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revision 1.7 by adcroft, Mon Jun 22 16:24:50 1998 UTC revision 1.109 by jmc, Tue Dec 10 04:28:01 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
7    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
8      when using P-coordinate; only implemented for atmospheric config.
9    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
10      NOTES: requires option NONLIN_FRSURF to be "#define".
11    o update advect_xz/results/output.txt (left from checkpoint44g_post)
12    
13    checkpoint47b_post
14    Merging from release1_p9:
15    o pkg/seaice
16      - removed GOTO's and added taf directives
17      - double precision constants to reduce the g77 (Linux)
18        to F77 (SGI) differences reported in release1_p8
19    o tools/genmake
20      - added SGI options
21    o verification/testscript
22      - updated to that of checkpoint47a_post
23    o verification/global_ocean.90x40x15/input/eedata
24      - modified for SGI f77 compatibility
25    o verification/lab_sea
26      - added description of sea-ice model
27      - added missing matlab routines
28      - added test of thermodynamics parallelization
29    
30    checkpoint47a_post
31    o new pkg: aim_v23
32     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
33       for now, keep the same surface forcing as before.
34     - Part-Cell implemented into AIM; check that Heat & Water are conserved
35     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
36     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
37    o add diagnostic of surface correction term in monitor output
38    
39    o bulk_force and therm_seaice
40    - Two packages:  bulk_force (Bulk forcing)
41      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
42    - Earlier integration from Stephaine Dutkiewicz
43      and Patrick Heimbach.
44    - Two ifdef statements for compile time,
45       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
46    
47    checkpoint47
48    differentiable version of checkpoint46n_post
49    o bug fix in quasihydrostaticterms
50    o * "clean" adjoint code (in terms of extensive recomputations)
51        can now be obtained for all GMREDI options (i.e. for
52        - GM_VISBECK_VARIABLE_K
53        - GM_NON_UNITY_DIAGONAL
54        - GM_EXTRA_DIAGONAL
55        - GM_BOLUS_ADVEC )
56      * However, wrong gradient check problem remains unsolved.
57      * New CPP options have been introduced for different
58        tapering schemes
59    o external_fields_load now part of differentiation list
60    o pressure needs multiple storing;
61      would be nice to have store_pressure at beginning or
62      end of forward_step, e.g. by having phiHyd global (5-dim.)
63      (NB: pressure is needed for certain cases in find_rho,
64      which is also invoked through convective_adjustment).
65    o recomputations in find_rho for cases
66     'JMD95'/'UNESCO' or 'MDJWF' are OK.
67    o #define ATMOSPHERIC_LOADING should be differentiable
68    o ini_forcing shifted to begining of initialise_varia
69    o Incorporating QNVS line search routines into MITgcm
70      (this is separate code, and therefore not under pkg)
71      lsopt/, optim/
72    o Updated verification/carbon/
73      - #define GM_VISBECK_VARIABLE_K
74      - GM_taper_scheme    = 'ldd97'    
75    
76    checkpoint46n_post
77    Merging from release1_p8:
78    o verification/natl_box:
79      updating new external_fields_load routine
80    o New package: pkg/seaice
81      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
82      The sea-ice code is based on Hibler (1979-1980).
83      Two sea-ice dynamic solvers, ADI and LSR, are included.
84      In addition to computing prognostic sea-ice variables and diagnosing
85      the forcing/external data fields that drive the ocean model,
86      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
87      The implied surface heat flux is then stored in variable
88      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
89      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
90      non-local transport term.  Because this call precedes model
91      thermodynamics, temperature under sea-ice may not be "exactly" at
92      the freezing point by the time theta is dumped or time-averaged.
