for output and interpolation of input fields onto model grid)
2803    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
2804       Affects results of exp. rotating_tank ; update output.txt.
2805    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
2806          and taking the square quantity and/or using a fraction-weight field.
2807    o fix aim_diagnostics_init.F mate numbers.
2808    o add mnc output capability to diagnostics/diagstat and update
2809      our cvsignore files for the ACSII output generated
2810    
2811    checkpoint57k_post (2005/07/02)
2812    o lab_sea now uses diagnostics package and provides a suite of
2813      new EXF diagnostics output.
2814    
2815    checkpoint57j_post (2005/06/30)
2816    o exf
2817      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
2818        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
2819        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
2820      * extended diagnostics output
2821        - now includes all EXF variables
2822        - hs, hl moved to common block
2823        - separate S/R for diagnostics, called after ctrl vector is added
2824        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
2825        - EXFqnet contains true Qnet (i.e. includes qsw)
2826      * updated verif. lab_sea, global_with_exf
2827      * Rearranging hflux (exf_mapfields -> exf_getforcing)
2828        to ensure that diagnostics sees a true EXFqnet
2829    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
2830    o diagnostics pkg: change pointers so that 1 diagnostic can be used
2831      several times with different frequencies.
2832    o mnc-ify the thsice package as requested by Daniel Enderton
2833      - the monitor--MNC output needs work
2834      - many attributes need to be added (most are currently blank)
2835    o mnc-ify theaim_v23 package as requested by Daniel Enderton
2836      - many attributes need to be added (most are currently blank)
2837    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
2838    o add Sadourny like discretization to the 4th.O vorticity advection scheme
2839    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
2840      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
2841         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
2842    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
2843     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
2844    
2845    checkpoint57i_post (2005/06/19)
2846    o Diagnostics package was changed: diagnostic allocation is now deactivated
2847      by setting an empty file name in the namelist (used to be by setting 0 frequency)
2848    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
2849      add 1rst Order upwind vertical Shear.
2850    o add a quick fix for A/B checkpointing in OFFLINE mode
2851    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
2852      end-run around the C/Fortran linking horror in eesup/src/timers.F
2853    o added pkg/runclock: allows user to terminate run based on wall clock
2854    o added non-hydrostatic scaling parameter: nh_am2
2855    o pkg/my82: futile attempt to make results compiler-independent by adding
2856      some "_d 0", etc. no effect.
2857    o for mnc output, fill the 'T' coordinate var with myTime and create a
2858      separate 'iter' variable for iteration count
2859    o pkg/diagnostics:
2860      add new capability: output of Global/Regional & per-level statistics ;
2861      tested against monitor output (including land & thSIce) on various exp.
2862    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
2863    
2864    checkpoint57h_done (2005/05/19)
2865      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
2866      data.diagnostics, data.gchem, data.ptracers) is done.
2867    
2868    o pkg/diagnostics: prepare for Global/Regional statistics.
2869      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
2870    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
2871      and rename it: DIFFERENT_MULTIPLE
2872    
2873    checkpoint57h_post (2005/05/14)
2874    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
2875    o pkg/diagnostics: change output frequency, now in seconds (instead
2876      of Nb of iterations). This requires to change data.diagnostics.
2877    checkpoint57h_pre (2005/05/12)
2878    
2879    o in mnc, let the user create the output dir if both mnc_outdir_date
2880      and mnc_outdir_num are false
2881    o add fflags() to pkg/diagnostics which allows one to specify, on a
2882      per-file basis, the file precision [default behavior is unchanged]
2883    o added diagnostics to pkg/kpp, including computation of mixed layer
2884      depth based on a temperature/density criterion
2885    o updated verification/natl_box to test the new pkg/kpp diagnostics
2886    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
2887    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
2888    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
2889      not mnc -- this mistake was found by JMC and is now corrected
2890    
2891    checkpoint57g_post (2005/04/15)
2892    o add Adams-Bashforth 3rd Order time stepping:
2893      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
2894      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
2895    checkpoint57g_pre (2005/04/15)
2896    
2897    o make lambda[Theta,Salt]ClimRelax spatially varying
2898      (default remains spatially uniform constant based on tau)
2899    o added new control variables
2900      * init. uVel, vVel, etanN
2901      * lambda[Theta,Salt]ClimRelax
2902    o separate masks used for ctrl_pack/unpack 'from write_grid' output
2903      (suggested by G. Forget)
2904    
2905    checkpoint57f_post (2005/04/06)
2906    o add parameter "baseTime" = model base time = time at iteration zero
2907      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
2908      account for baseTime shift
2909    o move Coriolis arrays from PARAMS.h to GRID.h
2910    checkpoint57f_pre (2005/04/06)
2911    
2912    o mnc-ifying the seaice package
2913    o introduced an alternative length scale calculation for use in the limiting
2914      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2915    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
2916    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
2917      as well as grad(vort3).  Made it compatible with both approximate form
2918      for the cubed sphere and full form of these gradients.  Added flag
2919      useFullLeith to select between approximate and full form.  
2920    o add "d0" in getcon.F to reduce differences between compilers/platforms
2921      update output.txt of exp. fizhi-gridalt-hs
2922    o change port_rand funtion to allow to set the seed.
2923    o fix obscure MNC bug involving conversion between reals and integers
2924      - it caused no problems with certain (eg. gcc, ifc) compilers but the
2925        new version is now more standards-compliant
2926    o adjoint-related modifications
2927      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
2928      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
2929      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
2930    
2931    checkpoint57e_post (2005/02/28)
2932    o Adding eddy stress controls a la Ferreira et al.
2933    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
2934    
2935    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
2936      update output.txt of exp. fizhi-gridalt-hs
2937    o add more "Z" dimensions and associated coordinate vars to MNC
2938    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
2939    o parameter calendarDumps: when set, approximate months (30-31 days) and years
2940      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
2941      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
2942      months and years.  Requires pkg/cal.
2943    o diagnostics: add pickup functionality
2944      - off by default for backwards compatibility
2945      - current version only uses MDSIO -- MNC will be added
2946    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
2947    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
2948    
2949    checkpoint57d_post (2005/02/11)
2950    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
2951    o modify verification/ideal_2D_oce so that it tests the creation of mnc
2952      output from the diagnostics package
2953    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
2954    o make genmake2 more portable by using ".$FS" instead of ".f" for more
2955      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
2956    o add coordinate variables to the MNC output from the diagnostics package
2957    o change MNC-flags default value: true when useMNC=TRUE
2958    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
2959      the ability (off by default) to read the grid information using MNC
2960    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
2961    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
2962    o do snap-shot diagnostics at the middle of the time-interval (instead of
2963      at the end).
2964    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
2965      new test for AIM with thSIce + slab-ocean
2966    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
2967    o move state variable diagnostics to the beginning of the time step ;
2968      (note: still needs some work specially for snap-shot diagnostics)
2969      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
2970    
2971    checkpoint57c_post (2005/01/27)
2972    o Change testing option (-ieee) to get closer agreement between g77 & ifort
2973    o generate new output.txt files on faulks with g77 & the new -ieee option
2974    checkpoint57c_pre (2005/01/27)
2975    
2976    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
2977      update output.txt of exp. global_ocean.90x40x15
2978    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
2979      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
2980    o add saltFlux(+File) forcing capability with periodicExternalForcing
2981    o allow to use pkg diagnostics for GM-Redi & ThSIce output
2982    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
2983    o improvements for the MNC output from DIAGNOSTICS:
2984      - correct handling of the unlimitied dimension
2985      - all dims now have associated coordinate variables
2986      - variables located at U, V, and Corner ("Z") points are now written
2987        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
2988        *all* data points are output
2989    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
2990    o added pkg/seaice/seaice_monitor.F
2991    o mdsio_readfield.F can now read files visible only to master MPI process.
2992    o pkg/seaice: some test code for ice-modified ocean stress
2993    o exf_getffields interpolation defaults to bilinear for all scalar forcing
2994      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
2995      spurious negative numbers for precipitation and humidity.  Will cause
2996      some small numerical differences for integrations using pkg/exf/exf_interp.F.
2997    o pkg/ctrl/
2998      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
2999        May be enabled via doPackDiag
3000      *  introduce z-scaling of
3001         + gradient (doZscalePack) and
3002         + control (doZscaleUnpack)
3003    o pkg/mdsio/
3004      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
3005      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
3006    
3007    checkpoint57b_post (2004/12/20)
3008    o simplify options in diagnostics_fill arguments (remove weird combinations)
3009    o fix MNC coordinate variables so that they now contain per-face index
3010      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
3011      general, EXCH2 grids are only aligned to a "local" coordinate system
3012    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
3013    o Implement instantaneous output within pkg diagnostics:
3014      setting a negative frequency in data.diagnostics produces
3015     "snap-shot" output (as opposed to time-average if freq > 0)
3016    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
3017      NOTE: change ptracer diagnostics name: use 2 characters to work with
3018            more than 9 tracers. Add also diagnostics of advect & diffus flux.
