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revision 1.1018 by jmc, Sun Aug 24 22:03:51 2008 UTC revision 1.1407 by jmc, Thu Apr 14 22:23:58 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o external_fields_load:
8      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
9       interpolation weights) to use in a periodic time-series ; do not divide by
10       time-step to convert to integer:
11       - this fixes case where externForcingPeriod is not multiple of time-step
12          (Thanks to Christopher L. Wolfe)
13       - this fixes case where externForcingPeriod is an odd multiple of time-step
14         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
15      store index of time-record which is currently loaded:
16       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
17       - needed for the adjoint but not yet used because of extensive recomputations;
18         (to be fixed soon)
19    
20    checkpoint62v (2011/04/02)
21    o verification/1D_ocean_ice_column added to test Ian Fenty's
22      pkg/seaice_growth.F modifications for improving sea ice code differentiability
23    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
24      (new velocity statistics after changing maskInW & maskInS definition)
25    o pkg/generic_advdiff with OBCS:
26      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
27      equivalent to assumption of no tracer gradient outside the OB region.
28      This will affect the results if using obcs+biharmonic diffusion.
29      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
30    o pkg/obcs:
31      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
32      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
33      in Interior region. No impact on solution but affects Velocity monitor stats.
34    o pkg/ptracers (adjoint)
35      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
36      tape file for each tracer
37    o model/inc/src and pkg/autodiff: add parameters that allow to turn
38      of parts of the adjoint code at run time. For now, there are only
39      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
40      parameters are set in data.pkg.
41      This is the lazy coward's version of doing this, but still useful for
42      debugging. In order to do it right, everything needs to be moved to
43      pkg/autodiff.
44    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
45      the end; this fixes the adjoint balancing code for open boundaries.
46    o pkg/ctrl:
47      - change behavior of xx_${varname}period to be analogous to exf-conventions:
48        xx_${varname}period =   0.,  means time-independent control part
49        xx_${varname}period = -12., means one-year-periodic monthly control part
50      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
51        clean up ctrl_init a little, remove unused variables
52      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
53      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
54    
55    checkpoint62u (2011/03/15)
56    o model/src:
57      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
58        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
59      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
60        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
61    o pkg/ctrl/obcs/ecco:
62      - remove obsolete, unused, and partially broken code:
63        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
64        ALLOW_CTRL_OBCS_BALANCE
65      - put a stop statement into ecco/cost_obcsvol.F, but also add
66        cost_obcsvol to ecco_ad_diff.list
67    o pkg/ecco: fix counting cost function contributions for obcs (code
68      by Matt M.) and diffkr for diagnostics
69    o pkg/ecco, pkg/ctrl, pkg/grdchk:
70      add cost penalty terms for initial uvel, vvel, eta controls
71      and I/O for prior error files
72    o pkg/mdsio:
73       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
74       (new argument) to check for tiled file in mdsioLocalDir : this fix the
75       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
76    o pkg/ctrl:
77     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
78       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
79       unused and superfluous variables
80     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
81    o pkg/ecco
82     - enable adjoint of Stevens OB
83    o pkg/ctrl/ecco/grdchk:
84      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
85        Fortunately, we do not have any tests for the numerous cpp-flagged
86        option of "obcs as control parameters" so we will never know
87        if this is an improvement (but at least now things compile).
88      - remove an obsolete initialization from ecco_cost_init_barfiles.F
89      - fix some problems within never used ifdefs to make the code compile
90    o pkg/obcs:
91     - Refine Interior mask definition to work with more complex OB (e.g.
92       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
93       read in Interior mask from file. Check if Interior mask is consistent
94       with OB list of indices.
95    o pkg/seaice
96     - beginning code for a seaice tracer package,
97       but currently only used for seaice age: SEAICE_AGE
98       SEAICE_num = 4
99       iTracer = 1: area-weighted ice age
100               = 2: volume-weighted ice age
101               = 3, 4: template for one-year vs. multi-year ice
102       data.seaice has new namelist SEAICE_PARM03 for arrays related to
103       SEAICE_num
104    
105    checkpoint62t (2011/03/05)
106    o pkg/obcs:
107     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
108       then normal component. This ensures that the normal component is set
109       correctly even when it conficts with tangential setting from an other OB.
110       Affects results of test-experiment seaice_obcs: update the output.txt
111    o pkg/obcs:
112     - add code to monitor statistics of dynamical fields at OB.
113     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
114       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
115       - change default: balance the Net inflow through all OB (instead of balancing
116         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
117     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
118       to match Nortern OB inflow (OBCS_balanceFacN=0).
119    o pkg/seaice:
120     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
121    o pkg/seaice (seaice_growth v 1.113):
122     - reverting seaice_growth to v 1.111 in order to have code with exact bit
123       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
124       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
125       runtime flag SEAICEareaFormula is kept but is inactive
126    o model/src:
127     - add new param to scale curvilinear grid distance and area when using
128       a different sphere radius from the grid-files.
129     - test/check multi-threads EXCH applied to local variable (cg2d_x)
130    o adjoint:
131     - enable adjoint of Stevens OB
132     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
133       (a bit delicate because of potentially modified adj. common block structure;
134       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
135    
136    checkpoint62s (2011/02/15)
137    o pkg/seaice (seaice_growth v 1.112):
138     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
139       computing the ice cover tendency from effective thickness tendencies. Include
140       Ian Fenty's formula.
141     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
142       SEAICEareaFormula.
143     - simplify notations for the various d_HEFF/d_AREA terms.
144    o pkg/gmredi:
145     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
146       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
147       add a verification test-run (front_relax.bvp) to test GM_useBVP.
148    o pkg/seaice (seaice_growth v 1.111):
149     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
150     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
151       also melt ice.
152    o pkg/seaice:
153     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
154     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
155    o pkg/cheapaml:
156     - from Nico Wienders: New version of this package.
157    o pkg/flt:
158     - add CPP options to prevent floats to re-enter the opposite side of
159       a periodic domain (default: keep periodicity)
160    o pkg/gmredi:
161     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
162       (needed for multi-dim advection).
163     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
164    o model/src:
165     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
166    o tutorial_tracer_adjsens
167     - extend to NLFS and replace maskC by hFacC
168       (change reference output accordingly)
169    
170    checkpoint62r (2011/01/24)
171    o testreport:
172     - add option -deloutp (-do) to remove output file after successful run
173     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
174       extract exact list of procs from this file ; adjust COMMAND by
175       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
176    o pkg/ecco: replace old ineffective way of penalizing deviations from
177      first guess (of obcs) with code by Matt Mazloff
178    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
179      exf/cal
180      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
181        and handle case of obcs?period == 0
182        Not affected by these changes: There is still an inconsistency in
183        the computation of start/endrec for the obcs variables for ALLOW_CAL
184        defined (see comment by Menemenlis, 7-Mar-2003)
185      - make S/R ctrl_get_gen_rec return something meaningful even if
186        ALLOW_CAL is not defined
187      - ctrl_getobcs?: simplify code so that it does not need to use
188                       S/R exf_swapfields
189    o testreport:
190       allow to test MPI with different number of processors for each experiment:
191       create file "SIZE.h.mpi" in each build dir.
192       Note: update of "-command" argument not yet implemented.
193    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
194      alleviate the need for additional 3D tapes when using
195      the non-inear free surface in the adjoint. This is done
196      by adding an 'update' of hfacc etc. to their current
197      value at the beginning of forward_step.F.
198    o pkg/seaice
199      seaice_lsr: move stress-divergence computations out of outer pseudo-
200      timestepping loop
201    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
202      up, so that the calls of the ctrl_* subroutines are really at the end
203      of the routine.
204    o pkg/gmredi:
205      allow to specify a 2-D horizontal map and a 1-D vertical profil
206      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
207    o pkg/seaice:
208      move lsr iterations from seaice_dynsolver to seaice_lsr.
209    o pkg/seaice:
210      reduce memory footprint of seaice mutldim advection tapes,
211      by using a 2D tape independent of the generic_advdiff ones,
212      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
213    
214    checkpoint62q (2010/12/29)
215    o model/src:
216      - check horizontal grid-spacing for unset or zero/negative values.
217      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
218    o pkg/flt:
219      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
220      - precision of input and output files set according to readBinaryPrec
221        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
222      - initial float position from tiled file was not converted to index space
223        (looks like a bug): fixed to make it similar to initial pos. global file.
224    o global_ocean.cs32x15:
225       change SIZE.h of AD set-up to get same tiling as with MPI.
226       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
227    o model/src:
228       add flag to control printing of domain fields (bathymetry, hFac ...) in
229       ini_mask_etc (call to plot_fieds_xy*).
230    o pkg/thsice:
231       if useEXF, some forcing fields are not valid in overlap: fixed by computing
232       over the interior only + apply EXCH at the end (like with SEAICE advection).
233    o pkg/mdsio:
234      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
235        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
236      - change barrier call for safe multi-threads access to 3-D shared buffer.
237      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
238      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
239        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
240    o pkg/flt:
241      - add fourth-order Runge-Kutta integration
242      - add basic exch2 support (only 1 facet supported so far!)
243    o pkg/mdsio+rw:
244      new S/R to read local (or tile independent) vector (read counterpart of
245       mds_writevec_loc, and front-end write_glvec_rl/rs).
246    o global_ocean.cs32x15: additional input_ad.seaice experiment
247        that uses pkg/seaice rather than pkg/thsice.
248        (using multidim advection for seaice)
249    o towards more F95 syntax for array specification in namelist:
250      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
251        of all verification experiments.
252           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
253          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
254      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
255    o global_ocean.cs32x15: additional input.seaice experiment
256        that uses pkg/seaice rather than pkg/thsice.
257    
258    checkpoint62p (2010/12/17)
259    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
260        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
261    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
262        allow for use of multim. advection in seaice adjoint.
263    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
264      - first attempt to close budgets by taking into account the freshwater
265        flux implied by the sublimation of snow and ice. So far only the
266        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
267        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
268    o eesupp/src:
269      new S/R with new option (NML_EXTENDED_F77) to change array specification
270      from F95 standard to commonly accepted extended F77 form.
271      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
272      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
273      for less tolerant f77 compiler (e.g., pgf77, g77).
274    o globalFiles:
275      commented out in parameter file "data" since it's not safe with MPI
276      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
277      in this case); no longer commented out in restart test (tst_2+2).
278    o add adTapeDir to specify a special directory where adjoint tapes are
279      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
280      and cannot be used together with mdsioLocalDir.
281    o nesting pkgs:
282      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
283      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
284      - add parameter files + utils dir + output from short run on beagle.
285    o pkg/seaice:
286        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
287    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
288      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
289    
290    checkpoint62o (2010/11/25)
291    o pkg/exf:
292      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
293    o pkg/seaice:
294      - seaice_ocean_stress: split a loop for better vectorization of the
295        adjoint code
296      - seaice_growth.F: fix bug in conservation of freshwater connected to
297        capping of heff, put contribution into d_HEFFbyNEG
298      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
299        by something more sensible (parameters that are what their name implies)
300      - change some defaults, so that by default exf-parameters are used for
301        things like rhoAir, cpAir,latent/sensible heat parameters, in order
302        to reproduce the old results, many data.seaice now contain funny values
303        for cpAir and latent heat of sublimation
304    o packages_readparms.F: move exf_readparms up in line so that
305        exf-parameters are visible for other packages (e.g. seaice)
306    o debugMode & debugLevel=2:
307      - differentiate between debugMode & debugLevel=2:
308        debugMode: controls printing of debug messages (sequence of S/R calls).
309        debugLevel: controls printing of algorithm intermediate results and stats.
310      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
311        => allows to print debug-stats without all sequence of call messages.
312      - switch control of debug print from debugLevel to debugMode in many S/R.
313    o pkg/obcs (obcs-sponge):
314        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
315        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
316    o pkg/generic_advdiff:
317      - record overlap minimum size for each advection scheme;
318      - refine criteria on overlap minimum size;
319      - check and stop (in gad_check) if overlap size is too small.
320    o pkg/obcs:
321      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
322        once, in ptracers_implicit.F)
323      - with seaice: remove test on empty file name in obcs_apply_seaice (always
324        apply OB values when tile has OB)
325    o model/src, coriolis setting:
326      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
327        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
328        files (selectCoriMap=3) with any grid.
329      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
330    o pkg/seaice/seaice_growth.F:
331        a few cosmetic changes that reduce the number of lines of code
332    o pkg/obcs: add boundary conditions following Stevens (1990)
333      - the code follows old MOM/NAOSIM code
334      - so far it is only implemented for the eastern and western boundaries
335        and NOT for pTracers
336    o pkg/rbcs:
337      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
338        beginning of the first rbcs forcing period.
339      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
340        offline package, i.e., one file per time, labeled by iteration number;
341        deltaTrbcs sets the timestep with which the data was generated;
342        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
343      - rbcsForcingCycle=0 makes forcing non-cyclic.
344      - make arithmetic safe for negative times and odd forcing periods.
345    
346    checkpoint62n (2010/11/09)
347    o pkg/seaice:
348        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
349    o pkg/obcs:
350       New S/R to copy tracer value from the OB location to narrow band region
351        (width = same as overlap) beyond the OB: preserve OB value (needed for
352        high-order scheme) which were overwritten by EXCH call if in overlap
353        region. Applied to theta, salt, ptracer and advected seaice variables.
354       With seaice: use maskInC in similar way as in gad_advection.F,
355        in seaice_advection.F and advect.F.
356       Update output of experiment seaice_obcs and change exp4 to test OBCS with
357        4th order Adv.Scheme. for pasive salt and ptracer.
358    o tools/genmake2:
359      - when looking for an optfile (not specified), only search for Fortran compiler
360        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
361      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
362        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
363      - set default for CPP to "cpp -traditional -P" (was the case without specifying
364        an optfile, but otherwise default was just "cpp".
365      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
366      - when "CC" is not set in the optfile, look for possible C compiler
367        (instead of just setting CC=cc)
368      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
369        => add a ".F" to ".o" rule for source files with no "#include" (such as
370           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
371      - move gfortran before g77 in list of possible Fortran compiler (consistent
372        with reference compiler switch from g77 to gfortran)
373    o pkg/seaice:
374      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
375        seaice_check that stops the model, when the CPP flag is used.
376      o seaice_growth.F: make capping of ice volume conserving by returning the
377        capped ice as freshwater to EmPmR. This does not change the verification
378        experiments but will change runs where the capping is acutally active
379    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
380      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
381         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
382         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
383    o tools/genmake2:
384      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
385      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
386      - clean previous genmake log files before anything else.
387      - change Makefile to remove testreport log files (*.tr_log) and genmake log
388        files only with "CLEAN" target (instead of "Clean");
389    o pkg/generic_advdiff:
390      Change OBCS in multiDim advection (gad_advection.F):
391       Use maskInC to prevent intermediate update of tracer-field in OB regions,
392       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
393       which were applying future time-step OB values.
394      This way, all explicit calculations use current-time-step OB values
395       (simpler and more consistent).
396      Affects results when set-up uses time-varying OBC and multi-dim advection;
397       update output of experiment seaice_obcs.
398    o pkg/seaice:
399      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
400       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
401         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
402      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
403       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
404       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
405    o pkg aim (2010/10/26):
406      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
407        formulation with obliquity, eccentricity, ... as run-time parameters,
408      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
409        upward shortwave radition at the surface (all-sky and clear-sky).
410    o pkg/obcs:
411      - writing sections with globalFiles=T does not work: switch to tiled-files
412        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
413      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
414      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
415    
416    checkpoint62m (2010/10/21)
417    o pkg/seaice: vectorize seaice_solve4temp.F
418      - move iterations loops outside of i/j-loops
419      - requires 2D arrays for TB and effConduct
420      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
421        modified in this routine
422      - a little bit of clean up, adjusting indentation, etc.
423      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
424        performance and '**TWO' by '**2' (because TWO is a float),
425        replaced ONE, ZERO
426    o eesupp/src:
427       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
428    o pkg/seaice/seaice_growth.F
429      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
430      merging process. The merged routine has two branches, and one activates the 'evolution'
431      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
432      In summary, here is what the '10/10 revision' did consist of
433        part 1: seaice_growth.F revisions 1.71 to 1.75
434          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
435            The emphasis here was on improving readability (e.g. by trying to use meaningful
436            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
437        part 1.5:
438          - revising the lab_sea experiment to make it a more useful (i.e. stable
439            and representative of an actual model run). This was done by generating a
440            (winter) pickup to start from, switching back the main experiment dynamic
441            solver from evp to lsr, having one of the experiments use the free drift solution.
442        part 2: seaice_growth.F revisions 1.76 to 1.85
443          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
444          - Sorting out the various fields units and sign (set early on and reset at the end)
445            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
446            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
447          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
448            and simplifying logical expressions to further improve readibility.
449        part 3: seaice_growth.F revisions 1.86 to 1.89
450          - Re-organize the blocks of code more logically.
451          - Merging the '_if.F' pieces that add something new.
452    o pkg/thsice:
453      - vectorize thsice_solve4temp and thsice_get_exf.
454        Problem: thsice_solve4temp has an unvectorizable statement that
455        might also be problematic for TAF
456      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
457        does not change the verifcation experiment, but will change all
458        experiments that have this flag undefined (not tested in verification);
459        a little reorganization to save a few 2D fields and recomputations
460      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
461      - 2nd step:  fix some store dirs
462        o seems to work somewhat, i.e. using ifort but not g77
463        o likely cause are incomplete init. or recomputation
464        o start verification/global_ocean.cs32x15/input_ad.thsice
465    o pkg/obcs: add support for exch2
466      - the position of the boundary and prescribed values are specified using
467        a global domain with exch2 facets stacked
468        - in x for N,S boundaries (like W2_mapIO=-1)
469        - in y for E,W boundaries (so E,W boundaries do not overlap)
470    o pkg/mdsio: add support for writing global sections with exch2
471        file layout is as for obcs described above:
472        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
473        - for y-z sections, facets are stacked in y
474    o pkg/thsice:
475       - change a few routines for better vectorization: thsice_albedo.F,
476         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
477         not affected, but in particular the latter routine has changed
478         dramatically (not necessarily easier to read now).
479       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
480       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
481    o verification/lab_sea:
482      - overhaul of the forward model experiments. The main motivation
483        for this revision is that lab_sea has proven quite fragile (when
484        changing the sea-ice code, and switching platforms) to a point
485        when failures were very hard to attribute to specific code problems.
486      - the suspected reason for this fragility is noise amplification by evp so,
487        to start with, we decided to replace evp with lsr in the main experiment.
488      - the input.lsr experiment thus became obsolete and was removed.
489      - it was replaced with the input.fd experiment that uses an
490        analytical "free drift" solution as the ice velocity field.
491      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
492        will hopefully allow us to discriminate problems due to dynamic solvers
493        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
494        us to test additional options, along with the salt plume package.
495      - Finally a pickup was generated (at the end of a one year run) to
496        make the tests more representative of an actual model run. Previously
497        the tests starting point was a 1m thickness of ice everywhere.
498    o pkg/seaice:
499      - introducing S\R seaice_freedrift.F that compute the
500        analytical solution to an approximate ice momentum
501        equation (i.e. the simple stress/coriolis balance).
502      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
503        of the free drift velocity field, and enable its use.
504        To actually use the free drift solution as the model ice
505        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
506    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
507    
508    checkpoint62l (2010/10/04)
509    o pkg/seaice:
510      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
511      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
512       version (with USE_ORIGINAL_SBI undef);
513    o add hooks for new packages OASIS, the package will follow
514      (hooks exclude the seaice pkg for now)
515    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
516      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
517      rather than mdsio_readvector.F/mdsio_writevector.F, within
518      adread_adwrite.F to read/write adjoint-related tapes to disk.