93      N.B.: fairly large differences in accuracy occur across
94            different platforms/compilers; comparison between
95            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
96            generated output gives:
97       T           S           U           V
98      C D M    c        m  s        m  s        m  s        m  s
99      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
100      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
101      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
102    
103      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
104    o GAD:
105      - generated new common blocks to account for call of
106        same gad routines with differing traceridentities
107        (needed to modify tracerIdentity indices in GAD.h)
108      - generated separate common blocks for case useCubedSphereExchange
109        (Department of Futurology)
110      - parameter lists to gmredi_?transport: added tracerIdentity
111      - added new key indices to tamc.h
112    o external_fields_load:
113      - added this routine to TAF list
114      - needed to make some common blocks global and additional storing
115        along the same lines as exf package (checkpoint_lev?_directives.h)
116    o exf:
117      updated external forcing package
118      - bug fixes carried over from ecco-branch
119        (missing OBCS_OPTIONS.h in two routines)
120      - enable easy to use "no forcing".
121      - added exf I/O for atmospheric loading
122      - added exf I/O for runoff data
123      - transfered scaling between exf <-> MITgcm to exf namelist
124    o Adding new verification experiment global_with_exf.
125      This verification experiment is almost identical to the
126      global_ocean.90x40x15 experiment, except that it uses
127      the exf (and cal) package instead of the
128      external_fields_load routine (cf README file).
129    
130    checkpoint46m_post
131    o modified testscript to return -- when there are no lines of "%MON" output
132    o added new flag "quasiHydrostatic" for QH mode
133      and new routine quasihydrostaticterms()
134    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
135      New routine: mom_u_coriolis_nh()
136    o fixed sign of non-hydrostatic metric terms in u and v equations.
137      Depend on correct sign of gravitySign.
138    o added work.pc* to .cvsignore in aim directories using ifc
139    o introduced flag for controllin non-hydrostatic metric terms
140    o removed gravitySign from PARM04
141    o switched to g77/ifc from pgf77 in aim experiments
142    
143    checkpoint46l_post
144    o made convective adjustment work with pressure coordinates:
145     - changed the direction of k-loop in convective_adjustment.F for the
146       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
147     - adjusted the reference pressure k-index in convective_adjustment.F
148     - adjusted the convection condition in convect.F (in analogy to
149       calc_ivdc.F)
150     - convective_adjustment no longer computes anything on the halos
151     - removed the warnings about negative salinity from find_rho.F and
152       find_alpha.F; instead the new routine look_for_neg_salinity, called
153       at the beginning of find_rho, find_alpha, and find_beta, does a
154       check of the entire slice, if CPP-option
155       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
156    checkpoint46l_pre
157    
158    checkpoint46k_post
159    o fixed the verification/global_ocean.90x40x15 experiment:
160     - new bathymetry (the world according to A., JMC, and M.)
161     - new initial fields and forcing fields (*.bin files)
162     - new POLY3.COEFFS (for the next release one should switch to a full
163       equation of state: JMD95P or MDJWF)
164     - fixed several errors and redundancies in the data file
165     - experiment uses looped cells
166     - added matlab directory with diagnostic scripts for plotting of output
167    
168    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
169     - read AIM physics parameters from a file (data.aimphys)
170     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
171    
172    checkpoint46j_post
173    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
174    o move wVel computation at the end of the time step, in S/R integr_continuity
175    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
176    o update timeave pkg for wVel diagnostic.
177    checkpoint46j_pre
178    
179    checkpoint46i_post
180    o Clean up AIM package (and keep the results unchanged):
181      include CPP_OPTION and use IMPLICT NONE in all routines ;
182      declare all the variables _RL ; use _d 0 for all numerical constants.
183      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
184    
185    checkpoint46h_post
186    o cleaned up the use of rhoNil and rhoConst.
187      - rhoNil should only appear in the LINEAR equation of state, everywhere
188        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
189        and the dynamical equations are all divided by rhoConst
190    o introduced new parameter rhoConstFresh, a reference density of fresh
191      water, to remove the fresh water flux's dependence on rhoNil. The default
192      value is 999.8 kg/m^3
193    o cleanup up external_forcing.F and external_forcing_surf.F
194      - can now be used by both OCEANIC and OCEANICP
195    checkpoint46h_pre
196    
197     Added code to convert surface volume flux (fresh water) into
198     a mass flux when using P coordinates in the ocean (OCEANICP).