3019    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
3020      becomes the coordinate variable for the 'T' dimension
3021    o add CF-style coordinate variables to MNC
3022      - just a first cut:  numbers are meaningless on the cubesphere and
3023        missing along the T axis but otherwise it works!
3024    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
3025    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
3026    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
3027      this is based directly on what the model compute, so that the content of
3028      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
3029    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
3030    o clean up build options files for SunOS, in particular
3031      - remove -traditional from xmakedepend
3032      - change -xarch=v9 to -xarch=native for f77
3033      - restore use of make (not gmake)
3034      - add CC=gcc if using g77
3035    o changes per discussion of AM, JMC, & EH3 today:
3036      - move redundant "grid" variables out of "state" -- in preparation of
3037        creating proper CF-style coordinate variables and in recognition
3038        that any/all grid variables can be easily copied (eg. w/NCO) from
3039        the grid files into any of the other NetCDF files
3040      - *always* output grid variables with MDSIO (this will eventually be
3041        changed)
3042      - output MNC grid file if useMNC is true
3043    o every instance of _END_MASTER() has been found and replaced with
3044      _END_MASTER( myThid ) in order to satisfy certain picky Sun
3045      preprocessors
3046    o re-arrange diagnostics pkg initialisation:
3047     - allow each package to extend the available diagnostics list
3048     - add some checking and fix small problems (multi-threaded, ...)
3049     - new S/R diagnostics_fill (replace fill_diagnostics):
3050       look through the short list of active diag. (instead of the long list)
3051       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
3052    
3053    checkpoint57a_post (2004/12/10)
3054    o this set of changes restores TAMC compatibility
3055      tested for global_ocean.90x40x15 adjoint on trough
3056      (what a pain)
3057    
3058    checkpoint57a_pre (2004/12/10)
3059    o some modifs in tools/build_options for sunos
3060    o call ctrl_pack for ctrl at end for optimcycle=0
3061    
3062    checkpoint57 (2004/12/09)
3063    o add horizontal bi-harmonic viscosity for vertical velocity
3064      - new parameter viscA4W (defaults to viscA4)
3065      - affects only non-hydrostatic code
3066      - to be done: no-slip lateral boundary conditions
3067    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
3068    o implement Implicit Vertical advection for pTracers
3069    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
3070      (implemented also for implicit vertical diffusion & advection)
3071    o OBCS: extend application of tracer open boundary conditions
3072      to a strip beyond the boundary of width Olx/Oly
3073    o add call monitor to TAF set of required calls (flow directives)
3074      and include in natl_box_adjoint
3075    o untangle a few ifdefs related to cost, ctrl, autodiff
3076      untangel a few ALLOW_ECCO_OPTIMIZATION
3077    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
3078      (theta2, salt2 in ecco_cost_weights)
3079    
3080    checkpoint56c_post (2004/12/03)
3081    o OBCS as control variables
3082      - update ctrl_ad_diff.list, obcs_ad_diff.list
3083      - remove balance of obcs controls from default
3084      - fix index bug nobcs in ctrl_init
3085      - fix dummy fields filen in ctrl_pack
3086      - add dummy weights for obcs
3087    o lsopt: comment out fort.94 output
3088    o optim:
3089      - remove unnecessary header files
3090      - adjusted namelists
3091      - add xerbla.F to Makefile
3092    o exf:
3093      - multiple modifications of exf_check_range
3094      - unit change in exf_init_runoff from [m/year] to [m/s]
3095    o mdsio:
3096      - i/o-vector change debugLevel from debLevA to debLevB
3097    
3098    checkpoint56b_post (2004/12/01)
3099    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
3100      is called from DO_THE_MODEL_IO
3101      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
3102      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
3103      - clean up PTRACERS_WRITE_TIMEAVE a little
3104    o add another verification experiment that tests both the cfc-pkg and
3105      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
3106      reactive tendencies treated inline with regular timestepping
3107    o testreport previously did a lousy job of comparing small numbers, so
3108      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
3109      implemented in the little c-progam tmp_cmpnum.c which is embedded in
3110      testreport.
3111    o ptracers_monitor: bug fix for MPI
3112    
3113    checkpoint56a_post (2004/11/28)
3114    o GCHEM: finish reorganizating the package
3115      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
3116        (introduces another 3D-array for each passive tracer, but only if
3117        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
3118        gchemTendency is not needed because the timestep is done separately)
3119      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
3120      - GCHEM is now---more or less cleanly---separate from PTRACERS
3121      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
3122        so clear to me how that should be done in a general way.
3123    o CFC: improve formatting of output in CFC_ATMOS
3124    o PTRACERS:
3125      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
3126        that ALL experiments with ptracers enable can be checked. This makes
3127        GCHEM_MONITOR obsolete.
3128      - include a runtime parameter PTRACERS_monitorFreq that defaults to
3129        monitorFreq
3130      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
3131    o add PTRACERS (PTR0[1-5]) to testreport output
3132    o exf_check_range:
3133      * default changed to .TRUE.
3134      * will check values for niter0 if debLevA, every timestep if debLevB
3135      * STOP in exf_check_range if 'out of range'
3136      * range chosen generous to allow for potential extema
3137      TBD: a version with stricter range
3138           permitted range would be runtime parameters
3139    o GMredi:
3140      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
3141      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
3142      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
3143    o GCHEM:
3144      - move call to GCHEM_FORCING_SEP, so that it is now called before
3145        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
3146      - introduced a useGCHEM runtime flag and applied it everywhere.
3147      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
3148        this flag is now only visible within GCHEM-pkg routines.
3149      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
3150        be replaced by a 3D array that is computed before thermodynamics; for
3151        this, the tracer ID iTracer had to be included into the parameter list
3152        of ptracers_forcing
3153      - set up forward_step to call gchem_forcing, that will replace
3154        gchem_forcing_int in ptracers_forcing
3155      - cleaning up
3156    o small cleaning of exch2: remove files that are also in eesupp/src
3157    
3158    checkpoint56 (2004/11/17)
3159    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
3160    o mnc: cleanup "full" files--fixes out-of-memory problem
3161    o ECCO-GODAE
3162      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
3163      * fully merged and updated from SIO code
3164        windstress sign change affects
3165        - exf_inscal_[u/v]stress
3166        - sign of xx_tau[u/v] adjustments
3167        - signs in cost_scat
3168      * ctrl_get_gen: avoid update of tau[u/v] for first few days
3169      * natl_box_adjoint updated and compressed
3170      * 2-level checkpoint switch added
3171        (tested in EXP. 1 of natl_box_adjoint)
3172      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
3173    o SVD
3174      * first complete, non-hacked version for SVD calculations
3175      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
3176        performed via direct access files admtlm_vector.it????
3177        (via ctrl_[un]pack)
3178      * optimcycle is used for ARPACK iteration counter
3179        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
3180      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
3181        and add linear transforms where necessary
3182      * controls are initial/final SST, SSS (can be extended; need to check
3183        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
3184    o mdsio: filename info to both stderr, stdout
3185    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
3186      from sign change
3187    
3188    checkpoint55j_post (2004/11/10)
3189    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
3190      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3191    o add consistent build directories and .cvsignore files to verification
3192    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
3193    o make all subroutines 30 or less characters in length for certain older
3194      compilers to work (a thorough search only turns up two routines in
3195      pkg/ptracers)
3196    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
3197      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3198    
3199    checkpoint55i_post (2004/10/28)
3200    o change arrays for total vertical diffusivity (2.D if explicit,
3201      3.D if implicit) ; each ptracer uses its own background value.
3202    o added mnc/NetCDF output capability to ocn_compon_interf
3203      - added bits to verification/cpl_aim+ocn so that it can run on
3204        ITRDA and other clusters without the mpirun "-wd" option
3205    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
3206      configuration
3207    o give MNC the ability to create additional files rather than
3208      exceeding a specified file size limit "MNC_MAX_FILESIZE"
3209      - the default is just less than 2GB which is a practical limit
3210        on many systems
3211    o Compute the non-local term using either KPP vertical diffusivity (=default)
3212       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
3213    
3214    checkpoint55h_post (2004/10/20)
3215    o add verification test "vermix"
3216    o remove all the *_ioinc flags and replace with the single global
3217      outputTypesInclusive flag
3218    o allow to set a vertical profile of vertical diffusivity for T & S
3219    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
3220    o useMNC moved from data.mnc to data.pkg
3221    
3222    checkpoint55g_post (2004/10/14)
3223    o Renaming carbon AD experiments to comply with testreport conventions
3224    o Updating adjoint of Held-Suarez hs94.1x64x5
3225    o Fixing directives for non-ECCO forward_step, after ECCO directives
3226      have been fixed to avoid recomp. of do_oceanic_phys
3227      Works well for global_ocean.90x40x15,
3228      but recomp. issue remains for carbon
3229    o Updating adjoint output for natl_box_adjoint after
3230      pkg/ecco has been modified (see taga c55d_post)
3231    
3232    checkpoint55f_post (2004/10/13)
3233    o rename to timeave_init_fixed
3234    
3235    checkpoint55e_post (2004/10/13)
3236    o some delicate re-shuffle of store directives to avoid one
3237      extra call of do_oceanic_physics
3238      affects ecco_the_main_loop.F, do_oceanic_physics.F
3239      checkpoint_lev1_directives.h
3240    o NB: this may break global_ocean adjoint temporarily,
3241      but it is clear how to fix it. Will do later, need this now.
