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revision 1.3 by cnh, Mon Jun 8 19:25:25 1998 UTC revision 1.166 by heimbach, Tue Jun 24 16:14:59 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint51
7    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
8      - autodiff, ctrl, exf, grdchk, seaice
9      kept separate packages
10      - cost, ecco, obcs
11    
12    checkpoint50i_post
13    o Preparing next differentiable checkpoint and sync
14      of MAIN vs. ecco-branch
15      - 1st step: this one is differentiable
16      - 2nd step: next(! not this) checkpoint will have updated packages
17                  from ecco-branch)
18    
19    checkpoint50h_post
20    o new package "land": provide surface BC for AIM.
21    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
22    o AIM: use true log-P extrapolation for near surface temp (= as in
23        F.Molteni paper) ; update aim.5l_cs output.
24    o New variable in PARM03 for more flexible pickups
25    o somewhat cleaned package initialisation sequence for
26      ctrl/ cost/ ecco/ in packages_... routines
27    
28    checkpoint50g_post
29    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
30      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
31      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
32        made the default because of faster convergence than ADI
33    
34    checkpoint50f_post
35    o exf totally restructured
36      - replaced all exf_set_ routines by one generic exf_set_gen.F
37        and made sure it's still differentiable
38      - split exf_getffields.F into new exf_bulkformulae.F
39      - exf_inscal_/exf_outscal_ suffixes consistent with field names
40      - updated adjoint/makefile and relevant verif. accordingly
41    
42    checkpoint50f_pre
43     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
44          + change Evap over land. (update aim.5l_cs output)
45     o added missing .cvsignores and made uniform across expts
46     o changed configuration of tidal_basin_2d expt
47     o added pkg/debug functions for tracing code in fatal crashes
48     o tidied pkg/monitor to use MONITOR_OPTIONS.h
49     o new fn in pkg/monitor to stop model if solution grows too big
50     o removed lots of single quotes from comments
51    
52    checkpoint50e_post
53    o make KPP work with PTRACERS
54     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
55       nearly a copy of kpp_transport_s
56     - there is no analogue to SurfaceTendencyS, so I have to use
57       gPtr(of the surface layer) instead
58    o add a new platform SunFire+mpi (SunFire 15000) to genmake
59    checkpoint50e_pre
60    
61    checkpoint50d_post
62    o change kpp output from multiple-record state files to single-record state
63      files analogous to write_state.F
64    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
65      analogous to the cg2d-related output.
66    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
67      so that writing to internal file fn (with length 512) fails.
68    checkpoint50d_pre
69    
70    checkpoint50c_post
71    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
72    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
73    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
74    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
75    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
76    
77    checkpoint50c_pre
78    Merging from release1_p13:
79    o bug fix for pkg/seaice dynamic solver
80    o Added SEAICE_initialHEFF to pkg/seaice
81    
82    checkpoint50b_post
83    o store u*,v* in gU,V instead of in guNm1,gvNm1
84    o in order to put the momForcing out of the Adams-Bashforth:
85      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
86      to timestep.F
87    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
88    o re-generate output for highly sensitive test-exp:
89       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
90    
91    checkpoint50b_pre
92    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
93    o corrected CPP option mismatch in exf_Bulk... functions for case
94      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
95    
96    checkpoint50a_post
97    o Bug fix for merging between c50 and KPP.
98      ikey was passed from thermodynamics to kpp_calc via
99      common block rather than being recomputed in kpp_calc,
100      in contradiction with new key itdkey.
101      New key ikppkey created, and tamc.h headers updated.
102    
103    checkpoint50
104    - 2nd step of merge with ecco-branch:
105      merge changes in ecco-branch back into main trunk
106    - bug fix in find_alpha
107    - more storing in gmredi_calc_tensor.F, kpp_routines.F
108    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
109    - merged some sliced AD support routines
110    
111    checkpoint49
112    merged from ecco-branch:
113    o exf:
114      - Enable initialisation of forcing fields to constant
115        (runtime) values.
116      - in exf_getffields.F
117        Reduce i-/j-loop to interior domain, discarding overlaps.
118        That also fixes wrong TAF-key computations for key_1, key_2
119        with bulf formulae.
120      - exf_init.F modify #ifdef for exf_init_evap
121      - exf_getffieldrec.F, ctrl_getrec.F
122        The following INT-usages are not safe:
123          fldsecs  = int(fldsecs/fldperiod)*fldperiod
124          fldcount = int(fldsecs/fldperiod) + 1
125        and were modified.
126    o autodiff: checkpoint_lev...
127      - updated storing for bulk formulae (some arrays were missing)
128      - added state for seaice package
129      - synchronized with main branch
130    o DIVA:
131      Modif.s in
132      - the_main_loop.F
133      - the_model_main.F
134      and added cost_final_restore.F cost_final_store.F
135      o With these changes, it is possible to fully separate
136        the first forward run to compute the cost function (mdthe_main_loop)
137        and adjoint runs over individual DIVA intervals (adthe_main_loop)
138        into separate model executions.
139        This enables better tuning of DIVA to given queue sizes.
140      o Loss of cost function value in consecutive DIVA runs is
141        fixed by storing to 'costfinal' file.
142      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
143        beginning/end of adjoint integration is accounted for.
144      The current changes apply to TAF-1.4.26.
145      TAF has one remaining bug, requiring one manual change
146      (see MITgcm manual).
147    o cal: synchronized between MAIN and ecco-branch
148    
149    checkpoint48i_post
150    o Changes to restore differentiability of code w.r.t. previous tag
151      (mostly adding new routines to make list and replacing
152      pressure by totPhiHyd).
153    o Updated and merged grdchk package
154      - has both ADM and TLM checks
155      - works for single- and multi-proc.