519    o eesupp and pkg/mdsio: ALLOW_WHIO
520      Option to write/read 2D fields to files including tiles halos.
521      The main purpose is for adjoint related "tape I/O".
522      The secondary purpose is for debugging phases.
523      A word on those rather specifically intended purposes.
524      The code was meant to be stripped down to the bare minimum.
525      Typically, there is a unique and basic mapping to the global
526      buffer (tile by tile, then proc by proc, then level by level), and
527      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
528      meant to generate user friendly outputs of various shapes and forms.
529      Rather it is intended, for the knowledgeabale developers,
530      to be largely independent of the many mdsio options, to allow
531      outputs of tiles+halos in debugging phases and in adjoint runs,
532      and to allow some flexibility in tuning (adoint) I/O depending on each
533      file system behavior. With regard to tuning, most of the potential knobs
534      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
535      to specify directories, to specify the typical size of I/O calls, etc.)
536      are not yet included, and will be added if they prove useful.
537    o pkg/seaice:
538       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
539    o pkg/seaice:
540       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
541       code (seaice_budget_ice_if.F) which enable to recover old standard
542       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
543       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
544    o model/src (rStar):
545       use simple average (not area weighted) of rStarFac at U,V point when using
546       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
547       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
548    
549    checkpoint62k (2010/09/17)
550    o adjoint
551       * changed verification/global_ocean.cs32x15 ; adjoint now tests
552         Adams-Bashforth 3 + NLFS + RSTAR
553       * some more modifs required for ECCO-GODAE v4
554    o pkg/seaice
555       add SEAICE_AGE_VOL option to use volume instead of area for
556       integrating SEAICE_AGE
557    o model/src:
558       first check-in of sigma & hybrid-sigma coordinate code ; also includes
559       non-linear free-surface parts ; but pressure-gradient not yet coded.
560    o pkg/ptracers:
561       option for ptracer to convert Salt Relax into additional EmP.
562        tested in exp. global_ocean.90x40x15.dwnslp (update output)
563    
564    checkpoint62j (2010/08/25)
565    o pkg/ggl90:
566       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
567    o pkg/dic: car_flux.F, phos_flux.F
568      - reduce number of exp-calls in order to improve performance
569      - clean up a little (replace fields by their macros, etc., fix
570        typo in CPP-flag)
571    o pkg/ggl90: minor changes
572      - GGL90diffKrS was removed --> always use GGL90diffKr
573      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
574      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
575        (commented out for now)
576      - change in max/min operations to ensure that smoothing is ok
577      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
578      - always use diffKrNrT as background profile (i.e. never use diffKr field)
579    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
580    o pkg/dic:
581      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
582        vectorization
583      - small bug fix in insol for the unlikely case of a cartesian grid
584      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
585        + now vectorize, which also removes adjoint recomputations;
586        + replace integer maksp1 by _RL maskp1
587        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
588    
589    checkpoint62i (2010/07/21)
590    o pkg/flt:
591      - with OBCS: stop floats which enter the OB region
592    o model/src:
593      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
594        for implicit vertical advection.
595    o pkg/seaice:
596     - account for melting in seaice age evolution.
597     - remove double counting of seaice ridging effect on seaice age.
598    
599    checkpoint62h (2010/06/18)
600    o pkg/exch2:
601     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
602    o tools/genmake2
603      - remove "-pdefault" option: redundant with the use of "packages.conf";
604      - remove file pkg/pkg_default : set the default as a pkg group
605        ("default_pkg_list") defined in pkg/pkg_groups;
606      - fix for case pkg/pkg_depend is missing (was hanging before);
607      - add option "-pgroups" to specify a different pkg_groups than the default.
608    o verification/adjustment.cs-32x32x1:
609       add a "minimal" set-up test (code_min & input_min) which only compiles
610       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
611    o tools/genmake2
612      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
613      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
614    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
615      files are nearly the same anyway.
616      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
617       - redefinition of tau(i,i) (by a factor of ustar)
618       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
619       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
620       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
621       - replace
622         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
623         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
624         by
625         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
626         (changes results)
627       -> exf_bulkformulae v1.22,
628          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
629          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
630                    output.txt 1.63
631           offline_exf_seaice: output.seaicetd.txt 1.7
632           seaice_obcs: output.txt 1.10)
633      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
634       -> exf_bulkformulae v1.23,
635          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
636          and global_ocean.cs32x15.icedyn (only 11 matching digits)
637      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
638    o adjoint of exch-1:
639     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
640       (note: was already like this when using EXCH-2) and remove flow dir
641       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
642     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
643     - update pkg/exch2 diff list.
644    
645    checkpoint62g (2010/05/19)
646    o eesupp/src (exch-1):
647     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
648       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
649       (renamed to exch1_*rx_cube.F).
650     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
651       to call new exch1 S/R ; update Makefile and .cvsignore.
652     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
653       exch2_xy_rx later)
654      Note: after updating your code, need to run "make clean" in eesupp/src
655    o test experiment bottom_ctrl_5x5:
656       new output_adm.txt with fewer grdchk & less monitor output.
657    o model/src:
658      remove the call to ini_cori in initialise_varia.F (just keep the usual one
659       in initialise_fixed.F). More consistent with coriolis & horizontal grid
660       beeing treated in the same way (ini_grid is not called a 2nd time).
661    o pkg/exf:
662      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
663      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
664      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
665      - cosmetic changes to exf_bulkformulae.F to make it look more like
666        exf_bulk_largeyeager04.F
667    o eesupp/src (exch-1):
668      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
669      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
670        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
671        (even without using MPI).
672      - Message mode: move RecvAck setting (indicator of buffer being ready)
673        from send_put to recv_get S/R (was useless before, but not sure if
674        it's much more useful now);
675      - Switch the order of sync: MPI-proc 1rst and then threads;
676      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
677      - fix AD code for communication mode ='get' (but not used).
678    o model/src:
679      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
680      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
681    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
682    o pkg/ctrl: require a specific set of control variables and exf-flags for
683      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
684    o model/src:
685     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
686       1rst forward sweep, to avoid over-writing output files during recomputations
687       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
688     b) 2nd version:
689      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
690      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
691         writePickupAtEnd) + seaice & ptracers output;
692      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
693    o model/src:
694      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
695    o pkg/exch2:
696      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
697      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
698    o pkg/autodiff & exch2:
699      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
700      (for now, only if ALLOW_EXCH2 is defined).
701    o pkg/autodiff:
702      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
703        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
704       + clean-up comments (_RS is not always real*4)
705      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
706      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
707        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
708    o testreport (AD-tests):
709      no longer link files from dir "../input" (1rst link files from
710      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
711    
712    checkpoint62f (2010/04/29)
713    o model/src/the_main_loop.F:
714      adjust store directives for seaice evp and multicategory according to
715      pkg/ecco/the_main_loop.F
716    o adjoint:
717      global_sum_ad was incomplete (noted many times by many people ;)
718      nice description by Jean U. as follows:
719      * allreduce(var) in global_sum.F can be interpreted as
720        reduce(sum) followed by broadcast of sum.
721      * The adjoint of that is
722        sum(adjoint) followed by broadcast(summed adjoint value)
723        or in other words, allreduce(sum, adjoint vars)
724      We were missing the sum(adjoint)!
725      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
726      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
727      The fix should produce 16-digit accuracy between
728      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
729      multi-CPU single-tile (e.g. nSx=1, nPx-2)
730      We'll probably change this yet again shortly
731    o eesupp/src:
732      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
733    o pkg/icefront
734      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
735        specification of addmass array based on a 2D field, which is added
736        at bottommost wet level at each horizontal location.
737    o model/src:
738     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
739     layout; (not always compatible with delX,delY setting; commented out for now).
740    o pkg/exch2:
741     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
742     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
743    
744    checkpoint62e (2010/04/15)
745    o pkg/obcs:
746      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
747    o pkg/dic:
748      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
749        (note: not presently tested in any forward verification exp.)
750       update tutorial_global_oce_biogeo AD output file.
751    o pkg/exf:
752      - account for the variation of albedo as a function of zenith angle
753        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
754    o build_options:
755     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
756    o pkg/dic:
757      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
758      - use binary pickup file for restart;
759      - initialise atmos-CO2 box from dic_pCO2 parameter;
760      - fix multi-threaded.
761    o pkg/rbcs:
762     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
763       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
764     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
765       and update output.txt
766    o pkg/kpp:
767     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
768     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
769       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
770       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
771     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
772       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
773    o pkg/offline:
774      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
775      (bug was added in version 1.10 on 2007-08-23).
776    o pkg/offline:
777      - no need to specify periodicExternalForcing, etc ... to use offline pack
778      - offline input files no longer just single prec --> parameter offlineLoadPrec
779    o verification/lab_sea:
780      change AD test to multi-tile setup and update all 4 AD output.
781      NOTE: while cost function values remain very similar,
782      gradients are very different, although gradient checks are self-consistent
783      Should try to get to the bottom of this (cost function summation order?)
784    o pkg/dic:
785      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
786      a weakness of TAF that drops part of double precision in log10 derivative.
787      <= changes removed since problem has been fixed in current TAF version 1.9.71
788      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
789    o pkg/ecco:
790      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
791      update all 4 lab_sea AD output.
792    
793    checkpoint62d (2010/03/22)
794    o build_options:
795      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
796    o remove unbalanced quote (single or double) in commented line of source code
797      (may cause some warning with some preprocessor/makedepend versions).
798    o pkg/seaice:
799      fix seaice_model.F for adjoint (gael) and update AD results of experiments
800       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
801    o testreport:
802      add option '-runonly' (short: '-ro') to just do the run part (without make).
803    o eesupp: remove JAM communication code (obsolete).
804    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
805      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
806      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
807      (update also the output).
808    
809    checkpoint62c (2010/03/02)
810    o tools/build_options :
811       move (some) old optfiles from build_options/ to build_options/unsupported/
812    o model/src and pkg/exf
813       surface relaxation -- separating data and data.exf options
814       The point is to ensure that we specify the surface relaxation
815       either in data or in data.exf (but not half and half) and to
816       avoid an accidental relaxation to 0 (which happened if a time
817       scale was specified but the file name was left empty)
818    o model/src model/inc and pkg/mom_common
819       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
820       => addition to the viscosity field as computed by others schemes
821    o tools/build_options:
822      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
823        but keep the former optfile for few weeks for smooth transition
824    o pkg/ecco
825      - allow user defined cost function contributions
826         CPP: ALLOW_USERCOST_CONTRIBUTION
827         USAGE: compute contributions in cost_usercost_all.F
828      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
829          the two options are complementary.
830    o pkg/smooth
831      - migration from contrib to the main repository
832    
833    checkpoint62b (2010/01/26)
834    o pkg/monitor:
835      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
836        (in case someone forgot to update customized pieces of code)
837    o nonHydrostatic:
838      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
839      - add a simple 2-D experiment (short_surf_wave) to test it.
840    o pkg/icefront:
841       adding the shell of, and the hooks to, a new package that
842       will model melting and freezing of vertical glacier ice fronts
843    o momentum:
844      add diagnostics of momentum tendency from Hydrostatic pressure gradient
845       (without surf.pressure term: would need a 2nd filling since implicit term).
846    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
847      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
848      cannot deal with the former
849    o cleaning:
850      - remove all (except OpenAD) old TLM output from results_ad dirs.
851      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
852      - comment out maskH definition (replaced by maskInC)
853    o pkg/monitor:
854      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
855        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
856    
857    checkpoint62a (2010/01/15)
858    o model/src:
859      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
860    o pkg/diagnostics:
861      - add optional level number diagnostics (i.e., level number to be define
862        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
863      - strictly check for valid parser-code(10) ;
864      - check if adding diag to the list from the right place.
865    o pkg/longstep:
866      - change parameters and fix tracer conservation with rstar/nonlinear free surface
867    o diagnostics:
868     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
869       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
870    o pkg/diagnostics:
871     - Add option for writing vertical integral (sum of selected levels) of an output
872        field instead of writing output field levels. Activate this option on a per
873        output-file basis, by setting the 2nd character of fileflag to 'I'.
874     - Add field-specific information relative to level integral in 3rd postion
875        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
876        vertically (x level-thickness x hFac), "r"=same but without hFac.
877    o do_the_model_io:
878      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
879        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
880        writing pickups and stopping.
881    o pkg/diagnostics (for now, only with mdsio):
882      - write time information to meta file (and modify accordingly rdmds.m) :
883        time-averaged diagnostics output: write starting and ending time of the
884        time-averaging interval ; snap-shot diagnostics output remains unchanged;
885    o pkg/timeave:
886      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
887        always Nr), now assumed to be equal to number of levels of averaged field;
888        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
889    o pkg/sbo:
890      - fix ocean bottom pressure global-average & 2-D time-ave output (was
891        neither initialised nor filled).
892      - add starting iteration in suffix of global-average output file
893        (to avoid over-writing the file after a restart)
894      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
895    o time-average:
896      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
897        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
898         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
899        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
900      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
901      - fix missing accumulation for pkg/opps.
902      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
903         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
904      - fix initialisation of time-ave vars and do only full time-step increment
905        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
906    o pkg/layers:
907      - use standard RW pkg S/R to write the output
908        and remove local write_fld version (which had a problem).
909      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
910      - fix LAYERS_CALC argument list.
911    o pkg/timeave:
912      - store cumulative-time in a simple tiled array (drop the level index)
913      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
914    o pkg/ocn,aim_compon_interf
915      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
916    
917    checkpoint62  (2009/12/23)
918    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
919        (was not previously tested in any other exp.)
920    o pkg/monitor:
921      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
922        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
923        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
924      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
925      - change del2 calculation.
926      - use interior masks (instead of maskH, <- to be remove).
927      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
928    o mask & obcs:
929      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
930      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
931        (called after packages_init_fixed)
932    o pkg/obcs:
933      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
934        Fixes bug in obcs+exf with nSx*nSy.GT.1
935      - fix multi-tile handling in obcs balance code
936    o nonHydrostatic:
937      - Implement AB-3 for non-hydrostatic vertical momentum ;
938        (change ordering of var. stored in pickup file when using NH)
939      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
940      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
941        (in prep. for new NH free surface form).
942    o pkg/obcs:
943      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
944    o model/src:
945      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
946    
947    checkpoint61z (2009/12/01)
948    o nonHydrostatic:
949      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
950        a spurious source of energy in simple baroclinic adjusment test case.
951      Update all non-hydrostatic exp output.
952    o model/src (3-d solver):
953      Change again 3-D solver free-surface RHS term when exactConserv=T:
954        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
955        (which was not the case with previous formulation).
956      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
957      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
958    o nonHydrostatic:
959      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
960        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
961      - change 3-D solver to work with r* (for now, only with linear free-surf.)
962      - add few debug diagnostics (cg3d_x, residual)
963    o model/src:
964      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
965        update output of exp. global_ocean.cs32x15.viscA4
966    o update output of exp. global_ocean.cs32x15.icedyn after removing
967      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
968    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
969    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
970      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
971    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
972      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
973      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
974      to test this code
975    o pkg/cd_code:
976      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
977       C-grid momentum. D-grid velocity used to be stepped forward in time with
978       Adams-Bashforth only on surface pressure term. Tests show that using AB on
979       D-grid coriolis term improves stability (as expected from CD-scheme paper).
980      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
981      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
982       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
983       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
984      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
985           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
986    o pkg/obcs:
987     - fix bug in initialisation (broken since Oct 1rst modification)
988       for useOBCSprescribe without useEXF.
989    
990    checkpoint61y (2009/11/15)
991    o pkg/seaice
992     - change (once again) the discretization for the evp solver: rather than
993       squaring the averages of strain rates, average the squares to give
994       a better approximation to VP behavior (in simple test); this breaks
995       verification experiments that use EVP (lab_sea and lab_sea.hb87)
996        --> update outputs
997    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
998      to improve vectorization of adjoint code on TARGET_NEC_SX
999    o verification/vermix:
1000      - change vermix to a more "classical" 1d column with high vertical
1001        resolution, seasonal heat flux forcing and constant wind forcing
1002        --> update outputs
1003    o pkg/seaice
1004     - fix diagnostics of principal stress components for EVP
1005     - add optional diagnostics of non-linear convergence for LSOR solver
1006     - make maximum zeta a runtime parameter
1007    o model/src (3-d solver):
1008      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
1009       which consisted in removing the Surf. Non-Hydrostatic pressure from the
1010       whole column and adding it to Eta (inspired from Casualli, 1999):
1011       Only affects 3-D solver initial guess and only if using ExactConserv,
1012       but tests did show a degradation of solver convergence. For this reason,
1013       decide to disable this piece of code.
1014       to recover previous version, just set zeroPsNH = exactConserv (line 78).
1015      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
1016    o pkg/ggl90:
1017     - fix previous modif (unfortunatly has not been documented here).
1018    o pkg/seaice/autodiff:
1019     - add CPP flag to include clipping of zeta in EVP code;
1020       although clipping of zeta is not necessary for EVP and not recommended
1021       it was done by default, now clipping is disabled by default
1022     - modify computation and store zetaC/Z in seaice_evp for TAF
1023     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
1024     - change seaice_calc_viscosities/strainrates for better
1025       vectorization after AD by TAF
1026     - rearrange common blocks in SEAICE.h once again for easier dumps of
1027       adjoint output, adjust adcommon.h and g_common.h
1028     - change flux form of default advection scheme for better vectorization
1029       of adjoint code
1030     - modify lab_sea/input.lsr to test the flux form of default advection
1031       scheme
1032    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
1033      transition in checkpoint61r)
1034    
1035    checkpoint61x (2009/10/19)
1036    o adjoint: adding two new verification experiments
1037      * tutorial_global_biogeo: an online dic sensitivity experiment
1038        (work with G. Forget)
1039      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
1040        (an update of the Dutkiewicz et al., 2006 paper)
1041      Both use the same CO2FLUX cost function, but different controls
1042      Gradient checks look good, but some recomp. could still be traightened out
1043      Should add xx_dic control variable to test at some point
1044    o model/src:
1045      add run-time parameters to check and/or mask initial Temp & Salt
1046    o pkg/ptracers:
1047      apply zonal filter (if used) to all passive tracers
1048    
1049    checkpoint61w (2009/10/12)
1050    o adjoint:
1051      * update and finish work on adjoint of dic package (G. Forget)
1052      * start adjoint of offline package
1053      * bug fix for cube-sphere TLM code (active_file_g.F)
1054    o tutorial_global_oce_optim:
1055      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
1056      and add SIZE.h_mpi for MPI testing
1057    o pkg autodiff
1058     - fix bug in autodiff_restore
1059     - make genmake2 remove comments and empty lines from ad_input_code.f in
1060       order to reduce file size (new script file remove_comments_sed)
1061    o allows to specify vertical profile of vertical viscosity (viscArNr)
1062    o pkg autodiff
1063      autodiff_ini_model_io: comment out writing of grid information to netcdf
1064      files, because at this time the grid fields are a bunch of zeros
1065      (this is analogous to ini_mnc_vars.F)
1066    o pkg seaice/autodiff:
1067     left-over from removing the 3-time-level fields:
1068     - small rearrangement of common blocks (SEAICE.h)
1069     - fix field declaration in order to get meaningful output in
1070       adseaice.*.nc (adcommon.h)
1071    o pkg obcs:
1072     - go through NH code only if nonHydrostatic=T
1073     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
1074     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
1075       => Update output of experiment seaice_obcs
1076     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
1077     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
1078     - fix restart for useOBCSprescribe + useEXF
1079    o pkg ctrl
1080     - make obcs as control parameter work also with useSingleCPUio
1081     - replace a few sny and snx by Ny and Nx to be consistent with
1082       ctrl_set_globfld_x/yz.F
1083    o pkg seaice
1084     - re-introduce global field frWtrAtm for the case of
1085       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
1086     - catch the case of an empty filename in seaice_cost_init_fixed.F
1087    o pkg ecco:
1088     - small bug fixes in the_main_loop
1089      . fix order of monitor arguments
1090      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
1091      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
1092        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
1093     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
1094       imbalance diagnostics for wmean_h/sflux = 0
1095     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
1096     - catch the case of empty filenames in ecco_cost_init_fixed.F
1097       and ecco_readparms.F
1098     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
1099       to make this statement meaningfull in ecco_cost_weights.F
1100    o pkg zonal_filt:
1101      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
1102      - when using rStar, filter uVel*hFacW instead of uVel
1103       (tested without topography: fix a Pb of growing instability with NLFS)
1104    o pkg/aim/thsice:
1105     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
1106      (works as SST restoring)
1107    o pkg/thsice:
1108     -add specific parameter for salt restoring in slab mixed-layer
1109       (by default equal to the temperature restoring)
1110    
1111    checkpoint61v (2009/09/21)
1112    o pkg/kpp:
1113     -add double diffusive contributions as a hack, turned off by default
1114      for now, and the code can be excluded with a CPP-flag
1115      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
1116     -add a verification experiments to "vermix" to test this code
1117    o pkg/mom_common:
1118      Move computation of length scales to mom_init_fixed.F (avoid recomputation
1119      at each time-steps*levels).
