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Revision 1.156 - (hide annotations) (download)
Thu May 15 16:15:57 2003 UTC (20 years, 11 months ago) by adcroft
Branch: MAIN
Changes since 1.155: +10 -1 lines
Recorded updates by AJA

1 adcroft 1.156 $Header: /u/gcmpack/models/MITgcmUV/doc/tag-index,v 1.155 2003/05/14 09:22:09 mlosch Exp $
2 cnh 1.1
3     Notes on tags used in MITgcmUV
4     ==============================
5 adcroft 1.156
6     o added missing .cvsignores and made uniform across expts
7     o changed configuration of tidal_basin_2d expt
8     o added pkg/debug functions for tracing code in fatal crashes
9     o tidied pkg/monitor to use MONITOR_OPTIONS.h
10     o new fn in pkg/monitor to stop model if solution grows too big
11     o removed lots of single quotes from comments
12     o fixed gather/scatter inital MPI dialogue in ini_procs.F
13    
14 mlosch 1.155 checkpoint50e_post
15     o make KPP work with PTRACERS
16     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
17     nearly a copy of kpp_transport_s
18     - there is no analogue to SurfaceTendencyS, so I have to use
19     gPtr(of the surface layer) instead
20     o add a new platform SunFire+mpi (SunFire 15000) to genmake
21     checkpoint50e_pre
22    
23     checkpoint50d_post
24 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
25     files analogous to write_state.F
26     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
27     analogous to the cg2d-related output.
28 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
29     so that writing to internal file fn (with length 512) fails.
30 mlosch 1.154 checkpoint50d_pre
31 jmc 1.151
32 jmc 1.153 checkpoint50c_post
33     o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
34 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
35 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
36     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
37     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
38 dimitri 1.150
39     checkpoint50c_pre
40     Merging from release1_p13:
41     o bug fix for pkg/seaice dynamic solver
42     o Added SEAICE_initialHEFF to pkg/seaice
43 jmc 1.149
44     checkpoint50b_post
45     o store u*,v* in gU,V instead of in guNm1,gvNm1
46     o in order to put the momForcing out of the Adams-Bashforth:
47     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
48     to timestep.F
49     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
50     o re-generate output for highly sensitive test-exp:
51     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
52 heimbach 1.146
53 jmc 1.148 checkpoint50b_pre
54 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
55 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
56     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
57 heimbach 1.145
58     checkpoint50a_post
59     o Bug fix for merging between c50 and KPP.
60     ikey was passed from thermodynamics to kpp_calc via
61     common block rather than being recomputed in kpp_calc,
62     in contradiction with new key itdkey.
63     New key ikppkey created, and tamc.h headers updated.
64 heimbach 1.143
65 heimbach 1.144 checkpoint50
66     - 2nd step of merge with ecco-branch:
67     merge changes in ecco-branch back into main trunk
68     - bug fix in find_alpha
69     - more storing in gmredi_calc_tensor.F, kpp_routines.F
70     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
71     - merged some sliced AD support routines
72    
73 heimbach 1.143 checkpoint49
74     merged from ecco-branch:
75     o exf:
76     - Enable initialisation of forcing fields to constant
77     (runtime) values.
78     - in exf_getffields.F
79     Reduce i-/j-loop to interior domain, discarding overlaps.
80     That also fixes wrong TAF-key computations for key_1, key_2
81     with bulf formulae.
82     - exf_init.F modify #ifdef for exf_init_evap
83     - exf_getffieldrec.F, ctrl_getrec.F
84     The following INT-usages are not safe:
85     fldsecs = int(fldsecs/fldperiod)*fldperiod
86     fldcount = int(fldsecs/fldperiod) + 1
87     and were modified.
88     o autodiff: checkpoint_lev...
89     - updated storing for bulk formulae (some arrays were missing)
90     - added state for seaice package
91     - synchronized with main branch
92     o DIVA:
93     Modif.s in
94 heimbach 1.144 - the_main_loop.F
95     - the_model_main.F
96 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
97     o With these changes, it is possible to fully separate
98     the first forward run to compute the cost function (mdthe_main_loop)
99     and adjoint runs over individual DIVA intervals (adthe_main_loop)
100     into separate model executions.
101     This enables better tuning of DIVA to given queue sizes.
102     o Loss of cost function value in consecutive DIVA runs is
103     fixed by storing to 'costfinal' file.
104     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
105     beginning/end of adjoint integration is accounted for.
106     The current changes apply to TAF-1.4.26.
107     TAF has one remaining bug, requiring one manual change
108     (see MITgcm manual).
109     o cal: synchronized between MAIN and ecco-branch
110 heimbach 1.141
111 heimbach 1.142 checkpoint48i_post
112 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
113     (mostly adding new routines to make list and replacing
114     pressure by totPhiHyd).
115     o Updated and merged grdchk package
116     - has both ADM and TLM checks
117     - works for single- and multi-proc.
118     - output cleaned
119     - worked successfully for parallel DIVA
120     o genmake:
121     - Adding -platform=SP4
122     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
123     o Modif. for DIVA:
124     ctrl_unpack should not be called in intermediate DIVA interval.
