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revision 1.6 by adcroft, Mon Jun 22 16:09:37 1998 UTC revision 1.110 by cheisey, Mon Dec 16 17:12:23 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint47c_post
7    o Added a verification experiment for a global cubed-sphere ocean run
8      -  verification/global_ocean.cubed32x32x30
9      -  uses pkg/therm_seaice and pkg/bulk_forcing
10    
11    
12    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
13    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
14      when using P-coordinate; only implemented for atmospheric config.
15    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
16      NOTES: requires option NONLIN_FRSURF to be "#define".
17    o update advect_xz/results/output.txt (left from checkpoint44g_post)
18    
19    checkpoint47b_post
20    Merging from release1_p9:
21    o pkg/seaice
22      - removed GOTO's and added taf directives
23      - double precision constants to reduce the g77 (Linux)
24        to F77 (SGI) differences reported in release1_p8
25    o tools/genmake
26      - added SGI options
27    o verification/testscript
28      - updated to that of checkpoint47a_post
29    o verification/global_ocean.90x40x15/input/eedata
30      - modified for SGI f77 compatibility
31    o verification/lab_sea
32      - added description of sea-ice model
33      - added missing matlab routines
34      - added test of thermodynamics parallelization
35    
36    checkpoint47a_post
37    o new pkg: aim_v23
38     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
39       for now, keep the same surface forcing as before.
40     - Part-Cell implemented into AIM; check that Heat & Water are conserved
41     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
42     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
43    o add diagnostic of surface correction term in monitor output
44    
45    o bulk_force and therm_seaice
46    - Two packages:  bulk_force (Bulk forcing)
47      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
48    - Earlier integration from Stephaine Dutkiewicz
49      and Patrick Heimbach.
50    - Two ifdef statements for compile time,
51       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
52    
53    checkpoint47
54    differentiable version of checkpoint46n_post
55    o bug fix in quasihydrostaticterms
56    o * "clean" adjoint code (in terms of extensive recomputations)
57        can now be obtained for all GMREDI options (i.e. for
58        - GM_VISBECK_VARIABLE_K
59        - GM_NON_UNITY_DIAGONAL
60        - GM_EXTRA_DIAGONAL
61        - GM_BOLUS_ADVEC )
62      * However, wrong gradient check problem remains unsolved.
63      * New CPP options have been introduced for different
64        tapering schemes
65    o external_fields_load now part of differentiation list
66    o pressure needs multiple storing;
67      would be nice to have store_pressure at beginning or
68      end of forward_step, e.g. by having phiHyd global (5-dim.)
69      (NB: pressure is needed for certain cases in find_rho,
70      which is also invoked through convective_adjustment).
71    o recomputations in find_rho for cases
72     'JMD95'/'UNESCO' or 'MDJWF' are OK.
73    o #define ATMOSPHERIC_LOADING should be differentiable
74    o ini_forcing shifted to begining of initialise_varia
75    o Incorporating QNVS line search routines into MITgcm
76      (this is separate code, and therefore not under pkg)
77      lsopt/, optim/
78    o Updated verification/carbon/
79      - #define GM_VISBECK_VARIABLE_K
80      - GM_taper_scheme    = 'ldd97'    
81    
82    checkpoint46n_post
83    Merging from release1_p8:
84    o verification/natl_box:
85      updating new external_fields_load routine
86    o New package: pkg/seaice
87      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
88      The sea-ice code is based on Hibler (1979-1980).
89      Two sea-ice dynamic solvers, ADI and LSR, are included.
90      In addition to computing prognostic sea-ice variables and diagnosing
91      the forcing/external data fields that drive the ocean model,
92      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
93      The implied surface heat flux is then stored in variable
94      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
95      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
96      non-local transport term.  Because this call precedes model
97      thermodynamics, temperature under sea-ice may not be "exactly" at
98      the freezing point by the time theta is dumped or time-averaged.