199     Note: It assumes you have set rho0=rhoConst=density of fresh water.
200    
201    checkpoint46g_post
202    o Include a new diagnostic variable phiHydLow for the ocean model
203      - in z-coordinates, it is the bottom pressure anomaly
204      - in p-coordinates, it is the sea surface elevation
205      - in both cases, these variable have global drift, reflecting the mass
206        drift in z-coordinates and the volume drift in p-coordinates
207      - included time averaging for phiHydLow, be aware of the drift!
208    o depth-dependent computation of Bo_surf for pressure coordinates
209      in the ocean (buoyancyRelation='OCEANICP')
210      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
211        Theta, Salinity, and Pressure in the parameter list. This routine is
212        presently contained in find_rho.F. This routine does not give the
213        correct density for 'POLY3', which would be a z-dependent reference
214        density.
215    o cleaned up find_rho
216      - removed obsolete 'eqn' from the parameter list.
217    o added two new verification experiments: gop and goz
218      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
219    checkpoint46g_pre
220    
221    checkpoint46f_post
222    o Enable tangent linear (forward mode) gradient checks:
223      - extended active file handling to g_... files
224      - added TANGENT_SIMULATION to theSimulationMode
225      - extended grdchk package accordingly
226    o added tangent linear setup in verification/carbon/code_ftl
227    o added adjoint setup in verification/front_relax/code_ad
228    
229    checkpoint46e_post
230    o Added new equation of state -> MDJWF
231      - EOS of McDougall et al., 2002, JAOT, submitted
232      - caveat: the equation of state is only valid for a smaller (more
233        realistic?) range of values than JMD95P/Z and UNESCO
234      - added masks to the calculation of pressure in store_pressure
235      - added more check values for density in check_eos (ini_eos.F), some of
236        the old check values are out of the range of the MDJWF-eos, so don't
237        expect perfect matches for those
238    checkpoint46e_pre
239    
240    checkpoint46d_post
241    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
242      'OCEANICP', also initialised field pressure correctly in ini_eos in the
243      case of pressure coordinates. eosType='JMD95Z' in
244      combination with buoyancyRelation='OCEANICP' now causes an error.
245    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
246      in find_alpha/beta.
247    checkpoint46d_pre
248    
249    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
250      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
251    
252    checkpoint46c_post
253    o Changes necessary for ocean in p-coordinates
254     -  Added new buoyancy relation = 'OCEANICP'
255     -  Added new parameters = gravitySign (this used to be contained inside
256        the factor dRdZ which I added when we first switched to R coordinates).
257     X GM/Redi is not compatible (yet)
258     X bottom drag and no-slip need to be debugged.
259    checkpoint46c_pre
260    
261    checkpoint46b_post
262    o Added new equation of state -> JMD95Z and JMD95P
263      - EOS of Jackett and McDougall, 1995, JAOT
264      - moved all EOS parameters into EOS.h
265      - new routines ini_eos.F, store_pressure.F
266    o Added UNESCO EOS, but not recommended because it requires
267      in-situ temperature (see JMD95)
268    o Modified formatting for knudsen2.f in utils/knudsen2 and added
269      unesco.f to be used with POLY3
270    checkpoint46b_pre
271    
272    checkpoint46a_post
273    o Added (atmospheric) pressure loading
274      - new field in FFIELDS.h, etc...
275      - new cpp flag ATMOSPHERIC_LOADING
276    o Changed hFacC to _hFacC in calc_phi_hyd.F
277    o Added SHORTWAVE_HEATING to some files for consistency
278    checkpoint46a_pre
279    
280    checkpoint46
281    further merges from release1_p5
282    o new ctrl package
283      - adopted from ECCO environment to enable optimization
284      - added Eliassen Palm fluxes to controls
285    o added Eliassen Palm flux controls to gradient check package
286    o cost package
287      - Compatible with new ctrl package
288      - added Eliassen Palm cost hooks
289      - modif's of existing cost functions
290    o Adjoint-related bug fixes in kpp:
291      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
292      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
293    o autodiff package
294      - flow directives:
295        + new for S/R do_the_model_io
296        + enhanced for S/R checkpoint
297        + new gmredi.flow
298      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
299        disable adcommon.h/g_common.h by default.