1120    o pkg/layers:
1121      Created a new package for computing volume fluxes in temperature or
1122      [not yet implemented] density layers, e.g. for calculating residual
1123      overturning circulations.
1124    o pkg/diagnostics:
1125      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
1126    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
1127    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
1128      To avoid mixing type (RS/RL) of input/output array argument,
1129      replace single mixed-type array with a pair from each type (RS/RL).
1130    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
1131      is now implemented for all pkgs (previously only done for the main pickup)
1132    
1133    checkpoint61u (2009/08/25)
1134    o pkg/obcs:
1135      - change OB?eta from _RS to _RL and put them into a separate commen block
1136      - add code to read OB?eta from a file via obcs_prescribe_read: the code
1137        compiles and does not destroy any other experiments, the data is read
1138        properly, but the code is not tested in actual applications
1139    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
1140      create a meaningful unit attribute for the time coordinate variable
1141    o pkg/ebm: add plenty of missing "_d 0" ;
1142       update results of experiment global_ocean_ebm (fwd + adjoint tests)
1143      Notes: several pieces of code only works for (very) specific set up
1144       (domain size, lat range, etc ...); should be documented & stop if one
1145       of those assumptions is not meet.
1146    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
1147       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
1148          and offline_exf_seaice (seaicetd + adjoint).
1149    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
1150       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
1151        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
1152    o few changes to pass when compiling with strick checking of arguments
1153       across S/R (allow to find few bugs in S/R calls).
1154    o pkg/seaice:
1155     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
1156       2d-fields, for slightly better performance
1157    
1158    checkpoint61t (2009/07/22)
1159    o pkg/seaice:
1160     - remove unused variables in seaice_evp
1161     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
1162    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
1163       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
1164       each processor opens a different file (a fix from Matt).
1165    o cg2d:
1166       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
1167       this reduces number of EXCH calls by 2 when using exch2.
1168       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
1169       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
1170    o pkg/thsice:
1171       add code for Near Infra-Red albedo (from Jeff)
1172       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
1173    o ini_model_io:
1174       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
1175       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
1176       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
1177    
1178    checkpoint61s (2009/06/30)
1179    o pkg/exch2 (exch2_rxN_cube*):
1180       remove last BARRIER (no need to synchronise after getting data from shared
1181       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
1182    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
1183      and generate new output (for the 2 tests) using default rotationPeriod.
1184    o pkg/exch2:
1185      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
1186        (was already the case with AUTODIFF_EXCH2 defined)
1187      - add bj in exch2 arrays and S/R.
1188      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
1189        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
1190    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
1191      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
1192        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
1193      - verification experiment natl_box.longstep
1194    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
1195      allow different versions of ifort (8 or 9) and different versions
1196       of mpi (mpich or mpich2) to be used with the same optfile.
1197      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
1198       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
1199    o pkg/seaice:
1200      fix previous modif (3-level field removed) for old-pickup reading
1201    
1202    checkpoint61r (2009/06/25)
1203    o pkg/seaice:
1204     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
1205      1. introduce fields for time step (N-1)
1206      2. do not use levels 2 and 3 anymore (but keep them)
1207      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
1208         includes changes to pkg/thsice/thsice_get_velocity.F,
1209         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
1210         pkg/obcs/obcs_apply_uvice.F.
1211     - completely remove code for leap-frog time stepping for second order
1212       advection
1213     - adjusted adjoint accordingly;
1214       gradient checks have improved by an order of magnitude!
1215    
1216    checkpoint61q (2009/06/22)
1217    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
1218     - the boundary conditions along open boundaries are unclear, because the
1219       associated masks are set to zero and are thus treated as closed when
1220       applying the slip-boundary conditions.
1221     - move initialisation of grid variables from seaice_init_varia to _fixed
1222    o adding doc/diags_changes.txt
1223    o model/src:
1224      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
1225       to avoid "_diags" naming if no relation to pkg/diagnostics.
1226      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
1227       file and only call PLOT_FIELD_XYZ if debugMode=T.
1228      remove few PLOT_FIELD_XY calls outside initialisation.
1229      remove few unnecessary BARRIER.
1230    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
1231      of salt_plume package in Southern Ocean
1232    o pkg/thsice:
1233     - fix hOceMxL in overlap (needed for sea-ice advection);
1234       update output of experiment global_ocean.cs32x15.icedyn.
1235    o pkg/seaice:
1236     - make the (placeholder-)tracer IceAge a little more meaningful
1237      by avoiding ridging of age due to convergent ice flow
1238     - add diagnostics for surface temperature, atmospheric and oceanic
1239       heat flux, and atmospheric and oceanic ice growth
1240    
1241    checkpoint61p (2009/06/10)
1242    o eesupp (global_max & global_sum):
1243     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
1244     - remove starting & endding barrier (no longer needed)
1245    o pkg/mdsio, writelocal:
1246       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
1247       (remove the STOP): uses shared buffer IO to store data from all threads
1248       and then let master-thread write nThreads tiles.
1249    o pkg/mdsio (read/write field):
1250     - tiled IO done in 1 piece (all levels at a time);
1251     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
1252     - multi-threaded: allow to read/write local (non-shared) array
1253       (was already working with singleCpuIO ; now works also without);
1254       => no longer needs barrier call after reading a file (added inside
1255       mds_read/write field).
1256     - move barrier calls outside gather/scatter_2d to mds_read/write_field
1257    o pkg/obcs/exf
1258      - exf_getffieldrec.F: add a few ". _d 0" and
1259                            add code to catch the case fldperiod = 0.  
1260      - obcs_precribe_read.F: change if statements so that they match
1261                              the variable type (_RL)
1262      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
1263        exf_iprec) as part of namelist EXF_NML_01
1264    o pkg/mdsio:
1265      - read/write tiled (local) files: read/write 1-level tile chunk at a time
1266        (instead of segment of length sNx); expected to speed up tiled IO.
1267    o pkg/exch2:
1268      - take buffer copy from/to array out of S/R exch2_send/recv into new
1269        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
1270        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
1271      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
1272      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
1273        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
1274        including Topology header file (and common blocks).
1275      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
1276        remove 2nd exch call in exch2_s3d_rx (no longer needed).
1277      - document S/R arg. list (+ update some comments)
1278    o pkg/seaice:
1279      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
1280        temperature and humidity over sea ice based on climatological values.
1281      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
1282        of LSR (this change is expected to change the results slightly because now
1283        it uses slightly difference moduli from the second last LSR solution, but
1284        that is more consistent with the stress computations; this part of the code
1285        is not tested in the verification experiments)
1286      - fix diagnostics for flux of ice in case of B-grid
1287      - turn strain rates eij and press into global fields within global
1288        common block in SEAICE.h for more straighforward diagnostics
1289      - fix diagnostics for principal stress components, press, zeta, eta
1290        to give something meaning full
1291    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
1292      new output (all 4 tests) using default rotationPeriod.
1293    o pkg KPP:
1294      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
1295      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
1296        and normal grid from 1 to Nr)
1297    o Fix computations of L4rdt in mom_calc_visc.F
1298    o eesupp:
1299      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
1300      should be called before a "stop" if we know that all process are going
1301      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
1302    
1303    checkpoint61o (2009/05/26)
1304    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
1305    o model/src/ini_curvilinear_grid.F:
1306       compute angleSin/CosC when they are not read from a file
1307    o pkg/seaice:
1308       add pseudo time stepping for LSOR
1309    o pkg/exch2:
1310       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
1311    o pkg/seaice:
1312       Adding separate sea ice albedo, drag coefficients, and HO in Southern
1313       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
1314    o SingleCpuIO:
1315       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
1316    o pkg/seaice:
1317       put exchanged variable in (local) common block for MPI+Multi-Threads
1318       to work (necessary with exch1, and for now with exch2 too).
1319    o verification: to get more experiments tested with mpi, mth and mpi+mth,
1320      change tiling of:
1321       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
1322       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
1323      update output of exp:
1324       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
1325       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
1326      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
1327                       (note: output.txt generated on faulks using only 1 tile)
1328    o eesupp & mdsio (SingleCpuIO):
1329     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
1330       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
1331       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
1332     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
1333     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
1334       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
1335    o pkg/exch2:
1336     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
1337       read parameter file "data.exch2" if it exists; otherwise try default regular
1338       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
1339     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
1340       with new code (not to be used, just as a backup solution).
1341     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
1342       in utils/exch2/input.
1343    
1344    checkpoint61n (2009/05/12)
1345    o eesupp & mdsio (SingleCpuIO):
1346      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
1347        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
1348        receive real*4 array (instead of real*8) to read/write 32.bit files.
1349        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
1350         and remove new mapping S/R)
1351    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
1352      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
1353        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
1354        when using exch2. Add S/R to map global io-buffer to global model array.
1355      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
1356    
1357    checkpoint61m (2009/04/29)
1358    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
1359      and add 3 other S/R for other types (R4,R8,RS).
1360      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
1361    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
1362     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
1363     - reduce number of macro definitions (keep only those which are used);
1364       can always call directly the corrresponding S/R if needed.
1365     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
1366       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
1367     Fixed wrong type of arg in:
1368       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
1369       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
1370     To fix: global_sum of var in common block is wrong (multi-threaded) in:
1371       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
1372     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
1373    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
1374      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
1375    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
1376    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
1377      edges are closed (zero depth); might happen with "blank tiles";
1378      for now, disabled if using OBCS.
1379    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
1380      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
1381    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
1382      to reduce length of 1.D array print in STDOUT.
1383    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
1384      + use 48 tiles (16x8): this will allow to test "blank tiles".
1385    o start to test MPI + multi-threaded (change testreport to skip tests
1386      where number of tiles do not match).
1387    o genmake2: add option "-omp" to turn on Open-MP ;
1388      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
1389    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
1390      and keep the original tile numbering. Note: compatible with old
1391      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
1392    
1393    checkpoint61l (2009/04/07)
1394    o Overlaps had been forgotten in calculating ijk keys : fixed
1395    o fix cyrus makedepend for gcc 4.4
1396    o experiment fizhi-cs-aqualev20:
1397      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
1398      and generate new output. Note: new output is much closer to the old
1399      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
1400      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
1401    o pkg/fizhi:
1402     - change to avoid indices going deliberately over array-bounds
1403     - remove unnecessary MPI stuff
1404     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
1405     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
1406       does not go over array-bounds and therefore returns reliable output.
1407     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
1408       this S/R has 4 output arguments, which are used inside "get_alarm";
1409       when it is called with the same variable "ndum" in place of several
1410       output arguments, this produces weird side effect inside "get_alarm"
1411      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
1412       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
1413       address) and produces error.
1414    o tools/gemake2: (March 27-29 2009)
1415      with option "-mpi": link *_mpi files from "MODS" dir (this is what
1416      testreport does).
1417    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
1418    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
1419       update lab_sea.lsr & lab_sea.salt_plume results
1420    o pkg/seaice:
1421      Major overhaul of the LSOR solver: change discretization from original
1422      finite differences to finite volume. The old routine is still in the
1423      file seaice_lsr.F and can be turned on with the CPP-flag
1424      SEAICE_OLD_AND_BAD_DISCRETIZATION
1425      Along with this change, the discretization of the strain rates is changed.
1426      The same flag turns on the old discretization in seaice_calc_strainrates.F
1427      All verification experiments with seaice are affected (except for
1428      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
1429      results by setting the above flag.
1430      Further changes involve changes in defaults:
1431      - ALLOW_FLOODING is defined and turned on by default
1432      - SEAICEadvSnow = .true. is now the default
1433      - SEAICEadvSalt = .true. is now the default
1434      - SEAICEadvAge  = .true. is now the default
1435      - SEAICE_clipVelocities  = .false. is now the default
1436                                         (as per J. Zhang's recommendation)
1437      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
1438        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
1439      - seaice_growth: replace computation of UG by a simple copy from wspeed
1440    
1441    checkpoint61k (2009/03/18)
1442    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
1443      seaice_lsr: fixed a few metric terms,
1444                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
1445                  add more debugging diagnostics
1446      seaice_evp: removed superfluous many metric terms of FV discretization
1447                  of stress divergence
1448                  affects lab_sea, lab_sea.hb87
1449      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
1450                  of stress divergence for non-evp solver
1451                  (this part is not tested anywhere)
1452      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
1453                  they were effectively only half slip
1454                  affects lab_sea.hb87
1455      updated all relevant verification experiments (except lab_sea//output_adm.txt
1456        which was left over, but fails at level 7 & 6)
1457    
1458    checkpoint61j (2009/03/17)
1459    o pkg/seaice: turn a few hard wired parameters into run time parameters
1460    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
1461      time in seconds as promised by the usints in seaice_monitor and exf_monitor
1462    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
1463      that are not cubed-sphere grids
1464    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
1465    o pkg/ctrl:
1466      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
1467    o non-hydrostatic (calc_gw.F):
1468      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
1469      update output of exp. global_ocean.cs32x15.viscA4
1470    o remove backward compatibility for thetaMin,phiMin
1471      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
1472    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
1473      interpolated wind field not only for curvilineargrid=.true., but also
1474      for a rotated grid (rotateGrid=.true.)
1475    o pkg/exf: add capability to bypass interpolation for runoff
1476      by setting yet another CPP-flag
1477    o eesupp/src, B-grid exchange:
1478      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
1479    o autodiff
1480      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
1481      allows to switch to single-prec common blocks;
1482      corresponding switch occurs in tamc.h, integer isbyte
1483      TAF store directivs "byte" and "kind" seem equivalent;
1484      Most tamc.h have been updated correspondingly.
1485    
1486    checkpoint61i (2009/02/13)
1487    o autodiff:
1488      fix autodiff_sore/_restore indices for obcs
1489      (spotted by I. Hoteit, M. Mazloff)
1490    o pkg/autodiff, pkg/ctrl:
1491      Add flag to reduce all tapelev I/O to single-prec.
1492      In data.ctrl set
1493        doSinglePrecTapelev = .TRUE.
1494    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
1495      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
1496    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
1497      real fresh water flux (not yet)
1498    o pkg/mdsio & rw:
1499     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
1500     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
1501    o pkg/flt:
1502     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
1503       init_fixed & ini_varia.
1504     - clean-up & simplify linear interpolation S/R:
1505       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
1506     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
1507     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
1508     - add vert. coordinate & horiz. indices to output files.
1509     - change vertical position in initial condition, from index to depth [m].
1510     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
1511       (easier to get to a curvilinear grid) ; delX,delY no longer used.
1512    o pkg/ggl90: a few modifications:
1513     - fix bottom boundary condition, and interpolation of KappaE
1514       near top and bottom
1515     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
1516     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
1517     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
1518    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
1519      (maintain temporary backward compatibility, until next checkpoint)
1520    
1521    checkpoint61h (2009/01/27)
1522    o pkg/diagnostics with "periodic averaging diagnostics":
1523      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
1524    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
1525    o pkg/obcs: fix loop ranges for balancing code
1526    o pkg/flt:
1527     - improve criteria for finding which tile owns a float.
1528     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
1529    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
1530      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
1531      with ocean biogeo)
1532    o pkg/flt:
1533     - do some cleaning and fix the restart ;
1534     - add output.txt in flt_example/results to get this pkg tested.
1535    o genmake2: add an EXTENDED_SRC option and flag.
1536       for now, cannot be turned on on command line (only through genmake_local)
1537    o pkg/mdsio: read/write vector:
1538     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
1539     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
1540       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
1541     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
1542      (drop to 4 digits matching for grad). But this test does not look very
1543      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
1544    
1545    checkpoint61g (2008/12/29)
1546    o pkg/flt:
1547      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
1548       + make OPTIONS file more standard.
1549      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
1550      - fix _BYTESWAPIO CPP-Flag
1551      - standard reading of file-parameter "data.flt"
1552      - fix argument list of S/R FLT_RESTART
1553      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
1554    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
1555    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
1556      a still unfixed compiler/optimization bug
1557    
1558    checkpoint61f (2008/11/21)
1559    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
1560      update results of global_ocean.cs32x15.icedyn test.
1561    o move getcon.F from model/src to pkg/fizhi.
1562    o pkg/exf: add parameter for extrapolation of temp up to the surface
1563       and option to prevent negative evap (in bulk_largeyeager04 only).
1564    o Prather Advection scheme: fix tracer conservation for divergent flow
1565      (e.g., when using NonLin Free-Surface).
1566    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
1567    o gmredi (Visbeck-variable-K):
1568     - add more parameters to Visbeck-variable-K.
1569     - use a 5 points average for dSigmaR in Visbeck-K calculation
1570       (more "homogenous": same stencil and same weights as in dSigmaH)
1571     - update output of ideal_2D_oce experiment.
1572    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
1573      (#undef REAL4_IS_SLOW)
1574     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
1575       coordinate variable
1576     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
1577       (surface forcing fields), removes some of the functionality
1578     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
1579     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
1580       probably not all: copy _RS surface flux fields to RL field before
1581       calling DIAGNOSTICS_FILL
1582     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
1583       real*4 (CALL EXCH_*_RS) versions.
1584     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
1585       (generate new output).
1586    
1587    checkpoint61e (2008/10/23)
1588    o gmredi (Visbeck-variable-K):
1589      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
1590      - change computation of Visbeck-K where Slope > Smax :        
1591        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
1592        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
1593    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
1594      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
1595    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
1596    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
1597      does not become too large (to avoid precision problems in implicit-diffusion
1598      solver); update ideal_2D_oce output.
1599    o pkg ggl90:
1600      - in ggl90_cal.F: compute only one set of visc/diff, used to
1601        step forward TKE/T/S/momentum
1602      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
1603        have Prandlt =1)
1604    o gmredi (fm07):
1605      - add lower limit on Transition layer thickness + lower limit on 1/lambda
1606      - allow to set few more params from data.gmredi
1607    o pkg ggl90:
1608          - add missing sqrt(2) factor in computation of mixing length
1609            scale in ggl90_calc.F
1610            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
1611    
1612    checkpoint61d (2008/09/25)
1613    o adjoint modifs
1614      - adapt to new field rhoInSitu
1615      - allow to revert from StoreDynVars2D, StoreDynVars3D
1616        to individual fields
1617        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
1618    o store 3-D (in-situ) density in commom block (DYNVARS.h)
1619     - save 1 rho computation.
1620     - no longer modify T & S inland when using down_slope pkg.
1621    o gad_som : allow to switch to SOM advection for T & S without corresponding
1622      pickup files (using new S/R: MDS_CHECK4FILE).
