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revision 1.286 by dimitri, Mon May 3 07:12:25 2004 UTC revision 1.1271 by mlosch, Mon May 17 14:23:42 2010 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/exf/exf_bulk_largeyeager04.F: rewrite for better vectorization, changes
8      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
9    o eesupp/src (exch-1):
10      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
11      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
12        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
13        (even without using MPI).
14      - Message mode: move RecvAck setting (indicator of buffer being ready)
15        from send_put to recv_get S/R (was useless before, but not sure if
16        it's much more useful now);
17      - switch the order of sync: MPI-proc 1rst and then threads;
18      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
19    o model/src:
20      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
21      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
22    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
23    o pkg/ctrl: require a specific set of control variables and exf-flags for
24      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
25    o model/src:
26     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
27       1rst forward sweep, to avoid over-writing output files during recomputations
28       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
29     b) 2nd version:
30      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
31      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
32         writePickupAtEnd) + seaice & ptracers output;
33      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
34    o model/src:
35      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
36    o pkg/exch2:
37      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
38      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
39    o pkg/autodiff & exch2:
40      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
41      (for now, only if ALLOW_EXCH2 is defined).
42    o pkg/autodiff:
43      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
44        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
45       + clean-up comments (_RS is not always real*4)
46      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
47      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
48        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
49    o testreport (AD-tests):
50      no longer link files from dir "../input" (1rst link files from
51      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
52    
53    checkpoint62f (2010/04/29)
54    o model/src/the_main_loop.F:
55      adjust store directives for seaice evp and multicategory according to
56      pkg/ecco/the_main_loop.F
57    o adjoint:
58      global_sum_ad was incomplete (noted many times by many people ;)
59      nice description by Jean U. as follows:
60      * allreduce(var) in global_sum.F can be interpreted as
61        reduce(sum) followed by broadcast of sum.
62      * The adjoint of that is
63        sum(adjoint) followed by broadcast(summed adjoint value)
64        or in other words, allreduce(sum, adjoint vars)
65      We were missing the sum(adjoint)!
66      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
67      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
68      The fix should produce 16-digit accuracy between
69      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
70      multi-CPU single-tile (e.g. nSx=1, nPx-2)
71      We'll probably change this yet again shortly
72    o eesupp/src:
73      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
74    o pkg/icefront
75      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
76        specification of addmass array based on a 2D field, which is added
77        at bottommost wet level at each horizontal location.
78    o model/src:
79     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
80     layout; (not always compatible with delX,delY setting; commented out for now).
81    o pkg/exch2:
82     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
83     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
84    
85    checkpoint62e (2010/04/15)
86    o pkg/obcs:
87      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
88    o pkg/dic:
89      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
90        (note: not presently tested in any forward verification exp.)
91       update tutorial_global_oce_biogeo AD output file.
92    o pkg/exf:
93      - account for the variation of albedo as a function of zenith angle
94        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
95    o build_options:
96     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
97    o pkg/dic:
98      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
99      - use binary pickup file for restart;
100      - initialise atmos-CO2 box from dic_pCO2 parameter;
101      - fix multi-threaded.
102    o pkg/rbcs:
103     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
104       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
105     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
106       and update output.txt
107    o pkg/kpp:
108     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
109     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
110       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
111       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
112     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
113       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
114    o pkg/offline:
115      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
116      (bug was added in version 1.10 on 2007-08-23).
117    o pkg/offline:
118      - no need to specify periodicExternalForcing, etc ... to use offline pack
119      - offline input files no longer just single prec --> parameter offlineLoadPrec
120    o verification/lab_sea:
121      change AD test to multi-tile setup and update all 4 AD output.
122      NOTE: while cost function values remain very similar,
123      gradients are very different, although gradient checks are self-consistent
124      Should try to get to the bottom of this (cost function summation order?)
125    o pkg/dic:
126      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
127      a weakness of TAF that drops part of double precision in log10 derivative.
128      <= changes removed since problem has been fixed in current TAF version 1.9.71
129      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
130    o pkg/ecco:
131      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
132      update all 4 lab_sea AD output.
133    
134    checkpoint62d (2010/03/22)
135    o build_options:
136      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
137    o remove unbalanced quote (single or double) in commented line of source code
138      (may cause some warning with some preprocessor/makedepend versions).
139    o pkg/seaice:
140      fix seaice_model.F for adjoint (gael) and update AD results of experiments
141       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
142    o testreport:
143      add option '-runonly' (short: '-ro') to just do the run part (without make).
144    o eesupp: remove JAM communication code (obsolete).
145    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
146      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
147      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
148      (update also the output).
149    
150    checkpoint62c (2010/03/02)
151    o tools/build_options :
152       move (some) old optfiles from build_options/ to build_options/unsupported/
153    o model/src and pkg/exf
154       surface relaxation -- separating data and data.exf options
155       The point is to ensure that we specify the surface relaxation
156       either in data or in data.exf (but not half and half) and to
157       avoid an accidental relaxation to 0 (which happened if a time
158       scale was specified but the file name was left empty)
159    o model/src model/inc and pkg/mom_common
160       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
161       => addition to the viscosity field as computed by others schemes
162    o tools/build_options:
163      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
164        but keep the former optfile for few weeks for smooth transition
165    o pkg/ecco
166      - allow user defined cost function contributions
167            CPP: ALLOW_USERCOST_CONTRIBUTION
168            USAGE: compute contributions in cost_usercost_all.F
169      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
170          the two options are complementary.
171    o pkg/smooth
172      - migration from contrib to the main repository
173    
174    checkpoint62b (2010/01/26)
175    o pkg/monitor:
176      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
177        (in case someone forgot to update customized pieces of code)
178    o nonHydrostatic:
179      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
180      - add a simple 2-D experiment (short_surf_wave) to test it.
181    o pkg/icefront:
182       adding the shell of, and the hooks to, a new package that
183       will model melting and freezing of vertical glacier ice fronts
184    o momentum:
185      add diagnostics of momentum tendency from Hydrostatic pressure gradient
186       (without surf.pressure term: would need a 2nd filling since implicit term).
187    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
188      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
189      cannot deal with the former
190    o cleaning:
191      - remove all (except OpenAD) old TLM output from results_ad dirs.
192      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
193      - comment out maskH definition (replaced by maskInC)
194    o pkg/monitor:
195      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
196        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
197    
198    checkpoint62a (2010/01/15)
199    o model/src:
200      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
201    o pkg/diagnostics:
202      - add optional level number diagnostics (i.e., level number to be define
203        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
204      - strictly check for valid parser-code(10) ;
205      - check if adding diag to the list from the right place.
206    o pkg/longstep:
207      - change parameters and fix tracer conservation with rstar/nonlinear free surface
208    o diagnostics:
209     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
210       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
211    o pkg/diagnostics:
212     - Add option for writing vertical integral (sum of selected levels) of an output
213        field instead of writing output field levels. Activate this option on a per
214        output-file basis, by setting the 2nd character of fileflag to 'I'.
215     - Add field-specific information relative to level integral in 3rd postion
216        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
217        vertically (x level-thickness x hFac), "r"=same but without hFac.
218    o do_the_model_io:
219      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
220        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
221        writing pickups and stopping.
222    o pkg/diagnostics (for now, only with mdsio):
223      - write time information to meta file (and modify accordingly rdmds.m) :
224        time-averaged diagnostics output: write starting and ending time of the
225        time-averaging interval ; snap-shot diagnostics output remains unchanged;
226    o pkg/timeave:
227      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
228        always Nr), now assumed to be equal to number of levels of averaged field;
229        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
230    o pkg/sbo:
231      - fix ocean bottom pressure global-average & 2-D time-ave output (was
232        neither initialised nor filled).
233      - add starting iteration in suffix of global-average output file
234        (to avoid over-writing the file after a restart)
235      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
236    o time-average:
237      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
238        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
239         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
240        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
241      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
242      - fix missing accumulation for pkg/opps.
243      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
244         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
245      - fix initialisation of time-ave vars and do only full time-step increment
246        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
247    o pkg/layers:
248      - use standard RW pkg S/R to write the output
249        and remove local write_fld version (which had a problem).
250      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
251      - fix LAYERS_CALC argument list.
252    o pkg/timeave:
253      - store cumulative-time in a simple tiled array (drop the level index)
254      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
255    o pkg/ocn,aim_compon_interf
256      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
257    
258    checkpoint62  (2009/12/23)
259    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
260        (was not previously tested in any other exp.)
261    o pkg/monitor:
262      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
263        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
264        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
265      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
266      - change del2 calculation.
267      - use interior masks (instead of maskH, <- to be remove).
268      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
269    o mask & obcs:
270      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
271      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
272        (called after packages_init_fixed)
273    o pkg/obcs:
274      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
275        Fixes bug in obcs+exf with nSx*nSy.GT.1
276      - fix multi-tile handling in obcs balance code
277    o nonHydrostatic:
278      - Implement AB-3 for non-hydrostatic vertical momentum ;
279        (change ordering of var. stored in pickup file when using NH)
280      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
281      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
282        (in prep. for new NH free surface form).
283    o pkg/obcs:
284      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
285    o model/src:
286      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
287    
288    checkpoint61z (2009/12/01)
289    o nonHydrostatic:
290      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
291        a spurious source of energy in simple baroclinic adjusment test case.
292      Update all non-hydrostatic exp output.
293    o model/src (3-d solver):
294      Change again 3-D solver free-surface RHS term when exactConserv=T:
295        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
296        (which was not the case with previous formulation).
297      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
298      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
299    o nonHydrostatic:
300      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
301        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
302      - change 3-D solver to work with r* (for now, only with linear free-surf.)
303      - add few debug diagnostics (cg3d_x, residual)
304    o model/src:
305      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
306        update output of exp. global_ocean.cs32x15.viscA4
307    o update output of exp. global_ocean.cs32x15.icedyn after removing
308      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
309    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
310    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
311      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
312    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
313      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
314      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
315      to test this code
316    o pkg/cd_code:
317      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
318       C-grid momentum. D-grid velocity used to be stepped forward in time with
319       Adams-Bashforth only on surface pressure term. Tests show that using AB on
320       D-grid coriolis term improves stability (as expected from CD-scheme paper).
321      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
322      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
323       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
324       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
325      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
326           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
327    o pkg/obcs:
328     - fix bug in initialisation (broken since Oct 1rst modification)
329       for useOBCSprescribe without useEXF.
330    
331    checkpoint61y (2009/11/15)
332    o pkg/seaice
333     - change (once again) the discretization for the evp solver: rather than
334       squaring the averages of strain rates, average the squares to give
335       a better approximation to VP behavior (in simple test); this breaks
336       verification experiments that use EVP (lab_sea and lab_sea.hb87)
337        --> update outputs
338    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
339      to improve vectorization of adjoint code on TARGET_NEC_SX
340    o verification/vermix:
341      - change vermix to a more "classical" 1d column with high vertical
342        resolution, seasonal heat flux forcing and constant wind forcing
343        --> update outputs
344    o pkg/seaice
345     - fix diagnostics of principal stress components for EVP
346     - add optional diagnostics of non-linear convergence for LSOR solver
347     - make maximum zeta a runtime parameter
348    o model/src (3-d solver):
349      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
350       which consisted in removing the Surf. Non-Hydrostatic pressure from the
351       whole column and adding it to Eta (inspired from Casualli, 1999):
352       Only affects 3-D solver initial guess and only if using ExactConserv,
353       but tests did show a degradation of solver convergence. For this reason,
354       decide to disable this piece of code.
355       to recover previous version, just set zeroPsNH = exactConserv (line 78).
356      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
357    o pkg/ggl90:
358     - fix previous modif (unfortunatly has not been documented here).
359    o pkg/seaice/autodiff:
360     - add CPP flag to include clipping of zeta in EVP code;
361       although clipping of zeta is not necessary for EVP and not recommended
362       it was done by default, now clipping is disabled by default
363     - modify computation and store zetaC/Z in seaice_evp for TAF
364     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
365     - change seaice_calc_viscosities/strainrates for better
366       vectorization after AD by TAF
367     - rearrange common blocks in SEAICE.h once again for easier dumps of
368       adjoint output, adjust adcommon.h and g_common.h
369     - change flux form of default advection scheme for better vectorization
370       of adjoint code
371     - modify lab_sea/input.lsr to test the flux form of default advection
372       scheme
373    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
374      transition in checkpoint61r)
375    
376    checkpoint61x (2009/10/19)
377    o adjoint: adding two new verification experiments
378      * tutorial_global_biogeo: an online dic sensitivity experiment
379        (work with G. Forget)
380      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
381        (an update of the Dutkiewicz et al., 2006 paper)
382      Both use the same CO2FLUX cost function, but different controls
383      Gradient checks look good, but some recomp. could still be traightened out
384      Should add xx_dic control variable to test at some point
385    o model/src:
386      add run-time parameters to check and/or mask initial Temp & Salt
387    o pkg/ptracers:
388      apply zonal filter (if used) to all passive tracers
389    
390    checkpoint61w (2009/10/12)
391    o adjoint:
392      * update and finish work on adjoint of dic package (G. Forget)
393      * start adjoint of offline package
394      * bug fix for cube-sphere TLM code (active_file_g.F)
395    o tutorial_global_oce_optim:
396      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
397      and add SIZE.h_mpi for MPI testing
398    o pkg autodiff
399     - fix bug in autodiff_restore
400     - make genmake2 remove comments and empty lines from ad_input_code.f in
401       order to reduce file size (new script file remove_comments_sed)
402    o allows to specify vertical profile of vertical viscosity (viscArNr)
403    o pkg autodiff
404      autodiff_ini_model_io: comment out writing of grid information to netcdf
405      files, because at this time the grid fields are a bunch of zeros
406      (this is analogous to ini_mnc_vars.F)
407    o pkg seaice/autodiff:
408     left-over from removing the 3-time-level fields:
409     - small rearrangement of common blocks (SEAICE.h)
410     - fix field declaration in order to get meaningful output in
411       adseaice.*.nc (adcommon.h)
412    o pkg obcs:
413     - go through NH code only if nonHydrostatic=T
414     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
415     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
416       => Update output of experiment seaice_obcs
417     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
418     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
419     - fix restart for useOBCSprescribe + useEXF
420    o pkg ctrl
421     - make obcs as control parameter work also with useSingleCPUio
422     - replace a few sny and snx by Ny and Nx to be consistent with
423       ctrl_set_globfld_x/yz.F
424    o pkg seaice
425     - re-introduce global field frWtrAtm for the case of
426       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
427     - catch the case of an empty filename in seaice_cost_init_fixed.F
428    o pkg ecco:
429     - small bug fixes in the_main_loop
430      . fix order of monitor arguments
431      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
432      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
433        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
434     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
435       imbalance diagnostics for wmean_h/sflux = 0
436     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
437     - catch the case of empty filenames in ecco_cost_init_fixed.F
438       and ecco_readparms.F
439     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
440       to make this statement meaningfull in ecco_cost_weights.F
441    o pkg zonal_filt:
442      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
443      - when using rStar, filter uVel*hFacW instead of uVel
444       (tested without topography: fix a Pb of growing instability with NLFS)
445    o pkg/aim/thsice:
446     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
447      (works as SST restoring)
448    o pkg/thsice:
449     -add specific parameter for salt restoring in slab mixed-layer
450       (by default equal to the temperature restoring)
451    
452    checkpoint61v (2009/09/21)
453    o pkg/kpp:
454     -add double diffusive contributions as a hack, turned off by default
455      for now, and the code can be excluded with a CPP-flag
456      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
457     -add a verification experiments to "vermix" to test this code
458    o pkg/mom_common:
459      Move computation of length scales to mom_init_fixed.F (avoid recomputation
460      at each time-steps*levels).
461    o pkg/layers:
462      Created a new package for computing volume fluxes in temperature or
463      [not yet implemented] density layers, e.g. for calculating residual
464      overturning circulations.
465    o pkg/diagnostics:
466      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
467    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
468    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
469      To avoid mixing type (RS/RL) of input/output array argument,
470      replace single mixed-type array with a pair from each type (RS/RL).
471    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
472      is now implemented for all pkgs (previously only done for the main pickup)
473    
474    checkpoint61u (2009/08/25)
475    o pkg/obcs:
476      - change OB?eta from _RS to _RL and put them into a separate commen block
477      - add code to read OB?eta from a file via obcs_prescribe_read: the code
478        compiles and does not destroy any other experiments, the data is read
479        properly, but the code is not tested in actual applications
480    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
481      create a meaningful unit attribute for the time coordinate variable
482    o pkg/ebm: add plenty of missing "_d 0" ;
483       update results of experiment global_ocean_ebm (fwd + adjoint tests)
484      Notes: several pieces of code only works for (very) specific set up
485       (domain size, lat range, etc ...); should be documented & stop if one
486       of those assumptions is not meet.
487    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
488       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
489          and offline_exf_seaice (seaicetd + adjoint).
490    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
491       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
492        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
493    o few changes to pass when compiling with strick checking of arguments
494       across S/R (allow to find few bugs in S/R calls).
495    o pkg/seaice:
496     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
497       2d-fields, for slightly better performance
498    
499    checkpoint61t (2009/07/22)
500    o pkg/seaice:
501     - remove unused variables in seaice_evp
502     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
503    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
504       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
505       each processor opens a different file (a fix from Matt).
506    o cg2d:
507       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
508       this reduces number of EXCH calls by 2 when using exch2.
509       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
510       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
511    o pkg/thsice:
512       add code for Near Infra-Red albedo (from Jeff)
513       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
514    o ini_model_io:
515       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
516       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
517       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
518    
519    checkpoint61s (2009/06/30)
520    o pkg/exch2 (exch2_rxN_cube*):
521       remove last BARRIER (no need to synchronise after getting data from shared
522       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
523    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
524      and generate new output (for the 2 tests) using default rotationPeriod.
525    o pkg/exch2:
526      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
527        (was already the case with AUTODIFF_EXCH2 defined)
528      - add bj in exch2 arrays and S/R.
529      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
530        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
531    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
532      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
533        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
534      - verification experiment natl_box.longstep
535    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
536      allow different versions of ifort (8 or 9) and different versions
537       of mpi (mpich or mpich2) to be used with the same optfile.
538      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
539       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
540    o pkg/seaice:
541      fix previous modif (3-level field removed) for old-pickup reading
542    
543    checkpoint61r (2009/06/25)
544    o pkg/seaice:
545     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
546      1. introduce fields for time step (N-1)
547      2. do not use levels 2 and 3 anymore (but keep them)
548      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
549         includes changes to pkg/thsice/thsice_get_velocity.F,
550         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
551         pkg/obcs/obcs_apply_uvice.F.
552     - completely remove code for leap-frog time stepping for second order
553       advection
554     - adjusted adjoint accordingly;
555       gradient checks have improved by an order of magnitude!
556    
557    checkpoint61q (2009/06/22)
558    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
559     - the boundary conditions along open boundaries are unclear, because the
560       associated masks are set to zero and are thus treated as closed when
561       applying the slip-boundary conditions.
562     - move initialisation of grid variables from seaice_init_varia to _fixed
563    o adding doc/diags_changes.txt
564    o model/src:
565      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
566       to avoid "_diags" naming if no relation to pkg/diagnostics.
567      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
568       file and only call PLOT_FIELD_XYZ if debugMode=T.
569      remove few PLOT_FIELD_XY calls outside initialisation.
570      remove few unnecessary BARRIER.
571    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
572      of salt_plume package in Southern Ocean
573    o pkg/thsice:
574     - fix hOceMxL in overlap (needed for sea-ice advection);
575       update output of experiment global_ocean.cs32x15.icedyn.
576    o pkg/seaice:
577     - make the (placeholder-)tracer IceAge a little more meaningful
578      by avoiding ridging of age due to convergent ice flow
579     - add diagnostics for surface temperature, atmospheric and oceanic
580       heat flux, and atmospheric and oceanic ice growth
581    
582    checkpoint61p (2009/06/10)
583    o eesupp (global_max & global_sum):
584     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
585     - remove starting & endding barrier (no longer needed)
586    o pkg/mdsio, writelocal:
587       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
588       (remove the STOP): uses shared buffer IO to store data from all threads
589       and then let master-thread write nThreads tiles.
590    o pkg/mdsio (read/write field):
591     - tiled IO done in 1 piece (all levels at a time);
592     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
593     - multi-threaded: allow to read/write local (non-shared) array
594       (was already working with singleCpuIO ; now works also without);
595       => no longer needs barrier call after reading a file (added inside
596       mds_read/write field).