3242    
3243    checkpoint55d_post (2004/10/11)
3244    o ECCO specific cost function terms (up-to-date with 1x1 runs)
3245    o ecco_cost_weights is modified to 1x1 runs
3246    o modifs to allow observations to be read in as
3247      single file or yearly files
3248    o enable to read exf forcing fields as either
3249      single file or yearly files (flag useExfYearlyFields)
3250    checkpoint55d_pre (2004/10/08)
3251    
3252    o switch between 2-level and 3-level checkpointing
3253    o add ability of MNC to write local and "partial" (eg. 2D slices where
3254      the full 3D field is never actually stored) arrays to NetCDF files
3255      with the correct (that is, the complete multi-dimensional) set of
3256      array indicies
3257      - used in mom_vecinv() to write the diagFreq output
3258      - tested (demonstrated) in verification/aim.5l_cs
3259    o further mnc-ification
3260      - add verification/lab_sea to the list with mnc setups
3261      - fix undefined mnc v-names in cd_code
3262      - add kpp to mnc output (both snapshot and timeave)
3263    o non-hydrostatic code
3264      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
3265        in calc_gw.F
3266      - defaults to viscAh
3267      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
3268        friction or Leith) in non-hydrostatic mode, as long as there is
3269        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
3270    o pkg/cost
3271      extend simple cost functions to treat time mean quantities
3272      (T,U,V) via cost_accumulate_state from cost_tile
3273    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
3274        be 2 times larger than the minimum size the advection scheme requires.
3275        now get a perfect conservation of salt in advect_cs test-exp (updated)
3276    o GGL90 (Gaspar's TKE mixed layer)
3277      - add horizontal diffusion of TKE, requires exchanges in
3278        do_fields_blocking_exchanges, horizontal diffusivity is zero by
3279        default. In OPA there is no horizontal diffusion of TKE but the
3280        mixing coefficients are computed from a horizontal average of TKE of
3281        6 points or so. I think that diffusion has a little more physical
3282        justification.
3283      - clean up ggl90_calc in the hope of reducing memory usage (this hope
3284        was in vain)
3285      - mask tke-variable in ggl90_init
3286    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
3287    o fix biharmonic diffusion on CS-grid.
3288    o more obcs stuff
3289      - added obcs_external_fields_load as an alternative to the EXF-pkg option
3290        for reading boundary values. This routine is called from
3291        obcs_prescribe_read
3292      - updated obcs_check
3293      - changed sponge layer relaxation parameter units for days to seconds
3294      - turned off sponge layer by default
3295      - changed argument list of OBCS_CALC to myTime+deltaTclock
3296      - fixed about 35 bugs in obcs_external_fields_load
3297    
3298    checkpoint55c_post (2004/09/23)
3299    o obcs stuff
3300      - new runtime flags useOBCSprescribe, useOBCSbalance
3301      - re-arranged obcs_calc
3302      - moved exf_getobcs to obcs_prescibe_read
3303        obcs_prescibe_read is called after ORLANSKI stuff
3304        and independent of it (executable can contain all).
3305      - updated obcs_check
3306      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
3307        These may be necessary only if tangential velocities are
3308        prescribed at OB, not sure, needs testing.
3309    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
3310      which simplifies the calls and passes the ifc check-bounds test
3311    
3312    checkpoint55b_post (2004/09/22)
3313    o add a 2D scalar, Z location, exchange_2 routine.
3314    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
3315      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
3316      affects advect_cs results (for the wrong reason): update output.txt
3317    o use a more standard discretization for biharmonic viscosity ;
3318     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
3319      affects results of dome set-up: update output.txt
3320    o fix gad_advection.F (CubedSphere part), back to version 1.23
3321    o fix bug in mom_vi_del2uv.F (CubedSphere part).
3322    
3323    checkpoint55a_post (2004/09/20)
3324    o merged code to
3325      * prescribe/read time-dependent open boundaries
3326        (works in conjunction with exf, cal)
3327      * sponge layer code for open boundaries
3328      * each boundary N/S/E/W now has its own CPP option
3329        (healthy for the adjoint)
3330    
3331    checkpoint55 (2004/09/17)
3332    o up-to-date adjoint of previous breaks
3333      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
3334      - global_ocean_ebm: adjoint still needs fix (TLM ok)
3335      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
3336      - carbon: * remove tr1-related adjoint verification
3337                * add ptracer as control variable
3338    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
3339      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
3340    
3341    checkpoint54f_post (2004/09/16)
3342    o in verification/carbin/ remove experiment related to
3343      ALLOW_PASSIVE_TRACER (array tr1 etc)
3344      code_ad/ input_ad/ results_ad
3345    
3346    o add two new packages
3347      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
3348        + subject to optimization (memory)
3349      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
3350        + subject to reordering (many GOTOs in the original code)
3351        + so far opps is called for every (i,j) point, and then operates in
3352          the vertical; one may want to reorder the scheme in order operate in
3353          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
3354          fields)
3355    o overhaul of IO so that we now have flags for MDSIO and/or MNC
3356      - all verification tests compile and run with linux_ia32_g77
3357      - defaults are compatible with current input files--nothing
3358        should change if you were not previously using MNC
3359      - MNC output has been added in numerous places (eg. timeave)
3360        but there are still a few writes not yet do-able with MNC
3361        (this is in progress)
3362      - flags now allow for either/or/both use of MDSIO and MNC and
3363        documentation will soon follow
3364      - numerous small formatting cleanups for ProTeX
3365    o add version info (via BUILD_INFO.h) to MNC and stdout
3366    
3367    checkpoint54e_post (2004/09/02)
3368    o add two new packages
3369      - pp81 (Packanowski and Philander, 1981), Richardson number and
3370        stratification dependent mixing
3371      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
3372      - these scheme operate in a similar manner as KPP (without ghat, of
3373        course), however there is only one diffusivity that is used for both
3374        temperature and salinity (and passive tracers)
3375    o add offline package
3376    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
3377      provided by Stephanie Dutkiewicz
3378    o genmake2: add ability to search for C compilers and cleanup test output
3379      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
3380    
3381    checkpoint54d_post (2004/07/27)
3382    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
3383    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
3384      leading to additional shift by 5 days each year of integration
3385       (i.e. leading to considerable offset over the years)
3386    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
3387    o start with no AB and no initial filtering (staggerTimeStep):
3388      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
3389    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
3390      (external loading & cpl import/export stay in forward_step.F)
3391    o update coupling interface to work with new staggerTimeStep
3392    o change MDSIO ptracers_pickup.
3393    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
3394    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
3395    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
3396    
3397    checkpoint54c_post (2004/07/18)
3398    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
3399      this affects (truncation error) output.txt of test-exp:
3400       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
3401    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
3402    o change Qnet to always be the net heat flux, (+upward).
3403      affects (truncation error) output of natl_box exp.: updated
3404    o define the max number of passive tracers in PTRACERS_SIZE.h
3405    o start to test mnc routinely in exp0
3406    o add sea-ice loading (sIceLoad) as a new forcing field.
3407    
3408    checkpoint54b_post (2004/07/08)
3409    o add testreport "-j JOBS" option for parallel builds (tested and pretty
3410       impressive on Altix and Opteron systems)
3411    o diagnostics can now write NetCDF files through the mnc package
3412    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
3413    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
3414    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
3415      affects (truncation error) output of lab_sea & natl_box exp.: updated
3416    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
3417    
3418    checkpoint54a_post (2004/07/06)
3419    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
3420    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
3421    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
3422    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
3423      + internal_wave (shift in writing cg2d_ini_res)
3424    checkpoint54a_pre (2004/07/05)
3425    
3426    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
3427      - modified verification/lab_sea and natl_box_adjoint accordingly
3428    
3429    checkpoint54 (2004/07/02)
3430    checkpoint53g_post (2004/07/02)
3431    o prepare splitting of thermodynamics: store convect.counter in common block
3432    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
3433      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
3434    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
3435    o new parameter "nShapS": allow to treat differently S from T (nShapT)
3436    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
3437    o restore adjointability
3438    
3439    checkpoint53f_post (2004/06/25)
3440    o modifications that affect AIM experiment results (update output.txt):
3441      - no advection of S at top interface Nr (pkg/generic_advdiff)
3442      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
3443    o AIM pkg:
3444      - include stability function into surf.Flux derivative relative to Tsurf
3445      - calculate clear-sky radiation & surface temp. change (for diagnostics)
3446    
3447    checkpoint53e_post
3448    o merged cylindrical coord configuration
3449    o added rotating_tank experiment
3450    checkpoint53e_pre
3451    
3452    checkpoint53d_post (2004/06/14)
3453    o faulks upgraded: re-generate output.txt that have changed:
3454       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
3455    o Added Bryan and Lewis, 1979, vertical diffusivity profile
3456    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
3457    o added Sadourny discretization of Coriolis
3458      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
3459      - re-enabled use of omega3 (useAbsVorticity)
3460    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
3461      vector-invariant equations
3462      - note: does *NOT* yet use same variable visc. for no-slip BC's.