300      - fixed problem for adjoint of global_max
301    o modified verification/carbon/
302    o New setup for adjoint of global_ocean
303    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
304    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
305    o incorporated hooks for sponge layer code (external_forcing.F)
306    
307    checkpoint45d_post
308    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
309    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
310      (affects plume_on_slope "cg2d" output)
311    o add new parameter deltaTfreesurf for free-surface time stepping
312    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
313    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
314    o change phiMin in exp1 (to agree with documentation)
315    o add new flags:
316     - T,S forcing inside/outside Adams-Bashforth
317     - turn off temp,salt advection and/or forcing
318     - for each tracer, define internal flag for multiDimAdvection & A-B
319    o monitor: change definition of KE to check conservation of Energy
320    
321    checkpoint45c_post
322    o Removed f90 comments ("!")
323    o Modified initialisations to enable exf package for MITgcm
324      (without invoking ECCO_PACKAGE).
325    o modifications to gradient check package (Martin Losch)
326      - enable centered differences
327      - modified format of standard output
328    
329    checkpoint45b_post
330    o cleaned exchange calls in cg2d
331    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
332    o included CPP option SINGLE_LAYER_MODE in thermodynamics
333      to configure barotropic setup (Martin Losch)
334    o moved some initialisations within bi,bj loop in dynamics
335      (TAF flow dependency)
336    o in initialise_varia, moved call packages_init_variables
337      before convective_adjustment_init
338      (corresponding adjustment of TAF tape initialisation).
339    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
340    
341    checkpoint45a_post
342    o compute Rho over the whole domain (extend iMin,jMin indices)
343    o specific exchange for X-slice domain (case Ny=1)
344    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
345    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
346    
347    checkpoint44h_post = checkpoint45
348    o Fix to restore differentiability:
349      place at which packages_init_variables is called in
350      initialise_varia is crucial for reverse control flow.
351    o modifications in GMRedi to enable stable adjoint
352      (corresponding modif's in thermodynamics, dynamics)
353    o added missing hook for sponge layer code in external_forcing
354    o modified test cost functions
355    o storing in gad_advection (plus removal of write(0,*)!
356    o missing headers TR1.h added in convective_adjustment routines
357    o errorMessageUnit set non-equal zero in eeboot
358      (conflict on some platforms, e.g. IBM SP3)
359    o modified carbon verif.
360    
361    checkpoint44h_pre
362    o vertical grid option: allow to put the Interface at the middle between
363      2 cell-centers ; replace delZ in pkg/kpp by drF.
364    o GM Advective form: Tracers are advected using the residual transport (=
365      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
366    
367    checkpoint44g_post
368    o fix surface correction term in multiDimAdvection (affects plume_on_slope
369      results) ; ifdef missing in thermodynamics.F
370    
371    checkpoint44f_pre,checkpoint44f_post
372    o added PTRACERS package
373      This allows an arbitrary number of passive tracers to be integrated
374      forward simultaneously with the dynamicaly model.
375      + Implemented so far:
376        - basic forward algorithm (time-stepping, advection, diffusion, convection)
377        - I/O and checkpointing
378        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
379      + Not implemented so far:
380        - KPP
381        - OBCS
382      + No specific example supplied (yet) but global_ocean.90x40x15 has the
383        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
384        line in data.pkg.
385      + This package is disabled by default since it increases storage.
386    
387    
388    o testscript: added -cleanup option
389    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
390                 b) enable to filter 2D fields.