597     - move barrier calls outside gather/scatter_2d to mds_read/write_field
598    o pkg/obcs/exf
599      - exf_getffieldrec.F: add a few ". _d 0" and
600                            add code to catch the case fldperiod = 0.  
601      - obcs_precribe_read.F: change if statements so that they match
602                              the variable type (_RL)
603      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
604        exf_iprec) as part of namelist EXF_NML_01
605    o pkg/mdsio:
606      - read/write tiled (local) files: read/write 1-level tile chunk at a time
607        (instead of segment of length sNx); expected to speed up tiled IO.
608    o pkg/exch2:
609      - take buffer copy from/to array out of S/R exch2_send/recv into new
610        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
611        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
612      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
613      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
614        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
615        including Topology header file (and common blocks).
616      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
617        remove 2nd exch call in exch2_s3d_rx (no longer needed).
618      - document S/R arg. list (+ update some comments)
619    o pkg/seaice:
620      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
621        temperature and humidity over sea ice based on climatological values.
622      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
623        of LSR (this change is expected to change the results slightly because now
624        it uses slightly difference moduli from the second last LSR solution, but
625        that is more consistent with the stress computations; this part of the code
626        is not tested in the verification experiments)
627      - fix diagnostics for flux of ice in case of B-grid
628      - turn strain rates eij and press into global fields within global
629        common block in SEAICE.h for more straighforward diagnostics
630      - fix diagnostics for principal stress components, press, zeta, eta
631        to give something meaning full
632    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
633      new output (all 4 tests) using default rotationPeriod.
634    o pkg KPP:
635      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
636      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
637        and normal grid from 1 to Nr)
638    o Fix computations of L4rdt in mom_calc_visc.F
639    o eesupp:
640      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
641      should be called before a "stop" if we know that all process are going
642      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
643    
644    checkpoint61o (2009/05/26)
645    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
646    o model/src/ini_curvilinear_grid.F:
647       compute angleSin/CosC when they are not read from a file
648    o pkg/seaice:
649       add pseudo time stepping for LSOR
650    o pkg/exch2:
651       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
652    o pkg/seaice:
653       Adding separate sea ice albedo, drag coefficients, and HO in Southern
654       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
655    o SingleCpuIO:
656       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
657    o pkg/seaice:
658       put exchanged variable in (local) common block for MPI+Multi-Threads
659       to work (necessary with exch1, and for now with exch2 too).
660    o verification: to get more experiments tested with mpi, mth and mpi+mth,
661      change tiling of:
662       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
663       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
664      update output of exp:
665       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
666       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
667      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
668                       (note: output.txt generated on faulks using only 1 tile)
669    o eesupp & mdsio (SingleCpuIO):
670     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
671       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
672       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
673     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
674     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
675       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
676    o pkg/exch2:
677     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
678       read parameter file "data.exch2" if it exists; otherwise try default regular
679       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
680     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
681       with new code (not to be used, just as a backup solution).
682     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
683       in utils/exch2/input.
684    
685    checkpoint61n (2009/05/12)
686    o eesupp & mdsio (SingleCpuIO):
687      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
688        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
689        receive real*4 array (instead of real*8) to read/write 32.bit files.
690        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
691         and remove new mapping S/R)
692    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
693      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
694        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
695        when using exch2. Add S/R to map global io-buffer to global model array.
696      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
697    
698    checkpoint61m (2009/04/29)
699    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
700      and add 3 other S/R for other types (R4,R8,RS).
701      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
702    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
703     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
704     - reduce number of macro definitions (keep only those which are used);
705       can always call directly the corrresponding S/R if needed.
706     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
707       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
708     Fixed wrong type of arg in:
709       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
710       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
711     To fix: global_sum of var in common block is wrong (multi-threaded) in:
712       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
713     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
714    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
715      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
716    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
717    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
718      edges are closed (zero depth); might happen with "blank tiles";
719      for now, disabled if using OBCS.
720    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
721      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
722    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
723      to reduce length of 1.D array print in STDOUT.
724    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
725      + use 48 tiles (16x8): this will allow to test "blank tiles".
726    o start to test MPI + multi-threaded (change testreport to skip tests
727      where number of tiles do not match).
728    o genmake2: add option "-omp" to turn on Open-MP ;
729      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
730    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
731      and keep the original tile numbering. Note: compatible with old
732      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
733    
734    checkpoint61l (2009/04/07)
735    o Overlaps had been forgotten in calculating ijk keys : fixed
736    o fix cyrus makedepend for gcc 4.4
737    o experiment fizhi-cs-aqualev20:
738      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
739      and generate new output. Note: new output is much closer to the old
740      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
741      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
742    o pkg/fizhi:
743     - change to avoid indices going deliberately over array-bounds
744     - remove unnecessary MPI stuff
745     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
746     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
747       does not go over array-bounds and therefore returns reliable output.
748     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
749       this S/R has 4 output arguments, which are used inside "get_alarm";
750       when it is called with the same variable "ndum" in place of several
751       output arguments, this produces weird side effect inside "get_alarm"
752      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
753       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
754       address) and produces error.
755    o tools/gemake2: (March 27-29 2009)
756      with option "-mpi": link *_mpi files from "MODS" dir (this is what
757      testreport does).
758    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
759    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
760       update lab_sea.lsr & lab_sea.salt_plume results
761    o pkg/seaice:
762      Major overhaul of the LSOR solver: change discretization from original
763      finite differences to finite volume. The old routine is still in the
764      file seaice_lsr.F and can be turned on with the CPP-flag
765      SEAICE_OLD_AND_BAD_DISCRETIZATION
766      Along with this change, the discretization of the strain rates is changed.
767      The same flag turns on the old discretization in seaice_calc_strainrates.F
768      All verification experiments with seaice are affected (except for
769      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
770      results by setting the above flag.
771      Further changes involve changes in defaults:
772      - ALLOW_FLOODING is defined and turned on by default
773      - SEAICEadvSnow = .true. is now the default
774      - SEAICEadvSalt = .true. is now the default
775      - SEAICEadvAge  = .true. is now the default
776      - SEAICE_clipVelocities  = .false. is now the default
777                                         (as per J. Zhang's recommendation)
778      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
779        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
780      - seaice_growth: replace computation of UG by a simple copy from wspeed
781    
782    checkpoint61k (2009/03/18)
783    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
784      seaice_lsr: fixed a few metric terms,
785                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
786                  add more debugging diagnostics
787      seaice_evp: removed superfluous many metric terms of FV discretization
788                  of stress divergence
789                  affects lab_sea, lab_sea.hb87
790      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
791                  of stress divergence for non-evp solver
792                  (this part is not tested anywhere)
793      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
794                  they were effectively only half slip
795                  affects lab_sea.hb87
796      updated all relevant verification experiments (except lab_sea//output_adm.txt
797        which was left over, but fails at level 7 & 6)
798    
799    checkpoint61j (2009/03/17)
800    o pkg/seaice: turn a few hard wired parameters into run time parameters
801    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
802      time in seconds as promised by the usints in seaice_monitor and exf_monitor
803    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
804      that are not cubed-sphere grids
805    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
806    o pkg/ctrl:
807      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
808    o non-hydrostatic (calc_gw.F):
809      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
810      update output of exp. global_ocean.cs32x15.viscA4
811    o remove backward compatibility for thetaMin,phiMin
812      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
813    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
814      interpolated wind field not only for curvilineargrid=.true., but also
815      for a rotated grid (rotateGrid=.true.)
816    o pkg/exf: add capability to bypass interpolation for runoff
817      by setting yet another CPP-flag
818    o eesupp/src, B-grid exchange:
819      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
820    o autodiff
821      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
822      allows to switch to single-prec common blocks;
823      corresponding switch occurs in tamc.h, integer isbyte
824      TAF store directivs "byte" and "kind" seem equivalent;
825      Most tamc.h have been updated correspondingly.
826    
827    checkpoint61i (2009/02/13)
828    o autodiff:
829      fix autodiff_sore/_restore indices for obcs
830      (spotted by I. Hoteit, M. Mazloff)
831    o pkg/autodiff, pkg/ctrl:
832      Add flag to reduce all tapelev I/O to single-prec.
833      In data.ctrl set
834        doSinglePrecTapelev = .TRUE.
835    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
836      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
837    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
838      real fresh water flux (not yet)
839    o pkg/mdsio & rw:
840     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
841     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
842    o pkg/flt:
843     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
844       init_fixed & ini_varia.
845     - clean-up & simplify linear interpolation S/R:
846       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
847     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
848     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
849     - add vert. coordinate & horiz. indices to output files.
850     - change vertical position in initial condition, from index to depth [m].
851     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
852       (easier to get to a curvilinear grid) ; delX,delY no longer used.
853    o pkg/ggl90: a few modifications:
854     - fix bottom boundary condition, and interpolation of KappaE
855       near top and bottom
856     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
857     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
858     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
859    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
860      (maintain temporary backward compatibility, until next checkpoint)
861    
862    checkpoint61h (2009/01/27)
863    o pkg/diagnostics with "periodic averaging diagnostics":
864      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
865    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
866    o pkg/obcs: fix loop ranges for balancing code
867    o pkg/flt:
868     - improve criteria for finding which tile owns a float.
869     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
870    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
871      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
872      with ocean biogeo)
873    o pkg/flt:
874     - do some cleaning and fix the restart ;
875     - add output.txt in flt_example/results to get this pkg tested.
876    o genmake2: add an EXTENDED_SRC option and flag.
877       for now, cannot be turned on on command line (only through genmake_local)
878    o pkg/mdsio: read/write vector:
879     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
880     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
881       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
882     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
883      (drop to 4 digits matching for grad). But this test does not look very
884      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
885    
886    checkpoint61g (2008/12/29)
887    o pkg/flt:
888      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
889       + make OPTIONS file more standard.
890      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
891      - fix _BYTESWAPIO CPP-Flag
892      - standard reading of file-parameter "data.flt"
893      - fix argument list of S/R FLT_RESTART
894      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
895    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
896    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
897      a still unfixed compiler/optimization bug
898    
899    checkpoint61f (2008/11/21)
900    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
901      update results of global_ocean.cs32x15.icedyn test.
902    o move getcon.F from model/src to pkg/fizhi.
903    o pkg/exf: add parameter for extrapolation of temp up to the surface
904       and option to prevent negative evap (in bulk_largeyeager04 only).
905    o Prather Advection scheme: fix tracer conservation for divergent flow
906      (e.g., when using NonLin Free-Surface).
907    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
908    o gmredi (Visbeck-variable-K):
909     - add more parameters to Visbeck-variable-K.
910     - use a 5 points average for dSigmaR in Visbeck-K calculation
911       (more "homogenous": same stencil and same weights as in dSigmaH)
912     - update output of ideal_2D_oce experiment.
913    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
914      (#undef REAL4_IS_SLOW)
915     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
916       coordinate variable
917     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
918       (surface forcing fields), removes some of the functionality
919     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
920     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
921       probably not all: copy _RS surface flux fields to RL field before
922       calling DIAGNOSTICS_FILL
923     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
924       real*4 (CALL EXCH_*_RS) versions.
925     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
926       (generate new output).
927    
928    checkpoint61e (2008/10/23)
929    o gmredi (Visbeck-variable-K):
930      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
931      - change computation of Visbeck-K where Slope > Smax :        
932        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
933        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
934    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
935      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
936    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
937    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
938      does not become too large (to avoid precision problems in implicit-diffusion
939      solver); update ideal_2D_oce output.
940    o pkg ggl90:
941      - in ggl90_cal.F: compute only one set of visc/diff, used to
942        step forward TKE/T/S/momentum
943      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
944        have Prandlt =1)
945    o gmredi (fm07):
946      - add lower limit on Transition layer thickness + lower limit on 1/lambda
947      - allow to set few more params from data.gmredi
948    o pkg ggl90:
949          - add missing sqrt(2) factor in computation of mixing length
950            scale in ggl90_calc.F
951            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
952    
953    checkpoint61d (2008/09/25)
954    o adjoint modifs
955      - adapt to new field rhoInSitu
956      - allow to revert from StoreDynVars2D, StoreDynVars3D
957        to individual fields
958        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
959    o store 3-D (in-situ) density in commom block (DYNVARS.h)
960     - save 1 rho computation.
961     - no longer modify T & S inland when using down_slope pkg.
962    o gad_som : allow to switch to SOM advection for T & S without corresponding
963      pickup files (using new S/R: MDS_CHECK4FILE).
964    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
965      (for useSingleCpuIO to work in multi-threaded)
966    o pkg/shelfice:
967     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
968       with SHELFICEtopoFile in data.shelfice
969     - move code for reading ice shelf topography and modifying hFacC into separate
970       subroutines of the shelfice package
971     - separate initialisation of "fixed" and "variable" variables
972     - kTopC is not (yet) replaced by kSurfC, although this is possible
973    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
974    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
975      and rename:
976      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
977      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
978    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
979    
980    checkpoint61c (2008/08/30)
981    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
982      to add mass source/sink of fluid in the interior (3-D generalisation
983      of oceanic real-fresh water flux).
984    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
985    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
986    o new pkg: down_slope
987      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
988      - presently, modify T & S inland (dwnslp_calc_rho.F).
989        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
990      - implementation for ocean in P-coords not tested.
991      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
992    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
993      (to facilitate conversion of oceanic pkg to p-coordinate).
994    o change FIND_RHO to FIND_RHO_2D :
995      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
996    o new pkg: cheapaml
997    
998    checkpoint61b (2008/08/05)
999    o exch2:
1000      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
1001      - no longer depend on the order sequence (N,S,E,W).
1002      - 3rd exchange no longer needed (tested with 24 tiles).
1003      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
1004      - exch_UV_A-grid readily available (but not yet tested).
1005      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
1006      (both are no longer needed) in exch_uv: no effect in forward run; but
1007       get truncation error differences with adjoint exch.
1008    o exch2:
1009     - change index-bounds storage (moved from target to local tile,
1010       more intuitive this way) ; rename/remove some variables.
1011     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
1012    
1013    checkpoint61a (2008/07/29)
1014    o exch2/matlab-topology-generator:
1015      fix bug in index bounds for N-S internal exchange (hard to tell if this
1016      had any effect on the solution).
1017    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
1018      is exceeded
1019    o testreport: modify syntax of awk, so that it works also with
1020      awk, and not only with nawk and gawk
1021    
1022    checkpoint61 (2008/06/24)
1023    o autodiff
1024      Change default for TAF usage by removing argument '-nonew_arg'
1025      This changes TAF subroutine argument list (ordering of active var.)
1026      Omission of this flag leads to incompatibility w.r.t. TAMC
1027      To restore TAMC-compatibility, need following modifs:
1028      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
1029      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
1030      Tested TAF version is 1.9.22
1031      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
1032    
1033    checkpoint60 (2008/06/19)
1034    --->>> This is the last checkpoint for which generating the adjoint
1035    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
1036    --->>> by default.
1037    --->>> Future checkpoints will ommit this flag by default.
1038    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
1039    o pkg/grdchk: Add gradient check to etan0 perturbations.
1040    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
1041    o pkg/autodiff: more flexibility in zeroadj.
1042      model/src: modifying do_oceanic_phys.F accordingly.
1043    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
1044    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
1045      special setup of gmredi for which the adjoint is stable
1046      enough for parameter optimization.
1047    o bridging the gap between eddy stress and GM.
1048      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
1049          along with a change in CPP option (now ALLOW_EDDYPSI).
1050      -> when using GM w/ GM_AdvForm:
1051          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
1052          is applied either in the tracer Eq. or in momentum Eq.
1053          depending on data.gmredi (intro. GM_InMomAsStress).
1054      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
1055      The key modifications are in model/src/taueddy_external_forcing.F
1056      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
1057    
1058    checkpoint59r (2008/05/29)
1059    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
1060      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
1061      fix option to read coriolis(@ cell-corner) from files with CS-grid.
1062    o pkg/mnc: add some attributes to standard 1D-coordinate variables
1063    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
1064      mass points, when using mnc for output
1065      - add runtime parameter (missing_value, missing_value_int) to override
1066        default (which is the value of getcon('UNDEF'))
1067    o pkg/mnc: prepare mnc for the actual use of missing values with the
1068      diagnostics package: small fix in mnc_cw_readwrite.template and more
1069      initialisation of never used fields
1070      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
1071      versions
1072    o pkg/thsice/thsice_ini_vars.F added default initial values so that
1073      thermodynamics sea ice solver does not blow up when some initial fields
1074      are missing.
1075    o move from external_forcing_surf.F to ini_forcing.F
1076      the p-coord. hack consisting in using pLoad to set phi0surf ;
1077      update output of tutorial_global_oce_in_p (affected @ truncation level).
1078    o Freshen up a bit hs94.1x64x5, notably:
1079      remove rotationPeriod and tRef=5*0. (adjoint only), and add
1080      exactConserv=.TRUE.
1081    o pkg/generic_advdiff:
1082      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
1083      applies to files where Temperature & Salinity 2nd Order moments are used.
1084    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
1085      this uses a dynamically allocated internal state data structure
1086      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
1087      and requires a fortran 90 compiler
1088    
1089    checkpoint59q (2008/05/06)
1090    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
1091       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
1092    o Refresh tutorial_global_oce_biogeo, notably:
1093      - change bathymetry (put back seamounts in ACC, use hFacs)
1094      - change EOS (POLY3 --> JMD95Z)
1095      - use Bryan-Lewis vertical diffusivity
1096      - use multidimensional advection
1097      - remove old virtual virtual in dic pkg, now done through ptracer pkg
1098      - change a couple of parameters in dic pkg
1099    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
1100    o pkg/obcs: change default to OBCSfixTopo = .true.,
1101      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
1102      - replace "debugMode" with "debugLevel .GE. debLevB"
1103    o implementation of TAF directives for gchem,cfc,dic
1104    o remove "exp5" (replaced by tutorial_deep_convection).
1105    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
1106      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
1107      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
1108      --> changes results in exp4, seaice_obcs
1109    o tutorial_deep_convection :
1110      update the set-up and increase resolution and domain size ; start
1111      from pseudo initial conditions = output at t=120mn in order to see
1112      something happening when running testreport.
1113    o pkg/seaice: add os7mp as an advection scheme
1114                  add check for advection schemes
1115                  add a flag for restoring T and S underneath sea ice
1116    o pkg/my82: add netcdf-support and diagnostics
1117    o thsice pkg:
1118      - Now hsMax limits snow height by turning it into ice following
1119        flooding scheme (and now conserving energy)
1120      - Slight rewriting of the formula in thsice_calc_thick.F
1121      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
1122      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
1123    
1124    checkpoint59p (2008/04/10)
1125    o gchem / dic / cfc :
1126      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
1127      - add new parameter files: "data.dic" & "data.cfc" ;
1128      - various re-arrangement in initialisation & header file ;
1129      - fix tutorial_global_oce_biogeo for multi-threaded test.
1130    o pkg/dic: test for "pickup_dic" file when restarting ;
1131      if no pickup-file, can restart with a re-initialised pH (same as it did
1132      before) providing pickupStrictlyMatch is set to False.
1133    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
1134      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
1135    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
1136      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
1137    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
1138     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
1139       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
1140    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
1141       scheme to use for vorticty-term ;
1142     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
1143       (with default selectVortScheme, return to original discretisation)
1144     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
1145    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
1146    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
1147      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
1148      also fix diagnostics VISCAHW & VISCA4W.
1149    
1150    checkpoint59o (2008/03/07)
1151    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
1152    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
1153      move a few statemens out the main loop into separate loops
1154    o pkg/shelfice:
1155      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
1156        (kg/m^2/s), does not break tests, because in verification/isomip,
1157        rhoConstFresh=rhoConst (by accident)
1158      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
1159      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
1160        new file model/src/seawater.F, so that they are available for all pkgs.
1161      - convert potential temperature into in-situ temperature. This changes the
1162        isomip tests => update tests
1163    o add a flag writePickupAtEnd (default=true) to be able to suppress
1164      writing a pickup at the last timestep
1165    o tools/mpack-1.6 :
1166      - disable automake (not working) and autoconf (not needed).
1167      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
1168        also cleaner with much less compilation warnings.