3463    o recoded the lateral boundary conditions for non-hydrostatic w, this time
3464      hopefully without new bugs
3465      - still to do: biharmonic friction for non-hydrostatic w
3466    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
3467    o regenerated output for global_ocean_ebm (using -ieee)
3468    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
3469      of mom_common/
3470      - simple re-arrangement of instructions within computing loop
3471    checkpoint53d_pre (2004/05/21)
3472    
3473    checkpoint53c_post (2004/05/21)
3474    o new version of coupler for AIM+thSIce and Ocean models
3475     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
3476     - land: change Evaporation of snow
3477     - aim with thSIce: fix bug in snow-precip.
3478    o changes to calc_gw.F
3479     - bug fix for w^2 term near the bottom boundary
3480     - (hopefully) improve the lateral slip boundary condtions for use with
3481        partial/looped cells
3482      - because the bug fix changes two verification experiments anyway (exp5
3483        and plume on slope), change the lateral boundary condition from half slip
3484        to the value of no_slip_sides
3485    o ebm package wasnt quite up to the parallel task. Fixed that.
3486    o Adjoint of EBM package + verification
3487      * TLM OK
3488      * ADM not sufficient accuracy yet (needs further testing)
3489    
3490    checkpoint53b_post (2004/05/14)
3491    o Commiting new energy balance model to repository
3492      * package is pkg/ebm
3493      * verif. is verification/global_ocean_ebm
3494      * references are in ebm_driver.F
3495    C      * X. Wang, P. Stone and J. Marotzke, 1999:
3496    C        Global thermohaline circulation. Part I:
3497    C        Sensitivity to atmospheric moisture transport.
3498    C        J. Climate 12(1), 71-82
3499    C      * X. Wang, P. Stone and J. Marotzke, 1999:
3500    C        Global thermohaline circulation. Part II:
3501    C        Sensitivity with interactive transport.
3502    C        J. Climate 12(1), 83-91
3503    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
3504    C        Destabilization of the thermohaline circulation
3505    C        by atmospheric eddy transports.
3506    C        J. Climate 7(12), 1870-1882
3507    o Will need long integration testing.
3508    checkpoint53b_pre (2004/05/14)
3509    
3510    o created pkg/mom_common in preparation for variable viscosity code
3511    o renamed and split ini_mnc_io
3512    o pkg/land: only liquid water can diffuse or run-off
3513    o AIM using land: soil wetness availability account for snow
3514    o added printMapIncludesZeros to EEPARMS namelist
3515    
3516    checkpoint53a_post (2004/05/11)
3517    o restore TAMC compatiility for exf_constants.h
3518      (no usage of _d in .h)
3519    o Additional storing in KPP in an attempt to fix
3520      TAMC problem with adjoint of KPP code.
3521      (no success...)
3522      Identical code works fine with TAF.
3523    o Fixed verification/natl_box_adjoint experiments.
3524      Initial conditions for Experiments 4 and 5 are now
3525      set to "SEAICE_initialHEFF=0", which is more reasonable,
3526      and hence gives results closer to that of Experiment 2.
3527      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
3528    
3529    checkpoint53 (2004/05/06)
3530    o stable checkpoint with up to date adjoint
3531      TLM tests only run for 1st grdchk at the moment. Its unclear if
3532      this is a code problem or a problem with resetting code for g_
3533      variables that is being autogenerated wrong.
3534      Otherwise:
3535       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
3536       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
3537         are both still in chaos following their security messes.
3538    
3539    checkpoint52n_post (2004/05/06)
3540    o various build (mostly genmake2) changes including:
3541      - ability to build/run more easily within Cygwin and MacOS X
3542      - more complicated Makefiles with a stronger dependence on Gnu Make
3543    o pkg/seaice modifications
3544      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
3545        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
3546        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
3547      - changed proxy for geostrophic velocity and updated
3548        verification/lab_sea/results/* accordingly
3549      - removed ADI dynamic solver from pkg/seaice
3550      - replaced all occurrences of 1/CSTICE or 1/CSUICE
3551        they caused a segmentation fault under certain circumstances
3552      - removed unused field WATR
3553    o bug fix in exf-package:
3554      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
3555         now reflect that.
3556    o small fixes in the cal-package:
3557      - set reference date to first of January for the 'model'-calendar
3558      - failing of cal_CheckDate in cal_FullDate now actually results in a
3559        warning
3560    o small modifications in exf-package to increase flexibility:
3561      - change climtempfreeze from a constant to a runtime parameter that
3562        is specified in data.exf_clim (default = -1.9)
3563      - introduce runtime parameter windstressmax (default = 2.0) that is
3564        specified in data.exf
3565    o fix in pkg/thsice:
3566      - update Evap (Tsf changes) to be consistent with Latent heat flux
3567      - maintain snow precipitation unchanged (even if Tsf >=0).
3568     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
3569    
3570    checkpoint52m_post (2004/04/18)
3571    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
3572      this does not change any of the results, because myIter=0 in swfrac always
3573      lead to jwtype=2 (the default anyway), but the call makes little sense
3574      as a default
3575    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
3576    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
3577      atmospheric model (AIM) to use it ; add a "slab ocean" component.
3578    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
3579    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
3580    o extending useSingleCpuIO option to work with new exch2 I/O format
3581      - old-style, missing-tile I/O is still accessible by defining CPP
3582        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
3583    o monitor package can write to NetCDF files and/or STDOUT
3584    o fix re-definition bug in MNC_GRID_INIT_ALL()
3585    o doc/api_reference added
3586      - a framework for building an API Reference Manual using all
3587        the "protex" comments embedded in the code
3588      - see pkg/generic_advdiff, pkg/mnc for examples
3589    o MNC:
3590      - make myThid the last argument for all subroutines
3591      - new default for the grid files: NO halos
3592      - add useMNC and other run-time flags
3593      - separate per-file-group handling of the unlimited dimension
3594      - early initialization of MNC w/ flags read at the eeboot stage
3595        and lookup tables set in initialize_fixed
3596      - write all MNC output to a freshly-created directory
3597    o thermodynamics sea-ice (thsice) is now tested with testreport.
3598    o test exp. advect_cs: use the standard cs32 grid ; update output.
3599    o Added functionality to grdchk:
3600      pick global i,j,k position (or nearest wet) where to perform check.
3601    
3602    checkpoint52l_post (2004/03/11)
3603    o new land formulation:
3604      a) use ground enthalpy as prognostic variable to ensure exact
3605         energy conservation.
3606      b) account for water temperature and for latent heat of freezing
3607         in all processes (rain, run-off, ground storage)
3608      c) compute surface and ground temperature implicitly.
3609    o aim_v23 modification for new land model:
3610      a) Treat separately land / ocean / sea-ice surface fluxes
3611         to allow implicit computation of land & sea-ice surface temp.
3612      b) add snow precipitation.
3613    checkpoint52l_pre (2004/03/11)
3614    
3615    o fix problem (when 1 tile is empty) in min/max monitor.
3616    o fix bug in timeAve (u,vZetatave in common block)
3617    o no restoring terms under ice for pkg/seaice
3618    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
3619    o bug fix for pkg/seaice pickups
3620    o change MNC call locations and add coordinate attributes
3621    o mask vorticity at the corner ; affects global_ocean.cs output
3622    o fix ini_curvilinear_grid ; test CS experiments with mpi
3623    o aim.5l_cs: modify sea-ice fraction input file ; update output
3624    o exf: Adding simple range check routine for exf fields after read
3625    
3626    checkpoint52k_post (2004/02/23)
3627    o removed top-level directory "diags"
3628      - we migrated these functions to pkg/timeave a long time ago
3629    o fixed bug introduced in pkg/monitor
3630    o accuracy ctrlprec = 32 insuffient for gradient checks using
3631      averaged fields (I/O via cost_averages)
3632      -> use ctrl.h in active_file*.F to control I/O precision.
3633    o paramter list of CALL ADTHE_MAIN_LOOP
3634    o added initial do_the_model_io to ecco
3635    o set all ...Freq to zero after cost_final
3636      taveFreq, dumpFreq, pChkptFreq
3637    o MAIN and ECCO differentiability restored
3638    
3639    checkpoint52j_post (2004/02/18)
3640    o fix nchklev in tamc.h for global_ocean...
3641    o Bringing flow and store directives up-to-date
3642    o Really weird thing!