99      N.B.: fairly large differences in accuracy occur across
100            different platforms/compilers; comparison between
101            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
102            generated output gives:
103       T           S           U           V
104      C D M    c        m  s        m  s        m  s        m  s
105      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
106      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
107      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
108    
109      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
110    o GAD:
111      - generated new common blocks to account for call of
112        same gad routines with differing traceridentities
113        (needed to modify tracerIdentity indices in GAD.h)
114      - generated separate common blocks for case useCubedSphereExchange
115        (Department of Futurology)
116      - parameter lists to gmredi_?transport: added tracerIdentity
117      - added new key indices to tamc.h
118    o external_fields_load:
119      - added this routine to TAF list
120      - needed to make some common blocks global and additional storing
121        along the same lines as exf package (checkpoint_lev?_directives.h)
122    o exf:
123      updated external forcing package
124      - bug fixes carried over from ecco-branch
125        (missing OBCS_OPTIONS.h in two routines)
126      - enable easy to use "no forcing".
127      - added exf I/O for atmospheric loading
128      - added exf I/O for runoff data
129      - transfered scaling between exf <-> MITgcm to exf namelist
130    o Adding new verification experiment global_with_exf.
131      This verification experiment is almost identical to the
132      global_ocean.90x40x15 experiment, except that it uses
133      the exf (and cal) package instead of the
134      external_fields_load routine (cf README file).
135    
136    checkpoint46m_post
137    o modified testscript to return -- when there are no lines of "%MON" output
138    o added new flag "quasiHydrostatic" for QH mode
139      and new routine quasihydrostaticterms()
140    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
141      New routine: mom_u_coriolis_nh()
142    o fixed sign of non-hydrostatic metric terms in u and v equations.
143      Depend on correct sign of gravitySign.
144    o added work.pc* to .cvsignore in aim directories using ifc
145    o introduced flag for controllin non-hydrostatic metric terms
146    o removed gravitySign from PARM04
147    o switched to g77/ifc from pgf77 in aim experiments
148    
149    checkpoint46l_post
150    o made convective adjustment work with pressure coordinates:
151     - changed the direction of k-loop in convective_adjustment.F for the
152       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
153     - adjusted the reference pressure k-index in convective_adjustment.F
154     - adjusted the convection condition in convect.F (in analogy to
155       calc_ivdc.F)
156     - convective_adjustment no longer computes anything on the halos
157     - removed the warnings about negative salinity from find_rho.F and
158       find_alpha.F; instead the new routine look_for_neg_salinity, called
159       at the beginning of find_rho, find_alpha, and find_beta, does a
160       check of the entire slice, if CPP-option
161       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
162    checkpoint46l_pre
163    
164    checkpoint46k_post
165    o fixed the verification/global_ocean.90x40x15 experiment:
166     - new bathymetry (the world according to A., JMC, and M.)
167     - new initial fields and forcing fields (*.bin files)
168     - new POLY3.COEFFS (for the next release one should switch to a full
169       equation of state: JMD95P or MDJWF)
170     - fixed several errors and redundancies in the data file
171     - experiment uses looped cells
172     - added matlab directory with diagnostic scripts for plotting of output
173    
174    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
175     - read AIM physics parameters from a file (data.aimphys)
176     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
177    
178    checkpoint46j_post
179    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
180    o move wVel computation at the end of the time step, in S/R integr_continuity
181    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
182    o update timeave pkg for wVel diagnostic.
183    checkpoint46j_pre
184    
185    checkpoint46i_post
186    o Clean up AIM package (and keep the results unchanged):
187      include CPP_OPTION and use IMPLICT NONE in all routines ;
188      declare all the variables _RL ; use _d 0 for all numerical constants.
189      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
190    
191    checkpoint46h_post
192    o cleaned up the use of rhoNil and rhoConst.
193      - rhoNil should only appear in the LINEAR equation of state, everywhere
194        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
195        and the dynamical equations are all divided by rhoConst
196    o introduced new parameter rhoConstFresh, a reference density of fresh
197      water, to remove the fresh water flux's dependence on rhoNil. The default
198      value is 999.8 kg/m^3
199    o cleanup up external_forcing.F and external_forcing_surf.F
200      - can now be used by both OCEANIC and OCEANICP
201    checkpoint46h_pre
202    
203     Added code to convert surface volume flux (fresh water) into
204     a mass flux when using P coordinates in the ocean (OCEANICP).