1169    o pkg/profiles:
1170      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
1171      (for "less than 32 characters name" compiler requirement)
1172    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
1173      conditions that have a different sampling frequency than S/T/U/V obcs
1174    o pkg/diagnostics (stats-diags):
1175      - fix global Min/Max in case 1 processor get only empty tiles
1176    o genmake2: replace (4 times)
1177         make genmake_tc_1.o >> genmake_warnings 2>&1
1178      with
1179         COMM="$CC $CFLAGS -c genmake_tc_1.c"
1180         echo $COMM >> genmake_warnings
1181         $COMM >> genmake_warnings 2>&1
1182      to make genmake2 always see the value of CC as specified in the optfile.
1183    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
1184      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
1185      - modify verification advect_cs test to test SOM-advection on CS-grid.
1186    o pkg/ctrl:
1187      - Rewrite of ctrl_map_ini_ecco.F,
1188        introducing a generic routine (ctrl_map_ini_gen.F).
1189      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
1190    
1191    checkpoint59n (2008/02/09)
1192    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
1193      number in dedicate array "hdiag":
1194      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
1195        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
1196      - many small changes (integer format) for large number of diagnostics
1197      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
1198        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
1199    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
1200      usingSphericalGrid, this allows to define the rotated grid coordinates
1201      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
1202      geographical coordinates according to the inverse of the rotation defined
1203      by the Euler angles, so that Coriolis parameter and online-interpolation by
1204      exf works with the geographical coordinates on XC/YC/XG/YG.
1205      Naturally, this feature does not work with all packages, so some
1206      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
1207      profiles), because there the coordinates are assumed to be regular
1208      spherical grid coordinates.
1209    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
1210      - introduce isopycnal diffusion coefficient control.
1211    o tools/adjoint_options:
1212      - additional control vector components.
1213    o pkg/mnc: have mnc create marginally meaning full coordinate variables
1214      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
1215    o pkg/mypackage:
1216      - add example of read/write pickup for state-var ;
1217      - add entry points to the main code for state-vars diags & write-pickup.
1218    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
1219      transitions for useExfYearlyFields
1220      - add new subroutine that determines the file to read from for
1221        use*YearlyFields = .TRUE. and .FALSE.
1222      - add a verification experiment to global_with_exf that tests
1223        useExfYearlyFields with USE_EXF_INTERPOLATION defined
1224    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
1225      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
1226      subroutines (which could be generated from a template, because they are
1227      almost identical), for now they are included in obcs_prescribe_read.F for
1228      simplicity
1229    o pkg/exf:
1230      - add a little more diagnostic to exf_interp_read (in analogy to
1231        mds_read_field, can be turned off with debugLevel < debugLevA=1)
1232      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
1233        ugly but fast by unrolling short inner loops, inserting a unroll=8
1234        directive in routine lagran, and splitting a loop and making do while the
1235        outermost loop (the latter requires the intoduction of index arrays)
1236    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
1237    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
1238      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
1239    o verification/seaice_obcs: updated for restart test and latest options
1240    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
1241      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
1242      for now this is only available for the C-grid code and also within
1243      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
1244    
1245    checkpoint59m (2008/01/14)
1246    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
1247      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
1248    o gad_som : fix flux output (& diagnostics) to have same units as other  
1249      advection scheme fluxes (was previously multiplied by deltaT).  
1250    o added verification/seaice_obcs both to test seaice open boundaries
1251      and to provide an example matlab scrpt for generating them
1252    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
1253    o pkg/salt_plume: clean up salt_plume_frac.F to
1254      remove redundancy in PlumeMethod 1 and 4
1255    o pkg/kpp: added saltplume diagnostics
1256    o pkg/obcs and pkg/seaice:
1257      - do not set uice and vice to zero when OB*icefile are unspecified
1258      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
1259      - moved seaice tracer obcs after call to seaice_growth
1260    o pkg/salt_plume: added various options for salt plume depth
1261      criterion and for vertical distribution of the salt
1262    
1263    checkpoint59l (2007/12/18)
1264    o pkg/ptracers: new version of ptracers pickup:
1265      read meta file and write only fields which are needed to restart.
1266      ( same logic as main pickup file ; also using pickupStrictlyMatch )
1267    o pkg/seaice:
1268      - add timescale for melting due to warm mixed layer as a means of
1269        setting SEAICE_availHeatFrac more conveniently
1270      - add a CPP-flag/runtime parameter check for flooding algorithm
1271      - reformulated availHeat in seaice_growth.F to be independent of AREA
1272    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
1273      unit changes
1274    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
1275    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
1276      SX vector computer.
1277    o pkg/seaice:
1278      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
1279        seaice forcing fields can now be read only through pkg/exf
1280      - removed some unused halos
1281    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
1282    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
1283      or U/VICE from U/VWIND before computing U/VSTRESS
1284    
1285    checkpoint59k (2007/11/30)
1286    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
1287      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
1288    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
1289      all experiments pass when compile with un-initialised var. checking option.
1290    o added pkg/salt_plume
1291    o script to test restart (for now, in MITgcm_contrib/jmc_script)
1292    o pkg/seaice: new read/write pickup version.
1293      read meta file and write only fields which are needed to restart.
1294      ( same logic as main pickup file ; also using pickupStrictlyMatch )
1295    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
1296    o lab_sea.hb87: modify the domain & update output.hb87.txt :
1297      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
1298      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
1299      process. Fixed here by closing the domain at the Northern boundary.
1300    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
1301    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
1302      a set of consecutive levels in/from a 3-D array.
1303    o pkg/ptracers:
1304      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
1305      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
1306    
1307    checkpoint59j (2007/11/09)
1308    o in pkgs: dic, obcs, offline, rbcs:
1309      standard way to compute coeff. for time interpolation between 2 time reccords
1310      which retains full precision (& make results less dependent on compiler).
1311      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
1312    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
1313      packages instead of reading ice cover and wind speed separately
1314    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
1315     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
1316      to allow to compile customized code before the update)
1317    o cleaning-up:
1318      - fix CPP instruction syntax in pkg/obcs
1319      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
1320        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
1321      - fix some threads issue in IO parts.
1322    o pkg/dic:
1323      - add tons of "_d 0" (--> much better testreports !)
1324       and then update outputs of tutorial_global_oce_biogeo
1325    o pkg/mom_fluxform:
1326      add a special version of momentum advection intended to conserve momentum
1327      next to a bathymetry step or a coastline edge. (default = off = #undef)
1328    o new read/write pickup version:
1329      - for now, only implemented for main (mdsio) pickup file.
1330      - write out only what is needed to restart; merge pickup_nh , pickup_ph
1331        and main pickup together.
1332      - read meta file; read only what is needed to restart; stop if a field
1333        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
1334        if it make sense (even if the restart is not perfect).
1335      - if no meta file, assume that pickup to read corresponds exactly to
1336        a pickup that would currently be written.
1337      - read pickup written in the old format (until checkpoint59i) if it
1338        recognizes an old meta file (no field-list).
1339      - add a meta file in exp. which starts from a pickup: 2 cases:
1340        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
1341         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
1342        b) a meta file describing the content of the associated pickup file
1343         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
1344    o pkg/mdsio & pkg/rw:
1345      - new routine to read a meta file ; new set of routine to read
1346        Multiple-fields file (with meta file).
1347    o added open boundary conditions capability for seaice
1348        HSNOW, HSALT, UICE, and VICE
1349    
1350    checkpoint59i (2007/10/21)
1351    o adjoint:
1352      * fix multiDimAdvection adjoint
1353        (partial recomputation problem by TAF for fVerT(:,:,kDown)
1354        and comlev1 size definition (maxpass vs. max. number of tracers)
1355      * verification/global_ocean.90x45x15 adjoint now tests
1356        NLFS and multiDimAdvection using DST3 (=30)
1357      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
1358    o pkg/kpp: add "_d 0" to real constant (if missing);
1359      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
1360      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
1361    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
1362      for internal parameters related to restart process (formerly from PARAMS.h)
1363      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
1364    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
1365      as argument. (only atm2d & obcs write_pickup have not yet been updated)
1366    o pkg/monitor:
1367      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
1368      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
1369      - account for deep Atmosphere factor and density factor (anelastic)
1370    o added open boundary conditions capability for seaice HEFF and AREA
1371    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
1372      thermodynamics
1373      - requires a little reorganization, which affects the testreport results
1374        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
1375        so that now the conservative form is tested
1376      - add a few comments
1377    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
1378    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
1379    o add new diagnostics to seaice: advective, diffusive fluxes (only for
1380      multidim-advection, for scheme 2 they are not filled) and transports,
1381      thermodynamic growth rates
1382    o change units of EmPmR (inside the code, + within coupling interface)
1383      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
1384      Affects results @ truncation level (cg2d match) and update output of
1385       experiments: lab_sea(6), global_ocean.90x40x15(10),
1386      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
1387      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
1388      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
1389      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
1390    
1391    checkpoint59h (2007/09/29)
1392    o pkg/exf:
1393      - improve vectorization by moving if-statement out of loops in
1394        exf_mapfields, exf_radiation
1395      - exf_bulkformulae.F: introduce 2D fields and vectorize code
1396    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
1397    o testreport:
1398      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
1399        monitor & update offline_exf_seaice exp. output.
1400      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
1401    o pkg/seaice:
1402      - bug fix in the evp solver: boundary conditions were affected be
1403        masking of zMax/zMin (changes results)
1404      - minor bug fix in boundary conditions in seaice_calc_strainrates
1405        (changes results for no_slip)
1406      - seaice_lsr.F: make interpolation of eta dependent on boundaries
1407      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
1408      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
1409        stress formulation and no-slip boundary conditions
1410    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
1411      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
1412    o pkg/seaice: a first HSALT time stepping equation has been checked in
1413    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
1414      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
1415      without requiring DO-IF statements
1416    o pkg/thsice:
1417      use continuous power-law function for partition of energy between lateral
1418      melting/freezing and thinning/thickening ; old code using step function
1419      still available with #undef THSICE_FRACEN_POWERLAW
1420      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
1421    o testreport: change AD testing : check against results/output_adm.txt
1422      using same scripts as for forward test.
1423    
1424    checkpoint59g (2007/09/17)
1425    o adjoint testing: in preparation for changing testreport:
1426      - output format: cost and grad written on separated lines
1427      - ad output results in directory "results" (instead of "results_ad")
1428    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
1429    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
1430    o pkg/ecco: allow user defined cost function contributions
1431    o testreport:
1432      Allow to choose (per experiment) the list of tested output variables
1433       and the main variable (used to issue a pass/FAIL ) ;
1434      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
1435      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
1436      Also modify printing of summary:
1437       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
1438       b) echo the list of tested variables in the individual summary.txt of
1439          each experiment.
1440    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
1441      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
1442      (but still depend on the tile decompostion of the domain).
1443    o pkg/seaice: change a discretization detail to make the B-grid code
1444      "more symmetric". This change is likely to remove all "ridges/leads" that
1445      where quasi-aligned with the grid in B-grid solutions. It may also be
1446      the solution to the stress coupling issues with the B-grid.
1447    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1448      remove .cvsignore from input dir. (since testreport no longer run here).
1449    o pkg/thsice:
1450     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1451     - fix reshaping of sea-ice just after advection:
1452       melt all the ice only if ice-volume is too small.
1453     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1454       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1455     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1456    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1457      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1458    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1459      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1460      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1461      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1462      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1463      -> update output.txt
1464    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1465     this affects truncation error: -> update output.txt of exp:
1466      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1467      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1468    
1469    checkpoint59f (2007/08/21)
1470    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1471    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1472      a bounded range (in forward mode)
1473    o pkg/ecco, ctrl, autodiff and mom_common:
1474     internal parameter controls, completements of implementations
1475    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1476    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1477      (not seem any difference in testing results).
1478    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1479       at face corners.
1480    o pkg/generic_advdiff:
1481     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1482      loop range indices for computing vertical advection tendency
1483      and do the calculation in the interior only (no overlap) ;
1484      for now, only implemented for SOM advection (to save CPU time).
1485     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1486    o exch2 adjoint
1487      First set of changes:
1488      - add exch2 hand-written adjoint templates
1489      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1490        This will require cleanup in pkg/autodiff/*.F
1491        (changed routines currently kept separate in verif. code/)
1492      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1493        that used to hide exch2 or cubed-sphere specific code
1494        (commented via 'cph-exch2')
1495    o pkg/seaice
1496      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1497    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1498       output of global_ocean.cs32x15.thsice .
1499    
1500    checkpoint59e (2007/07/26)
1501    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1502      for B-grid vector (not yet tested) and C-grid vector (<- only used
1503      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1504    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1505      (#ifdef ALLOW_SALT_PLUME)
1506    o gather_2d/scatter_2d: removed halo regions
1507    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1508      scheme and the corresponding test case (under front_relax dir). For now,
1509      only available with Skew-flux form and not yet tested in realistic set-up.
1510      adjoint: store directives updated, but gradient checks deteriorated,
1511      so maybe GM/Redi adjoint is now broken.
1512    o seaice adjoint
1513      * add AREA, HEFF, HSNOW as control variable
1514        (should not change lab_sea results)
1515      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1516    o pkg/seaice:
1517      * added computation of saltFlux in seaice_growth;
1518        For time being, sea ice salinity is assumed constant
1519        contribution of snow flooding to freshening of sea ice is neglected.
1520        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1521        defaults to 0.0 in order to maintain backward compatibility.
1522        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1523      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1524      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1525        heat content used to melt or grow ice
1526      * commented out cap of HICE: it helps keep ice thinner
1527      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1528      * applied OBCS T/S mask to HEFFM sea ice mask
1529    
1530    checkpoint59d (2007/06/21)
1531    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1532     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1533     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1534    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1535     and change default value of parameter "GM_Small_Number";
1536     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1537       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1538       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1539    o pkg/ecco: cost function when applying pkg/smooth to controls
1540    o pkg/ctrl: add forcingPrecond run time parameter
1541    o pkg/seaice:
1542     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1543     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1544       changes verification/lab_sea
1545     - rearrange implicit part of u-equation in LSR solver to make it easier to
1546       read, understand, and debug. This causes changes at the truncation level.
1547     - fix (serious) bug in the boundary conditions (sign error in the implicit
1548       part) of the LSR solver. Changes all LSR results.
1549     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1550       is initilized with small values - does not change lab_sea results.
1551     - added HsnowFile initialization capability
1552    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1553     initialization of pkg/smooth and application to control vector
1554    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1555    o dependencies: pkg/profiles requires pkg/cal
1556    o pkg/profiles:
1557     - added option ALLOW_PROFILES_GENERICGRID
1558         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1559         that interpolation information (grid points and coefficients) is provided
1560         within the netcdf input files.
1561         -> sample matlab scripts can be found in MITgcm_contrib/gael
1562         that allow you to prepare netcdf input files.
1563     - also modified: cleaner include statements, cleaner error print statements,
1564       cleaner stops when error, and more tests of the netcdf input files consistency.
1565    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1566    o pkg/seaice:
1567     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1568       requires a new routine: seaice_diagnostics_fill.F
1569     - make sure that seaice does not move if not forced (pressure replacement
1570       method, Hibler and Ip, 1995), changes results
1571     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1572     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1573       It is turned off by default (=-1.), because it changes the results.
1574     - make it possible to read AREA from a file, too.
1575    
1576    checkpoint59c (2007/06/04)
1577    o add S/R and diagnostics for oceanic mixed-layer depth
1578    o move GMRedi call after all vertical mixing schemes (including KPP)
1579    o pkg/thsice:
1580     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1581      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1582    o pkg/obcs:
1583     - bug fix for balance code
1584    o pkg/seaice:
1585      - allow values of SEAICE_elasticParm > 1
1586      - add new parameter SEAICE_evpTauRelax as an alternative
1587        to SEAICE_elasticParm
1588      - make lsr boundary conditions free slip (by default), changes result
1589      - add code for no slip boundary conditions for lsr
1590      - set minimum of zeta to zero (and not 4e8) (changes results)
1591      - add a cap on AREA after advecting AREA if seaice_growth is not called
1592    o change calculation of Visbeck K:
1593      - no longer depend on tapering scheme; instead, compute slope (limited
1594        by GM_maxSlope). this is equivalent to what was comuted before with
1595        clipping or linear tappering.
1596      - fix vertical averaging (wrong by 1/2 level)
1597      - leave the old version (but will not be maintained) within
1598        #ifdef OLD_VISBECK_CALC / #endif
1599      - update output of exp. ideal_2D_oce
1600    o change error catch in calc_r_star to improve vectorization
1601    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1602      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1603    o adjoint:
1604      Re-organized adjoint checkpointing according to Matt Mazloff
1605      (but with modifs/completions/cleanups)
1606      Storing is now bundled into large arrays to optimized I/O
1607      (and second step in cleanup of the_main_loop)
1608    
1609    checkpoint59b (2007/05/16)
1610    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1611      - export/import (between ocean & coupler) fields needed for ocean DIC.
1612    o pkg/seaice:
1613      - get rid of three more exchanges seaice_calc_viscosities (required
1614        different loop boundaries in seaice_lsr and seaice_ocean_stress)
1615      - bug fix in seaice_ocean_stress (update of lab_sea required)
1616      - reduce loop boundaries to necessary minimum also in seaice_evp
1617      - go back to the old way of computing deltaC/Z as the adjoint likes that
1618        better
1619    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
1620      passive tracer to an Age Tracer) + update output.txt
1621    o pkg/exf:
1622      - implement A-grid / C-grid selection for wind-stress input files.
1623      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
1624      for now, in exf_bulk_largeyeager04.F only :
1625      - change implementation for case where windspeed + 2. components wind-stress
1626        are read-in. AND use rhoConstFresh to convert evap.
1627    o pkg/seaice:
1628      - use correct EXCH_UV for wind-forcing (on A-grid).
1629      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
1630        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1631    o pkg/exf:
1632      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1633      EXF_INTERPOLATION:
1634      - merge global_with_exf/code version of exf_interp_read.F
1635        to the main code ;
1636      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1637        reading the file ; Important: This options needs to be defined to recover
1638        previous code.
1639        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1640      - no longer loose real*8 precision along the way when using exf_iprec=64.
1641    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1642      - change discretisation of evp-solver in order to avoid another exchange
1643        (changes lab_sea) and clean up a little
1644      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1645        help the adjoint (this also changes the results slightly)
1646      - add a few "_d 0" where they had been missing in seaice_evp.F
1647      - cleaning up: remove unused seaice_calc_rhs.F
1648    o pkg/exf: some cleaning-up:
1649      - change various "constants" into runtime parameters
1650      - cleaned-up Large&Yeager04 routine which should eventually
1651        replace exf_bulkformulae.F (changed names of S/R and CPP)
1652        and merged various ALLOW_ATM_WIND options
1653     only used with thsice pkg (in thsice_get_exf.F):
1654      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1655        which are used when useStabilityFct_overIce=TRUE (= the default)
1656      - change default values of ice & snow emissivity and scale downward LW
1657        by ice & snow emissivity.
1658    o pkg/thsice:
1659     fix few little problems, in thsice_calc_thickn.F:
1660      - growth vertically (and not laterally) if iceFrac == iceMaskMax
1661      - melt only laterally if hIce < hThinIce (as the comments say)
1662      and in thsice_extend.F:
1663      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1664      - start to form ice as soon as the minimum ice-volume is reachable.
1665     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1666      and cpl_aim+ocn
1667    o pkg/kpp
1668     - move computation of surface related input fields to KPP into a new
1669       subroutine kpp_forcing_surf.F
1670     - remove wrong (within bi,bj loops) EXCH calls.
1671     - little cleaning (add argument myThid in last position, cvs header ...)
1672     - for now, fix conservation problem by exchanging KPPviscAz (may not
1673       be the best fix)
1674    o pkg/seaice
1675     - check for inconsistent evp parameter/cpp-flag combination
1676     - remove leftover errIO flat for obsolete name list error handling
1677    o OpenAD
1678     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1679    
1680    checkpoint59a (2007/05/01)
1681    o pkg/seaice: some parameter clarifications and a little bit of clean up
1682    o pkg/thsice: rename run-time parameters:
1683       himin       -> hIceMin
1684       himin0      -> hThinIce
1685       hihig       -> hThickIce
1686       i0          -> i0swFrac
1687       transCoef   -> bMeltCoef
1688       frac_energy -> fracMelting
1689      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
1690       with default values (for now) that do not change the results.
1691      remove old version of thsice vars advection in pkg/seaice.