1623    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
1624      (for useSingleCpuIO to work in multi-threaded)
1625    o pkg/shelfice:
1626     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
1627       with SHELFICEtopoFile in data.shelfice
1628     - move code for reading ice shelf topography and modifying hFacC into separate
1629       subroutines of the shelfice package
1630     - separate initialisation of "fixed" and "variable" variables
1631     - kTopC is not (yet) replaced by kSurfC, although this is possible
1632    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
1633    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
1634      and rename:
1635      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
1636      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
1637    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
1638    
1639    checkpoint61c (2008/08/30)
1640  o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"  o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
1641    to add mass source/sink of fluid in the interior (3-D generalisation    to add mass source/sink of fluid in the interior (3-D generalisation
1642    of oceanic real-fresh water flux).    of oceanic real-fresh water flux).
# Line 21  o change FIND_RHO to FIND_RHO_2D : Line 1654  o change FIND_RHO to FIND_RHO_2D :
1654    pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.    pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
1655  o new pkg: cheapaml  o new pkg: cheapaml
1656    
1657  checkpoint61b  checkpoint61b (2008/08/05)
1658  o exch2:  o exch2:
1659    change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)    change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
1660    - no longer depend on the order sequence (N,S,E,W).    - no longer depend on the order sequence (N,S,E,W).
# Line 36  o exch2: Line 1669  o exch2:
1669     more intuitive this way) ; rename/remove some variables.     more intuitive this way) ; rename/remove some variables.
1670   - change utils/exch2/matlab-topology-generator & code_mods accordingly.   - change utils/exch2/matlab-topology-generator & code_mods accordingly.
1671    
1672  checkpoint61a  checkpoint61a (2008/07/29)
1673  o exch2/matlab-topology-generator:  o exch2/matlab-topology-generator:
1674    fix bug in index bounds for N-S internal exchange (hard to tell if this    fix bug in index bounds for N-S internal exchange (hard to tell if this
1675    had any effect on the solution).    had any effect on the solution).
# Line 45  o pkg/mnc: small fix in mnc_handle_err: Line 1678  o pkg/mnc: small fix in mnc_handle_err:
1678  o testreport: modify syntax of awk, so that it works also with  o testreport: modify syntax of awk, so that it works also with
1679    awk, and not only with nawk and gawk    awk, and not only with nawk and gawk
1680    
1681  checkpoint61  checkpoint61 (2008/06/24)
1682  o autodiff  o autodiff
1683    Change default for TAF usage by removing argument '-nonew_arg'    Change default for TAF usage by removing argument '-nonew_arg'
1684    This changes TAF subroutine argument list (ordering of active var.)    This changes TAF subroutine argument list (ordering of active var.)
# Line 56  o autodiff Line 1689  o autodiff
1689    Tested TAF version is 1.9.22    Tested TAF version is 1.9.22
1690    N.B.: exch2 hand-written adjoint code currently not TAMC compatible    N.B.: exch2 hand-written adjoint code currently not TAMC compatible
1691    
1692  checkpoint60  checkpoint60 (2008/06/19)
1693  --->>> This is the last checkpoint for which generating the adjoint  --->>> This is the last checkpoint for which generating the adjoint
1694  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
1695  --->>> by default.  --->>> by default.
# Line 81  o bridging the gap between eddy stress a Line 1714  o bridging the gap between eddy stress a
1714    The key modifications are in model/src/taueddy_external_forcing.F    The key modifications are in model/src/taueddy_external_forcing.F
1715    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
1716    
1717  checkpoint59r  checkpoint59r (2008/05/29)
1718  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
1719    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
1720    fix option to read coriolis(@ cell-corner) from files with CS-grid.    fix option to read coriolis(@ cell-corner) from files with CS-grid.
# Line 112  o pkg/ptracers: add second-order moment Line 1745  o pkg/ptracers: add second-order moment
1745    (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)    (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
1746    and requires a fortran 90 compiler    and requires a fortran 90 compiler
1747    
1748  checkpoint59q  checkpoint59q (2008/05/06)
1749  o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)  o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
1750     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
1751  o Refresh tutorial_global_oce_biogeo, notably:  o Refresh tutorial_global_oce_biogeo, notably:
# Line 147  o thsice pkg: Line 1780  o thsice pkg:
1780    - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos    - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
1781    --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice    --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
1782    
1783  checkpoint59p  checkpoint59p (2008/04/10)
1784  o gchem / dic / cfc :  o gchem / dic / cfc :
1785    - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);    - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
1786    - add new parameter files: "data.dic" & "data.cfc" ;    - add new parameter files: "data.dic" & "data.cfc" ;
# Line 173  o in mom_calc_visc, fix average value of Line 1806  o in mom_calc_visc, fix average value of
1806    bottom ; only used with variable horizontal viscosity and non-hydrostatic.    bottom ; only used with variable horizontal viscosity and non-hydrostatic.
1807    also fix diagnostics VISCAHW & VISCA4W.    also fix diagnostics VISCAHW & VISCA4W.
1808    
1809  checkpoint59o  checkpoint59o (2008/03/07)
1810  o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).  o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
1811  o change the loop ordering in most gad_*_adv_x.F to improve vectorization:  o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
1812    move a few statemens out the main loop into separate loops    move a few statemens out the main loop into separate loops
# Line 214  o pkg/ctrl: Line 1847  o pkg/ctrl:
1847      introducing a generic routine (ctrl_map_ini_gen.F).      introducing a generic routine (ctrl_map_ini_gen.F).
1848    - Modification of ctrl_bound/adctrl_bound handling control vector bounds.    - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
1849    
1850  checkpoint59n  checkpoint59n (2008/02/09)
1851  o pkg/diagnostics: for large number of diagnostics, store diagnostic mate  o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
1852    number in dedicate array "hdiag":    number in dedicate array "hdiag":
1853    - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST    - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
# Line 268  o pkg/seaice: add a new flag SEAICEuseTE Line 1901  o pkg/seaice: add a new flag SEAICEuseTE
1901    for now this is only available for the C-grid code and also within    for now this is only available for the C-grid code and also within
1902    #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code    #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
1903    
1904  checkpoint59m  checkpoint59m (2008/01/14)
1905  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
1906    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
1907  o gad_som : fix flux output (& diagnostics) to have same units as other    o gad_som : fix flux output (& diagnostics) to have same units as other  
# Line 286  o pkg/obcs and pkg/seaice: Line 1919  o pkg/obcs and pkg/seaice:
1919  o pkg/salt_plume: added various options for salt plume depth  o pkg/salt_plume: added various options for salt plume depth
1920    criterion and for vertical distribution of the salt    criterion and for vertical distribution of the salt
1921    
1922  checkpoint59l  checkpoint59l (2007/12/18)
1923  o pkg/ptracers: new version of ptracers pickup:  o pkg/ptracers: new version of ptracers pickup:
1924    read meta file and write only fields which are needed to restart.    read meta file and write only fields which are needed to restart.
1925    ( same logic as main pickup file ; also using pickupStrictlyMatch )    ( same logic as main pickup file ; also using pickupStrictlyMatch )
# Line 308  o no longer write pickup from THE_MODEL_ Line 1941  o no longer write pickup from THE_MODEL_
1941  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
1942    or U/VICE from U/VWIND before computing U/VSTRESS    or U/VICE from U/VWIND before computing U/VSTRESS
1943    
1944  checkpoint59k  checkpoint59k (2007/11/30)
1945  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
1946    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
1947  o fix un-initialised variable problem (in mom_vecinv & shap_filt):  o fix un-initialised variable problem (in mom_vecinv & shap_filt):
# Line 330  o pkg/ptracers: Line 1963  o pkg/ptracers:
1963    use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).    use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
1964    to-do: fix pkg/diagnostics when large number of diagnostics are defined.    to-do: fix pkg/diagnostics when large number of diagnostics are defined.
1965    
1966  checkpoint59j  checkpoint59j (2007/11/09)
1967  o in pkgs: dic, obcs, offline, rbcs:  o in pkgs: dic, obcs, offline, rbcs:
1968    standard way to compute coeff. for time interpolation between 2 time reccords    standard way to compute coeff. for time interpolation between 2 time reccords
1969    which retains full precision (& make results less dependent on compiler).    which retains full precision (& make results less dependent on compiler).
# Line 373  o pkg/mdsio & pkg/rw: Line 2006  o pkg/mdsio & pkg/rw:
2006  o added open boundary conditions capability for seaice  o added open boundary conditions capability for seaice
2007      HSNOW, HSALT, UICE, and VICE      HSNOW, HSALT, UICE, and VICE
2008    
2009  checkpoint59i  checkpoint59i (2007/10/21)
2010  o adjoint:  o adjoint:
2011    * fix multiDimAdvection adjoint    * fix multiDimAdvection adjoint
2012      (partial recomputation problem by TAF for fVerT(:,:,kDown)      (partial recomputation problem by TAF for fVerT(:,:,kDown)
# Line 414  o change units of EmPmR (inside the code Line 2047  o change units of EmPmR (inside the code
2047    Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).    Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
2048    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
2049    
2050  checkpoint59h  checkpoint59h (2007/09/29)
2051  o pkg/exf:  o pkg/exf:
2052    - improve vectorization by moving if-statement out of loops in    - improve vectorization by moving if-statement out of loops in
2053      exf_mapfields, exf_radiation      exf_mapfields, exf_radiation
# Line 447  o pkg/thsice: Line 2080  o pkg/thsice:
2080  o testreport: change AD testing : check against results/output_adm.txt  o testreport: change AD testing : check against results/output_adm.txt
2081    using same scripts as for forward test.    using same scripts as for forward test.
2082    
2083  checkpoint59g  checkpoint59g (2007/09/17)
2084  o adjoint testing: in preparation for changing testreport:  o adjoint testing: in preparation for changing testreport:
2085    - output format: cost and grad written on separated lines    - output format: cost and grad written on separated lines
2086    - ad output results in directory "results" (instead of "results_ad")    - ad output results in directory "results" (instead of "results_ad")
# Line 492  o pkg/cd_code: add brackets in multiple Line 2125  o pkg/cd_code: add brackets in multiple
2125    global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,    global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
2126    ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.    ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
2127    
2128  checkpoint59f  checkpoint59f (2007/08/21)
2129  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
2130  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
2131    a bounded range (in forward mode)    a bounded range (in forward mode)
# Line 523  o pkg/seaice Line 2156  o pkg/seaice
2156  o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update  o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
2157     output of global_ocean.cs32x15.thsice .     output of global_ocean.cs32x15.thsice .
2158    
2159  checkpoint59e  checkpoint59e (2007/07/26)
2160  o exch2: new S/R that only use the cube-tracer (center-position) exchange:  o exch2: new S/R that only use the cube-tracer (center-position) exchange:
2161    for B-grid vector (not yet tested) and C-grid vector (<- only used    for B-grid vector (not yet tested) and C-grid vector (<- only used
2162    when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).    when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
# Line 553  o pkg/seaice: Line 2186  o pkg/seaice:
2186    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
2187    * applied OBCS T/S mask to HEFFM sea ice mask    * applied OBCS T/S mask to HEFFM sea ice mask
2188    
2189  checkpoint59d  checkpoint59d (2007/06/21)
2190  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
2191   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
2192   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
# Line 599  o pkg/seaice: Line 2232  o pkg/seaice:
2232     It is turned off by default (=-1.), because it changes the results.     It is turned off by default (=-1.), because it changes the results.
2233   - make it possible to read AREA from a file, too.   - make it possible to read AREA from a file, too.
2234    
2235  checkpoint59c  checkpoint59c (2007/06/04)
2236  o add S/R and diagnostics for oceanic mixed-layer depth  o add S/R and diagnostics for oceanic mixed-layer depth
2237  o move GMRedi call after all vertical mixing schemes (including KPP)  o move GMRedi call after all vertical mixing schemes (including KPP)
2238  o pkg/thsice:  o pkg/thsice:
# Line 632  o adjoint: Line 2265  o adjoint:
2265    Storing is now bundled into large arrays to optimized I/O    Storing is now bundled into large arrays to optimized I/O
2266    (and second step in cleanup of the_main_loop)    (and second step in cleanup of the_main_loop)
2267    
2268  checkpoint59b  checkpoint59b (2007/05/16)
2269  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
2270    - export/import (between ocean & coupler) fields needed for ocean DIC.    - export/import (between ocean & coupler) fields needed for ocean DIC.
2271  o pkg/seaice:  o pkg/seaice:
# Line 703  o pkg/seaice Line 2336  o pkg/seaice
2336  o OpenAD  o OpenAD
2337   - changed verification/OpenAD to full baroclinic setup (including GM/Redi)   - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
2338    
2339  checkpoint59a  checkpoint59a (2007/05/01)
2340  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
2341  o pkg/thsice: rename run-time parameters:  o pkg/thsice: rename run-time parameters:
2342     himin       -> hIceMin     himin       -> hIceMin
# Line 745  o pkg/seaice: fix bug in evp solver, whi Line 2378  o pkg/seaice: fix bug in evp solver, whi
2378  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
2379    - add myThid to all kpp routines (long overdue)    - add myThid to all kpp routines (long overdue)
2380    
2381  checkpoint59  checkpoint59 (2007/04/19)
2382  o pkg/exf:  o pkg/exf:
2383    - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &    - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
2384      ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid      ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
# Line 771  o pkg/thsise Line 2404  o pkg/thsise
2404    - 2nd set of modifs for thsice adjoint in conjunction with exf    - 2nd set of modifs for thsice adjoint in conjunction with exf
2405  o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)  o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
2406    
2407  checkpoint58y_post  checkpoint58y_post (2007/04/15)
2408  o Added capability for latitudinal dependence of Bryan and Lewis, 1979  o Added capability for latitudinal dependence of Bryan and Lewis, 1979
2409    vertical diffusivity, similar to that in MOM4; turned on using    vertical diffusivity, similar to that in MOM4; turned on using
2410    #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using    #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
# Line 787  o ice dynamics (pkg/seaice) with thsice Line 2420  o ice dynamics (pkg/seaice) with thsice
2420         - better when using non-linear advection scheme (not yet fully tested)         - better when using non-linear advection scheme (not yet fully tested)
2421         - can also be used in atmospheric set-up (for now, only the diffusion).         - can also be used in atmospheric set-up (for now, only the diffusion).
2422    
2423  checkpoint58x_post  checkpoint58x_post (2007/04/04)
2424  o IO option for global-file compact format:  o IO option for global-file compact format:
2425    - add options when generating topology (utils/exch2/matlab-topology-generator)    - add options when generating topology (utils/exch2/matlab-topology-generator)
2426    - add I/O capability (pkg/mdsio).    - add I/O capability (pkg/mdsio).
# Line 795  o IO option for global-file compact form Line 2428  o IO option for global-file compact form
2428    for now long-line format not yet supported by pkg/mdsio (& exch2).    for now long-line format not yet supported by pkg/mdsio (& exch2).
2429  o shelfice: add a few diagnostics  o shelfice: add a few diagnostics
2430    
2431  checkpoint58w_post  checkpoint58w_post (2007/03/13)
2432  o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:  o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
2433    rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref    rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
2434    (and replace horiVertRatio in NH code).    (and replace horiVertRatio in NH code).
# Line 816  o cpl_aim+ocn exp.: use consistent rhoCo Line 2449  o cpl_aim+ocn exp.: use consistent rhoCo
2449  o move call to cal_readparms up to make calendar parameters/variable available  o move call to cal_readparms up to make calendar parameters/variable available
2450    to all packages    to all packages
2451    
2452  checkpoint58v_post  checkpoint58v_post (2007/02/08)
2453  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
2454    useDynP_inEos_Zc tested.    useDynP_inEos_Zc tested.
2455  o pkg/exf: changes to properly interpolate/mask/scale initial fields  o pkg/exf: changes to properly interpolate/mask/scale initial fields
# Line 835  o 2nd-Order Moment Advection Scheme (Pra Line 2468  o 2nd-Order Moment Advection Scheme (Pra
2468   - use this scheme for temperature & salinity in 2 advection test exp.:   - use this scheme for temperature & salinity in 2 advection test exp.:
2469     advect_xy & advect_xz, respectively.     advect_xy & advect_xz, respectively.
2470    
2471  checkpoint58u_post  checkpoint58u_post (2007/01/12)
2472  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
2473  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
2474  o testreport: add option "-skipdir" to skip some test.  o testreport: add option "-skipdir" to skip some test.
# Line 850  o add option (linFSConserveTr) to correc Line 2483  o add option (linFSConserveTr) to correc
2483  o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine  o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
2484  o pkg/thsice: fix reading mnc-pickups  o pkg/thsice: fix reading mnc-pickups
2485    
2486  checkpoint58t_post  checkpoint58t_post (2006/12/30)
2487  o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)  o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
2488  o pkg/mdsio:  o pkg/mdsio:
2489   - clean-up mdsio_readfield.F & mdsio_writefield_new.F and   - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
# Line 893  o pkg/seaice: overhaul of thermodynamics Line 2526  o pkg/seaice: overhaul of thermodynamics
2526   - introduce a few local fields to avoid modifying external fields such   - introduce a few local fields to avoid modifying external fields such
2527     as atemp, etc.     as atemp, etc.
2528    
2529  checkpoint58s_post  checkpoint58s_post (2006/12/11)
2530  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
2531    changed exf_set_gen.F so that    changed exf_set_gen.F so that
2532      genperiod=0 means input file is one time-constant field and      genperiod=0 means input file is one time-constant field and
# Line 927  o modifications to pkg/seaice/growth.F a Line 2560  o modifications to pkg/seaice/growth.F a
2560    as actual snow thickness.  It now refers everywhere to effective snow    as actual snow thickness.  It now refers everywhere to effective snow
2561    thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.    thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
2562    
2563  checkpoint58r_post  checkpoint58r_post (2006/11/17)
2564  o modifications to pkg/seaice/growth.F, which change results of  o modifications to pkg/seaice/growth.F, which change results of
2565    lab_sea experiment: fixes pertain to melting snow over open water, to    lab_sea experiment: fixes pertain to melting snow over open water, to
2566    masking EVAP under sea ice, and to using the correct AREA variable for    masking EVAP under sea ice, and to using the correct AREA variable for
# Line 951  o Adding some pkg/diagnostics capability Line 2584  o Adding some pkg/diagnostics capability
2584  o ctrl: adding new control variables:  o ctrl: adding new control variables:
2585    lwflux, lwdown, evap, snowprecip, apressure, runoff    lwflux, lwdown, evap, snowprecip, apressure, runoff
2586    
2587  checkpoint58q_post  checkpoint58q_post (2006/10/20)
2588  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
2589    1/6-deg Southern Ocean configuration by 8% on IBM Datastar and    1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
2590    high_res_cube configuration by 4% on Columbia.    high_res_cube configuration by 4% on Columbia.
# Line 962  o new function "MASTER_CPU_IO" (=T if ma Line 2595  o new function "MASTER_CPU_IO" (=T if ma
2595    single CPU io) so that TAF does not have to see EESUPPORT.h    single CPU io) so that TAF does not have to see EESUPPORT.h
2596  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
2597    
2598  checkpoint58p_post  checkpoint58p_post (2006/09/08)
2599  o obcs: stop if obcs is used with useCDscheme = .true.  o obcs: stop if obcs is used with useCDscheme = .true.
2600  o shelfice:  o shelfice:
2601   - fix a sign error so that no slip at shelfice interface works   - fix a sign error so that no slip at shelfice interface works
# Line 973  o diagnoctics: modify UVELPHI and VVELPH Line 2606  o diagnoctics: modify UVELPHI and VVELPH
2606  o added adjoint exch routined for all exch*3d* routines  o added adjoint exch routined for all exch*3d* routines
2607    and updated flow directives    and updated flow directives
2608    
2609  checkpoint58o_post  checkpoint58o_post (2006/08/28)
2610  o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;  o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
2611    remove old subroutines (_XY_ & _XYZ_); update the adjoint version.    remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
2612  o change controling S/R for writing pickup file (new S/R do_write_pickup)  o change controling S/R for writing pickup file (new S/R do_write_pickup)
# Line 987  o shelfice: Line 2620  o shelfice:
2620   - add a simple boundary layer scheme to reduce noise   - add a simple boundary layer scheme to reduce noise
2621   - fix the indexing in shelfice_u/v_drag so that there will be actually drag   - fix the indexing in shelfice_u/v_drag so that there will be actually drag
2622    
2623  checkpoint58n_post  checkpoint58n_post (2006/08/14)
2624  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
2625     local variable (not in common block).     local variable (not in common block).