391    
392    checkpoint44e_pre,post
393    o re-wrote convective adjustment to use pre-calculated weights
394      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
395      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
396      Original calls to convect() still in place.
397    
398    chkpt44d_pre,post
399    o added missing EXCLUDE_MONITOR flags
400    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
401      (incompatible typ in MIN/MAX expressions caused problems
402      on IBM SP3)
403    o in genmake added variable MAKEDEPEND
404      plus resetting for case SunOS
405    o added timer_stats.c routine for IBM SP3
406    o removed variables in dynamics
407    !!! I forgot to create tag chkpt44d_pre !!!
408    !!! But chkpt44d_pre = chkpt44c_post    !!!
409    
410    o real fresh water flux implemented with non-linear free-surface.
411    
412    chkpt44c_pre,post
413    o few fix (mask in shap_s2, EmPmR in external_field_load,
414      USE_NATURAL_BCS in solve_for_P);
415    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
416    
417    checkpoint44b_pre/_post
418    o merge of relevant stuff from the ecco-branch:
419      - genmake: removed $S64 overwrite for case SunOS
420      - pkg/exf: update and corrections for field swapping and obcs
421      - pkg/ecco: parameter lists for the_model_main, the_main_loop
422                  harmonized between ECCO and MITgcm
423      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
424                      updated checkpointing_lev... lists for obcs
425      - model/src: minor changes in forward_step, plot_field
426                   added directive for divided adjoint in the_main_loop
427      - pkg/mdsio: added mdsio_gl_slice
428    
429    o check parameters & config (chkpt44a_pre,post)
430    o OBC and NonLin_FrSurf.
431    
432    checkpoint44
433    o fix bug in mom_vi_del2uv
434    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
435    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
436    o update AIM experiments (NCEP input files)
437    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
438    o added some stuff for AD
439    
440    checkpoint43
441    o added two new advection tests
442    o added global 4x4 degree ocean test
443    o added test of H&S94 with free surface on cube
444    o some final mods for gradient check, adjoint,...
445    
446    checkpoint42
447      Fixed AD-related problems:
448    o Store directives up-to-date with re-arranged Adams-Bashforth
449      (mainly thermodynamics.F)
450    o New store directives for multi-dim. advection schemes
451      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
452      * new common block and key passkey
453      (mainly gad_advection.F)
454    o Modified store directives for split of dynamics/thermodynamics
455      for the case ALLOW_KPP
456    o Cleaned argument list for timestep_tracer.F
457    
458    checkpoint41
459    o re-formatted/added comments in prologues of key subroutines
460      to work with protex
461    
462    checkpoint40
463    o moved calc_gs, calc_gt and calc_tr1 back to model/src
464    o added FLT (floats) package from Arne along with demo. experiment
465    o re-arranged Adams-Bashforth scheme for tracers to allow easier
466      implementation of forward-in-time forcing terms
467    o more mods for non-linear free-surface including new variable
468    o modified multi-dim method to work on cube
469    o bug fix in KPP (from DM)
470    
471    checkpoint40pre9
472    o added DST advection schemes
473    o fix MPI bug on SGI's
474    o modifications for non-linear free-surface
475    o fixed conditionals for fixed flow/passive tracer only mode
476    o added tension/strain form of stress tensor
477    o changes to commenting of arguments for TAF/TAMC
478    o added/updated many matlab scripts
479    o added multi-dimensional advection method for tracers
480      
481    checkpoint40pre8
482    o new package rw/
483      Added method for dumping intermediate local arrays:
484      mdsio_writetile - same as mdsio_writefield except works from inside
485                        bi,bj loop
486      mdsio_writelocal - same as mdsio_writetile except works for local
487                         arrays
488      write_local_r? - higher-level wrapper for mdsio_writelocal
489      Controlled by diagFreq. Defaults to zero (ie. no dumps)
490      Example given at end of mom_vecinv.F that dumps some local arrays.
491    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
492      control flux-form versus vector invariant code.
493      Switch is runtime flag vectorInvariantMomentum (defaults to false)
494      or genmake -DISABLE ...
495    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
496      (additional storing is now needed for case vecinv;
497      currently nothing implemented to switch this storing off
498      in case fluxform is used since no CPP flag available).