1692    o in FFIELDS.h:
1693      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
1694      - make pLoad & sIceLoad always available (but still only used if
1695         ATMOSPHERIC_LOADING is #define).
1696    o pkg/kpp: replaced _KPP_RL with _RL
1697    o bug fixes for vertical diffusivity computations when both KPP and
1698        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1699        are no longer updating the vertical diffusivity array
1700        (passed as argument) but are (re-) setting those arrays.
1701    o pkg/seaice: fix bug in evp solver, while doing that
1702      - change (improve?) discretization of stress computations for both
1703        cgrid-lsr and evp solver
1704      - add a new routine to compute strain rates
1705      - the above changes lab_sea results
1706      - add no slip conditions for evp solver (off by default), lsr-version
1707        may follow
1708      - fix exchange for shear at Z-points (does not change lab_sea)
1709      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
1710        (to force the user to pick a time step since there is not "safe" way
1711        of choosing it)
1712      - add principal stress diagnostics
1713      - rearrange fields for evp a little to avoid having to call a: too many
1714        exchanges and b: exchanges for stress trensor components which we do
1715        not have.
1716      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
1717        of evp, complete rewrite for lsr case (latter is does not yet work
1718        in all cases)
1719    o pkg/kpp: add code to have mixing in shelf ice caverns
1720      - add myThid to all kpp routines (long overdue)
1721    
1722    checkpoint59 (2007/04/19)
1723    o pkg/exf:
1724      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1725        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
1726      - move exf header files from lower_case.h to UPPER_CASE.h ;
1727        add missing cvs Header & Name
1728      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
1729      - add namelist param. selectStressGridPosition, exf_monFreq
1730      - retire many _CLIM routines, and remove data.exf_clim
1731        + params moved to data.exf
1732        + climsst, climsss now handled by exf_set_gen, i.e.
1733          climss?period=0 refers to constant field,
1734          climss?period=-12 to monthly forcing
1735      - split up namelists in data.exf
1736    o pkg/seaice:
1737      - remove seaice_exch and seaice_exch_uv
1738      - remove superfluous exchange of theta
1739      - add myThid to seaice_budget_ocean/ice
1740      - add new interface for atmospheric wind forcing (C-grid only)
1741        + new routine
1742        + two new field (taux, tauy for stress over ice)
1743        + removed one global field (DAIRN) for C-grid case only
1744    o pkg/thsise
1745      - 2nd set of modifs for thsice adjoint in conjunction with exf
1746    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
1747    
1748    checkpoint58y_post (2007/04/15)
1749    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
1750      vertical diffusivity, similar to that in MOM4; turned on using
1751      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
1752      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
1753    o Added capability for 3D specification of background vertical diffusion
1754      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
1755      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
1756      "data" file that contains the 3D vertical diffusivity coefficients.
1757    o ice dynamics (pkg/seaice) with thsice thermodynamics:
1758      - add code within pkg thsice to advect & diffuse sea-ice fields
1759      similar to (and will replace) what has been added in  seaice_advdiff.F,
1760      but: - conserving Mass, Heat & Salt.
1761           - better when using non-linear advection scheme (not yet fully tested)
1762           - can also be used in atmospheric set-up (for now, only the diffusion).
1763    
1764    checkpoint58x_post (2007/04/04)
1765    o IO option for global-file compact format:
1766      - add options when generating topology (utils/exch2/matlab-topology-generator)
1767      - add I/O capability (pkg/mdsio).
1768      - adapt utils/matlab/rdmds.m to read this format.
1769      for now long-line format not yet supported by pkg/mdsio (& exch2).
1770    o shelfice: add a few diagnostics
1771    
1772    checkpoint58w_post (2007/03/13)
1773    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
1774      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
1775      (and replace horiVertRatio in NH code).
1776      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
1777                         and tutorial_plume_on_slope (sensitive to truncation)
1778    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
1779      directly to drive seaice model (C-grid only)
1780    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
1781     - reintroduce computation of wind from stress,
1782     - compute tau (in exf_bulkformulae.F) from windstress averaged to
1783       mass points to avoid tau = 0
1784     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
1785    o rdmnc.m: make it work with "global" files created with gluemnc
1786    o rdmnc.m : some improvements in dealing with singleton dimension
1787      (tested on all testreport mnc output files).
1788    o genmake2: disable pkg/profiles if netcdf test fails.
1789    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
1790    o move call to cal_readparms up to make calendar parameters/variable available
1791      to all packages
1792    
1793    checkpoint58v_post (2007/02/08)
1794    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
1795      useDynP_inEos_Zc tested.
1796    o pkg/exf: changes to properly interpolate/mask/scale initial fields
1797    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1798      and portions thereof.  See read_cs.txt for description and examples.
1799    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1800      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1801      following the great-circle arc between those 2 points.
1802    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1803      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1804    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1805     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1806     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1807     - still needs work (not working with some options ; efficiency to improve)
1808       and serious testing.
1809     - use this scheme for temperature & salinity in 2 advection test exp.:
1810       advect_xy & advect_xz, respectively.
1811    
1812    checkpoint58u_post (2007/01/12)
1813    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1814    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1815    o testreport: add option "-skipdir" to skip some test.
1816    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1817      momentum calculation.
1818    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1819    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1820      remove checkpoint.F and the_correction_step.F (no longer used);
1821      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1822    o add option (linFSConserveTr) to correct for tracer source/sink due to
1823      Linear Free surface
1824    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1825    o pkg/thsice: fix reading mnc-pickups
1826    
1827    checkpoint58t_post (2006/12/30)
1828    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1829    o pkg/mdsio:
1830     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1831       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1832       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1833     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1834     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1835       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1836     - new S/R (to replace MDSWRITEMETA), which allows to write more
1837       informations (variable names, time ...) to meta files.
1838     - modify rdmds.m to give back the meta file content.
1839    o pkg/diagnostics: change vertical interpolation to be safer, and more
1840       flexible (define p-levels to interpolate to in data.diagnostics);
1841      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1842       diagnostic pointer.
1843    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1844    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1845    o fix multi-category seaice:
1846     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1847       SEAICE_MULTICATEGORY
1848     - fix short wave heat flux
1849    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1850       and allow to use EVP solver. Change forward lab_sea: test both EVP
1851       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1852    o Initial check-in of lab_sea adjoint
1853      (very similar to natl_box_adjoint/code_seaice)
1854      * used C-grid and EVP solver
1855      * used KPP, GM/Redi
1856      * uses inAdExact=.TRUE.
1857      * gradient checks fail for both ADM and TLM
1858        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1859        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1860        issue is related to forward mismatch between g77 an ifort
1861    o pkg/seaice: overhaul of thermodynamics
1862     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1863     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1864     - move a few global fields out of SEAICE.h into seaice_growth.F and
1865       make them 2D (FICE/QNETO/ ...)
1866     - remove FO (it is the same as QNETO)
1867     - introduce a few local fields to avoid modifying external fields such
1868       as atemp, etc.
1869    
1870    checkpoint58s_post (2006/12/11)
1871    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1872      changed exf_set_gen.F so that
1873        genperiod=0 means input file is one time-constant field and
1874        genperiod=-12 means input file contains 12 monthly means
1875    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1876      this affects truncation error ; generate new output file for exp. which
1877      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1878        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1879        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1880        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1881        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1882        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1883    o start implementation of deep-atmosphere and anelastic formulation
1884    o verification: remove 2nd copy of input files and use script "prepare_run"
1885      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1886    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1887    o profiles: fix for multithreaded case
1888    
1889    o diagnostics: rename few diags:
1890      s/'PRESSURE'/'RCENTER '/g
1891      s/'TICE    '/'oceFreez'/g
1892      s/'TAUX    '/'oceTAUX '/g
1893      s/'TAUY    '/'oceTAUY '/g
1894      s/'SWFLUX  '/'oceQsw  '/g
1895      s/DIFx/DFxE/g
1896      s/DIFy/DFyE/g
1897      and add few ocean-forcing diagnostics:
1898      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1899    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1900      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1901      as actual snow thickness.  It now refers everywhere to effective snow
1902      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1903    
1904    checkpoint58r_post (2006/11/17)
1905    o modifications to pkg/seaice/growth.F, which change results of
1906      lab_sea experiment: fixes pertain to melting snow over open water, to
1907      masking EVAP under sea ice, and to using the correct AREA variable for
1908      computations of EVAP, PRECIP, HSNOW, and GHEFF
1909    o add ability to read bathy, salt, and theta using MNC (off by def)
1910    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1911      both are turned off by default and do no change any results
1912    o seaice advection with pkg/thsice: a step toward the use of non-linear
1913      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1914    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1915      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1916      in natl_box (affects results @ truncation level: update output.txt)
1917    o multi-threading and IO:
1918      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1919      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1920        (needed to work with SingleCpuIO): tested in all verif. exp.
1921    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1922      affects the results (but none of the verification test uses this scheme).
1923    o Adding some pkg/diagnostics capability to pkg/seaice
1924      (will certainly be subject to changes)
1925    o ctrl: adding new control variables:
1926      lwflux, lwdown, evap, snowprecip, apressure, runoff
1927    
1928    checkpoint58q_post (2006/10/20)
1929    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1930      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1931      high_res_cube configuration by 4% on Columbia.
1932    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1933      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1934      dynamical allocation (seems to work in multi-threaded).
1935    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1936      single CPU io) so that TAF does not have to see EESUPPORT.h
1937    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1938    
1939    checkpoint58p_post (2006/09/08)
1940    o obcs: stop if obcs is used with useCDscheme = .true.
1941    o shelfice:
1942     - fix a sign error so that no slip at shelfice interface works
1943     - remove stop for combination non-hydrostatic code and shelfice. That does
1944       not mean, that the results are correct, but at least they are numerically
1945       stable
1946    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1947    o added adjoint exch routined for all exch*3d* routines
1948      and updated flow directives
1949    
1950    checkpoint58o_post (2006/08/28)
1951    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1952      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1953    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1954      and clean-up reading/writing of pickup files.
1955    o fix local version of read/write pickup (NH part) in rotating_tank/code
1956    o simplify EXCH interface:
1957     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1958     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1959    o added the regrid package
1960    o shelfice:
1961     - add a simple boundary layer scheme to reduce noise
1962     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1963    
1964    checkpoint58n_post (2006/08/14)
1965    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1966       local variable (not in common block).
1967    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1968      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1969      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1970        to work with SingleCpuIO.
1971    o add "_d 0" to real constant of pkg/cfc subroutines ;
1972       update exp. cfc_exemple & tutorial_cfc_offline output files.
1973    o multi-threading and IO:
1974      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1975        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1976      - barrier before and after reading.
1977      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1978      - avoid using MDS_WRITELOCAL for LAND pkg output.
1979      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1980        common-block variables ; Allows multi-threading with master-thread IO.
1981    o change default MAX_NO_THREADS from 32 to 4 ;
1982      and stop cleanly when MAX_NO_THREADS is too small.
1983    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1984    
1985    checkpoint58m_post (2006/07/17)
1986    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1987       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1988    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1989       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1990       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1991    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1992        add MITgcm_tutorials (= code + all the tutorials)
1993    o ecco, option to compute cost for total ssh (mean+anom)
1994    o consistent with addition of ptracer and ssh in pkg/profiles
1995    o profiles: adding ptracer and ssh
1996    o testreport: change multi-test output-file name
1997      (from output.txt.{name} to output.{name}.txt)
1998    o profiles: now ok for mutli-tiles case
1999    o seaice: add 4 parameters for different advection schemes for area,
2000      (effective) seaice thickness, enthalphy, and snow height. Their default
2001      is the standard parameter SEAICEadvScheme
2002    o calc_gw:
2003     - add cosFacU in zonal viscous flux (harmonic.visc.).
2004     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
2005       of tutorial_plume_on_slope.
2006    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
2007    o calc_gw: true flux-form, account for horizontal grid spacing.
2008      update rotating_tank results, but not plume_on_slope (affected at
2009      truncation level, 11 digits).
2010    
2011    checkpoint58l_post (2006/07/12)
2012    o calc_gw:
2013     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
2014     - remove side-drag for now (need to fix it); update plume_on_slope results.
2015     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
2016    o commit code to make SST/SSS weights spatially variable
2017      (based on either variable in-situ or variable initial T/S weights)
2018    o pkg/ecco:
2019      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
2020        now based on horizontally varying weights wthetaLev, wsaltLev
2021      * cost_averagesflags now returns year indices in addition to day, month
2022      * sflux balance is performed on annual basis
2023        (sflxumm, sfluxmm2, bal_sfluxmm)
2024      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
2025        including separate counting and multipliers
2026    o pkg/rbcs
2027      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
2028    
2029    checkpoint58k_post (2006/07/06)
2030    o testreport:
2031     - always build in dir. "build" (if not there, mkdir build instead of building
2032       & running in input)
2033     - run in dir run (if it exists), in build otherwise.
2034     - call prepare_run (if input/prepare_run exists)
2035     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
2036    o pkg/exf modifications to interpolation and rotation routines for more
2037       reasonable treatment of North Pole singularity: for tracers North Pole
2038       value is set to northernmost zonal-mean value, for zonal velocity it is
2039       set to zero, and for meridional velocity it is set to northernmost value.
2040    o pkg/exf/exf_check_range.F
2041     - add tile index to diagnostics and move stop statement to the very
2042       end of the routine.
2043    o pkg/diagnostics: (diagnostics_main_init.F)
2044      define title of isomorphic variables according to the current config.
2045    o pkg/thsice with pkg/seaice dynamics:
2046    - fix domain of computation (interior only, required for exf) and do exchanges
2047    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
2048    o towards a standard way of dealing with multi-threading in MONITOR
2049      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
2050    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
2051       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
2052    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
2053    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
2054    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
2055       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
2056    o tracer advection:
2057     - clean-up and simplify calc_common_factors.F
2058     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
2059       advection subroutine (but still not used within DST advection S/R)
2060    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
2061    
2062    checkpoint58j_post (2006/06/15)
2063    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
2064      from file (collects calls previously in FORWARD_STEP)
2065    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
2066    o adjoint store dir. adjusted accordingly
2067    o genmake2
2068      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
2069    
2070    checkpoint58i_post (2006/06/14)
2071    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
2072      on wind stress (SEAICEstressFactor defaults to 1.)
2073    o Total number of Timers is finite (<=40): comment out 2 non-essential one
2074      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
2075    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
2076      on CS-grid: no longer loosing mass.
2077    o exf & curvilinear-grid: no longer modify longitude xC & xG.
2078    o pkg/ggl90: fix sloppy output and fix a bug
2079    o pkg/seaice: added SEAICEuseEVPpickup parameter
2080      - Set to false in order to start EVP solver with
2081        non-EVP pickup files when using SEAICEuseEVP
2082      - fix sign error in diffusion in seaice_calc_rhs
2083    
2084    checkpoint58h_post (2006/06/07)
2085    * Modifications for bottom topography control
2086      o replace hFacC by _hFacC at various places
2087      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
2088      o add non-self-adjoint cg2d_nsa
2089      o update autodiff support routines
2090      o re-initialise hfac after ctrl_depth_ini
2091      o works for 5x5 box, doesnt work for global_ocean.90x40x15
2092    * Adding verification for 5x5 box (4-layer) bottom topography control
2093    
2094    checkpoint58g_post (2006/06/07)
2095    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
2096       used for mean seasonal cycle, mean diurnal cycle); add an example
2097       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
2098    o pkg/ggl90:
2099      - add parameter (minimum surface kinetic energy)
2100      - fix bug (avoiding division by zero)
2101    o couple pkg/thsice to pkg/seaice:
2102      - modify advection in seaice to accomodate new scalar fields to be advected
2103      - only muliDimAdection scheme work with seaice/thsice
2104      - mapping of thsice-variables to seaice-variables, back and forth
2105      - does not break the verification experiments, but does not give the
2106        desired results either
2107    o pkg/seaice
2108      - make (default) second order advection a bit less confusing?
2109    
2110    checkpoint58f_post (2006/06/05)
2111    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
2112      to pkg/seaice):
2113      - new routines thsice_map_exf and thsice_get_exf provide the interface
2114      - add an additional formal parameter to thsice_solve4temp
2115    o pkg/exf:
2116      - add new fields wspeed, snowprecip (to be able to couple to thsice)
2117      - correct Stefan-Boltzmann constant
2118      - new parameter for longwave surface emittance
2119      - separate some stuff from exf_bulkformulae into new routines  
2120        exf_radiation, exf_wind
2121      - add new parameters and constants: longwave emissivity for ocean, ice
2122        and snow, evaporation parameters over ice
2123      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
2124        either wind from stress or stress from wind
2125    o pkg/thSIce:
2126    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
2127    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
2128       and THSICE_CALC_THICKN
2129    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
2130    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
2131      to make debugging easier.
2132    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
2133    o pkg/bulk_force:
2134      - clean-up comments and parameters ;
2135      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
2136    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
2137      generate new output for test-experiment: aim.5l_cs.thSI
2138    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
2139      testreport accordingly
2140    
2141    checkpoint58e_post (2006/05/17)
2142    o SEAICE_CGRID adjoint done
2143    o R_STAR adjoint implemented.
2144      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
2145      * need to sort out init. of h0facc, etc.
2146    o Make pkg/profile fully independent of ecco,cost, etc. stuff
2147      to be able to use it in pure forward.
2148    
2149    checkpoint58d_post (2006/04/21)
2150    o upgrade simple test-experiment to tutorial example:
2151     step.1: duplicate the experiment and (step.2) will remove the old copy.
2152      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
2153      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
2154      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
2155      tutorial_global_oce_biogeo    <- copy of dic_example
2156      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
2157      tutorial_plume_on_slope       <- copy of plume_on_slope
2158      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
2159      tutorial_global_oce_optim     <- empty for now (David ?)
2160      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
2161     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
2162    o correct a sign problem in cost_scat.F
2163    o obcs and ptracers: fix boundary conditions for advections schemes
2164      with larger stencil
2165    o thsice adjoint: start
2166    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
2167      completeness
2168    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
2169      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
2170    o ptracers adjoint:
2171      * avoid extensive recomputatations
2172      * fix missing re-init. of gptr (missed by TAF)
2173    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
2174      me to turn off the excessive output to STDOUT that this package produces
2175    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
2176      and add those terms in Vector-Invariant formulation.
2177    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
2178      if the control period (xx_hfluxperiod etc) is 0
2179    o in profiles pkg, clean routines and fix details
2180    o in ecco pkg, reading ssh data:
2181      fix problem in case the model does not start at iter0=0
2182    o fix mnc-pickup/restart for ptracers
2183    o new package prifiles:
2184      code to compute profile-based cost by Gael Forget
2185      (modifs in ecco, ctrl, autodiff)
2186    o Benign bug fix in initialization (spotted by M. Mazloff) of
2187      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
2188    
2189    checkpoint58c_post (2006/03/23)
2190    o adjoint: finish NLFS adjoint and provide reference output in
2191      verification/global_ocean.90x40x15/results_ad_nlfs
2192    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
2193      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
2194      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
2195      with SEAICE_CGRID defined.
2196    o move calendarDumps from "data" to "data.cal" and clean-up the code
2197      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
2198    o add useEXF & useCAL flags (for now, set in hard-coded way)
2199    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
2200      (were missing in NH mode, and wrong in quasihydrostatic mode).
2201      waiting for Chris updated version of calc_gw to add those CALLs.
2202    o fix bug in quasihydrostatic S/R ;
2203      add a test for this option: global_ocean.90x40x15.qshyd
2204    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
2205      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
2206    o add on/off flag useOffLine for package OFFLINE
2207    o seaice:
2208      - modify advection so that it works also on the C-grid
2209      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
2210        problem in multi-tile runs with C-grid
2211      - add flags for clipping ice velocities and/or masking solver forcing
2212      - fix drag (ocean on ice) formulation and a bug that caused noise in the
2213        C-grid solver
2214      - added a few comments to seaice_diffusion.F
2215      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
2216        are now exclusive)
2217      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
2218        required re-ordering the code a little:
2219       + make DAIRN global variable (defined in SEAICE)
2220       + move computation of the viscosities eta and zeta into a new separate
2221         routine (because I need to recompute them in seaice_ocean_stress.F)
2222    
2223    checkpoint58b_post (2006/03/13)
2224    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
2225      update output.txt of exp. aim.5l_cs.thSI
2226    o various mnc cleanups and improvements:
2227      + shrink lookup tables by factor of ~4
2228      + better error reporting when running out of lookup space
2229      + able to handle longer path/file names (up to 500 chars)
2230    o adjoint:
2231      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
2232      - TBD: "hidden" mom_vecinv recomp. in dynamics
2233    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
2234     (allow to differentiate between forcing components using new integer flags:
2235      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
2236     and add new flag to put Dissipation tendency out of Adams-Bashforth.