205     Note: It assumes you have set rho0=rhoConst=density of fresh water.
206    
207    checkpoint46g_post
208    o Include a new diagnostic variable phiHydLow for the ocean model
209      - in z-coordinates, it is the bottom pressure anomaly
210      - in p-coordinates, it is the sea surface elevation
211      - in both cases, these variable have global drift, reflecting the mass
212        drift in z-coordinates and the volume drift in p-coordinates
213      - included time averaging for phiHydLow, be aware of the drift!
214    o depth-dependent computation of Bo_surf for pressure coordinates
215      in the ocean (buoyancyRelation='OCEANICP')
216      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
217        Theta, Salinity, and Pressure in the parameter list. This routine is
218        presently contained in find_rho.F. This routine does not give the
219        correct density for 'POLY3', which would be a z-dependent reference
220        density.
221    o cleaned up find_rho
222      - removed obsolete 'eqn' from the parameter list.
223    o added two new verification experiments: gop and goz
224      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
225    checkpoint46g_pre
226    
227    checkpoint46f_post
228    o Enable tangent linear (forward mode) gradient checks:
229      - extended active file handling to g_... files
230      - added TANGENT_SIMULATION to theSimulationMode
231      - extended grdchk package accordingly
232    o added tangent linear setup in verification/carbon/code_ftl
233    o added adjoint setup in verification/front_relax/code_ad
234    
235    checkpoint46e_post
236    o Added new equation of state -> MDJWF
237      - EOS of McDougall et al., 2002, JAOT, submitted
238      - caveat: the equation of state is only valid for a smaller (more
239        realistic?) range of values than JMD95P/Z and UNESCO
240      - added masks to the calculation of pressure in store_pressure
241      - added more check values for density in check_eos (ini_eos.F), some of
242        the old check values are out of the range of the MDJWF-eos, so don't
243        expect perfect matches for those
244    checkpoint46e_pre
245    
246    checkpoint46d_post
247    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
248      'OCEANICP', also initialised field pressure correctly in ini_eos in the
249      case of pressure coordinates. eosType='JMD95Z' in
250      combination with buoyancyRelation='OCEANICP' now causes an error.
251    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
252      in find_alpha/beta.
253    checkpoint46d_pre
254    
255    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
256      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
257    
258    checkpoint46c_post
259    o Changes necessary for ocean in p-coordinates
260     -  Added new buoyancy relation = 'OCEANICP'
261     -  Added new parameters = gravitySign (this used to be contained inside
262        the factor dRdZ which I added when we first switched to R coordinates).
263     X GM/Redi is not compatible (yet)
264     X bottom drag and no-slip need to be debugged.
265    checkpoint46c_pre
266    
267    checkpoint46b_post
268    o Added new equation of state -> JMD95Z and JMD95P
269      - EOS of Jackett and McDougall, 1995, JAOT
270      - moved all EOS parameters into EOS.h
271      - new routines ini_eos.F, store_pressure.F
272    o Added UNESCO EOS, but not recommended because it requires
273      in-situ temperature (see JMD95)
274    o Modified formatting for knudsen2.f in utils/knudsen2 and added
275      unesco.f to be used with POLY3
276    checkpoint46b_pre
277    
278    checkpoint46a_post
279    o Added (atmospheric) pressure loading
280      - new field in FFIELDS.h, etc...
281      - new cpp flag ATMOSPHERIC_LOADING
282    o Changed hFacC to _hFacC in calc_phi_hyd.F
283    o Added SHORTWAVE_HEATING to some files for consistency
284    checkpoint46a_pre
285    
286    checkpoint46
287    further merges from release1_p5
288    o new ctrl package
289      - adopted from ECCO environment to enable optimization
290      - added Eliassen Palm fluxes to controls
291    o added Eliassen Palm flux controls to gradient check package
292    o cost package
293      - Compatible with new ctrl package
294      - added Eliassen Palm cost hooks
295      - modif's of existing cost functions
296    o Adjoint-related bug fixes in kpp:
297      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
298      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
299    o autodiff package
300      - flow directives:
301        + new for S/R do_the_model_io
302        + enhanced for S/R checkpoint
303        + new gmredi.flow
304      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
305        disable adcommon.h/g_common.h by default.