156      - output cleaned
157      - worked successfully for parallel DIVA
158    o genmake:
159      - Adding -platform=SP4
160      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
161    o Modif. for DIVA:
162      ctrl_unpack should not be called in intermediate DIVA interval.
163      (similar thing would apply for active files such as
164      tbar, sbar, psbar, which should not be reinitialised;
165      only relevant for ecco-branch)
166    
167    checkpoint48h_post
168    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
169    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
170    o Added SEAICE_initialHEFF to pkg/seaice
171    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
172    
173    checkpoint48g_post
174    --- EOS:
175    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
176      store total Potential in totPhyHyd for diagnostics & EOS.
177    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
178    --- Pressure/geopotential gradient:
179    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
180    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
181      ( changes results of global_ocean_pressure )
182    o NLFS + z-coord.: add eta*Rho' contribution.
183    o accurate phiHyd when using interface-W at the middle between 2 centers
184     ( changes results of ideal_2D_oce )
185    o includes r* 2nd term in potential gradient.
186    
187    checkpoint48f_post
188    Merging from release1_p12:
189    o Modifications for using pkg/exf with pkg/seaice
190      - improved description of the various forcing configurations
191      - added basic radiation bulk formulae to pkg/exf
192      - units/sign fix for evap computation in exf_getffields.F
193      - updated verification/global_with_exf/results/output.txt
194    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
195      (SBO) core products, including oceanic mass, center-of-mass,
196      angular, and bottom pressure (see pkg/sbo/README.sbo).
197    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
198      to avoid negative values in shallow regions.
199      - updated verification/natl_box/results/output.txt
200      - updated verification/lab_sea/results/output.txt
201    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
202    o Added useSingleCpuIO option (see PARAMS.h).
203    o Updated useSingleCpuIO option in mdsio_writefield.F to
204      work with multi-field files, e.g., for single-file pickup.
205    o pkg/seaice:
206      - bug fix in growth.F: QNET for no shortwave case
207      - added HeffFile for specifying initial sea-ice thickness
208      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
209    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
210      kpp_transport_t.F, forward_step.F, and the_main_loop.F
211    o pkg/seaice:
212      - adjoint-friendly modifications
213      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
214    
215    checkpoint48e_post
216    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
217    o dynamics: change definition of computational domain & adapt mom_fluxform
218      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
219    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
220        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
221        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
222        global_ocean.90x40x15 global_with_exf global_ocean_pressure
223        inverted_barometer solid-body.cs-32x32x1
224      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
225    
226    checkpoint48d_post
227    o in preparation for r*:
228     a) use pre-computed gradient of hydrostatic potential:
229        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
230     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
231        => affects results of glob_oce_pressure (different truncation error)  
232      update output.txt of ideal_2D_oce & global_ocean_pressure
233    
234    checkpoint48d_pre
235    o in preparation for r*:
236      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
237      pass the 2 comp. of the grad. as arguments to momentum S/R.
238      but for the moment, only used if it does not change the results.
239    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
240    
241    checkpoint48c_post
242    Modifications in treatment of initial flux forcing controls
243    to avoid extra storing of flux fields.
244    
245    checkpoint48c_pre
246    o Added tidal_basin_2d experiment (currently 1D!)
247    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
248    
249    checkpoint48b_post
250    o r* coordinate added in #ifdef NONLIN_FRSURF block.
251     (modification to pressure gradient not yet implemented)
252    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
253      (for U & V) that are used for vertical advection of momentum.
254    
255    checkpoint48a_post
256    o In preparation for r*, use temp. array to compute vertical transport
257       in flux-form momentum pkg. => change results of few test-exp.
258      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
259                        lab_sea, natl_box & plume_on_slope
260    
261    checkpoint48
262    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
263    
264    checkpoint47j_post
265    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
266    o moved adexch from forward_step to addummy_in_stepping
267    o added exch in ctrl_map_...
268    o aveFreq.=0. at end of cost_final to avoid overwrite in
269      reverse checkpointing loop
270    o Yet more changes in gmredi:
271      * adgmredi_calc_tensor
272        avoiding all recomputation of gmredi_slope_limit
273      * adgmredi_x/y/rtransport
274        added flag for excessive storing to avoid recomp. of
275        u/v/rtans, dTdx/y/z
276        -> this is not really necessary and very memory-consuming
277      * adgmredi_slope_psi:
278        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
279      * gmredi_slope_limit
280        re-activated full calculation of taperfct for case 'ac02'
281    o updating verification/ adjoints of carbon, global_ocean.90x40x15
282    
283    checkpoint47i_post
284    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
285    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
286      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
287    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
288    o gmredi: fix few bugs.
289    
290    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
291    This will be a good checkpoint to plug into the ecco-branch.
292    o few modif.'s to get latest version adjointed
293      (mainly kick out code in ini_linear_phisurf)
294    o modif's to run adjoint with exactConserv
295    o case GM_BOLUS_ADVEC should be cleaned
296      S/R gmredi_slope_psi should be cleaned
297    o verification/carbon now has exactConserv=.TRUE.
298    
299    checkpoint47g_post
300    o time-average AIM output: becomes independent from statvars time-average
301      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
302    o After TAF bug fix:
303      Tested adjoint of gmredi package.
304      Tests were done with checkpoint47 rather than with latest
305      checkpoint47f_post since the latter is broken for the adjoint
306      verification/carbon/ contains both ADM and TLM gradient checks.