2237    o ecco
2238      - enable trend removal from SSH anomaly obs.
2239    o adjoint
2240      - a fix for PmEpR when #undef EXACT_CONSERV
2241      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
2242      - try to fix "hidden" recomp. in forward_step for NLFS
2243        (NLFS seems broken sometimes after I checked it in)
2244    o seaice:
2245     - add c-grid version of the dynamic solver:
2246       + three new routines that are the c-grid substitute lsr, dynsolver
2247         and ostres
2248       + put a few fields that were local to dynsolver into global common
2249         blocks, so that I can move the computation of stresses etc into
2250         seaice_lsr (saves coding but may break the adjoint).
2251     - replace more hardwired parameters by runtime parameters
2252     - add ice masks that mask the rhs of the implicit solvers where there
2253       is no ice (commented out in seaice_dynsolver, because i am not sure
2254       if this works properly), eventually this should replace the clipping
2255       of ice velocities in seaice_dynsolver to +/-40cm/s.
2256    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
2257      include it only where its needed
2258    o move balancing of fluxes before the call of external_forcing_surf
2259    o seaice:
2260      - correct units of turning angles (now they are really in degrees)
2261      - move computation of GWATX/Y out of main routine into dynsolver
2262      - initialize GWATX/Y in seaice_init
2263    o Apply mask on Fresh-Water flux (needed for SSH forcing).
2264      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
2265    o seaice: add runtime flags for turning angles (default to zero)
2266    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
2267      and trend from exf forcing and ctrl control adjustments
2268    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
2269      (since checkpoint57x_post)
2270    o change the default rotation period to 86164.s = the Earth rotation
2271    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
2272      and based on a reference stratification. Tested within hs94.cs-32x32x5.
2273    o seaice advection: add code for choosing between the default (2nd order
2274      central differences) and multiDim advection schemes provided by
2275      pkg/generic_advdiff
2276    o seaice:
2277      - removed all references to SEAICE_GRID.h fields from
2278        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
2279        (cubed-sphere configuration will change a little)
2280      - grid computations in seaice_init are obsolete now.
2281      - cleaned up code a little so that is easier to read (hopefully).
2282      - added new (better?) discretizations of default advection and diffusion
2283        (turn on with SEAICEuseFluxForm)
2284      - replace 1 in 3d global fields by kSurface in growth.F
2285      
2286    checkpoint58a_post (2006/02/13)
2287    o seaice:
2288      - bug fix in advect.F
2289    o shelfice:
2290      - separate shelfice load anomaly from pload (breaks with time
2291        dependent forcing), => introduce constant field shelficeLoadAnomaly.
2292        Its default is 0., but it may be computed more cleverly from (unknown)
2293        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
2294        done offline. A good approximation of the pressure load anomaly is
2295        necessary to avoid large initial adjustment processes underneath
2296        deep-reaching shelfice.
2297      - small fix in ISOMIP shelfice_thermodynamics
2298      - add more sophisticated thermodynamics of Hellmer (1989), this is
2299        now the default
2300      - give a few constants more intuitive names
2301    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
2302      if bulk formulae are used in long integration (especially EmPmR). Turn
2303      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
2304      if balancePrintMean, the imbalance that is substracted is printed to
2305      STDOUT.
2306    o fix bug (typo) in obcs_apply_eta.F
2307    o add a new package shelfice which enables us to model the circulation
2308      underneath shelf-ice with draughts of hundreds of meters.
2309     - works
2310     - to do: + include improved thermodynamics
2311              + check whether kSurfC (from model/inc/SURFACE.h) can be used
2312                instead of new field kTopC
2313              + can we use topoFile, Ro_surf and existing code in ini_depth.F
2314                instead of new field R_shelfIce and new code in ini_depth.F
2315                and ini_mask_etc.F?
2316              + adjust vertical mixing schemes?
2317    o seaice pkg:
2318     - add a cpp-flag to include a simple formula for a salinity dependent
2319       freezing point of sea water at the surface
2320     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
2321       meridional stresses are now different (and hopefully correct)
2322    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
2323       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
2324       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
2325    o pkg/diagnostics: add options and parameters for regional-statistics
2326       diagnostics ; define regions by reading a region-mask from a file
2327       (might add other options later)
2328    o pkg/bulk_force:
2329     - add option and parameters to use AIM surface-flux formulae.
2330     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
2331       others forcing fields (defined in PARM05, parameter file "data") are loaded
2332       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
2333     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
2334     - use the right EXCH call for uwind,vwind (to work on CS-grid).
2335     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
2336       and parameters (note: calcWindStress replaces .NOT.readwindstress).
2337     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
2338    
2339    checkpoint58 (2006/01/12)
2340    o add "--embed-source" option to genmake2 which, when the supporting
2341      tools can be compiled (as determined by genmake2) will turn on the
2342      embed_files package which then embeds the entire MITgcm source code
2343      (*.[fFhc] + Makefile) used for the build within the executable
2344      - requested by CNH but off by default
2345      - adds a paltry <9MB to the mitgcmuv executable in most cases
2346      - only writes the output when useEMBEDSRC in eedata is true
2347    o clean up 3-dim. relaxation codes:
2348      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
2349      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
2350      * Thanks to Tom Haine for testing!
2351    
2352    checkpoint57z_post (2005/12/31)
2353    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
2354      affects output (@ truncation level) of exp. plume_on_slope ; updated.
2355    o fix the pickup behavior for obcs in combination with ptracers
2356    o fix a bug in ptracers_external_fields_load
2357    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
2358      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
2359    o transfered surface NH pressure to eta field (if exactConserv).
2360    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
2361         and update lab_sea output.txt file.
2362    o completing 3-dim. relaxation code: additional term
2363         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
2364      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
2365      * At compile time, in "EXF_OPTIONS.h" set
2366          #define  ALLOW_CLIMTEMP_RELAXATION
2367          #define  ALLOW_CLIMSALT_RELAXATION
2368      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
2369          tauThetaClimRelax3Dim = 15552000.0,
2370          tauSaltClimRelax3Dim  = 15552000.0,
2371      * 3 cases:
2372          1) Use a constant-in-time 3-dim. field
2373          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
2374          3) Real-time relax. to time-evolving prescribed field
2375    o Adding Laplacian-type smoothness constraint on
2376      initial and boundary (forcing) controls (ic, bc)
2377      * enable at compile-time via
2378        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
2379      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
2380      * Absolute scale somewhat unclear so far
2381      * no area weighting was included since no other cost term does so far
2382    
2383    checkpoint57y_post (2005/12/08)
2384    First step for a NLFS adjoint
2385    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
2386    o new init. routines for calc_r_star, calc_surf_dr
2387    o still need to deal with ini_masks_etc
2388    o testreport seemed happy
2389    checkpoint57y_pre (2005/12/08)
2390    
2391    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
2392    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
2393    o add new offset feature to offline pkg (plus minor cleanup)
2394    o cfc fixes for final year of integration
2395    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
2396      be in GCHEM_OPTIONS).
2397    
2398    checkpoint57x_post (2005/12/04)
2399    o fix testreport Pb in multiple test experiment.
2400    o cleanup our namelist syntax in verification:
2401      - make it more F95 standards compliant (some work still needed)
2402      - allows the vast majority of our tests to work with gfortran
2403    o Non-Hydrostatic:
2404     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
2405     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
2406    o Allow to apply AB on T,S rather than on AB(gT,gS):
2407     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
2408     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
2409       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
2410     - need a "clever" read_pickup to restart from the other AB formulation
2411    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
2412    o remove some unused variables (reduces number of compiler warnings)
2413    o adjoint
2414      * Disable useVariableViscosity for adjoint for time being
2415        (there are a number of extensive recomputations)
2416      * Initialize certain variables needed for adjoint
2417    
2418    checkpoint57w_post (2005/11/03)
2419    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
2420                 fix the singleCpuIO RS version of MDSWRITEFIELD
2421       and add a WARNING if using globalFiles=T with multi-processors.
2422    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
2423      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
2424    o tracer advection scheme:
2425      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
2426       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
2427       was not very convenient).
2428      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
2429       (further tests needed for the implicit DST & Flux-Limiter schemes).
2430    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
2431      and sRef for convenience, handy, when you want to initialize
2432      ptracers in a large domain with a constant non-zero value. Also,
2433      untangle ptracers_init.F a little.
2434    
2435    checkpoint57v_post (2005/10/13)
2436    o change dome exp. to use variable viscosity in side-drag terms.
2437    o remove all the files from the cfc_offline test since they are now
2438      incorporated into tutorial_cfc_offline which has been producing
2439      identical results for a few days of testing
2440    o add new parameter: sideDragFactor to enable half-slip-side BC
2441      and change side-drag S/R to use viscosity from mom_calc_visc
2442      (can switch back by setting sideDragFactor=0.); affects results at
2443      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
2444       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
2445    o vorticity & strain are now computed without masking, to account for
2446      no-slip-side BC in variable viscosity calculation ; mask is applied
2447      anyway later on, before computing advection/coriolis terms.
2448    o modify exp4 to test new obcs support for reading from external files
2449      and for passive tracers
2450    o fix behavior of ptracers_monitor when monitor output is written to a
2451      netcdf-file; still not independent of monitor.F (writes in the same
2452      file).
2453    o change default value of tRef (put a uniform, meaningful value for ocean
2454      & atmos) and initialize sRef (was missing, as Martin mentioned).
2455    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
2456      to be proportional to enstrophy dissipation length.  Thus,
2457       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
2458      This is now consistent with Smagorinsky and with the manual.
2459    
2460    checkpoint57u_post
2461    o OBCS and PTRACERS: add open boundary support for passive tracers
2462      - either use homogenous (pseudo) v.Neumann conditions or prescribe
2463        OB-values from file; this is not different from the way theta and salinity
2464        are treated
2465      - however, Orlanski-radiation conditions are not supported, and the model
2466        will stop if you use pTracers and Orlanski at the same time.
2467      - beefed up the rountine obcs_external_fields_load: now only those open
2468        boundary values are overwritten with values from files for which there
2469        are really files, otherwise the OB-fields remain untouched. This makes
2470        it possible to use different OBs at different ends of the domain (as
2471        with EXF)
2472    o reduce number of exch calls in shap_filt (s2).
2473    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
2474      truncation level) 4/5 MLAdjust test results (11&12 digits match).
2475    
2476    checkpoint57t_post (2005/10/03)
2477    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
2478    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
2479      same truncation, independent of the face number: affects affects several
2480      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
2481    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
2482      note that biharmonic viscosity + no-slip was not tested in any experiment.
2483    o fix bug in non-linear free-surf side-drag ; generate new output for
2484      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
2485    o make mnc honor the writeBinaryPrec flag for most kinds of output
2486    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
2487    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
2488      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
2489    o add brackets in multi-terms sum to get same truncation, independent of
2490      the face number (manage to get exactly same value of gU,gV at the cs-edge)
2491      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
2492    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
2493      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
2494      a maximum grid-scale Reynolds number.  Also, changes all length calculations
2495      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
2496      Suggested values of viscosity parameters found in mom_calc_visc.
2497      Many new viscosity diagnostics available.
2498    
2499    checkpoint57s_post (2005/09/20)
2500    o Add clearing-house for viscosity calculations, mom_calc_visc and
2501      correct numerous bugs in LeithD and Smagorinsky discretizations.  
2502      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
2503      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
2504      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
2505      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
2506      The Strain-Tension form is now called with useStrainTensonVisc=.true.
2507      ViscAhStrain and viscAhTension are now retired.
2508    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
2509    o In response to JMC's bug report, genmake2 now ignores any soft-links
2510      that it finds in the *current* directory when searching for files.
2511      Soft-links found in any other source directories will still work as
2512      they did before.
2513    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
2514      a C routine to unlimit the stack size
2515    o mnc-ify pkg/aim snapshot vars
2516    o mnc-ify pkg/land as requested by Daniel
2517    o various changes to mnc including:
2518      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
2519      - output can now be grouped so that all files within a group
2520          change the ITER portion of their names in lock-step together
2521      - can now read ("global") PER-FACE (in addition to PER-TILE) files
2522          and works with both EXCH1 and EXCH2 (but needs more testing)
2523      - writing works for all verification test cases w/ g77 on Linux
2524    
2525    checkpoint57r_post (2005/09/07)
2526    o make MNC variable initialization happen earlier
2527    o add diagnostics for (almost) each term of the momentum Eq.
2528    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2529    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
2530    o remove MINIMAL_TAVE_OUTPUT option ;
2531      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
2532    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
2533      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
2534    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
2535    o add time-dependent SST, SSS control
2536    o cost terms in ecco/ modularized (new cost_generic.F)
2537    o cost_averages routines are modularized (new cost_averagesgeneric.F)
2538    o new infrastructure for seaice model vs. obs misfits in seaice/
2539      * driver from the_main_loop.F is seaice_cost_driver.F
2540      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
2541      * gradient check in Exp. 6a of natl_box_adjoint/
2542    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2543      (see README file)
2544    
2545    checkpoint57q_post (2005/08/19)
2546    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2547    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2548      - bug was reported by Jean-Michel and Ian Fenty
2549    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
2550      update exp. cpl_aim+ocn output.
2551    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
2552      Needed for high-res. runs with large global files
2553      to be able to limit tapelev size
2554    o Changed some tests for adjoint:
2555      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
2556      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
2557      * global_ocean.90x40x15/ back to default 3-level checkpointing
2558    o Modifications to enable scripted COMMON to MODULE conversion
2559      * verification/OpenAD/code/ has necessary scripts and description;
2560      * converts, compiles and runs successfully;
2561    
2562    checkpoint57p_post (2005/08/01)
2563    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2564    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2565      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
2566    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
2567    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
2568      (was already the case for dissipation with mom_vecinv,
2569       and also the case for grad.PhiHyd when staggered-timeStep)
2570      This will allow to put dissipation out-off the AB time-stepping.
2571     Unfortunately, affects truncation error. Update output of exp. that "fails"
2572      (cg2d matching number) and leave the others for later: front_relax(10),
2573      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2574      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2575    
2576    checkpoint57o_post (2005/07/30)
2577    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
2578      (2) its ready to be documented during the 20050801 DocFest
2579    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
2580      for ideal_2D_oce and lab_sea on linux_ia32_g77
2581    o set to #undef CTRL_SET_OLD_MAXCVARS_30
2582      in global1x1_tot/code_seaice_adj to access indices 32, 33
2583      (worth another tag)
2584    
2585    checkpoint57n_post (2005/07/29)
2586    o adding precip control xx_precip 32
2587    o adding swflux control xx_swflux 33
2588    o Replacing 10 forcing penalty cost routines by 1 generic.
2589    o Implementing partitioning in time-mean and variable adjustment
2590      for atmos. state.
2591    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
2592    o in natl_box_adjoint:
2593      * updated exp 1 to 10
2594        (but does not have time-mean vs. variable split results yet)
2595    o updated global1x1/*_seaice_adj/
2596      to incorporate latest changes
2597    o enable useSingleCpuIO for mdsio vector routines
2598      (applies in particular to tapelev I/O)
2599    o removed inefficient K-loop in all active_file*control*.F
2600    
2601    checkpoint57m_post (2005/07/28)
2602    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
2603      and advect_cs (use EXCH-2 and standard cs-32 grid files).
2604    o pkg/exch2: filling of face-corner halo regions is optional
2605      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
2606    
2607    checkpoint57l_post (2005/07/14)
2608     tag before updating tutorials (pre-release-2)
2609    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
2610       for output and interpolation of input fields onto model grid)
2611    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
2612       Affects results of exp. rotating_tank ; update output.txt.
2613    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
2614          and taking the square quantity and/or using a fraction-weight field.
2615    o fix aim_diagnostics_init.F mate numbers.
2616    o add mnc output capability to diagnostics/diagstat and update
2617      our cvsignore files for the ACSII output generated
2618    
2619    checkpoint57k_post (2005/07/02)
2620    o lab_sea now uses diagnostics package and provides a suite of
2621      new EXF diagnostics output.
2622    
2623    checkpoint57j_post (2005/06/30)
2624    o exf
2625      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
2626        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
2627        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
2628      * extended diagnostics output
2629        - now includes all EXF variables
2630        - hs, hl moved to common block
2631        - separate S/R for diagnostics, called after ctrl vector is added
2632        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
2633        - EXFqnet contains true Qnet (i.e. includes qsw)
2634      * updated verif. lab_sea, global_with_exf
2635      * Rearranging hflux (exf_mapfields -> exf_getforcing)
2636        to ensure that diagnostics sees a true EXFqnet
2637    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
2638    o diagnostics pkg: change pointers so that 1 diagnostic can be used
2639      several times with different frequencies.
2640    o mnc-ify the thsice package as requested by Daniel Enderton
2641      - the monitor--MNC output needs work
2642      - many attributes need to be added (most are currently blank)
2643    o mnc-ify theaim_v23 package as requested by Daniel Enderton
2644      - many attributes need to be added (most are currently blank)
2645    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
2646    o add Sadourny like discretization to the 4th.O vorticity advection scheme
2647    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
2648      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
2649         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
2650    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
2651     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
2652    
2653    checkpoint57i_post (2005/06/19)
2654    o Diagnostics package was changed: diagnostic allocation is now deactivated
2655      by setting an empty file name in the namelist (used to be by setting 0 frequency)
2656    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
2657      add 1rst Order upwind vertical Shear.
2658    o add a quick fix for A/B checkpointing in OFFLINE mode
2659    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
2660      end-run around the C/Fortran linking horror in eesup/src/timers.F
2661    o added pkg/runclock: allows user to terminate run based on wall clock
2662    o added non-hydrostatic scaling parameter: nh_am2
2663    o pkg/my82: futile attempt to make results compiler-independent by adding
2664      some "_d 0", etc. no effect.
2665    o for mnc output, fill the 'T' coordinate var with myTime and create a
2666      separate 'iter' variable for iteration count
2667    o pkg/diagnostics:
2668      add new capability: output of Global/Regional & per-level statistics ;
2669      tested against monitor output (including land & thSIce) on various exp.
2670    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
2671    
2672    checkpoint57h_done (2005/05/19)
2673      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
2674      data.diagnostics, data.gchem, data.ptracers) is done.
2675    
2676    o pkg/diagnostics: prepare for Global/Regional statistics.
2677      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
2678    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
2679      and rename it: DIFFERENT_MULTIPLE
2680    
2681    checkpoint57h_post (2005/05/14)
2682    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
2683    o pkg/diagnostics: change output frequency, now in seconds (instead
2684      of Nb of iterations). This requires to change data.diagnostics.
2685    checkpoint57h_pre (2005/05/12)
2686    
2687    o in mnc, let the user create the output dir if both mnc_outdir_date
2688      and mnc_outdir_num are false
2689    o add fflags() to pkg/diagnostics which allows one to specify, on a
2690      per-file basis, the file precision [default behavior is unchanged]
2691    o added diagnostics to pkg/kpp, including computation of mixed layer
2692      depth based on a temperature/density criterion
2693    o updated verification/natl_box to test the new pkg/kpp diagnostics
2694    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
2695    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
2696    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
2697      not mnc -- this mistake was found by JMC and is now corrected
2698    
2699    checkpoint57g_post (2005/04/15)
2700    o add Adams-Bashforth 3rd Order time stepping:
2701      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
2702      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
2703    checkpoint57g_pre (2005/04/15)
2704    
2705    o make lambda[Theta,Salt]ClimRelax spatially varying
2706      (default remains spatially uniform constant based on tau)
2707    o added new control variables
2708      * init. uVel, vVel, etanN
2709      * lambda[Theta,Salt]ClimRelax
2710    o separate masks used for ctrl_pack/unpack 'from write_grid' output
2711      (suggested by G. Forget)
2712    
2713    checkpoint57f_post (2005/04/06)
2714    o add parameter "baseTime" = model base time = time at iteration zero
2715      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
2716      account for baseTime shift
2717    o move Coriolis arrays from PARAMS.h to GRID.h
2718    checkpoint57f_pre (2005/04/06)
2719    
2720    o mnc-ifying the seaice package
2721    o introduced an alternative length scale calculation for use in the limiting
2722      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2723    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
2724    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
2725      as well as grad(vort3).  Made it compatible with both approximate form
2726      for the cubed sphere and full form of these gradients.  Added flag
2727      useFullLeith to select between approximate and full form.  