306      - fixed problem for adjoint of global_max
307    o modified verification/carbon/
308    o New setup for adjoint of global_ocean
309    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
310    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
311    o incorporated hooks for sponge layer code (external_forcing.F)
312    
313    checkpoint45d_post
314    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
315    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
316      (affects plume_on_slope "cg2d" output)
317    o add new parameter deltaTfreesurf for free-surface time stepping
318    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
319    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
320    o change phiMin in exp1 (to agree with documentation)
321    o add new flags:
322     - T,S forcing inside/outside Adams-Bashforth
323     - turn off temp,salt advection and/or forcing
324     - for each tracer, define internal flag for multiDimAdvection & A-B
325    o monitor: change definition of KE to check conservation of Energy
326    
327    checkpoint45c_post
328    o Removed f90 comments ("!")
329    o Modified initialisations to enable exf package for MITgcm
330      (without invoking ECCO_PACKAGE).
331    o modifications to gradient check package (Martin Losch)
332      - enable centered differences
333      - modified format of standard output
334    
335    checkpoint45b_post
336    o cleaned exchange calls in cg2d
337    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
338    o included CPP option SINGLE_LAYER_MODE in thermodynamics
339      to configure barotropic setup (Martin Losch)
340    o moved some initialisations within bi,bj loop in dynamics
341      (TAF flow dependency)
342    o in initialise_varia, moved call packages_init_variables
343      before convective_adjustment_init
344      (corresponding adjustment of TAF tape initialisation).
345    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
346    
347    checkpoint45a_post
348    o compute Rho over the whole domain (extend iMin,jMin indices)
349    o specific exchange for X-slice domain (case Ny=1)
350    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
351    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
352    
353    checkpoint44h_post = checkpoint45
354    o Fix to restore differentiability:
355      place at which packages_init_variables is called in
356      initialise_varia is crucial for reverse control flow.
357    o modifications in GMRedi to enable stable adjoint
358      (corresponding modif's in thermodynamics, dynamics)
359    o added missing hook for sponge layer code in external_forcing
360    o modified test cost functions
361    o storing in gad_advection (plus removal of write(0,*)!
362    o missing headers TR1.h added in convective_adjustment routines
363    o errorMessageUnit set non-equal zero in eeboot
364      (conflict on some platforms, e.g. IBM SP3)
365    o modified carbon verif.
366    
367    checkpoint44h_pre
368    o vertical grid option: allow to put the Interface at the middle between
369      2 cell-centers ; replace delZ in pkg/kpp by drF.
370    o GM Advective form: Tracers are advected using the residual transport (=
371      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
372    
373    checkpoint44g_post
374    o fix surface correction term in multiDimAdvection (affects plume_on_slope
375      results) ; ifdef missing in thermodynamics.F
376    
377    checkpoint44f_pre,checkpoint44f_post
378    o added PTRACERS package
379      This allows an arbitrary number of passive tracers to be integrated
380      forward simultaneously with the dynamicaly model.
381      + Implemented so far:
382        - basic forward algorithm (time-stepping, advection, diffusion, convection)
383        - I/O and checkpointing
384        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
385      + Not implemented so far:
386        - KPP
387        - OBCS
388      + No specific example supplied (yet) but global_ocean.90x40x15 has the
389        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
390        line in data.pkg.
391      + This package is disabled by default since it increases storage.
392    
393    
394    o testscript: added -cleanup option
395    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
396                 b) enable to filter 2D fields.
