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revision 1.14 by cnh, Tue Sep 29 18:57:53 1998 UTC revision 1.119 by jmc, Mon Jan 13 23:52:38 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint47i_post
7    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
8    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
9      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
10    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
11    o gmredi: fix few bugs.
12    
13    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
14    This will be a good checkpoint to plug into the ecco-branch.
15    o few modif.'s to get latest version adjointed
16      (mainly kick out code in ini_linear_phisurf)
17    o modif's to run adjoint with exactConserv
18    o case GM_BOLUS_ADVEC should be cleaned
19      S/R gmredi_slope_psi should be cleaned
20    o verification/carbon now has exactConserv=.TRUE.
21    
22    checkpoint47g_post
23    o time-average AIM output: becomes independent from statvars time-average
24      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
25    o After TAF bug fix:
26      Tested adjoint of gmredi package.
27      Tests were done with checkpoint47 rather than with latest
28      checkpoint47f_post since the latter is broken for the adjoint
29      verification/carbon/ contains both ADM and TLM gradient checks.
30    Here they are, before they get changed/lost/stolen.
31    Mostly modif.'s to fix numerical sensitivities.
32    Gradient checks OK for
33    - GM_taper_scheme:
34      * clipping
35      * ac02
36      * linear
37      * glw91
38      * dm95
39      * ldd97
40    - GMREDI_OPTIONS:
41      * GM_VISBECK_VARIABLE_K
42      * GM_NON_UNITY_DIAGONAL
43      * GM_EXTRA_DIAGONAL
44      * GM_BOLUS_ADVEC
45    in conjunction with data.gmredi parameters to be checked in
46    in a few minutes under verification/carbon/code/
47    
48    checkpoint47f_post
49    Merging from release1_p10:
50    o modifications for using pkg/exf with pkg/seaice
51      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
52        and SEAICE_EXTERNAL_FLUXES
53      - pkg/exf CPP options EXF_READ_EVAP and
54        EXF_NO_BULK_COMPUTATIONS
55      - usage examples are Experiments 8 and 9 in
56        verification/lab_sea/README
57      - verification/lab_sea default experiment now uses
58        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
59    
60    checkpoint47e_post
61    o created a tag prior to creating a branch
62    
63    checkpoint47d_post
64    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
65      at the bottom boundary had an erroneous half slip boundary condition
66    o added bottom drag and no slip boundary condition capabilities to
67      oceanic pressure coordinates code
68    o added new verification experiment global_ocean_pressure, this experiment is
69      also described in the tutorial section of the manual
70    checkpoint47d_pre
71    
72    checkpoint47c_post
73    o Added a verification experiment for a global cubed-sphere ocean run
74      -  verification/global_ocean.cubed32x32x30
75      -  uses pkg/therm_seaice and pkg/bulk_forcing
76    
77    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
78    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
79      when using P-coordinate; only implemented for atmospheric config.
80    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
81      NOTES: requires option NONLIN_FRSURF to be "#define".
82    o update advect_xz/results/output.txt (left from checkpoint44g_post)
83    
84    checkpoint47b_post
85    Merging from release1_p9:
86    o pkg/seaice
87      - removed GOTO's and added taf directives
88      - double precision constants to reduce the g77 (Linux)
89        to F77 (SGI) differences reported in release1_p8
90    o tools/genmake
91      - added SGI options
92    o verification/testscript
93      - updated to that of checkpoint47a_post
94    o verification/global_ocean.90x40x15/input/eedata
95      - modified for SGI f77 compatibility
96    o verification/lab_sea
97      - added description of sea-ice model
98      - added missing matlab routines
99      - added test of thermodynamics parallelization
100    
101    checkpoint47a_post
102    o new pkg: aim_v23
103     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
104       for now, keep the same surface forcing as before.
105     - Part-Cell implemented into AIM; check that Heat & Water are conserved
106     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
107     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
108    o add diagnostic of surface correction term in monitor output
109    
110    o bulk_force and therm_seaice
111    - Two packages:  bulk_force (Bulk forcing)
112      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
113    - Earlier integration from Stephaine Dutkiewicz
114      and Patrick Heimbach.