125     (similar thing would apply for active files such as
126     tbar, sbar, psbar, which should not be reinitialised;
127     only relevant for ecco-branch)
128 dimitri 1.136
129 heimbach 1.140 checkpoint48h_post
130 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
131 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
132     o Added SEAICE_initialHEFF to pkg/seaice
133 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
134 jmc 1.135
135     checkpoint48g_post
136     --- EOS:
137     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
138     store total Potential in totPhyHyd for diagnostics & EOS.
139     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
140     --- Pressure/geopotential gradient:
141     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
142     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
143     ( changes results of global_ocean_pressure )
144     o NLFS + z-coord.: add eta*Rho' contribution.
145     o accurate phiHyd when using interface-W at the middle between 2 centers
146     ( changes results of ideal_2D_oce )
147     o includes r* 2nd term in potential gradient.
148 dimitri 1.134
149     checkpoint48f_post
150     Merging from release1_p12:
151     o Modifications for using pkg/exf with pkg/seaice
152     - improved description of the various forcing configurations
153     - added basic radiation bulk formulae to pkg/exf
154     - units/sign fix for evap computation in exf_getffields.F
155     - updated verification/global_with_exf/results/output.txt
156     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
157     (SBO) core products, including oceanic mass, center-of-mass,
158     angular, and bottom pressure (see pkg/sbo/README.sbo).
159     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
160     to avoid negative values in shallow regions.
161     - updated verification/natl_box/results/output.txt
162     - updated verification/lab_sea/results/output.txt
163     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
164     o Added useSingleCpuIO option (see PARAMS.h).
165     o Updated useSingleCpuIO option in mdsio_writefield.F to
166     work with multi-field files, e.g., for single-file pickup.
167     o pkg/seaice:
168     - bug fix in growth.F: QNET for no shortwave case
169     - added HeffFile for specifying initial sea-ice thickness
170     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
171     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
172     kpp_transport_t.F, forward_step.F, and the_main_loop.F
173     o pkg/seaice:
174     - adjoint-friendly modifications
175     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
176 jmc 1.131
177 jmc 1.133 checkpoint48e_post
178 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
179 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
180     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
181     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
182     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
183 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
184 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
185     inverted_barometer solid-body.cs-32x32x1
186     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
187 jmc 1.130
188     checkpoint48d_post
189     o in preparation for r*:
190     a) use pre-computed gradient of hydrostatic potential:
191     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
192     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
193     => affects results of glob_oce_pressure (different truncation error)
194     update output.txt of ideal_2D_oce & global_ocean_pressure
195 jmc 1.129
196     checkpoint48d_pre
197     o in preparation for r*:
198     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
199     pass the 2 comp. of the grad. as arguments to momentum S/R.
200     but for the moment, only used if it does not change the results.
201     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
202 jmc 1.126
203 heimbach 1.128 checkpoint48c_post
204     Modifications in treatment of initial flux forcing controls
205     to avoid extra storing of flux fields.
206    
207     checkpoint48c_pre
208 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
209 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
210 jmc 1.124
211 jmc 1.125 checkpoint48b_post
212 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
213     (modification to pressure gradient not yet implemented)
214     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
215     (for U & V) that are used for vertical advection of momentum.
216 jmc 1.123
217     checkpoint48a_post
218     o In preparation for r*, use temp. array to compute vertical transport
219     in flux-form momentum pkg. => change results of few test-exp.
220     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
221     lab_sea, natl_box & plume_on_slope
222 jmc 1.122
223     checkpoint48
224     o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
225 heimbach 1.121
226     checkpoint47j_post
227 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
228 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
229     o added exch in ctrl_map_...
230     o aveFreq.=0. at end of cost_final to avoid overwrite in
231     reverse checkpointing loop
232     o Yet more changes in gmredi:
233     * adgmredi_calc_tensor
234     avoiding all recomputation of gmredi_slope_limit
235     * adgmredi_x/y/rtransport
236     added flag for excessive storing to avoid recomp. of
237     u/v/rtans, dTdx/y/z
238     -> this is not really necessary and very memory-consuming
239     * adgmredi_slope_psi:
240     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
241     * gmredi_slope_limit
242     re-activated full calculation of taperfct for case 'ac02'
243     o updating verification/ adjoints of carbon, global_ocean.90x40x15
244 heimbach 1.116
245 jmc 1.119 checkpoint47i_post
246     o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
247     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
248     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
249     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
250     o gmredi: fix few bugs.
251    
252 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
253 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
254     o few modif.'s to get latest version adjointed
255     (mainly kick out code in ini_linear_phisurf)
256     o modif's to run adjoint with exactConserv
257     o case GM_BOLUS_ADVEC should be cleaned
258     S/R gmredi_slope_psi should be cleaned
259     o verification/carbon now has exactConserv=.TRUE.
260 jmc 1.114
261 heimbach 1.115 checkpoint47g_post
262 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
263     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
264 heimbach 1.115 o After TAF bug fix:
265     Tested adjoint of gmredi package.
266     Tests were done with checkpoint47 rather than with latest
267     checkpoint47f_post since the latter is broken for the adjoint
268     verification/carbon/ contains both ADM and TLM gradient checks.