307    Here they are, before they get changed/lost/stolen.
308    Mostly modif.'s to fix numerical sensitivities.
309    Gradient checks OK for
310    - GM_taper_scheme:
311      * clipping
312      * ac02
313      * linear
314      * glw91
315      * dm95
316      * ldd97
317    - GMREDI_OPTIONS:
318      * GM_VISBECK_VARIABLE_K
319      * GM_NON_UNITY_DIAGONAL
320      * GM_EXTRA_DIAGONAL
321      * GM_BOLUS_ADVEC
322    in conjunction with data.gmredi parameters to be checked in
323    in a few minutes under verification/carbon/code/
324    
325    checkpoint47f_post
326    Merging from release1_p10:
327    o modifications for using pkg/exf with pkg/seaice
328      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
329        and SEAICE_EXTERNAL_FLUXES
330      - pkg/exf CPP options EXF_READ_EVAP and
331        EXF_NO_BULK_COMPUTATIONS
332      - usage examples are Experiments 8 and 9 in
333        verification/lab_sea/README
334      - verification/lab_sea default experiment now uses
335        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
336    
337    checkpoint47e_post
338    o created a tag prior to creating a branch
339    
340    checkpoint47d_post
341    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
342      at the bottom boundary had an erroneous half slip boundary condition
343    o added bottom drag and no slip boundary condition capabilities to
344      oceanic pressure coordinates code
345    o added new verification experiment global_ocean_pressure, this experiment is
346      also described in the tutorial section of the manual
347    checkpoint47d_pre
348    
349    checkpoint47c_post
350    o Added a verification experiment for a global cubed-sphere ocean run
351      -  verification/global_ocean.cubed32x32x30
352      -  uses pkg/therm_seaice and pkg/bulk_forcing
353    
354    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
355    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
356      when using P-coordinate; only implemented for atmospheric config.
357    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
358      NOTES: requires option NONLIN_FRSURF to be "#define".
359    o update advect_xz/results/output.txt (left from checkpoint44g_post)
360    
361    checkpoint47b_post
362    Merging from release1_p9:
363    o pkg/seaice
364      - removed GOTO's and added taf directives
365      - double precision constants to reduce the g77 (Linux)
366        to F77 (SGI) differences reported in release1_p8
367    o tools/genmake
368      - added SGI options
369    o verification/testscript
370      - updated to that of checkpoint47a_post
371    o verification/global_ocean.90x40x15/input/eedata
372      - modified for SGI f77 compatibility
373    o verification/lab_sea
374      - added description of sea-ice model
375      - added missing matlab routines
376      - added test of thermodynamics parallelization
377    
378    checkpoint47a_post
379    o new pkg: aim_v23
380     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
381       for now, keep the same surface forcing as before.
382     - Part-Cell implemented into AIM; check that Heat & Water are conserved
383     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
384     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
385    o add diagnostic of surface correction term in monitor output
386    
387    o bulk_force and therm_seaice
388    - Two packages:  bulk_force (Bulk forcing)
389      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
390    - Earlier integration from Stephaine Dutkiewicz
391      and Patrick Heimbach.
392    - Two ifdef statements for compile time,
393       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
394    
395    checkpoint47
396    differentiable version of checkpoint46n_post
397    o bug fix in quasihydrostaticterms
398    o * "clean" adjoint code (in terms of extensive recomputations)
399        can now be obtained for all GMREDI options (i.e. for
400        - GM_VISBECK_VARIABLE_K
401        - GM_NON_UNITY_DIAGONAL
402        - GM_EXTRA_DIAGONAL
403        - GM_BOLUS_ADVEC )
404      * However, wrong gradient check problem remains unsolved.
405      * New CPP options have been introduced for different
406        tapering schemes
407    o external_fields_load now part of differentiation list
408    o pressure needs multiple storing;
409      would be nice to have store_pressure at beginning or
410      end of forward_step, e.g. by having phiHyd global (5-dim.)
411      (NB: pressure is needed for certain cases in find_rho,
412      which is also invoked through convective_adjustment).
413    o recomputations in find_rho for cases
414     'JMD95'/'UNESCO' or 'MDJWF' are OK.
415    o #define ATMOSPHERIC_LOADING should be differentiable
416    o ini_forcing shifted to begining of initialise_varia
417    o Incorporating QNVS line search routines into MITgcm
418      (this is separate code, and therefore not under pkg)
419      lsopt/, optim/
420    o Updated verification/carbon/
421      - #define GM_VISBECK_VARIABLE_K
422      - GM_taper_scheme    = 'ldd97'    
423    
424    checkpoint46n_post
425    Merging from release1_p8:
426    o verification/natl_box:
427      updating new external_fields_load routine
428    o New package: pkg/seaice
429      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
430      The sea-ice code is based on Hibler (1979-1980).
431      Two sea-ice dynamic solvers, ADI and LSR, are included.
432      In addition to computing prognostic sea-ice variables and diagnosing
433      the forcing/external data fields that drive the ocean model,
434      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
435      The implied surface heat flux is then stored in variable
436      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
437      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
438      non-local transport term.  Because this call precedes model
439      thermodynamics, temperature under sea-ice may not be "exactly" at
440      the freezing point by the time theta is dumped or time-averaged.
441      N.B.: fairly large differences in accuracy occur across
442            different platforms/compilers; comparison between
443            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
444            generated output gives:
445       T           S           U           V
446      C D M    c        m  s        m  s        m  s        m  s
447      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
448      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
449      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
450    
451      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
452    o GAD:
453      - generated new common blocks to account for call of
454        same gad routines with differing traceridentities
455        (needed to modify tracerIdentity indices in GAD.h)
456      - generated separate common blocks for case useCubedSphereExchange
457        (Department of Futurology)
458      - parameter lists to gmredi_?transport: added tracerIdentity
459      - added new key indices to tamc.h
460    o external_fields_load:
461      - added this routine to TAF list
462      - needed to make some common blocks global and additional storing
463        along the same lines as exf package (checkpoint_lev?_directives.h)
464    o exf:
465      updated external forcing package
466      - bug fixes carried over from ecco-branch
467        (missing OBCS_OPTIONS.h in two routines)
468      - enable easy to use "no forcing".