115    - Two ifdef statements for compile time,
116       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
117    
118    checkpoint47
119    differentiable version of checkpoint46n_post
120    o bug fix in quasihydrostaticterms
121    o * "clean" adjoint code (in terms of extensive recomputations)
122        can now be obtained for all GMREDI options (i.e. for
123        - GM_VISBECK_VARIABLE_K
124        - GM_NON_UNITY_DIAGONAL
125        - GM_EXTRA_DIAGONAL
126        - GM_BOLUS_ADVEC )
127      * However, wrong gradient check problem remains unsolved.
128      * New CPP options have been introduced for different
129        tapering schemes
130    o external_fields_load now part of differentiation list
131    o pressure needs multiple storing;
132      would be nice to have store_pressure at beginning or
133      end of forward_step, e.g. by having phiHyd global (5-dim.)
134      (NB: pressure is needed for certain cases in find_rho,
135      which is also invoked through convective_adjustment).
136    o recomputations in find_rho for cases
137     'JMD95'/'UNESCO' or 'MDJWF' are OK.
138    o #define ATMOSPHERIC_LOADING should be differentiable
139    o ini_forcing shifted to begining of initialise_varia
140    o Incorporating QNVS line search routines into MITgcm
141      (this is separate code, and therefore not under pkg)
142      lsopt/, optim/
143    o Updated verification/carbon/
144      - #define GM_VISBECK_VARIABLE_K
145      - GM_taper_scheme    = 'ldd97'    
146    
147    checkpoint46n_post
148    Merging from release1_p8:
149    o verification/natl_box:
150      updating new external_fields_load routine
151    o New package: pkg/seaice
152      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
153      The sea-ice code is based on Hibler (1979-1980).
154      Two sea-ice dynamic solvers, ADI and LSR, are included.
155      In addition to computing prognostic sea-ice variables and diagnosing
156      the forcing/external data fields that drive the ocean model,
157      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
158      The implied surface heat flux is then stored in variable
159      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
160      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
161      non-local transport term.  Because this call precedes model
162      thermodynamics, temperature under sea-ice may not be "exactly" at
163      the freezing point by the time theta is dumped or time-averaged.
164      N.B.: fairly large differences in accuracy occur across
165            different platforms/compilers; comparison between
166            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
167            generated output gives:
168       T           S           U           V
169      C D M    c        m  s        m  s        m  s        m  s
170      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
171      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
172      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
173    
174      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
175    o GAD:
176      - generated new common blocks to account for call of
177        same gad routines with differing traceridentities
178        (needed to modify tracerIdentity indices in GAD.h)
179      - generated separate common blocks for case useCubedSphereExchange
180        (Department of Futurology)
181      - parameter lists to gmredi_?transport: added tracerIdentity
182      - added new key indices to tamc.h
183    o external_fields_load:
184      - added this routine to TAF list
185      - needed to make some common blocks global and additional storing
186        along the same lines as exf package (checkpoint_lev?_directives.h)
187    o exf:
188      updated external forcing package
189      - bug fixes carried over from ecco-branch
190        (missing OBCS_OPTIONS.h in two routines)
191      - enable easy to use "no forcing".
192      - added exf I/O for atmospheric loading
193      - added exf I/O for runoff data
194      - transfered scaling between exf <-> MITgcm to exf namelist
195    o Adding new verification experiment global_with_exf.
196      This verification experiment is almost identical to the
197      global_ocean.90x40x15 experiment, except that it uses
198      the exf (and cal) package instead of the
199      external_fields_load routine (cf README file).
200    
201    checkpoint46m_post
202    o modified testscript to return -- when there are no lines of "%MON" output
203    o added new flag "quasiHydrostatic" for QH mode
204      and new routine quasihydrostaticterms()
205    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
206      New routine: mom_u_coriolis_nh()
207    o fixed sign of non-hydrostatic metric terms in u and v equations.