499    
500    checkpoint40pre7
501    o bug fix in dynamics.F
502      calc_viscosity called before k=1,Nr loop.
503    o added some #ifdef's ALLOW_PASSIVE_TRACER
504    o cleaned initialisations in ctrl_map_ini
505      related to TAF
506    
507    checkpoint40pre6
508    o split dynamics into thermodynamics & dynamics
509    o corresponding split of calc_diffusivity into
510      calc_diffusivity, calc_viscosity
511      (kpp_calc_diff, kpp_calc_visc).
512    o Added diffkr, kapgm to control variables
513    o bug fix in gmredi_slope_limit for ldd97
514    
515    checkpoint40pre5
516    o proper initialization of Adams-Bashforth time stepping
517      + uses forward step for very first step of model (iter=0)
518    o re-generated *all* output since almost all output is modified by this
519      change (sorry but we've been putting this one off for about 2 years)
520      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
521        *not* regenerated since they are already out of date and I don't
522        want to create the impression that they are suddenly working.
523    o removed KAP stuff for DEC's
524    o modified/added many .cvsignore files in */code and */input
525    o added new expt "solid-body.cs-32x32x1"
526      + this uses an alternative form of ini_curvilinear_grid.F which
527        is not necessarily any better than the current one...
528    
529    checkpoint40pre4
530    o added re-initialisations of utrans,vtrans,rtrans in
531      calc_common_factors which are crucial for TAF.
532    o extended iMin,jMin range for calc_common_factors,
533      calc_diffusivity
534    o added option ALLOW_PASSIVE_TRACER
535    o a few minor updates and fixes
536    
537    checkpoint40pre3
538    o created calc_gtr1.F for gad package
539    o split the_main_loop and re-introduced forward_step
540    o some recomputations of nIter0 for TAMC
541    
542    checkpoint40pre2
543    o Updated to latest branch of AJA, JMC
544    o Added gradient check package
545    o Added routines for passive tracer handling
546    o Added carbon sequestration sensitivity experiment
547    
548    checkpoint39
549     o Modifications and fixes to support TAMC
550       (mainly missing or wrong directives)
551     o Corrected common blocks when fooling TAMC to produce adjoint I/O
552       in addummy_in_stepping
553     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
554     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
555     o Included following packages:
556       cal: calendar
557       exf: external forcing
558       ecco: essential routines to control use of cal, exf
559             (NB: this is not the full ECCO environment)
560     o disabled some packages by default in genmake
561    
562    checkpoint38
563     o see notes_c37_adj.txt
564     o corrected wrong layer index in external_forcing_t
565     o replaced the_main_loop/forward_step by the_main_loop
566     o removed forceoutput from write_state
567       (replaced criteria for initial/final state)
568     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
569    
570    checkpoint37
571     o mdsio.F routine split and packaged in pkg/mdsio
572       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
573        used unless genmake -disable=mdsio)
574     o allow a more precise surface-geopotential gradient for the atmosphere
575       taking into account the change in space of Alpha (=1/rho) at the surface.
576     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
577       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
578     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
579       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
580       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
581     o Time-Average diagnostics defined as a pseudo package "timeave".
582     o pickup files : old pickup (before c35) did not work with new code (c35
583       and after) unless activating 2 commented lines in initialise-varia.
584     o Non-Hydrostatic pickup file Pb fixed.
585     o bug with Rigid-lid version (since c35) fixed.  
586    
587    checkpoint36
588     o implement Crank-Nickelson barotropic time-stepping
589     o recover Time-Average diagnostics
590     o fix Pb in checkpoint (PR#19)
591     o AIM become a standard package ; clean unused CPP_kees
592    
593    checkpoint35
594     o subtantial rewrite of dynamics.f
595     o allows staggered time-stepping
596     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
597     o added bottom drag (linear + quadratic)
598    
599    checkpoint34
600     o Modified exchange routines for correct reverse simulation.