397    
398    checkpoint44e_pre,post
399    o re-wrote convective adjustment to use pre-calculated weights
400      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
401      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
402      Original calls to convect() still in place.
403    
404    chkpt44d_pre,post
405    o added missing EXCLUDE_MONITOR flags
406    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
407      (incompatible typ in MIN/MAX expressions caused problems
408      on IBM SP3)
409    o in genmake added variable MAKEDEPEND
410      plus resetting for case SunOS
411    o added timer_stats.c routine for IBM SP3
412    o removed variables in dynamics
413    !!! I forgot to create tag chkpt44d_pre !!!
414    !!! But chkpt44d_pre = chkpt44c_post    !!!
415    
416    o real fresh water flux implemented with non-linear free-surface.
417    
418    chkpt44c_pre,post
419    o few fix (mask in shap_s2, EmPmR in external_field_load,
420      USE_NATURAL_BCS in solve_for_P);
421    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
422    
423    checkpoint44b_pre/_post
424    o merge of relevant stuff from the ecco-branch:
425      - genmake: removed $S64 overwrite for case SunOS
426      - pkg/exf: update and corrections for field swapping and obcs
427      - pkg/ecco: parameter lists for the_model_main, the_main_loop
428                  harmonized between ECCO and MITgcm
429      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
430                      updated checkpointing_lev... lists for obcs
431      - model/src: minor changes in forward_step, plot_field
432                   added directive for divided adjoint in the_main_loop
433      - pkg/mdsio: added mdsio_gl_slice
434    
435    o check parameters & config (chkpt44a_pre,post)
436    o OBC and NonLin_FrSurf.
437    
438    checkpoint44
439    o fix bug in mom_vi_del2uv
440    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
441    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
442    o update AIM experiments (NCEP input files)
443    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
444    o added some stuff for AD
445    
446    checkpoint43
447    o added two new advection tests
448    o added global 4x4 degree ocean test
449    o added test of H&S94 with free surface on cube
450    o some final mods for gradient check, adjoint,...
451    
452    checkpoint42
453      Fixed AD-related problems:
454    o Store directives up-to-date with re-arranged Adams-Bashforth
455      (mainly thermodynamics.F)
456    o New store directives for multi-dim. advection schemes
457      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
458      * new common block and key passkey
459      (mainly gad_advection.F)
460    o Modified store directives for split of dynamics/thermodynamics
461      for the case ALLOW_KPP
462    o Cleaned argument list for timestep_tracer.F
463    
464    checkpoint41
465    o re-formatted/added comments in prologues of key subroutines
466      to work with protex
467    
468    checkpoint40
469    o moved calc_gs, calc_gt and calc_tr1 back to model/src
470    o added FLT (floats) package from Arne along with demo. experiment
471    o re-arranged Adams-Bashforth scheme for tracers to allow easier
472      implementation of forward-in-time forcing terms
473    o more mods for non-linear free-surface including new variable
474    o modified multi-dim method to work on cube
475    o bug fix in KPP (from DM)
476    
477    checkpoint40pre9
478    o added DST advection schemes
479    o fix MPI bug on SGI's
480    o modifications for non-linear free-surface
481    o fixed conditionals for fixed flow/passive tracer only mode
482    o added tension/strain form of stress tensor
483    o changes to commenting of arguments for TAF/TAMC
484    o added/updated many matlab scripts
485    o added multi-dimensional advection method for tracers
486      
487    checkpoint40pre8
488    o new package rw/
489      Added method for dumping intermediate local arrays:
490      mdsio_writetile - same as mdsio_writefield except works from inside
491                        bi,bj loop
492      mdsio_writelocal - same as mdsio_writetile except works for local
493                         arrays
494      write_local_r? - higher-level wrapper for mdsio_writelocal
495      Controlled by diagFreq. Defaults to zero (ie. no dumps)
496      Example given at end of mom_vecinv.F that dumps some local arrays.
497    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
498      control flux-form versus vector invariant code.
499      Switch is runtime flag vectorInvariantMomentum (defaults to false)
500      or genmake -DISABLE ...
501    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
502      (additional storing is now needed for case vecinv;
503      currently nothing implemented to switch this storing off
504      in case fluxform is used since no CPP flag available).
