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revision 1.359 by heimbach, Mon Sep 27 14:56:42 2004 UTC revision 1.1244 by dfer, Tue Mar 30 18:43:34 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/offline:
8      - no need to specify periodicExternalForcing, etc ... to use offline pack
9      - offline input files no longer just single prec --> parameter offlineLoadPrec
10    o verification/lab_sea:
11      change to multi-tile setup.
12      NOTE: while cost function values remain very similar,
13      gradients are very different, although gradient checks are self-consistent
14      Should try to get to the bottom of this (cost function summation order?)
15    o pkg/dic:
16      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
17      a weakness of TAF that drops part of double precision in log10 derivative.
18      <= changes removed since problem has been fixed in current TAF version 1.9.71
19      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
20    o pkg/ecco:
21      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
22      update all 4 lab_sea AD output.
23    
24    checkpoint62d (2010/03/22)
25    o build_options:
26      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
27    o remove unbalanced quote (single or double) in commented line of source code
28      (may cause some warning with some preprocessor/makedepend versions).
29    o pkg/seaice:
30      fix seaice_model.F for adjoint (gael) and update AD results of experiments
31       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
32    o testreport:
33      add option '-runonly' (short: '-ro') to just do the run part (without make).
34    o eesupp: remove JAM communication code (obsolete).
35    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
36      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
37      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
38      (update also the output).
39    
40    checkpoint62c (2010/03/02)
41    o tools/build_options :
42       move (some) old optfiles from build_options/ to build_options/unsupported/
43    o model/src and pkg/exf
44       surface relaxation -- separating data and data.exf options
45       The point is to ensure that we specify the surface relaxation
46       either in data or in data.exf (but not half and half) and to
47       avoid an accidental relaxation to 0 (which happened if a time
48       scale was specified but the file name was left empty)
49    o model/src model/inc and pkg/mom_common
50       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
51       => addition to the viscosity field as computed by others schemes
52    o tools/build_options:
53      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
54        but keep the former optfile for few weeks for smooth transition
55    o pkg/ecco
56      - allow user defined cost function contributions
57            CPP: ALLOW_USERCOST_CONTRIBUTION
58            USAGE: compute contributions in cost_usercost_all.F
59      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
60          the two options are complementary.
61    o pkg/smooth
62      - migration from contrib to the main repository
63    
64    checkpoint62b (2010/01/26)
65    o pkg/monitor:
66      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
67        (in case someone forgot to update customized pieces of code)
68    o nonHydrostatic:
69      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
70      - add a simple 2-D experiment (short_surf_wave) to test it.
71    o pkg/icefront:
72       adding the shell of, and the hooks to, a new package that
73       will model melting and freezing of vertical glacier ice fronts
74    o momentum:
75      add diagnostics of momentum tendency from Hydrostatic pressure gradient
76       (without surf.pressure term: would need a 2nd filling since implicit term).
77    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
78      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
79      cannot deal with the former
80    o cleaning:
81      - remove all (except OpenAD) old TLM output from results_ad dirs.
82      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
83      - comment out maskH definition (replaced by maskInC)
84    o pkg/monitor:
85      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
86        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
87    
88    checkpoint62a (2010/01/15)
89    o model/src:
90      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
91    o pkg/diagnostics:
92      - add optional level number diagnostics (i.e., level number to be define
93        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
94      - strictly check for valid parser-code(10) ;
95      - check if adding diag to the list from the right place.
96    o pkg/longstep:
97      - change parameters and fix tracer conservation with rstar/nonlinear free surface
98    o diagnostics:
99     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
100       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
101    o pkg/diagnostics:
102     - Add option for writing vertical integral (sum of selected levels) of an output
103        field instead of writing output field levels. Activate this option on a per
104        output-file basis, by setting the 2nd character of fileflag to 'I'.
105     - Add field-specific information relative to level integral in 3rd postion
106        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
107        vertically (x level-thickness x hFac), "r"=same but without hFac.
108    o do_the_model_io:
109      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
110        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
111        writing pickups and stopping.
112    o pkg/diagnostics (for now, only with mdsio):
113      - write time information to meta file (and modify accordingly rdmds.m) :
114        time-averaged diagnostics output: write starting and ending time of the
115        time-averaging interval ; snap-shot diagnostics output remains unchanged;
116    o pkg/timeave:
117      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
118        always Nr), now assumed to be equal to number of levels of averaged field;
119        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
120    o pkg/sbo:
121      - fix ocean bottom pressure global-average & 2-D time-ave output (was
122        neither initialised nor filled).
123      - add starting iteration in suffix of global-average output file
124        (to avoid over-writing the file after a restart)
125      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
126    o time-average:
127      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
128        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
129         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
130        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
131      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
132      - fix missing accumulation for pkg/opps.
133      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
134         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
135      - fix initialisation of time-ave vars and do only full time-step increment
136        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
137    o pkg/layers:
138      - use standard RW pkg S/R to write the output
139        and remove local write_fld version (which had a problem).
140      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
141      - fix LAYERS_CALC argument list.
142    o pkg/timeave:
143      - store cumulative-time in a simple tiled array (drop the level index)
144      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
145    o pkg/ocn,aim_compon_interf
146      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
147    
148    checkpoint62  (2009/12/23)
149    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
150        (was not previously tested in any other exp.)
151    o pkg/monitor:
152      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
153        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
154        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
155      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
156      - change del2 calculation.
157      - use interior masks (instead of maskH, <- to be remove).
158      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
159    o mask & obcs:
160      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
161      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
162        (called after packages_init_fixed)
163    o pkg/obcs:
164      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
165        Fixes bug in obcs+exf with nSx*nSy.GT.1
166      - fix multi-tile handling in obcs balance code
167    o nonHydrostatic:
168      - Implement AB-3 for non-hydrostatic vertical momentum ;
169        (change ordering of var. stored in pickup file when using NH)
170      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
171      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
172        (in prep. for new NH free surface form).
173    o pkg/obcs:
174      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
175    o model/src:
176      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
177    
178    checkpoint61z (2009/12/01)
179    o nonHydrostatic:
180      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
181        a spurious source of energy in simple baroclinic adjusment test case.
182      Update all non-hydrostatic exp output.
183    o model/src (3-d solver):
184      Change again 3-D solver free-surface RHS term when exactConserv=T:
185        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
186        (which was not the case with previous formulation).
187      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
188      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
189    o nonHydrostatic:
190      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
191        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
192      - change 3-D solver to work with r* (for now, only with linear free-surf.)
193      - add few debug diagnostics (cg3d_x, residual)
194    o model/src:
195      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
196        update output of exp. global_ocean.cs32x15.viscA4
197    o update output of exp. global_ocean.cs32x15.icedyn after removing
198      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
199    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
200    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
201      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
202    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
203      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
204      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
205      to test this code
206    o pkg/cd_code:
207      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
208       C-grid momentum. D-grid velocity used to be stepped forward in time with
209       Adams-Bashforth only on surface pressure term. Tests show that using AB on
210       D-grid coriolis term improves stability (as expected from CD-scheme paper).
211      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
212      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
213       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
214       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
215      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
216           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
217    o pkg/obcs:
218     - fix bug in initialisation (broken since Oct 1rst modification)
219       for useOBCSprescribe without useEXF.
220    
221    checkpoint61y (2009/11/15)
222    o pkg/seaice
223     - change (once again) the discretization for the evp solver: rather than
224       squaring the averages of strain rates, average the squares to give
225       a better approximation to VP behavior (in simple test); this breaks
226       verification experiments that use EVP (lab_sea and lab_sea.hb87)
227        --> update outputs
228    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
229      to improve vectorization of adjoint code on TARGET_NEC_SX
230    o verification/vermix:
231      - change vermix to a more "classical" 1d column with high vertical
232        resolution, seasonal heat flux forcing and constant wind forcing
233        --> update outputs
234    o pkg/seaice
235     - fix diagnostics of principal stress components for EVP
236     - add optional diagnostics of non-linear convergence for LSOR solver
237     - make maximum zeta a runtime parameter
238    o model/src (3-d solver):
239      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
240       which consisted in removing the Surf. Non-Hydrostatic pressure from the
241       whole column and adding it to Eta (inspired from Casualli, 1999):
242       Only affects 3-D solver initial guess and only if using ExactConserv,
243       but tests did show a degradation of solver convergence. For this reason,
244       decide to disable this piece of code.
245       to recover previous version, just set zeroPsNH = exactConserv (line 78).
246      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
247    o pkg/ggl90:
248     - fix previous modif (unfortunatly has not been documented here).
249    o pkg/seaice/autodiff:
250     - add CPP flag to include clipping of zeta in EVP code;
251       although clipping of zeta is not necessary for EVP and not recommended
252       it was done by default, now clipping is disabled by default
253     - modify computation and store zetaC/Z in seaice_evp for TAF
254     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
255     - change seaice_calc_viscosities/strainrates for better
256       vectorization after AD by TAF
257     - rearrange common blocks in SEAICE.h once again for easier dumps of
258       adjoint output, adjust adcommon.h and g_common.h
259     - change flux form of default advection scheme for better vectorization
260       of adjoint code
261     - modify lab_sea/input.lsr to test the flux form of default advection
262       scheme
263    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
264      transition in checkpoint61r)
265    
266    checkpoint61x (2009/10/19)
267    o adjoint: adding two new verification experiments
268      * tutorial_global_biogeo: an online dic sensitivity experiment
269        (work with G. Forget)
270      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
271        (an update of the Dutkiewicz et al., 2006 paper)
272      Both use the same CO2FLUX cost function, but different controls
273      Gradient checks look good, but some recomp. could still be traightened out
274      Should add xx_dic control variable to test at some point
275    o model/src:
276      add run-time parameters to check and/or mask initial Temp & Salt
277    o pkg/ptracers:
278      apply zonal filter (if used) to all passive tracers
279    
280    checkpoint61w (2009/10/12)
281    o adjoint:
282      * update and finish work on adjoint of dic package (G. Forget)
283      * start adjoint of offline package
284      * bug fix for cube-sphere TLM code (active_file_g.F)
285    o tutorial_global_oce_optim:
286      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
287      and add SIZE.h_mpi for MPI testing
288    o pkg autodiff
289     - fix bug in autodiff_restore
290     - make genmake2 remove comments and empty lines from ad_input_code.f in
291       order to reduce file size (new script file remove_comments_sed)
292    o allows to specify vertical profile of vertical viscosity (viscArNr)
293    o pkg autodiff
294      autodiff_ini_model_io: comment out writing of grid information to netcdf
295      files, because at this time the grid fields are a bunch of zeros
296      (this is analogous to ini_mnc_vars.F)
297    o pkg seaice/autodiff:
298     left-over from removing the 3-time-level fields:
299     - small rearrangement of common blocks (SEAICE.h)
300     - fix field declaration in order to get meaningful output in
301       adseaice.*.nc (adcommon.h)
302    o pkg obcs:
303     - go through NH code only if nonHydrostatic=T
304     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
305     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
306       => Update output of experiment seaice_obcs
307     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
308     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
309     - fix restart for useOBCSprescribe + useEXF
310    o pkg ctrl
311     - make obcs as control parameter work also with useSingleCPUio
312     - replace a few sny and snx by Ny and Nx to be consistent with
313       ctrl_set_globfld_x/yz.F
314    o pkg seaice
315     - re-introduce global field frWtrAtm for the case of
316       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
317     - catch the case of an empty filename in seaice_cost_init_fixed.F
318    o pkg ecco:
319     - small bug fixes in the_main_loop
320      . fix order of monitor arguments
321      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
322      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
323        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
324     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
325       imbalance diagnostics for wmean_h/sflux = 0
326     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
327     - catch the case of empty filenames in ecco_cost_init_fixed.F
328       and ecco_readparms.F
329     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
330       to make this statement meaningfull in ecco_cost_weights.F
331    o pkg zonal_filt:
332      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
333      - when using rStar, filter uVel*hFacW instead of uVel
334       (tested without topography: fix a Pb of growing instability with NLFS)
335    o pkg/aim/thsice:
336     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
337      (works as SST restoring)
338    o pkg/thsice:
339     -add specific parameter for salt restoring in slab mixed-layer
340       (by default equal to the temperature restoring)
341    
342    checkpoint61v (2009/09/21)
343    o pkg/kpp:
344     -add double diffusive contributions as a hack, turned off by default
345      for now, and the code can be excluded with a CPP-flag
346      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
347     -add a verification experiments to "vermix" to test this code
348    o pkg/mom_common:
349      Move computation of length scales to mom_init_fixed.F (avoid recomputation
350      at each time-steps*levels).
351    o pkg/layers:
352      Created a new package for computing volume fluxes in temperature or
353      [not yet implemented] density layers, e.g. for calculating residual
354      overturning circulations.
355    o pkg/diagnostics:
356      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
357    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
358    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
359      To avoid mixing type (RS/RL) of input/output array argument,
360      replace single mixed-type array with a pair from each type (RS/RL).
361    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
362      is now implemented for all pkgs (previously only done for the main pickup)
363    
364    checkpoint61u (2009/08/25)
365    o pkg/obcs:
366      - change OB?eta from _RS to _RL and put them into a separate commen block
367      - add code to read OB?eta from a file via obcs_prescribe_read: the code
368        compiles and does not destroy any other experiments, the data is read
369        properly, but the code is not tested in actual applications
370    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
371      create a meaningful unit attribute for the time coordinate variable
372    o pkg/ebm: add plenty of missing "_d 0" ;
373       update results of experiment global_ocean_ebm (fwd + adjoint tests)
374      Notes: several pieces of code only works for (very) specific set up
375       (domain size, lat range, etc ...); should be documented & stop if one
376       of those assumptions is not meet.
377    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
378       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
379          and offline_exf_seaice (seaicetd + adjoint).
380    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
381       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
382        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
383    o few changes to pass when compiling with strick checking of arguments
384       across S/R (allow to find few bugs in S/R calls).
385    o pkg/seaice:
386     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
387       2d-fields, for slightly better performance
388    
389    checkpoint61t (2009/07/22)
390    o pkg/seaice:
391     - remove unused variables in seaice_evp
392     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
393    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
394       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
395       each processor opens a different file (a fix from Matt).
396    o cg2d:
397       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
398       this reduces number of EXCH calls by 2 when using exch2.
399       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
400       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
401    o pkg/thsice:
402       add code for Near Infra-Red albedo (from Jeff)
403       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
404    o ini_model_io:
405       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
406       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
407       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
408    
409    checkpoint61s (2009/06/30)
410    o pkg/exch2 (exch2_rxN_cube*):
411       remove last BARRIER (no need to synchronise after getting data from shared
412       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
413    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
414      and generate new output (for the 2 tests) using default rotationPeriod.
415    o pkg/exch2:
416      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
417        (was already the case with AUTODIFF_EXCH2 defined)
418      - add bj in exch2 arrays and S/R.
419      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
420        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
421    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
422      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
423        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
424      - verification experiment natl_box.longstep
425    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
426      allow different versions of ifort (8 or 9) and different versions
427       of mpi (mpich or mpich2) to be used with the same optfile.
428      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
429       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
430    o pkg/seaice:
431      fix previous modif (3-level field removed) for old-pickup reading
432    
433    checkpoint61r (2009/06/25)
434    o pkg/seaice:
435     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
436      1. introduce fields for time step (N-1)
437      2. do not use levels 2 and 3 anymore (but keep them)
438      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
439         includes changes to pkg/thsice/thsice_get_velocity.F,
440         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
441         pkg/obcs/obcs_apply_uvice.F.
442     - completely remove code for leap-frog time stepping for second order
443       advection
444     - adjusted adjoint accordingly;
445       gradient checks have improved by an order of magnitude!
446    
447    checkpoint61q (2009/06/22)
448    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
449     - the boundary conditions along open boundaries are unclear, because the
450       associated masks are set to zero and are thus treated as closed when
451       applying the slip-boundary conditions.
452     - move initialisation of grid variables from seaice_init_varia to _fixed
453    o adding doc/diags_changes.txt
454    o model/src:
455      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
456       to avoid "_diags" naming if no relation to pkg/diagnostics.
457      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
458       file and only call PLOT_FIELD_XYZ if debugMode=T.
459      remove few PLOT_FIELD_XY calls outside initialisation.
460      remove few unnecessary BARRIER.
461    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
462      of salt_plume package in Southern Ocean
463    o pkg/thsice:
464     - fix hOceMxL in overlap (needed for sea-ice advection);
465       update output of experiment global_ocean.cs32x15.icedyn.
466    o pkg/seaice:
467     - make the (placeholder-)tracer IceAge a little more meaningful
468      by avoiding ridging of age due to convergent ice flow
469     - add diagnostics for surface temperature, atmospheric and oceanic
470       heat flux, and atmospheric and oceanic ice growth
471    
472    checkpoint61p (2009/06/10)
473    o eesupp (global_max & global_sum):
474     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
475     - remove starting & endding barrier (no longer needed)
476    o pkg/mdsio, writelocal:
477       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
478       (remove the STOP): uses shared buffer IO to store data from all threads
479       and then let master-thread write nThreads tiles.
480    o pkg/mdsio (read/write field):
481     - tiled IO done in 1 piece (all levels at a time);
482     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
483     - multi-threaded: allow to read/write local (non-shared) array
484       (was already working with singleCpuIO ; now works also without);
485       => no longer needs barrier call after reading a file (added inside
486       mds_read/write field).
487     - move barrier calls outside gather/scatter_2d to mds_read/write_field
488    o pkg/obcs/exf
489      - exf_getffieldrec.F: add a few ". _d 0" and
490                            add code to catch the case fldperiod = 0.  
491      - obcs_precribe_read.F: change if statements so that they match
492                              the variable type (_RL)
493      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
494        exf_iprec) as part of namelist EXF_NML_01
495    o pkg/mdsio:
496      - read/write tiled (local) files: read/write 1-level tile chunk at a time
497        (instead of segment of length sNx); expected to speed up tiled IO.
498    o pkg/exch2:
499      - take buffer copy from/to array out of S/R exch2_send/recv into new
500        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
501        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
502      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
503      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
504        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
505        including Topology header file (and common blocks).
506      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
507        remove 2nd exch call in exch2_s3d_rx (no longer needed).
508      - document S/R arg. list (+ update some comments)
509    o pkg/seaice:
510      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
511        temperature and humidity over sea ice based on climatological values.
512      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
513        of LSR (this change is expected to change the results slightly because now
514        it uses slightly difference moduli from the second last LSR solution, but
515        that is more consistent with the stress computations; this part of the code
516        is not tested in the verification experiments)
517      - fix diagnostics for flux of ice in case of B-grid
518      - turn strain rates eij and press into global fields within global
519        common block in SEAICE.h for more straighforward diagnostics
520      - fix diagnostics for principal stress components, press, zeta, eta
521        to give something meaning full
522    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
523      new output (all 4 tests) using default rotationPeriod.
524    o pkg KPP:
525      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
526      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
527        and normal grid from 1 to Nr)
528    o Fix computations of L4rdt in mom_calc_visc.F
529    o eesupp:
530      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
531      should be called before a "stop" if we know that all process are going
532      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
533    
534    checkpoint61o (2009/05/26)
535    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
536    o model/src/ini_curvilinear_grid.F:
537       compute angleSin/CosC when they are not read from a file
538    o pkg/seaice:
539       add pseudo time stepping for LSOR
540    o pkg/exch2:
541       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
542    o pkg/seaice:
543       Adding separate sea ice albedo, drag coefficients, and HO in Southern
544       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
545    o SingleCpuIO:
546       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
547    o pkg/seaice:
548       put exchanged variable in (local) common block for MPI+Multi-Threads
549       to work (necessary with exch1, and for now with exch2 too).
550    o verification: to get more experiments tested with mpi, mth and mpi+mth,
551      change tiling of:
552       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
553       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
554      update output of exp:
555       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
556       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
557      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
558                       (note: output.txt generated on faulks using only 1 tile)
559    o eesupp & mdsio (SingleCpuIO):
560     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
561       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
562       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
563     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
564     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
565       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
566    o pkg/exch2:
567     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
568       read parameter file "data.exch2" if it exists; otherwise try default regular
569       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
570     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
571       with new code (not to be used, just as a backup solution).