469      - added exf I/O for atmospheric loading
470      - added exf I/O for runoff data
471      - transfered scaling between exf <-> MITgcm to exf namelist
472    o Adding new verification experiment global_with_exf.
473      This verification experiment is almost identical to the
474      global_ocean.90x40x15 experiment, except that it uses
475      the exf (and cal) package instead of the
476      external_fields_load routine (cf README file).
477    
478    checkpoint46m_post
479    o modified testscript to return -- when there are no lines of "%MON" output
480    o added new flag "quasiHydrostatic" for QH mode
481      and new routine quasihydrostaticterms()
482    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
483      New routine: mom_u_coriolis_nh()
484    o fixed sign of non-hydrostatic metric terms in u and v equations.
485      Depend on correct sign of gravitySign.
486    o added work.pc* to .cvsignore in aim directories using ifc
487    o introduced flag for controllin non-hydrostatic metric terms
488    o removed gravitySign from PARM04
489    o switched to g77/ifc from pgf77 in aim experiments
490    
491    checkpoint46l_post
492    o made convective adjustment work with pressure coordinates:
493     - changed the direction of k-loop in convective_adjustment.F for the
494       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
495     - adjusted the reference pressure k-index in convective_adjustment.F
496     - adjusted the convection condition in convect.F (in analogy to
497       calc_ivdc.F)
498     - convective_adjustment no longer computes anything on the halos
499     - removed the warnings about negative salinity from find_rho.F and
500       find_alpha.F; instead the new routine look_for_neg_salinity, called
501       at the beginning of find_rho, find_alpha, and find_beta, does a
502       check of the entire slice, if CPP-option
503       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
504    checkpoint46l_pre
505    
506    checkpoint46k_post
507    o fixed the verification/global_ocean.90x40x15 experiment:
508     - new bathymetry (the world according to A., JMC, and M.)
509     - new initial fields and forcing fields (*.bin files)
510     - new POLY3.COEFFS (for the next release one should switch to a full
511       equation of state: JMD95P or MDJWF)
512     - fixed several errors and redundancies in the data file
513     - experiment uses looped cells
514     - added matlab directory with diagnostic scripts for plotting of output
515    
516    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
517     - read AIM physics parameters from a file (data.aimphys)
518     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
519    
520    checkpoint46j_post
521    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
522    o move wVel computation at the end of the time step, in S/R integr_continuity
523    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
524    o update timeave pkg for wVel diagnostic.
525    checkpoint46j_pre
526    
527    checkpoint46i_post
528    o Clean up AIM package (and keep the results unchanged):
529      include CPP_OPTION and use IMPLICT NONE in all routines ;
530      declare all the variables _RL ; use _d 0 for all numerical constants.
531      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
532    
533    checkpoint46h_post
534    o cleaned up the use of rhoNil and rhoConst.
535      - rhoNil should only appear in the LINEAR equation of state, everywhere
536        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
537        and the dynamical equations are all divided by rhoConst
538    o introduced new parameter rhoConstFresh, a reference density of fresh
539      water, to remove the fresh water flux's dependence on rhoNil. The default
540      value is 999.8 kg/m^3
541    o cleanup up external_forcing.F and external_forcing_surf.F
542      - can now be used by both OCEANIC and OCEANICP
543    checkpoint46h_pre
544    
545     Added code to convert surface volume flux (fresh water) into
546     a mass flux when using P coordinates in the ocean (OCEANICP).
547     Note: It assumes you have set rho0=rhoConst=density of fresh water.
548    
549    checkpoint46g_post
550    o Include a new diagnostic variable phiHydLow for the ocean model
551      - in z-coordinates, it is the bottom pressure anomaly
552      - in p-coordinates, it is the sea surface elevation
553      - in both cases, these variable have global drift, reflecting the mass
554        drift in z-coordinates and the volume drift in p-coordinates
555      - included time averaging for phiHydLow, be aware of the drift!
556    o depth-dependent computation of Bo_surf for pressure coordinates
557      in the ocean (buoyancyRelation='OCEANICP')
558      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
559        Theta, Salinity, and Pressure in the parameter list. This routine is
560        presently contained in find_rho.F. This routine does not give the
561        correct density for 'POLY3', which would be a z-dependent reference
562        density.
563    o cleaned up find_rho
564      - removed obsolete 'eqn' from the parameter list.
565    o added two new verification experiments: gop and goz
566      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
567    checkpoint46g_pre
568    
569    checkpoint46f_post
570    o Enable tangent linear (forward mode) gradient checks:
571      - extended active file handling to g_... files
572      - added TANGENT_SIMULATION to theSimulationMode
573      - extended grdchk package accordingly
574    o added tangent linear setup in verification/carbon/code_ftl
575    o added adjoint setup in verification/front_relax/code_ad
576    
577    checkpoint46e_post
578    o Added new equation of state -> MDJWF
579      - EOS of McDougall et al., 2002, JAOT, submitted
580      - caveat: the equation of state is only valid for a smaller (more
581        realistic?) range of values than JMD95P/Z and UNESCO
582      - added masks to the calculation of pressure in store_pressure
583      - added more check values for density in check_eos (ini_eos.F), some of
584        the old check values are out of the range of the MDJWF-eos, so don't
585        expect perfect matches for those
586    checkpoint46e_pre
587    
588    checkpoint46d_post
589    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
590      'OCEANICP', also initialised field pressure correctly in ini_eos in the
591      case of pressure coordinates. eosType='JMD95Z' in
592      combination with buoyancyRelation='OCEANICP' now causes an error.