3643      call do_the_model_io from the_main_loop with parameters
3644      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
3645      TAF places a faulty re-call of initialise_varia
3646      after cost_final call which should not be there!
3647    checkpoint52j_pre (2004/02/03)
3648    
3649    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
3650      error messages
3651    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
3652    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
3653      debug output
3654    o modfied mdsio_writefield.F to handle non-global files under exch2
3655    o update AIM Cubed-Sphere exp (aim.5l_cs):
3656      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
3657    o update AIM Equatorial Channel exp:
3658      use standard aim_v23 pkg and change the SST fields to be more realistic.
3659    o globalFile now works with exch2
3660    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
3661      mon_vort3.F to make exch2 friendly with >1 tile per cube face
3662    o limit timeave output for hi-res integrations
3663    
3664    checkpoint52i_post (2004/01/21)
3665    o removed CPP_EEOPTIONS.h from verification/*/code
3666    o updated the tiling for global_ocean_pressure
3667    checkpoint52i_pre (2004/01/20)
3668    
3669    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
3670      the old pkg/aim).
3671    
3672    checkpoint52h_pre (2004/01/20)
3673    o shortened offending lines in exch2_send_rx?.template
3674    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
3675    o genmake2: add build & execute test for NetCDF code
3676    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
3677      old grid files, moved CPP_EEMACROS.h to pkg/exch2
3678    o added useSingleCPUIO flag to monitor.F and mon_out.F
3679    o added temporary hack for sea-ice dynamics on the cube:
3680      metric terms are ignored and it is assumed that
3681      there is no sea-ice on cube faces 1, 2, 4, and 5.
3682    
3683    checkpoint52f_post (2004/01/09)
3684    o added exch2 cube routines to pkg/exch2
3685    o modified hs94.cs-32x32x5 to use it
3686    o added new grid files to hs94.cs-32x32x5
3687    checkpoint52f_pre (2004/01/07)
3688    
3689    checkpoint52e_post (2004/01/07)
3690    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
3691      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
3692    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
3693      to work with implicit vertical advection and AB ;
3694    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
3695    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
3696     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
3697    checkpoint52e_pre (2004/01/02)
3698    
3699    o fix bug in impldiff when Nr=1 or Nr=2.
3700    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
3701    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
3702    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
3703      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
3704    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
3705    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
3706    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
3707    
3708    checkpoint52d_post (2003/12/16)
3709    o re-tiled many expts to allow comparison in multi-processor mode
3710      - updated output accordingly
3711      - changed hs94.128x64x5 to use intial T from file rather than use the
3712        random number generator
3713    o add infrastructure in model routines for fizhi and gridalt packages
3714  o change global_ocean.cs32x15 because of Pb with GM on CS-grid.  o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
3715  o changes to permit hi-res, cubed-sphere, configuration  o changes to permit hi-res, cubed-sphere, configuration
3716    - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F    - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
# Line 14  o changes to permit hi-res, cubed-sphere Line 3722  o changes to permit hi-res, cubed-sphere
3722     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
3723     complete with example surface forcing files and matlab scripts to look     complete with example surface forcing files and matlab scripts to look
3724     at the output and compare it with that of global_ocean.cs32x15.)     at the output and compare it with that of global_ocean.cs32x15.)
3725    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
3726       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
3727       to conform to the common rule.
3728    o check-in the first version of the coupler + interfaces for multi-components
3729       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
3730       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
3731       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
3732       - ocean and atmos. share the same horizontal grid (no interpolation).
3733       - exchanges between component and coupler is done in forward_step
3734    o new verification experiment, cpl_aim+ocn:
3735       coupled ocean - AIM atmosphere on cs32 grid.
3736    
3737  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
3738  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
3739  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
3740    
3741  checkpoint52c_post  checkpoint52c_post (2003/11/25)
3742  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
3743    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
3744    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 33  o Removed all CPP options for cal packag Line 3752  o Removed all CPP options for cal packag
3752  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
3753  o corrected key comp. for passkey  o corrected key comp. for passkey
3754    
3755  checkpoint52b_post  checkpoint52b_post (2003/11/23)
3756  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
3757   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
3758   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 41  o new version: "thsice" of thermodynamic Line 3760  o new version: "thsice" of thermodynamic
3760   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
3761     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
3762  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
3763  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
3764    
3765  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
3766  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 51  o missing PTRACERS headers in some routi Line 3770  o missing PTRACERS headers in some routi
3770  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
3771    to ensure proper customization    to ensure proper customization
3772    
3773  checkpoint52a_post  checkpoint52a_post (2003/11/17)
3774  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
3775    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3776    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 66  o fix problem with ECCO-related divided Line 3785  o fix problem with ECCO-related divided
3785    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
3786    but no warning issued by TAF    but no warning issued by TAF
3787    
3788  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
3789  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
3790    
3791  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
3792  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
3793    
3794  checkpoint51u_post  checkpoint51u_post (2003/11/06)
3795  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
3796    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
3797  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 87  o top level routines the_main_loop, forw Line 3806  o top level routines the_main_loop, forw
3806    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
3807  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
3808    
3809  checkpoint51t_post  checkpoint51t_post (2003/11/04)
3810  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
3811    
3812  checkpoint51s_post  checkpoint51s_post (2003/11/04)
3813  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
3814  o pkg/grdchk  o pkg/grdchk
3815    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 99  o pkg/grdchk Line 3818  o pkg/grdchk
3818    - additional high-precision output for testreport    - additional high-precision output for testreport
3819      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
3820    
3821  checkpoint51r_post  checkpoint51r_post (2003/11/03)
3822  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
3823  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
3824    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
3825    
3826  checkpoint51q_post  checkpoint51q_post (2003/10/30)
3827  o cd_code:  o cd_code:
3828    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
3829    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 120  o ctrl package totally restructured Line 3839  o ctrl package totally restructured
3839    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
3840  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
3841    
3842  checkpoint51p_post  checkpoint51p_post (2003/10/30)
3843  o create initial cd_code package  o create initial cd_code package
3844    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
3845      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 135  o create initial cd_code package Line 3854  o create initial cd_code package
3854  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
3855  o cleanup testreport  o cleanup testreport
3856    
3857  checkpoint51o_post  checkpoint51o_post (2003/10/27)
3858  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
3859    - carbon/    - carbon/
3860    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 156  o Correcting initialisations for fVerU, Line 3875  o Correcting initialisations for fVerU,
3875  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
3876    fVerU, fVerV    fVerU, fVerV
3877  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
3878  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
3879    
3880  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
3881  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 164  o added the [#include "AD_CONFIG.h"] sta Line 3883  o added the [#include "AD_CONFIG.h"] sta
3883   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
3884   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
3885    
3886  checkpoint51n_post  checkpoint51n_post (2003/10/23)
3887  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
3888    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3889    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 173  o modifications to make FREEZE flux visi Line 3892  o modifications to make FREEZE flux visi
3892       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
3893  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
3894    
3895  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
3896  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
3897  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
3898    defines:    defines:
# Line 181  o added [#include "AD_CONFIG.h"] to all Line 3900  o added [#include "AD_CONFIG.h"] to all
3900    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
3901    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
3902    
3903  checkpoint51m_post  checkpoint51m_post (2003/10/21)
3904  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
3905    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
3906    - various cleanups related to package handling    - various cleanups related to package handling
3907    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
3908    
3909  checkpoint51l_post  checkpoint51l_post (2003/10/20)
3910  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
3911   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
3912   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
3913   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
3914     model integration time     model integration time
3915    
3916  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
3917  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)
3918  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.
3919  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
3920     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
3921    
3922  checkpoint51k_post  checkpoint51k_post (2003/10/16)
3923  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
3924   - 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):
3925     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 214  o added an include barrier to the defaul Line 3933  o added an include barrier to the defaul
3933    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
3934  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
3935    
3936  checkpoint51j_post  checkpoint51j_post (2003/10/10)
3937  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
3938  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
3939  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 228  o Moving pkg-specific flow directives to Line 3947  o Moving pkg-specific flow directives to
3947         - pkg_ad_diff.list         - pkg_ad_diff.list
3948         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
3949    
3950  checkpoint51i_post  checkpoint51i_post (2003/10/09)
3951  o merge of the branch-genmake2  o merge of the branch-genmake2
3952    - knowingly breaks the older genmake    - knowingly breaks the older genmake
3953    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
3954    - new testreport supersedes older testscript    - new testreport supersedes older testscript
3955  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
3956  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
3957    
3958  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
3959  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 246  o modify gchem pkg to be more versatile Line 3965  o modify gchem pkg to be more versatile
3965  o modifications to clean up dic pkg  o modifications to clean up dic pkg
3966  o add pkg/cfc  o add pkg/cfc
3967    
3968  checkpoint51g_post  checkpoint51g_post (2003/10/02)
3969  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
3970  o start removing verification/vero/  o start removing verification/vero/
3971  o update AD-related stuff  o update AD-related stuff
# Line 254  o update AD-related stuff Line 3973  o update AD-related stuff
3973  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
3974    vector invariant setup    vector invariant setup
3975    
3976  checkpoint51f_post  checkpoint51f_post (2003/10/02)
3977  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)
3978  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
3979    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
3980    
3981  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
3982  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
3983      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
3984    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 271  o Bug fix to pkg/ptracers, pkg/generic_a Line 3990  o Bug fix to pkg/ptracers, pkg/generic_a
3990      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
3991      non-local transport term.      non-local transport term.