572     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
573       in utils/exch2/input.
574    
575    checkpoint61n (2009/05/12)
576    o eesupp & mdsio (SingleCpuIO):
577      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
578        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
579        receive real*4 array (instead of real*8) to read/write 32.bit files.
580        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
581         and remove new mapping S/R)
582    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
583      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
584        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
585        when using exch2. Add S/R to map global io-buffer to global model array.
586      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
587    
588    checkpoint61m (2009/04/29)
589    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
590      and add 3 other S/R for other types (R4,R8,RS).
591      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
592    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
593     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
594     - reduce number of macro definitions (keep only those which are used);
595       can always call directly the corrresponding S/R if needed.
596     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
597       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
598     Fixed wrong type of arg in:
599       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
600       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
601     To fix: global_sum of var in common block is wrong (multi-threaded) in:
602       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
603     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
604    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
605      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
606    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
607    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
608      edges are closed (zero depth); might happen with "blank tiles";
609      for now, disabled if using OBCS.
610    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
611      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
612    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
613      to reduce length of 1.D array print in STDOUT.
614    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
615      + use 48 tiles (16x8): this will allow to test "blank tiles".
616    o start to test MPI + multi-threaded (change testreport to skip tests
617      where number of tiles do not match).
618    o genmake2: add option "-omp" to turn on Open-MP ;
619      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
620    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
621      and keep the original tile numbering. Note: compatible with old
622      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
623    
624    checkpoint61l (2009/04/07)
625    o Overlaps had been forgotten in calculating ijk keys : fixed
626    o fix cyrus makedepend for gcc 4.4
627    o experiment fizhi-cs-aqualev20:
628      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
629      and generate new output. Note: new output is much closer to the old
630      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
631      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
632    o pkg/fizhi:
633     - change to avoid indices going deliberately over array-bounds
634     - remove unnecessary MPI stuff
635     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
636     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
637       does not go over array-bounds and therefore returns reliable output.
638     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
639       this S/R has 4 output arguments, which are used inside "get_alarm";
640       when it is called with the same variable "ndum" in place of several
641       output arguments, this produces weird side effect inside "get_alarm"
642      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
643       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
644       address) and produces error.
645    o tools/gemake2: (March 27-29 2009)
646      with option "-mpi": link *_mpi files from "MODS" dir (this is what
647      testreport does).
648    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
649    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
650       update lab_sea.lsr & lab_sea.salt_plume results
651    o pkg/seaice:
652      Major overhaul of the LSOR solver: change discretization from original
653      finite differences to finite volume. The old routine is still in the
654      file seaice_lsr.F and can be turned on with the CPP-flag
655      SEAICE_OLD_AND_BAD_DISCRETIZATION
656      Along with this change, the discretization of the strain rates is changed.
657      The same flag turns on the old discretization in seaice_calc_strainrates.F
658      All verification experiments with seaice are affected (except for
659      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
660      results by setting the above flag.
661      Further changes involve changes in defaults:
662      - ALLOW_FLOODING is defined and turned on by default
663      - SEAICEadvSnow = .true. is now the default
664      - SEAICEadvSalt = .true. is now the default
665      - SEAICEadvAge  = .true. is now the default
666      - SEAICE_clipVelocities  = .false. is now the default
667                                         (as per J. Zhang's recommendation)
668      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
669        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
670      - seaice_growth: replace computation of UG by a simple copy from wspeed
671    
672    checkpoint61k (2009/03/18)
673    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
674      seaice_lsr: fixed a few metric terms,
675                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
676                  add more debugging diagnostics
677      seaice_evp: removed superfluous many metric terms of FV discretization
678                  of stress divergence
679                  affects lab_sea, lab_sea.hb87
680      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
681                  of stress divergence for non-evp solver
682                  (this part is not tested anywhere)
683      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
684                  they were effectively only half slip
685                  affects lab_sea.hb87
686      updated all relevant verification experiments (except lab_sea//output_adm.txt
687        which was left over, but fails at level 7 & 6)
688    
689    checkpoint61j (2009/03/17)
690    o pkg/seaice: turn a few hard wired parameters into run time parameters
691    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
692      time in seconds as promised by the usints in seaice_monitor and exf_monitor
693    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
694      that are not cubed-sphere grids
695    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
696    o pkg/ctrl:
697      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
698    o non-hydrostatic (calc_gw.F):
699      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
700      update output of exp. global_ocean.cs32x15.viscA4
701    o remove backward compatibility for thetaMin,phiMin
702      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
703    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
704      interpolated wind field not only for curvilineargrid=.true., but also
705      for a rotated grid (rotateGrid=.true.)
706    o pkg/exf: add capability to bypass interpolation for runoff
707      by setting yet another CPP-flag
708    o eesupp/src, B-grid exchange:
709      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
710    o autodiff
711      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
712      allows to switch to single-prec common blocks;
713      corresponding switch occurs in tamc.h, integer isbyte
714      TAF store directivs "byte" and "kind" seem equivalent;
715      Most tamc.h have been updated correspondingly.
716    
717    checkpoint61i (2009/02/13)
718    o autodiff:
719      fix autodiff_sore/_restore indices for obcs
720      (spotted by I. Hoteit, M. Mazloff)
721    o pkg/autodiff, pkg/ctrl:
722      Add flag to reduce all tapelev I/O to single-prec.
723      In data.ctrl set
724        doSinglePrecTapelev = .TRUE.
725    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
726      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
727    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
728      real fresh water flux (not yet)
729    o pkg/mdsio & rw:
730     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
731     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
732    o pkg/flt:
733     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
734       init_fixed & ini_varia.
735     - clean-up & simplify linear interpolation S/R:
736       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
737     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
738     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
739     - add vert. coordinate & horiz. indices to output files.
740     - change vertical position in initial condition, from index to depth [m].
741     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
742       (easier to get to a curvilinear grid) ; delX,delY no longer used.
743    o pkg/ggl90: a few modifications:
744     - fix bottom boundary condition, and interpolation of KappaE
745       near top and bottom
746     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
747     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
748     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
749    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
750      (maintain temporary backward compatibility, until next checkpoint)
751    
752    checkpoint61h (2009/01/27)
753    o pkg/diagnostics with "periodic averaging diagnostics":
754      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
755    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
756    o pkg/obcs: fix loop ranges for balancing code
757    o pkg/flt:
758     - improve criteria for finding which tile owns a float.
759     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
760    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
761      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
762      with ocean biogeo)
763    o pkg/flt:
764     - do some cleaning and fix the restart ;
765     - add output.txt in flt_example/results to get this pkg tested.
766    o genmake2: add an EXTENDED_SRC option and flag.
767       for now, cannot be turned on on command line (only through genmake_local)
768    o pkg/mdsio: read/write vector:
769     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
770     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
771       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
772     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
773      (drop to 4 digits matching for grad). But this test does not look very
774      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
775    
776    checkpoint61g (2008/12/29)
777    o pkg/flt:
778      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
779       + make OPTIONS file more standard.
780      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
781      - fix _BYTESWAPIO CPP-Flag
782      - standard reading of file-parameter "data.flt"
783      - fix argument list of S/R FLT_RESTART
784      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
785    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
786    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
787      a still unfixed compiler/optimization bug
788    
789    checkpoint61f (2008/11/21)
790    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
791      update results of global_ocean.cs32x15.icedyn test.
792    o move getcon.F from model/src to pkg/fizhi.
793    o pkg/exf: add parameter for extrapolation of temp up to the surface
794       and option to prevent negative evap (in bulk_largeyeager04 only).
795    o Prather Advection scheme: fix tracer conservation for divergent flow
796      (e.g., when using NonLin Free-Surface).
797    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
798    o gmredi (Visbeck-variable-K):
799     - add more parameters to Visbeck-variable-K.
800     - use a 5 points average for dSigmaR in Visbeck-K calculation
801       (more "homogenous": same stencil and same weights as in dSigmaH)
802     - update output of ideal_2D_oce experiment.
803    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
804      (#undef REAL4_IS_SLOW)
805     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
806       coordinate variable
807     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
808       (surface forcing fields), removes some of the functionality
809     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
810     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
811       probably not all: copy _RS surface flux fields to RL field before
812       calling DIAGNOSTICS_FILL
813     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
814       real*4 (CALL EXCH_*_RS) versions.
815     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
816       (generate new output).
817    
818    checkpoint61e (2008/10/23)
819    o gmredi (Visbeck-variable-K):
820      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
821      - change computation of Visbeck-K where Slope > Smax :        
822        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
823        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
824    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
825      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
826    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
827    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
828      does not become too large (to avoid precision problems in implicit-diffusion
829      solver); update ideal_2D_oce output.
830    o pkg ggl90:
831      - in ggl90_cal.F: compute only one set of visc/diff, used to
832        step forward TKE/T/S/momentum
833      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
834        have Prandlt =1)
835    o gmredi (fm07):
836      - add lower limit on Transition layer thickness + lower limit on 1/lambda
837      - allow to set few more params from data.gmredi
838    o pkg ggl90:
839          - add missing sqrt(2) factor in computation of mixing length
840            scale in ggl90_calc.F
841            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
842    
843    checkpoint61d (2008/09/25)
844    o adjoint modifs
845      - adapt to new field rhoInSitu
846      - allow to revert from StoreDynVars2D, StoreDynVars3D
847        to individual fields
848        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
849    o store 3-D (in-situ) density in commom block (DYNVARS.h)
850     - save 1 rho computation.
851     - no longer modify T & S inland when using down_slope pkg.
852    o gad_som : allow to switch to SOM advection for T & S without corresponding
853      pickup files (using new S/R: MDS_CHECK4FILE).
854    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
855      (for useSingleCpuIO to work in multi-threaded)
856    o pkg/shelfice:
857     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
858       with SHELFICEtopoFile in data.shelfice
859     - move code for reading ice shelf topography and modifying hFacC into separate
860       subroutines of the shelfice package
861     - separate initialisation of "fixed" and "variable" variables
862     - kTopC is not (yet) replaced by kSurfC, although this is possible
863    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
864    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
865      and rename:
866      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
867      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
868    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
869    
870    checkpoint61c (2008/08/30)
871    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
872      to add mass source/sink of fluid in the interior (3-D generalisation
873      of oceanic real-fresh water flux).
874    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
875    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
876    o new pkg: down_slope
877      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
878      - presently, modify T & S inland (dwnslp_calc_rho.F).
879        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
880      - implementation for ocean in P-coords not tested.
881      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
882    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
883      (to facilitate conversion of oceanic pkg to p-coordinate).
884    o change FIND_RHO to FIND_RHO_2D :
885      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
886    o new pkg: cheapaml
887    
888    checkpoint61b (2008/08/05)
889    o exch2:
890      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
891      - no longer depend on the order sequence (N,S,E,W).
892      - 3rd exchange no longer needed (tested with 24 tiles).
893      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
894      - exch_UV_A-grid readily available (but not yet tested).
895      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
896      (both are no longer needed) in exch_uv: no effect in forward run; but
897       get truncation error differences with adjoint exch.
898    o exch2:
899     - change index-bounds storage (moved from target to local tile,
900       more intuitive this way) ; rename/remove some variables.
901     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
902    
903    checkpoint61a (2008/07/29)
904    o exch2/matlab-topology-generator:
905      fix bug in index bounds for N-S internal exchange (hard to tell if this
906      had any effect on the solution).
907    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
908      is exceeded
909    o testreport: modify syntax of awk, so that it works also with
910      awk, and not only with nawk and gawk
911    
912    checkpoint61 (2008/06/24)
913    o autodiff
914      Change default for TAF usage by removing argument '-nonew_arg'
915      This changes TAF subroutine argument list (ordering of active var.)
916      Omission of this flag leads to incompatibility w.r.t. TAMC
917      To restore TAMC-compatibility, need following modifs:
918      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
919      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
920      Tested TAF version is 1.9.22
921      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
922    
923    checkpoint60 (2008/06/19)
924    --->>> This is the last checkpoint for which generating the adjoint
925    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
926    --->>> by default.
927    --->>> Future checkpoints will ommit this flag by default.
928    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
929    o pkg/grdchk: Add gradient check to etan0 perturbations.
930    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
931    o pkg/autodiff: more flexibility in zeroadj.
932      model/src: modifying do_oceanic_phys.F accordingly.
933    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
934    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
935      special setup of gmredi for which the adjoint is stable
936      enough for parameter optimization.
937    o bridging the gap between eddy stress and GM.
938      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
939          along with a change in CPP option (now ALLOW_EDDYPSI).
940      -> when using GM w/ GM_AdvForm:
941          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
942          is applied either in the tracer Eq. or in momentum Eq.
943          depending on data.gmredi (intro. GM_InMomAsStress).
944      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
945      The key modifications are in model/src/taueddy_external_forcing.F
946      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
947    
948    checkpoint59r (2008/05/29)
949    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
950      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
951      fix option to read coriolis(@ cell-corner) from files with CS-grid.
952    o pkg/mnc: add some attributes to standard 1D-coordinate variables
953    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
954      mass points, when using mnc for output
955      - add runtime parameter (missing_value, missing_value_int) to override
956        default (which is the value of getcon('UNDEF'))
957    o pkg/mnc: prepare mnc for the actual use of missing values with the
958      diagnostics package: small fix in mnc_cw_readwrite.template and more
959      initialisation of never used fields
960      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
961      versions
962    o pkg/thsice/thsice_ini_vars.F added default initial values so that
963      thermodynamics sea ice solver does not blow up when some initial fields
964      are missing.
965    o move from external_forcing_surf.F to ini_forcing.F
966      the p-coord. hack consisting in using pLoad to set phi0surf ;
967      update output of tutorial_global_oce_in_p (affected @ truncation level).
968    o Freshen up a bit hs94.1x64x5, notably:
969      remove rotationPeriod and tRef=5*0. (adjoint only), and add
970      exactConserv=.TRUE.
971    o pkg/generic_advdiff:
972      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
973      applies to files where Temperature & Salinity 2nd Order moments are used.
974    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
975      this uses a dynamically allocated internal state data structure
976      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
977      and requires a fortran 90 compiler
978    
979    checkpoint59q (2008/05/06)
980    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
981       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
982    o Refresh tutorial_global_oce_biogeo, notably:
983      - change bathymetry (put back seamounts in ACC, use hFacs)
984      - change EOS (POLY3 --> JMD95Z)
985      - use Bryan-Lewis vertical diffusivity
986      - use multidimensional advection
987      - remove old virtual virtual in dic pkg, now done through ptracer pkg
988      - change a couple of parameters in dic pkg
989    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
990    o pkg/obcs: change default to OBCSfixTopo = .true.,
991      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
992      - replace "debugMode" with "debugLevel .GE. debLevB"
993    o implementation of TAF directives for gchem,cfc,dic
994    o remove "exp5" (replaced by tutorial_deep_convection).
995    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
996      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
997      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
998      --> changes results in exp4, seaice_obcs
999    o tutorial_deep_convection :
1000      update the set-up and increase resolution and domain size ; start
1001      from pseudo initial conditions = output at t=120mn in order to see
1002      something happening when running testreport.
1003    o pkg/seaice: add os7mp as an advection scheme
1004                  add check for advection schemes
1005                  add a flag for restoring T and S underneath sea ice
1006    o pkg/my82: add netcdf-support and diagnostics
1007    o thsice pkg:
1008      - Now hsMax limits snow height by turning it into ice following
1009        flooding scheme (and now conserving energy)
1010      - Slight rewriting of the formula in thsice_calc_thick.F
1011      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
1012      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
1013    
1014    checkpoint59p (2008/04/10)
1015    o gchem / dic / cfc :
1016      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
1017      - add new parameter files: "data.dic" & "data.cfc" ;
1018      - various re-arrangement in initialisation & header file ;
1019      - fix tutorial_global_oce_biogeo for multi-threaded test.
1020    o pkg/dic: test for "pickup_dic" file when restarting ;
1021      if no pickup-file, can restart with a re-initialised pH (same as it did
1022      before) providing pickupStrictlyMatch is set to False.
1023    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
1024      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
1025    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
1026      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
1027    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
1028     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
1029       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
1030    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
1031       scheme to use for vorticty-term ;
1032     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
1033       (with default selectVortScheme, return to original discretisation)
1034     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
1035    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
1036    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
1037      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
1038      also fix diagnostics VISCAHW & VISCA4W.
1039    
1040    checkpoint59o (2008/03/07)
1041    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
1042    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
1043      move a few statemens out the main loop into separate loops
1044    o pkg/shelfice:
1045      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
1046        (kg/m^2/s), does not break tests, because in verification/isomip,
1047        rhoConstFresh=rhoConst (by accident)
1048      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
1049      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
1050        new file model/src/seawater.F, so that they are available for all pkgs.
1051      - convert potential temperature into in-situ temperature. This changes the
1052        isomip tests => update tests
1053    o add a flag writePickupAtEnd (default=true) to be able to suppress
1054      writing a pickup at the last timestep
1055    o tools/mpack-1.6 :
1056      - disable automake (not working) and autoconf (not needed).
1057      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
1058        also cleaner with much less compilation warnings.
1059    o pkg/profiles:
1060      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
1061      (for "less than 32 characters name" compiler requirement)
1062    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
1063      conditions that have a different sampling frequency than S/T/U/V obcs
1064    o pkg/diagnostics (stats-diags):
1065      - fix global Min/Max in case 1 processor get only empty tiles
1066    o genmake2: replace (4 times)
1067         make genmake_tc_1.o >> genmake_warnings 2>&1
1068      with
1069         COMM="$CC $CFLAGS -c genmake_tc_1.c"
1070         echo $COMM >> genmake_warnings
1071         $COMM >> genmake_warnings 2>&1
1072      to make genmake2 always see the value of CC as specified in the optfile.
1073    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
1074      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
1075      - modify verification advect_cs test to test SOM-advection on CS-grid.
1076    o pkg/ctrl:
1077      - Rewrite of ctrl_map_ini_ecco.F,
1078        introducing a generic routine (ctrl_map_ini_gen.F).
1079      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
1080    
1081    checkpoint59n (2008/02/09)
1082    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
1083      number in dedicate array "hdiag":
1084      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
1085        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
1086      - many small changes (integer format) for large number of diagnostics
1087      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
1088        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
1089    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
1090      usingSphericalGrid, this allows to define the rotated grid coordinates
1091      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
1092      geographical coordinates according to the inverse of the rotation defined
1093      by the Euler angles, so that Coriolis parameter and online-interpolation by
1094      exf works with the geographical coordinates on XC/YC/XG/YG.
1095      Naturally, this feature does not work with all packages, so some
1096      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
1097      profiles), because there the coordinates are assumed to be regular
1098      spherical grid coordinates.
1099    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
1100      - introduce isopycnal diffusion coefficient control.
1101    o tools/adjoint_options:
1102      - additional control vector components.
1103    o pkg/mnc: have mnc create marginally meaning full coordinate variables
1104      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
1105    o pkg/mypackage:
1106      - add example of read/write pickup for state-var ;
1107      - add entry points to the main code for state-vars diags & write-pickup.
1108    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
1109      transitions for useExfYearlyFields
1110      - add new subroutine that determines the file to read from for
1111        use*YearlyFields = .TRUE. and .FALSE.
1112      - add a verification experiment to global_with_exf that tests
1113        useExfYearlyFields with USE_EXF_INTERPOLATION defined
1114    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
1115      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
1116      subroutines (which could be generated from a template, because they are
1117      almost identical), for now they are included in obcs_prescribe_read.F for
1118      simplicity
1119    o pkg/exf:
1120      - add a little more diagnostic to exf_interp_read (in analogy to
1121        mds_read_field, can be turned off with debugLevel < debugLevA=1)
1122      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
1123        ugly but fast by unrolling short inner loops, inserting a unroll=8
1124        directive in routine lagran, and splitting a loop and making do while the
1125        outermost loop (the latter requires the intoduction of index arrays)
1126    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
1127    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
1128      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
1129    o verification/seaice_obcs: updated for restart test and latest options
1130    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
1131      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
1132      for now this is only available for the C-grid code and also within
1133      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
1134    
1135    checkpoint59m (2008/01/14)
1136    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
1137      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
1138    o gad_som : fix flux output (& diagnostics) to have same units as other  
1139      advection scheme fluxes (was previously multiplied by deltaT).  