593    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
594      in find_alpha/beta.
595    checkpoint46d_pre
596    
597    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
598      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
599    
600    checkpoint46c_post
601    o Changes necessary for ocean in p-coordinates
602     -  Added new buoyancy relation = 'OCEANICP'
603     -  Added new parameters = gravitySign (this used to be contained inside
604        the factor dRdZ which I added when we first switched to R coordinates).
605     X GM/Redi is not compatible (yet)
606     X bottom drag and no-slip need to be debugged.
607    checkpoint46c_pre
608    
609    checkpoint46b_post
610    o Added new equation of state -> JMD95Z and JMD95P
611      - EOS of Jackett and McDougall, 1995, JAOT
612      - moved all EOS parameters into EOS.h
613      - new routines ini_eos.F, store_pressure.F
614    o Added UNESCO EOS, but not recommended because it requires
615      in-situ temperature (see JMD95)
616    o Modified formatting for knudsen2.f in utils/knudsen2 and added
617      unesco.f to be used with POLY3
618    checkpoint46b_pre
619    
620    checkpoint46a_post
621    o Added (atmospheric) pressure loading
622      - new field in FFIELDS.h, etc...
623      - new cpp flag ATMOSPHERIC_LOADING
624    o Changed hFacC to _hFacC in calc_phi_hyd.F
625    o Added SHORTWAVE_HEATING to some files for consistency
626    checkpoint46a_pre
627    
628    checkpoint46
629    further merges from release1_p5
630    o new ctrl package
631      - adopted from ECCO environment to enable optimization
632      - added Eliassen Palm fluxes to controls
633    o added Eliassen Palm flux controls to gradient check package
634    o cost package
635      - Compatible with new ctrl package
636      - added Eliassen Palm cost hooks
637      - modif's of existing cost functions
638    o Adjoint-related bug fixes in kpp:
639      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
640      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
641    o autodiff package
642      - flow directives:
643        + new for S/R do_the_model_io
644        + enhanced for S/R checkpoint
645        + new gmredi.flow
646      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
647        disable adcommon.h/g_common.h by default.
648      - fixed problem for adjoint of global_max
649    o modified verification/carbon/
650    o New setup for adjoint of global_ocean
651    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
652    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
653    o incorporated hooks for sponge layer code (external_forcing.F)
654    
655    checkpoint45d_post
656    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
657    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
658      (affects plume_on_slope "cg2d" output)
659    o add new parameter deltaTfreesurf for free-surface time stepping
660    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
661    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
662    o change phiMin in exp1 (to agree with documentation)
663    o add new flags:
664     - T,S forcing inside/outside Adams-Bashforth
665     - turn off temp,salt advection and/or forcing
666     - for each tracer, define internal flag for multiDimAdvection & A-B
667    o monitor: change definition of KE to check conservation of Energy
668    
669    checkpoint45c_post
670    o Removed f90 comments ("!")
671    o Modified initialisations to enable exf package for MITgcm
672      (without invoking ECCO_PACKAGE).
673    o modifications to gradient check package (Martin Losch)
674      - enable centered differences
675      - modified format of standard output
676    
677    checkpoint45b_post
678    o cleaned exchange calls in cg2d
679    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
680    o included CPP option SINGLE_LAYER_MODE in thermodynamics
681      to configure barotropic setup (Martin Losch)
682    o moved some initialisations within bi,bj loop in dynamics
683      (TAF flow dependency)
684    o in initialise_varia, moved call packages_init_variables
685      before convective_adjustment_init
686      (corresponding adjustment of TAF tape initialisation).
687    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
688    
689    checkpoint45a_post
690    o compute Rho over the whole domain (extend iMin,jMin indices)
691    o specific exchange for X-slice domain (case Ny=1)
692    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
693    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
694    
695    checkpoint44h_post = checkpoint45
696    o Fix to restore differentiability:
697      place at which packages_init_variables is called in
698      initialise_varia is crucial for reverse control flow.
699    o modifications in GMRedi to enable stable adjoint
700      (corresponding modif's in thermodynamics, dynamics)
701    o added missing hook for sponge layer code in external_forcing
702    o modified test cost functions
703    o storing in gad_advection (plus removal of write(0,*)!
704    o missing headers TR1.h added in convective_adjustment routines
705    o errorMessageUnit set non-equal zero in eeboot
706      (conflict on some platforms, e.g. IBM SP3)
707    o modified carbon verif.
708    
709    checkpoint44h_pre
710    o vertical grid option: allow to put the Interface at the middle between
711      2 cell-centers ; replace delZ in pkg/kpp by drF.
712    o GM Advective form: Tracers are advected using the residual transport (=
713      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
714    
715    checkpoint44g_post
716    o fix surface correction term in multiDimAdvection (affects plume_on_slope
717      results) ; ifdef missing in thermodynamics.F
718    
719    checkpoint44f_pre,checkpoint44f_post
720    o added PTRACERS package
721      This allows an arbitrary number of passive tracers to be integrated
722      forward simultaneously with the dynamicaly model.
723      + Implemented so far:
724        - basic forward algorithm (time-stepping, advection, diffusion, convection)
725        - I/O and checkpointing
726        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
727      + Not implemented so far:
728        - KPP
729        - OBCS
730      + No specific example supplied (yet) but global_ocean.90x40x15 has the
731        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
732        line in data.pkg.
733      + This package is disabled by default since it increases storage.
734    
735    
736    o testscript: added -cleanup option
737    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
738                 b) enable to filter 2D fields.