269     Here they are, before they get changed/lost/stolen.
270     Mostly modif.'s to fix numerical sensitivities.
271     Gradient checks OK for
272     - GM_taper_scheme:
273     * clipping
274     * ac02
275     * linear
276     * glw91
277     * dm95
278     * ldd97
279     - GMREDI_OPTIONS:
280     * GM_VISBECK_VARIABLE_K
281     * GM_NON_UNITY_DIAGONAL
282     * GM_EXTRA_DIAGONAL
283     * GM_BOLUS_ADVEC
284     in conjunction with data.gmredi parameters to be checked in
285     in a few minutes under verification/carbon/code/
286 cheisey 1.112
287 dimitri 1.113 checkpoint47f_post
288     Merging from release1_p10:
289     o modifications for using pkg/exf with pkg/seaice
290     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
291     and SEAICE_EXTERNAL_FLUXES
292     - pkg/exf CPP options EXF_READ_EVAP and
293     EXF_NO_BULK_COMPUTATIONS
294     - usage examples are Experiments 8 and 9 in
295     verification/lab_sea/README
296     - verification/lab_sea default experiment now uses
297     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
298    
299 cheisey 1.112 checkpoint47e_post
300     o created a tag prior to creating a branch
301    
302 mlosch 1.111 checkpoint47d_post
303     o fixed bug in the oceanic pressure coordinates code: vertical viscosity
304     at the bottom boundary had an erroneous half slip boundary condition
305     o added bottom drag and no slip boundary condition capabilities to
306     oceanic pressure coordinates code
307     o added new verification experiment global_ocean_pressure, this experiment is
308     also described in the tutorial section of the manual
309     checkpoint47d_pre
310 cheisey 1.110
311     checkpoint47c_post
312     o Added a verification experiment for a global cubed-sphere ocean run
313     - verification/global_ocean.cubed32x32x30
314     - uses pkg/therm_seaice and pkg/bulk_forcing
315 jmc 1.109
316     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
317     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
318     when using P-coordinate; only implemented for atmospheric config.
319     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
320     NOTES: requires option NONLIN_FRSURF to be "#define".
321     o update advect_xz/results/output.txt (left from checkpoint44g_post)
322 dimitri 1.108
323     checkpoint47b_post
324     Merging from release1_p9:
325     o pkg/seaice
326     - removed GOTO's and added taf directives
327     - double precision constants to reduce the g77 (Linux)
328     to F77 (SGI) differences reported in release1_p8
329     o tools/genmake
330     - added SGI options
331     o verification/testscript
332     - updated to that of checkpoint47a_post
333     o verification/global_ocean.90x40x15/input/eedata
334     - modified for SGI f77 compatibility
335     o verification/lab_sea
336     - added description of sea-ice model
337     - added missing matlab routines
338     - added test of thermodynamics parallelization
339 jmc 1.105
340 jmc 1.106 checkpoint47a_post
341 jmc 1.105 o new pkg: aim_v23
342     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
343     for now, keep the same surface forcing as before.
344     - Part-Cell implemented into AIM; check that Heat & Water are conserved
345     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
346     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
347     o add diagnostic of surface correction term in monitor output
348 jmc 1.106
349     o bulk_force and therm_seaice
350 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
351     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
352     - Earlier integration from Stephaine Dutkiewicz
353     and Patrick Heimbach.
354     - Two ifdef statements for compile time,
355     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
356 heimbach 1.104
357     checkpoint47
358     differentiable version of checkpoint46n_post
359     o bug fix in quasihydrostaticterms
360     o * "clean" adjoint code (in terms of extensive recomputations)
361     can now be obtained for all GMREDI options (i.e. for
362     - GM_VISBECK_VARIABLE_K
363     - GM_NON_UNITY_DIAGONAL
364     - GM_EXTRA_DIAGONAL
365     - GM_BOLUS_ADVEC )
366     * However, wrong gradient check problem remains unsolved.
367     * New CPP options have been introduced for different
368     tapering schemes
369     o external_fields_load now part of differentiation list
370     o pressure needs multiple storing;
371     would be nice to have store_pressure at beginning or
372     end of forward_step, e.g. by having phiHyd global (5-dim.)
373     (NB: pressure is needed for certain cases in find_rho,
374     which is also invoked through convective_adjustment).
375     o recomputations in find_rho for cases
376     'JMD95'/'UNESCO' or 'MDJWF' are OK.
377     o #define ATMOSPHERIC_LOADING should be differentiable
378     o ini_forcing shifted to begining of initialise_varia
379     o Incorporating QNVS line search routines into MITgcm
380     (this is separate code, and therefore not under pkg)
381     lsopt/, optim/
382     o Updated verification/carbon/
383     - #define GM_VISBECK_VARIABLE_K
384     - GM_taper_scheme = 'ldd97'
385 heimbach 1.103
386     checkpoint46n_post
387     Merging from release1_p8:
388     o verification/natl_box:
389     updating new external_fields_load routine
390     o New package: pkg/seaice
391     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
392     The sea-ice code is based on Hibler (1979-1980).
393     Two sea-ice dynamic solvers, ADI and LSR, are included.
394     In addition to computing prognostic sea-ice variables and diagnosing
395     the forcing/external data fields that drive the ocean model,
396     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
397     The implied surface heat flux is then stored in variable
398     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
399     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
400     non-local transport term. Because this call precedes model
401     thermodynamics, temperature under sea-ice may not be "exactly" at
402     the freezing point by the time theta is dumped or time-averaged.