1140    o added verification/seaice_obcs both to test seaice open boundaries
1141      and to provide an example matlab scrpt for generating them
1142    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
1143    o pkg/salt_plume: clean up salt_plume_frac.F to
1144      remove redundancy in PlumeMethod 1 and 4
1145    o pkg/kpp: added saltplume diagnostics
1146    o pkg/obcs and pkg/seaice:
1147      - do not set uice and vice to zero when OB*icefile are unspecified
1148      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
1149      - moved seaice tracer obcs after call to seaice_growth
1150    o pkg/salt_plume: added various options for salt plume depth
1151      criterion and for vertical distribution of the salt
1152    
1153    checkpoint59l (2007/12/18)
1154    o pkg/ptracers: new version of ptracers pickup:
1155      read meta file and write only fields which are needed to restart.
1156      ( same logic as main pickup file ; also using pickupStrictlyMatch )
1157    o pkg/seaice:
1158      - add timescale for melting due to warm mixed layer as a means of
1159        setting SEAICE_availHeatFrac more conveniently
1160      - add a CPP-flag/runtime parameter check for flooding algorithm
1161      - reformulated availHeat in seaice_growth.F to be independent of AREA
1162    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
1163      unit changes
1164    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
1165    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
1166      SX vector computer.
1167    o pkg/seaice:
1168      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
1169        seaice forcing fields can now be read only through pkg/exf
1170      - removed some unused halos
1171    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
1172    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
1173      or U/VICE from U/VWIND before computing U/VSTRESS
1174    
1175    checkpoint59k (2007/11/30)
1176    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
1177      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
1178    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
1179      all experiments pass when compile with un-initialised var. checking option.
1180    o added pkg/salt_plume
1181    o script to test restart (for now, in MITgcm_contrib/jmc_script)
1182    o pkg/seaice: new read/write pickup version.
1183      read meta file and write only fields which are needed to restart.
1184      ( same logic as main pickup file ; also using pickupStrictlyMatch )
1185    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
1186    o lab_sea.hb87: modify the domain & update output.hb87.txt :
1187      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
1188      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
1189      process. Fixed here by closing the domain at the Northern boundary.
1190    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
1191    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
1192      a set of consecutive levels in/from a 3-D array.
1193    o pkg/ptracers:
1194      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
1195      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
1196    
1197    checkpoint59j (2007/11/09)
1198    o in pkgs: dic, obcs, offline, rbcs:
1199      standard way to compute coeff. for time interpolation between 2 time reccords
1200      which retains full precision (& make results less dependent on compiler).
1201      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
1202    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
1203      packages instead of reading ice cover and wind speed separately
1204    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
1205     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
1206      to allow to compile customized code before the update)
1207    o cleaning-up:
1208      - fix CPP instruction syntax in pkg/obcs
1209      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
1210        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
1211      - fix some threads issue in IO parts.
1212    o pkg/dic:
1213      - add tons of "_d 0" (--> much better testreports !)
1214       and then update outputs of tutorial_global_oce_biogeo
1215    o pkg/mom_fluxform:
1216      add a special version of momentum advection intended to conserve momentum
1217      next to a bathymetry step or a coastline edge. (default = off = #undef)
1218    o new read/write pickup version:
1219      - for now, only implemented for main (mdsio) pickup file.
1220      - write out only what is needed to restart; merge pickup_nh , pickup_ph
1221        and main pickup together.
1222      - read meta file; read only what is needed to restart; stop if a field
1223        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
1224        if it make sense (even if the restart is not perfect).
1225      - if no meta file, assume that pickup to read corresponds exactly to
1226        a pickup that would currently be written.
1227      - read pickup written in the old format (until checkpoint59i) if it
1228        recognizes an old meta file (no field-list).
1229      - add a meta file in exp. which starts from a pickup: 2 cases:
1230        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
1231         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
1232        b) a meta file describing the content of the associated pickup file
1233         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
1234    o pkg/mdsio & pkg/rw:
1235      - new routine to read a meta file ; new set of routine to read
1236        Multiple-fields file (with meta file).
1237    o added open boundary conditions capability for seaice
1238        HSNOW, HSALT, UICE, and VICE
1239    
1240    checkpoint59i (2007/10/21)
1241    o adjoint:
1242      * fix multiDimAdvection adjoint
1243        (partial recomputation problem by TAF for fVerT(:,:,kDown)
1244        and comlev1 size definition (maxpass vs. max. number of tracers)
1245      * verification/global_ocean.90x45x15 adjoint now tests
1246        NLFS and multiDimAdvection using DST3 (=30)
1247      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
1248    o pkg/kpp: add "_d 0" to real constant (if missing);
1249      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
1250      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
1251    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
1252      for internal parameters related to restart process (formerly from PARAMS.h)
1253      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
1254    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
1255      as argument. (only atm2d & obcs write_pickup have not yet been updated)
1256    o pkg/monitor:
1257      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
1258      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
1259      - account for deep Atmosphere factor and density factor (anelastic)
1260    o added open boundary conditions capability for seaice HEFF and AREA
1261    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
1262      thermodynamics
1263      - requires a little reorganization, which affects the testreport results
1264        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
1265        so that now the conservative form is tested
1266      - add a few comments
1267    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
1268    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
1269    o add new diagnostics to seaice: advective, diffusive fluxes (only for
1270      multidim-advection, for scheme 2 they are not filled) and transports,
1271      thermodynamic growth rates
1272    o change units of EmPmR (inside the code, + within coupling interface)
1273      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
1274      Affects results @ truncation level (cg2d match) and update output of
1275       experiments: lab_sea(6), global_ocean.90x40x15(10),
1276      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
1277      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
1278      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
1279      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
1280    
1281    checkpoint59h (2007/09/29)
1282    o pkg/exf:
1283      - improve vectorization by moving if-statement out of loops in
1284        exf_mapfields, exf_radiation
1285      - exf_bulkformulae.F: introduce 2D fields and vectorize code
1286    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
1287    o testreport:
1288      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
1289        monitor & update offline_exf_seaice exp. output.
1290      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
1291    o pkg/seaice:
1292      - bug fix in the evp solver: boundary conditions were affected be
1293        masking of zMax/zMin (changes results)
1294      - minor bug fix in boundary conditions in seaice_calc_strainrates
1295        (changes results for no_slip)
1296      - seaice_lsr.F: make interpolation of eta dependent on boundaries
1297      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
1298      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
1299        stress formulation and no-slip boundary conditions
1300    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
1301      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
1302    o pkg/seaice: a first HSALT time stepping equation has been checked in
1303    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
1304      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
1305      without requiring DO-IF statements
1306    o pkg/thsice:
1307      use continuous power-law function for partition of energy between lateral
1308      melting/freezing and thinning/thickening ; old code using step function
1309      still available with #undef THSICE_FRACEN_POWERLAW
1310      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
1311    o testreport: change AD testing : check against results/output_adm.txt
1312      using same scripts as for forward test.
1313    
1314    checkpoint59g (2007/09/17)
1315    o adjoint testing: in preparation for changing testreport:
1316      - output format: cost and grad written on separated lines
1317      - ad output results in directory "results" (instead of "results_ad")
1318    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
1319    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
1320    o pkg/ecco: allow user defined cost function contributions
1321    o testreport:
1322      Allow to choose (per experiment) the list of tested output variables
1323       and the main variable (used to issue a pass/FAIL ) ;
1324      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
1325      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
1326      Also modify printing of summary:
1327       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
1328       b) echo the list of tested variables in the individual summary.txt of
1329          each experiment.
1330    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
1331      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
1332      (but still depend on the tile decompostion of the domain).
1333    o pkg/seaice: change a discretization detail to make the B-grid code
1334      "more symmetric". This change is likely to remove all "ridges/leads" that
1335      where quasi-aligned with the grid in B-grid solutions. It may also be
1336      the solution to the stress coupling issues with the B-grid.
1337    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1338      remove .cvsignore from input dir. (since testreport no longer run here).
1339    o pkg/thsice:
1340     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1341     - fix reshaping of sea-ice just after advection:
1342       melt all the ice only if ice-volume is too small.
1343     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1344       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1345     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1346    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1347      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1348    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1349      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1350      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1351      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1352      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1353      -> update output.txt
1354    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1355     this affects truncation error: -> update output.txt of exp:
1356      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1357      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1358    
1359    checkpoint59f (2007/08/21)
1360    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1361    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1362      a bounded range (in forward mode)
1363    o pkg/ecco, ctrl, autodiff and mom_common:
1364     internal parameter controls, completements of implementations
1365    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1366    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1367      (not seem any difference in testing results).
1368    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1369       at face corners.
1370    o pkg/generic_advdiff:
1371     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1372      loop range indices for computing vertical advection tendency
1373      and do the calculation in the interior only (no overlap) ;
1374      for now, only implemented for SOM advection (to save CPU time).
1375     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1376    o exch2 adjoint
1377      First set of changes:
1378      - add exch2 hand-written adjoint templates
1379      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1380        This will require cleanup in pkg/autodiff/*.F
1381        (changed routines currently kept separate in verif. code/)
1382      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1383        that used to hide exch2 or cubed-sphere specific code
1384        (commented via 'cph-exch2')
1385    o pkg/seaice
1386      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1387    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1388       output of global_ocean.cs32x15.thsice .
1389    
1390    checkpoint59e (2007/07/26)
1391    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1392      for B-grid vector (not yet tested) and C-grid vector (<- only used
1393      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1394    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1395      (#ifdef ALLOW_SALT_PLUME)
1396    o gather_2d/scatter_2d: removed halo regions
1397    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1398      scheme and the corresponding test case (under front_relax dir). For now,
1399      only available with Skew-flux form and not yet tested in realistic set-up.
1400      adjoint: store directives updated, but gradient checks deteriorated,
1401      so maybe GM/Redi adjoint is now broken.
1402    o seaice adjoint
1403      * add AREA, HEFF, HSNOW as control variable
1404        (should not change lab_sea results)
1405      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1406    o pkg/seaice:
1407      * added computation of saltFlux in seaice_growth;
1408        For time being, sea ice salinity is assumed constant
1409        contribution of snow flooding to freshening of sea ice is neglected.
1410        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1411        defaults to 0.0 in order to maintain backward compatibility.
1412        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1413      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1414      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1415        heat content used to melt or grow ice
1416      * commented out cap of HICE: it helps keep ice thinner
1417      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1418      * applied OBCS T/S mask to HEFFM sea ice mask
1419    
1420    checkpoint59d (2007/06/21)
1421    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1422     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1423     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1424    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1425     and change default value of parameter "GM_Small_Number";
1426     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1427       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1428       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1429    o pkg/ecco: cost function when applying pkg/smooth to controls
1430    o pkg/ctrl: add forcingPrecond run time parameter
1431    o pkg/seaice:
1432     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1433     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1434       changes verification/lab_sea
1435     - rearrange implicit part of u-equation in LSR solver to make it easier to
1436       read, understand, and debug. This causes changes at the truncation level.
1437     - fix (serious) bug in the boundary conditions (sign error in the implicit
1438       part) of the LSR solver. Changes all LSR results.
1439     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1440       is initilized with small values - does not change lab_sea results.
1441     - added HsnowFile initialization capability
1442    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1443     initialization of pkg/smooth and application to control vector
1444    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1445    o dependencies: pkg/profiles requires pkg/cal
1446    o pkg/profiles:
1447     - added option ALLOW_PROFILES_GENERICGRID
1448         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1449         that interpolation information (grid points and coefficients) is provided
1450         within the netcdf input files.
1451         -> sample matlab scripts can be found in MITgcm_contrib/gael
1452         that allow you to prepare netcdf input files.
1453     - also modified: cleaner include statements, cleaner error print statements,
1454       cleaner stops when error, and more tests of the netcdf input files consistency.
1455    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1456    o pkg/seaice:
1457     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1458       requires a new routine: seaice_diagnostics_fill.F
1459     - make sure that seaice does not move if not forced (pressure replacement
1460       method, Hibler and Ip, 1995), changes results
1461     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1462     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1463       It is turned off by default (=-1.), because it changes the results.
1464     - make it possible to read AREA from a file, too.
1465    
1466    checkpoint59c (2007/06/04)
1467    o add S/R and diagnostics for oceanic mixed-layer depth
1468    o move GMRedi call after all vertical mixing schemes (including KPP)
1469    o pkg/thsice:
1470     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1471      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1472    o pkg/obcs:
1473     - bug fix for balance code
1474    o pkg/seaice:
1475      - allow values of SEAICE_elasticParm > 1
1476      - add new parameter SEAICE_evpTauRelax as an alternative
1477        to SEAICE_elasticParm
1478      - make lsr boundary conditions free slip (by default), changes result
1479      - add code for no slip boundary conditions for lsr
1480      - set minimum of zeta to zero (and not 4e8) (changes results)
1481      - add a cap on AREA after advecting AREA if seaice_growth is not called
1482    o change calculation of Visbeck K:
1483      - no longer depend on tapering scheme; instead, compute slope (limited
1484        by GM_maxSlope). this is equivalent to what was comuted before with
1485        clipping or linear tappering.
1486      - fix vertical averaging (wrong by 1/2 level)
1487      - leave the old version (but will not be maintained) within
1488        #ifdef OLD_VISBECK_CALC / #endif
1489      - update output of exp. ideal_2D_oce
1490    o change error catch in calc_r_star to improve vectorization
1491    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1492      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1493    o adjoint:
1494      Re-organized adjoint checkpointing according to Matt Mazloff
1495      (but with modifs/completions/cleanups)
1496      Storing is now bundled into large arrays to optimized I/O
1497      (and second step in cleanup of the_main_loop)
1498    
1499    checkpoint59b (2007/05/16)
1500    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1501      - export/import (between ocean & coupler) fields needed for ocean DIC.
1502    o pkg/seaice:
1503      - get rid of three more exchanges seaice_calc_viscosities (required
1504        different loop boundaries in seaice_lsr and seaice_ocean_stress)
1505      - bug fix in seaice_ocean_stress (update of lab_sea required)
1506      - reduce loop boundaries to necessary minimum also in seaice_evp
1507      - go back to the old way of computing deltaC/Z as the adjoint likes that
1508        better
1509    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
1510      passive tracer to an Age Tracer) + update output.txt
1511    o pkg/exf:
1512      - implement A-grid / C-grid selection for wind-stress input files.
1513      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
1514      for now, in exf_bulk_largeyeager04.F only :
1515      - change implementation for case where windspeed + 2. components wind-stress
1516        are read-in. AND use rhoConstFresh to convert evap.
1517    o pkg/seaice:
1518      - use correct EXCH_UV for wind-forcing (on A-grid).
1519      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
1520        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1521    o pkg/exf:
1522      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1523      EXF_INTERPOLATION:
1524      - merge global_with_exf/code version of exf_interp_read.F
1525        to the main code ;
1526      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1527        reading the file ; Important: This options needs to be defined to recover
1528        previous code.
1529        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1530      - no longer loose real*8 precision along the way when using exf_iprec=64.
1531    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1532      - change discretisation of evp-solver in order to avoid another exchange
1533        (changes lab_sea) and clean up a little
1534      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1535        help the adjoint (this also changes the results slightly)
1536      - add a few "_d 0" where they had been missing in seaice_evp.F
1537      - cleaning up: remove unused seaice_calc_rhs.F
1538    o pkg/exf: some cleaning-up:
1539      - change various "constants" into runtime parameters
1540      - cleaned-up Large&Yeager04 routine which should eventually
1541        replace exf_bulkformulae.F (changed names of S/R and CPP)
1542        and merged various ALLOW_ATM_WIND options
1543     only used with thsice pkg (in thsice_get_exf.F):
1544      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1545        which are used when useStabilityFct_overIce=TRUE (= the default)
1546      - change default values of ice & snow emissivity and scale downward LW
1547        by ice & snow emissivity.
1548    o pkg/thsice:
1549     fix few little problems, in thsice_calc_thickn.F:
1550      - growth vertically (and not laterally) if iceFrac == iceMaskMax
1551      - melt only laterally if hIce < hThinIce (as the comments say)
1552      and in thsice_extend.F:
1553      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1554      - start to form ice as soon as the minimum ice-volume is reachable.
1555     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1556      and cpl_aim+ocn
1557    o pkg/kpp
1558     - move computation of surface related input fields to KPP into a new
1559       subroutine kpp_forcing_surf.F
1560     - remove wrong (within bi,bj loops) EXCH calls.
1561     - little cleaning (add argument myThid in last position, cvs header ...)
1562     - for now, fix conservation problem by exchanging KPPviscAz (may not
1563       be the best fix)
1564    o pkg/seaice
1565     - check for inconsistent evp parameter/cpp-flag combination
1566     - remove leftover errIO flat for obsolete name list error handling
1567    o OpenAD
1568     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1569    
1570    checkpoint59a (2007/05/01)
1571    o pkg/seaice: some parameter clarifications and a little bit of clean up
1572    o pkg/thsice: rename run-time parameters:
1573       himin       -> hIceMin
1574       himin0      -> hThinIce
1575       hihig       -> hThickIce
1576       i0          -> i0swFrac
1577       transCoef   -> bMeltCoef
1578       frac_energy -> fracMelting
1579      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
1580       with default values (for now) that do not change the results.
1581      remove old version of thsice vars advection in pkg/seaice.
1582    o in FFIELDS.h:
1583      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
1584      - make pLoad & sIceLoad always available (but still only used if
1585         ATMOSPHERIC_LOADING is #define).
1586    o pkg/kpp: replaced _KPP_RL with _RL
1587    o bug fixes for vertical diffusivity computations when both KPP and
1588        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1589        are no longer updating the vertical diffusivity array
1590        (passed as argument) but are (re-) setting those arrays.
1591    o pkg/seaice: fix bug in evp solver, while doing that
1592      - change (improve?) discretization of stress computations for both
1593        cgrid-lsr and evp solver
1594      - add a new routine to compute strain rates
1595      - the above changes lab_sea results
1596      - add no slip conditions for evp solver (off by default), lsr-version
1597        may follow
1598      - fix exchange for shear at Z-points (does not change lab_sea)
1599      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
1600        (to force the user to pick a time step since there is not "safe" way
1601        of choosing it)
1602      - add principal stress diagnostics
1603      - rearrange fields for evp a little to avoid having to call a: too many
1604        exchanges and b: exchanges for stress trensor components which we do
1605        not have.
1606      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
1607        of evp, complete rewrite for lsr case (latter is does not yet work
1608        in all cases)
1609    o pkg/kpp: add code to have mixing in shelf ice caverns
1610      - add myThid to all kpp routines (long overdue)
1611    
1612    checkpoint59 (2007/04/19)
1613    o pkg/exf:
1614      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1615        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
1616      - move exf header files from lower_case.h to UPPER_CASE.h ;
1617        add missing cvs Header & Name
1618      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
1619      - add namelist param. selectStressGridPosition, exf_monFreq
1620      - retire many _CLIM routines, and remove data.exf_clim
1621        + params moved to data.exf
1622        + climsst, climsss now handled by exf_set_gen, i.e.