739    
740    checkpoint44e_pre,post
741    o re-wrote convective adjustment to use pre-calculated weights
742      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
743      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
744      Original calls to convect() still in place.
745    
746    chkpt44d_pre,post
747    o added missing EXCLUDE_MONITOR flags
748    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
749      (incompatible typ in MIN/MAX expressions caused problems
750      on IBM SP3)
751    o in genmake added variable MAKEDEPEND
752      plus resetting for case SunOS
753    o added timer_stats.c routine for IBM SP3
754    o removed variables in dynamics
755    !!! I forgot to create tag chkpt44d_pre !!!
756    !!! But chkpt44d_pre = chkpt44c_post    !!!
757    
758    o real fresh water flux implemented with non-linear free-surface.
759    
760    chkpt44c_pre,post
761    o few fix (mask in shap_s2, EmPmR in external_field_load,
762      USE_NATURAL_BCS in solve_for_P);
763    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
764    
765    checkpoint44b_pre/_post
766    o merge of relevant stuff from the ecco-branch:
767      - genmake: removed $S64 overwrite for case SunOS
768      - pkg/exf: update and corrections for field swapping and obcs
769      - pkg/ecco: parameter lists for the_model_main, the_main_loop
770                  harmonized between ECCO and MITgcm
771      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
772                      updated checkpointing_lev... lists for obcs
773      - model/src: minor changes in forward_step, plot_field
774                   added directive for divided adjoint in the_main_loop
775      - pkg/mdsio: added mdsio_gl_slice
776    
777    o check parameters & config (chkpt44a_pre,post)
778    o OBC and NonLin_FrSurf.
779    
780    checkpoint44
781    o fix bug in mom_vi_del2uv
782    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
783    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
784    o update AIM experiments (NCEP input files)
785    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
786    o added some stuff for AD
787    
788    checkpoint43
789    o added two new advection tests
790    o added global 4x4 degree ocean test
791    o added test of H&S94 with free surface on cube
792    o some final mods for gradient check, adjoint,...
793    
794    checkpoint42
795      Fixed AD-related problems:
796    o Store directives up-to-date with re-arranged Adams-Bashforth
797      (mainly thermodynamics.F)
798    o New store directives for multi-dim. advection schemes
799      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
800      * new common block and key passkey
801      (mainly gad_advection.F)
802    o Modified store directives for split of dynamics/thermodynamics
803      for the case ALLOW_KPP
804    o Cleaned argument list for timestep_tracer.F
805    
806    checkpoint41
807    o re-formatted/added comments in prologues of key subroutines
808      to work with protex
809    
810    checkpoint40
811    o moved calc_gs, calc_gt and calc_tr1 back to model/src
812    o added FLT (floats) package from Arne along with demo. experiment
813    o re-arranged Adams-Bashforth scheme for tracers to allow easier
814      implementation of forward-in-time forcing terms
815    o more mods for non-linear free-surface including new variable
816    o modified multi-dim method to work on cube
817    o bug fix in KPP (from DM)
818    
819    checkpoint40pre9
820    o added DST advection schemes
821    o fix MPI bug on SGI's
822    o modifications for non-linear free-surface
823    o fixed conditionals for fixed flow/passive tracer only mode
824    o added tension/strain form of stress tensor
825    o changes to commenting of arguments for TAF/TAMC
826    o added/updated many matlab scripts
827    o added multi-dimensional advection method for tracers
828      
829    checkpoint40pre8
830    o new package rw/
831      Added method for dumping intermediate local arrays:
832      mdsio_writetile - same as mdsio_writefield except works from inside
833                        bi,bj loop
834      mdsio_writelocal - same as mdsio_writetile except works for local
835                         arrays
836      write_local_r? - higher-level wrapper for mdsio_writelocal
837      Controlled by diagFreq. Defaults to zero (ie. no dumps)
838      Example given at end of mom_vecinv.F that dumps some local arrays.
839    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
840      control flux-form versus vector invariant code.
841      Switch is runtime flag vectorInvariantMomentum (defaults to false)
842      or genmake -DISABLE ...
843    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
844      (additional storing is now needed for case vecinv;
845      currently nothing implemented to switch this storing off
846      in case fluxform is used since no CPP flag available).
847    
848    checkpoint40pre7
849    o bug fix in dynamics.F
850      calc_viscosity called before k=1,Nr loop.
851    o added some #ifdef's ALLOW_PASSIVE_TRACER
852    o cleaned initialisations in ctrl_map_ini
853      related to TAF
854    
855    checkpoint40pre6
856    o split dynamics into thermodynamics & dynamics
857    o corresponding split of calc_diffusivity into
858      calc_diffusivity, calc_viscosity
859      (kpp_calc_diff, kpp_calc_visc).
860    o Added diffkr, kapgm to control variables
861    o bug fix in gmredi_slope_limit for ldd97
862    
863    checkpoint40pre5
864    o proper initialization of Adams-Bashforth time stepping
865      + uses forward step for very first step of model (iter=0)
866    o re-generated *all* output since almost all output is modified by this
867      change (sorry but we've been putting this one off for about 2 years)
868      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
869        *not* regenerated since they are already out of date and I don't
870        want to create the impression that they are suddenly working.
871    o removed KAP stuff for DEC's
872    o modified/added many .cvsignore files in */code and */input
873    o added new expt "solid-body.cs-32x32x1"
874      + this uses an alternative form of ini_curvilinear_grid.F which
875        is not necessarily any better than the current one...
876    
877    checkpoint40pre4
878    o added re-initialisations of utrans,vtrans,rtrans in
879      calc_common_factors which are crucial for TAF.