3992    
3993  checkpoint51e_post  checkpoint51e_post (2003/08/03)
3994  o pkg/mom_vecinv:  o pkg/mom_vecinv:
3995    - 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)
3996    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 281  o atmospheric geopotential: - include wa Line 4000  o atmospheric geopotential: - include wa
4000  o land pkg: read initial state from files.  o land pkg: read initial state from files.
4001  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
4002    
4003  checkpoint51d_post  checkpoint51d_post (2003/07/18)
4004  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
4005    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
4006  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 294  o Use cluster local disks for purely loc Line 4013  o Use cluster local disks for purely loc
4013    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
4014    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
4015    
4016  checkpoint51c_post  checkpoint51c_post (2003/07/08)
4017  o introducing integer flag debugLevel  o introducing integer flag debugLevel
4018    - debLevZero: suppress all output    - debLevZero: suppress all output
4019    - debLevA: standard    - debLevA: standard
# Line 317  o added verification for adjoint with pt Line 4036  o added verification for adjoint with pt
4036    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
4037  <<<checkpoint51b_pre  <<<checkpoint51b_pre
4038    
4039  checkpoint51a_post  checkpoint51a_post (2003/06/25)
4040  o added code for biogeochemistry package  o added code for biogeochemistry package
4041    - new pkgs: dic, gchem    - new pkgs: dic, gchem
4042    - new subroutine in ptracers    - new subroutine in ptracers
4043  o modify code for biogeo packages  o modify code for biogeo packages
4044    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
4045    
4046  checkpoint51  checkpoint51 (2003/06/24)
4047  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
4048    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
4049    kept separate packages    kept separate packages
# Line 332  o merged improved packages from ecco-bra Line 4051  o merged improved packages from ecco-bra
4051  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
4052    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
4053    
4054  checkpoint50i_post  checkpoint50i_post (2003/06/23)
4055  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
4056    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
4057    - 1st step: this one is differentiable    - 1st step: this one is differentiable
4058    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
4059                from ecco-branch)                from ecco-branch)
4060    
4061  checkpoint50h_post  checkpoint50h_post (2003/06/20)
4062  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
4063  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
4064  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 348  o New variable in PARM03 for more flexib Line 4067  o New variable in PARM03 for more flexib
4067  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
4068    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
4069    
4070  checkpoint50g_post  checkpoint50g_post (2003/05/23)
4071  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
4072    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
4073    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
4074      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
4075    
4076  checkpoint50f_post  checkpoint50f_post (2003/05/23)
4077  o exf totally restructured  o exf totally restructured
4078    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
4079      and made sure it's still differentiable      and made sure it's still differentiable
# Line 362  o exf totally restructured Line 4081  o exf totally restructured
4081    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
4082    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
4083    
4084  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
4085   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 ;
4086        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
4087   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 372  checkpoint50f_pre Line 4091  checkpoint50f_pre
4091   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
4092   o removed lots of single quotes from comments   o removed lots of single quotes from comments
4093    
4094  checkpoint50e_post  checkpoint50e_post (2003/05/14)
4095  o make KPP work with PTRACERS  o make KPP work with PTRACERS
4096   - 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
4097     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
4098   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
4099     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
4100  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
4101  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
4102    
4103  checkpoint50d_post  checkpoint50d_post (2003/05/13)
4104  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
4105    files analogous to write_state.F    files analogous to write_state.F
4106  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,
4107    analogous to the cg2d-related output.    analogous to the cg2d-related output.
4108  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,
4109    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
4110  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
4111    
4112  checkpoint50c_post  checkpoint50c_post (2003/05/12)
4113  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)
4114  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
4115  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.
4116  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
4117  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
4118    
4119  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
4120  Merging from release1_p13:  Merging from release1_p13:
4121  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
4122  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4123    
4124  checkpoint50b_post  checkpoint50b_post (2003/04/17)
4125  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
4126  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
4127    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 411  o new flag "useCDscheme" (default=F); re Line 4130  o new flag "useCDscheme" (default=F); re
4130  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
4131     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
4132    
4133  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
4134  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
4135  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
4136    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
4137    
4138  checkpoint50a_post  checkpoint50a_post (2003/03/21)
4139  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
4140    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
4141    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
4142    in contradiction with new key itdkey.    in contradiction with new key itdkey.
4143    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
4144    
4145  checkpoint50  checkpoint50 (2003/03/08)
4146  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
4147    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
4148  - bug fix in find_alpha  - bug fix in find_alpha
# Line 431  checkpoint50 Line 4150  checkpoint50
4150  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
4151  - merged some sliced AD support routines  - merged some sliced AD support routines
4152    
4153  checkpoint49  checkpoint49 (2003/03/06)
4154  merged from ecco-branch:  merged from ecco-branch:
4155  o exf:  o exf:
4156    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 469  o DIVA: Line 4188  o DIVA:
4188    (see MITgcm manual).    (see MITgcm manual).
4189  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
4190    
4191  checkpoint48i_post  checkpoint48i_post (2003/03/05)
4192  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
4193    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
4194    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 487  o Modif. for DIVA: Line 4206  o Modif. for DIVA:
4206    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
4207    only relevant for ecco-branch)    only relevant for ecco-branch)
4208    
4209  checkpoint48h_post  checkpoint48h_post (2003/02/28)
4210  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
4211  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
4212  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4213  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
4214    
4215  checkpoint48g_post  checkpoint48g_post (2003/02/18)
4216  --- EOS:  --- EOS:
4217  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
4218    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 507  o accurate phiHyd when using interface-W Line 4226  o accurate phiHyd when using interface-W
4226   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
4227  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
4228    
4229  checkpoint48f_post  checkpoint48f_post (2003/02/18)
4230  Merging from release1_p12:  Merging from release1_p12:
4231  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
4232    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 535  o pkg/seaice: Line 4254  o pkg/seaice:
4254    - adjoint-friendly modifications    - adjoint-friendly modifications
4255    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
4256    
4257  checkpoint48e_post  checkpoint48e_post (2003/02/12)
4258  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)
4259  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
4260    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 546  o following exp works with Olx=Oly=2 (an Line 4265  o following exp works with Olx=Oly=2 (an
4265      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
4266    (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)
4267    
4268  checkpoint48d_post  checkpoint48d_post (2003/02/09)
4269  o in preparation for r*:  o in preparation for r*:
4270   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
4271      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 554  o in preparation for r*: Line 4273  o in preparation for r*:
4273      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
4274    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
4275    
4276  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
4277  o in preparation for r*:  o in preparation for r*:
4278    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.
4279    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.
4280    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.
4281  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
4282    
4283  checkpoint48c_post  checkpoint48c_post (2003/02/06)
4284  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
4285  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
4286    
4287  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
4288  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
4289  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)
4290    
4291  checkpoint48b_post  checkpoint48b_post (2003/01/27)
4292  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
4293   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
4294  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
4295    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
4296    
4297  checkpoint48a_post  checkpoint48a_post (2003/01/24)
4298  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
4299     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
4300    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
4301                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
4302    
4303  checkpoint48  checkpoint48 (2003/01/23)
4304  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')
4305    
4306  checkpoint47j_post  checkpoint47j_post (2003/01/21)
4307  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.
4308  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
4309  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 603  o Yet more changes in gmredi: Line 4322  o Yet more changes in gmredi:
4322      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
4323  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
4324    
4325  checkpoint47i_post  checkpoint47i_post (2003/01/13)
4326  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.