601     o Added verification output to comply with bug fix in impldiff.F
602       as of c33 (exp2, natl_box).
603     o Corrected store directives in dynamics.F
604     o Corrected array boundaries in impldiff.F
605     o Corrected array dimensions in gmredi.
606       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
607     o Added routine GLOBAL_SUM_INT to global_sum.F
608     o Added mdsio_gl.F for ECCO purposes.
609    
610    checkpoint33
611     o Fixed bug in lower BC in impldiff.F
612     o Fixed confusion about units of forcing arrays in FFIELDS.h
613       namely Fu,Fv,Qnet,Qsw,EmPmR:
614       - Removed verification/natl_box/code/external_fields_scale.F
615         (did not differ from that in model/src)
616       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
617         (see FFIELDS.h for description)
618       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
619         kpp_calc.F and kpp_transport_t.F
620       - Removed model/src/external_fields_scale.F and calls to it
621       - verification/natl_box uses flux data with "atmospheric" sign so
622         a special version of external_fields_load.F is used to
623         change the data as it's read in. This way, the arrays
624         have the right units and signs at all times tha a user could
625         possibly use them.
626     o Corrected genmake to delete a temporary file during configuration
627    
628    checkpoint32
629     o Scaling of forcing fields moved from external_forcing.F to
630       external_fields_scale.F, called directly after loading fields.
631     o Surface relaxation terms added to surface tendency fields in
632       extra subroutine.
633     o impldiff.F changed to avoid storing by TAMC of huge intermediate
634       fields.
635     o Changes in GMRedi to comply with packaging structure.
636     o Modifications and bug fixes in KPP package.
637     o Verification experiment for KPP added (verification/nat_box/)
638    
639    checkpoint31
640     o Packages interface brought in line with defined standard
641       -> new routines packages_...F
642       -> changes in initialise_fixed.F, initialise_varia.F
643       -> enables initialisation interface for ECCO package
644     o Rescaling of external forcing fields immediately after read
645       (removed from external_forcing.F)
646       -> new: surface_fields_scale.F
647       -> affects ini_foorcing.F, external_fields_load.F
648     o Computation of surface tendencies before tendency updates.
649       -> new: external_forcing_surf.F
650     o Change of variable names useGMRedi, useKPP, useECCO
651     o Further changes in dynamics.F, impldiff.F for TAMC
652     o Tested for experiments 0, 2, 4.
653       - not yet tested for GMRedi.
654       - not yet tested for KPP.
655    
656    checkpoint30
657     o Updates for OBCs
658     o New experiment for test OBCs (internal_wave)
659     o New output.txt in verification/exp4/results/
660     o Updates for KPP: calculation of viscosity corrected, new variables
661       kpp_dumpFreq and kpp_taveFreq
662     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
663       and entry for T90 in genmake
664    
665    checkpoint29
666     o packaged KPP and GM/Redi
667    
668    checkpoint28
669     o Corrected initialization of hFacMin for difference vertical coordinates
670     o Modified calculation of partial cell thickness to more robust algorithm
671     o config_summary.F: replaced write_1D_... by write_0D_...
672       read_write.F: added subroutines write_0D_...
673     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
674       included some initialisations required for TAMC.
675     o routine calc_isoslopes: modified sqrt computation to make it
676       differentiable for zero argument.
677     o routines dynamics, impldiff:
678       included store directives and tape key computations required for TAMC.
679     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
680    
681    checkpoint27
682     o fixed calc_isoslopes() to so that cancellation of terms in tensor
683       formulation works properly with variable resolution.
684     o restructured the calling tree between the_model_main() and dynamics()
685     o split initialise() into initialise_fixed() and initialise_varia()
686     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
687       in new routine ini_psurf()
688    
689    checkpoint26
690     o moved some #ifdef in optional routines to encompass everything
691       except the argument declarations. This was using up some memory.