208      Depend on correct sign of gravitySign.
209    o added work.pc* to .cvsignore in aim directories using ifc
210    o introduced flag for controllin non-hydrostatic metric terms
211    o removed gravitySign from PARM04
212    o switched to g77/ifc from pgf77 in aim experiments
213    
214    checkpoint46l_post
215    o made convective adjustment work with pressure coordinates:
216     - changed the direction of k-loop in convective_adjustment.F for the
217       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
218     - adjusted the reference pressure k-index in convective_adjustment.F
219     - adjusted the convection condition in convect.F (in analogy to
220       calc_ivdc.F)
221     - convective_adjustment no longer computes anything on the halos
222     - removed the warnings about negative salinity from find_rho.F and
223       find_alpha.F; instead the new routine look_for_neg_salinity, called
224       at the beginning of find_rho, find_alpha, and find_beta, does a
225       check of the entire slice, if CPP-option
226       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
227    checkpoint46l_pre
228    
229    checkpoint46k_post
230    o fixed the verification/global_ocean.90x40x15 experiment:
231     - new bathymetry (the world according to A., JMC, and M.)
232     - new initial fields and forcing fields (*.bin files)
233     - new POLY3.COEFFS (for the next release one should switch to a full
234       equation of state: JMD95P or MDJWF)
235     - fixed several errors and redundancies in the data file
236     - experiment uses looped cells
237     - added matlab directory with diagnostic scripts for plotting of output
238    
239    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
240     - read AIM physics parameters from a file (data.aimphys)
241     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
242    
243    checkpoint46j_post
244    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
245    o move wVel computation at the end of the time step, in S/R integr_continuity
246    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
247    o update timeave pkg for wVel diagnostic.
248    checkpoint46j_pre
249    
250    checkpoint46i_post
251    o Clean up AIM package (and keep the results unchanged):
252      include CPP_OPTION and use IMPLICT NONE in all routines ;
253      declare all the variables _RL ; use _d 0 for all numerical constants.
254      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
255    
256    checkpoint46h_post
257    o cleaned up the use of rhoNil and rhoConst.
258      - rhoNil should only appear in the LINEAR equation of state, everywhere
259        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
260        and the dynamical equations are all divided by rhoConst
261    o introduced new parameter rhoConstFresh, a reference density of fresh
262      water, to remove the fresh water flux's dependence on rhoNil. The default
263      value is 999.8 kg/m^3
264    o cleanup up external_forcing.F and external_forcing_surf.F
265      - can now be used by both OCEANIC and OCEANICP
266    checkpoint46h_pre
267    
268     Added code to convert surface volume flux (fresh water) into
269     a mass flux when using P coordinates in the ocean (OCEANICP).
270     Note: It assumes you have set rho0=rhoConst=density of fresh water.
271    
272    checkpoint46g_post
273    o Include a new diagnostic variable phiHydLow for the ocean model
274      - in z-coordinates, it is the bottom pressure anomaly
275      - in p-coordinates, it is the sea surface elevation
276      - in both cases, these variable have global drift, reflecting the mass
277        drift in z-coordinates and the volume drift in p-coordinates
278      - included time averaging for phiHydLow, be aware of the drift!
279    o depth-dependent computation of Bo_surf for pressure coordinates
280      in the ocean (buoyancyRelation='OCEANICP')
281      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
282        Theta, Salinity, and Pressure in the parameter list. This routine is
283        presently contained in find_rho.F. This routine does not give the
284        correct density for 'POLY3', which would be a z-dependent reference
285        density.
286    o cleaned up find_rho
287      - removed obsolete 'eqn' from the parameter list.
288    o added two new verification experiments: gop and goz
289      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
290    checkpoint46g_pre
291    
292    checkpoint46f_post
293    o Enable tangent linear (forward mode) gradient checks:
294      - extended active file handling to g_... files
295      - added TANGENT_SIMULATION to theSimulationMode
296      - extended grdchk package accordingly
297    o added tangent linear setup in verification/carbon/code_ftl
298    o added adjoint setup in verification/front_relax/code_ad
299    
300    checkpoint46e_post
301    o Added new equation of state -> MDJWF
302      - EOS of McDougall et al., 2002, JAOT, submitted
303      - caveat: the equation of state is only valid for a smaller (more
304        realistic?) range of values than JMD95P/Z and UNESCO
305      - added masks to the calculation of pressure in store_pressure
306      - added more check values for density in check_eos (ini_eos.F), some of
307        the old check values are out of the range of the MDJWF-eos, so don't
308        expect perfect matches for those
309    checkpoint46e_pre
310    
311    checkpoint46d_post
312    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
313      'OCEANICP', also initialised field pressure correctly in ini_eos in the
314      case of pressure coordinates. eosType='JMD95Z' in
315      combination with buoyancyRelation='OCEANICP' now causes an error.