403     N.B.: fairly large differences in accuracy occur across
404     different platforms/compilers; comparison between
405     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
406     generated output gives:
407     T S U V
408     C D M c m s m s m s m s
409     n p a R g m m e . m m e . m m e . m m e .
410     f n k u 2 i a a d i a a d i a a d i a a d
411     g d e n d n x n . n x n . n x n . n x n .
412    
413     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
414     o GAD:
415     - generated new common blocks to account for call of
416     same gad routines with differing traceridentities
417     (needed to modify tracerIdentity indices in GAD.h)
418     - generated separate common blocks for case useCubedSphereExchange
419     (Department of Futurology)
420     - parameter lists to gmredi_?transport: added tracerIdentity
421     - added new key indices to tamc.h
422     o external_fields_load:
423     - added this routine to TAF list
424     - needed to make some common blocks global and additional storing
425     along the same lines as exf package (checkpoint_lev?_directives.h)
426     o exf:
427     updated external forcing package
428     - bug fixes carried over from ecco-branch
429     (missing OBCS_OPTIONS.h in two routines)
430     - enable easy to use "no forcing".
431     - added exf I/O for atmospheric loading
432     - added exf I/O for runoff data
433     - transfered scaling between exf <-> MITgcm to exf namelist
434     o Adding new verification experiment global_with_exf.
435     This verification experiment is almost identical to the
436     global_ocean.90x40x15 experiment, except that it uses
437     the exf (and cal) package instead of the
438     external_fields_load routine (cf README file).
439 adcroft 1.94
440 adcroft 1.102 checkpoint46m_post
441 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
442 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
443     and new routine quasihydrostaticterms()
444 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
445     New routine: mom_u_coriolis_nh()
446 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
447     Depend on correct sign of gravitySign.
448 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
449 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
450 adcroft 1.95 o removed gravitySign from PARM04
451 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
452 mlosch 1.93
453     checkpoint46l_post
454     o made convective adjustment work with pressure coordinates:
455     - changed the direction of k-loop in convective_adjustment.F for the
456     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
457     - adjusted the reference pressure k-index in convective_adjustment.F
458     - adjusted the convection condition in convect.F (in analogy to
459     calc_ivdc.F)
460     - convective_adjustment no longer computes anything on the halos
461     - removed the warnings about negative salinity from find_rho.F and
462     find_alpha.F; instead the new routine look_for_neg_salinity, called
463     at the beginning of find_rho, find_alpha, and find_beta, does a
464     check of the entire slice, if CPP-option
465     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
466     checkpoint46l_pre
467 mlosch 1.91
468 mlosch 1.92 checkpoint46k_post
469 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
470     - new bathymetry (the world according to A., JMC, and M.)
471     - new initial fields and forcing fields (*.bin files)
472     - new POLY3.COEFFS (for the next release one should switch to a full
473     equation of state: JMD95P or MDJWF)
474     - fixed several errors and redundancies in the data file
475     - experiment uses looped cells
476     - added matlab directory with diagnostic scripts for plotting of output
477 jmc 1.90
478     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
479     - read AIM physics parameters from a file (data.aimphys)
480     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
481 jmc 1.89
482     checkpoint46j_post
483     o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
484     o move wVel computation at the end of the time step, in S/R integr_continuity
485     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
486     o update timeave pkg for wVel diagnostic.
487     checkpoint46j_pre
488 mlosch 1.87
489 jmc 1.88 checkpoint46i_post
490     o Clean up AIM package (and keep the results unchanged):
491     include CPP_OPTION and use IMPLICT NONE in all routines ;
492     declare all the variables _RL ; use _d 0 for all numerical constants.
493     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
494 mlosch 1.87
495     checkpoint46h_post
496     o cleaned up the use of rhoNil and rhoConst.
497     - rhoNil should only appear in the LINEAR equation of state, everywhere
498     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
499     and the dynamical equations are all divided by rhoConst
500     o introduced new parameter rhoConstFresh, a reference density of fresh
501     water, to remove the fresh water flux's dependence on rhoNil. The default
502     value is 999.8 kg/m^3
503     o cleanup up external_forcing.F and external_forcing_surf.F
504     - can now be used by both OCEANIC and OCEANICP
505     checkpoint46h_pre
506    
507     Added code to convert surface volume flux (fresh water) into
508     a mass flux when using P coordinates in the ocean (OCEANICP).
509     Note: It assumes you have set rho0=rhoConst=density of fresh water.
510 mlosch 1.86
511     checkpoint46g_post
512     o Include a new diagnostic variable phiHydLow for the ocean model
513     - in z-coordinates, it is the bottom pressure anomaly
514     - in p-coordinates, it is the sea surface elevation
515     - in both cases, these variable have global drift, reflecting the mass
516     drift in z-coordinates and the volume drift in p-coordinates
517     - included time averaging for phiHydLow, be aware of the drift!