1623          climss?period=0 refers to constant field,
1624          climss?period=-12 to monthly forcing
1625      - split up namelists in data.exf
1626    o pkg/seaice:
1627      - remove seaice_exch and seaice_exch_uv
1628      - remove superfluous exchange of theta
1629      - add myThid to seaice_budget_ocean/ice
1630      - add new interface for atmospheric wind forcing (C-grid only)
1631        + new routine
1632        + two new field (taux, tauy for stress over ice)
1633        + removed one global field (DAIRN) for C-grid case only
1634    o pkg/thsise
1635      - 2nd set of modifs for thsice adjoint in conjunction with exf
1636    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
1637    
1638    checkpoint58y_post (2007/04/15)
1639    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
1640      vertical diffusivity, similar to that in MOM4; turned on using
1641      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
1642      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
1643    o Added capability for 3D specification of background vertical diffusion
1644      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
1645      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
1646      "data" file that contains the 3D vertical diffusivity coefficients.
1647    o ice dynamics (pkg/seaice) with thsice thermodynamics:
1648      - add code within pkg thsice to advect & diffuse sea-ice fields
1649      similar to (and will replace) what has been added in  seaice_advdiff.F,
1650      but: - conserving Mass, Heat & Salt.
1651           - better when using non-linear advection scheme (not yet fully tested)
1652           - can also be used in atmospheric set-up (for now, only the diffusion).
1653    
1654    checkpoint58x_post (2007/04/04)
1655    o IO option for global-file compact format:
1656      - add options when generating topology (utils/exch2/matlab-topology-generator)
1657      - add I/O capability (pkg/mdsio).
1658      - adapt utils/matlab/rdmds.m to read this format.
1659      for now long-line format not yet supported by pkg/mdsio (& exch2).
1660    o shelfice: add a few diagnostics
1661    
1662    checkpoint58w_post (2007/03/13)
1663    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
1664      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
1665      (and replace horiVertRatio in NH code).
1666      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
1667                         and tutorial_plume_on_slope (sensitive to truncation)
1668    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
1669      directly to drive seaice model (C-grid only)
1670    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
1671     - reintroduce computation of wind from stress,
1672     - compute tau (in exf_bulkformulae.F) from windstress averaged to
1673       mass points to avoid tau = 0
1674     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
1675    o rdmnc.m: make it work with "global" files created with gluemnc
1676    o rdmnc.m : some improvements in dealing with singleton dimension
1677      (tested on all testreport mnc output files).
1678    o genmake2: disable pkg/profiles if netcdf test fails.
1679    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
1680    o move call to cal_readparms up to make calendar parameters/variable available
1681      to all packages
1682    
1683    checkpoint58v_post (2007/02/08)
1684    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
1685      useDynP_inEos_Zc tested.
1686    o pkg/exf: changes to properly interpolate/mask/scale initial fields
1687    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1688      and portions thereof.  See read_cs.txt for description and examples.
1689    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1690      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1691      following the great-circle arc between those 2 points.
1692    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1693      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1694    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1695     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1696     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1697     - still needs work (not working with some options ; efficiency to improve)
1698       and serious testing.
1699     - use this scheme for temperature & salinity in 2 advection test exp.:
1700       advect_xy & advect_xz, respectively.
1701    
1702    checkpoint58u_post (2007/01/12)
1703    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1704    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1705    o testreport: add option "-skipdir" to skip some test.
1706    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1707      momentum calculation.
1708    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1709    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1710      remove checkpoint.F and the_correction_step.F (no longer used);
1711      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1712    o add option (linFSConserveTr) to correct for tracer source/sink due to
1713      Linear Free surface
1714    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1715    o pkg/thsice: fix reading mnc-pickups
1716    
1717    checkpoint58t_post (2006/12/30)
1718    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1719    o pkg/mdsio:
1720     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1721       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1722       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1723     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1724     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1725       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1726     - new S/R (to replace MDSWRITEMETA), which allows to write more
1727       informations (variable names, time ...) to meta files.
1728     - modify rdmds.m to give back the meta file content.
1729    o pkg/diagnostics: change vertical interpolation to be safer, and more
1730       flexible (define p-levels to interpolate to in data.diagnostics);
1731      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1732       diagnostic pointer.
1733    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1734    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1735    o fix multi-category seaice:
1736     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1737       SEAICE_MULTICATEGORY
1738     - fix short wave heat flux
1739    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1740       and allow to use EVP solver. Change forward lab_sea: test both EVP
1741       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1742    o Initial check-in of lab_sea adjoint
1743      (very similar to natl_box_adjoint/code_seaice)
1744      * used C-grid and EVP solver
1745      * used KPP, GM/Redi
1746      * uses inAdExact=.TRUE.
1747      * gradient checks fail for both ADM and TLM
1748        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1749        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1750        issue is related to forward mismatch between g77 an ifort
1751    o pkg/seaice: overhaul of thermodynamics
1752     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1753     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1754     - move a few global fields out of SEAICE.h into seaice_growth.F and
1755       make them 2D (FICE/QNETO/ ...)
1756     - remove FO (it is the same as QNETO)
1757     - introduce a few local fields to avoid modifying external fields such
1758       as atemp, etc.
1759    
1760    checkpoint58s_post (2006/12/11)
1761    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1762      changed exf_set_gen.F so that
1763        genperiod=0 means input file is one time-constant field and
1764        genperiod=-12 means input file contains 12 monthly means
1765    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1766      this affects truncation error ; generate new output file for exp. which
1767      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1768        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1769        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1770        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1771        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1772        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1773    o start implementation of deep-atmosphere and anelastic formulation
1774    o verification: remove 2nd copy of input files and use script "prepare_run"
1775      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1776    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1777    o profiles: fix for multithreaded case
1778    
1779    o diagnostics: rename few diags:
1780      s/'PRESSURE'/'RCENTER '/g
1781      s/'TICE    '/'oceFreez'/g
1782      s/'TAUX    '/'oceTAUX '/g
1783      s/'TAUY    '/'oceTAUY '/g
1784      s/'SWFLUX  '/'oceQsw  '/g
1785      s/DIFx/DFxE/g
1786      s/DIFy/DFyE/g
1787      and add few ocean-forcing diagnostics:
1788      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1789    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1790      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1791      as actual snow thickness.  It now refers everywhere to effective snow
1792      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1793    
1794    checkpoint58r_post (2006/11/17)
1795    o modifications to pkg/seaice/growth.F, which change results of
1796      lab_sea experiment: fixes pertain to melting snow over open water, to
1797      masking EVAP under sea ice, and to using the correct AREA variable for
1798      computations of EVAP, PRECIP, HSNOW, and GHEFF
1799    o add ability to read bathy, salt, and theta using MNC (off by def)
1800    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1801      both are turned off by default and do no change any results
1802    o seaice advection with pkg/thsice: a step toward the use of non-linear
1803      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1804    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1805      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1806      in natl_box (affects results @ truncation level: update output.txt)
1807    o multi-threading and IO:
1808      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1809      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1810        (needed to work with SingleCpuIO): tested in all verif. exp.
1811    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1812      affects the results (but none of the verification test uses this scheme).
1813    o Adding some pkg/diagnostics capability to pkg/seaice
1814      (will certainly be subject to changes)
1815    o ctrl: adding new control variables:
1816      lwflux, lwdown, evap, snowprecip, apressure, runoff
1817    
1818    checkpoint58q_post (2006/10/20)
1819    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1820      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1821      high_res_cube configuration by 4% on Columbia.
1822    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1823      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1824      dynamical allocation (seems to work in multi-threaded).
1825    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1826      single CPU io) so that TAF does not have to see EESUPPORT.h
1827    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1828    
1829    checkpoint58p_post (2006/09/08)
1830    o obcs: stop if obcs is used with useCDscheme = .true.
1831    o shelfice:
1832     - fix a sign error so that no slip at shelfice interface works
1833     - remove stop for combination non-hydrostatic code and shelfice. That does
1834       not mean, that the results are correct, but at least they are numerically
1835       stable
1836    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1837    o added adjoint exch routined for all exch*3d* routines
1838      and updated flow directives
1839    
1840    checkpoint58o_post (2006/08/28)
1841    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1842      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1843    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1844      and clean-up reading/writing of pickup files.
1845    o fix local version of read/write pickup (NH part) in rotating_tank/code
1846    o simplify EXCH interface:
1847     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1848     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1849    o added the regrid package
1850    o shelfice:
1851     - add a simple boundary layer scheme to reduce noise
1852     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1853    
1854    checkpoint58n_post (2006/08/14)
1855    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1856       local variable (not in common block).
1857    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1858      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1859      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1860        to work with SingleCpuIO.
1861    o add "_d 0" to real constant of pkg/cfc subroutines ;
1862       update exp. cfc_exemple & tutorial_cfc_offline output files.
1863    o multi-threading and IO:
1864      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1865        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1866      - barrier before and after reading.
1867      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1868      - avoid using MDS_WRITELOCAL for LAND pkg output.
1869      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1870        common-block variables ; Allows multi-threading with master-thread IO.
1871    o change default MAX_NO_THREADS from 32 to 4 ;
1872      and stop cleanly when MAX_NO_THREADS is too small.
1873    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1874    
1875    checkpoint58m_post (2006/07/17)
1876    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1877       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1878    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1879       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1880       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1881    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1882        add MITgcm_tutorials (= code + all the tutorials)
1883    o ecco, option to compute cost for total ssh (mean+anom)
1884    o consistent with addition of ptracer and ssh in pkg/profiles
1885    o profiles: adding ptracer and ssh
1886    o testreport: change multi-test output-file name
1887      (from output.txt.{name} to output.{name}.txt)
1888    o profiles: now ok for mutli-tiles case
1889    o seaice: add 4 parameters for different advection schemes for area,
1890      (effective) seaice thickness, enthalphy, and snow height. Their default
1891      is the standard parameter SEAICEadvScheme
1892    o calc_gw:
1893     - add cosFacU in zonal viscous flux (harmonic.visc.).
1894     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1895       of tutorial_plume_on_slope.
1896    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1897    o calc_gw: true flux-form, account for horizontal grid spacing.
1898      update rotating_tank results, but not plume_on_slope (affected at
1899      truncation level, 11 digits).
1900    
1901    checkpoint58l_post (2006/07/12)
1902    o calc_gw:
1903     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1904     - remove side-drag for now (need to fix it); update plume_on_slope results.
1905     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1906    o commit code to make SST/SSS weights spatially variable
1907      (based on either variable in-situ or variable initial T/S weights)
1908    o pkg/ecco:
1909      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
1910        now based on horizontally varying weights wthetaLev, wsaltLev
1911      * cost_averagesflags now returns year indices in addition to day, month
1912      * sflux balance is performed on annual basis
1913        (sflxumm, sfluxmm2, bal_sfluxmm)
1914      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
1915        including separate counting and multipliers
1916    o pkg/rbcs
1917      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
1918    
1919    checkpoint58k_post (2006/07/06)
1920    o testreport:
1921     - always build in dir. "build" (if not there, mkdir build instead of building
1922       & running in input)
1923     - run in dir run (if it exists), in build otherwise.
1924     - call prepare_run (if input/prepare_run exists)
1925     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
1926    o pkg/exf modifications to interpolation and rotation routines for more
1927       reasonable treatment of North Pole singularity: for tracers North Pole
1928       value is set to northernmost zonal-mean value, for zonal velocity it is
1929       set to zero, and for meridional velocity it is set to northernmost value.
1930    o pkg/exf/exf_check_range.F
1931     - add tile index to diagnostics and move stop statement to the very
1932       end of the routine.
1933    o pkg/diagnostics: (diagnostics_main_init.F)
1934      define title of isomorphic variables according to the current config.
1935    o pkg/thsice with pkg/seaice dynamics:
1936    - fix domain of computation (interior only, required for exf) and do exchanges
1937    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
1938    o towards a standard way of dealing with multi-threading in MONITOR
1939      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
1940    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
1941       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
1942    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
1943    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
1944    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
1945       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
1946    o tracer advection:
1947     - clean-up and simplify calc_common_factors.F
1948     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
1949       advection subroutine (but still not used within DST advection S/R)
1950    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
1951    
1952    checkpoint58j_post (2006/06/15)
1953    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
1954      from file (collects calls previously in FORWARD_STEP)
1955    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
1956    o adjoint store dir. adjusted accordingly
1957    o genmake2
1958      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
1959    
1960    checkpoint58i_post (2006/06/14)
1961    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
1962      on wind stress (SEAICEstressFactor defaults to 1.)
1963    o Total number of Timers is finite (<=40): comment out 2 non-essential one
1964      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
1965    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
1966      on CS-grid: no longer loosing mass.
1967    o exf & curvilinear-grid: no longer modify longitude xC & xG.
1968    o pkg/ggl90: fix sloppy output and fix a bug
1969    o pkg/seaice: added SEAICEuseEVPpickup parameter
1970      - Set to false in order to start EVP solver with
1971        non-EVP pickup files when using SEAICEuseEVP
1972      - fix sign error in diffusion in seaice_calc_rhs
1973    
1974    checkpoint58h_post (2006/06/07)
1975    * Modifications for bottom topography control
1976      o replace hFacC by _hFacC at various places
1977      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
1978      o add non-self-adjoint cg2d_nsa
1979      o update autodiff support routines
1980      o re-initialise hfac after ctrl_depth_ini
1981      o works for 5x5 box, doesnt work for global_ocean.90x40x15
1982    * Adding verification for 5x5 box (4-layer) bottom topography control
1983    
1984    checkpoint58g_post (2006/06/07)
1985    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
1986       used for mean seasonal cycle, mean diurnal cycle); add an example
1987       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
1988    o pkg/ggl90:
1989      - add parameter (minimum surface kinetic energy)
1990      - fix bug (avoiding division by zero)
1991    o couple pkg/thsice to pkg/seaice:
1992      - modify advection in seaice to accomodate new scalar fields to be advected
1993      - only muliDimAdection scheme work with seaice/thsice
1994      - mapping of thsice-variables to seaice-variables, back and forth
1995      - does not break the verification experiments, but does not give the
1996        desired results either
1997    o pkg/seaice
1998      - make (default) second order advection a bit less confusing?
1999    
2000    checkpoint58f_post (2006/06/05)
2001    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
2002      to pkg/seaice):
2003      - new routines thsice_map_exf and thsice_get_exf provide the interface
2004      - add an additional formal parameter to thsice_solve4temp
2005    o pkg/exf:
2006      - add new fields wspeed, snowprecip (to be able to couple to thsice)
2007      - correct Stefan-Boltzmann constant
2008      - new parameter for longwave surface emittance
2009      - separate some stuff from exf_bulkformulae into new routines  
2010        exf_radiation, exf_wind
2011      - add new parameters and constants: longwave emissivity for ocean, ice
2012        and snow, evaporation parameters over ice
2013      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
2014        either wind from stress or stress from wind
2015    o pkg/thSIce:
2016    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
2017    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
2018       and THSICE_CALC_THICKN
2019    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
2020    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
2021      to make debugging easier.
2022    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
2023    o pkg/bulk_force:
2024      - clean-up comments and parameters ;
2025      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
2026    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
2027      generate new output for test-experiment: aim.5l_cs.thSI
2028    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
2029      testreport accordingly
2030    
2031    checkpoint58e_post (2006/05/17)
2032    o SEAICE_CGRID adjoint done
2033    o R_STAR adjoint implemented.
2034      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
2035      * need to sort out init. of h0facc, etc.
2036    o Make pkg/profile fully independent of ecco,cost, etc. stuff
2037      to be able to use it in pure forward.
2038    
2039    checkpoint58d_post (2006/04/21)
2040    o upgrade simple test-experiment to tutorial example:
2041     step.1: duplicate the experiment and (step.2) will remove the old copy.
2042      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
2043      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
2044      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
2045      tutorial_global_oce_biogeo    <- copy of dic_example
2046      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
2047      tutorial_plume_on_slope       <- copy of plume_on_slope
2048      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
2049      tutorial_global_oce_optim     <- empty for now (David ?)
2050      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
2051     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
2052    o correct a sign problem in cost_scat.F
2053    o obcs and ptracers: fix boundary conditions for advections schemes
2054      with larger stencil
2055    o thsice adjoint: start
2056    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
2057      completeness
2058    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
2059      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
2060    o ptracers adjoint:
2061      * avoid extensive recomputatations
2062      * fix missing re-init. of gptr (missed by TAF)
2063    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
2064      me to turn off the excessive output to STDOUT that this package produces
2065    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
2066      and add those terms in Vector-Invariant formulation.
2067    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
2068      if the control period (xx_hfluxperiod etc) is 0
2069    o in profiles pkg, clean routines and fix details
2070    o in ecco pkg, reading ssh data:
2071      fix problem in case the model does not start at iter0=0
2072    o fix mnc-pickup/restart for ptracers
2073    o new package prifiles:
2074      code to compute profile-based cost by Gael Forget
2075      (modifs in ecco, ctrl, autodiff)
2076    o Benign bug fix in initialization (spotted by M. Mazloff) of
2077      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
2078    
2079    checkpoint58c_post (2006/03/23)
2080    o adjoint: finish NLFS adjoint and provide reference output in
2081      verification/global_ocean.90x40x15/results_ad_nlfs
2082    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
2083      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
2084      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
2085      with SEAICE_CGRID defined.
2086    o move calendarDumps from "data" to "data.cal" and clean-up the code
2087      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
2088    o add useEXF & useCAL flags (for now, set in hard-coded way)
2089    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
2090      (were missing in NH mode, and wrong in quasihydrostatic mode).
2091      waiting for Chris updated version of calc_gw to add those CALLs.
2092    o fix bug in quasihydrostatic S/R ;
2093      add a test for this option: global_ocean.90x40x15.qshyd
2094    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
2095      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
2096    o add on/off flag useOffLine for package OFFLINE
2097    o seaice:
2098      - modify advection so that it works also on the C-grid
2099      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
2100        problem in multi-tile runs with C-grid
2101      - add flags for clipping ice velocities and/or masking solver forcing
2102      - fix drag (ocean on ice) formulation and a bug that caused noise in the
2103        C-grid solver
2104      - added a few comments to seaice_diffusion.F
2105      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
2106        are now exclusive)
2107      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
2108        required re-ordering the code a little:
2109       + make DAIRN global variable (defined in SEAICE)
2110       + move computation of the viscosities eta and zeta into a new separate
2111         routine (because I need to recompute them in seaice_ocean_stress.F)
2112    
2113    checkpoint58b_post (2006/03/13)
2114    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
2115      update output.txt of exp. aim.5l_cs.thSI
2116    o various mnc cleanups and improvements:
2117      + shrink lookup tables by factor of ~4
2118      + better error reporting when running out of lookup space
2119      + able to handle longer path/file names (up to 500 chars)
2120    o adjoint:
2121      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
2122      - TBD: "hidden" mom_vecinv recomp. in dynamics
2123    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
2124     (allow to differentiate between forcing components using new integer flags:
2125      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
2126     and add new flag to put Dissipation tendency out of Adams-Bashforth.
2127    o ecco
2128      - enable trend removal from SSH anomaly obs.
2129    o adjoint
2130      - a fix for PmEpR when #undef EXACT_CONSERV
2131      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
2132      - try to fix "hidden" recomp. in forward_step for NLFS
2133        (NLFS seems broken sometimes after I checked it in)
2134    o seaice:
2135     - add c-grid version of the dynamic solver:
2136       + three new routines that are the c-grid substitute lsr, dynsolver
2137         and ostres
2138       + put a few fields that were local to dynsolver into global common
2139         blocks, so that I can move the computation of stresses etc into
2140         seaice_lsr (saves coding but may break the adjoint).
2141     - replace more hardwired parameters by runtime parameters
2142     - add ice masks that mask the rhs of the implicit solvers where there
2143       is no ice (commented out in seaice_dynsolver, because i am not sure
2144       if this works properly), eventually this should replace the clipping
2145       of ice velocities in seaice_dynsolver to +/-40cm/s.
2146    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
2147      include it only where its needed
2148    o move balancing of fluxes before the call of external_forcing_surf
2149    o seaice:
2150      - correct units of turning angles (now they are really in degrees)
2151      - move computation of GWATX/Y out of main routine into dynsolver
2152      - initialize GWATX/Y in seaice_init
2153    o Apply mask on Fresh-Water flux (needed for SSH forcing).