316    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
317      in find_alpha/beta.
318    checkpoint46d_pre
319    
320    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
321      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
322    
323    checkpoint46c_post
324    o Changes necessary for ocean in p-coordinates
325     -  Added new buoyancy relation = 'OCEANICP'
326     -  Added new parameters = gravitySign (this used to be contained inside
327        the factor dRdZ which I added when we first switched to R coordinates).
328     X GM/Redi is not compatible (yet)
329     X bottom drag and no-slip need to be debugged.
330    checkpoint46c_pre
331    
332    checkpoint46b_post
333    o Added new equation of state -> JMD95Z and JMD95P
334      - EOS of Jackett and McDougall, 1995, JAOT
335      - moved all EOS parameters into EOS.h
336      - new routines ini_eos.F, store_pressure.F
337    o Added UNESCO EOS, but not recommended because it requires
338      in-situ temperature (see JMD95)
339    o Modified formatting for knudsen2.f in utils/knudsen2 and added
340      unesco.f to be used with POLY3
341    checkpoint46b_pre
342    
343    checkpoint46a_post
344    o Added (atmospheric) pressure loading
345      - new field in FFIELDS.h, etc...
346      - new cpp flag ATMOSPHERIC_LOADING
347    o Changed hFacC to _hFacC in calc_phi_hyd.F
348    o Added SHORTWAVE_HEATING to some files for consistency
349    checkpoint46a_pre
350    
351    checkpoint46
352    further merges from release1_p5
353    o new ctrl package
354      - adopted from ECCO environment to enable optimization
355      - added Eliassen Palm fluxes to controls
356    o added Eliassen Palm flux controls to gradient check package
357    o cost package
358      - Compatible with new ctrl package
359      - added Eliassen Palm cost hooks
360      - modif's of existing cost functions
361    o Adjoint-related bug fixes in kpp:
362      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
363      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
364    o autodiff package
365      - flow directives:
366        + new for S/R do_the_model_io
367        + enhanced for S/R checkpoint
368        + new gmredi.flow
369      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
370        disable adcommon.h/g_common.h by default.
371      - fixed problem for adjoint of global_max
372    o modified verification/carbon/
373    o New setup for adjoint of global_ocean
374    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
375    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
376    o incorporated hooks for sponge layer code (external_forcing.F)
377    
378    checkpoint45d_post
379    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
380    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
381      (affects plume_on_slope "cg2d" output)
382    o add new parameter deltaTfreesurf for free-surface time stepping
383    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
384    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
385    o change phiMin in exp1 (to agree with documentation)
386    o add new flags:
387     - T,S forcing inside/outside Adams-Bashforth
388     - turn off temp,salt advection and/or forcing
389     - for each tracer, define internal flag for multiDimAdvection & A-B
390    o monitor: change definition of KE to check conservation of Energy
391    
392    checkpoint45c_post
393    o Removed f90 comments ("!")
394    o Modified initialisations to enable exf package for MITgcm
395      (without invoking ECCO_PACKAGE).
396    o modifications to gradient check package (Martin Losch)
397      - enable centered differences
398      - modified format of standard output
399    
400    checkpoint45b_post
401    o cleaned exchange calls in cg2d
402    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
403    o included CPP option SINGLE_LAYER_MODE in thermodynamics
404      to configure barotropic setup (Martin Losch)
405    o moved some initialisations within bi,bj loop in dynamics
406      (TAF flow dependency)
407    o in initialise_varia, moved call packages_init_variables
408      before convective_adjustment_init
409      (corresponding adjustment of TAF tape initialisation).