518     o depth-dependent computation of Bo_surf for pressure coordinates
519     in the ocean (buoyancyRelation='OCEANICP')
520     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
521     Theta, Salinity, and Pressure in the parameter list. This routine is
522     presently contained in find_rho.F. This routine does not give the
523     correct density for 'POLY3', which would be a z-dependent reference
524     density.
525     o cleaned up find_rho
526     - removed obsolete 'eqn' from the parameter list.
527     o added two new verification experiments: gop and goz
528     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
529     checkpoint46g_pre
530 heimbach 1.85
531     checkpoint46f_post
532     o Enable tangent linear (forward mode) gradient checks:
533     - extended active file handling to g_... files
534     - added TANGENT_SIMULATION to theSimulationMode
535     - extended grdchk package accordingly
536     o added tangent linear setup in verification/carbon/code_ftl
537     o added adjoint setup in verification/front_relax/code_ad
538 mlosch 1.82
539 cnh 1.84 checkpoint46e_post
540 mlosch 1.83 o Added new equation of state -> MDJWF
541     - EOS of McDougall et al., 2002, JAOT, submitted
542     - caveat: the equation of state is only valid for a smaller (more
543     realistic?) range of values than JMD95P/Z and UNESCO
544     - added masks to the calculation of pressure in store_pressure
545     - added more check values for density in check_eos (ini_eos.F), some of
546     the old check values are out of the range of the MDJWF-eos, so don't
547     expect perfect matches for those
548 cnh 1.84 checkpoint46e_pre
549 mlosch 1.83
550 mlosch 1.82 checkpoint46d_post
551     o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
552     'OCEANICP', also initialised field pressure correctly in ini_eos in the
553     case of pressure coordinates. eosType='JMD95Z' in
554     combination with buoyancyRelation='OCEANICP' now causes an error.
555     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
556     in find_alpha/beta.
557     checkpoint46d_pre
558    
559     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
560     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
561 adcroft 1.81
562     checkpoint46c_post
563     o Changes necessary for ocean in p-coordinates
564     - Added new buoyancy relation = 'OCEANICP'
565     - Added new parameters = gravitySign (this used to be contained inside
566     the factor dRdZ which I added when we first switched to R coordinates).
567     X GM/Redi is not compatible (yet)
568     X bottom drag and no-slip need to be debugged.
569     checkpoint46c_pre
570 mlosch 1.80
571     checkpoint46b_post
572     o Added new equation of state -> JMD95Z and JMD95P
573 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
574 mlosch 1.80 - moved all EOS parameters into EOS.h
575     - new routines ini_eos.F, store_pressure.F
576     o Added UNESCO EOS, but not recommended because it requires
577     in-situ temperature (see JMD95)
578     o Modified formatting for knudsen2.f in utils/knudsen2 and added
579     unesco.f to be used with POLY3
580     checkpoint46b_pre
581 mlosch 1.79
582     checkpoint46a_post
583     o Added (atmospheric) pressure loading
584     - new field in FFIELDS.h, etc...
585     - new cpp flag ATMOSPHERIC_LOADING
586     o Changed hFacC to _hFacC in calc_phi_hyd.F
587     o Added SHORTWAVE_HEATING to some files for consistency
588     checkpoint46a_pre
589 heimbach 1.78
590     checkpoint46
591     further merges from release1_p5
592     o new ctrl package
593     - adopted from ECCO environment to enable optimization
594     - added Eliassen Palm fluxes to controls
595     o added Eliassen Palm flux controls to gradient check package
596     o cost package
597     - Compatible with new ctrl package
598     - added Eliassen Palm cost hooks
599     - modif's of existing cost functions
600     o Adjoint-related bug fixes in kpp:
601     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
602     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
603     o autodiff package
604     - flow directives:
605     + new for S/R do_the_model_io
606     + enhanced for S/R checkpoint
607     + new gmredi.flow
608     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
609     disable adcommon.h/g_common.h by default.
610     - fixed problem for adjoint of global_max
611     o modified verification/carbon/
612     o New setup for adjoint of global_ocean
613     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
614     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
615     o incorporated hooks for sponge layer code (external_forcing.F)
616    
617 jmc 1.77 checkpoint45d_post
618     o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
619 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
620     (affects plume_on_slope "cg2d" output)
621 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
622     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
623 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
624 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
625     o add new flags:
626     - T,S forcing inside/outside Adams-Bashforth
627     - turn off temp,salt advection and/or forcing
628     - for each tracer, define internal flag for multiDimAdvection & A-B
629     o monitor: change definition of KE to check conservation of Energy
630 heimbach 1.73
631     checkpoint45c_post
632     o Removed f90 comments ("!")
633     o Modified initialisations to enable exf package for MITgcm
634     (without invoking ECCO_PACKAGE).