505    
506    checkpoint40pre7
507    o bug fix in dynamics.F
508      calc_viscosity called before k=1,Nr loop.
509    o added some #ifdef's ALLOW_PASSIVE_TRACER
510    o cleaned initialisations in ctrl_map_ini
511      related to TAF
512    
513    checkpoint40pre6
514    o split dynamics into thermodynamics & dynamics
515    o corresponding split of calc_diffusivity into
516      calc_diffusivity, calc_viscosity
517      (kpp_calc_diff, kpp_calc_visc).
518    o Added diffkr, kapgm to control variables
519    o bug fix in gmredi_slope_limit for ldd97
520    
521    checkpoint40pre5
522    o proper initialization of Adams-Bashforth time stepping
523      + uses forward step for very first step of model (iter=0)
524    o re-generated *all* output since almost all output is modified by this
525      change (sorry but we've been putting this one off for about 2 years)
526      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
527        *not* regenerated since they are already out of date and I don't
528        want to create the impression that they are suddenly working.
529    o removed KAP stuff for DEC's
530    o modified/added many .cvsignore files in */code and */input
531    o added new expt "solid-body.cs-32x32x1"
532      + this uses an alternative form of ini_curvilinear_grid.F which
533        is not necessarily any better than the current one...
534    
535    checkpoint40pre4
536    o added re-initialisations of utrans,vtrans,rtrans in
537      calc_common_factors which are crucial for TAF.
538    o extended iMin,jMin range for calc_common_factors,
539      calc_diffusivity
540    o added option ALLOW_PASSIVE_TRACER
541    o a few minor updates and fixes
542    
543    checkpoint40pre3
544    o created calc_gtr1.F for gad package
545    o split the_main_loop and re-introduced forward_step
546    o some recomputations of nIter0 for TAMC
547    
548    checkpoint40pre2
549    o Updated to latest branch of AJA, JMC
550    o Added gradient check package
551    o Added routines for passive tracer handling
552    o Added carbon sequestration sensitivity experiment
553    
554    checkpoint39
555     o Modifications and fixes to support TAMC
556       (mainly missing or wrong directives)
557     o Corrected common blocks when fooling TAMC to produce adjoint I/O
558       in addummy_in_stepping
559     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
560     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
561     o Included following packages:
562       cal: calendar
563       exf: external forcing
564       ecco: essential routines to control use of cal, exf
565             (NB: this is not the full ECCO environment)
566     o disabled some packages by default in genmake
567    
568    checkpoint38
569     o see notes_c37_adj.txt
570     o corrected wrong layer index in external_forcing_t
571     o replaced the_main_loop/forward_step by the_main_loop
572     o removed forceoutput from write_state
573       (replaced criteria for initial/final state)
574     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
575    
576    checkpoint37
577     o mdsio.F routine split and packaged in pkg/mdsio
578       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
579        used unless genmake -disable=mdsio)
580     o allow a more precise surface-geopotential gradient for the atmosphere
581       taking into account the change in space of Alpha (=1/rho) at the surface.
582     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
583       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
584     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
585       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
586       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
587     o Time-Average diagnostics defined as a pseudo package "timeave".
588     o pickup files : old pickup (before c35) did not work with new code (c35
589       and after) unless activating 2 commented lines in initialise-varia.
590     o Non-Hydrostatic pickup file Pb fixed.
591     o bug with Rigid-lid version (since c35) fixed.  
592    
593    checkpoint36
594     o implement Crank-Nickelson barotropic time-stepping
595     o recover Time-Average diagnostics
596     o fix Pb in checkpoint (PR#19)
597     o AIM become a standard package ; clean unused CPP_kees
598    
599    checkpoint35
600     o subtantial rewrite of dynamics.f
601     o allows staggered time-stepping
602     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
603     o added bottom drag (linear + quadratic)
604    
605    checkpoint34
606     o Modified exchange routines for correct reverse simulation.
607     o Added verification output to comply with bug fix in impldiff.F
608       as of c33 (exp2, natl_box).