2154      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
2155    o seaice: add runtime flags for turning angles (default to zero)
2156    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
2157      and trend from exf forcing and ctrl control adjustments
2158    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
2159      (since checkpoint57x_post)
2160    o change the default rotation period to 86164.s = the Earth rotation
2161    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
2162      and based on a reference stratification. Tested within hs94.cs-32x32x5.
2163    o seaice advection: add code for choosing between the default (2nd order
2164      central differences) and multiDim advection schemes provided by
2165      pkg/generic_advdiff
2166    o seaice:
2167      - removed all references to SEAICE_GRID.h fields from
2168        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
2169        (cubed-sphere configuration will change a little)
2170      - grid computations in seaice_init are obsolete now.
2171      - cleaned up code a little so that is easier to read (hopefully).
2172      - added new (better?) discretizations of default advection and diffusion
2173        (turn on with SEAICEuseFluxForm)
2174      - replace 1 in 3d global fields by kSurface in growth.F
2175      
2176    checkpoint58a_post (2006/02/13)
2177    o seaice:
2178      - bug fix in advect.F
2179    o shelfice:
2180      - separate shelfice load anomaly from pload (breaks with time
2181        dependent forcing), => introduce constant field shelficeLoadAnomaly.
2182        Its default is 0., but it may be computed more cleverly from (unknown)
2183        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
2184        done offline. A good approximation of the pressure load anomaly is
2185        necessary to avoid large initial adjustment processes underneath
2186        deep-reaching shelfice.
2187      - small fix in ISOMIP shelfice_thermodynamics
2188      - add more sophisticated thermodynamics of Hellmer (1989), this is
2189        now the default
2190      - give a few constants more intuitive names
2191    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
2192      if bulk formulae are used in long integration (especially EmPmR). Turn
2193      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
2194      if balancePrintMean, the imbalance that is substracted is printed to
2195      STDOUT.
2196    o fix bug (typo) in obcs_apply_eta.F
2197    o add a new package shelfice which enables us to model the circulation
2198      underneath shelf-ice with draughts of hundreds of meters.
2199     - works
2200     - to do: + include improved thermodynamics
2201              + check whether kSurfC (from model/inc/SURFACE.h) can be used
2202                instead of new field kTopC
2203              + can we use topoFile, Ro_surf and existing code in ini_depth.F
2204                instead of new field R_shelfIce and new code in ini_depth.F
2205                and ini_mask_etc.F?
2206              + adjust vertical mixing schemes?
2207    o seaice pkg:
2208     - add a cpp-flag to include a simple formula for a salinity dependent
2209       freezing point of sea water at the surface
2210     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
2211       meridional stresses are now different (and hopefully correct)
2212    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
2213       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
2214       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
2215    o pkg/diagnostics: add options and parameters for regional-statistics
2216       diagnostics ; define regions by reading a region-mask from a file
2217       (might add other options later)
2218    o pkg/bulk_force:
2219     - add option and parameters to use AIM surface-flux formulae.
2220     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
2221       others forcing fields (defined in PARM05, parameter file "data") are loaded
2222       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
2223     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
2224     - use the right EXCH call for uwind,vwind (to work on CS-grid).
2225     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
2226       and parameters (note: calcWindStress replaces .NOT.readwindstress).
2227     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
2228    
2229    checkpoint58 (2006/01/12)
2230    o add "--embed-source" option to genmake2 which, when the supporting
2231      tools can be compiled (as determined by genmake2) will turn on the
2232      embed_files package which then embeds the entire MITgcm source code
2233      (*.[fFhc] + Makefile) used for the build within the executable
2234      - requested by CNH but off by default
2235      - adds a paltry <9MB to the mitgcmuv executable in most cases
2236      - only writes the output when useEMBEDSRC in eedata is true
2237    o clean up 3-dim. relaxation codes:
2238      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
2239      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
2240      * Thanks to Tom Haine for testing!
2241    
2242    checkpoint57z_post (2005/12/31)
2243    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
2244      affects output (@ truncation level) of exp. plume_on_slope ; updated.
2245    o fix the pickup behavior for obcs in combination with ptracers
2246    o fix a bug in ptracers_external_fields_load
2247    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
2248      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
2249    o transfered surface NH pressure to eta field (if exactConserv).
2250    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
2251         and update lab_sea output.txt file.
2252    o completing 3-dim. relaxation code: additional term
2253         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
2254      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
2255      * At compile time, in "EXF_OPTIONS.h" set
2256          #define  ALLOW_CLIMTEMP_RELAXATION
2257          #define  ALLOW_CLIMSALT_RELAXATION
2258      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
2259          tauThetaClimRelax3Dim = 15552000.0,
2260          tauSaltClimRelax3Dim  = 15552000.0,
2261      * 3 cases:
2262          1) Use a constant-in-time 3-dim. field
2263          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
2264          3) Real-time relax. to time-evolving prescribed field
2265    o Adding Laplacian-type smoothness constraint on
2266      initial and boundary (forcing) controls (ic, bc)
2267      * enable at compile-time via
2268        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
2269      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
2270      * Absolute scale somewhat unclear so far
2271      * no area weighting was included since no other cost term does so far
2272    
2273    checkpoint57y_post (2005/12/08)
2274    First step for a NLFS adjoint
2275    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
2276    o new init. routines for calc_r_star, calc_surf_dr
2277    o still need to deal with ini_masks_etc
2278    o testreport seemed happy
2279    checkpoint57y_pre (2005/12/08)
2280    
2281    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
2282    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
2283    o add new offset feature to offline pkg (plus minor cleanup)
2284    o cfc fixes for final year of integration
2285    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
2286      be in GCHEM_OPTIONS).
2287    
2288    checkpoint57x_post (2005/12/04)
2289    o fix testreport Pb in multiple test experiment.
2290    o cleanup our namelist syntax in verification:
2291      - make it more F95 standards compliant (some work still needed)
2292      - allows the vast majority of our tests to work with gfortran
2293    o Non-Hydrostatic:
2294     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
2295     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
2296    o Allow to apply AB on T,S rather than on AB(gT,gS):
2297     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
2298     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
2299       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
2300     - need a "clever" read_pickup to restart from the other AB formulation
2301    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
2302    o remove some unused variables (reduces number of compiler warnings)
2303    o adjoint
2304      * Disable useVariableViscosity for adjoint for time being
2305        (there are a number of extensive recomputations)
2306      * Initialize certain variables needed for adjoint
2307    
2308    checkpoint57w_post (2005/11/03)
2309    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
2310                 fix the singleCpuIO RS version of MDSWRITEFIELD
2311       and add a WARNING if using globalFiles=T with multi-processors.
2312    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
2313      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
2314    o tracer advection scheme:
2315      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
2316       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
2317       was not very convenient).
2318      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
2319       (further tests needed for the implicit DST & Flux-Limiter schemes).
2320    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
2321      and sRef for convenience, handy, when you want to initialize
2322      ptracers in a large domain with a constant non-zero value. Also,
2323      untangle ptracers_init.F a little.
2324    
2325    checkpoint57v_post (2005/10/13)
2326    o change dome exp. to use variable viscosity in side-drag terms.
2327    o remove all the files from the cfc_offline test since they are now
2328      incorporated into tutorial_cfc_offline which has been producing
2329      identical results for a few days of testing
2330    o add new parameter: sideDragFactor to enable half-slip-side BC
2331      and change side-drag S/R to use viscosity from mom_calc_visc
2332      (can switch back by setting sideDragFactor=0.); affects results at
2333      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
2334       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
2335    o vorticity & strain are now computed without masking, to account for
2336      no-slip-side BC in variable viscosity calculation ; mask is applied
2337      anyway later on, before computing advection/coriolis terms.
2338    o modify exp4 to test new obcs support for reading from external files
2339      and for passive tracers
2340    o fix behavior of ptracers_monitor when monitor output is written to a
2341      netcdf-file; still not independent of monitor.F (writes in the same
2342      file).
2343    o change default value of tRef (put a uniform, meaningful value for ocean
2344      & atmos) and initialize sRef (was missing, as Martin mentioned).
2345    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
2346      to be proportional to enstrophy dissipation length.  Thus,
2347       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
2348      This is now consistent with Smagorinsky and with the manual.
2349    
2350    checkpoint57u_post
2351    o OBCS and PTRACERS: add open boundary support for passive tracers
2352      - either use homogenous (pseudo) v.Neumann conditions or prescribe
2353        OB-values from file; this is not different from the way theta and salinity
2354        are treated
2355      - however, Orlanski-radiation conditions are not supported, and the model
2356        will stop if you use pTracers and Orlanski at the same time.
2357      - beefed up the rountine obcs_external_fields_load: now only those open
2358        boundary values are overwritten with values from files for which there
2359        are really files, otherwise the OB-fields remain untouched. This makes
2360        it possible to use different OBs at different ends of the domain (as
2361        with EXF)
2362    o reduce number of exch calls in shap_filt (s2).
2363    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
2364      truncation level) 4/5 MLAdjust test results (11&12 digits match).
2365    
2366    checkpoint57t_post (2005/10/03)
2367    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
2368    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
2369      same truncation, independent of the face number: affects affects several
2370      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
2371    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
2372      note that biharmonic viscosity + no-slip was not tested in any experiment.
2373    o fix bug in non-linear free-surf side-drag ; generate new output for
2374      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
2375    o make mnc honor the writeBinaryPrec flag for most kinds of output
2376    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
2377    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
2378      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
2379    o add brackets in multi-terms sum to get same truncation, independent of
2380      the face number (manage to get exactly same value of gU,gV at the cs-edge)
2381      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
2382    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
2383      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
2384      a maximum grid-scale Reynolds number.  Also, changes all length calculations
2385      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
2386      Suggested values of viscosity parameters found in mom_calc_visc.
2387      Many new viscosity diagnostics available.
2388    
2389    checkpoint57s_post (2005/09/20)
2390    o Add clearing-house for viscosity calculations, mom_calc_visc and
2391      correct numerous bugs in LeithD and Smagorinsky discretizations.  
2392      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
2393      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
2394      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
2395      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
2396      The Strain-Tension form is now called with useStrainTensonVisc=.true.
2397      ViscAhStrain and viscAhTension are now retired.
2398    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
2399    o In response to JMC's bug report, genmake2 now ignores any soft-links
2400      that it finds in the *current* directory when searching for files.
2401      Soft-links found in any other source directories will still work as
2402      they did before.
2403    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
2404      a C routine to unlimit the stack size
2405    o mnc-ify pkg/aim snapshot vars
2406    o mnc-ify pkg/land as requested by Daniel
2407    o various changes to mnc including:
2408      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
2409      - output can now be grouped so that all files within a group
2410          change the ITER portion of their names in lock-step together
2411      - can now read ("global") PER-FACE (in addition to PER-TILE) files
2412          and works with both EXCH1 and EXCH2 (but needs more testing)
2413      - writing works for all verification test cases w/ g77 on Linux
2414    
2415    checkpoint57r_post (2005/09/07)
2416    o make MNC variable initialization happen earlier
2417    o add diagnostics for (almost) each term of the momentum Eq.
2418    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2419    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
2420    o remove MINIMAL_TAVE_OUTPUT option ;
2421      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
2422    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
2423      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
2424    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
2425    o add time-dependent SST, SSS control
2426    o cost terms in ecco/ modularized (new cost_generic.F)
2427    o cost_averages routines are modularized (new cost_averagesgeneric.F)
2428    o new infrastructure for seaice model vs. obs misfits in seaice/
2429      * driver from the_main_loop.F is seaice_cost_driver.F
2430      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
2431      * gradient check in Exp. 6a of natl_box_adjoint/
2432    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2433      (see README file)
2434    
2435    checkpoint57q_post (2005/08/19)
2436    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2437    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2438      - bug was reported by Jean-Michel and Ian Fenty
2439    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
2440      update exp. cpl_aim+ocn output.
2441    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
2442      Needed for high-res. runs with large global files
2443      to be able to limit tapelev size
2444    o Changed some tests for adjoint:
2445      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
2446      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
2447      * global_ocean.90x40x15/ back to default 3-level checkpointing
2448    o Modifications to enable scripted COMMON to MODULE conversion
2449      * verification/OpenAD/code/ has necessary scripts and description;
2450      * converts, compiles and runs successfully;
2451    
2452    checkpoint57p_post (2005/08/01)
2453    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2454    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2455      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
2456    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
2457    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
2458      (was already the case for dissipation with mom_vecinv,
2459       and also the case for grad.PhiHyd when staggered-timeStep)
2460      This will allow to put dissipation out-off the AB time-stepping.
2461     Unfortunately, affects truncation error. Update output of exp. that "fails"
2462      (cg2d matching number) and leave the others for later: front_relax(10),
2463      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2464      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2465    
2466    checkpoint57o_post (2005/07/30)
2467    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
2468      (2) its ready to be documented during the 20050801 DocFest
2469    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
2470      for ideal_2D_oce and lab_sea on linux_ia32_g77
2471    o set to #undef CTRL_SET_OLD_MAXCVARS_30
2472      in global1x1_tot/code_seaice_adj to access indices 32, 33
2473      (worth another tag)
2474    
2475    checkpoint57n_post (2005/07/29)
2476    o adding precip control xx_precip 32
2477    o adding swflux control xx_swflux 33
2478    o Replacing 10 forcing penalty cost routines by 1 generic.
2479    o Implementing partitioning in time-mean and variable adjustment
2480      for atmos. state.
2481    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
2482    o in natl_box_adjoint:
2483      * updated exp 1 to 10
2484        (but does not have time-mean vs. variable split results yet)
2485    o updated global1x1/*_seaice_adj/
2486      to incorporate latest changes
2487    o enable useSingleCpuIO for mdsio vector routines
2488      (applies in particular to tapelev I/O)
2489    o removed inefficient K-loop in all active_file*control*.F
2490    
2491    checkpoint57m_post (2005/07/28)
2492    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
2493      and advect_cs (use EXCH-2 and standard cs-32 grid files).
2494    o pkg/exch2: filling of face-corner halo regions is optional
2495      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
2496    
2497    checkpoint57l_post (2005/07/14)
2498     tag before updating tutorials (pre-release-2)
2499    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
2500       for output and interpolation of input fields onto model grid)
2501    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
2502       Affects results of exp. rotating_tank ; update output.txt.
2503    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
2504          and taking the square quantity and/or using a fraction-weight field.
2505    o fix aim_diagnostics_init.F mate numbers.
2506    o add mnc output capability to diagnostics/diagstat and update
2507      our cvsignore files for the ACSII output generated
2508    
2509    checkpoint57k_post (2005/07/02)
2510    o lab_sea now uses diagnostics package and provides a suite of
2511      new EXF diagnostics output.
2512    
2513    checkpoint57j_post (2005/06/30)
2514    o exf
2515      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
2516        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
2517        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
2518      * extended diagnostics output
2519        - now includes all EXF variables
2520        - hs, hl moved to common block
2521        - separate S/R for diagnostics, called after ctrl vector is added
2522        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
2523        - EXFqnet contains true Qnet (i.e. includes qsw)
2524      * updated verif. lab_sea, global_with_exf
2525      * Rearranging hflux (exf_mapfields -> exf_getforcing)
2526        to ensure that diagnostics sees a true EXFqnet
2527    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
2528    o diagnostics pkg: change pointers so that 1 diagnostic can be used
2529      several times with different frequencies.
2530    o mnc-ify the thsice package as requested by Daniel Enderton
2531      - the monitor--MNC output needs work
2532      - many attributes need to be added (most are currently blank)
2533    o mnc-ify theaim_v23 package as requested by Daniel Enderton
2534      - many attributes need to be added (most are currently blank)
2535    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
2536    o add Sadourny like discretization to the 4th.O vorticity advection scheme
2537    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
2538      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
2539         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
2540    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
2541     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
2542    
2543    checkpoint57i_post (2005/06/19)
2544    o Diagnostics package was changed: diagnostic allocation is now deactivated
2545      by setting an empty file name in the namelist (used to be by setting 0 frequency)
2546    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
2547      add 1rst Order upwind vertical Shear.
2548    o add a quick fix for A/B checkpointing in OFFLINE mode
2549    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
2550      end-run around the C/Fortran linking horror in eesup/src/timers.F
2551    o added pkg/runclock: allows user to terminate run based on wall clock
2552    o added non-hydrostatic scaling parameter: nh_am2
2553    o pkg/my82: futile attempt to make results compiler-independent by adding
2554      some "_d 0", etc. no effect.
2555    o for mnc output, fill the 'T' coordinate var with myTime and create a
2556      separate 'iter' variable for iteration count
2557    o pkg/diagnostics:
2558      add new capability: output of Global/Regional & per-level statistics ;
2559      tested against monitor output (including land & thSIce) on various exp.
2560    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
2561    
2562    checkpoint57h_done (2005/05/19)
2563      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
2564      data.diagnostics, data.gchem, data.ptracers) is done.
2565    
2566    o pkg/diagnostics: prepare for Global/Regional statistics.
2567      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
2568    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
2569      and rename it: DIFFERENT_MULTIPLE
2570    
2571    checkpoint57h_post (2005/05/14)
2572    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
2573    o pkg/diagnostics: change output frequency, now in seconds (instead
2574      of Nb of iterations). This requires to change data.diagnostics.
2575    checkpoint57h_pre (2005/05/12)
2576    
2577    o in mnc, let the user create the output dir if both mnc_outdir_date
2578      and mnc_outdir_num are false
2579    o add fflags() to pkg/diagnostics which allows one to specify, on a
2580      per-file basis, the file precision [default behavior is unchanged]
2581    o added diagnostics to pkg/kpp, including computation of mixed layer
2582      depth based on a temperature/density criterion
2583    o updated verification/natl_box to test the new pkg/kpp diagnostics
2584    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
2585    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
2586    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
2587      not mnc -- this mistake was found by JMC and is now corrected
2588    
2589    checkpoint57g_post (2005/04/15)
2590    o add Adams-Bashforth 3rd Order time stepping:
2591      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
2592      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
2593    checkpoint57g_pre (2005/04/15)
2594    
2595    o make lambda[Theta,Salt]ClimRelax spatially varying
2596      (default remains spatially uniform constant based on tau)
2597    o added new control variables
2598      * init. uVel, vVel, etanN
2599      * lambda[Theta,Salt]ClimRelax
2600    o separate masks used for ctrl_pack/unpack 'from write_grid' output
2601      (suggested by G. Forget)
2602    
2603    checkpoint57f_post (2005/04/06)
2604    o add parameter "baseTime" = model base time = time at iteration zero
2605      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
2606      account for baseTime shift
2607    o move Coriolis arrays from PARAMS.h to GRID.h
2608    checkpoint57f_pre (2005/04/06)
2609    
2610    o mnc-ifying the seaice package
2611    o introduced an alternative length scale calculation for use in the limiting
2612      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2613    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
2614    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
2615      as well as grad(vort3).  Made it compatible with both approximate form
2616      for the cubed sphere and full form of these gradients.  Added flag
2617      useFullLeith to select between approximate and full form.  
2618    o add "d0" in getcon.F to reduce differences between compilers/platforms
2619      update output.txt of exp. fizhi-gridalt-hs
2620    o change port_rand funtion to allow to set the seed.
2621    o fix obscure MNC bug involving conversion between reals and integers
2622      - it caused no problems with certain (eg. gcc, ifc) compilers but the
2623        new version is now more standards-compliant
2624    o adjoint-related modifications
2625      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
2626      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
2627      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
2628    
2629    checkpoint57e_post (2005/02/28)
2630    o Adding eddy stress controls a la Ferreira et al.
2631    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
2632    
2633    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
2634      update output.txt of exp. fizhi-gridalt-hs
2635    o add more "Z" dimensions and associated coordinate vars to MNC
2636    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
2637    o parameter calendarDumps: when set, approximate months (30-31 days) and years
2638      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
2639      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
2640      months and years.  Requires pkg/cal.