410    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
411    
412    checkpoint45a_post
413    o compute Rho over the whole domain (extend iMin,jMin indices)
414    o specific exchange for X-slice domain (case Ny=1)
415    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
416    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
417    
418    checkpoint44h_post = checkpoint45
419    o Fix to restore differentiability:
420      place at which packages_init_variables is called in
421      initialise_varia is crucial for reverse control flow.
422    o modifications in GMRedi to enable stable adjoint
423      (corresponding modif's in thermodynamics, dynamics)
424    o added missing hook for sponge layer code in external_forcing
425    o modified test cost functions
426    o storing in gad_advection (plus removal of write(0,*)!
427    o missing headers TR1.h added in convective_adjustment routines
428    o errorMessageUnit set non-equal zero in eeboot
429      (conflict on some platforms, e.g. IBM SP3)
430    o modified carbon verif.
431    
432    checkpoint44h_pre
433    o vertical grid option: allow to put the Interface at the middle between
434      2 cell-centers ; replace delZ in pkg/kpp by drF.
435    o GM Advective form: Tracers are advected using the residual transport (=
436      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
437    
438    checkpoint44g_post
439    o fix surface correction term in multiDimAdvection (affects plume_on_slope
440      results) ; ifdef missing in thermodynamics.F
441    
442    checkpoint44f_pre,checkpoint44f_post
443    o added PTRACERS package
444      This allows an arbitrary number of passive tracers to be integrated
445      forward simultaneously with the dynamicaly model.
446      + Implemented so far:
447        - basic forward algorithm (time-stepping, advection, diffusion, convection)
448        - I/O and checkpointing
449        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
450      + Not implemented so far:
451        - KPP
452        - OBCS
453      + No specific example supplied (yet) but global_ocean.90x40x15 has the
454        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
455        line in data.pkg.
456      + This package is disabled by default since it increases storage.
457    
458    
459    o testscript: added -cleanup option
460    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
461                 b) enable to filter 2D fields.
462    
463    checkpoint44e_pre,post
464    o re-wrote convective adjustment to use pre-calculated weights
465      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
466      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
467      Original calls to convect() still in place.
468    
469    chkpt44d_pre,post
470    o added missing EXCLUDE_MONITOR flags
471    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
472      (incompatible typ in MIN/MAX expressions caused problems
473      on IBM SP3)
474    o in genmake added variable MAKEDEPEND
475      plus resetting for case SunOS
476    o added timer_stats.c routine for IBM SP3
477    o removed variables in dynamics
478    !!! I forgot to create tag chkpt44d_pre !!!
479    !!! But chkpt44d_pre = chkpt44c_post    !!!
480    
481    o real fresh water flux implemented with non-linear free-surface.
482    
483    chkpt44c_pre,post
484    o few fix (mask in shap_s2, EmPmR in external_field_load,
485      USE_NATURAL_BCS in solve_for_P);
486    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
487    
488    checkpoint44b_pre/_post
489    o merge of relevant stuff from the ecco-branch:
490      - genmake: removed $S64 overwrite for case SunOS
491      - pkg/exf: update and corrections for field swapping and obcs
492      - pkg/ecco: parameter lists for the_model_main, the_main_loop
493                  harmonized between ECCO and MITgcm
494      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
495                      updated checkpointing_lev... lists for obcs
496      - model/src: minor changes in forward_step, plot_field
497                   added directive for divided adjoint in the_main_loop
498      - pkg/mdsio: added mdsio_gl_slice
499    
500    o check parameters & config (chkpt44a_pre,post)
501    o OBC and NonLin_FrSurf.
502    
503    checkpoint44
504    o fix bug in mom_vi_del2uv
505    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
506    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
507    o update AIM experiments (NCEP input files)
508    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
509    o added some stuff for AD
510    
511    checkpoint43
512    o added two new advection tests
513    o added global 4x4 degree ocean test
514    o added test of H&S94 with free surface on cube
515    o some final mods for gradient check, adjoint,...