609     o Corrected store directives in dynamics.F
610     o Corrected array boundaries in impldiff.F
611     o Corrected array dimensions in gmredi.
612       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
613     o Added routine GLOBAL_SUM_INT to global_sum.F
614     o Added mdsio_gl.F for ECCO purposes.
615    
616    checkpoint33
617     o Fixed bug in lower BC in impldiff.F
618     o Fixed confusion about units of forcing arrays in FFIELDS.h
619       namely Fu,Fv,Qnet,Qsw,EmPmR:
620       - Removed verification/natl_box/code/external_fields_scale.F
621         (did not differ from that in model/src)
622       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
623         (see FFIELDS.h for description)
624       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
625         kpp_calc.F and kpp_transport_t.F
626       - Removed model/src/external_fields_scale.F and calls to it
627       - verification/natl_box uses flux data with "atmospheric" sign so
628         a special version of external_fields_load.F is used to
629         change the data as it's read in. This way, the arrays
630         have the right units and signs at all times tha a user could
631         possibly use them.
632     o Corrected genmake to delete a temporary file during configuration
633    
634    checkpoint32
635     o Scaling of forcing fields moved from external_forcing.F to
636       external_fields_scale.F, called directly after loading fields.
637     o Surface relaxation terms added to surface tendency fields in
638       extra subroutine.
639     o impldiff.F changed to avoid storing by TAMC of huge intermediate
640       fields.
641     o Changes in GMRedi to comply with packaging structure.
642     o Modifications and bug fixes in KPP package.
643     o Verification experiment for KPP added (verification/nat_box/)
644    
645    checkpoint31
646     o Packages interface brought in line with defined standard
647       -> new routines packages_...F
648       -> changes in initialise_fixed.F, initialise_varia.F
649       -> enables initialisation interface for ECCO package
650     o Rescaling of external forcing fields immediately after read
651       (removed from external_forcing.F)
652       -> new: surface_fields_scale.F
653       -> affects ini_foorcing.F, external_fields_load.F
654     o Computation of surface tendencies before tendency updates.
655       -> new: external_forcing_surf.F
656     o Change of variable names useGMRedi, useKPP, useECCO
657     o Further changes in dynamics.F, impldiff.F for TAMC
658     o Tested for experiments 0, 2, 4.
659       - not yet tested for GMRedi.
660       - not yet tested for KPP.
661    
662    checkpoint30
663     o Updates for OBCs
664     o New experiment for test OBCs (internal_wave)
665     o New output.txt in verification/exp4/results/
666     o Updates for KPP: calculation of viscosity corrected, new variables
667       kpp_dumpFreq and kpp_taveFreq
668     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
669       and entry for T90 in genmake
670    
671    checkpoint29
672     o packaged KPP and GM/Redi
673    
674    checkpoint28
675     o Corrected initialization of hFacMin for difference vertical coordinates
676     o Modified calculation of partial cell thickness to more robust algorithm
677     o config_summary.F: replaced write_1D_... by write_0D_...
678       read_write.F: added subroutines write_0D_...
679     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
680       included some initialisations required for TAMC.
681     o routine calc_isoslopes: modified sqrt computation to make it
682       differentiable for zero argument.
683     o routines dynamics, impldiff:
684       included store directives and tape key computations required for TAMC.
685     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
686    
687    checkpoint27
688     o fixed calc_isoslopes() to so that cancellation of terms in tensor
689       formulation works properly with variable resolution.
690     o restructured the calling tree between the_model_main() and dynamics()
691     o split initialise() into initialise_fixed() and initialise_varia()
692     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
693       in new routine ini_psurf()
694    
695    checkpoint26
696     o moved some #ifdef in optional routines to encompass everything
697       except the argument declarations. This was using up some memory.