2641    o diagnostics: add pickup functionality
2642      - off by default for backwards compatibility
2643      - current version only uses MDSIO -- MNC will be added
2644    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
2645    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
2646    
2647    checkpoint57d_post (2005/02/11)
2648    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
2649    o modify verification/ideal_2D_oce so that it tests the creation of mnc
2650      output from the diagnostics package
2651    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
2652    o make genmake2 more portable by using ".$FS" instead of ".f" for more
2653      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
2654    o add coordinate variables to the MNC output from the diagnostics package
2655    o change MNC-flags default value: true when useMNC=TRUE
2656    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
2657      the ability (off by default) to read the grid information using MNC
2658    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
2659    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
2660    o do snap-shot diagnostics at the middle of the time-interval (instead of
2661      at the end).
2662    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
2663      new test for AIM with thSIce + slab-ocean
2664    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
2665    o move state variable diagnostics to the beginning of the time step ;
2666      (note: still needs some work specially for snap-shot diagnostics)
2667      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
2668    
2669    checkpoint57c_post (2005/01/27)
2670    o Change testing option (-ieee) to get closer agreement between g77 & ifort
2671    o generate new output.txt files on faulks with g77 & the new -ieee option
2672    checkpoint57c_pre (2005/01/27)
2673    
2674    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
2675      update output.txt of exp. global_ocean.90x40x15
2676    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
2677      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
2678    o add saltFlux(+File) forcing capability with periodicExternalForcing
2679    o allow to use pkg diagnostics for GM-Redi & ThSIce output
2680    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
2681    o improvements for the MNC output from DIAGNOSTICS:
2682      - correct handling of the unlimitied dimension
2683      - all dims now have associated coordinate variables
2684      - variables located at U, V, and Corner ("Z") points are now written
2685        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
2686        *all* data points are output
2687    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
2688    o added pkg/seaice/seaice_monitor.F
2689    o mdsio_readfield.F can now read files visible only to master MPI process.
2690    o pkg/seaice: some test code for ice-modified ocean stress
2691    o exf_getffields interpolation defaults to bilinear for all scalar forcing
2692      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
2693      spurious negative numbers for precipitation and humidity.  Will cause
2694      some small numerical differences for integrations using pkg/exf/exf_interp.F.
2695    o pkg/ctrl/
2696      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
2697        May be enabled via doPackDiag
2698      *  introduce z-scaling of
2699         + gradient (doZscalePack) and
2700         + control (doZscaleUnpack)
2701    o pkg/mdsio/
2702      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
2703      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
2704    
2705    checkpoint57b_post (2004/12/20)
2706    o simplify options in diagnostics_fill arguments (remove weird combinations)
2707    o fix MNC coordinate variables so that they now contain per-face index
2708      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
2709      general, EXCH2 grids are only aligned to a "local" coordinate system
2710    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
2711    o Implement instantaneous output within pkg diagnostics:
2712      setting a negative frequency in data.diagnostics produces
2713     "snap-shot" output (as opposed to time-average if freq > 0)
2714    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
2715      NOTE: change ptracer diagnostics name: use 2 characters to work with
2716            more than 9 tracers. Add also diagnostics of advect & diffus flux.
2717    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
2718      becomes the coordinate variable for the 'T' dimension
2719    o add CF-style coordinate variables to MNC
2720      - just a first cut:  numbers are meaningless on the cubesphere and
2721        missing along the T axis but otherwise it works!
2722    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
2723    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
2724    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
2725      this is based directly on what the model compute, so that the content of
2726      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
2727    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
2728    o clean up build options files for SunOS, in particular
2729      - remove -traditional from xmakedepend
2730      - change -xarch=v9 to -xarch=native for f77
2731      - restore use of make (not gmake)
2732      - add CC=gcc if using g77
2733    o changes per discussion of AM, JMC, & EH3 today:
2734      - move redundant "grid" variables out of "state" -- in preparation of
2735        creating proper CF-style coordinate variables and in recognition
2736        that any/all grid variables can be easily copied (eg. w/NCO) from
2737        the grid files into any of the other NetCDF files
2738      - *always* output grid variables with MDSIO (this will eventually be
2739        changed)
2740      - output MNC grid file if useMNC is true
2741    o every instance of _END_MASTER() has been found and replaced with
2742      _END_MASTER( myThid ) in order to satisfy certain picky Sun
2743      preprocessors
2744    o re-arrange diagnostics pkg initialisation:
2745     - allow each package to extend the available diagnostics list
2746     - add some checking and fix small problems (multi-threaded, ...)
2747     - new S/R diagnostics_fill (replace fill_diagnostics):
2748       look through the short list of active diag. (instead of the long list)
2749       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
2750    
2751    checkpoint57a_post (2004/12/10)
2752    o this set of changes restores TAMC compatibility
2753      tested for global_ocean.90x40x15 adjoint on trough
2754      (what a pain)
2755    
2756    checkpoint57a_pre (2004/12/10)
2757    o some modifs in tools/build_options for sunos
2758    o call ctrl_pack for ctrl at end for optimcycle=0
2759    
2760    checkpoint57 (2004/12/09)
2761    o add horizontal bi-harmonic viscosity for vertical velocity
2762      - new parameter viscA4W (defaults to viscA4)
2763      - affects only non-hydrostatic code
2764      - to be done: no-slip lateral boundary conditions
2765    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
2766    o implement Implicit Vertical advection for pTracers
2767    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
2768      (implemented also for implicit vertical diffusion & advection)
2769    o OBCS: extend application of tracer open boundary conditions
2770      to a strip beyond the boundary of width Olx/Oly
2771    o add call monitor to TAF set of required calls (flow directives)
2772      and include in natl_box_adjoint
2773    o untangle a few ifdefs related to cost, ctrl, autodiff
2774      untangel a few ALLOW_ECCO_OPTIMIZATION
2775    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
2776      (theta2, salt2 in ecco_cost_weights)
2777    
2778    checkpoint56c_post (2004/12/03)
2779    o OBCS as control variables
2780      - update ctrl_ad_diff.list, obcs_ad_diff.list
2781      - remove balance of obcs controls from default
2782      - fix index bug nobcs in ctrl_init
2783      - fix dummy fields filen in ctrl_pack
2784      - add dummy weights for obcs
2785    o lsopt: comment out fort.94 output
2786    o optim:
2787      - remove unnecessary header files
2788      - adjusted namelists
2789      - add xerbla.F to Makefile
2790    o exf:
2791      - multiple modifications of exf_check_range
2792      - unit change in exf_init_runoff from [m/year] to [m/s]
2793    o mdsio:
2794      - i/o-vector change debugLevel from debLevA to debLevB
2795    
2796    checkpoint56b_post (2004/12/01)
2797    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
2798      is called from DO_THE_MODEL_IO
2799      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
2800      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
2801      - clean up PTRACERS_WRITE_TIMEAVE a little
2802    o add another verification experiment that tests both the cfc-pkg and
2803      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
2804      reactive tendencies treated inline with regular timestepping
2805    o testreport previously did a lousy job of comparing small numbers, so
2806      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
2807      implemented in the little c-progam tmp_cmpnum.c which is embedded in
2808      testreport.
2809    o ptracers_monitor: bug fix for MPI
2810    
2811    checkpoint56a_post (2004/11/28)
2812    o GCHEM: finish reorganizating the package
2813      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
2814        (introduces another 3D-array for each passive tracer, but only if
2815        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
2816        gchemTendency is not needed because the timestep is done separately)
2817      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
2818      - GCHEM is now---more or less cleanly---separate from PTRACERS
2819      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
2820        so clear to me how that should be done in a general way.
2821    o CFC: improve formatting of output in CFC_ATMOS
2822    o PTRACERS:
2823      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
2824        that ALL experiments with ptracers enable can be checked. This makes
2825        GCHEM_MONITOR obsolete.
2826      - include a runtime parameter PTRACERS_monitorFreq that defaults to
2827        monitorFreq
2828      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
2829    o add PTRACERS (PTR0[1-5]) to testreport output
2830    o exf_check_range:
2831      * default changed to .TRUE.
2832      * will check values for niter0 if debLevA, every timestep if debLevB
2833      * STOP in exf_check_range if 'out of range'
2834      * range chosen generous to allow for potential extema
2835      TBD: a version with stricter range
2836           permitted range would be runtime parameters
2837    o GMredi:
2838      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
2839      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
2840      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
2841    o GCHEM:
2842      - move call to GCHEM_FORCING_SEP, so that it is now called before
2843        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
2844      - introduced a useGCHEM runtime flag and applied it everywhere.
2845      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
2846        this flag is now only visible within GCHEM-pkg routines.
2847      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
2848        be replaced by a 3D array that is computed before thermodynamics; for
2849        this, the tracer ID iTracer had to be included into the parameter list
2850        of ptracers_forcing
2851      - set up forward_step to call gchem_forcing, that will replace
2852        gchem_forcing_int in ptracers_forcing
2853      - cleaning up
2854    o small cleaning of exch2: remove files that are also in eesupp/src
2855    
2856    checkpoint56 (2004/11/17)
2857    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
2858    o mnc: cleanup "full" files--fixes out-of-memory problem
2859    o ECCO-GODAE
2860      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
2861      * fully merged and updated from SIO code
2862        windstress sign change affects
2863        - exf_inscal_[u/v]stress
2864        - sign of xx_tau[u/v] adjustments
2865        - signs in cost_scat
2866      * ctrl_get_gen: avoid update of tau[u/v] for first few days
2867      * natl_box_adjoint updated and compressed
2868      * 2-level checkpoint switch added
2869        (tested in EXP. 1 of natl_box_adjoint)
2870      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
2871    o SVD
2872      * first complete, non-hacked version for SVD calculations
2873      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
2874        performed via direct access files admtlm_vector.it????
2875        (via ctrl_[un]pack)
2876      * optimcycle is used for ARPACK iteration counter
2877        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
2878      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
2879        and add linear transforms where necessary
2880      * controls are initial/final SST, SSS (can be extended; need to check
2881        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
2882    o mdsio: filename info to both stderr, stdout
2883    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
2884      from sign change
2885    
2886    checkpoint55j_post (2004/11/10)
2887    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
2888      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2889    o add consistent build directories and .cvsignore files to verification
2890    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
2891    o make all subroutines 30 or less characters in length for certain older
2892      compilers to work (a thorough search only turns up two routines in
2893      pkg/ptracers)
2894    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
2895      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2896    
2897    checkpoint55i_post (2004/10/28)
2898    o change arrays for total vertical diffusivity (2.D if explicit,
2899      3.D if implicit) ; each ptracer uses its own background value.
2900    o added mnc/NetCDF output capability to ocn_compon_interf
2901      - added bits to verification/cpl_aim+ocn so that it can run on
2902        ITRDA and other clusters without the mpirun "-wd" option
2903    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
2904      configuration
2905    o give MNC the ability to create additional files rather than
2906      exceeding a specified file size limit "MNC_MAX_FILESIZE"
2907      - the default is just less than 2GB which is a practical limit
2908        on many systems
2909    o Compute the non-local term using either KPP vertical diffusivity (=default)
2910       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
2911    
2912    checkpoint55h_post (2004/10/20)
2913    o add verification test "vermix"
2914    o remove all the *_ioinc flags and replace with the single global
2915      outputTypesInclusive flag
2916    o allow to set a vertical profile of vertical diffusivity for T & S
2917    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
2918    o useMNC moved from data.mnc to data.pkg
2919    
2920    checkpoint55g_post (2004/10/14)
2921    o Renaming carbon AD experiments to comply with testreport conventions
2922    o Updating adjoint of Held-Suarez hs94.1x64x5
2923    o Fixing directives for non-ECCO forward_step, after ECCO directives
2924      have been fixed to avoid recomp. of do_oceanic_phys
2925      Works well for global_ocean.90x40x15,
2926      but recomp. issue remains for carbon
2927    o Updating adjoint output for natl_box_adjoint after
2928      pkg/ecco has been modified (see taga c55d_post)
2929    
2930    checkpoint55f_post (2004/10/13)
2931    o rename to timeave_init_fixed
2932    
2933    checkpoint55e_post (2004/10/13)
2934    o some delicate re-shuffle of store directives to avoid one
2935      extra call of do_oceanic_physics
2936      affects ecco_the_main_loop.F, do_oceanic_physics.F
2937      checkpoint_lev1_directives.h
2938    o NB: this may break global_ocean adjoint temporarily,
2939      but it is clear how to fix it. Will do later, need this now.
2940    
2941    checkpoint55d_post (2004/10/11)
2942    o ECCO specific cost function terms (up-to-date with 1x1 runs)
2943    o ecco_cost_weights is modified to 1x1 runs
2944    o modifs to allow observations to be read in as
2945      single file or yearly files
2946    o enable to read exf forcing fields as either
2947      single file or yearly files (flag useExfYearlyFields)
2948    checkpoint55d_pre (2004/10/08)
2949    
2950    o switch between 2-level and 3-level checkpointing
2951    o add ability of MNC to write local and "partial" (eg. 2D slices where
2952      the full 3D field is never actually stored) arrays to NetCDF files
2953      with the correct (that is, the complete multi-dimensional) set of
2954      array indicies
2955      - used in mom_vecinv() to write the diagFreq output
2956      - tested (demonstrated) in verification/aim.5l_cs
2957    o further mnc-ification
2958      - add verification/lab_sea to the list with mnc setups
2959      - fix undefined mnc v-names in cd_code
2960      - add kpp to mnc output (both snapshot and timeave)
2961    o non-hydrostatic code
2962      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
2963        in calc_gw.F
2964      - defaults to viscAh
2965      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
2966        friction or Leith) in non-hydrostatic mode, as long as there is
2967        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
2968    o pkg/cost
2969      extend simple cost functions to treat time mean quantities
2970      (T,U,V) via cost_accumulate_state from cost_tile
2971  o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to  o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
2972      be 2 times larger than the minimum size the advection scheme requires.      be 2 times larger than the minimum size the advection scheme requires.
2973      now get a perfect conservation of salt in advect_cs test-exp (updated)      now get a perfect conservation of salt in advect_cs test-exp (updated)
# Line 26  o more obcs stuff Line 2991  o more obcs stuff
2991    - changed sponge layer relaxation parameter units for days to seconds    - changed sponge layer relaxation parameter units for days to seconds
2992    - turned off sponge layer by default    - turned off sponge layer by default
2993    - changed argument list of OBCS_CALC to myTime+deltaTclock    - changed argument list of OBCS_CALC to myTime+deltaTclock
2994      - fixed about 35 bugs in obcs_external_fields_load
2995    
2996  checkpoint55c_post  checkpoint55c_post (2004/09/23)
2997  o obcs stuff  o obcs stuff
2998    - new runtime flags useOBCSprescribe, useOBCSbalance    - new runtime flags useOBCSprescribe, useOBCSbalance
2999    - re-arranged obcs_calc    - re-arranged obcs_calc
# Line 41  o obcs stuff Line 3007  o obcs stuff
3007  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
3008    which simplifies the calls and passes the ifc check-bounds test    which simplifies the calls and passes the ifc check-bounds test
3009    
3010  checkpoint55b_post  checkpoint55b_post (2004/09/22)
3011  o add a 2D scalar, Z location, exchange_2 routine.  o add a 2D scalar, Z location, exchange_2 routine.
3012  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
3013    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
# Line 52  o use a more standard discretization for Line 3018  o use a more standard discretization for
3018  o fix gad_advection.F (CubedSphere part), back to version 1.23  o fix gad_advection.F (CubedSphere part), back to version 1.23
3019  o fix bug in mom_vi_del2uv.F (CubedSphere part).  o fix bug in mom_vi_del2uv.F (CubedSphere part).
3020    
3021  checkpoint55a_post  checkpoint55a_post (2004/09/20)
3022  o merged code to  o merged code to
3023    * prescribe/read time-dependent open boundaries    * prescribe/read time-dependent open boundaries
3024      (works in conjunction with exf, cal)      (works in conjunction with exf, cal)
# Line 60  o merged code to Line 3026  o merged code to
3026    * each boundary N/S/E/W now has its own CPP option    * each boundary N/S/E/W now has its own CPP option
3027      (healthy for the adjoint)      (healthy for the adjoint)
3028    
3029  checkpoint55  checkpoint55 (2004/09/17)
3030  o up-to-date adjoint of previous breaks  o up-to-date adjoint of previous breaks
3031    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
3032    - global_ocean_ebm: adjoint still needs fix (TLM ok)    - global_ocean_ebm: adjoint still needs fix (TLM ok)
# Line 70  o up-to-date adjoint of previous breaks Line 3036  o up-to-date adjoint of previous breaks
3036  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
3037    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
3038    
3039  checkpoint54f_post  checkpoint54f_post (2004/09/16)
3040  o in verification/carbin/ remove experiment related to  o in verification/carbin/ remove experiment related to
3041    ALLOW_PASSIVE_TRACER (array tr1 etc)    ALLOW_PASSIVE_TRACER (array tr1 etc)
3042    code_ad/ input_ad/ results_ad    code_ad/ input_ad/ results_ad
# Line 96  o overhaul of IO so that we now have fla Line 3062  o overhaul of IO so that we now have fla
3062    - numerous small formatting cleanups for ProTeX    - numerous small formatting cleanups for ProTeX
3063  o add version info (via BUILD_INFO.h) to MNC and stdout  o add version info (via BUILD_INFO.h) to MNC and stdout
3064    
3065  checkpoint54e_post  checkpoint54e_post (2004/09/02)
3066  o add two new packages  o add two new packages
3067    - pp81 (Packanowski and Philander, 1981), Richardson number and    - pp81 (Packanowski and Philander, 1981), Richardson number and
3068      stratification dependent mixing      stratification dependent mixing
3069    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
3070    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
3071      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
3072      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
3073  o add offline package  o add offline package
3074  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
3075    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
3076  o genmake2: add ability to search for C compilers and cleanup test output  o genmake2: add ability to search for C compilers and cleanup test output
3077    - fixes recent SX-6 problems and should help with others (eg. HP-UX)    - fixes recent SX-6 problems and should help with others (eg. HP-UX)
3078    
3079  checkpoint54d_post  checkpoint54d_post (2004/07/27)
3080  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
3081  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
3082    leading to additional shift by 5 days each year of integration    leading to additional shift by 5 days each year of integration
# Line 126  o fix a bug in Flux deriv. vs Ts (pkg/ai Line 3092  o fix a bug in Flux deriv. vs Ts (pkg/ai
3092  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
3093  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
3094    
3095  checkpoint54c_post  checkpoint54c_post (2004/07/18)
3096  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
3097    this affects (truncation error) output.txt of test-exp:    this affects (truncation error) output.txt of test-exp:
3098     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
# Line 137  o define the max number of passive trace Line 3103  o define the max number of passive trace
3103  o start to test mnc routinely in exp0  o start to test mnc routinely in exp0
3104  o add sea-ice loading (sIceLoad) as a new forcing field.  o add sea-ice loading (sIceLoad) as a new forcing field.