880    o extended iMin,jMin range for calc_common_factors,
881      calc_diffusivity
882    o added option ALLOW_PASSIVE_TRACER
883    o a few minor updates and fixes
884    
885    checkpoint40pre3
886    o created calc_gtr1.F for gad package
887    o split the_main_loop and re-introduced forward_step
888    o some recomputations of nIter0 for TAMC
889    
890    checkpoint40pre2
891    o Updated to latest branch of AJA, JMC
892    o Added gradient check package
893    o Added routines for passive tracer handling
894    o Added carbon sequestration sensitivity experiment
895    
896    checkpoint39
897     o Modifications and fixes to support TAMC
898       (mainly missing or wrong directives)
899     o Corrected common blocks when fooling TAMC to produce adjoint I/O
900       in addummy_in_stepping
901     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
902     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
903     o Included following packages:
904       cal: calendar
905       exf: external forcing
906       ecco: essential routines to control use of cal, exf
907             (NB: this is not the full ECCO environment)
908     o disabled some packages by default in genmake
909    
910    checkpoint38
911     o see notes_c37_adj.txt
912     o corrected wrong layer index in external_forcing_t
913     o replaced the_main_loop/forward_step by the_main_loop
914     o removed forceoutput from write_state
915       (replaced criteria for initial/final state)
916     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
917    
918    checkpoint37
919     o mdsio.F routine split and packaged in pkg/mdsio
920       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
921        used unless genmake -disable=mdsio)
922     o allow a more precise surface-geopotential gradient for the atmosphere
923       taking into account the change in space of Alpha (=1/rho) at the surface.
924     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
925       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
926     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
927       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
928       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
929     o Time-Average diagnostics defined as a pseudo package "timeave".
930     o pickup files : old pickup (before c35) did not work with new code (c35
931       and after) unless activating 2 commented lines in initialise-varia.
932     o Non-Hydrostatic pickup file Pb fixed.
933     o bug with Rigid-lid version (since c35) fixed.  
934    
935    checkpoint36
936     o implement Crank-Nickelson barotropic time-stepping
937     o recover Time-Average diagnostics
938     o fix Pb in checkpoint (PR#19)
939     o AIM become a standard package ; clean unused CPP_kees
940    
941    checkpoint35
942     o subtantial rewrite of dynamics.f
943     o allows staggered time-stepping
944     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
945     o added bottom drag (linear + quadratic)
946    
947    checkpoint34
948     o Modified exchange routines for correct reverse simulation.
949     o Added verification output to comply with bug fix in impldiff.F
950       as of c33 (exp2, natl_box).
951     o Corrected store directives in dynamics.F
952     o Corrected array boundaries in impldiff.F
953     o Corrected array dimensions in gmredi.
954       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
955     o Added routine GLOBAL_SUM_INT to global_sum.F
956     o Added mdsio_gl.F for ECCO purposes.
957    
958    checkpoint33
959     o Fixed bug in lower BC in impldiff.F
960     o Fixed confusion about units of forcing arrays in FFIELDS.h
961       namely Fu,Fv,Qnet,Qsw,EmPmR:
962       - Removed verification/natl_box/code/external_fields_scale.F
963         (did not differ from that in model/src)
964       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
965         (see FFIELDS.h for description)
966       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
967         kpp_calc.F and kpp_transport_t.F
968       - Removed model/src/external_fields_scale.F and calls to it
969       - verification/natl_box uses flux data with "atmospheric" sign so
970         a special version of external_fields_load.F is used to
971         change the data as it's read in. This way, the arrays
972         have the right units and signs at all times tha a user could
973         possibly use them.
974     o Corrected genmake to delete a temporary file during configuration
975    
976    checkpoint32
977     o Scaling of forcing fields moved from external_forcing.F to
978       external_fields_scale.F, called directly after loading fields.
979     o Surface relaxation terms added to surface tendency fields in
980       extra subroutine.
981     o impldiff.F changed to avoid storing by TAMC of huge intermediate
982       fields.
983     o Changes in GMRedi to comply with packaging structure.
984     o Modifications and bug fixes in KPP package.
985     o Verification experiment for KPP added (verification/nat_box/)
986    
987    checkpoint31
988     o Packages interface brought in line with defined standard
989       -> new routines packages_...F
990       -> changes in initialise_fixed.F, initialise_varia.F
991       -> enables initialisation interface for ECCO package
992     o Rescaling of external forcing fields immediately after read
993       (removed from external_forcing.F)
994       -> new: surface_fields_scale.F
995       -> affects ini_foorcing.F, external_fields_load.F
996     o Computation of surface tendencies before tendency updates.
997       -> new: external_forcing_surf.F
998     o Change of variable names useGMRedi, useKPP, useECCO
999     o Further changes in dynamics.F, impldiff.F for TAMC
1000     o Tested for experiments 0, 2, 4.
1001       - not yet tested for GMRedi.
1002       - not yet tested for KPP.
1003    
1004    checkpoint30
1005     o Updates for OBCs
1006     o New experiment for test OBCs (internal_wave)
1007     o New output.txt in verification/exp4/results/
1008     o Updates for KPP: calculation of viscosity corrected, new variables
1009       kpp_dumpFreq and kpp_taveFreq
1010     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1011       and entry for T90 in genmake
1012    
1013    checkpoint29
1014     o packaged KPP and GM/Redi
1015    
1016    checkpoint28
1017     o Corrected initialization of hFacMin for difference vertical coordinates
1018     o Modified calculation of partial cell thickness to more robust algorithm
1019     o config_summary.F: replaced write_1D_... by write_0D_...
1020       read_write.F: added subroutines write_0D_...
1021     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1022       included some initialisations required for TAMC.
1023     o routine calc_isoslopes: modified sqrt computation to make it
1024       differentiable for zero argument.
1025     o routines dynamics, impldiff:
1026       included store directives and tape key computations required for TAMC.
1027     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1028    
1029    checkpoint27
1030     o fixed calc_isoslopes() to so that cancellation of terms in tensor
1031       formulation works properly with variable resolution.