516    
517    checkpoint42
518      Fixed AD-related problems:
519    o Store directives up-to-date with re-arranged Adams-Bashforth
520      (mainly thermodynamics.F)
521    o New store directives for multi-dim. advection schemes
522      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
523      * new common block and key passkey
524      (mainly gad_advection.F)
525    o Modified store directives for split of dynamics/thermodynamics
526      for the case ALLOW_KPP
527    o Cleaned argument list for timestep_tracer.F
528    
529    checkpoint41
530    o re-formatted/added comments in prologues of key subroutines
531      to work with protex
532    
533    checkpoint40
534    o moved calc_gs, calc_gt and calc_tr1 back to model/src
535    o added FLT (floats) package from Arne along with demo. experiment
536    o re-arranged Adams-Bashforth scheme for tracers to allow easier
537      implementation of forward-in-time forcing terms
538    o more mods for non-linear free-surface including new variable
539    o modified multi-dim method to work on cube
540    o bug fix in KPP (from DM)
541    
542    checkpoint40pre9
543    o added DST advection schemes
544    o fix MPI bug on SGI's
545    o modifications for non-linear free-surface
546    o fixed conditionals for fixed flow/passive tracer only mode
547    o added tension/strain form of stress tensor
548    o changes to commenting of arguments for TAF/TAMC
549    o added/updated many matlab scripts
550    o added multi-dimensional advection method for tracers
551      
552    checkpoint40pre8
553    o new package rw/
554      Added method for dumping intermediate local arrays:
555      mdsio_writetile - same as mdsio_writefield except works from inside
556                        bi,bj loop
557      mdsio_writelocal - same as mdsio_writetile except works for local
558                         arrays
559      write_local_r? - higher-level wrapper for mdsio_writelocal
560      Controlled by diagFreq. Defaults to zero (ie. no dumps)
561      Example given at end of mom_vecinv.F that dumps some local arrays.
562    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
563      control flux-form versus vector invariant code.
564      Switch is runtime flag vectorInvariantMomentum (defaults to false)
565      or genmake -DISABLE ...
566    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
567      (additional storing is now needed for case vecinv;
568      currently nothing implemented to switch this storing off
569      in case fluxform is used since no CPP flag available).
570    
571    checkpoint40pre7
572    o bug fix in dynamics.F
573      calc_viscosity called before k=1,Nr loop.
574    o added some #ifdef's ALLOW_PASSIVE_TRACER
575    o cleaned initialisations in ctrl_map_ini
576      related to TAF
577    
578    checkpoint40pre6
579    o split dynamics into thermodynamics & dynamics
580    o corresponding split of calc_diffusivity into
581      calc_diffusivity, calc_viscosity
582      (kpp_calc_diff, kpp_calc_visc).
583    o Added diffkr, kapgm to control variables
584    o bug fix in gmredi_slope_limit for ldd97
585    
586    checkpoint40pre5
587    o proper initialization of Adams-Bashforth time stepping
588      + uses forward step for very first step of model (iter=0)
589    o re-generated *all* output since almost all output is modified by this
590      change (sorry but we've been putting this one off for about 2 years)
591      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
592        *not* regenerated since they are already out of date and I don't
593        want to create the impression that they are suddenly working.
594    o removed KAP stuff for DEC's
595    o modified/added many .cvsignore files in */code and */input
596    o added new expt "solid-body.cs-32x32x1"
597      + this uses an alternative form of ini_curvilinear_grid.F which
598        is not necessarily any better than the current one...
599    
600    checkpoint40pre4
601    o added re-initialisations of utrans,vtrans,rtrans in
602      calc_common_factors which are crucial for TAF.