3105    
3106  checkpoint54b_post  checkpoint54b_post (2004/07/08)
3107  o add testreport "-j JOBS" option for parallel builds (tested and pretty  o add testreport "-j JOBS" option for parallel builds (tested and pretty
3108     impressive on Altix and Opteron systems)     impressive on Altix and Opteron systems)
3109  o diagnostics can now write NetCDF files through the mnc package  o diagnostics can now write NetCDF files through the mnc package
# Line 147  o staggerTimeStep & NLFS: rescale T & S Line 3113  o staggerTimeStep & NLFS: rescale T & S
3113    affects (truncation error) output of lab_sea & natl_box exp.: updated    affects (truncation error) output of lab_sea & natl_box exp.: updated
3114  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
3115    
3116  checkpoint54a_post  checkpoint54a_post (2004/07/06)
3117  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
3118  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
3119  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
3120  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
3121    + internal_wave (shift in writing cg2d_ini_res)    + internal_wave (shift in writing cg2d_ini_res)
3122  checkpoint54a_pre  checkpoint54a_pre (2004/07/05)
3123    
3124  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
3125    - modified verification/lab_sea and natl_box_adjoint accordingly    - modified verification/lab_sea and natl_box_adjoint accordingly
3126    
3127  checkpoint54  checkpoint54 (2004/07/02)
3128  checkpoint53g_post  checkpoint53g_post (2004/07/02)
3129  o prepare splitting of thermodynamics: store convect.counter in common block  o prepare splitting of thermodynamics: store convect.counter in common block
3130  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
3131    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
# Line 168  o new parameter "nShapS": allow to treat Line 3134  o new parameter "nShapS": allow to treat
3134  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
3135  o restore adjointability  o restore adjointability
3136    
3137  checkpoint53f_post  checkpoint53f_post (2004/06/25)
3138  o modifications that affect AIM experiment results (update output.txt):  o modifications that affect AIM experiment results (update output.txt):
3139    - no advection of S at top interface Nr (pkg/generic_advdiff)    - no advection of S at top interface Nr (pkg/generic_advdiff)
3140    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
# Line 181  o merged cylindrical coord configuration Line 3147  o merged cylindrical coord configuration
3147  o added rotating_tank experiment  o added rotating_tank experiment
3148  checkpoint53e_pre  checkpoint53e_pre
3149    
3150  checkpoint53d_post  checkpoint53d_post (2004/06/14)
3151  o faulks upgraded: re-generate output.txt that have changed:  o faulks upgraded: re-generate output.txt that have changed:
3152     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
3153  o Added Bryan and Lewis, 1979, vertical diffusivity profile  o Added Bryan and Lewis, 1979, vertical diffusivity profile
# Line 200  o regenerated output for global_ocean_eb Line 3166  o regenerated output for global_ocean_eb
3166  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
3167    of mom_common/    of mom_common/
3168    - simple re-arrangement of instructions within computing loop    - simple re-arrangement of instructions within computing loop
3169  checkpoint53d_pre  checkpoint53d_pre (2004/05/21)
3170    
3171  checkpoint53c_post  checkpoint53c_post (2004/05/21)
3172  o new version of coupler for AIM+thSIce and Ocean models  o new version of coupler for AIM+thSIce and Ocean models
3173   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
3174   - land: change Evaporation of snow   - land: change Evaporation of snow
# Line 219  o Adjoint of EBM package + verification Line 3185  o Adjoint of EBM package + verification
3185    * TLM OK    * TLM OK
3186    * ADM not sufficient accuracy yet (needs further testing)    * ADM not sufficient accuracy yet (needs further testing)
3187    
3188  checkpoint53b_post  checkpoint53b_post (2004/05/14)
3189  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository
3190    * package is pkg/ebm    * package is pkg/ebm
3191    * verif. is verification/global_ocean_ebm    * verif. is verification/global_ocean_ebm
# Line 237  C        Destabilization of the thermoha Line 3203  C        Destabilization of the thermoha
3203  C        by atmospheric eddy transports.  C        by atmospheric eddy transports.
3204  C        J. Climate 7(12), 1870-1882  C        J. Climate 7(12), 1870-1882
3205  o Will need long integration testing.  o Will need long integration testing.
3206  checkpoint53b_pre  checkpoint53b_pre (2004/05/14)
3207    
3208  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code
3209  o renamed and split ini_mnc_io  o renamed and split ini_mnc_io
# Line 245  o pkg/land: only liquid water can diffus Line 3211  o pkg/land: only liquid water can diffus
3211  o AIM using land: soil wetness availability account for snow  o AIM using land: soil wetness availability account for snow
3212  o added printMapIncludesZeros to EEPARMS namelist  o added printMapIncludesZeros to EEPARMS namelist
3213    
3214  checkpoint53a_post  checkpoint53a_post (2004/05/11)
3215  o restore TAMC compatiility for exf_constants.h  o restore TAMC compatiility for exf_constants.h
3216    (no usage of _d in .h)    (no usage of _d in .h)
3217  o Additional storing in KPP in an attempt to fix  o Additional storing in KPP in an attempt to fix
# Line 258  o Fixed verification/natl_box_adjoint ex Line 3224  o Fixed verification/natl_box_adjoint ex
3224    and hence gives results closer to that of Experiment 2.    and hence gives results closer to that of Experiment 2.
3225    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
3226    
3227  checkpoint53  checkpoint53 (2004/05/06)
3228  o stable checkpoint with up to date adjoint  o stable checkpoint with up to date adjoint
3229    TLM tests only run for 1st grdchk at the moment. Its unclear if    TLM tests only run for 1st grdchk at the moment. Its unclear if
3230    this is a code problem or a problem with resetting code for g_    this is a code problem or a problem with resetting code for g_
# Line 268  o stable checkpoint with up to date adjo Line 3234  o stable checkpoint with up to date adjo
3234     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
3235       are both still in chaos following their security messes.       are both still in chaos following their security messes.
3236    
3237  checkpoint52n_post  checkpoint52n_post (2004/05/06)
3238  o various build (mostly genmake2) changes including:  o various build (mostly genmake2) changes including:
3239    - ability to build/run more easily within Cygwin and MacOS X    - ability to build/run more easily within Cygwin and MacOS X
3240    - more complicated Makefiles with a stronger dependence on Gnu Make    - more complicated Makefiles with a stronger dependence on Gnu Make
# Line 299  o fix in pkg/thsice: Line 3265  o fix in pkg/thsice:
3265    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
3266   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
3267    
3268  checkpoint52m_post  checkpoint52m_post (2004/04/18)
3269  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;
3270    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
3271    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 331  o test exp. advect_cs: use the standard Line 3297  o test exp. advect_cs: use the standard
3297  o Added functionality to grdchk:  o Added functionality to grdchk:
3298    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.
3299    
3300  checkpoint52l_post  checkpoint52l_post (2004/03/11)
3301  o new land formulation:  o new land formulation:
3302    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
3303       energy conservation.       energy conservation.
# Line 342  o aim_v23 modification for new land mode Line 3308  o aim_v23 modification for new land mode
3308    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
3309       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
3310    b) add snow precipitation.    b) add snow precipitation.
3311  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
3312    
3313  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
3314  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 355  o fix ini_curvilinear_grid ; test CS exp Line 3321  o fix ini_curvilinear_grid ; test CS exp
3321  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
3322  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
3323    
3324  checkpoint52k_post  checkpoint52k_post (2004/02/23)
3325  o removed top-level directory "diags"  o removed top-level directory "diags"
3326    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
3327  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 368  o set all ...Freq to zero after cost_fin Line 3334  o set all ...Freq to zero after cost_fin
3334    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
3335  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
3336    
3337  checkpoint52j_post  checkpoint52j_post (2004/02/18)
3338  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
3339  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
3340  o Really weird thing!  o Really weird thing!
# Line 376  o Really weird thing! Line 3342  o Really weird thing!
3342    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
3343    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
3344    after cost_final call which should not be there!    after cost_final call which should not be there!
3345  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
3346    
3347  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
3348    error messages    error messages
# Line 393  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 3359  o merged mom_vi_calc_relvort3.F, mom_vi_
3359    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
3360  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
3361    
3362  checkpoint52i_post  checkpoint52i_post (2004/01/21)
3363  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
3364  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
3365  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
3366    
3367  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
3368    the old pkg/aim).    the old pkg/aim).
3369    
3370  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
3371  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
3372  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
3373  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 412  o added temporary hack for sea-ice dynam Line 3378  o added temporary hack for sea-ice dynam
3378    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
3379    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.
3380    
3381  checkpoint52f_post  checkpoint52f_post (2004/01/09)
3382  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
3383  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
3384  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
3385  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
3386    
3387  checkpoint52e_post  checkpoint52e_post (2004/01/07)
3388  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
3389    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
3390  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 426  o step.1 : rewrite (as in MultiDimAdvec) Line 3392  o step.1 : rewrite (as in MultiDimAdvec)
3392  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.
3393  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:
3394   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
3395  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
3396    
3397  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
3398  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 437  o added exf_offset_atemp for Celsius to Line 3403  o added exf_offset_atemp for Celsius to
3403  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
3404  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
3405    
3406  checkpoint52d_post  checkpoint52d_post (2003/12/16)
3407  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
3408    - updated output accordingly    - updated output accordingly
3409    - 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 466  o check-in the first version of the coup Line 3432  o check-in the first version of the coup
3432  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
3433     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
3434    
3435  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
3436  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
3437  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
3438    
3439  checkpoint52c_post  checkpoint52c_post (2003/11/25)
3440  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
3441    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
3442    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 484  o Removed all CPP options for cal packag Line 3450  o Removed all CPP options for cal packag
3450  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
3451  o corrected key comp. for passkey  o corrected key comp. for passkey
3452    
3453  checkpoint52b_post  checkpoint52b_post (2003/11/23)
3454  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
3455   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
3456   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 492  o new version: "thsice" of thermodynamic Line 3458  o new version: "thsice" of thermodynamic
3458   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
3459     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
3460  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
3461  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
3462    
3463  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
3464  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 502  o missing PTRACERS headers in some routi Line 3468  o missing PTRACERS headers in some routi
3468  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
3469    to ensure proper customization    to ensure proper customization
3470    
3471  checkpoint52a_post  checkpoint52a_post (2003/11/17)
3472  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
3473    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3474    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 517  o fix problem with ECCO-related divided Line 3483  o fix problem with ECCO-related divided
3483    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
3484    but no warning issued by TAF    but no warning issued by TAF
3485    
3486  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
3487  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
3488    
3489  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
3490  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
3491    
3492  checkpoint51u_post  checkpoint51u_post (2003/11/06)
3493  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
3494    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
3495  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 538  o top level routines the_main_loop, forw Line 3504  o top level routines the_main_loop, forw
3504    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
3505  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
3506    
3507  checkpoint51t_post  checkpoint51t_post (2003/11/04)
3508  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
3509    
3510  checkpoint51s_post  checkpoint51s_post (2003/11/04)
3511  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
3512  o pkg/grdchk  o pkg/grdchk
3513    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 550  o pkg/grdchk Line 3516  o pkg/grdchk
3516    - additional high-precision output for testreport    - additional high-precision output for testreport
3517      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
3518    
3519  checkpoint51r_post  checkpoint51r_post (2003/11/03)
3520  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
3521  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
3522    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
3523    
3524  checkpoint51q_post  checkpoint51q_post (2003/10/30)
3525  o cd_code:  o cd_code:
3526    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
3527    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 571  o ctrl package totally restructured Line 3537  o ctrl package totally restructured
3537    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
3538  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
3539    
3540  checkpoint51p_post  checkpoint51p_post (2003/10/30)
3541  o create initial cd_code package  o create initial cd_code package
3542    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
3543      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 586  o create initial cd_code package Line 3552  o create initial cd_code package
3552  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
3553  o cleanup testreport  o cleanup testreport
3554    
3555  checkpoint51o_post  checkpoint51o_post (2003/10/27)
3556  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
3557    - carbon/    - carbon/
3558    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 607  o Correcting initialisations for fVerU, Line 3573  o Correcting initialisations for fVerU,
3573  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
3574    fVerU, fVerV    fVerU, fVerV
3575  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
3576  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
3577    
3578  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
3579  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 615  o added the [#include "AD_CONFIG.h"] sta Line 3581  o added the [#include "AD_CONFIG.h"] sta
3581   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
3582   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
3583    
3584  checkpoint51n_post  checkpoint51n_post (2003/10/23)
3585  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
3586    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3587    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 624  o modifications to make FREEZE flux visi Line 3590  o modifications to make FREEZE flux visi
3590       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
3591  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
3592    
3593  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
3594  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
3595  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
3596    defines:    defines:
# Line 632  o added [#include "AD_CONFIG.h"] to all Line 3598  o added [#include "AD_CONFIG.h"] to all
3598    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
3599    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
3600    
3601  checkpoint51m_post  checkpoint51m_post (2003/10/21)
3602  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
3603    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
3604    - various cleanups related to package handling    - various cleanups related to package handling
3605    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
3606    
3607  checkpoint51l_post  checkpoint51l_post (2003/10/20)
3608  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
3609   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
3610   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
3611   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
3612     model integration time     model integration time
3613    
3614  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
3615  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)
3616  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.
3617  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
3618     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
3619    
3620  checkpoint51k_post  checkpoint51k_post (2003/10/16)
3621  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
3622   - 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):
3623     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 665  o added an include barrier to the defaul Line 3631  o added an include barrier to the defaul
3631    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
3632  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
3633    
3634  checkpoint51j_post  checkpoint51j_post (2003/10/10)
3635  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
3636  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
3637  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 679  o Moving pkg-specific flow directives to Line 3645  o Moving pkg-specific flow directives to
3645         - pkg_ad_diff.list         - pkg_ad_diff.list
3646         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
3647    
3648  checkpoint51i_post  checkpoint51i_post (2003/10/09)
3649  o merge of the branch-genmake2  o merge of the branch-genmake2
3650    - knowingly breaks the older genmake    - knowingly breaks the older genmake
3651    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
3652    - new testreport supersedes older testscript    - new testreport supersedes older testscript
3653  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
3654  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
3655    
3656  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
3657  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 697  o modify gchem pkg to be more versatile Line 3663  o modify gchem pkg to be more versatile
3663  o modifications to clean up dic pkg  o modifications to clean up dic pkg
3664  o add pkg/cfc  o add pkg/cfc
3665    
3666  checkpoint51g_post  checkpoint51g_post (2003/10/02)
3667  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
3668  o start removing verification/vero/  o start removing verification/vero/
3669  o update AD-related stuff  o update AD-related stuff
# Line 705  o update AD-related stuff Line 3671  o update AD-related stuff
3671  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
3672    vector invariant setup    vector invariant setup
3673    
3674  checkpoint51f_post  checkpoint51f_post (2003/10/02)
3675  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)
3676  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
3677    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
3678    
3679  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
3680  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
3681      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
3682    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 722  o Bug fix to pkg/ptracers, pkg/generic_a Line 3688  o Bug fix to pkg/ptracers, pkg/generic_a
3688      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
3689      non-local transport term.      non-local transport term.
3690    
3691  checkpoint51e_post  checkpoint51e_post (2003/08/03)
3692  o pkg/mom_vecinv:  o pkg/mom_vecinv:
3693    - 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)
3694    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 732  o atmospheric geopotential: - include wa Line 3698  o atmospheric geopotential: - include wa
3698  o land pkg: read initial state from files.  o land pkg: read initial state from files.
3699  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
3700    
3701  checkpoint51d_post  checkpoint51d_post (2003/07/18)
3702  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
3703    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
3704  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 745  o Use cluster local disks for purely loc Line 3711  o Use cluster local disks for purely loc
3711    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
3712    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
3713    
3714  checkpoint51c_post  checkpoint51c_post (2003/07/08)
3715  o introducing integer flag debugLevel  o introducing integer flag debugLevel
3716    - debLevZero: suppress all output    - debLevZero: suppress all output
3717    - debLevA: standard    - debLevA: standard
# Line 768  o added verification for adjoint with pt Line 3734  o added verification for adjoint with pt
3734    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
3735  <<<checkpoint51b_pre  <<<checkpoint51b_pre
3736    
3737  checkpoint51a_post  checkpoint51a_post (2003/06/25)
3738  o added code for biogeochemistry package  o added code for biogeochemistry package
3739    - new pkgs: dic, gchem    - new pkgs: dic, gchem
3740    - new subroutine in ptracers    - new subroutine in ptracers
3741  o modify code for biogeo packages  o modify code for biogeo packages
3742    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
3743    
3744  checkpoint51  checkpoint51 (2003/06/24)
3745  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
3746    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
3747    kept separate packages    kept separate packages
# Line 783  o merged improved packages from ecco-bra Line 3749  o merged improved packages from ecco-bra
3749  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
3750    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
3751    
3752  checkpoint50i_post  checkpoint50i_post (2003/06/23)
3753  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
3754    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
3755    - 1st step: this one is differentiable    - 1st step: this one is differentiable
3756    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
3757                from ecco-branch)                from ecco-branch)
3758    
3759  checkpoint50h_post  checkpoint50h_post (2003/06/20)
3760  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
3761  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
3762  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 799  o New variable in PARM03 for more flexib Line 3765  o New variable in PARM03 for more flexib
3765  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
3766    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
3767    
3768  checkpoint50g_post  checkpoint50g_post (2003/05/23)
3769  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
3770    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
3771    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
3772      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
3773    
3774  checkpoint50f_post  checkpoint50f_post (2003/05/23)
3775  o exf totally restructured  o exf totally restructured
3776    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
3777      and made sure it's still differentiable      and made sure it's still differentiable
# Line 813  o exf totally restructured Line 3779  o exf totally restructured
3779    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
3780    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
3781    
3782  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
3783   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 ;
3784        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
3785   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 823  checkpoint50f_pre Line 3789  checkpoint50f_pre
3789   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
3790   o removed lots of single quotes from comments   o removed lots of single quotes from comments
3791    
3792  checkpoint50e_post  checkpoint50e_post (2003/05/14)
3793  o make KPP work with PTRACERS  o make KPP work with PTRACERS
3794   - 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
3795     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
3796   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
3797     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
3798  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
3799  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
3800    
3801  checkpoint50d_post  checkpoint50d_post (2003/05/13)
3802  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
3803    files analogous to write_state.F    files analogous to write_state.F
3804  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,
3805    analogous to the cg2d-related output.    analogous to the cg2d-related output.
3806  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,
3807    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
3808  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
3809    
3810  checkpoint50c_post  checkpoint50c_post (2003/05/12)
3811  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)
3812  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
3813  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.
3814  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
3815  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
3816    
3817  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
3818  Merging from release1_p13:  Merging from release1_p13:
3819  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
3820  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
3821    
3822  checkpoint50b_post  checkpoint50b_post (2003/04/17)
3823  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
3824  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
3825    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 862  o new flag "useCDscheme" (default=F); re Line 3828  o new flag "useCDscheme" (default=F); re
3828  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
3829     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
3830    
3831  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
3832  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
3833  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
3834    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
3835    
3836  checkpoint50a_post  checkpoint50a_post (2003/03/21)
3837  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
3838    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
3839    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
3840    in contradiction with new key itdkey.    in contradiction with new key itdkey.
3841    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
3842    
3843  checkpoint50  checkpoint50 (2003/03/08)
3844  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
3845    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
3846  - bug fix in find_alpha  - bug fix in find_alpha
# Line 882  checkpoint50 Line 3848  checkpoint50
3848  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
3849  - merged some sliced AD support routines  - merged some sliced AD support routines
3850    
3851  checkpoint49  checkpoint49 (2003/03/06)
3852  merged from ecco-branch:  merged from ecco-branch:
3853  o exf:  o exf:
3854    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 920  o DIVA: Line 3886  o DIVA:
3886    (see MITgcm manual).    (see MITgcm manual).
3887  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
3888    
3889  checkpoint48i_post  checkpoint48i_post (2003/03/05)
3890  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
3891    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
3892    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 938  o Modif. for DIVA: Line 3904  o Modif. for DIVA:
3904    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
3905    only relevant for ecco-branch)    only relevant for ecco-branch)
3906    
3907  checkpoint48h_post  checkpoint48h_post (2003/02/28)
3908  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
3909  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
3910  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
3911  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
3912    
3913  checkpoint48g_post  checkpoint48g_post (2003/02/18)
3914  --- EOS:  --- EOS:
3915  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
3916    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 958  o accurate phiHyd when using interface-W Line 3924  o accurate phiHyd when using interface-W
3924   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
3925  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
3926    
3927  checkpoint48f_post  checkpoint48f_post (2003/02/18)
3928  Merging from release1_p12:  Merging from release1_p12:
3929  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
3930    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 986  o pkg/seaice: Line 3952  o pkg/seaice:
3952    - adjoint-friendly modifications    - adjoint-friendly modifications
3953    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
3954    
3955  checkpoint48e_post  checkpoint48e_post (2003/02/12)
3956  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)
3957  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
3958    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 997  o following exp works with Olx=Oly=2 (an Line 3963  o following exp works with Olx=Oly=2 (an
3963      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
3964    (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)
3965    
3966  checkpoint48d_post  checkpoint48d_post (2003/02/09)
3967  o in preparation for r*:  o in preparation for r*:
3968   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
3969      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 1005  o in preparation for r*: Line 3971  o in preparation for r*:
3971      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
3972    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
3973    
3974  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
3975  o in preparation for r*:  o in preparation for r*:
3976    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.