2626  o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.  o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
# Line 1008  o change default MAX_NO_THREADS from 32 Line 2641  o change default MAX_NO_THREADS from 32
2641    and stop cleanly when MAX_NO_THREADS is too small.    and stop cleanly when MAX_NO_THREADS is too small.
2642  o add S/R BAR_CHECK to check multi-threaded barrier synchronization  o add S/R BAR_CHECK to check multi-threaded barrier synchronization
2643    
2644  checkpoint58m_post  checkpoint58m_post (2006/07/17)
2645  o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.  o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
2646     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
2647  o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.  o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
# Line 1034  o calc_gw: true flux-form, account for h Line 2667  o calc_gw: true flux-form, account for h
2667    update rotating_tank results, but not plume_on_slope (affected at    update rotating_tank results, but not plume_on_slope (affected at
2668    truncation level, 11 digits).    truncation level, 11 digits).
2669    
2670  checkpoint58l_post  checkpoint58l_post (2006/07/12)
2671  o calc_gw:  o calc_gw:
2672   - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V   - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
2673   - remove side-drag for now (need to fix it); update plume_on_slope results.   - remove side-drag for now (need to fix it); update plume_on_slope results.
# Line 1052  o pkg/ecco: Line 2685  o pkg/ecco:
2685  o pkg/rbcs  o pkg/rbcs
2686    * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing    * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
2687    
2688  checkpoint58k_post  checkpoint58k_post (2006/07/06)
2689  o testreport:  o testreport:
2690   - always build in dir. "build" (if not there, mkdir build instead of building   - always build in dir. "build" (if not there, mkdir build instead of building
2691     & running in input)     & running in input)
# Line 1085  o tracer advection: Line 2718  o tracer advection:
2718     advection subroutine (but still not used within DST advection S/R)     advection subroutine (but still not used within DST advection S/R)
2719  o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)  o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
2720    
2721  checkpoint58j_post  checkpoint58j_post (2006/06/15)
2722  o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields  o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
2723    from file (collects calls previously in FORWARD_STEP)    from file (collects calls previously in FORWARD_STEP)
2724  o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS  o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
# Line 1093  o adjoint store dir. adjusted accordingl Line 2726  o adjoint store dir. adjusted accordingl
2726  o genmake2  o genmake2
2727    replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.    replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
2728    
2729  checkpoint58i_post  checkpoint58i_post (2006/06/14)
2730  o pkg/seaice: add parameter that allows to scale/turn off effect of seaice  o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
2731    on wind stress (SEAICEstressFactor defaults to 1.)    on wind stress (SEAICEstressFactor defaults to 1.)
2732  o Total number of Timers is finite (<=40): comment out 2 non-essential one  o Total number of Timers is finite (<=40): comment out 2 non-essential one
# Line 1107  o pkg/seaice: added SEAICEuseEVPpickup p Line 2740  o pkg/seaice: added SEAICEuseEVPpickup p
2740      non-EVP pickup files when using SEAICEuseEVP      non-EVP pickup files when using SEAICEuseEVP
2741    - fix sign error in diffusion in seaice_calc_rhs    - fix sign error in diffusion in seaice_calc_rhs
2742    
2743  checkpoint58h_post  checkpoint58h_post (2006/06/07)
2744  * Modifications for bottom topography control  * Modifications for bottom topography control
2745    o replace hFacC by _hFacC at various places    o replace hFacC by _hFacC at various places
2746    o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL    o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
# Line 1117  checkpoint58h_post Line 2750  checkpoint58h_post
2750    o works for 5x5 box, doesnt work for global_ocean.90x40x15    o works for 5x5 box, doesnt work for global_ocean.90x40x15
2751  * Adding verification for 5x5 box (4-layer) bottom topography control  * Adding verification for 5x5 box (4-layer) bottom topography control
2752    
2753  checkpoint58g_post  checkpoint58g_post (2006/06/07)
2754  o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,  o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
2755     used for mean seasonal cycle, mean diurnal cycle); add an example     used for mean seasonal cycle, mean diurnal cycle); add an example
2756     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
# Line 1133  o couple pkg/thsice to pkg/seaice: Line 2766  o couple pkg/thsice to pkg/seaice:
2766  o pkg/seaice  o pkg/seaice
2767    - make (default) second order advection a bit less confusing?    - make (default) second order advection a bit less confusing?
2768    
2769  checkpoint58f_post  checkpoint58f_post (2006/06/05)
2770  o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice  o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
2771    to pkg/seaice):    to pkg/seaice):
2772    - new routines thsice_map_exf and thsice_get_exf provide the interface    - new routines thsice_map_exf and thsice_get_exf provide the interface
# Line 1164  o fix bug in aim+thsice albedo: snow & i Line 2797  o fix bug in aim+thsice albedo: snow & i
2797  o results_ad : rename "output.txt_adm" to "output_adm.txt" and change  o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
2798    testreport accordingly    testreport accordingly
2799    
2800  checkpoint58e_post  checkpoint58e_post (2006/05/17)
2801  o SEAICE_CGRID adjoint done  o SEAICE_CGRID adjoint done
2802  o R_STAR adjoint implemented.  o R_STAR adjoint implemented.
2803    * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )    * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
# Line 1172  o R_STAR adjoint implemented. Line 2805  o R_STAR adjoint implemented.
2805  o Make pkg/profile fully independent of ecco,cost, etc. stuff  o Make pkg/profile fully independent of ecco,cost, etc. stuff
2806    to be able to use it in pure forward.    to be able to use it in pure forward.
2807    
2808  checkpoint58d_post  checkpoint58d_post (2006/04/21)
2809  o upgrade simple test-experiment to tutorial example:  o upgrade simple test-experiment to tutorial example:
2810   step.1: duplicate the experiment and (step.2) will remove the old copy.   step.1: duplicate the experiment and (step.2) will remove the old copy.
2811    tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)    tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
# Line 1212  o new package prifiles: Line 2845  o new package prifiles:
2845  o Benign bug fix in initialization (spotted by M. Mazloff) of  o Benign bug fix in initialization (spotted by M. Mazloff) of
2846    ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F    ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
2847    
2848  checkpoint58c_post  checkpoint58c_post (2006/03/23)
2849  o adjoint: finish NLFS adjoint and provide reference output in  o adjoint: finish NLFS adjoint and provide reference output in
2850    verification/global_ocean.90x40x15/results_ad_nlfs    verification/global_ocean.90x40x15/results_ad_nlfs
2851  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
# Line 1246  o seaice: Line 2879  o seaice:
2879     + move computation of the viscosities eta and zeta into a new separate     + move computation of the viscosities eta and zeta into a new separate
2880       routine (because I need to recompute them in seaice_ocean_stress.F)       routine (because I need to recompute them in seaice_ocean_stress.F)
2881    
2882  checkpoint58b_post  checkpoint58b_post (2006/03/13)
2883  o AIM+thSIce: fix sign of Short-Wave through the Ice ;  o AIM+thSIce: fix sign of Short-Wave through the Ice ;
2884    update output.txt of exp. aim.5l_cs.thSI    update output.txt of exp. aim.5l_cs.thSI
2885  o various mnc cleanups and improvements:  o various mnc cleanups and improvements:
# Line 1309  o seaice: Line 2942  o seaice:
2942      (turn on with SEAICEuseFluxForm)      (turn on with SEAICEuseFluxForm)
2943    - replace 1 in 3d global fields by kSurface in growth.F    - replace 1 in 3d global fields by kSurface in growth.F
2944        
2945  checkpoint58a_post  checkpoint58a_post (2006/02/13)
2946  o seaice:  o seaice:
2947    - bug fix in advect.F    - bug fix in advect.F
2948  o shelfice:  o shelfice:
# Line 1362  o pkg/bulk_force: Line 2995  o pkg/bulk_force:
2995     and parameters (note: calcWindStress replaces .NOT.readwindstress).     and parameters (note: calcWindStress replaces .NOT.readwindstress).
2996   - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).   - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
2997    
2998  checkpoint58  checkpoint58 (2006/01/12)
2999  o add "--embed-source" option to genmake2 which, when the supporting  o add "--embed-source" option to genmake2 which, when the supporting
3000    tools can be compiled (as determined by genmake2) will turn on the    tools can be compiled (as determined by genmake2) will turn on the
3001    embed_files package which then embeds the entire MITgcm source code    embed_files package which then embeds the entire MITgcm source code
# Line 1375  o clean up 3-dim. relaxation codes: Line 3008  o clean up 3-dim. relaxation codes:
3008    * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)    * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
3009    * Thanks to Tom Haine for testing!    * Thanks to Tom Haine for testing!
3010    
3011  checkpoint57z_post  checkpoint57z_post (2005/12/31)
3012  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
3013    affects output (@ truncation level) of exp. plume_on_slope ; updated.    affects output (@ truncation level) of exp. plume_on_slope ; updated.
3014  o fix the pickup behavior for obcs in combination with ptracers  o fix the pickup behavior for obcs in combination with ptracers
# Line 1406  o Adding Laplacian-type smoothness const Line 3039  o Adding Laplacian-type smoothness const
3039    * Absolute scale somewhat unclear so far    * Absolute scale somewhat unclear so far
3040    * no area weighting was included since no other cost term does so far    * no area weighting was included since no other cost term does so far
3041    
3042  checkpoint57y_post  checkpoint57y_post (2005/12/08)
3043  First step for a NLFS adjoint  First step for a NLFS adjoint
3044  o initially suppress rStar (new flag DISABLE_RSTAR_CODE)  o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
3045  o new init. routines for calc_r_star, calc_surf_dr  o new init. routines for calc_r_star, calc_surf_dr
3046  o still need to deal with ini_masks_etc  o still need to deal with ini_masks_etc
3047  o testreport seemed happy  o testreport seemed happy
3048  checkpoint57y_pre  checkpoint57y_pre (2005/12/08)
3049    
3050  o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.  o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
3051  o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)  o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
# Line 1421  o cfc fixes for final year of integratio Line 3054  o cfc fixes for final year of integratio
3054  o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should  o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
3055    be in GCHEM_OPTIONS).    be in GCHEM_OPTIONS).
3056    
3057  checkpoint57x_post  checkpoint57x_post (2005/12/04)
3058  o fix testreport Pb in multiple test experiment.  o fix testreport Pb in multiple test experiment.
3059  o cleanup our namelist syntax in verification:  o cleanup our namelist syntax in verification:
3060    - make it more F95 standards compliant (some work still needed)    - make it more F95 standards compliant (some work still needed)
# Line 1441  o adjoint Line 3074  o adjoint
3074      (there are a number of extensive recomputations)      (there are a number of extensive recomputations)
3075    * Initialize certain variables needed for adjoint    * Initialize certain variables needed for adjoint
3076    
3077  checkpoint57w_post  checkpoint57w_post (2005/11/03)
3078  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
3079               fix the singleCpuIO RS version of MDSWRITEFIELD               fix the singleCpuIO RS version of MDSWRITEFIELD
3080     and add a WARNING if using globalFiles=T with multi-processors.     and add a WARNING if using globalFiles=T with multi-processors.
# Line 1458  o PTRACERS: added namelist parameter PTR Line 3091  o PTRACERS: added namelist parameter PTR
3091    ptracers in a large domain with a constant non-zero value. Also,    ptracers in a large domain with a constant non-zero value. Also,
3092    untangle ptracers_init.F a little.    untangle ptracers_init.F a little.
3093    
3094  checkpoint57v_post  checkpoint57v_post (2005/10/13)
3095  o change dome exp. to use variable viscosity in side-drag terms.  o change dome exp. to use variable viscosity in side-drag terms.
3096  o remove all the files from the cfc_offline test since they are now  o remove all the files from the cfc_offline test since they are now
3097    incorporated into tutorial_cfc_offline which has been producing    incorporated into tutorial_cfc_offline which has been producing
# Line 1499  o reduce number of exch calls in shap_fi Line 3132  o reduce number of exch calls in shap_fi
3132  o CS-grid: fix divergence contribution to Leith viscosity. Affects (@  o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
3133    truncation level) 4/5 MLAdjust test results (11&12 digits match).    truncation level) 4/5 MLAdjust test results (11&12 digits match).
3134    
3135  checkpoint57t_post  checkpoint57t_post (2005/10/03)
3136  o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4  o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
3137  o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get  o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
3138    same truncation, independent of the face number: affects affects several    same truncation, independent of the face number: affects affects several
# Line 1522  o Clean, new version of mom_calc_visc. Line 3155  o Clean, new version of mom_calc_visc.
3155    Suggested values of viscosity parameters found in mom_calc_visc.    Suggested values of viscosity parameters found in mom_calc_visc.
3156    Many new viscosity diagnostics available.    Many new viscosity diagnostics available.
3157    
3158  checkpoint57s_post  checkpoint57s_post (2005/09/20)
3159  o Add clearing-house for viscosity calculations, mom_calc_visc and  o Add clearing-house for viscosity calculations, mom_calc_visc and
3160    correct numerous bugs in LeithD and Smagorinsky discretizations.      correct numerous bugs in LeithD and Smagorinsky discretizations.  
3161    mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be    mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
# Line 1548  o various changes to mnc including: Line 3181  o various changes to mnc including:
3181        and works with both EXCH1 and EXCH2 (but needs more testing)        and works with both EXCH1 and EXCH2 (but needs more testing)
3182    - writing works for all verification test cases w/ g77 on Linux    - writing works for all verification test cases w/ g77 on Linux
3183    
3184  checkpoint57r_post  checkpoint57r_post (2005/09/07)
3185  o make MNC variable initialization happen earlier  o make MNC variable initialization happen earlier
3186  o add diagnostics for (almost) each term of the momentum Eq.  o add diagnostics for (almost) each term of the momentum Eq.
3187  o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.  o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
# Line 1568  o new infrastructure for seaice model vs Line 3201  o new infrastructure for seaice model vs
3201  o natl_box_adjoint input_seaice for Lab. Sea now available online via wget  o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
3202    (see README file)    (see README file)
3203    
3204  checkpoint57q_post  checkpoint57q_post (2005/08/19)
3205  o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)  o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
3206  o fix annoying months-old bug in mnc/mdsio output for seaice pkg  o fix annoying months-old bug in mnc/mdsio output for seaice pkg
3207    - bug was reported by Jean-Michel and Ian Fenty    - bug was reported by Jean-Michel and Ian Fenty
# Line 1585  o Modifications to enable scripted COMMO Line 3218  o Modifications to enable scripted COMMO
3218    * verification/OpenAD/code/ has necessary scripts and description;    * verification/OpenAD/code/ has necessary scripts and description;
3219    * converts, compiles and runs successfully;    * converts, compiles and runs successfully;
3220    
3221  checkpoint57p_post  checkpoint57p_post (2005/08/01)
3222  o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F  o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
3223  o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED  o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
3224    (already the case for some pkgs, including recent MNC_init, e.g. thsice)    (already the case for some pkgs, including recent MNC_init, e.g. thsice)
# Line 1599  o Dissipation & phiHyd gradient are alwa Line 3232  o Dissipation & phiHyd gradient are alwa
3232    global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),    global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
3233    matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).    matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
3234    
3235  checkpoint57o_post  checkpoint57o_post (2005/07/30)
3236  o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and  o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
3237    (2) its ready to be documented during the 20050801 DocFest    (2) its ready to be documented during the 20050801 DocFest
3238  o MNC-ify the gmredi package -- tested and works w/ and w/o mnc  o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
# Line 1608  o set to #undef CTRL_SET_OLD_MAXCVARS_30 Line 3241  o set to #undef CTRL_SET_OLD_MAXCVARS_30
3241    in global1x1_tot/code_seaice_adj to access indices 32, 33    in global1x1_tot/code_seaice_adj to access indices 32, 33
3242    (worth another tag)    (worth another tag)
3243    
3244  checkpoint57n_post  checkpoint57n_post (2005/07/29)
3245  o adding precip control xx_precip 32  o adding precip control xx_precip 32
3246  o adding swflux control xx_swflux 33  o adding swflux control xx_swflux 33
3247  o Replacing 10 forcing penalty cost routines by 1 generic.  o Replacing 10 forcing penalty cost routines by 1 generic.
# Line 1624  o enable useSingleCpuIO for mdsio vector Line 3257  o enable useSingleCpuIO for mdsio vector
3257    (applies in particular to tapelev I/O)    (applies in particular to tapelev I/O)
3258  o removed inefficient K-loop in all active_file*control*.F  o removed inefficient K-loop in all active_file*control*.F
3259    
3260  checkpoint57m_post  checkpoint57m_post (2005/07/28)
3261  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
3262    and advect_cs (use EXCH-2 and standard cs-32 grid files).    and advect_cs (use EXCH-2 and standard cs-32 grid files).
3263  o pkg/exch2: filling of face-corner halo regions is optional  o pkg/exch2: filling of face-corner halo regions is optional
3264    (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.    (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
3265    
3266  checkpoint57l_post  checkpoint57l_post (2005/07/14)
3267   tag before updating tutorials (pre-release-2)   tag before updating tutorials (pre-release-2)
3268  o add cos & sin of grid-direction orientation angle (curvilinear grid only,  o add cos & sin of grid-direction orientation angle (curvilinear grid only,
3269     for output and interpolation of input fields onto model grid)     for output and interpolation of input fields onto model grid)
# Line 1642  o fix aim_diagnostics_init.F mate number Line 3275  o fix aim_diagnostics_init.F mate number
3275  o add mnc output capability to diagnostics/diagstat and update  o add mnc output capability to diagnostics/diagstat and update
3276    our cvsignore files for the ACSII output generated    our cvsignore files for the ACSII output generated
3277    
3278  checkpoint57k_post  checkpoint57k_post (2005/07/02)
3279  o lab_sea now uses diagnostics package and provides a suite of  o lab_sea now uses diagnostics package and provides a suite of
3280    new EXF diagnostics output.    new EXF diagnostics output.
3281    
3282  checkpoint57j_post  checkpoint57j_post (2005/06/30)
3283  o exf  o exf
3284    * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):    * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
3285      Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);      Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
# Line 1676  o fix bug in rStar code (calc_r_star.F) Line 3309  o fix bug in rStar code (calc_r_star.F)
3309  o fix few little things to avoid floating error with -ftrapuv (ifort v9)  o fix few little things to avoid floating error with -ftrapuv (ifort v9)
3310   (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)   (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
3311    
3312  checkpoint57i_post  checkpoint57i_post (2005/06/19)
3313  o Diagnostics package was changed: diagnostic allocation is now deactivated  o Diagnostics package was changed: diagnostic allocation is now deactivated
3314    by setting an empty file name in the namelist (used to be by setting 0 frequency)    by setting an empty file name in the namelist (used to be by setting 0 frequency)
3315  o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;  o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
# Line 1695  o pkg/diagnostics: Line 3328  o pkg/diagnostics:
3328    tested against monitor output (including land & thSIce) on various exp.    tested against monitor output (including land & thSIce) on various exp.
3329  o make seaice-pkg I/O type flags (MNC/MDS) more standard.  o make seaice-pkg I/O type flags (MNC/MDS) more standard.