2728    o add "d0" in getcon.F to reduce differences between compilers/platforms
2729      update output.txt of exp. fizhi-gridalt-hs
2730    o change port_rand funtion to allow to set the seed.
2731    o fix obscure MNC bug involving conversion between reals and integers
2732      - it caused no problems with certain (eg. gcc, ifc) compilers but the
2733        new version is now more standards-compliant
2734    o adjoint-related modifications
2735      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
2736      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
2737      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
2738    
2739    checkpoint57e_post (2005/02/28)
2740    o Adding eddy stress controls a la Ferreira et al.
2741    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
2742    
2743    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
2744      update output.txt of exp. fizhi-gridalt-hs
2745    o add more "Z" dimensions and associated coordinate vars to MNC
2746    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
2747    o parameter calendarDumps: when set, approximate months (30-31 days) and years
2748      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
2749      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
2750      months and years.  Requires pkg/cal.
2751    o diagnostics: add pickup functionality
2752      - off by default for backwards compatibility
2753      - current version only uses MDSIO -- MNC will be added
2754    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
2755    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
2756    
2757    checkpoint57d_post (2005/02/11)
2758    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
2759    o modify verification/ideal_2D_oce so that it tests the creation of mnc
2760      output from the diagnostics package
2761    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
2762    o make genmake2 more portable by using ".$FS" instead of ".f" for more
2763      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
2764    o add coordinate variables to the MNC output from the diagnostics package
2765    o change MNC-flags default value: true when useMNC=TRUE
2766    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
2767      the ability (off by default) to read the grid information using MNC
2768    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
2769    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
2770    o do snap-shot diagnostics at the middle of the time-interval (instead of
2771      at the end).
2772    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
2773      new test for AIM with thSIce + slab-ocean
2774    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
2775    o move state variable diagnostics to the beginning of the time step ;
2776      (note: still needs some work specially for snap-shot diagnostics)
2777      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
2778    
2779    checkpoint57c_post (2005/01/27)
2780    o Change testing option (-ieee) to get closer agreement between g77 & ifort
2781    o generate new output.txt files on faulks with g77 & the new -ieee option
2782    checkpoint57c_pre (2005/01/27)
2783    
2784    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
2785      update output.txt of exp. global_ocean.90x40x15
2786    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
2787      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
2788    o add saltFlux(+File) forcing capability with periodicExternalForcing
2789    o allow to use pkg diagnostics for GM-Redi & ThSIce output
2790    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
2791    o improvements for the MNC output from DIAGNOSTICS:
2792      - correct handling of the unlimitied dimension
2793      - all dims now have associated coordinate variables
2794      - variables located at U, V, and Corner ("Z") points are now written
2795        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
2796        *all* data points are output
2797    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
2798    o added pkg/seaice/seaice_monitor.F
2799    o mdsio_readfield.F can now read files visible only to master MPI process.
2800    o pkg/seaice: some test code for ice-modified ocean stress
2801    o exf_getffields interpolation defaults to bilinear for all scalar forcing
2802      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
2803      spurious negative numbers for precipitation and humidity.  Will cause
2804      some small numerical differences for integrations using pkg/exf/exf_interp.F.
2805    o pkg/ctrl/
2806      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
2807        May be enabled via doPackDiag
2808      *  introduce z-scaling of
2809         + gradient (doZscalePack) and
2810         + control (doZscaleUnpack)
2811    o pkg/mdsio/
2812      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
2813      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
2814    
2815    checkpoint57b_post (2004/12/20)
2816    o simplify options in diagnostics_fill arguments (remove weird combinations)
2817    o fix MNC coordinate variables so that they now contain per-face index
2818      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
2819      general, EXCH2 grids are only aligned to a "local" coordinate system
2820    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
2821    o Implement instantaneous output within pkg diagnostics:
2822      setting a negative frequency in data.diagnostics produces
2823     "snap-shot" output (as opposed to time-average if freq > 0)
2824    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
2825      NOTE: change ptracer diagnostics name: use 2 characters to work with
2826            more than 9 tracers. Add also diagnostics of advect & diffus flux.
2827    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
2828      becomes the coordinate variable for the 'T' dimension
2829    o add CF-style coordinate variables to MNC
2830      - just a first cut:  numbers are meaningless on the cubesphere and
2831        missing along the T axis but otherwise it works!
2832    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
2833    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
2834    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
2835      this is based directly on what the model compute, so that the content of
2836      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
2837    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
2838    o clean up build options files for SunOS, in particular
2839      - remove -traditional from xmakedepend
2840      - change -xarch=v9 to -xarch=native for f77
2841      - restore use of make (not gmake)
2842      - add CC=gcc if using g77
2843    o changes per discussion of AM, JMC, & EH3 today:
2844      - move redundant "grid" variables out of "state" -- in preparation of
2845        creating proper CF-style coordinate variables and in recognition
2846        that any/all grid variables can be easily copied (eg. w/NCO) from
2847        the grid files into any of the other NetCDF files
2848      - *always* output grid variables with MDSIO (this will eventually be
2849        changed)
2850      - output MNC grid file if useMNC is true
2851    o every instance of _END_MASTER() has been found and replaced with
2852      _END_MASTER( myThid ) in order to satisfy certain picky Sun
2853      preprocessors
2854    o re-arrange diagnostics pkg initialisation:
2855     - allow each package to extend the available diagnostics list
2856     - add some checking and fix small problems (multi-threaded, ...)
2857     - new S/R diagnostics_fill (replace fill_diagnostics):
2858       look through the short list of active diag. (instead of the long list)
2859       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
2860    
2861    checkpoint57a_post (2004/12/10)
2862    o this set of changes restores TAMC compatibility
2863      tested for global_ocean.90x40x15 adjoint on trough
2864      (what a pain)
2865    
2866    checkpoint57a_pre (2004/12/10)
2867    o some modifs in tools/build_options for sunos
2868    o call ctrl_pack for ctrl at end for optimcycle=0
2869    
2870    checkpoint57 (2004/12/09)
2871    o add horizontal bi-harmonic viscosity for vertical velocity
2872      - new parameter viscA4W (defaults to viscA4)
2873      - affects only non-hydrostatic code
2874      - to be done: no-slip lateral boundary conditions
2875    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
2876    o implement Implicit Vertical advection for pTracers
2877    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
2878      (implemented also for implicit vertical diffusion & advection)
2879    o OBCS: extend application of tracer open boundary conditions
2880      to a strip beyond the boundary of width Olx/Oly
2881    o add call monitor to TAF set of required calls (flow directives)
2882      and include in natl_box_adjoint
2883    o untangle a few ifdefs related to cost, ctrl, autodiff
2884      untangel a few ALLOW_ECCO_OPTIMIZATION
2885    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
2886      (theta2, salt2 in ecco_cost_weights)
2887    
2888    checkpoint56c_post (2004/12/03)
2889    o OBCS as control variables
2890      - update ctrl_ad_diff.list, obcs_ad_diff.list
2891      - remove balance of obcs controls from default
2892      - fix index bug nobcs in ctrl_init
2893      - fix dummy fields filen in ctrl_pack
2894      - add dummy weights for obcs
2895    o lsopt: comment out fort.94 output
2896    o optim:
2897      - remove unnecessary header files
2898      - adjusted namelists
2899      - add xerbla.F to Makefile
2900    o exf:
2901      - multiple modifications of exf_check_range
2902      - unit change in exf_init_runoff from [m/year] to [m/s]
2903    o mdsio:
2904      - i/o-vector change debugLevel from debLevA to debLevB
2905    
2906    checkpoint56b_post (2004/12/01)
2907    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
2908      is called from DO_THE_MODEL_IO
2909      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
2910      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
2911      - clean up PTRACERS_WRITE_TIMEAVE a little
2912    o add another verification experiment that tests both the cfc-pkg and
2913      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
2914      reactive tendencies treated inline with regular timestepping
2915    o testreport previously did a lousy job of comparing small numbers, so
2916      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
2917      implemented in the little c-progam tmp_cmpnum.c which is embedded in
2918      testreport.
2919    o ptracers_monitor: bug fix for MPI
2920    
2921    checkpoint56a_post (2004/11/28)
2922    o GCHEM: finish reorganizating the package
2923      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
2924        (introduces another 3D-array for each passive tracer, but only if
2925        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
2926        gchemTendency is not needed because the timestep is done separately)
2927      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
2928      - GCHEM is now---more or less cleanly---separate from PTRACERS
2929      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
2930        so clear to me how that should be done in a general way.
2931    o CFC: improve formatting of output in CFC_ATMOS
2932    o PTRACERS:
2933      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
2934        that ALL experiments with ptracers enable can be checked. This makes
2935        GCHEM_MONITOR obsolete.
2936      - include a runtime parameter PTRACERS_monitorFreq that defaults to
2937        monitorFreq
2938      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
2939    o add PTRACERS (PTR0[1-5]) to testreport output
2940    o exf_check_range:
2941      * default changed to .TRUE.
2942      * will check values for niter0 if debLevA, every timestep if debLevB
2943      * STOP in exf_check_range if 'out of range'
2944      * range chosen generous to allow for potential extema
2945      TBD: a version with stricter range
2946           permitted range would be runtime parameters
2947    o GMredi:
2948      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
2949      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
2950      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
2951    o GCHEM:
2952      - move call to GCHEM_FORCING_SEP, so that it is now called before
2953        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
2954      - introduced a useGCHEM runtime flag and applied it everywhere.
2955      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
2956        this flag is now only visible within GCHEM-pkg routines.
2957      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
2958        be replaced by a 3D array that is computed before thermodynamics; for
2959        this, the tracer ID iTracer had to be included into the parameter list
2960        of ptracers_forcing
2961      - set up forward_step to call gchem_forcing, that will replace
2962        gchem_forcing_int in ptracers_forcing
2963      - cleaning up
2964    o small cleaning of exch2: remove files that are also in eesupp/src
2965    
2966    checkpoint56 (2004/11/17)
2967    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
2968    o mnc: cleanup "full" files--fixes out-of-memory problem
2969    o ECCO-GODAE
2970      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
2971      * fully merged and updated from SIO code
2972        windstress sign change affects
2973        - exf_inscal_[u/v]stress
2974        - sign of xx_tau[u/v] adjustments
2975        - signs in cost_scat
2976      * ctrl_get_gen: avoid update of tau[u/v] for first few days
2977      * natl_box_adjoint updated and compressed
2978      * 2-level checkpoint switch added
2979        (tested in EXP. 1 of natl_box_adjoint)
2980      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
2981    o SVD
2982      * first complete, non-hacked version for SVD calculations
2983      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
2984        performed via direct access files admtlm_vector.it????
2985        (via ctrl_[un]pack)
2986      * optimcycle is used for ARPACK iteration counter
2987        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
2988      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
2989        and add linear transforms where necessary
2990      * controls are initial/final SST, SSS (can be extended; need to check
2991        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
2992    o mdsio: filename info to both stderr, stdout
2993    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
2994      from sign change
2995    
2996    checkpoint55j_post (2004/11/10)
2997    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
2998      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2999    o add consistent build directories and .cvsignore files to verification
3000    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
3001    o make all subroutines 30 or less characters in length for certain older
3002      compilers to work (a thorough search only turns up two routines in
3003      pkg/ptracers)
3004    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
3005      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3006    
3007    checkpoint55i_post (2004/10/28)
3008    o change arrays for total vertical diffusivity (2.D if explicit,
3009      3.D if implicit) ; each ptracer uses its own background value.
3010    o added mnc/NetCDF output capability to ocn_compon_interf
3011      - added bits to verification/cpl_aim+ocn so that it can run on
3012        ITRDA and other clusters without the mpirun "-wd" option
3013    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
3014      configuration
3015    o give MNC the ability to create additional files rather than
3016      exceeding a specified file size limit "MNC_MAX_FILESIZE"
3017      - the default is just less than 2GB which is a practical limit
3018        on many systems
3019    o Compute the non-local term using either KPP vertical diffusivity (=default)
3020       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
3021    
3022    checkpoint55h_post (2004/10/20)
3023    o add verification test "vermix"
3024    o remove all the *_ioinc flags and replace with the single global
3025      outputTypesInclusive flag
3026    o allow to set a vertical profile of vertical diffusivity for T & S
3027    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
3028    o useMNC moved from data.mnc to data.pkg
3029    
3030    checkpoint55g_post (2004/10/14)
3031    o Renaming carbon AD experiments to comply with testreport conventions
3032    o Updating adjoint of Held-Suarez hs94.1x64x5
3033    o Fixing directives for non-ECCO forward_step, after ECCO directives
3034      have been fixed to avoid recomp. of do_oceanic_phys
3035      Works well for global_ocean.90x40x15,
3036      but recomp. issue remains for carbon
3037    o Updating adjoint output for natl_box_adjoint after
3038      pkg/ecco has been modified (see taga c55d_post)
3039    
3040    checkpoint55f_post (2004/10/13)
3041    o rename to timeave_init_fixed
3042    
3043    checkpoint55e_post (2004/10/13)
3044    o some delicate re-shuffle of store directives to avoid one
3045      extra call of do_oceanic_physics
3046      affects ecco_the_main_loop.F, do_oceanic_physics.F
3047      checkpoint_lev1_directives.h
3048    o NB: this may break global_ocean adjoint temporarily,
3049      but it is clear how to fix it. Will do later, need this now.
3050    
3051    checkpoint55d_post (2004/10/11)
3052    o ECCO specific cost function terms (up-to-date with 1x1 runs)
3053    o ecco_cost_weights is modified to 1x1 runs
3054    o modifs to allow observations to be read in as
3055      single file or yearly files
3056    o enable to read exf forcing fields as either
3057      single file or yearly files (flag useExfYearlyFields)
3058    checkpoint55d_pre (2004/10/08)
3059    
3060    o switch between 2-level and 3-level checkpointing
3061    o add ability of MNC to write local and "partial" (eg. 2D slices where
3062      the full 3D field is never actually stored) arrays to NetCDF files
3063      with the correct (that is, the complete multi-dimensional) set of
3064      array indicies
3065      - used in mom_vecinv() to write the diagFreq output
3066      - tested (demonstrated) in verification/aim.5l_cs
3067    o further mnc-ification
3068      - add verification/lab_sea to the list with mnc setups
3069      - fix undefined mnc v-names in cd_code
3070      - add kpp to mnc output (both snapshot and timeave)
3071    o non-hydrostatic code
3072      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
3073        in calc_gw.F
3074      - defaults to viscAh
3075      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
3076        friction or Leith) in non-hydrostatic mode, as long as there is
3077        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
3078    o pkg/cost
3079      extend simple cost functions to treat time mean quantities
3080      (T,U,V) via cost_accumulate_state from cost_tile
3081    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
3082        be 2 times larger than the minimum size the advection scheme requires.
3083        now get a perfect conservation of salt in advect_cs test-exp (updated)
3084    o GGL90 (Gaspar's TKE mixed layer)
3085      - add horizontal diffusion of TKE, requires exchanges in
3086        do_fields_blocking_exchanges, horizontal diffusivity is zero by
3087        default. In OPA there is no horizontal diffusion of TKE but the
3088        mixing coefficients are computed from a horizontal average of TKE of
3089        6 points or so. I think that diffusion has a little more physical
3090        justification.
3091      - clean up ggl90_calc in the hope of reducing memory usage (this hope
3092        was in vain)
3093      - mask tke-variable in ggl90_init
3094    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
3095    o fix biharmonic diffusion on CS-grid.
3096    o more obcs stuff
3097      - added obcs_external_fields_load as an alternative to the EXF-pkg option
3098        for reading boundary values. This routine is called from
3099        obcs_prescribe_read
3100      - updated obcs_check
3101      - changed sponge layer relaxation parameter units for days to seconds
3102      - turned off sponge layer by default
3103      - changed argument list of OBCS_CALC to myTime+deltaTclock
3104      - fixed about 35 bugs in obcs_external_fields_load
3105    
3106    checkpoint55c_post (2004/09/23)
3107    o obcs stuff
3108      - new runtime flags useOBCSprescribe, useOBCSbalance
3109      - re-arranged obcs_calc
3110      - moved exf_getobcs to obcs_prescibe_read
3111        obcs_prescibe_read is called after ORLANSKI stuff
3112        and independent of it (executable can contain all).
3113      - updated obcs_check
3114      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
3115        These may be necessary only if tangential velocities are
3116        prescribed at OB, not sure, needs testing.
3117    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
3118      which simplifies the calls and passes the ifc check-bounds test
3119    
3120    checkpoint55b_post (2004/09/22)
3121    o add a 2D scalar, Z location, exchange_2 routine.
3122    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
3123      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
3124      affects advect_cs results (for the wrong reason): update output.txt
3125    o use a more standard discretization for biharmonic viscosity ;
3126     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
3127      affects results of dome set-up: update output.txt
3128    o fix gad_advection.F (CubedSphere part), back to version 1.23
3129    o fix bug in mom_vi_del2uv.F (CubedSphere part).
3130    
3131    checkpoint55a_post (2004/09/20)
3132    o merged code to
3133      * prescribe/read time-dependent open boundaries
3134        (works in conjunction with exf, cal)
3135      * sponge layer code for open boundaries
3136      * each boundary N/S/E/W now has its own CPP option
3137        (healthy for the adjoint)
3138    
3139    checkpoint55 (2004/09/17)
3140    o up-to-date adjoint of previous breaks
3141      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
3142      - global_ocean_ebm: adjoint still needs fix (TLM ok)
3143      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
3144      - carbon: * remove tr1-related adjoint verification
3145                * add ptracer as control variable
3146    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
3147      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
3148    
3149    checkpoint54f_post (2004/09/16)
3150    o in verification/carbin/ remove experiment related to
3151      ALLOW_PASSIVE_TRACER (array tr1 etc)
3152      code_ad/ input_ad/ results_ad
3153    
3154    o add two new packages
3155      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
3156        + subject to optimization (memory)
3157      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
3158        + subject to reordering (many GOTOs in the original code)
3159        + so far opps is called for every (i,j) point, and then operates in
3160          the vertical; one may want to reorder the scheme in order operate in
3161          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
3162          fields)
3163    o overhaul of IO so that we now have flags for MDSIO and/or MNC
3164      - all verification tests compile and run with linux_ia32_g77
3165      - defaults are compatible with current input files--nothing
3166        should change if you were not previously using MNC
3167      - MNC output has been added in numerous places (eg. timeave)
3168        but there are still a few writes not yet do-able with MNC
3169        (this is in progress)
3170      - flags now allow for either/or/both use of MDSIO and MNC and
3171        documentation will soon follow
3172      - numerous small formatting cleanups for ProTeX
3173    o add version info (via BUILD_INFO.h) to MNC and stdout
3174    
3175    checkpoint54e_post (2004/09/02)
3176    o add two new packages
3177      - pp81 (Packanowski and Philander, 1981), Richardson number and
3178        stratification dependent mixing
3179      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
3180      - these scheme operate in a similar manner as KPP (without ghat, of
3181        course), however there is only one diffusivity that is used for both
3182        temperature and salinity (and passive tracers)
3183    o add offline package
3184    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
3185      provided by Stephanie Dutkiewicz
3186    o genmake2: add ability to search for C compilers and cleanup test output
3187      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
3188    
3189    checkpoint54d_post (2004/07/27)
3190    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
3191    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
3192      leading to additional shift by 5 days each year of integration
3193       (i.e. leading to considerable offset over the years)
3194    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
3195    o start with no AB and no initial filtering (staggerTimeStep):
3196      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
3197    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
3198      (external loading & cpl import/export stay in forward_step.F)
3199    o update coupling interface to work with new staggerTimeStep
3200    o change MDSIO ptracers_pickup.
3201    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
3202    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
3203    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
3204    
3205    checkpoint54c_post (2004/07/18)
3206    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
3207      this affects (truncation error) output.txt of test-exp:
3208       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
3209    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
3210    o change Qnet to always be the net heat flux, (+upward).
3211      affects (truncation error) output of natl_box exp.: updated
3212    o define the max number of passive tracers in PTRACERS_SIZE.h
3213    o start to test mnc routinely in exp0
3214    o add sea-ice loading (sIceLoad) as a new forcing field.