3977    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.
3978    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.
3979  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
3980    
3981  checkpoint48c_post  checkpoint48c_post (2003/02/06)
3982  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
3983  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
3984    
3985  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
3986  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
3987  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)
3988    
3989  checkpoint48b_post  checkpoint48b_post (2003/01/27)
3990  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
3991   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
3992  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
3993    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
3994    
3995  checkpoint48a_post  checkpoint48a_post (2003/01/24)
3996  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
3997     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
3998    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
3999                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
4000    
4001  checkpoint48  checkpoint48 (2003/01/23)
4002  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')
4003    
4004  checkpoint47j_post  checkpoint47j_post (2003/01/21)
4005  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.
4006  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
4007  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 1054  o Yet more changes in gmredi: Line 4020  o Yet more changes in gmredi:
4020      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
4021  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
4022    
4023  checkpoint47i_post  checkpoint47i_post (2003/01/13)
4024  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.
4025  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)
4026    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 1070  o case GM_BOLUS_ADVEC should be cleaned Line 4036  o case GM_BOLUS_ADVEC should be cleaned
4036    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
4037  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
4038    
4039  checkpoint47g_post  checkpoint47g_post (2003/01/10)
4040  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
4041    (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)
4042  o After TAF bug fix:  o After TAF bug fix:
# Line 1096  Gradient checks OK for Line 4062  Gradient checks OK for
4062  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
4063  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
4064    
4065  checkpoint47f_post  checkpoint47f_post (2002/12/28)
4066  Merging from release1_p10:  Merging from release1_p10:
4067  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
4068    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 1108  o modifications for using pkg/exf with p Line 4074  o modifications for using pkg/exf with p
4074    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
4075      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
4076    
4077  checkpoint47e_post  checkpoint47e_post (2002/12/27)
4078  o created a tag prior to creating a branch  o created a tag prior to creating a branch
4079    
4080  checkpoint47d_post  checkpoint47d_post (2002/12/16)
4081  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
4082    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
4083  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
4084    oceanic pressure coordinates code    oceanic pressure coordinates code
4085  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
4086    also described in the tutorial section of the manual    also described in the tutorial section of the manual
4087  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
4088    
4089  checkpoint47c_post  checkpoint47c_post (2002/12/16)
4090  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
4091    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
4092    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 1132  o OCEANICP & realFreshWater: include P-E Line 4098  o OCEANICP & realFreshWater: include P-E
4098    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
4099  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
4100    
4101  checkpoint47b_post  checkpoint47b_post (2002/12/05)
4102  Merging from release1_p9:  Merging from release1_p9:
4103  o pkg/seaice  o pkg/seaice
4104    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 1149  o verification/lab_sea Line 4115  o verification/lab_sea
4115    - added missing matlab routines    - added missing matlab routines
4116    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
4117    
4118  checkpoint47a_post  checkpoint47a_post (2002/11/23)
4119  o new pkg: aim_v23  o new pkg: aim_v23
4120   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
4121     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 1166  o bulk_force and therm_seaice Line 4132  o bulk_force and therm_seaice
4132  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
4133     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
4134    
4135  checkpoint47  checkpoint47 (2002/11/15)
4136  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
4137  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
4138  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 1195  o Updated verification/carbon/ Line 4161  o Updated verification/carbon/
4161    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
4162    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
4163    
4164  checkpoint46n_post  checkpoint46n_post (2002/11/12)
4165  Merging from release1_p8:  Merging from release1_p8:
4166  o verification/natl_box:  o verification/natl_box:
4167    updating new external_fields_load routine    updating new external_fields_load routine
# Line 1249  o Adding new verification experiment glo Line 4215  o Adding new verification experiment glo
4215    the exf (and cal) package instead of the    the exf (and cal) package instead of the
4216    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
4217    
4218  checkpoint46m_post  checkpoint46m_post (2002/11/07)
4219  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
4220  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
4221    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 1262  o introduced flag for controllin non-hyd Line 4228  o introduced flag for controllin non-hyd
4228  o removed gravitySign from PARM04  o removed gravitySign from PARM04
4229  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
4230    
4231  checkpoint46l_post  checkpoint46l_post (2002/11/01)
4232  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
4233   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
4234     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 1275  o made convective adjustment work with p Line 4241  o made convective adjustment work with p
4241     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
4242     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
4243     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
4244  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
4245    
4246  checkpoint46k_post  checkpoint46k_post (2002/10/23)
4247  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
4248   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
4249   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 1291  o S/R aim_initialise.F replace S/R aim_i Line 4257  o S/R aim_initialise.F replace S/R aim_i
4257   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
4258   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
4259    
4260  checkpoint46j_post  checkpoint46j_post (2002/10/07)
4261  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
4262  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
4263  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)
4264  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
4265  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
4266    
4267  checkpoint46i_post  checkpoint46i_post (2002/09/25)
4268  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
4269    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
4270    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
4271    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 !
4272    
4273  checkpoint46h_post  checkpoint46h_post (2002/09/25)
4274  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
4275    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
4276      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 1314  o introduced new parameter rhoConstFresh Line 4280  o introduced new parameter rhoConstFresh
4280    value is 999.8 kg/m^3    value is 999.8 kg/m^3
4281  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
4282    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
4283  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
4284    
4285   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
4286   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
4287   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
4288    
4289  checkpoint46g_post  checkpoint46g_post (2002/09/18)
4290  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
4291    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
4292    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 1338  o cleaned up find_rho Line 4304  o cleaned up find_rho
4304    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
4305  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
4306    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
4307  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
4308    
4309  checkpoint46f_post  checkpoint46f_post (2002/09/16)
4310  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
4311    - extended active file handling to g_... files    - extended active file handling to g_... files
4312    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 1348  o Enable tangent linear (forward mode) g Line 4314  o Enable tangent linear (forward mode) g
4314  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
4315  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
4316    
4317  checkpoint46e_post  checkpoint46e_post (2002/09/05)
4318  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
4319    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
4320    - 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 1357  o Added new equation of state -> MDJWF Line 4323  o Added new equation of state -> MDJWF
4323    - 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
4324      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
4325      expect perfect matches for those      expect perfect matches for those
4326  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
4327    
4328  checkpoint46d_post  checkpoint46d_post (2002/08/19)
4329  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
4330    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
4331    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
4332    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
4333  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)
4334    in find_alpha/beta.    in find_alpha/beta.
4335  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
4336    
4337  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)
4338    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
4339    
4340  checkpoint46c_post  checkpoint46c_post (2002/08/15)
4341  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
4342   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
4343   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
4344      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).
4345   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
4346   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
4347  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
4348    
4349  checkpoint46b_post  checkpoint46b_post (2002/08/07)
4350  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
4351    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
4352    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 1389  o Added UNESCO EOS, but not recommended Line 4355  o Added UNESCO EOS, but not recommended
4355    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
4356  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
4357    unesco.f to be used with POLY3    unesco.f to be used with POLY3
4358  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
4359    
4360  checkpoint46a_post  checkpoint46a_post (2002/07/31)
4361  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
4362    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
4363    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
4364  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
4365  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
4366  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
4367    
4368  checkpoint46  checkpoint46 (2002/07/13)
4369  further merges from release1_p5  further merges from release1_p5
4370  o new ctrl package  o new ctrl package
4371    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 1426  o added hooks for Eliassen Palm fluxes ( Line 4392  o added hooks for Eliassen Palm fluxes (
4392  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
4393  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
4394    
4395  checkpoint45d_post  checkpoint45d_post (2002/07/12)
4396  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
4397  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
4398    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 1440  o add new flags: Line 4406  o add new flags:
4406   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
4407  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
4408    
4409  checkpoint45c_post  checkpoint45c_post (2002/05/30)
4410  o Removed f90 comments ("!")  o Removed f90 comments ("!")
4411  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
4412    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 1448  o modifications to gradient check packag Line 4414  o modifications to gradient check packag
4414    - enable centered differences    - enable centered differences
4415    - modified format of standard output    - modified format of standard output
4416    
4417  checkpoint45b_post  checkpoint45b_post (2002/05/30)
4418  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
4419  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
4420  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1460  o in initialise_varia, moved call packag Line 4426  o in initialise_varia, moved call packag
4426    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
4427  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
4428    
4429  checkpoint45a_post  checkpoint45a_post (2002/05/01)
4430  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
4431  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
4432  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 1480  o errorMessageUnit set non-equal zero in Line 4446  o errorMessageUnit set non-equal zero in
4446    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
4447  o modified carbon verif.  o modified carbon verif.
4448    
4449  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
4450  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
4451    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
4452  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
4453    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.
4454    
4455  checkpoint44g_post  checkpoint44g_post (2002/03/05)
4456  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
4457    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
4458    
# Line 1551  o merge of relevant stuff from the ecco- Line 4517  o merge of relevant stuff from the ecco-
4517  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
4518  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
4519    
4520  checkpoint44  checkpoint44 (2002/01/18)
4521  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
4522  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)
4523  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 1559  o update AIM experiments (NCEP input fil Line 4525  o update AIM experiments (NCEP input fil
4525  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
4526  o added some stuff for AD  o added some stuff for AD
4527    
4528  checkpoint43  checkpoint43 (2001/09/28)
4529  o added two new advection tests  o added two new advection tests
4530  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
4531  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
4532  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
4533    
4534  checkpoint42  checkpoint42 (2001/09/27)
4535    Fixed AD-related problems:    Fixed AD-related problems:
4536  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
4537    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1577  o Modified store directives for split of Line 4543  o Modified store directives for split of
4543    for the case ALLOW_KPP    for the case ALLOW_KPP
4544  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
4545    
4546  checkpoint41  checkpoint41 (2001/09/27)
4547  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
4548    to work with protex    to work with protex
4549    
4550  checkpoint40  checkpoint40 (2001/09/27)
4551  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
4552  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
4553  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1590  o more mods for non-linear free-surface Line 4556  o more mods for non-linear free-surface
4556  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
4557  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
4558    
4559  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
4560  o added DST advection schemes  o added DST advection schemes
4561  o fix MPI bug on SGI's  o fix MPI bug on SGI's
4562  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1600  o changes to commenting of arguments for Line 4566  o changes to commenting of arguments for
4566  o added/updated many matlab scripts  o added/updated many matlab scripts
4567  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
4568        
4569  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
4570  o new package rw/  o new package rw/
4571    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
4572    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1619  o TAMC-related update to cope with mom_f Line 4585  o TAMC-related update to cope with mom_f
4585    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
4586    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
4587    
4588  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
4589  o bug fix in dynamics.F  o bug fix in dynamics.F
4590    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
4591  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
4592  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
4593    related to TAF    related to TAF
4594    
4595  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
4596  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
4597  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
4598    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1634  o corresponding split of calc_diffusivit Line 4600  o corresponding split of calc_diffusivit
4600  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
4601  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
4602    
4603  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
4604  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
4605    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
4606  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 1648  o added new expt "solid-body.cs-32x32x1" Line 4614  o added new expt "solid-body.cs-32x32x1"
4614    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
4615      is not necessarily any better than the current one...      is not necessarily any better than the current one...
4616    
4617  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
4618  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
4619    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
4620  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1656  o extended iMin,jMin range for calc_comm Line 4622  o extended iMin,jMin range for calc_comm
4622  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
4623  o a few minor updates and fixes  o a few minor updates and fixes
4624    
4625  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
4626  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
4627  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
4628  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
4629    
4630  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
4631  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
4632  o Added gradient check package  o Added gradient check package
4633  o Added routines for passive tracer handling  o Added routines for passive tracer handling
4634  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
4635    
4636  checkpoint39  checkpoint39 (2001/05/14)
4637   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
4638     (mainly missing or wrong directives)     (mainly missing or wrong directives)
4639   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 1681  checkpoint39 Line 4647  checkpoint39
4647           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
4648   o disabled some packages by default in genmake   o disabled some packages by default in genmake
4649    
4650  checkpoint38  checkpoint38 (2001/04/10)
4651   o see notes_c37_adj.txt   o see notes_c37_adj.txt
4652   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
4653   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1689  checkpoint38 Line 4655  checkpoint38
4655     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
4656   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
4657    
4658  checkpoint37  checkpoint37 (2001/03/13)
4659   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
4660     (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
4661      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1706  checkpoint37 Line 4672  checkpoint37
4672   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
4673   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
4674    
4675  checkpoint36  checkpoint36 (2001/02/20)
4676   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
4677   o recover Time-Average diagnostics   o recover Time-Average diagnostics
4678   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
4679   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
4680    
4681  checkpoint35  checkpoint35 (2001/02/08)
4682   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
4683   o allows staggered time-stepping   o allows staggered time-stepping
4684   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
4685   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
4686    
4687  checkpoint34  checkpoint34 (2001/01/30)
4688   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
4689   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
4690     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1729  checkpoint34 Line 4695  checkpoint34
4695   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
4696   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
4697    
4698  checkpoint33  checkpoint33 (2000/11/30)
4699   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
4700   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
4701     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1747  checkpoint33 Line 4713  checkpoint33
4713       possibly use them.       possibly use them.
4714   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
4715    
4716  checkpoint32  checkpoint32 (2000/11/13)
4717   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
4718     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
4719   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1758  checkpoint32 Line 4724  checkpoint32
4724   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
4725   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
4726    
4727  checkpoint31  checkpoint31 (2000/09/11)
4728   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
4729     -> new routines packages_...F     -> new routines packages_...F
4730     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1775  checkpoint31 Line 4741  checkpoint31
4741     - not yet tested for GMRedi.     - not yet tested for GMRedi.
4742     - not yet tested for KPP.     - not yet tested for KPP.
4743    
4744  checkpoint30  checkpoint30 (2000/07/13)
4745   o Updates for OBCs   o Updates for OBCs
4746   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
4747   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1784  checkpoint30 Line 4750  checkpoint30
4750   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.)
4751     and entry for T90 in genmake     and entry for T90 in genmake
4752    
4753  checkpoint29  checkpoint29 (2000/06/21)
4754   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
4755    
4756  checkpoint28  checkpoint28 (2000/06/09)
4757   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
4758   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
4759   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 1800  checkpoint28 Line 4766  checkpoint28
4766     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
4767   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
4768    
4769  checkpoint27  checkpoint27 (2000/04/10)
4770   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
4771     formulation works properly with variable resolution.     formulation works properly with variable resolution.
4772   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 1808  checkpoint27 Line 4774  checkpoint27
4774   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
4775     in new routine ini_psurf()     in new routine ini_psurf()
4776    
4777  checkpoint26  checkpoint26 (2000/04/05)
4778   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
4779     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
4780   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 1818  checkpoint26 Line 4784  checkpoint26
4784     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
4785   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
4786    
4787  checkpoint25  checkpoint25 (2000/03/15)
4788   o updates for OBCs and NH   o updates for OBCs and NH
4789   o dramatically reduced memory usage   o dramatically reduced memory usage
4790   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 1829  checkpoint25 Line 4795  checkpoint25
4795      an explicit free-surface option)      an explicit free-surface option)
4796   o initial state input files for U and V   o initial state input files for U and V
4797    
4798  checkpoint24  checkpoint24 (1999/08/02)
4799   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
4800   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
4801   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
4802    
4803  checkpoint23  checkpoint23 (1999/05/26)
4804   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
4805   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
4806    
4807  checkpoint22  checkpoint22 (1999/05/18)
4808   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
4809   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
4810    
4811  checkpoint21  checkpoint21 (1999/05/18)
4812   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)
4813   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
4814   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
4815   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
4816    
4817  checkpoint20  checkpoint20 (1999/03/22)
4818   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
4819   o Added non-hydrostatic code   o Added non-hydrostatic code
4820   o Fixed some input data   o Fixed some input data
4821   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
4822    
4823  checkpoint19  checkpoint19 (1998/12/15)
4824   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
4825   o Added new code for open boundaries.   o Added new code for open boundaries.
4826   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 1862  checkpoint19 Line 4828  checkpoint19
4828   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
4829   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.
4830    
4831  checkpoint18  checkpoint18 (1998/11/30)
4832   o Further changes for optional code generation with   o Further changes for optional code generation with
4833     CPP - ugh!     CPP - ugh!
4834    
4835  checkpoint17  checkpoint17 (1998/11/03)
4836   o Beginning to incorporating modularity   o Beginning to incorporating modularity
4837     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
4838   o Small changes for TAMC complinace   o Small changes for TAMC complinace
4839   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
4840     configuration "exp0".     configuration "exp0".
4841    
4842  checkpoint16  checkpoint16 (1998/10/28)
4843   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
4844     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
4845     assignment is an addition.     assignment is an addition.
# Line 1881  checkpoint16 Line 4847  checkpoint16
4847     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
4848     limit ).     limit ).
4849    
4850  checkpoint15  checkpoint15 (1998/09/29)
4851   Rewrote exchange routines to allow   Rewrote exchange routines to allow
4852   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
4853   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 1890  checkpoint15 Line 4856  checkpoint15
4856     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
4857     communication method.     communication method.
4858    
4859  checkpoint14  checkpoint14 (1998/09/09)
4860   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
4861   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
4862    
4863  checkpoint13  checkpoint13 (1998/07/17)
4864   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
4865   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
4866   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 1909  branch-point-rdot Line 4875  branch-point-rdot
4875   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
4876   we've actually tested it...   we've actually tested it...
4877    
4878  checkpoint12  checkpoint12 (1998/07/08)
4879   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
4880   configure script).   configure script).
4881   Released to testers.   Released to testers.
4882    
4883  checkpoint11  checkpoint11 (1998/07/02)
4884   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
4885   and ini_masks_etc().   and ini_masks_etc().
4886    
4887  checkpoint10  checkpoint10 (1998/07/01)
4888   Introduced the configure script.   Introduced the configure script.
4889   Separated out the diags package.   Separated out the diags package.
4890   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
4891   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
4892    
4893  checkpoint9  checkpoint9 (1998/06/22)
4894   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
4895   General tidy-up.   General tidy-up.
4896   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
4897    
4898  checkpoint8  checkpoint8 (1998/06/22)
4899   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
4900   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
4901    
# Line 1939  checkpoint7-4degree-ref Line 4905  checkpoint7-4degree-ref
4905   model etc..   model etc..
4906   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
4907    
4908  checkpoint7  checkpoint7 (1998/06/15)
4909   Created by cnh   Created by cnh
4910   Simple 4 degree global simulation   Simple 4 degree global simulation
4911   configuration.   configuration.
# Line 1947  checkpoint7 Line 4913  checkpoint7
4913   hydrography, bathymetry etc   hydrography, bathymetry etc
4914   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
4915    
4916  checkpoint6  checkpoint6 (1998/06/08)
4917   Created by cnh   Created by cnh
4918   merged checkpoint5 with CD and   merged checkpoint5 with CD and
4919   spherical polar code.   spherical polar code.
4920   Still some problems with GM Redi   Still some problems with GM Redi
4921   abd full topography.   abd full topography.
4922    
4923  checkpoint5  checkpoint5 (1998/06/08)
4924   Created by AJA   Created by AJA
4925   contains updates to GM Redi   contains updates to GM Redi
4926   and reordered timestepping loop   and reordered timestepping loop
4927   for Implicit Diffusion.   for Implicit Diffusion.
4928    
4929  checkpoint4  checkpoint4 (1998/05/30)
4930   Created by cnh   Created by cnh
4931   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
4932   grid variations are limited.   grid variations are limited.
4933   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
4934   for generation.   for generation.
4935    
4936  checkpoint3  checkpoint3 (1998/05/26)
4937   Created by cnh   Created by cnh
4938   Added extra flags for runtime options   Added extra flags for runtime options
4939   Added this file   Added this file

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