698     o fixed macros like _ADT to work with both versions of Linux cpp
699     o cleaned up some unused and uninitialized variables
700       (helps when debugging with strict compile options)
701     o split up CPP_EEOPTIONS.h into options and macros
702       (macros are now in eesupp/inc/CPP_EEMACROS.h)
703     o patch for 2 processor JAM mode
704    
705    checkpoint25
706     o updates for OBCs and NH
707     o dramatically reduced memory usage
708     o added "JAM" routines for use on Artic network
709     o parameterization of convection by implicit vertical diffusion
710     o added a diagnostic of convective index
711     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
712       (this is was partly for OBCs and NH but also in anticipation of
713        an explicit free-surface option)
714     o initial state input files for U and V
715    
716    checkpoint24
717     o Removed some spurious "REAL"s
718     o Updated KPP to latest version from JPL
719     o Added a COS(latitude) in horizontal viscosity
720    
721    checkpoint23
722     o Added del^4 diffusion for salt and temperature
723     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
724    
725    checkpoint22
726     o Made many small changes: implicit none, format(i5), etc...
727     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
728    
729    checkpoint21
730     o Introduced new I/O package that supports direct-access records (mdsio.F)
731     o Split-up mid-level I/O routines
732     o Updated input data for experiments 0,1,2,4 and 5
733     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
734    
735    checkpoint20
736     o Tidied up open-boundaries some more
737     o Added non-hydrostatic code
738     o Fixed some input data
739     o Modified MPI start-up to work in "coupled" context.
740    
741    checkpoint19
742     o Tidied up directory structure for verification experiments.
743     o Added new code for open boundaries.
744     o Corrected advective terms near boundaries.
745     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
746     o Implemented free-slip/no-slip BCs and del^4 dissipation.
747     o Split default parameters out of ini_parms.F into set_defaults.F.
748    
749    checkpoint18
750     o Further changes for optional code generation with
751       CPP - ugh!
752    
753    checkpoint17
754     o Beginning to incorporating modularity
755       for supporting atmos. and ocean configs.
756     o Small changes for TAMC complinace
757     o New ultra simple test case. Barotropic box
758       configuration "exp0".
759    
760    checkpoint16
761     o Minor changes to exchange routines to support
762       accumulation in reverse mode. Adjoint of an
763       assignment is an addition.
764     o Changes to support compilation by TAMC (LR(1)
765       syntax) and by g77 under Linux ( 72 character
766       limit ).
767    
768    checkpoint15
769     Rewrote exchange routines to allow
770     o General tile <-> tile connectivity.
771     o TAMC reverse mode flag ( is this really needed? )
772     o Variable width overlap and exchange region widths.
773     o Hooks for sharing data via DMA, Arctic, Memory Channel,
774       shmput/shmget, VIA, SYSV shmem and every other cool
775       communication method.
776    
777    checkpoint14
778     Consistent isomorphism chages made. These allow dynamical core
779     to support both pressure and meters as a vertical coordinate.
780    
781    checkpoint13
782     Release which corrects global_max problem and a couple
783     of KGM time-averaging diagnostic errors. Also contains
784     a double-gyre experiment setup as well as the baseline
785     4 degree global template. The double gyre template is
786     organised to allow it to be applied automatically to
787     the baseline configuration.
788    
789    branch-point-rdot
790     A few tidy-ups have been made bt the real point of this
791     check-point (excuse the pun) is to allow a branch to be
792     made for the purposes of adding the rDot alterations.
793     I don't want to commit the rDot to the main-trunk until
794     we've actually tested it...
795    
796    checkpoint12
797     Tidy up and added generic genmake script (formerly
798     configure script).
799     Released to testers.
800    
801    checkpoint11
802     Re-arranged initialise() and introduced ini_vertical_grid()
803     and ini_masks_etc().
804    
805    checkpoint10
806     Introduced the configure script.
807     Separated out the diags package.
808     Added template for writing time-averages of tile/intermediate quantities.
809     Updated SIZE.h in exp2 and made the data big-endian.
810    
811    checkpoint9
812     MPI fix. Filename changes (meta/data). salbin*y stuff.
813     General tidy-up.
814     SST.bin SSS.bin added to verification/exp2
815    
816  checkpoint8  checkpoint8
817   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
818   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global

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