635     o modifications to gradient check package (Martin Losch)
636     - enable centered differences
637     - modified format of standard output
638 heimbach 1.72
639     checkpoint45b_post
640     o cleaned exchange calls in cg2d
641     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
642     o included CPP option SINGLE_LAYER_MODE in thermodynamics
643     to configure barotropic setup (Martin Losch)
644     o moved some initialisations within bi,bj loop in dynamics
645     (TAF flow dependency)
646     o in initialise_varia, moved call packages_init_variables
647     before convective_adjustment_init
648     (corresponding adjustment of TAF tape initialisation).
649     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
650 jmc 1.70
651 jmc 1.71 checkpoint45a_post
652     o compute Rho over the whole domain (extend iMin,jMin indices)
653     o specific exchange for X-slice domain (case Ny=1)
654 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
655     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
656 jmc 1.67
657 heimbach 1.69 checkpoint44h_post = checkpoint45
658     o Fix to restore differentiability:
659     place at which packages_init_variables is called in
660     initialise_varia is crucial for reverse control flow.
661     o modifications in GMRedi to enable stable adjoint
662     (corresponding modif's in thermodynamics, dynamics)
663     o added missing hook for sponge layer code in external_forcing
664     o modified test cost functions
665     o storing in gad_advection (plus removal of write(0,*)!
666     o missing headers TR1.h added in convective_adjustment routines
667     o errorMessageUnit set non-equal zero in eeboot
668     (conflict on some platforms, e.g. IBM SP3)
669     o modified carbon verif.
670    
671     checkpoint44h_pre
672 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
673     2 cell-centers ; replace delZ in pkg/kpp by drF.
674 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
675     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
676 jmc 1.66
677     checkpoint44g_post
678     o fix surface correction term in multiDimAdvection (affects plume_on_slope
679     results) ; ifdef missing in thermodynamics.F
680 adcroft 1.65
681     checkpoint44f_pre,checkpoint44f_post
682     o added PTRACERS package
683     This allows an arbitrary number of passive tracers to be integrated
684     forward simultaneously with the dynamicaly model.
685     + Implemented so far:
686     - basic forward algorithm (time-stepping, advection, diffusion, convection)
687     - I/O and checkpointing
688     - GM/Redi *but* using the GM/Redi coefficient of Salt
689     + Not implemented so far:
690     - KPP
691     - OBCS
692     + No specific example supplied (yet) but global_ocean.90x40x15 has the
693     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
694     line in data.pkg.
695     + This package is disabled by default since it increases storage.
696    
697 jmc 1.60
698 adcroft 1.64 o testscript: added -cleanup option
699 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
700     b) enable to filter 2D fields.
701 adcroft 1.62
702     checkpoint44e_pre,post
703     o re-wrote convective adjustment to use pre-calculated weights
704     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
705     Adds: model/src/convective_weights.F, convectively_mixtracer.F
706     Original calls to convect() still in place.
707 heimbach 1.61
708     chkpt44d_pre,post
709     o added missing EXCLUDE_MONITOR flags
710     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
711     (incompatible typ in MIN/MAX expressions caused problems
712     on IBM SP3)
713     o in genmake added variable MAKEDEPEND
714     plus resetting for case SunOS
715     o added timer_stats.c routine for IBM SP3
716     o removed variables in dynamics
717     !!! I forgot to create tag chkpt44d_pre !!!
718     !!! But chkpt44d_pre = chkpt44c_post !!!
719 jmc 1.63
720     o real fresh water flux implemented with non-linear free-surface.
721 heimbach 1.58
722 jmc 1.59 chkpt44c_pre,post
723     o few fix (mask in shap_s2, EmPmR in external_field_load,
724     USE_NATURAL_BCS in solve_for_P);
725     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
726    
727 heimbach 1.58 checkpoint44b_pre/_post
728     o merge of relevant stuff from the ecco-branch:
729     - genmake: removed $S64 overwrite for case SunOS
730     - pkg/exf: update and corrections for field swapping and obcs
731     - pkg/ecco: parameter lists for the_model_main, the_main_loop
732     harmonized between ECCO and MITgcm
733     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
734     updated checkpointing_lev... lists for obcs
735     - model/src: minor changes in forward_step, plot_field
736     added directive for divided adjoint in the_main_loop
737     - pkg/mdsio: added mdsio_gl_slice
738 jmc 1.57
739     o check parameters & config (chkpt44a_pre,post)
740 jmc 1.56 o OBC and NonLin_FrSurf.
741    
742 heimbach 1.55 checkpoint44
743 jmc 1.54 o fix bug in mom_vi_del2uv
744 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
745     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
746     o update AIM experiments (NCEP input files)
747     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
748 heimbach 1.55 o added some stuff for AD
749 adcroft 1.53
750     checkpoint43
751     o added two new advection tests
752     o added global 4x4 degree ocean test
753     o added test of H&S94 with free surface on cube
754     o some final mods for gradient check, adjoint,...