1032     o restructured the calling tree between the_model_main() and dynamics()
1033     o split initialise() into initialise_fixed() and initialise_varia()
1034     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1035       in new routine ini_psurf()
1036    
1037    checkpoint26
1038     o moved some #ifdef in optional routines to encompass everything
1039       except the argument declarations. This was using up some memory.
1040     o fixed macros like _ADT to work with both versions of Linux cpp
1041     o cleaned up some unused and uninitialized variables
1042       (helps when debugging with strict compile options)
1043     o split up CPP_EEOPTIONS.h into options and macros
1044       (macros are now in eesupp/inc/CPP_EEMACROS.h)
1045     o patch for 2 processor JAM mode
1046    
1047    checkpoint25
1048     o updates for OBCs and NH
1049     o dramatically reduced memory usage
1050     o added "JAM" routines for use on Artic network
1051     o parameterization of convection by implicit vertical diffusion
1052     o added a diagnostic of convective index
1053     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1054       (this is was partly for OBCs and NH but also in anticipation of
1055        an explicit free-surface option)
1056     o initial state input files for U and V
1057    
1058    checkpoint24
1059     o Removed some spurious "REAL"s
1060     o Updated KPP to latest version from JPL
1061     o Added a COS(latitude) in horizontal viscosity
1062    
1063    checkpoint23
1064     o Added del^4 diffusion for salt and temperature
1065     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1066    
1067    checkpoint22
1068     o Made many small changes: implicit none, format(i5), etc...
1069     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1070    
1071    checkpoint21
1072     o Introduced new I/O package that supports direct-access records (mdsio.F)
1073     o Split-up mid-level I/O routines
1074     o Updated input data for experiments 0,1,2,4 and 5
1075     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1076    
1077    checkpoint20
1078     o Tidied up open-boundaries some more
1079     o Added non-hydrostatic code
1080     o Fixed some input data
1081     o Modified MPI start-up to work in "coupled" context.
1082    
1083    checkpoint19
1084     o Tidied up directory structure for verification experiments.
1085     o Added new code for open boundaries.
1086     o Corrected advective terms near boundaries.
1087     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1088     o Implemented free-slip/no-slip BCs and del^4 dissipation.
1089     o Split default parameters out of ini_parms.F into set_defaults.F.
1090    
1091    checkpoint18
1092     o Further changes for optional code generation with
1093       CPP - ugh!
1094    
1095    checkpoint17
1096     o Beginning to incorporating modularity
1097       for supporting atmos. and ocean configs.
1098     o Small changes for TAMC complinace
1099     o New ultra simple test case. Barotropic box
1100       configuration "exp0".
1101    
1102    checkpoint16
1103     o Minor changes to exchange routines to support
1104       accumulation in reverse mode. Adjoint of an
1105       assignment is an addition.
1106     o Changes to support compilation by TAMC (LR(1)
1107       syntax) and by g77 under Linux ( 72 character
1108       limit ).
1109    
1110    checkpoint15
1111     Rewrote exchange routines to allow
1112     o General tile <-> tile connectivity.
1113     o TAMC reverse mode flag ( is this really needed? )
1114     o Variable width overlap and exchange region widths.
1115     o Hooks for sharing data via DMA, Arctic, Memory Channel,
1116       shmput/shmget, VIA, SYSV shmem and every other cool
1117       communication method.
1118    
1119    checkpoint14
1120     Consistent isomorphism chages made. These allow dynamical core
1121     to support both pressure and meters as a vertical coordinate.
1122    
1123    checkpoint13
1124     Release which corrects global_max problem and a couple
1125     of KGM time-averaging diagnostic errors. Also contains
1126     a double-gyre experiment setup as well as the baseline
1127     4 degree global template. The double gyre template is
1128     organised to allow it to be applied automatically to
1129     the baseline configuration.
1130    
1131    branch-point-rdot
1132     A few tidy-ups have been made bt the real point of this
1133     check-point (excuse the pun) is to allow a branch to be
1134     made for the purposes of adding the rDot alterations.
1135     I don't want to commit the rDot to the main-trunk until
1136     we've actually tested it...
1137    
1138    checkpoint12
1139     Tidy up and added generic genmake script (formerly
1140     configure script).
1141     Released to testers.
1142    
1143    checkpoint11
1144     Re-arranged initialise() and introduced ini_vertical_grid()
1145     and ini_masks_etc().
1146    
1147    checkpoint10
1148     Introduced the configure script.
1149     Separated out the diags package.
1150     Added template for writing time-averages of tile/intermediate quantities.
1151     Updated SIZE.h in exp2 and made the data big-endian.
1152    
1153    checkpoint9
1154     MPI fix. Filename changes (meta/data). salbin*y stuff.
1155     General tidy-up.
1156     SST.bin SSS.bin added to verification/exp2
1157    
1158    checkpoint8
1159     Inludes time-dependant forcing and time-averaging.
1160     Works at 4x4 and 2.8125x2.8125 global
1161    
1162    checkpoint7-4degree-ref
1163     Branch from checkpoint7. Released for application to
1164     global modeling and general modeling - process studies, regional
1165     model etc..
1166     Configured for verification/exp2 - 4 degree global, two process.
1167    
1168    checkpoint7
1169     Created by cnh
1170     Simple 4 degree global simulation
1171     configuration.
1172     Includes climatological wind,
1173     hydrography, bathymetry etc
1174     Does not include Heat Flux and E-P
1175    
1176    checkpoint6
1177     Created by cnh
1178     merged checkpoint5 with CD and
1179     spherical polar code.
1180     Still some problems with GM Redi
1181     abd full topography.
1182    
1183  checkpoint5  checkpoint5
1184   Created by AJA   Created by AJA
1185   contains updates to GM Redi   contains updates to GM Redi

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