3330    
3331  checkpoint57h_done  checkpoint57h_done (2005/05/19)
3332    tag after changing user customized files (DIAGNOSTICS_SIZE.h,    tag after changing user customized files (DIAGNOSTICS_SIZE.h,
3333    data.diagnostics, data.gchem, data.ptracers) is done.    data.diagnostics, data.gchem, data.ptracers) is done.
3334    
# Line 1704  o pkg/diagnostics: prepare for Global/Re Line 3337  o pkg/diagnostics: prepare for Global/Re
3337  o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE  o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
3338    and rename it: DIFFERENT_MULTIPLE    and rename it: DIFFERENT_MULTIPLE
3339    
3340  checkpoint57h_post  checkpoint57h_post (2005/05/14)
3341  o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers  o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
3342  o pkg/diagnostics: change output frequency, now in seconds (instead  o pkg/diagnostics: change output frequency, now in seconds (instead
3343    of Nb of iterations). This requires to change data.diagnostics.    of Nb of iterations). This requires to change data.diagnostics.
3344  checkpoint57h_pre  checkpoint57h_pre (2005/05/12)
3345    
3346  o in mnc, let the user create the output dir if both mnc_outdir_date  o in mnc, let the user create the output dir if both mnc_outdir_date
3347    and mnc_outdir_num are false    and mnc_outdir_num are false
# Line 1722  o test AB-3 code with 4th.Order advectio Line 3355  o test AB-3 code with 4th.Order advectio
3355  o fix mnc flags in pkg/seaice so that they are "owned" by seaice,  o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
3356    not mnc -- this mistake was found by JMC and is now corrected    not mnc -- this mistake was found by JMC and is now corrected
3357    
3358  checkpoint57g_post  checkpoint57g_post (2005/04/15)
3359  o add Adams-Bashforth 3rd Order time stepping:  o add Adams-Bashforth 3rd Order time stepping:
3360    - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)    - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
3361    - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...    - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
3362  checkpoint57g_pre  checkpoint57g_pre (2005/04/15)
3363    
3364  o make lambda[Theta,Salt]ClimRelax spatially varying  o make lambda[Theta,Salt]ClimRelax spatially varying
3365    (default remains spatially uniform constant based on tau)    (default remains spatially uniform constant based on tau)
# Line 1736  o added new control variables Line 3369  o added new control variables
3369  o separate masks used for ctrl_pack/unpack 'from write_grid' output  o separate masks used for ctrl_pack/unpack 'from write_grid' output
3370    (suggested by G. Forget)    (suggested by G. Forget)
3371    
3372  checkpoint57f_post  checkpoint57f_post (2005/04/06)
3373  o add parameter "baseTime" = model base time = time at iteration zero  o add parameter "baseTime" = model base time = time at iteration zero
3374    new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to    new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
3375    account for baseTime shift    account for baseTime shift
3376  o move Coriolis arrays from PARAMS.h to GRID.h  o move Coriolis arrays from PARAMS.h to GRID.h
3377  checkpoint57f_pre  checkpoint57f_pre (2005/04/06)
3378    
3379  o mnc-ifying the seaice package  o mnc-ifying the seaice package
3380  o introduced an alternative length scale calculation for use in the limiting  o introduced an alternative length scale calculation for use in the limiting
# Line 1762  o adjoint-related modifications Line 3395  o adjoint-related modifications
3395    * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33    * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
3396    * mom_vi_hdissip: to be able to use Leith scheme in adjoint    * mom_vi_hdissip: to be able to use Leith scheme in adjoint
3397    
3398  checkpoint57e_post  checkpoint57e_post (2005/02/28)
3399  o Adding eddy stress controls a la Ferreira et al.  o Adding eddy stress controls a la Ferreira et al.
3400  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
3401    
# Line 1780  o diagnostics: add pickup functionality Line 3413  o diagnostics: add pickup functionality
3413  o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.  o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
3414  o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)  o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
3415    
3416  checkpoint57d_post  checkpoint57d_post (2005/02/11)
3417  o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing  o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
3418  o modify verification/ideal_2D_oce so that it tests the creation of mnc  o modify verification/ideal_2D_oce so that it tests the creation of mnc
3419    output from the diagnostics package    output from the diagnostics package
# Line 1802  o move state variable diagnostics to the Line 3435  o move state variable diagnostics to the
3435    (note: still needs some work specially for snap-shot diagnostics)    (note: still needs some work specially for snap-shot diagnostics)
3436    duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z    duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
3437    
3438  checkpoint57c_post  checkpoint57c_post (2005/01/27)
3439  o Change testing option (-ieee) to get closer agreement between g77 & ifort  o Change testing option (-ieee) to get closer agreement between g77 & ifort
3440  o generate new output.txt files on faulks with g77 & the new -ieee option  o generate new output.txt files on faulks with g77 & the new -ieee option
3441  checkpoint57c_pre  checkpoint57c_pre (2005/01/27)
3442    
3443  o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);  o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
3444    update output.txt of exp. global_ocean.90x40x15    update output.txt of exp. global_ocean.90x40x15
# Line 1838  o pkg/mdsio/ Line 3471  o pkg/mdsio/
3471    * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F    * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
3472    * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)    * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
3473    
3474  checkpoint57b_post  checkpoint57b_post (2004/12/20)
3475  o simplify options in diagnostics_fill arguments (remove weird combinations)  o simplify options in diagnostics_fill arguments (remove weird combinations)
3476  o fix MNC coordinate variables so that they now contain per-face index  o fix MNC coordinate variables so that they now contain per-face index
3477    values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in    values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
# Line 1884  o re-arrange diagnostics pkg initialisat Line 3517  o re-arrange diagnostics pkg initialisat
3517     look through the short list of active diag. (instead of the long list)     look through the short list of active diag. (instead of the long list)
3518     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
3519    
3520  checkpoint57a_post  checkpoint57a_post (2004/12/10)
3521  o this set of changes restores TAMC compatibility  o this set of changes restores TAMC compatibility
3522    tested for global_ocean.90x40x15 adjoint on trough    tested for global_ocean.90x40x15 adjoint on trough
3523    (what a pain)    (what a pain)
3524    
3525  checkpoint57a_pre  checkpoint57a_pre (2004/12/10)
3526  o some modifs in tools/build_options for sunos  o some modifs in tools/build_options for sunos
3527  o call ctrl_pack for ctrl at end for optimcycle=0  o call ctrl_pack for ctrl at end for optimcycle=0
3528    
3529  checkpoint57  checkpoint57 (2004/12/09)
3530  o add horizontal bi-harmonic viscosity for vertical velocity  o add horizontal bi-harmonic viscosity for vertical velocity
3531    - new parameter viscA4W (defaults to viscA4)    - new parameter viscA4W (defaults to viscA4)
3532    - affects only non-hydrostatic code    - affects only non-hydrostatic code
# Line 1911  o untangle a few ifdefs related to cost, Line 3544  o untangle a few ifdefs related to cost,
3544  o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)  o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
3545    (theta2, salt2 in ecco_cost_weights)    (theta2, salt2 in ecco_cost_weights)
3546    
3547  checkpoint56c_post  checkpoint56c_post (2004/12/03)
3548  o OBCS as control variables  o OBCS as control variables
3549    - update ctrl_ad_diff.list, obcs_ad_diff.list    - update ctrl_ad_diff.list, obcs_ad_diff.list
3550    - remove balance of obcs controls from default    - remove balance of obcs controls from default
# Line 1929  o exf: Line 3562  o exf:
3562  o mdsio:  o mdsio:
3563    - i/o-vector change debugLevel from debLevA to debLevB    - i/o-vector change debugLevel from debLevA to debLevB
3564    
3565  checkpoint56b_post  checkpoint56b_post (2004/12/01)
3566  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
3567    is called from DO_THE_MODEL_IO    is called from DO_THE_MODEL_IO
3568    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
# Line 1944  o testreport previously did a lousy job Line 3577  o testreport previously did a lousy job
3577    testreport.    testreport.
3578  o ptracers_monitor: bug fix for MPI  o ptracers_monitor: bug fix for MPI
3579    
3580  checkpoint56a_post  checkpoint56a_post (2004/11/28)
3581  o GCHEM: finish reorganizating the package  o GCHEM: finish reorganizating the package
3582    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
3583      (introduces another 3D-array for each passive tracer, but only if      (introduces another 3D-array for each passive tracer, but only if
# Line 1989  o GCHEM: Line 3622  o GCHEM:
3622    - cleaning up    - cleaning up
3623  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
3624    
3625  checkpoint56  checkpoint56 (2004/11/17)
3626  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
3627  o mnc: cleanup "full" files--fixes out-of-memory problem  o mnc: cleanup "full" files--fixes out-of-memory problem
3628  o ECCO-GODAE  o ECCO-GODAE
# Line 2019  o mdsio: filename info to both stderr, s Line 3652  o mdsio: filename info to both stderr, s
3652  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
3653    from sign change    from sign change
3654    
3655  checkpoint55j_post  checkpoint55j_post (2004/11/10)
3656  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
3657    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3658  o add consistent build directories and .cvsignore files to verification  o add consistent build directories and .cvsignore files to verification
# Line 2030  o make all subroutines 30 or less charac Line 3663  o make all subroutines 30 or less charac
3663  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
3664    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3665    
3666  checkpoint55i_post  checkpoint55i_post (2004/10/28)
3667  o change arrays for total vertical diffusivity (2.D if explicit,  o change arrays for total vertical diffusivity (2.D if explicit,
3668    3.D if implicit) ; each ptracer uses its own background value.    3.D if implicit) ; each ptracer uses its own background value.
3669  o added mnc/NetCDF output capability to ocn_compon_interf  o added mnc/NetCDF output capability to ocn_compon_interf
# Line 2045  o give MNC the ability to create additio Line 3678  o give MNC the ability to create additio
3678  o Compute the non-local term using either KPP vertical diffusivity (=default)  o Compute the non-local term using either KPP vertical diffusivity (=default)
3679     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
3680    
3681  checkpoint55h_post  checkpoint55h_post (2004/10/20)
3682  o add verification test "vermix"  o add verification test "vermix"
3683  o remove all the *_ioinc flags and replace with the single global  o remove all the *_ioinc flags and replace with the single global
3684    outputTypesInclusive flag    outputTypesInclusive flag
# Line 2053  o allow to set a vertical profile of ver Line 3686  o allow to set a vertical profile of ver
3686  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
3687  o useMNC moved from data.mnc to data.pkg  o useMNC moved from data.mnc to data.pkg
3688    
3689  checkpoint55g_post  checkpoint55g_post (2004/10/14)
3690  o Renaming carbon AD experiments to comply with testreport conventions  o Renaming carbon AD experiments to comply with testreport conventions
3691  o Updating adjoint of Held-Suarez hs94.1x64x5  o Updating adjoint of Held-Suarez hs94.1x64x5
3692  o Fixing directives for non-ECCO forward_step, after ECCO directives  o Fixing directives for non-ECCO forward_step, after ECCO directives
# Line 2063  o Fixing directives for non-ECCO forward Line 3696  o Fixing directives for non-ECCO forward
3696  o Updating adjoint output for natl_box_adjoint after  o Updating adjoint output for natl_box_adjoint after
3697    pkg/ecco has been modified (see taga c55d_post)    pkg/ecco has been modified (see taga c55d_post)
3698    
3699  checkpoint55f_post  checkpoint55f_post (2004/10/13)
3700  o rename to timeave_init_fixed  o rename to timeave_init_fixed
3701    
3702  checkpoint55e_post  checkpoint55e_post (2004/10/13)
3703  o some delicate re-shuffle of store directives to avoid one  o some delicate re-shuffle of store directives to avoid one
3704    extra call of do_oceanic_physics    extra call of do_oceanic_physics
3705    affects ecco_the_main_loop.F, do_oceanic_physics.F    affects ecco_the_main_loop.F, do_oceanic_physics.F
# Line 2074  o some delicate re-shuffle of store dire Line 3707  o some delicate re-shuffle of store dire
3707  o NB: this may break global_ocean adjoint temporarily,  o NB: this may break global_ocean adjoint temporarily,
3708    but it is clear how to fix it. Will do later, need this now.    but it is clear how to fix it. Will do later, need this now.
3709    
3710  checkpoint55d_post  checkpoint55d_post (2004/10/11)
3711  o ECCO specific cost function terms (up-to-date with 1x1 runs)  o ECCO specific cost function terms (up-to-date with 1x1 runs)
3712  o ecco_cost_weights is modified to 1x1 runs  o ecco_cost_weights is modified to 1x1 runs
3713  o modifs to allow observations to be read in as  o modifs to allow observations to be read in as
3714    single file or yearly files    single file or yearly files
3715  o enable to read exf forcing fields as either  o enable to read exf forcing fields as either
3716    single file or yearly files (flag useExfYearlyFields)    single file or yearly files (flag useExfYearlyFields)
3717  checkpoint55d_pre  checkpoint55d_pre (2004/10/08)
3718    
3719  o switch between 2-level and 3-level checkpointing  o switch between 2-level and 3-level checkpointing
3720  o add ability of MNC to write local and "partial" (eg. 2D slices where  o add ability of MNC to write local and "partial" (eg. 2D slices where
# Line 2129  o more obcs stuff Line 3762  o more obcs stuff
3762    - changed argument list of OBCS_CALC to myTime+deltaTclock    - changed argument list of OBCS_CALC to myTime+deltaTclock
3763    - fixed about 35 bugs in obcs_external_fields_load    - fixed about 35 bugs in obcs_external_fields_load
3764    
3765  checkpoint55c_post  checkpoint55c_post (2004/09/23)
3766  o obcs stuff  o obcs stuff
3767    - new runtime flags useOBCSprescribe, useOBCSbalance    - new runtime flags useOBCSprescribe, useOBCSbalance
3768    - re-arranged obcs_calc    - re-arranged obcs_calc
# Line 2143  o obcs stuff Line 3776  o obcs stuff
3776  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
3777    which simplifies the calls and passes the ifc check-bounds test    which simplifies the calls and passes the ifc check-bounds test
3778    
3779  checkpoint55b_post  checkpoint55b_post (2004/09/22)
3780  o add a 2D scalar, Z location, exchange_2 routine.  o add a 2D scalar, Z location, exchange_2 routine.
3781  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
3782    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
# Line 2154  o use a more standard discretization for Line 3787  o use a more standard discretization for
3787  o fix gad_advection.F (CubedSphere part), back to version 1.23  o fix gad_advection.F (CubedSphere part), back to version 1.23
3788  o fix bug in mom_vi_del2uv.F (CubedSphere part).  o fix bug in mom_vi_del2uv.F (CubedSphere part).
3789    
3790  checkpoint55a_post  checkpoint55a_post (2004/09/20)
3791  o merged code to  o merged code to
3792    * prescribe/read time-dependent open boundaries    * prescribe/read time-dependent open boundaries
3793      (works in conjunction with exf, cal)      (works in conjunction with exf, cal)
# Line 2162  o merged code to Line 3795  o merged code to
3795    * each boundary N/S/E/W now has its own CPP option    * each boundary N/S/E/W now has its own CPP option
3796      (healthy for the adjoint)      (healthy for the adjoint)
3797    
3798  checkpoint55  checkpoint55 (2004/09/17)
3799  o up-to-date adjoint of previous breaks  o up-to-date adjoint of previous breaks
3800    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
3801    - global_ocean_ebm: adjoint still needs fix (TLM ok)    - global_ocean_ebm: adjoint still needs fix (TLM ok)
# Line 2172  o up-to-date adjoint of previous breaks Line 3805  o up-to-date adjoint of previous breaks
3805  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
3806    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
3807    
3808  checkpoint54f_post  checkpoint54f_post (2004/09/16)
3809  o in verification/carbin/ remove experiment related to  o in verification/carbin/ remove experiment related to
3810    ALLOW_PASSIVE_TRACER (array tr1 etc)    ALLOW_PASSIVE_TRACER (array tr1 etc)
3811    code_ad/ input_ad/ results_ad    code_ad/ input_ad/ results_ad
# Line 2198  o overhaul of IO so that we now have fla Line 3831  o overhaul of IO so that we now have fla
3831    - numerous small formatting cleanups for ProTeX    - numerous small formatting cleanups for ProTeX
3832  o add version info (via BUILD_INFO.h) to MNC and stdout  o add version info (via BUILD_INFO.h) to MNC and stdout
3833    
3834  checkpoint54e_post  checkpoint54e_post (2004/09/02)
3835  o add two new packages  o add two new packages
3836    - pp81 (Packanowski and Philander, 1981), Richardson number and    - pp81 (Packanowski and Philander, 1981), Richardson number and
3837      stratification dependent mixing      stratification dependent mixing
3838    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
3839    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
3840      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
3841      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
3842  o add offline package  o add offline package
3843  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
3844    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
3845  o genmake2: add ability to search for C compilers and cleanup test output  o genmake2: add ability to search for C compilers and cleanup test output
3846    - fixes recent SX-6 problems and should help with others (eg. HP-UX)    - fixes recent SX-6 problems and should help with others (eg. HP-UX)
3847    
3848  checkpoint54d_post  checkpoint54d_post (2004/07/27)
3849  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
3850  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
3851    leading to additional shift by 5 days each year of integration    leading to additional shift by 5 days each year of integration
# Line 2228  o fix a bug in Flux deriv. vs Ts (pkg/ai Line 3861  o fix a bug in Flux deriv. vs Ts (pkg/ai
3861  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
3862  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
3863    
3864  checkpoint54c_post  checkpoint54c_post (2004/07/18)
3865  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
3866    this affects (truncation error) output.txt of test-exp:    this affects (truncation error) output.txt of test-exp:
3867     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
# Line 2239  o define the max number of passive trace Line 3872  o define the max number of passive trace
3872  o start to test mnc routinely in exp0  o start to test mnc routinely in exp0
3873  o add sea-ice loading (sIceLoad) as a new forcing field.  o add sea-ice loading (sIceLoad) as a new forcing field.