755 heimbach 1.52
756     checkpoint42
757     Fixed AD-related problems:
758     o Store directives up-to-date with re-arranged Adams-Bashforth
759     (mainly thermodynamics.F)
760     o New store directives for multi-dim. advection schemes
761     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
762     * new common block and key passkey
763     (mainly gad_advection.F)
764     o Modified store directives for split of dynamics/thermodynamics
765     for the case ALLOW_KPP
766     o Cleaned argument list for timestep_tracer.F
767 adcroft 1.51
768     checkpoint41
769     o re-formatted/added comments in prologues of key subroutines
770     to work with protex
771 heimbach 1.47
772 adcroft 1.50 checkpoint40
773     o moved calc_gs, calc_gt and calc_tr1 back to model/src
774     o added FLT (floats) package from Arne along with demo. experiment
775     o re-arranged Adams-Bashforth scheme for tracers to allow easier
776     implementation of forward-in-time forcing terms
777     o more mods for non-linear free-surface including new variable
778     o modified multi-dim method to work on cube
779     o bug fix in KPP (from DM)
780    
781 adcroft 1.49 checkpoint40pre9
782     o added DST advection schemes
783     o fix MPI bug on SGI's
784     o modifications for non-linear free-surface
785     o fixed conditionals for fixed flow/passive tracer only mode
786     o added tension/strain form of stress tensor
787     o changes to commenting of arguments for TAF/TAMC
788     o added/updated many matlab scripts
789 adcroft 1.50 o added multi-dimensional advection method for tracers
790 adcroft 1.49
791 adcroft 1.48 checkpoint40pre8
792 heimbach 1.47 o new package rw/
793     Added method for dumping intermediate local arrays:
794     mdsio_writetile - same as mdsio_writefield except works from inside
795     bi,bj loop
796     mdsio_writelocal - same as mdsio_writetile except works for local
797     arrays
798     write_local_r? - higher-level wrapper for mdsio_writelocal
799     Controlled by diagFreq. Defaults to zero (ie. no dumps)
800     Example given at end of mom_vecinv.F that dumps some local arrays.
801     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
802     control flux-form versus vector invariant code.
803     Switch is runtime flag vectorInvariantMomentum (defaults to false)
804     or genmake -DISABLE ...
805     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
806     (additional storing is now needed for case vecinv;
807     currently nothing implemented to switch this storing off
808     in case fluxform is used since no CPP flag available).
809 heimbach 1.46
810     checkpoint40pre7
811     o bug fix in dynamics.F
812     calc_viscosity called before k=1,Nr loop.
813     o added some #ifdef's ALLOW_PASSIVE_TRACER
814     o cleaned initialisations in ctrl_map_ini
815     related to TAF
816 heimbach 1.45
817     checkpoint40pre6
818     o split dynamics into thermodynamics & dynamics
819     o corresponding split of calc_diffusivity into
820     calc_diffusivity, calc_viscosity
821     (kpp_calc_diff, kpp_calc_visc).
822     o Added diffkr, kapgm to control variables
823     o bug fix in gmredi_slope_limit for ldd97
824 adcroft 1.44
825     checkpoint40pre5
826     o proper initialization of Adams-Bashforth time stepping
827     + uses forward step for very first step of model (iter=0)
828     o re-generated *all* output since almost all output is modified by this
829     change (sorry but we've been putting this one off for about 2 years)
830     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
831     *not* regenerated since they are already out of date and I don't
832     want to create the impression that they are suddenly working.
833     o removed KAP stuff for DEC's
834     o modified/added many .cvsignore files in */code and */input
835     o added new expt "solid-body.cs-32x32x1"
836     + this uses an alternative form of ini_curvilinear_grid.F which
837     is not necessarily any better than the current one...
838 heimbach 1.43
839     checkpoint40pre4
840     o added re-initialisations of utrans,vtrans,rtrans in
841     calc_common_factors which are crucial for TAF.
842     o extended iMin,jMin range for calc_common_factors,
843     calc_diffusivity
844     o added option ALLOW_PASSIVE_TRACER
845     o a few minor updates and fixes
846    
847 heimbach 1.42 checkpoint40pre3
848     o created calc_gtr1.F for gad package
849     o split the_main_loop and re-introduced forward_step
850     o some recomputations of nIter0 for TAMC
851    
852 heimbach 1.41 checkpoint40pre2
853     o Updated to latest branch of AJA, JMC
854     o Added gradient check package
855     o Added routines for passive tracer handling
856     o Added carbon sequestration sensitivity experiment
857    
858 heimbach 1.39 checkpoint39
859     o Modifications and fixes to support TAMC
860     (mainly missing or wrong directives)
861     o Corrected common blocks when fooling TAMC to produce adjoint I/O
862     in addummy_in_stepping
863     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
864     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
865     o Included following packages:
866     cal: calendar
867     exf: external forcing
868     ecco: essential routines to control use of cal, exf
869     (NB: this is not the full ECCO environment)
870 heimbach 1.40 o disabled some packages by default in genmake
871 heimbach 1.39
872 heimbach 1.38 checkpoint38
873     o see notes_c37_adj.txt
874     o corrected wrong layer index in external_forcing_t
875     o replaced the_main_loop/forward_step by the_main_loop
876     o removed forceoutput from write_state
877     (replaced criteria for initial/final state)
878     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
879 jmc 1.36
880 jmc 1.37 checkpoint37
881     o mdsio.F routine split and packaged in pkg/mdsio
882     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
883     used unless genmake -disable=mdsio)
884     o allow a more precise surface-geopotential gradient for the atmosphere
885     taking into account the change in space of Alpha (=1/rho) at the surface.