4327  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)
4328    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 619  o case GM_BOLUS_ADVEC should be cleaned Line 4338  o case GM_BOLUS_ADVEC should be cleaned
4338    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
4339  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
4340    
4341  checkpoint47g_post  checkpoint47g_post (2003/01/10)
4342  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
4343    (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)
4344  o After TAF bug fix:  o After TAF bug fix:
# Line 645  Gradient checks OK for Line 4364  Gradient checks OK for
4364  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
4365  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
4366    
4367  checkpoint47f_post  checkpoint47f_post (2002/12/28)
4368  Merging from release1_p10:  Merging from release1_p10:
4369  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
4370    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 657  o modifications for using pkg/exf with p Line 4376  o modifications for using pkg/exf with p
4376    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
4377      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
4378    
4379  checkpoint47e_post  checkpoint47e_post (2002/12/27)
4380  o created a tag prior to creating a branch  o created a tag prior to creating a branch
4381    
4382  checkpoint47d_post  checkpoint47d_post (2002/12/16)
4383  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
4384    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
4385  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
4386    oceanic pressure coordinates code    oceanic pressure coordinates code
4387  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
4388    also described in the tutorial section of the manual    also described in the tutorial section of the manual
4389  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
4390    
4391  checkpoint47c_post  checkpoint47c_post (2002/12/16)
4392  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
4393    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
4394    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 681  o OCEANICP & realFreshWater: include P-E Line 4400  o OCEANICP & realFreshWater: include P-E
4400    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
4401  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
4402    
4403  checkpoint47b_post  checkpoint47b_post (2002/12/05)
4404  Merging from release1_p9:  Merging from release1_p9:
4405  o pkg/seaice  o pkg/seaice
4406    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 698  o verification/lab_sea Line 4417  o verification/lab_sea
4417    - added missing matlab routines    - added missing matlab routines
4418    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
4419    
4420  checkpoint47a_post  checkpoint47a_post (2002/11/23)
4421  o new pkg: aim_v23  o new pkg: aim_v23
4422   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
4423     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 715  o bulk_force and therm_seaice Line 4434  o bulk_force and therm_seaice
4434  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
4435     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
4436    
4437  checkpoint47  checkpoint47 (2002/11/15)
4438  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
4439  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
4440  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 744  o Updated verification/carbon/ Line 4463  o Updated verification/carbon/
4463    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
4464    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
4465    
4466  checkpoint46n_post  checkpoint46n_post (2002/11/12)
4467  Merging from release1_p8:  Merging from release1_p8:
4468  o verification/natl_box:  o verification/natl_box:
4469    updating new external_fields_load routine    updating new external_fields_load routine
# Line 798  o Adding new verification experiment glo Line 4517  o Adding new verification experiment glo
4517    the exf (and cal) package instead of the    the exf (and cal) package instead of the
4518    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
4519    
4520  checkpoint46m_post  checkpoint46m_post (2002/11/07)
4521  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
4522  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
4523    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 811  o introduced flag for controllin non-hyd Line 4530  o introduced flag for controllin non-hyd
4530  o removed gravitySign from PARM04  o removed gravitySign from PARM04
4531  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
4532    
4533  checkpoint46l_post  checkpoint46l_post (2002/11/01)
4534  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
4535   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
4536     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 824  o made convective adjustment work with p Line 4543  o made convective adjustment work with p
4543     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
4544     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
4545     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
4546  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
4547    
4548  checkpoint46k_post  checkpoint46k_post (2002/10/23)
4549  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
4550   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
4551   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 840  o S/R aim_initialise.F replace S/R aim_i Line 4559  o S/R aim_initialise.F replace S/R aim_i
4559   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
4560   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
4561    
4562  checkpoint46j_post  checkpoint46j_post (2002/10/07)
4563  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
4564  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
4565  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)
4566  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
4567  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
4568    
4569  checkpoint46i_post  checkpoint46i_post (2002/09/25)
4570  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
4571    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
4572    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
4573    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 !
4574    
4575  checkpoint46h_post  checkpoint46h_post (2002/09/25)
4576  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
4577    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
4578      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 863  o introduced new parameter rhoConstFresh Line 4582  o introduced new parameter rhoConstFresh
4582    value is 999.8 kg/m^3    value is 999.8 kg/m^3
4583  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
4584    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
4585  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
4586    
4587   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
4588   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
4589   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
4590    
4591  checkpoint46g_post  checkpoint46g_post (2002/09/18)
4592  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
4593    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
4594    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 887  o cleaned up find_rho Line 4606  o cleaned up find_rho
4606    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
4607  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
4608    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
4609  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
4610    
4611  checkpoint46f_post  checkpoint46f_post (2002/09/16)
4612  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
4613    - extended active file handling to g_... files    - extended active file handling to g_... files
4614    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 897  o Enable tangent linear (forward mode) g Line 4616  o Enable tangent linear (forward mode) g
4616  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
4617  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
4618    
4619  checkpoint46e_post  checkpoint46e_post (2002/09/05)
4620  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
4621    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
4622    - 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 906  o Added new equation of state -> MDJWF Line 4625  o Added new equation of state -> MDJWF
4625    - 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
4626      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
4627      expect perfect matches for those      expect perfect matches for those
4628  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
4629    
4630  checkpoint46d_post  checkpoint46d_post (2002/08/19)
4631  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
4632    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
4633    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
4634    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
4635  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)
4636    in find_alpha/beta.    in find_alpha/beta.
4637  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
4638    
4639  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)
4640    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
4641    
4642  checkpoint46c_post  checkpoint46c_post (2002/08/15)
4643  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
4644   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
4645   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
4646      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).
4647   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
4648   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
4649  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
4650    
4651  checkpoint46b_post  checkpoint46b_post (2002/08/07)
4652  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
4653    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
4654    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 938  o Added UNESCO EOS, but not recommended Line 4657  o Added UNESCO EOS, but not recommended
4657    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
4658  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
4659    unesco.f to be used with POLY3    unesco.f to be used with POLY3
4660  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
4661    
4662  checkpoint46a_post  checkpoint46a_post (2002/07/31)
4663  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
4664    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
4665    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
4666  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
4667  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
4668  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
4669    
4670  checkpoint46  checkpoint46 (2002/07/13)
4671  further merges from release1_p5  further merges from release1_p5
4672  o new ctrl package  o new ctrl package
4673    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 975  o added hooks for Eliassen Palm fluxes ( Line 4694  o added hooks for Eliassen Palm fluxes (
4694  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
4695  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
4696    
4697  checkpoint45d_post  checkpoint45d_post (2002/07/12)
4698  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
4699  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
4700    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 989  o add new flags: Line 4708  o add new flags:
4708   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
4709  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
4710    
4711  checkpoint45c_post  checkpoint45c_post (2002/05/30)
4712  o Removed f90 comments ("!")  o Removed f90 comments ("!")
4713  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
4714    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 997  o modifications to gradient check packag Line 4716  o modifications to gradient check packag
4716    - enable centered differences    - enable centered differences
4717    - modified format of standard output    - modified format of standard output
4718    
4719  checkpoint45b_post  checkpoint45b_post (2002/05/30)
4720  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
4721  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
4722  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1009  o in initialise_varia, moved call packag Line 4728  o in initialise_varia, moved call packag
4728    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
4729  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
4730    
4731  checkpoint45a_post  checkpoint45a_post (2002/05/01)
4732  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
4733  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
4734  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 1029  o errorMessageUnit set non-equal zero in Line 4748  o errorMessageUnit set non-equal zero in
4748    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
4749  o modified carbon verif.  o modified carbon verif.
4750    
4751  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
4752  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
4753    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
4754  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
4755    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.
4756    
4757  checkpoint44g_post  checkpoint44g_post (2002/03/05)
4758  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
4759    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
4760    
# Line 1100  o merge of relevant stuff from the ecco- Line 4819  o merge of relevant stuff from the ecco-
4819  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
4820  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
4821    
4822  checkpoint44  checkpoint44 (2002/01/18)
4823  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
4824  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)
4825  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 1108  o update AIM experiments (NCEP input fil Line 4827  o update AIM experiments (NCEP input fil
4827  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
4828  o added some stuff for AD  o added some stuff for AD
4829    
4830  checkpoint43  checkpoint43 (2001/09/28)
4831  o added two new advection tests  o added two new advection tests
4832  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
4833  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
4834  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
4835    
4836  checkpoint42  checkpoint42 (2001/09/27)
4837    Fixed AD-related problems:    Fixed AD-related problems:
4838  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
4839    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1126  o Modified store directives for split of Line 4845  o Modified store directives for split of
4845    for the case ALLOW_KPP    for the case ALLOW_KPP
4846  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
4847    
4848  checkpoint41  checkpoint41 (2001/09/27)
4849  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
4850    to work with protex    to work with protex
4851    
4852  checkpoint40  checkpoint40 (2001/09/27)
4853  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
4854  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
4855  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1139  o more mods for non-linear free-surface Line 4858  o more mods for non-linear free-surface
4858  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
4859  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
4860    
4861  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
4862  o added DST advection schemes  o added DST advection schemes
4863  o fix MPI bug on SGI's  o fix MPI bug on SGI's
4864  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1149  o changes to commenting of arguments for Line 4868  o changes to commenting of arguments for
4868  o added/updated many matlab scripts  o added/updated many matlab scripts
4869  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
4870        
4871  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
4872  o new package rw/  o new package rw/
4873    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
4874    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1168  o TAMC-related update to cope with mom_f Line 4887  o TAMC-related update to cope with mom_f
4887    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
4888    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
4889    
4890  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
4891  o bug fix in dynamics.F  o bug fix in dynamics.F
4892    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
4893  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
4894  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
4895    related to TAF    related to TAF
4896    
4897  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
4898  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
4899  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
4900    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1183  o corresponding split of calc_diffusivit Line 4902  o corresponding split of calc_diffusivit
4902  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
4903  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
4904    
4905  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
4906  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
4907    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
4908  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 1197  o added new expt "solid-body.cs-32x32x1" Line 4916  o added new expt "solid-body.cs-32x32x1"
4916    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
4917      is not necessarily any better than the current one...      is not necessarily any better than the current one...