3874    
3875  checkpoint54b_post  checkpoint54b_post (2004/07/08)
3876  o add testreport "-j JOBS" option for parallel builds (tested and pretty  o add testreport "-j JOBS" option for parallel builds (tested and pretty
3877     impressive on Altix and Opteron systems)     impressive on Altix and Opteron systems)
3878  o diagnostics can now write NetCDF files through the mnc package  o diagnostics can now write NetCDF files through the mnc package
# Line 2249  o staggerTimeStep & NLFS: rescale T & S Line 3882  o staggerTimeStep & NLFS: rescale T & S
3882    affects (truncation error) output of lab_sea & natl_box exp.: updated    affects (truncation error) output of lab_sea & natl_box exp.: updated
3883  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
3884    
3885  checkpoint54a_post  checkpoint54a_post (2004/07/06)
3886  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
3887  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
3888  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
3889  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
3890    + internal_wave (shift in writing cg2d_ini_res)    + internal_wave (shift in writing cg2d_ini_res)
3891  checkpoint54a_pre  checkpoint54a_pre (2004/07/05)
3892    
3893  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
3894    - modified verification/lab_sea and natl_box_adjoint accordingly    - modified verification/lab_sea and natl_box_adjoint accordingly
3895    
3896  checkpoint54  checkpoint54 (2004/07/02)
3897  checkpoint53g_post  checkpoint53g_post (2004/07/02)
3898  o prepare splitting of thermodynamics: store convect.counter in common block  o prepare splitting of thermodynamics: store convect.counter in common block
3899  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
3900    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
# Line 2270  o new parameter "nShapS": allow to treat Line 3903  o new parameter "nShapS": allow to treat
3903  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
3904  o restore adjointability  o restore adjointability
3905    
3906  checkpoint53f_post  checkpoint53f_post (2004/06/25)
3907  o modifications that affect AIM experiment results (update output.txt):  o modifications that affect AIM experiment results (update output.txt):
3908    - no advection of S at top interface Nr (pkg/generic_advdiff)    - no advection of S at top interface Nr (pkg/generic_advdiff)
3909    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
# Line 2283  o merged cylindrical coord configuration Line 3916  o merged cylindrical coord configuration
3916  o added rotating_tank experiment  o added rotating_tank experiment
3917  checkpoint53e_pre  checkpoint53e_pre
3918    
3919  checkpoint53d_post  checkpoint53d_post (2004/06/14)
3920  o faulks upgraded: re-generate output.txt that have changed:  o faulks upgraded: re-generate output.txt that have changed:
3921     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
3922  o Added Bryan and Lewis, 1979, vertical diffusivity profile  o Added Bryan and Lewis, 1979, vertical diffusivity profile
# Line 2302  o regenerated output for global_ocean_eb Line 3935  o regenerated output for global_ocean_eb
3935  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
3936    of mom_common/    of mom_common/
3937    - simple re-arrangement of instructions within computing loop    - simple re-arrangement of instructions within computing loop
3938  checkpoint53d_pre  checkpoint53d_pre (2004/05/21)
3939    
3940  checkpoint53c_post  checkpoint53c_post (2004/05/21)
3941  o new version of coupler for AIM+thSIce and Ocean models  o new version of coupler for AIM+thSIce and Ocean models
3942   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
3943   - land: change Evaporation of snow   - land: change Evaporation of snow
# Line 2321  o Adjoint of EBM package + verification Line 3954  o Adjoint of EBM package + verification
3954    * TLM OK    * TLM OK
3955    * ADM not sufficient accuracy yet (needs further testing)    * ADM not sufficient accuracy yet (needs further testing)
3956    
3957  checkpoint53b_post  checkpoint53b_post (2004/05/14)
3958  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository
3959    * package is pkg/ebm    * package is pkg/ebm
3960    * verif. is verification/global_ocean_ebm    * verif. is verification/global_ocean_ebm
# Line 2339  C        Destabilization of the thermoha Line 3972  C        Destabilization of the thermoha
3972  C        by atmospheric eddy transports.  C        by atmospheric eddy transports.
3973  C        J. Climate 7(12), 1870-1882  C        J. Climate 7(12), 1870-1882
3974  o Will need long integration testing.  o Will need long integration testing.
3975  checkpoint53b_pre  checkpoint53b_pre (2004/05/14)
3976    
3977  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code
3978  o renamed and split ini_mnc_io  o renamed and split ini_mnc_io
# Line 2347  o pkg/land: only liquid water can diffus Line 3980  o pkg/land: only liquid water can diffus
3980  o AIM using land: soil wetness availability account for snow  o AIM using land: soil wetness availability account for snow
3981  o added printMapIncludesZeros to EEPARMS namelist  o added printMapIncludesZeros to EEPARMS namelist
3982    
3983  checkpoint53a_post  checkpoint53a_post (2004/05/11)
3984  o restore TAMC compatiility for exf_constants.h  o restore TAMC compatiility for exf_constants.h
3985    (no usage of _d in .h)    (no usage of _d in .h)
3986  o Additional storing in KPP in an attempt to fix  o Additional storing in KPP in an attempt to fix
# Line 2360  o Fixed verification/natl_box_adjoint ex Line 3993  o Fixed verification/natl_box_adjoint ex
3993    and hence gives results closer to that of Experiment 2.    and hence gives results closer to that of Experiment 2.
3994    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
3995    
3996  checkpoint53  checkpoint53 (2004/05/06)
3997  o stable checkpoint with up to date adjoint  o stable checkpoint with up to date adjoint
3998    TLM tests only run for 1st grdchk at the moment. Its unclear if    TLM tests only run for 1st grdchk at the moment. Its unclear if
3999    this is a code problem or a problem with resetting code for g_    this is a code problem or a problem with resetting code for g_
# Line 2370  o stable checkpoint with up to date adjo Line 4003  o stable checkpoint with up to date adjo
4003     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
4004       are both still in chaos following their security messes.       are both still in chaos following their security messes.
4005    
4006  checkpoint52n_post  checkpoint52n_post (2004/05/06)
4007  o various build (mostly genmake2) changes including:  o various build (mostly genmake2) changes including:
4008    - ability to build/run more easily within Cygwin and MacOS X    - ability to build/run more easily within Cygwin and MacOS X
4009    - more complicated Makefiles with a stronger dependence on Gnu Make    - more complicated Makefiles with a stronger dependence on Gnu Make
# Line 2401  o fix in pkg/thsice: Line 4034  o fix in pkg/thsice:
4034    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
4035   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
4036    
4037  checkpoint52m_post  checkpoint52m_post (2004/04/18)
4038  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
4039    this does not change any of the results, because myIter=0 in swfrac always    this does not change any of the results, because myIter=0 in swfrac always
4040    lead to jwtype=2 (the default anyway), but the call makes little sense    lead to jwtype=2 (the default anyway), but the call makes little sense
# Line 2433  o test exp. advect_cs: use the standard Line 4066  o test exp. advect_cs: use the standard
4066  o Added functionality to grdchk:  o Added functionality to grdchk:
4067    pick global i,j,k position (or nearest wet) where to perform check.    pick global i,j,k position (or nearest wet) where to perform check.
4068    
4069  checkpoint52l_post  checkpoint52l_post (2004/03/11)
4070  o new land formulation:  o new land formulation:
4071    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
4072       energy conservation.       energy conservation.
# Line 2444  o aim_v23 modification for new land mode Line 4077  o aim_v23 modification for new land mode
4077    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
4078       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
4079    b) add snow precipitation.    b) add snow precipitation.
4080  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
4081    
4082  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
4083  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 2457  o fix ini_curvilinear_grid ; test CS exp Line 4090  o fix ini_curvilinear_grid ; test CS exp
4090  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
4091  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
4092    
4093  checkpoint52k_post  checkpoint52k_post (2004/02/23)
4094  o removed top-level directory "diags"  o removed top-level directory "diags"
4095    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
4096  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 2470  o set all ...Freq to zero after cost_fin Line 4103  o set all ...Freq to zero after cost_fin
4103    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
4104  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
4105    
4106  checkpoint52j_post  checkpoint52j_post (2004/02/18)
4107  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
4108  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
4109  o Really weird thing!  o Really weird thing!
# Line 2478  o Really weird thing! Line 4111  o Really weird thing!
4111    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
4112    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
4113    after cost_final call which should not be there!    after cost_final call which should not be there!
4114  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
4115    
4116  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
4117    error messages    error messages
# Line 2495  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 4128  o merged mom_vi_calc_relvort3.F, mom_vi_
4128    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
4129  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
4130    
4131  checkpoint52i_post  checkpoint52i_post (2004/01/21)
4132  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
4133  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
4134  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
4135    
4136  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
4137    the old pkg/aim).    the old pkg/aim).
4138    
4139  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
4140  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
4141  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
4142  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 2514  o added temporary hack for sea-ice dynam Line 4147  o added temporary hack for sea-ice dynam
4147    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
4148    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
4149    
4150  checkpoint52f_post  checkpoint52f_post (2004/01/09)
4151  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
4152  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
4153  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
4154  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
4155    
4156  checkpoint52e_post  checkpoint52e_post (2004/01/07)
4157  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
4158    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
4159  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 2528  o step.1 : rewrite (as in MultiDimAdvec) Line 4161  o step.1 : rewrite (as in MultiDimAdvec)
4161  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
4162  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
4163   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
4164  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
4165    
4166  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
4167  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 2539  o added exf_offset_atemp for Celsius to Line 4172  o added exf_offset_atemp for Celsius to
4172  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
4173  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
4174    
4175  checkpoint52d_post  checkpoint52d_post (2003/12/16)
4176  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
4177    - updated output accordingly    - updated output accordingly
4178    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 2568  o check-in the first version of the coup Line 4201  o check-in the first version of the coup
4201  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
4202     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
4203    
4204  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
4205  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
4206  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
4207    
4208  checkpoint52c_post  checkpoint52c_post (2003/11/25)
4209  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
4210    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
4211    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 2586  o Removed all CPP options for cal packag Line 4219  o Removed all CPP options for cal packag
4219  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
4220  o corrected key comp. for passkey  o corrected key comp. for passkey
4221    
4222  checkpoint52b_post  checkpoint52b_post (2003/11/23)
4223  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
4224   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
4225   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 2594  o new version: "thsice" of thermodynamic Line 4227  o new version: "thsice" of thermodynamic
4227   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
4228     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
4229  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
4230  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
4231    
4232  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
4233  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 2604  o missing PTRACERS headers in some routi Line 4237  o missing PTRACERS headers in some routi
4237  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
4238    to ensure proper customization    to ensure proper customization
4239    
4240  checkpoint52a_post  checkpoint52a_post (2003/11/17)
4241  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
4242    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
4243    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 2619  o fix problem with ECCO-related divided Line 4252  o fix problem with ECCO-related divided
4252    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
4253    but no warning issued by TAF    but no warning issued by TAF
4254    
4255  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
4256  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
4257    
4258  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
4259  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
4260    
4261  checkpoint51u_post  checkpoint51u_post (2003/11/06)
4262  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
4263    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
4264  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 2640  o top level routines the_main_loop, forw Line 4273  o top level routines the_main_loop, forw
4273    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
4274  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
4275    
4276  checkpoint51t_post  checkpoint51t_post (2003/11/04)
4277  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
4278    
4279  checkpoint51s_post  checkpoint51s_post (2003/11/04)
4280  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
4281  o pkg/grdchk  o pkg/grdchk
4282    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 2652  o pkg/grdchk Line 4285  o pkg/grdchk
4285    - additional high-precision output for testreport    - additional high-precision output for testreport
4286      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
4287    
4288  checkpoint51r_post  checkpoint51r_post (2003/11/03)
4289  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
4290  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
4291    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
4292    
4293  checkpoint51q_post  checkpoint51q_post (2003/10/30)
4294  o cd_code:  o cd_code:
4295    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
4296    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 2673  o ctrl package totally restructured Line 4306  o ctrl package totally restructured
4306    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
4307  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
4308    
4309  checkpoint51p_post  checkpoint51p_post (2003/10/30)
4310  o create initial cd_code package  o create initial cd_code package
4311    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
4312      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 2688  o create initial cd_code package Line 4321  o create initial cd_code package
4321  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
4322  o cleanup testreport  o cleanup testreport
4323    
4324  checkpoint51o_post  checkpoint51o_post (2003/10/27)
4325  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
4326    - carbon/    - carbon/
4327    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 2709  o Correcting initialisations for fVerU, Line 4342  o Correcting initialisations for fVerU,
4342  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
4343    fVerU, fVerV    fVerU, fVerV
4344  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
4345  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
4346    
4347  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
4348  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 2717  o added the [#include "AD_CONFIG.h"] sta Line 4350  o added the [#include "AD_CONFIG.h"] sta
4350   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
4351   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
4352    
4353  checkpoint51n_post  checkpoint51n_post (2003/10/23)
4354  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
4355    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
4356    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 2726  o modifications to make FREEZE flux visi Line 4359  o modifications to make FREEZE flux visi
4359       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
4360  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
4361    
4362  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
4363  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
4364  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
4365    defines:    defines:
# Line 2734  o added [#include "AD_CONFIG.h"] to all Line 4367  o added [#include "AD_CONFIG.h"] to all
4367    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
4368    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
4369    
4370  checkpoint51m_post  checkpoint51m_post (2003/10/21)
4371  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
4372    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
4373    - various cleanups related to package handling    - various cleanups related to package handling
4374    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
4375    
4376  checkpoint51l_post  checkpoint51l_post (2003/10/20)
4377  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
4378   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
4379   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
4380   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
4381     model integration time     model integration time
4382    
4383  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
4384  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)
4385  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.
4386  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
4387     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
4388    
4389  checkpoint51k_post  checkpoint51k_post (2003/10/16)
4390  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
4391   - 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):
4392     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 2767  o added an include barrier to the defaul Line 4400  o added an include barrier to the defaul
4400    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
4401  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
4402    
4403  checkpoint51j_post  checkpoint51j_post (2003/10/10)
4404  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
4405  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
4406  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 2781  o Moving pkg-specific flow directives to Line 4414  o Moving pkg-specific flow directives to
4414         - pkg_ad_diff.list         - pkg_ad_diff.list
4415         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
4416    
4417  checkpoint51i_post  checkpoint51i_post (2003/10/09)
4418  o merge of the branch-genmake2  o merge of the branch-genmake2
4419    - knowingly breaks the older genmake    - knowingly breaks the older genmake
4420    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
4421    - new testreport supersedes older testscript    - new testreport supersedes older testscript
4422  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
4423  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
4424    
4425  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
4426  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 2799  o modify gchem pkg to be more versatile Line 4432  o modify gchem pkg to be more versatile
4432  o modifications to clean up dic pkg  o modifications to clean up dic pkg
4433  o add pkg/cfc  o add pkg/cfc
4434    
4435  checkpoint51g_post  checkpoint51g_post (2003/10/02)
4436  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
4437  o start removing verification/vero/  o start removing verification/vero/
4438  o update AD-related stuff  o update AD-related stuff
# Line 2807  o update AD-related stuff Line 4440  o update AD-related stuff
4440  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
4441    vector invariant setup    vector invariant setup
4442    
4443  checkpoint51f_post  checkpoint51f_post (2003/10/02)
4444  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)
4445  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
4446    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
4447    
4448  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
4449  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
4450      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
4451    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 2824  o Bug fix to pkg/ptracers, pkg/generic_a Line 4457  o Bug fix to pkg/ptracers, pkg/generic_a
4457      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
4458      non-local transport term.      non-local transport term.
4459    
4460  checkpoint51e_post  checkpoint51e_post (2003/08/03)
4461  o pkg/mom_vecinv:  o pkg/mom_vecinv:
4462    - 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)
4463    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 2834  o atmospheric geopotential: - include wa Line 4467  o atmospheric geopotential: - include wa
4467  o land pkg: read initial state from files.  o land pkg: read initial state from files.
4468  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
4469    
4470  checkpoint51d_post  checkpoint51d_post (2003/07/18)
4471  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
4472    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
4473  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 2847  o Use cluster local disks for purely loc Line 4480  o Use cluster local disks for purely loc
4480    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
4481    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
4482    
4483  checkpoint51c_post  checkpoint51c_post (2003/07/08)
4484  o introducing integer flag debugLevel  o introducing integer flag debugLevel
4485    - debLevZero: suppress all output    - debLevZero: suppress all output
4486    - debLevA: standard    - debLevA: standard
# Line 2870  o added verification for adjoint with pt Line 4503  o added verification for adjoint with pt
4503    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
4504  <<<checkpoint51b_pre  <<<checkpoint51b_pre
4505    
4506  checkpoint51a_post  checkpoint51a_post (2003/06/25)
4507  o added code for biogeochemistry package  o added code for biogeochemistry package
4508    - new pkgs: dic, gchem    - new pkgs: dic, gchem
4509    - new subroutine in ptracers    - new subroutine in ptracers
4510  o modify code for biogeo packages  o modify code for biogeo packages
4511    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
4512    
4513  checkpoint51  checkpoint51 (2003/06/24)
4514  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
4515    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
4516    kept separate packages    kept separate packages
# Line 2885  o merged improved packages from ecco-bra Line 4518  o merged improved packages from ecco-bra
4518  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
4519    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
4520    
4521  checkpoint50i_post  checkpoint50i_post (2003/06/23)
4522  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
4523    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
4524    - 1st step: this one is differentiable    - 1st step: this one is differentiable
4525    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
4526                from ecco-branch)                from ecco-branch)
4527    
4528  checkpoint50h_post  checkpoint50h_post (2003/06/20)
4529  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
4530  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
4531  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 2901  o New variable in PARM03 for more flexib Line 4534  o New variable in PARM03 for more flexib
4534  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
4535    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
4536    
4537  checkpoint50g_post  checkpoint50g_post (2003/05/23)
4538  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
4539    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
4540    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
4541      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
4542    
4543  checkpoint50f_post  checkpoint50f_post (2003/05/23)
4544  o exf totally restructured  o exf totally restructured
4545    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
4546      and made sure it's still differentiable      and made sure it's still differentiable
# Line 2915  o exf totally restructured Line 4548  o exf totally restructured
4548    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
4549    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
4550    
4551  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
4552   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 ;
4553        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
4554   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 2925  checkpoint50f_pre Line 4558  checkpoint50f_pre
4558   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
4559   o removed lots of single quotes from comments   o removed lots of single quotes from comments
4560    
4561  checkpoint50e_post  checkpoint50e_post (2003/05/14)
4562  o make KPP work with PTRACERS  o make KPP work with PTRACERS
4563   - 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
4564     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
4565   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
4566     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
4567  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
4568  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
4569    
4570  checkpoint50d_post  checkpoint50d_post (2003/05/13)
4571  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
4572    files analogous to write_state.F    files analogous to write_state.F
4573  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,
4574    analogous to the cg2d-related output.    analogous to the cg2d-related output.
4575  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,
4576    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
4577  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
4578    
4579  checkpoint50c_post  checkpoint50c_post (2003/05/12)
4580  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)
4581  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
4582  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.
4583  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
4584  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
4585    
4586  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
4587  Merging from release1_p13:  Merging from release1_p13:
4588  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
4589  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4590    
4591  checkpoint50b_post  checkpoint50b_post (2003/04/17)
4592  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
4593  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
4594    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 2964  o new flag "useCDscheme" (default=F); re Line 4597  o new flag "useCDscheme" (default=F); re
4597  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
4598     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
4599    
4600  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
4601  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
4602  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
4603    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
4604    
4605  checkpoint50a_post  checkpoint50a_post (2003/03/21)
4606  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
4607    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
4608    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
4609    in contradiction with new key itdkey.    in contradiction with new key itdkey.
4610    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
4611    
4612  checkpoint50  checkpoint50 (2003/03/08)
4613  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
4614    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
4615  - bug fix in find_alpha  - bug fix in find_alpha
# Line 2984  checkpoint50 Line 4617  checkpoint50
4617  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
4618  - merged some sliced AD support routines  - merged some sliced AD support routines
4619    
4620  checkpoint49  checkpoint49 (2003/03/06)
4621  merged from ecco-branch:  merged from ecco-branch:
4622  o exf:  o exf:
4623    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 3022  o DIVA: Line 4655  o DIVA:
4655    (see MITgcm manual).    (see MITgcm manual).
4656  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
4657    
4658  checkpoint48i_post  checkpoint48i_post (2003/03/05)
4659  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
4660    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
4661    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 3040  o Modif. for DIVA: Line 4673  o Modif. for DIVA:
4673    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
4674    only relevant for ecco-branch)    only relevant for ecco-branch)
4675    
4676  checkpoint48h_post  checkpoint48h_post (2003/02/28)
4677  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
4678  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
4679  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4680  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
4681    
4682  checkpoint48g_post  checkpoint48g_post (2003/02/18)
4683  --- EOS:  --- EOS:
4684  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
4685    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 3060  o accurate phiHyd when using interface-W Line 4693  o accurate phiHyd when using interface-W
4693   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
4694  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
4695    
4696  checkpoint48f_post  checkpoint48f_post (2003/02/18)
4697  Merging from release1_p12:  Merging from release1_p12:
4698  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
4699    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 3088  o pkg/seaice: Line 4721  o pkg/seaice:
4721    - adjoint-friendly modifications    - adjoint-friendly modifications
4722    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
4723    
4724  checkpoint48e_post  checkpoint48e_post (2003/02/12)
4725  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)
4726  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
4727    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 3099  o following exp works with Olx=Oly=2 (an Line 4732  o following exp works with Olx=Oly=2 (an
4732      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
4733    (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)
4734    
4735  checkpoint48d_post  checkpoint48d_post (2003/02/09)
4736  o in preparation for r*:  o in preparation for r*:
4737   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
4738      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 3107  o in preparation for r*: Line 4740  o in preparation for r*:
4740      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
4741    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
4742    
4743  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
4744  o in preparation for r*:  o in preparation for r*:
4745    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.