603    o extended iMin,jMin range for calc_common_factors,
604      calc_diffusivity
605    o added option ALLOW_PASSIVE_TRACER
606    o a few minor updates and fixes
607    
608    checkpoint40pre3
609    o created calc_gtr1.F for gad package
610    o split the_main_loop and re-introduced forward_step
611    o some recomputations of nIter0 for TAMC
612    
613    checkpoint40pre2
614    o Updated to latest branch of AJA, JMC
615    o Added gradient check package
616    o Added routines for passive tracer handling
617    o Added carbon sequestration sensitivity experiment
618    
619    checkpoint39
620     o Modifications and fixes to support TAMC
621       (mainly missing or wrong directives)
622     o Corrected common blocks when fooling TAMC to produce adjoint I/O
623       in addummy_in_stepping
624     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
625     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
626     o Included following packages:
627       cal: calendar
628       exf: external forcing
629       ecco: essential routines to control use of cal, exf
630             (NB: this is not the full ECCO environment)
631     o disabled some packages by default in genmake
632    
633    checkpoint38
634     o see notes_c37_adj.txt
635     o corrected wrong layer index in external_forcing_t
636     o replaced the_main_loop/forward_step by the_main_loop
637     o removed forceoutput from write_state
638       (replaced criteria for initial/final state)
639     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
640    
641    checkpoint37
642     o mdsio.F routine split and packaged in pkg/mdsio
643       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
644        used unless genmake -disable=mdsio)
645     o allow a more precise surface-geopotential gradient for the atmosphere
646       taking into account the change in space of Alpha (=1/rho) at the surface.
647     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
648       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
649     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
650       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
651       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
652     o Time-Average diagnostics defined as a pseudo package "timeave".
653     o pickup files : old pickup (before c35) did not work with new code (c35
654       and after) unless activating 2 commented lines in initialise-varia.
655     o Non-Hydrostatic pickup file Pb fixed.
656     o bug with Rigid-lid version (since c35) fixed.  
657    
658    checkpoint36
659     o implement Crank-Nickelson barotropic time-stepping
660     o recover Time-Average diagnostics
661     o fix Pb in checkpoint (PR#19)
662     o AIM become a standard package ; clean unused CPP_kees
663    
664    checkpoint35
665     o subtantial rewrite of dynamics.f
666     o allows staggered time-stepping
667     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
668     o added bottom drag (linear + quadratic)
669    
670    checkpoint34
671     o Modified exchange routines for correct reverse simulation.
672     o Added verification output to comply with bug fix in impldiff.F
673       as of c33 (exp2, natl_box).
674     o Corrected store directives in dynamics.F
675     o Corrected array boundaries in impldiff.F
676     o Corrected array dimensions in gmredi.
677       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
678     o Added routine GLOBAL_SUM_INT to global_sum.F
679     o Added mdsio_gl.F for ECCO purposes.
680    
681    checkpoint33
682     o Fixed bug in lower BC in impldiff.F
683     o Fixed confusion about units of forcing arrays in FFIELDS.h
684       namely Fu,Fv,Qnet,Qsw,EmPmR:
685       - Removed verification/natl_box/code/external_fields_scale.F
686         (did not differ from that in model/src)
687       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
688         (see FFIELDS.h for description)
689       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
690         kpp_calc.F and kpp_transport_t.F
691       - Removed model/src/external_fields_scale.F and calls to it
692       - verification/natl_box uses flux data with "atmospheric" sign so
693         a special version of external_fields_load.F is used to
694         change the data as it's read in. This way, the arrays
695         have the right units and signs at all times tha a user could
696         possibly use them.
697     o Corrected genmake to delete a temporary file during configuration
698    
699    checkpoint32
700     o Scaling of forcing fields moved from external_forcing.F to
701       external_fields_scale.F, called directly after loading fields.
702     o Surface relaxation terms added to surface tendency fields in
703       extra subroutine.
704     o impldiff.F changed to avoid storing by TAMC of huge intermediate
705       fields.
706     o Changes in GMRedi to comply with packaging structure.
707     o Modifications and bug fixes in KPP package.
708     o Verification experiment for KPP added (verification/nat_box/)
709    
710    checkpoint31
711     o Packages interface brought in line with defined standard
712       -> new routines packages_...F
713       -> changes in initialise_fixed.F, initialise_varia.F
714       -> enables initialisation interface for ECCO package
715     o Rescaling of external forcing fields immediately after read
716       (removed from external_forcing.F)
717       -> new: surface_fields_scale.F
718       -> affects ini_foorcing.F, external_fields_load.F
719     o Computation of surface tendencies before tendency updates.
720       -> new: external_forcing_surf.F
721     o Change of variable names useGMRedi, useKPP, useECCO
722     o Further changes in dynamics.F, impldiff.F for TAMC
723     o Tested for experiments 0, 2, 4.