3215    
3216    checkpoint54b_post (2004/07/08)
3217    o add testreport "-j JOBS" option for parallel builds (tested and pretty
3218       impressive on Altix and Opteron systems)
3219    o diagnostics can now write NetCDF files through the mnc package
3220    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
3221    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
3222    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
3223      affects (truncation error) output of lab_sea & natl_box exp.: updated
3224    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
3225    
3226    checkpoint54a_post (2004/07/06)
3227    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
3228    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
3229    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
3230    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
3231      + internal_wave (shift in writing cg2d_ini_res)
3232    checkpoint54a_pre (2004/07/05)
3233    
3234    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
3235      - modified verification/lab_sea and natl_box_adjoint accordingly
3236    
3237    checkpoint54 (2004/07/02)
3238    checkpoint53g_post (2004/07/02)
3239    o prepare splitting of thermodynamics: store convect.counter in common block
3240    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
3241      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
3242    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
3243    o new parameter "nShapS": allow to treat differently S from T (nShapT)
3244    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
3245    o restore adjointability
3246    
3247    checkpoint53f_post (2004/06/25)
3248    o modifications that affect AIM experiment results (update output.txt):
3249      - no advection of S at top interface Nr (pkg/generic_advdiff)
3250      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
3251    o AIM pkg:
3252      - include stability function into surf.Flux derivative relative to Tsurf
3253      - calculate clear-sky radiation & surface temp. change (for diagnostics)
3254    
3255    checkpoint53e_post
3256    o merged cylindrical coord configuration
3257    o added rotating_tank experiment
3258    checkpoint53e_pre
3259    
3260    checkpoint53d_post (2004/06/14)
3261    o faulks upgraded: re-generate output.txt that have changed:
3262       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
3263    o Added Bryan and Lewis, 1979, vertical diffusivity profile
3264    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
3265    o added Sadourny discretization of Coriolis
3266      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
3267      - re-enabled use of omega3 (useAbsVorticity)
3268    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
3269      vector-invariant equations
3270      - note: does *NOT* yet use same variable visc. for no-slip BC's.
3271    o recoded the lateral boundary conditions for non-hydrostatic w, this time
3272      hopefully without new bugs
3273      - still to do: biharmonic friction for non-hydrostatic w
3274    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
3275    o regenerated output for global_ocean_ebm (using -ieee)
3276    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
3277      of mom_common/
3278      - simple re-arrangement of instructions within computing loop
3279    checkpoint53d_pre (2004/05/21)
3280    
3281    checkpoint53c_post (2004/05/21)
3282    o new version of coupler for AIM+thSIce and Ocean models
3283     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
3284     - land: change Evaporation of snow
3285     - aim with thSIce: fix bug in snow-precip.
3286    o changes to calc_gw.F
3287     - bug fix for w^2 term near the bottom boundary
3288     - (hopefully) improve the lateral slip boundary condtions for use with
3289        partial/looped cells
3290      - because the bug fix changes two verification experiments anyway (exp5
3291        and plume on slope), change the lateral boundary condition from half slip
3292        to the value of no_slip_sides
3293    o ebm package wasnt quite up to the parallel task. Fixed that.
3294    o Adjoint of EBM package + verification
3295      * TLM OK
3296      * ADM not sufficient accuracy yet (needs further testing)
3297    
3298    checkpoint53b_post (2004/05/14)
3299    o Commiting new energy balance model to repository
3300      * package is pkg/ebm
3301      * verif. is verification/global_ocean_ebm
3302      * references are in ebm_driver.F
3303    C      * X. Wang, P. Stone and J. Marotzke, 1999:
3304    C        Global thermohaline circulation. Part I:
3305    C        Sensitivity to atmospheric moisture transport.
3306    C        J. Climate 12(1), 71-82
3307    C      * X. Wang, P. Stone and J. Marotzke, 1999:
3308    C        Global thermohaline circulation. Part II:
3309    C        Sensitivity with interactive transport.
3310    C        J. Climate 12(1), 83-91
3311    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
3312    C        Destabilization of the thermohaline circulation
3313    C        by atmospheric eddy transports.
3314    C        J. Climate 7(12), 1870-1882
3315    o Will need long integration testing.
3316    checkpoint53b_pre (2004/05/14)
3317    
3318    o created pkg/mom_common in preparation for variable viscosity code
3319    o renamed and split ini_mnc_io
3320    o pkg/land: only liquid water can diffuse or run-off
3321    o AIM using land: soil wetness availability account for snow
3322    o added printMapIncludesZeros to EEPARMS namelist
3323    
3324    checkpoint53a_post (2004/05/11)
3325    o restore TAMC compatiility for exf_constants.h
3326      (no usage of _d in .h)
3327    o Additional storing in KPP in an attempt to fix
3328      TAMC problem with adjoint of KPP code.
3329      (no success...)
3330      Identical code works fine with TAF.
3331    o Fixed verification/natl_box_adjoint experiments.
3332      Initial conditions for Experiments 4 and 5 are now
3333      set to "SEAICE_initialHEFF=0", which is more reasonable,
3334      and hence gives results closer to that of Experiment 2.
3335      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
3336    
3337    checkpoint53 (2004/05/06)
3338    o stable checkpoint with up to date adjoint
3339      TLM tests only run for 1st grdchk at the moment. Its unclear if
3340      this is a code problem or a problem with resetting code for g_
3341      variables that is being autogenerated wrong.
3342      Otherwise:
3343       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
3344       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
3345         are both still in chaos following their security messes.
3346    
3347    checkpoint52n_post (2004/05/06)
3348    o various build (mostly genmake2) changes including:
3349      - ability to build/run more easily within Cygwin and MacOS X
3350      - more complicated Makefiles with a stronger dependence on Gnu Make
3351  o pkg/seaice modifications  o pkg/seaice modifications
3352      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
3353        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
3354        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
3355    - changed proxy for geostrophic velocity and updated    - changed proxy for geostrophic velocity and updated
3356      verification/lab_sea/results/* accordingly      verification/lab_sea/results/* accordingly
3357    - removed ADI dynamic solver from pkg/seaice    - removed ADI dynamic solver from pkg/seaice
# Line 27  o fix in pkg/thsice: Line 3375  o fix in pkg/thsice:
3375    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
3376   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
3377    
3378  checkpoint52m_post  checkpoint52m_post (2004/04/18)
3379  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;
3380    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
3381    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 59  o test exp. advect_cs: use the standard Line 3407  o test exp. advect_cs: use the standard
3407  o Added functionality to grdchk:  o Added functionality to grdchk:
3408    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.
3409    
3410  checkpoint52l_post  checkpoint52l_post (2004/03/11)
3411  o new land formulation:  o new land formulation:
3412    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
3413       energy conservation.       energy conservation.
# Line 70  o aim_v23 modification for new land mode Line 3418  o aim_v23 modification for new land mode
3418    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
3419       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
3420    b) add snow precipitation.    b) add snow precipitation.
3421  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
3422    
3423  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
3424  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 83  o fix ini_curvilinear_grid ; test CS exp Line 3431  o fix ini_curvilinear_grid ; test CS exp
3431  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
3432  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
3433    
3434  checkpoint52k_post  checkpoint52k_post (2004/02/23)
3435  o removed top-level directory "diags"  o removed top-level directory "diags"
3436    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
3437  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 96  o set all ...Freq to zero after cost_fin Line 3444  o set all ...Freq to zero after cost_fin
3444    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
3445  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
3446    
3447  checkpoint52j_post  checkpoint52j_post (2004/02/18)
3448  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
3449  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
3450  o Really weird thing!  o Really weird thing!
# Line 104  o Really weird thing! Line 3452  o Really weird thing!
3452    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
3453    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
3454    after cost_final call which should not be there!    after cost_final call which should not be there!
3455  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
3456    
3457  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
3458    error messages    error messages
# Line 121  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 3469  o merged mom_vi_calc_relvort3.F, mom_vi_
3469    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
3470  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
3471    
3472  checkpoint52i_post  checkpoint52i_post (2004/01/21)
3473  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
3474  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
3475  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
3476    
3477  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
3478    the old pkg/aim).    the old pkg/aim).
3479    
3480  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
3481  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
3482  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
3483  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 140  o added temporary hack for sea-ice dynam Line 3488  o added temporary hack for sea-ice dynam
3488    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
3489    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.
3490    
3491  checkpoint52f_post  checkpoint52f_post (2004/01/09)
3492  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
3493  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
3494  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
3495  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
3496    
3497  checkpoint52e_post  checkpoint52e_post (2004/01/07)
3498  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
3499    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
3500  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 154  o step.1 : rewrite (as in MultiDimAdvec) Line 3502  o step.1 : rewrite (as in MultiDimAdvec)
3502  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.
3503  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:
3504   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
3505  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
3506    
3507  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
3508  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 165  o added exf_offset_atemp for Celsius to Line 3513  o added exf_offset_atemp for Celsius to
3513  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
3514  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
3515    
3516  checkpoint52d_post  checkpoint52d_post (2003/12/16)
3517  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
3518    - updated output accordingly    - updated output accordingly
3519    - 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 194  o check-in the first version of the coup Line 3542  o check-in the first version of the coup
3542  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
3543     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
3544    
3545  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
3546  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
3547  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
3548    
3549  checkpoint52c_post  checkpoint52c_post (2003/11/25)
3550  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
3551    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
3552    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 212  o Removed all CPP options for cal packag Line 3560  o Removed all CPP options for cal packag
3560  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
3561  o corrected key comp. for passkey  o corrected key comp. for passkey
3562    
3563  checkpoint52b_post  checkpoint52b_post (2003/11/23)
3564  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
3565   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
3566   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 220  o new version: "thsice" of thermodynamic Line 3568  o new version: "thsice" of thermodynamic
3568   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
3569     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
3570  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
3571  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
3572    
3573  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
3574  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 230  o missing PTRACERS headers in some routi Line 3578  o missing PTRACERS headers in some routi
3578  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
3579    to ensure proper customization    to ensure proper customization
3580    
3581  checkpoint52a_post  checkpoint52a_post (2003/11/17)
3582  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
3583    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3584    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 245  o fix problem with ECCO-related divided Line 3593  o fix problem with ECCO-related divided
3593    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
3594    but no warning issued by TAF    but no warning issued by TAF
3595    
3596  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
3597  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
3598    
3599  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
3600  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
3601    
3602  checkpoint51u_post  checkpoint51u_post (2003/11/06)
3603  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
3604    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
3605  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 266  o top level routines the_main_loop, forw Line 3614  o top level routines the_main_loop, forw
3614    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
3615  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
3616    
3617  checkpoint51t_post  checkpoint51t_post (2003/11/04)
3618  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
3619    
3620  checkpoint51s_post  checkpoint51s_post (2003/11/04)
3621  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
3622  o pkg/grdchk  o pkg/grdchk
3623    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 278  o pkg/grdchk Line 3626  o pkg/grdchk
3626    - additional high-precision output for testreport    - additional high-precision output for testreport
3627      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
3628    
3629  checkpoint51r_post  checkpoint51r_post (2003/11/03)
3630  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
3631  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
3632    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
3633    
3634  checkpoint51q_post  checkpoint51q_post (2003/10/30)
3635  o cd_code:  o cd_code:
3636    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
3637    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 299  o ctrl package totally restructured Line 3647  o ctrl package totally restructured
3647    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
3648  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
3649    
3650  checkpoint51p_post  checkpoint51p_post (2003/10/30)
3651  o create initial cd_code package  o create initial cd_code package
3652    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
3653      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 314  o create initial cd_code package Line 3662  o create initial cd_code package
3662  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
3663  o cleanup testreport  o cleanup testreport
3664    
3665  checkpoint51o_post  checkpoint51o_post (2003/10/27)
3666  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
3667    - carbon/    - carbon/
3668    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 335  o Correcting initialisations for fVerU, Line 3683  o Correcting initialisations for fVerU,
3683  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
3684    fVerU, fVerV    fVerU, fVerV
3685  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
3686  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
3687    
3688  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
3689  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 343  o added the [#include "AD_CONFIG.h"] sta Line 3691  o added the [#include "AD_CONFIG.h"] sta
3691   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
3692   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
3693    
3694  checkpoint51n_post  checkpoint51n_post (2003/10/23)
3695  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
3696    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3697    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 352  o modifications to make FREEZE flux visi Line 3700  o modifications to make FREEZE flux visi
3700       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
3701  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
3702    
3703  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
3704  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
3705  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
3706    defines:    defines:
# Line 360  o added [#include "AD_CONFIG.h"] to all Line 3708  o added [#include "AD_CONFIG.h"] to all
3708    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
3709    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
3710    
3711  checkpoint51m_post  checkpoint51m_post (2003/10/21)
3712  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
3713    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
3714    - various cleanups related to package handling    - various cleanups related to package handling
3715    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
3716    
3717  checkpoint51l_post  checkpoint51l_post (2003/10/20)
3718  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
3719   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
3720   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
3721   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
3722     model integration time     model integration time
3723    
3724  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
3725  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)
3726  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.
3727  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
3728     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
3729    
3730  checkpoint51k_post  checkpoint51k_post (2003/10/16)
3731  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
3732   - 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):
3733     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 393  o added an include barrier to the defaul Line 3741  o added an include barrier to the defaul
3741    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
3742  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
3743    
3744  checkpoint51j_post  checkpoint51j_post (2003/10/10)
3745  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
3746  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
3747  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 407  o Moving pkg-specific flow directives to Line 3755  o Moving pkg-specific flow directives to
3755         - pkg_ad_diff.list         - pkg_ad_diff.list
3756         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
3757    
3758  checkpoint51i_post  checkpoint51i_post (2003/10/09)
3759  o merge of the branch-genmake2  o merge of the branch-genmake2
3760    - knowingly breaks the older genmake    - knowingly breaks the older genmake
3761    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
3762    - new testreport supersedes older testscript    - new testreport supersedes older testscript
3763  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
3764  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
3765    
3766  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
3767  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 425  o modify gchem pkg to be more versatile Line 3773  o modify gchem pkg to be more versatile
3773  o modifications to clean up dic pkg  o modifications to clean up dic pkg
3774  o add pkg/cfc  o add pkg/cfc
3775    
3776  checkpoint51g_post  checkpoint51g_post (2003/10/02)
3777  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
3778  o start removing verification/vero/  o start removing verification/vero/
3779  o update AD-related stuff  o update AD-related stuff
# Line 433  o update AD-related stuff Line 3781  o update AD-related stuff
3781  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
3782    vector invariant setup    vector invariant setup
3783    
3784  checkpoint51f_post  checkpoint51f_post (2003/10/02)
3785  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)
3786  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
3787    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
3788    
3789  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
3790  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
3791      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
3792    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 450  o Bug fix to pkg/ptracers, pkg/generic_a Line 3798  o Bug fix to pkg/ptracers, pkg/generic_a
3798      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
3799      non-local transport term.      non-local transport term.
3800    
3801  checkpoint51e_post  checkpoint51e_post (2003/08/03)
3802  o pkg/mom_vecinv:  o pkg/mom_vecinv:
3803    - 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)
3804    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 460  o atmospheric geopotential: - include wa Line 3808  o atmospheric geopotential: - include wa
3808  o land pkg: read initial state from files.  o land pkg: read initial state from files.
3809  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
3810    
3811  checkpoint51d_post  checkpoint51d_post (2003/07/18)
3812  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
3813    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
3814  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 473  o Use cluster local disks for purely loc Line 3821  o Use cluster local disks for purely loc
3821    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
3822    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
3823    
3824  checkpoint51c_post  checkpoint51c_post (2003/07/08)
3825  o introducing integer flag debugLevel  o introducing integer flag debugLevel
3826    - debLevZero: suppress all output    - debLevZero: suppress all output
3827    - debLevA: standard    - debLevA: standard
# Line 496  o added verification for adjoint with pt Line 3844  o added verification for adjoint with pt
3844    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
3845  <<<checkpoint51b_pre  <<<checkpoint51b_pre
3846    
3847  checkpoint51a_post  checkpoint51a_post (2003/06/25)
3848  o added code for biogeochemistry package  o added code for biogeochemistry package
3849    - new pkgs: dic, gchem    - new pkgs: dic, gchem
3850    - new subroutine in ptracers    - new subroutine in ptracers
3851  o modify code for biogeo packages  o modify code for biogeo packages
3852    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
3853    
3854  checkpoint51  checkpoint51 (2003/06/24)
3855  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
3856    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
3857    kept separate packages    kept separate packages
# Line 511  o merged improved packages from ecco-bra Line 3859  o merged improved packages from ecco-bra
3859  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
3860    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
3861    
3862  checkpoint50i_post  checkpoint50i_post (2003/06/23)
3863  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
3864    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
3865    - 1st step: this one is differentiable    - 1st step: this one is differentiable
3866    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
3867                from ecco-branch)                from ecco-branch)
3868    
3869  checkpoint50h_post  checkpoint50h_post (2003/06/20)
3870  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
3871  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
3872  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 527  o New variable in PARM03 for more flexib Line 3875  o New variable in PARM03 for more flexib
3875  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
3876    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
3877    
3878  checkpoint50g_post  checkpoint50g_post (2003/05/23)
3879  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
3880    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
3881    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
3882      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
3883    
3884  checkpoint50f_post  checkpoint50f_post (2003/05/23)
3885  o exf totally restructured  o exf totally restructured
3886    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
3887      and made sure it's still differentiable      and made sure it's still differentiable
# Line 541  o exf totally restructured Line 3889  o exf totally restructured
3889    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
3890    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
3891    
3892  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
3893   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 ;
3894        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
3895   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 551  checkpoint50f_pre Line 3899  checkpoint50f_pre
3899   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
3900   o removed lots of single quotes from comments   o removed lots of single quotes from comments
3901    
3902  checkpoint50e_post  checkpoint50e_post (2003/05/14)
3903  o make KPP work with PTRACERS  o make KPP work with PTRACERS
3904   - 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
3905     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
3906   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
3907     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
3908  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
3909  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
3910    
3911  checkpoint50d_post  checkpoint50d_post (2003/05/13)
3912  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
3913    files analogous to write_state.F    files analogous to write_state.F
3914  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,
3915    analogous to the cg2d-related output.    analogous to the cg2d-related output.
3916  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,
3917    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
3918  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
3919    
3920  checkpoint50c_post  checkpoint50c_post (2003/05/12)
3921  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)
3922  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
3923  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.
3924  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
3925  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
3926    
3927  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
3928  Merging from release1_p13:  Merging from release1_p13:
3929  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
3930  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
3931    
3932  checkpoint50b_post  checkpoint50b_post (2003/04/17)
3933  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
3934  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
3935    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 590  o new flag "useCDscheme" (default=F); re Line 3938  o new flag "useCDscheme" (default=F); re
3938  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
3939     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
3940    
3941  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
3942  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
3943  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
3944    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
3945    
3946  checkpoint50a_post  checkpoint50a_post (2003/03/21)
3947  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
3948    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
3949    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
3950    in contradiction with new key itdkey.    in contradiction with new key itdkey.
3951    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
3952    
3953  checkpoint50  checkpoint50 (2003/03/08)
3954  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
3955    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
3956  - bug fix in find_alpha  - bug fix in find_alpha
# Line 610  checkpoint50 Line 3958  checkpoint50
3958  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
3959  - merged some sliced AD support routines  - merged some sliced AD support routines
3960    
3961  checkpoint49  checkpoint49 (2003/03/06)
3962  merged from ecco-branch:  merged from ecco-branch:
3963  o exf:  o exf:
3964    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 648  o DIVA: Line 3996  o DIVA:
3996    (see MITgcm manual).    (see MITgcm manual).