4746    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.
4747    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.
4748  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
4749    
4750  checkpoint48c_post  checkpoint48c_post (2003/02/06)
4751  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
4752  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
4753    
4754  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
4755  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
4756  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)
4757    
4758  checkpoint48b_post  checkpoint48b_post (2003/01/27)
4759  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
4760   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
4761  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
4762    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
4763    
4764  checkpoint48a_post  checkpoint48a_post (2003/01/24)
4765  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
4766     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
4767    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
4768                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
4769    
4770  checkpoint48  checkpoint48 (2003/01/23)
4771  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')
4772    
4773  checkpoint47j_post  checkpoint47j_post (2003/01/21)
4774  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.
4775  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
4776  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 3156  o Yet more changes in gmredi: Line 4789  o Yet more changes in gmredi:
4789      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
4790  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
4791    
4792  checkpoint47i_post  checkpoint47i_post (2003/01/13)
4793  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.
4794  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)
4795    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 3172  o case GM_BOLUS_ADVEC should be cleaned Line 4805  o case GM_BOLUS_ADVEC should be cleaned
4805    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
4806  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
4807    
4808  checkpoint47g_post  checkpoint47g_post (2003/01/10)
4809  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
4810    (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)
4811  o After TAF bug fix:  o After TAF bug fix:
# Line 3198  Gradient checks OK for Line 4831  Gradient checks OK for
4831  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
4832  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
4833    
4834  checkpoint47f_post  checkpoint47f_post (2002/12/28)
4835  Merging from release1_p10:  Merging from release1_p10:
4836  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
4837    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 3210  o modifications for using pkg/exf with p Line 4843  o modifications for using pkg/exf with p
4843    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
4844      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
4845    
4846  checkpoint47e_post  checkpoint47e_post (2002/12/27)
4847  o created a tag prior to creating a branch  o created a tag prior to creating a branch
4848    
4849  checkpoint47d_post  checkpoint47d_post (2002/12/16)
4850  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
4851    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
4852  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
4853    oceanic pressure coordinates code    oceanic pressure coordinates code
4854  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
4855    also described in the tutorial section of the manual    also described in the tutorial section of the manual
4856  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
4857    
4858  checkpoint47c_post  checkpoint47c_post (2002/12/16)
4859  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
4860    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
4861    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 3234  o OCEANICP & realFreshWater: include P-E Line 4867  o OCEANICP & realFreshWater: include P-E
4867    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
4868  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
4869    
4870  checkpoint47b_post  checkpoint47b_post (2002/12/05)
4871  Merging from release1_p9:  Merging from release1_p9:
4872  o pkg/seaice  o pkg/seaice
4873    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 3251  o verification/lab_sea Line 4884  o verification/lab_sea
4884    - added missing matlab routines    - added missing matlab routines
4885    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
4886    
4887  checkpoint47a_post  checkpoint47a_post (2002/11/23)
4888  o new pkg: aim_v23  o new pkg: aim_v23
4889   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
4890     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 3268  o bulk_force and therm_seaice Line 4901  o bulk_force and therm_seaice
4901  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
4902     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
4903    
4904  checkpoint47  checkpoint47 (2002/11/15)
4905  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
4906  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
4907  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 3297  o Updated verification/carbon/ Line 4930  o Updated verification/carbon/
4930    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
4931    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
4932    
4933  checkpoint46n_post  checkpoint46n_post (2002/11/12)
4934  Merging from release1_p8:  Merging from release1_p8:
4935  o verification/natl_box:  o verification/natl_box:
4936    updating new external_fields_load routine    updating new external_fields_load routine
# Line 3351  o Adding new verification experiment glo Line 4984  o Adding new verification experiment glo
4984    the exf (and cal) package instead of the    the exf (and cal) package instead of the
4985    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
4986    
4987  checkpoint46m_post  checkpoint46m_post (2002/11/07)
4988  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
4989  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
4990    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 3364  o introduced flag for controllin non-hyd Line 4997  o introduced flag for controllin non-hyd
4997  o removed gravitySign from PARM04  o removed gravitySign from PARM04
4998  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
4999    
5000  checkpoint46l_post  checkpoint46l_post (2002/11/01)
5001  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
5002   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
5003     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 3377  o made convective adjustment work with p Line 5010  o made convective adjustment work with p
5010     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
5011     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
5012     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
5013  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
5014    
5015  checkpoint46k_post  checkpoint46k_post (2002/10/23)
5016  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
5017   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
5018   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 3393  o S/R aim_initialise.F replace S/R aim_i Line 5026  o S/R aim_initialise.F replace S/R aim_i
5026   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
5027   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
5028    
5029  checkpoint46j_post  checkpoint46j_post (2002/10/07)
5030  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
5031  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
5032  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)
5033  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
5034  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
5035    
5036  checkpoint46i_post  checkpoint46i_post (2002/09/25)
5037  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
5038    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
5039    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
5040    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 !
5041    
5042  checkpoint46h_post  checkpoint46h_post (2002/09/25)
5043  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
5044    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
5045      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 3416  o introduced new parameter rhoConstFresh Line 5049  o introduced new parameter rhoConstFresh
5049    value is 999.8 kg/m^3    value is 999.8 kg/m^3
5050  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
5051    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
5052  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
5053    
5054   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
5055   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
5056   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
5057    
5058  checkpoint46g_post  checkpoint46g_post (2002/09/18)
5059  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
5060    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
5061    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 3440  o cleaned up find_rho Line 5073  o cleaned up find_rho
5073    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
5074  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
5075    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
5076  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
5077    
5078  checkpoint46f_post  checkpoint46f_post (2002/09/16)
5079  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
5080    - extended active file handling to g_... files    - extended active file handling to g_... files
5081    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 3450  o Enable tangent linear (forward mode) g Line 5083  o Enable tangent linear (forward mode) g
5083  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
5084  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
5085    
5086  checkpoint46e_post  checkpoint46e_post (2002/09/05)
5087  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
5088    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
5089    - 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 3459  o Added new equation of state -> MDJWF Line 5092  o Added new equation of state -> MDJWF
5092    - 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
5093      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
5094      expect perfect matches for those      expect perfect matches for those
5095  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
5096    
5097  checkpoint46d_post  checkpoint46d_post (2002/08/19)
5098  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
5099    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
5100    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
5101    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
5102  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)
5103    in find_alpha/beta.    in find_alpha/beta.
5104  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
5105    
5106  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)
5107    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
5108    
5109  checkpoint46c_post  checkpoint46c_post (2002/08/15)
5110  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
5111   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
5112   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
5113      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).
5114   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
5115   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
5116  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
5117    
5118  checkpoint46b_post  checkpoint46b_post (2002/08/07)
5119  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
5120    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
5121    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 3491  o Added UNESCO EOS, but not recommended Line 5124  o Added UNESCO EOS, but not recommended
5124    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
5125  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
5126    unesco.f to be used with POLY3    unesco.f to be used with POLY3
5127  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
5128    
5129  checkpoint46a_post  checkpoint46a_post (2002/07/31)
5130  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
5131    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
5132    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
5133  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
5134  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
5135  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
5136    
5137  checkpoint46  checkpoint46 (2002/07/13)
5138  further merges from release1_p5  further merges from release1_p5
5139  o new ctrl package  o new ctrl package
5140    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 3528  o added hooks for Eliassen Palm fluxes ( Line 5161  o added hooks for Eliassen Palm fluxes (
5161  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
5162  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
5163    
5164  checkpoint45d_post  checkpoint45d_post (2002/07/12)
5165  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
5166  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
5167    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 3542  o add new flags: Line 5175  o add new flags:
5175   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
5176  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
5177    
5178  checkpoint45c_post  checkpoint45c_post (2002/05/30)
5179  o Removed f90 comments ("!")  o Removed f90 comments ("!")
5180  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
5181    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 3550  o modifications to gradient check packag Line 5183  o modifications to gradient check packag
5183    - enable centered differences    - enable centered differences
5184    - modified format of standard output    - modified format of standard output
5185    
5186  checkpoint45b_post  checkpoint45b_post (2002/05/30)
5187  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
5188  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
5189  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 3562  o in initialise_varia, moved call packag Line 5195  o in initialise_varia, moved call packag
5195    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
5196  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
5197    
5198  checkpoint45a_post  checkpoint45a_post (2002/05/01)
5199  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
5200  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
5201  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 3582  o errorMessageUnit set non-equal zero in Line 5215  o errorMessageUnit set non-equal zero in
5215    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
5216  o modified carbon verif.  o modified carbon verif.
5217    
5218  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
5219  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
5220    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
5221  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
5222    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.
5223    
5224  checkpoint44g_post  checkpoint44g_post (2002/03/05)
5225  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
5226    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
5227    
# Line 3653  o merge of relevant stuff from the ecco- Line 5286  o merge of relevant stuff from the ecco-
5286  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
5287  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
5288    
5289  checkpoint44  checkpoint44 (2002/01/18)
5290  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
5291  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)
5292  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 3661  o update AIM experiments (NCEP input fil Line 5294  o update AIM experiments (NCEP input fil
5294  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
5295  o added some stuff for AD  o added some stuff for AD
5296    
5297  checkpoint43  checkpoint43 (2001/09/28)
5298  o added two new advection tests  o added two new advection tests
5299  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
5300  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
5301  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
5302    
5303  checkpoint42  checkpoint42 (2001/09/27)
5304    Fixed AD-related problems:    Fixed AD-related problems:
5305  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
5306    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 3679  o Modified store directives for split of Line 5312  o Modified store directives for split of
5312    for the case ALLOW_KPP    for the case ALLOW_KPP
5313  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
5314    
5315  checkpoint41  checkpoint41 (2001/09/27)
5316  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
5317    to work with protex    to work with protex
5318    
5319  checkpoint40  checkpoint40 (2001/09/27)
5320  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
5321  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
5322  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 3692  o more mods for non-linear free-surface Line 5325  o more mods for non-linear free-surface
5325  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
5326  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
5327    
5328  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
5329  o added DST advection schemes  o added DST advection schemes
5330  o fix MPI bug on SGI's  o fix MPI bug on SGI's
5331  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 3702  o changes to commenting of arguments for Line 5335  o changes to commenting of arguments for
5335  o added/updated many matlab scripts  o added/updated many matlab scripts
5336  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
5337        
5338  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
5339  o new package rw/  o new package rw/
5340    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
5341    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 3721  o TAMC-related update to cope with mom_f Line 5354  o TAMC-related update to cope with mom_f
5354    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
5355    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
5356    
5357  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
5358  o bug fix in dynamics.F  o bug fix in dynamics.F
5359    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
5360  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
5361  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
5362    related to TAF    related to TAF
5363    
5364  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
5365  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
5366  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
5367    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 3736  o corresponding split of calc_diffusivit Line 5369  o corresponding split of calc_diffusivit
5369  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
5370  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
5371    
5372  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
5373  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
5374    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
5375  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 3750  o added new expt "solid-body.cs-32x32x1" Line 5383  o added new expt "solid-body.cs-32x32x1"
5383    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
5384      is not necessarily any better than the current one...      is not necessarily any better than the current one...
5385    
5386  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
5387  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
5388    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
5389  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 3758  o extended iMin,jMin range for calc_comm Line 5391  o extended iMin,jMin range for calc_comm
5391  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
5392  o a few minor updates and fixes  o a few minor updates and fixes
5393    
5394  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
5395  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
5396  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
5397  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
5398    
5399  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
5400  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
5401  o Added gradient check package  o Added gradient check package
5402  o Added routines for passive tracer handling  o Added routines for passive tracer handling
5403  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
5404    
5405  checkpoint39  checkpoint39 (2001/05/14)
5406   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
5407     (mainly missing or wrong directives)     (mainly missing or wrong directives)
5408   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 3783  checkpoint39 Line 5416  checkpoint39
5416           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
5417   o disabled some packages by default in genmake   o disabled some packages by default in genmake
5418    
5419  checkpoint38  checkpoint38 (2001/04/10)
5420   o see notes_c37_adj.txt   o see notes_c37_adj.txt
5421   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
5422   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 3791  checkpoint38 Line 5424  checkpoint38
5424     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
5425   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
5426    
5427  checkpoint37  checkpoint37 (2001/03/13)
5428   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
5429     (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
5430      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 3808  checkpoint37 Line 5441  checkpoint37
5441   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
5442   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
5443    
5444  checkpoint36  checkpoint36 (2001/02/20)
5445   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
5446   o recover Time-Average diagnostics   o recover Time-Average diagnostics
5447   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
5448   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
5449    
5450  checkpoint35  checkpoint35 (2001/02/08)
5451   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
5452   o allows staggered time-stepping   o allows staggered time-stepping
5453   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
5454   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
5455    
5456  checkpoint34  checkpoint34 (2001/01/30)
5457   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
5458   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
5459     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 3831  checkpoint34 Line 5464  checkpoint34
5464   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
5465   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
5466    
5467  checkpoint33  checkpoint33 (2000/11/30)
5468   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
5469   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
5470     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 3849  checkpoint33 Line 5482  checkpoint33
5482       possibly use them.       possibly use them.
5483   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
5484    
5485  checkpoint32  checkpoint32 (2000/11/13)
5486   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
5487     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
5488   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 3860  checkpoint32 Line 5493  checkpoint32
5493   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
5494   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
5495    
5496  checkpoint31  checkpoint31 (2000/09/11)
5497   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
5498     -> new routines packages_...F     -> new routines packages_...F
5499     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 3877  checkpoint31 Line 5510  checkpoint31
5510     - not yet tested for GMRedi.     - not yet tested for GMRedi.
5511     - not yet tested for KPP.     - not yet tested for KPP.
5512    
5513  checkpoint30  checkpoint30 (2000/07/13)
5514   o Updates for OBCs   o Updates for OBCs
5515   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
5516   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 3886  checkpoint30 Line 5519  checkpoint30
5519   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.)
5520     and entry for T90 in genmake     and entry for T90 in genmake
5521    
5522  checkpoint29  checkpoint29 (2000/06/21)
5523   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
5524    
5525  checkpoint28  checkpoint28 (2000/06/09)
5526   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
5527   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
5528   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 3902  checkpoint28 Line 5535  checkpoint28
5535     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
5536   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
5537    
5538  checkpoint27  checkpoint27 (2000/04/10)
5539   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
5540     formulation works properly with variable resolution.     formulation works properly with variable resolution.
5541   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 3910  checkpoint27 Line 5543  checkpoint27
5543   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
5544     in new routine ini_psurf()     in new routine ini_psurf()
5545    
5546  checkpoint26  checkpoint26 (2000/04/05)
5547   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
5548     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
5549   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 3920  checkpoint26 Line 5553  checkpoint26
5553     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
5554   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
5555    
5556  checkpoint25  checkpoint25 (2000/03/15)
5557   o updates for OBCs and NH   o updates for OBCs and NH
5558   o dramatically reduced memory usage   o dramatically reduced memory usage
5559   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 3931  checkpoint25 Line 5564  checkpoint25
5564      an explicit free-surface option)      an explicit free-surface option)
5565   o initial state input files for U and V   o initial state input files for U and V
5566    
5567  checkpoint24  checkpoint24 (1999/08/02)
5568   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
5569   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
5570   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
5571    
5572  checkpoint23  checkpoint23 (1999/05/26)
5573   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
5574   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
5575    
5576  checkpoint22  checkpoint22 (1999/05/18)
5577   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
5578   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
5579    
5580  checkpoint21  checkpoint21 (1999/05/18)
5581   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)
5582   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
5583   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
5584   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
5585    
5586  checkpoint20  checkpoint20 (1999/03/22)
5587   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
5588   o Added non-hydrostatic code   o Added non-hydrostatic code
5589   o Fixed some input data   o Fixed some input data
5590   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
5591    
5592  checkpoint19  checkpoint19 (1998/12/15)
5593   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
5594   o Added new code for open boundaries.   o Added new code for open boundaries.
5595   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 3964  checkpoint19 Line 5597  checkpoint19
5597   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
5598   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.
5599    
5600  checkpoint18  checkpoint18 (1998/11/30)
5601   o Further changes for optional code generation with   o Further changes for optional code generation with
5602     CPP - ugh!     CPP - ugh!
5603    
5604  checkpoint17  checkpoint17 (1998/11/03)
5605   o Beginning to incorporating modularity   o Beginning to incorporating modularity
5606     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
5607   o Small changes for TAMC complinace   o Small changes for TAMC complinace
5608   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
5609     configuration "exp0".     configuration "exp0".
5610    
5611  checkpoint16  checkpoint16 (1998/10/28)
5612   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
5613     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
5614     assignment is an addition.     assignment is an addition.
# Line 3983  checkpoint16 Line 5616  checkpoint16
5616     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
5617     limit ).     limit ).
5618    
5619  checkpoint15  checkpoint15 (1998/09/29)
5620   Rewrote exchange routines to allow   Rewrote exchange routines to allow
5621   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
5622   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 3992  checkpoint15 Line 5625  checkpoint15
5625     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
5626     communication method.     communication method.
5627    
5628  checkpoint14  checkpoint14 (1998/09/09)
5629   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
5630   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
5631    
5632  checkpoint13  checkpoint13 (1998/07/17)
5633   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
5634   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
5635   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 4011  branch-point-rdot Line 5644  branch-point-rdot
5644   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
5645   we've actually tested it...   we've actually tested it...
5646    
5647  checkpoint12  checkpoint12 (1998/07/08)
5648   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
5649   configure script).   configure script).
5650   Released to testers.   Released to testers.
5651    
5652  checkpoint11  checkpoint11 (1998/07/02)
5653   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
5654   and ini_masks_etc().   and ini_masks_etc().
5655    
5656  checkpoint10  checkpoint10 (1998/07/01)
5657   Introduced the configure script.   Introduced the configure script.
5658   Separated out the diags package.   Separated out the diags package.
5659   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
5660   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
5661    
5662  checkpoint9  checkpoint9 (1998/06/22)
5663   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
5664   General tidy-up.   General tidy-up.
5665   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
5666    
5667  checkpoint8  checkpoint8 (1998/06/22)
5668   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
5669   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
5670    
# Line 4041  checkpoint7-4degree-ref Line 5674  checkpoint7-4degree-ref
5674   model etc..   model etc..
5675   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
5676    
5677  checkpoint7  checkpoint7 (1998/06/15)
5678   Created by cnh   Created by cnh
5679   Simple 4 degree global simulation   Simple 4 degree global simulation
5680   configuration.   configuration.
# Line 4049  checkpoint7 Line 5682  checkpoint7
5682   hydrography, bathymetry etc   hydrography, bathymetry etc
5683   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
5684    
5685  checkpoint6  checkpoint6 (1998/06/08)
5686   Created by cnh   Created by cnh
5687   merged checkpoint5 with CD and   merged checkpoint5 with CD and
5688   spherical polar code.   spherical polar code.
5689   Still some problems with GM Redi   Still some problems with GM Redi
5690   abd full topography.   abd full topography.
5691    
5692  checkpoint5  checkpoint5 (1998/06/08)
5693   Created by AJA   Created by AJA
5694   contains updates to GM Redi   contains updates to GM Redi
5695   and reordered timestepping loop   and reordered timestepping loop
5696   for Implicit Diffusion.   for Implicit Diffusion.
5697    
5698  checkpoint4  checkpoint4 (1998/05/30)
5699   Created by cnh   Created by cnh
5700   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
5701   grid variations are limited.   grid variations are limited.
5702   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
5703   for generation.   for generation.
5704    
5705  checkpoint3  checkpoint3 (1998/05/26)
5706   Created by cnh   Created by cnh
5707   Added extra flags for runtime options   Added extra flags for runtime options
5708   Added this file   Added this file

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