724       - not yet tested for GMRedi.
725       - not yet tested for KPP.
726    
727    checkpoint30
728     o Updates for OBCs
729     o New experiment for test OBCs (internal_wave)
730     o New output.txt in verification/exp4/results/
731     o Updates for KPP: calculation of viscosity corrected, new variables
732       kpp_dumpFreq and kpp_taveFreq
733     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
734       and entry for T90 in genmake
735    
736    checkpoint29
737     o packaged KPP and GM/Redi
738    
739    checkpoint28
740     o Corrected initialization of hFacMin for difference vertical coordinates
741     o Modified calculation of partial cell thickness to more robust algorithm
742     o config_summary.F: replaced write_1D_... by write_0D_...
743       read_write.F: added subroutines write_0D_...
744     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
745       included some initialisations required for TAMC.
746     o routine calc_isoslopes: modified sqrt computation to make it
747       differentiable for zero argument.
748     o routines dynamics, impldiff:
749       included store directives and tape key computations required for TAMC.
750     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
751    
752    checkpoint27
753     o fixed calc_isoslopes() to so that cancellation of terms in tensor
754       formulation works properly with variable resolution.
755     o restructured the calling tree between the_model_main() and dynamics()
756     o split initialise() into initialise_fixed() and initialise_varia()
757     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
758       in new routine ini_psurf()
759    
760    checkpoint26
761     o moved some #ifdef in optional routines to encompass everything
762       except the argument declarations. This was using up some memory.
763     o fixed macros like _ADT to work with both versions of Linux cpp
764     o cleaned up some unused and uninitialized variables
765       (helps when debugging with strict compile options)
766     o split up CPP_EEOPTIONS.h into options and macros
767       (macros are now in eesupp/inc/CPP_EEMACROS.h)
768     o patch for 2 processor JAM mode
769    
770    checkpoint25
771     o updates for OBCs and NH
772     o dramatically reduced memory usage
773     o added "JAM" routines for use on Artic network
774     o parameterization of convection by implicit vertical diffusion
775     o added a diagnostic of convective index
776     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
777       (this is was partly for OBCs and NH but also in anticipation of
778        an explicit free-surface option)
779     o initial state input files for U and V
780    
781    checkpoint24
782     o Removed some spurious "REAL"s
783     o Updated KPP to latest version from JPL
784     o Added a COS(latitude) in horizontal viscosity
785    
786    checkpoint23
787     o Added del^4 diffusion for salt and temperature
788     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
789    
790    checkpoint22
791     o Made many small changes: implicit none, format(i5), etc...
792     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
793    
794    checkpoint21
795     o Introduced new I/O package that supports direct-access records (mdsio.F)
796     o Split-up mid-level I/O routines
797     o Updated input data for experiments 0,1,2,4 and 5
798     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
799    
800    checkpoint20
801     o Tidied up open-boundaries some more
802     o Added non-hydrostatic code
803     o Fixed some input data
804     o Modified MPI start-up to work in "coupled" context.
805    
806    checkpoint19
807     o Tidied up directory structure for verification experiments.
808     o Added new code for open boundaries.
809     o Corrected advective terms near boundaries.
810     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
811     o Implemented free-slip/no-slip BCs and del^4 dissipation.
812     o Split default parameters out of ini_parms.F into set_defaults.F.
813    
814    checkpoint18
815     o Further changes for optional code generation with
816       CPP - ugh!
817    
818    checkpoint17
819     o Beginning to incorporating modularity
820       for supporting atmos. and ocean configs.
821     o Small changes for TAMC complinace
822     o New ultra simple test case. Barotropic box
823       configuration "exp0".
824    
825    checkpoint16
826     o Minor changes to exchange routines to support
827       accumulation in reverse mode. Adjoint of an
828       assignment is an addition.
829     o Changes to support compilation by TAMC (LR(1)
830       syntax) and by g77 under Linux ( 72 character
831       limit ).
832    
833  checkpoint15  checkpoint15
834   Rewrote exchange routines to allow   Rewrote exchange routines to allow
835   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.

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