3997  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
3998    
3999  checkpoint48i_post  checkpoint48i_post (2003/03/05)
4000  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
4001    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
4002    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 666  o Modif. for DIVA: Line 4014  o Modif. for DIVA:
4014    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
4015    only relevant for ecco-branch)    only relevant for ecco-branch)
4016    
4017  checkpoint48h_post  checkpoint48h_post (2003/02/28)
4018  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
4019  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
4020  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4021  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
4022    
4023  checkpoint48g_post  checkpoint48g_post (2003/02/18)
4024  --- EOS:  --- EOS:
4025  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
4026    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 686  o accurate phiHyd when using interface-W Line 4034  o accurate phiHyd when using interface-W
4034   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
4035  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
4036    
4037  checkpoint48f_post  checkpoint48f_post (2003/02/18)
4038  Merging from release1_p12:  Merging from release1_p12:
4039  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
4040    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 714  o pkg/seaice: Line 4062  o pkg/seaice:
4062    - adjoint-friendly modifications    - adjoint-friendly modifications
4063    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
4064    
4065  checkpoint48e_post  checkpoint48e_post (2003/02/12)
4066  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)
4067  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
4068    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 725  o following exp works with Olx=Oly=2 (an Line 4073  o following exp works with Olx=Oly=2 (an
4073      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
4074    (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)
4075    
4076  checkpoint48d_post  checkpoint48d_post (2003/02/09)
4077  o in preparation for r*:  o in preparation for r*:
4078   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
4079      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 733  o in preparation for r*: Line 4081  o in preparation for r*:
4081      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
4082    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
4083    
4084  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
4085  o in preparation for r*:  o in preparation for r*:
4086    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.
4087    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.
4088    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.
4089  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
4090    
4091  checkpoint48c_post  checkpoint48c_post (2003/02/06)
4092  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
4093  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
4094    
4095  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
4096  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
4097  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)
4098    
4099  checkpoint48b_post  checkpoint48b_post (2003/01/27)
4100  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
4101   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
4102  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
4103    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
4104    
4105  checkpoint48a_post  checkpoint48a_post (2003/01/24)
4106  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
4107     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
4108    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
4109                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
4110    
4111  checkpoint48  checkpoint48 (2003/01/23)
4112  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')
4113    
4114  checkpoint47j_post  checkpoint47j_post (2003/01/21)
4115  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.
4116  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
4117  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 782  o Yet more changes in gmredi: Line 4130  o Yet more changes in gmredi:
4130      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
4131  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
4132    
4133  checkpoint47i_post  checkpoint47i_post (2003/01/13)
4134  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.
4135  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)
4136    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 798  o case GM_BOLUS_ADVEC should be cleaned Line 4146  o case GM_BOLUS_ADVEC should be cleaned
4146    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
4147  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
4148    
4149  checkpoint47g_post  checkpoint47g_post (2003/01/10)
4150  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
4151    (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)
4152  o After TAF bug fix:  o After TAF bug fix:
# Line 824  Gradient checks OK for Line 4172  Gradient checks OK for
4172  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
4173  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
4174    
4175  checkpoint47f_post  checkpoint47f_post (2002/12/28)
4176  Merging from release1_p10:  Merging from release1_p10:
4177  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
4178    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 836  o modifications for using pkg/exf with p Line 4184  o modifications for using pkg/exf with p
4184    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
4185      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
4186    
4187  checkpoint47e_post  checkpoint47e_post (2002/12/27)
4188  o created a tag prior to creating a branch  o created a tag prior to creating a branch
4189    
4190  checkpoint47d_post  checkpoint47d_post (2002/12/16)
4191  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
4192    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
4193  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
4194    oceanic pressure coordinates code    oceanic pressure coordinates code
4195  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
4196    also described in the tutorial section of the manual    also described in the tutorial section of the manual
4197  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
4198    
4199  checkpoint47c_post  checkpoint47c_post (2002/12/16)
4200  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
4201    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
4202    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 860  o OCEANICP & realFreshWater: include P-E Line 4208  o OCEANICP & realFreshWater: include P-E
4208    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
4209  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
4210    
4211  checkpoint47b_post  checkpoint47b_post (2002/12/05)
4212  Merging from release1_p9:  Merging from release1_p9:
4213  o pkg/seaice  o pkg/seaice
4214    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 877  o verification/lab_sea Line 4225  o verification/lab_sea
4225    - added missing matlab routines    - added missing matlab routines
4226    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
4227    
4228  checkpoint47a_post  checkpoint47a_post (2002/11/23)
4229  o new pkg: aim_v23  o new pkg: aim_v23
4230   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
4231     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 894  o bulk_force and therm_seaice Line 4242  o bulk_force and therm_seaice
4242  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
4243     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
4244    
4245  checkpoint47  checkpoint47 (2002/11/15)
4246  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
4247  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
4248  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 923  o Updated verification/carbon/ Line 4271  o Updated verification/carbon/
4271    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
4272    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
4273    
4274  checkpoint46n_post  checkpoint46n_post (2002/11/12)
4275  Merging from release1_p8:  Merging from release1_p8:
4276  o verification/natl_box:  o verification/natl_box:
4277    updating new external_fields_load routine    updating new external_fields_load routine
# Line 977  o Adding new verification experiment glo Line 4325  o Adding new verification experiment glo
4325    the exf (and cal) package instead of the    the exf (and cal) package instead of the
4326    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
4327    
4328  checkpoint46m_post  checkpoint46m_post (2002/11/07)
4329  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
4330  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
4331    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 990  o introduced flag for controllin non-hyd Line 4338  o introduced flag for controllin non-hyd
4338  o removed gravitySign from PARM04  o removed gravitySign from PARM04
4339  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
4340    
4341  checkpoint46l_post  checkpoint46l_post (2002/11/01)
4342  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
4343   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
4344     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 1003  o made convective adjustment work with p Line 4351  o made convective adjustment work with p
4351     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
4352     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
4353     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
4354  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
4355    
4356  checkpoint46k_post  checkpoint46k_post (2002/10/23)
4357  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
4358   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
4359   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 1019  o S/R aim_initialise.F replace S/R aim_i Line 4367  o S/R aim_initialise.F replace S/R aim_i
4367   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
4368   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
4369    
4370  checkpoint46j_post  checkpoint46j_post (2002/10/07)
4371  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
4372  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
4373  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)
4374  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
4375  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
4376    
4377  checkpoint46i_post  checkpoint46i_post (2002/09/25)
4378  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
4379    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
4380    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
4381    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 !
4382    
4383  checkpoint46h_post  checkpoint46h_post (2002/09/25)
4384  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
4385    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
4386      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 1042  o introduced new parameter rhoConstFresh Line 4390  o introduced new parameter rhoConstFresh
4390    value is 999.8 kg/m^3    value is 999.8 kg/m^3
4391  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
4392    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
4393  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
4394    
4395   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
4396   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
4397   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
4398    
4399  checkpoint46g_post  checkpoint46g_post (2002/09/18)
4400  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
4401    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
4402    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 1066  o cleaned up find_rho Line 4414  o cleaned up find_rho
4414    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
4415  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
4416    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
4417  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
4418    
4419  checkpoint46f_post  checkpoint46f_post (2002/09/16)
4420  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
4421    - extended active file handling to g_... files    - extended active file handling to g_... files
4422    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 1076  o Enable tangent linear (forward mode) g Line 4424  o Enable tangent linear (forward mode) g
4424  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
4425  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
4426    
4427  checkpoint46e_post  checkpoint46e_post (2002/09/05)
4428  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
4429    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
4430    - 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 1085  o Added new equation of state -> MDJWF Line 4433  o Added new equation of state -> MDJWF
4433    - 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
4434      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
4435      expect perfect matches for those      expect perfect matches for those
4436  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
4437    
4438  checkpoint46d_post  checkpoint46d_post (2002/08/19)
4439  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
4440    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
4441    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
4442    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
4443  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)
4444    in find_alpha/beta.    in find_alpha/beta.
4445  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
4446    
4447  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)
4448    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
4449    
4450  checkpoint46c_post  checkpoint46c_post (2002/08/15)
4451  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
4452   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
4453   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
4454      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).
4455   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
4456   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
4457  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
4458    
4459  checkpoint46b_post  checkpoint46b_post (2002/08/07)
4460  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
4461    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
4462    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 1117  o Added UNESCO EOS, but not recommended Line 4465  o Added UNESCO EOS, but not recommended
4465    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
4466  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
4467    unesco.f to be used with POLY3    unesco.f to be used with POLY3
4468  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
4469    
4470  checkpoint46a_post  checkpoint46a_post (2002/07/31)
4471  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
4472    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
4473    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
4474  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
4475  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
4476  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
4477    
4478  checkpoint46  checkpoint46 (2002/07/13)
4479  further merges from release1_p5  further merges from release1_p5
4480  o new ctrl package  o new ctrl package
4481    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 1154  o added hooks for Eliassen Palm fluxes ( Line 4502  o added hooks for Eliassen Palm fluxes (
4502  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
4503  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
4504    
4505  checkpoint45d_post  checkpoint45d_post (2002/07/12)
4506  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
4507  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
4508    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 1168  o add new flags: Line 4516  o add new flags:
4516   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
4517  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
4518    
4519  checkpoint45c_post  checkpoint45c_post (2002/05/30)
4520  o Removed f90 comments ("!")  o Removed f90 comments ("!")
4521  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
4522    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 1176  o modifications to gradient check packag Line 4524  o modifications to gradient check packag
4524    - enable centered differences    - enable centered differences
4525    - modified format of standard output    - modified format of standard output
4526    
4527  checkpoint45b_post  checkpoint45b_post (2002/05/30)
4528  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
4529  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
4530  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1188  o in initialise_varia, moved call packag Line 4536  o in initialise_varia, moved call packag
4536    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
4537  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
4538    
4539  checkpoint45a_post  checkpoint45a_post (2002/05/01)
4540  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
4541  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
4542  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 1208  o errorMessageUnit set non-equal zero in Line 4556  o errorMessageUnit set non-equal zero in
4556    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
4557  o modified carbon verif.  o modified carbon verif.
4558    
4559  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
4560  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
4561    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
4562  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
4563    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.
4564    
4565  checkpoint44g_post  checkpoint44g_post (2002/03/05)
4566  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
4567    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
4568    
# Line 1279  o merge of relevant stuff from the ecco- Line 4627  o merge of relevant stuff from the ecco-
4627  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
4628  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
4629    
4630  checkpoint44  checkpoint44 (2002/01/18)
4631  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
4632  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)
4633  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 1287  o update AIM experiments (NCEP input fil Line 4635  o update AIM experiments (NCEP input fil
4635  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
4636  o added some stuff for AD  o added some stuff for AD
4637    
4638  checkpoint43  checkpoint43 (2001/09/28)
4639  o added two new advection tests  o added two new advection tests
4640  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
4641  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
4642  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
4643    
4644  checkpoint42  checkpoint42 (2001/09/27)
4645    Fixed AD-related problems:    Fixed AD-related problems:
4646  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
4647    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1305  o Modified store directives for split of Line 4653  o Modified store directives for split of
4653    for the case ALLOW_KPP    for the case ALLOW_KPP
4654  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
4655    
4656  checkpoint41  checkpoint41 (2001/09/27)
4657  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
4658    to work with protex    to work with protex
4659    
4660  checkpoint40  checkpoint40 (2001/09/27)
4661  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
4662  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
4663  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1318  o more mods for non-linear free-surface Line 4666  o more mods for non-linear free-surface
4666  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
4667  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
4668    
4669  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
4670  o added DST advection schemes  o added DST advection schemes
4671  o fix MPI bug on SGI's  o fix MPI bug on SGI's
4672  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1328  o changes to commenting of arguments for Line 4676  o changes to commenting of arguments for
4676  o added/updated many matlab scripts  o added/updated many matlab scripts
4677  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
4678        
4679  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
4680  o new package rw/  o new package rw/
4681    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
4682    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1347  o TAMC-related update to cope with mom_f Line 4695  o TAMC-related update to cope with mom_f
4695    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
4696    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
4697    
4698  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
4699  o bug fix in dynamics.F  o bug fix in dynamics.F
4700    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
4701  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
4702  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
4703    related to TAF    related to TAF
4704    
4705  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
4706  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
4707  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
4708    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1362  o corresponding split of calc_diffusivit Line 4710  o corresponding split of calc_diffusivit
4710  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
4711  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
4712    
4713  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
4714  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
4715    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
4716  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 1376  o added new expt "solid-body.cs-32x32x1" Line 4724  o added new expt "solid-body.cs-32x32x1"
4724    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
4725      is not necessarily any better than the current one...      is not necessarily any better than the current one...
4726    
4727  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
4728  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
4729    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
4730  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1384  o extended iMin,jMin range for calc_comm Line 4732  o extended iMin,jMin range for calc_comm
4732  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
4733  o a few minor updates and fixes  o a few minor updates and fixes
4734    
4735  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
4736  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
4737  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
4738  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
4739    
4740  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
4741  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
4742  o Added gradient check package  o Added gradient check package
4743  o Added routines for passive tracer handling  o Added routines for passive tracer handling
4744  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
4745    
4746  checkpoint39  checkpoint39 (2001/05/14)
4747   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
4748     (mainly missing or wrong directives)     (mainly missing or wrong directives)
4749   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 1409  checkpoint39 Line 4757  checkpoint39
4757           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
4758   o disabled some packages by default in genmake   o disabled some packages by default in genmake
4759    
4760  checkpoint38  checkpoint38 (2001/04/10)
4761   o see notes_c37_adj.txt   o see notes_c37_adj.txt
4762   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
4763   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1417  checkpoint38 Line 4765  checkpoint38
4765     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
4766   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
4767    
4768  checkpoint37  checkpoint37 (2001/03/13)
4769   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
4770     (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
4771      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1434  checkpoint37 Line 4782  checkpoint37
4782   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
4783   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
4784    
4785  checkpoint36  checkpoint36 (2001/02/20)
4786   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
4787   o recover Time-Average diagnostics   o recover Time-Average diagnostics
4788   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
4789   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
4790    
4791  checkpoint35  checkpoint35 (2001/02/08)
4792   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
4793   o allows staggered time-stepping   o allows staggered time-stepping
4794   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
4795   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
4796    
4797  checkpoint34  checkpoint34 (2001/01/30)
4798   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
4799   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
4800     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1457  checkpoint34 Line 4805  checkpoint34
4805   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
4806   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
4807    
4808  checkpoint33  checkpoint33 (2000/11/30)
4809   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
4810   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
4811     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1475  checkpoint33 Line 4823  checkpoint33
4823       possibly use them.       possibly use them.
4824   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
4825    
4826  checkpoint32  checkpoint32 (2000/11/13)
4827   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
4828     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
4829   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1486  checkpoint32 Line 4834  checkpoint32
4834   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
4835   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
4836    
4837  checkpoint31  checkpoint31 (2000/09/11)
4838   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
4839     -> new routines packages_...F     -> new routines packages_...F
4840     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1503  checkpoint31 Line 4851  checkpoint31
4851     - not yet tested for GMRedi.     - not yet tested for GMRedi.
4852     - not yet tested for KPP.     - not yet tested for KPP.
4853    
4854  checkpoint30  checkpoint30 (2000/07/13)
4855   o Updates for OBCs   o Updates for OBCs
4856   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
4857   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1512  checkpoint30 Line 4860  checkpoint30
4860   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.)
4861     and entry for T90 in genmake     and entry for T90 in genmake
4862    
4863  checkpoint29  checkpoint29 (2000/06/21)
4864   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
4865    
4866  checkpoint28  checkpoint28 (2000/06/09)
4867   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
4868   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
4869   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 1528  checkpoint28 Line 4876  checkpoint28
4876     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
4877   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
4878    
4879  checkpoint27  checkpoint27 (2000/04/10)
4880   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
4881     formulation works properly with variable resolution.     formulation works properly with variable resolution.
4882   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 1536  checkpoint27 Line 4884  checkpoint27
4884   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
4885     in new routine ini_psurf()     in new routine ini_psurf()
4886    
4887  checkpoint26  checkpoint26 (2000/04/05)
4888   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
4889     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
4890   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 1546  checkpoint26 Line 4894  checkpoint26
4894     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
4895   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
4896    
4897  checkpoint25  checkpoint25 (2000/03/15)
4898   o updates for OBCs and NH   o updates for OBCs and NH
4899   o dramatically reduced memory usage   o dramatically reduced memory usage
4900   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 1557  checkpoint25 Line 4905  checkpoint25
4905      an explicit free-surface option)      an explicit free-surface option)
4906   o initial state input files for U and V   o initial state input files for U and V
4907    
4908  checkpoint24  checkpoint24 (1999/08/02)
4909   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
4910   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
4911   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
4912    
4913  checkpoint23  checkpoint23 (1999/05/26)
4914   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
4915   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
4916    
4917  checkpoint22  checkpoint22 (1999/05/18)
4918   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
4919   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
4920    
4921  checkpoint21  checkpoint21 (1999/05/18)
4922   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)
4923   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
4924   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
4925   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
4926    
4927  checkpoint20  checkpoint20 (1999/03/22)
4928   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
4929   o Added non-hydrostatic code   o Added non-hydrostatic code
4930   o Fixed some input data   o Fixed some input data
4931   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
4932    
4933  checkpoint19  checkpoint19 (1998/12/15)
4934   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
4935   o Added new code for open boundaries.   o Added new code for open boundaries.
4936   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 1590  checkpoint19 Line 4938  checkpoint19
4938   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
4939   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.
4940    
4941  checkpoint18  checkpoint18 (1998/11/30)
4942   o Further changes for optional code generation with   o Further changes for optional code generation with
4943     CPP - ugh!     CPP - ugh!
4944    
4945  checkpoint17  checkpoint17 (1998/11/03)
4946   o Beginning to incorporating modularity   o Beginning to incorporating modularity
4947     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
4948   o Small changes for TAMC complinace   o Small changes for TAMC complinace
4949   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
4950     configuration "exp0".     configuration "exp0".
4951    
4952  checkpoint16  checkpoint16 (1998/10/28)
4953   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
4954     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
4955     assignment is an addition.     assignment is an addition.
# Line 1609  checkpoint16 Line 4957  checkpoint16
4957     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
4958     limit ).     limit ).
4959    
4960  checkpoint15  checkpoint15 (1998/09/29)
4961   Rewrote exchange routines to allow   Rewrote exchange routines to allow
4962   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
4963   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 1618  checkpoint15 Line 4966  checkpoint15
4966     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
4967     communication method.     communication method.
4968    
4969  checkpoint14  checkpoint14 (1998/09/09)
4970   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
4971   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
4972    
4973  checkpoint13  checkpoint13 (1998/07/17)
4974   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
4975   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
4976   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 1637  branch-point-rdot Line 4985  branch-point-rdot
4985   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
4986   we've actually tested it...   we've actually tested it...
4987    
4988  checkpoint12  checkpoint12 (1998/07/08)
4989   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
4990   configure script).   configure script).
4991   Released to testers.   Released to testers.
4992    
4993  checkpoint11  checkpoint11 (1998/07/02)
4994   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
4995   and ini_masks_etc().   and ini_masks_etc().
4996    
4997  checkpoint10  checkpoint10 (1998/07/01)
4998   Introduced the configure script.   Introduced the configure script.
4999   Separated out the diags package.   Separated out the diags package.
5000   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
5001   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
5002    
5003  checkpoint9  checkpoint9 (1998/06/22)
5004   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
5005   General tidy-up.   General tidy-up.
5006   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
5007    
5008  checkpoint8  checkpoint8 (1998/06/22)
5009   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
5010   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
5011    
# Line 1667  checkpoint7-4degree-ref Line 5015  checkpoint7-4degree-ref
5015   model etc..   model etc..
5016   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
5017    
5018  checkpoint7  checkpoint7 (1998/06/15)
5019   Created by cnh   Created by cnh
5020   Simple 4 degree global simulation   Simple 4 degree global simulation
5021   configuration.   configuration.
# Line 1675  checkpoint7 Line 5023  checkpoint7
5023   hydrography, bathymetry etc   hydrography, bathymetry etc
5024   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
5025    
5026  checkpoint6  checkpoint6 (1998/06/08)
5027   Created by cnh   Created by cnh
5028   merged checkpoint5 with CD and   merged checkpoint5 with CD and
5029   spherical polar code.   spherical polar code.
5030   Still some problems with GM Redi   Still some problems with GM Redi
5031   abd full topography.   abd full topography.
5032    
5033  checkpoint5  checkpoint5 (1998/06/08)
5034   Created by AJA   Created by AJA
5035   contains updates to GM Redi   contains updates to GM Redi
5036   and reordered timestepping loop   and reordered timestepping loop
5037   for Implicit Diffusion.   for Implicit Diffusion.
5038    
5039  checkpoint4  checkpoint4 (1998/05/30)
5040   Created by cnh   Created by cnh
5041   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
5042   grid variations are limited.   grid variations are limited.
5043   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
5044   for generation.   for generation.
5045    
5046  checkpoint3  checkpoint3 (1998/05/26)
5047   Created by cnh   Created by cnh
5048   Added extra flags for runtime options   Added extra flags for runtime options
5049   Added this file   Added this file

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