4918    
4919  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
4920  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
4921    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
4922  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1205  o extended iMin,jMin range for calc_comm Line 4924  o extended iMin,jMin range for calc_comm
4924  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
4925  o a few minor updates and fixes  o a few minor updates and fixes
4926    
4927  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
4928  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
4929  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
4930  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
4931    
4932  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
4933  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
4934  o Added gradient check package  o Added gradient check package
4935  o Added routines for passive tracer handling  o Added routines for passive tracer handling
4936  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
4937    
4938  checkpoint39  checkpoint39 (2001/05/14)
4939   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
4940     (mainly missing or wrong directives)     (mainly missing or wrong directives)
4941   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 1230  checkpoint39 Line 4949  checkpoint39
4949           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
4950   o disabled some packages by default in genmake   o disabled some packages by default in genmake
4951    
4952  checkpoint38  checkpoint38 (2001/04/10)
4953   o see notes_c37_adj.txt   o see notes_c37_adj.txt
4954   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
4955   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1238  checkpoint38 Line 4957  checkpoint38
4957     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
4958   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
4959    
4960  checkpoint37  checkpoint37 (2001/03/13)
4961   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
4962     (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
4963      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1255  checkpoint37 Line 4974  checkpoint37
4974   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
4975   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
4976    
4977  checkpoint36  checkpoint36 (2001/02/20)
4978   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
4979   o recover Time-Average diagnostics   o recover Time-Average diagnostics
4980   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
4981   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
4982    
4983  checkpoint35  checkpoint35 (2001/02/08)
4984   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
4985   o allows staggered time-stepping   o allows staggered time-stepping
4986   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
4987   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
4988    
4989  checkpoint34  checkpoint34 (2001/01/30)
4990   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
4991   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
4992     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1278  checkpoint34 Line 4997  checkpoint34
4997   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
4998   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
4999    
5000  checkpoint33  checkpoint33 (2000/11/30)
5001   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
5002   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
5003     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1296  checkpoint33 Line 5015  checkpoint33
5015       possibly use them.       possibly use them.
5016   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
5017    
5018  checkpoint32  checkpoint32 (2000/11/13)
5019   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
5020     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
5021   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1307  checkpoint32 Line 5026  checkpoint32
5026   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
5027   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
5028    
5029  checkpoint31  checkpoint31 (2000/09/11)
5030   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
5031     -> new routines packages_...F     -> new routines packages_...F
5032     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1324  checkpoint31 Line 5043  checkpoint31
5043     - not yet tested for GMRedi.     - not yet tested for GMRedi.
5044     - not yet tested for KPP.     - not yet tested for KPP.
5045    
5046  checkpoint30  checkpoint30 (2000/07/13)
5047   o Updates for OBCs   o Updates for OBCs
5048   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
5049   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1333  checkpoint30 Line 5052  checkpoint30
5052   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.)
5053     and entry for T90 in genmake     and entry for T90 in genmake
5054    
5055  checkpoint29  checkpoint29 (2000/06/21)
5056   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
5057    
5058  checkpoint28  checkpoint28 (2000/06/09)
5059   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
5060   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
5061   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 1349  checkpoint28 Line 5068  checkpoint28
5068     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
5069   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
5070    
5071  checkpoint27  checkpoint27 (2000/04/10)
5072   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
5073     formulation works properly with variable resolution.     formulation works properly with variable resolution.
5074   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 1357  checkpoint27 Line 5076  checkpoint27
5076   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
5077     in new routine ini_psurf()     in new routine ini_psurf()
5078    
5079  checkpoint26  checkpoint26 (2000/04/05)
5080   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
5081     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
5082   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 1367  checkpoint26 Line 5086  checkpoint26
5086     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
5087   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
5088    
5089  checkpoint25  checkpoint25 (2000/03/15)
5090   o updates for OBCs and NH   o updates for OBCs and NH
5091   o dramatically reduced memory usage   o dramatically reduced memory usage
5092   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 1378  checkpoint25 Line 5097  checkpoint25
5097      an explicit free-surface option)      an explicit free-surface option)
5098   o initial state input files for U and V   o initial state input files for U and V
5099    
5100  checkpoint24  checkpoint24 (1999/08/02)
5101   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
5102   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
5103   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
5104    
5105  checkpoint23  checkpoint23 (1999/05/26)
5106   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
5107   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
5108    
5109  checkpoint22  checkpoint22 (1999/05/18)
5110   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
5111   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
5112    
5113  checkpoint21  checkpoint21 (1999/05/18)
5114   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)
5115   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
5116   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
5117   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
5118    
5119  checkpoint20  checkpoint20 (1999/03/22)
5120   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
5121   o Added non-hydrostatic code   o Added non-hydrostatic code
5122   o Fixed some input data   o Fixed some input data
5123   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
5124    
5125  checkpoint19  checkpoint19 (1998/12/15)
5126   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
5127   o Added new code for open boundaries.   o Added new code for open boundaries.
5128   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 1411  checkpoint19 Line 5130  checkpoint19
5130   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
5131   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.
5132    
5133  checkpoint18  checkpoint18 (1998/11/30)
5134   o Further changes for optional code generation with   o Further changes for optional code generation with
5135     CPP - ugh!     CPP - ugh!
5136    
5137  checkpoint17  checkpoint17 (1998/11/03)
5138   o Beginning to incorporating modularity   o Beginning to incorporating modularity
5139     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
5140   o Small changes for TAMC complinace   o Small changes for TAMC complinace
5141   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
5142     configuration "exp0".     configuration "exp0".
5143    
5144  checkpoint16  checkpoint16 (1998/10/28)
5145   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
5146     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
5147     assignment is an addition.     assignment is an addition.
# Line 1430  checkpoint16 Line 5149  checkpoint16
5149     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
5150     limit ).     limit ).
5151    
5152  checkpoint15  checkpoint15 (1998/09/29)
5153   Rewrote exchange routines to allow   Rewrote exchange routines to allow
5154   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
5155   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 1439  checkpoint15 Line 5158  checkpoint15
5158     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
5159     communication method.     communication method.
5160    
5161  checkpoint14  checkpoint14 (1998/09/09)
5162   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
5163   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
5164    
5165  checkpoint13  checkpoint13 (1998/07/17)
5166   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
5167   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
5168   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 1458  branch-point-rdot Line 5177  branch-point-rdot
5177   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
5178   we've actually tested it...   we've actually tested it...
5179    
5180  checkpoint12  checkpoint12 (1998/07/08)
5181   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
5182   configure script).   configure script).
5183   Released to testers.   Released to testers.
5184    
5185  checkpoint11  checkpoint11 (1998/07/02)
5186   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
5187   and ini_masks_etc().   and ini_masks_etc().
5188    
5189  checkpoint10  checkpoint10 (1998/07/01)
5190   Introduced the configure script.   Introduced the configure script.
5191   Separated out the diags package.   Separated out the diags package.
5192   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
5193   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
5194    
5195  checkpoint9  checkpoint9 (1998/06/22)
5196   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
5197   General tidy-up.   General tidy-up.
5198   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
5199    
5200  checkpoint8  checkpoint8 (1998/06/22)
5201   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
5202   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
5203    
# Line 1488  checkpoint7-4degree-ref Line 5207  checkpoint7-4degree-ref
5207   model etc..   model etc..
5208   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
5209    
5210  checkpoint7  checkpoint7 (1998/06/15)
5211   Created by cnh   Created by cnh
5212   Simple 4 degree global simulation   Simple 4 degree global simulation
5213   configuration.   configuration.
# Line 1496  checkpoint7 Line 5215  checkpoint7
5215   hydrography, bathymetry etc   hydrography, bathymetry etc
5216   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
5217    
5218  checkpoint6  checkpoint6 (1998/06/08)
5219   Created by cnh   Created by cnh
5220   merged checkpoint5 with CD and   merged checkpoint5 with CD and
5221   spherical polar code.   spherical polar code.
5222   Still some problems with GM Redi   Still some problems with GM Redi
5223   abd full topography.   abd full topography.
5224    
5225  checkpoint5  checkpoint5 (1998/06/08)
5226   Created by AJA   Created by AJA
5227   contains updates to GM Redi   contains updates to GM Redi
5228   and reordered timestepping loop   and reordered timestepping loop
5229   for Implicit Diffusion.   for Implicit Diffusion.
5230    
5231  checkpoint4  checkpoint4 (1998/05/30)
5232   Created by cnh   Created by cnh
5233   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
5234   grid variations are limited.   grid variations are limited.
5235   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
5236   for generation.   for generation.
5237    
5238  checkpoint3  checkpoint3 (1998/05/26)
5239   Created by cnh   Created by cnh
5240   Added extra flags for runtime options   Added extra flags for runtime options
5241   Added this file   Added this file

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