692     o fixed macros like _ADT to work with both versions of Linux cpp
693     o cleaned up some unused and uninitialized variables
694       (helps when debugging with strict compile options)
695     o split up CPP_EEOPTIONS.h into options and macros
696       (macros are now in eesupp/inc/CPP_EEMACROS.h)
697     o patch for 2 processor JAM mode
698    
699    checkpoint25
700     o updates for OBCs and NH
701     o dramatically reduced memory usage
702     o added "JAM" routines for use on Artic network
703     o parameterization of convection by implicit vertical diffusion
704     o added a diagnostic of convective index
705     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
706       (this is was partly for OBCs and NH but also in anticipation of
707        an explicit free-surface option)
708     o initial state input files for U and V
709    
710    checkpoint24
711     o Removed some spurious "REAL"s
712     o Updated KPP to latest version from JPL
713     o Added a COS(latitude) in horizontal viscosity
714    
715    checkpoint23
716     o Added del^4 diffusion for salt and temperature
717     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
718    
719    checkpoint22
720     o Made many small changes: implicit none, format(i5), etc...
721     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
722    
723    checkpoint21
724     o Introduced new I/O package that supports direct-access records (mdsio.F)
725     o Split-up mid-level I/O routines
726     o Updated input data for experiments 0,1,2,4 and 5
727     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
728    
729    checkpoint20
730     o Tidied up open-boundaries some more
731     o Added non-hydrostatic code
732     o Fixed some input data
733     o Modified MPI start-up to work in "coupled" context.
734    
735    checkpoint19
736     o Tidied up directory structure for verification experiments.
737     o Added new code for open boundaries.
738     o Corrected advective terms near boundaries.
739     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
740     o Implemented free-slip/no-slip BCs and del^4 dissipation.
741     o Split default parameters out of ini_parms.F into set_defaults.F.
742    
743    checkpoint18
744     o Further changes for optional code generation with
745       CPP - ugh!
746    
747    checkpoint17
748     o Beginning to incorporating modularity
749       for supporting atmos. and ocean configs.
750     o Small changes for TAMC complinace
751     o New ultra simple test case. Barotropic box
752       configuration "exp0".
753    
754    checkpoint16
755     o Minor changes to exchange routines to support
756       accumulation in reverse mode. Adjoint of an
757       assignment is an addition.
758     o Changes to support compilation by TAMC (LR(1)
759       syntax) and by g77 under Linux ( 72 character
760       limit ).
761    
762    checkpoint15
763     Rewrote exchange routines to allow
764     o General tile <-> tile connectivity.
765     o TAMC reverse mode flag ( is this really needed? )
766     o Variable width overlap and exchange region widths.
767     o Hooks for sharing data via DMA, Arctic, Memory Channel,
768       shmput/shmget, VIA, SYSV shmem and every other cool
769       communication method.
770    
771    checkpoint14
772     Consistent isomorphism chages made. These allow dynamical core
773     to support both pressure and meters as a vertical coordinate.
774    
775    checkpoint13
776     Release which corrects global_max problem and a couple
777     of KGM time-averaging diagnostic errors. Also contains
778     a double-gyre experiment setup as well as the baseline
779     4 degree global template. The double gyre template is
780     organised to allow it to be applied automatically to
781     the baseline configuration.
782    
783    branch-point-rdot
784     A few tidy-ups have been made bt the real point of this
785     check-point (excuse the pun) is to allow a branch to be
786     made for the purposes of adding the rDot alterations.
787     I don't want to commit the rDot to the main-trunk until
788     we've actually tested it...
789    
790    checkpoint12
791     Tidy up and added generic genmake script (formerly
792     configure script).
793     Released to testers.
794    
795    checkpoint11
796     Re-arranged initialise() and introduced ini_vertical_grid()
797     and ini_masks_etc().
798    
799    checkpoint10
800     Introduced the configure script.
801     Separated out the diags package.
802     Added template for writing time-averages of tile/intermediate quantities.
803     Updated SIZE.h in exp2 and made the data big-endian.
804    
805  checkpoint9  checkpoint9
806   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
807   General tidy-up.   General tidy-up.

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