886     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
887     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
888     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
889     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
890     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
891     o Time-Average diagnostics defined as a pseudo package "timeave".
892     o pickup files : old pickup (before c35) did not work with new code (c35
893     and after) unless activating 2 commented lines in initialise-varia.
894     o Non-Hydrostatic pickup file Pb fixed.
895     o bug with Rigid-lid version (since c35) fixed.
896    
897 jmc 1.36 checkpoint36
898 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
899 jmc 1.36 o recover Time-Average diagnostics
900     o fix Pb in checkpoint (PR#19)
901     o AIM become a standard package ; clean unused CPP_kees
902 jmc 1.35
903     checkpoint35
904     o subtantial rewrite of dynamics.f
905     o allows staggered time-stepping
906     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
907     o added bottom drag (linear + quadratic)
908 heimbach 1.33
909     checkpoint34
910     o Modified exchange routines for correct reverse simulation.
911     o Added verification output to comply with bug fix in impldiff.F
912     as of c33 (exp2, natl_box).
913     o Corrected store directives in dynamics.F
914     o Corrected array boundaries in impldiff.F
915     o Corrected array dimensions in gmredi.
916     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
917 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
918 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
919 adcroft 1.32
920     checkpoint33
921     o Fixed bug in lower BC in impldiff.F
922     o Fixed confusion about units of forcing arrays in FFIELDS.h
923     namely Fu,Fv,Qnet,Qsw,EmPmR:
924     - Removed verification/natl_box/code/external_fields_scale.F
925     (did not differ from that in model/src)
926     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
927     (see FFIELDS.h for description)
928     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
929     kpp_calc.F and kpp_transport_t.F
930     - Removed model/src/external_fields_scale.F and calls to it
931     - verification/natl_box uses flux data with "atmospheric" sign so
932     a special version of external_fields_load.F is used to
933     change the data as it's read in. This way, the arrays
934     have the right units and signs at all times tha a user could
935     possibly use them.
936     o Corrected genmake to delete a temporary file during configuration
937 heimbach 1.31
938     checkpoint32
939     o Scaling of forcing fields moved from external_forcing.F to
940     external_fields_scale.F, called directly after loading fields.
941     o Surface relaxation terms added to surface tendency fields in
942     extra subroutine.
943     o impldiff.F changed to avoid storing by TAMC of huge intermediate
944     fields.
945     o Changes in GMRedi to comply with packaging structure.
946     o Modifications and bug fixes in KPP package.
947     o Verification experiment for KPP added (verification/nat_box/)
948 heimbach 1.30
949     checkpoint31
950     o Packages interface brought in line with defined standard
951     -> new routines packages_...F
952     -> changes in initialise_fixed.F, initialise_varia.F
953     -> enables initialisation interface for ECCO package
954     o Rescaling of external forcing fields immediately after read
955     (removed from external_forcing.F)
956     -> new: surface_fields_scale.F
957     -> affects ini_foorcing.F, external_fields_load.F
958     o Computation of surface tendencies before tendency updates.
959     -> new: external_forcing_surf.F
960     o Change of variable names useGMRedi, useKPP, useECCO
961     o Further changes in dynamics.F, impldiff.F for TAMC
962     o Tested for experiments 0, 2, 4.
963     - not yet tested for GMRedi.
964     - not yet tested for KPP.
965 adcroft 1.29
966     checkpoint30
967     o Updates for OBCs
968     o New experiment for test OBCs (internal_wave)
969     o New output.txt in verification/exp4/results/
970     o Updates for KPP: calculation of viscosity corrected, new variables
971     kpp_dumpFreq and kpp_taveFreq
972     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
973     and entry for T90 in genmake
974 adcroft 1.28
975     checkpoint29
976     o packaged KPP and GM/Redi
977 heimbach 1.27
978     checkpoint28
979     o Corrected initialization of hFacMin for difference vertical coordinates
980     o Modified calculation of partial cell thickness to more robust algorithm
981     o config_summary.F: replaced write_1D_... by write_0D_...
982     read_write.F: added subroutines write_0D_...
983     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
984     included some initialisations required for TAMC.
985     o routine calc_isoslopes: modified sqrt computation to make it
986     differentiable for zero argument.
987     o routines dynamics, impldiff:
988     included store directives and tape key computations required for TAMC.
989     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
990 adcroft 1.26
991     checkpoint27
992     o fixed calc_isoslopes() to so that cancellation of terms in tensor
993     formulation works properly with variable resolution.
994     o restructured the calling tree between the_model_main() and dynamics()
995     o split initialise() into initialise_fixed() and initialise_varia()
996     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
997     in new routine ini_psurf()
998 adcroft 1.25
999     checkpoint26
1000     o moved some #ifdef in optional routines to encompass everything
1001     except the argument declarations. This was using up some memory.
1002     o fixed macros like _ADT to work with both versions of Linux cpp
1003     o cleaned up some unused and uninitialized variables
1004     (helps when debugging with strict compile options)
1005     o split up CPP_EEOPTIONS.h into options and macros
1006     (macros are now in eesupp/inc/CPP_EEMACROS.h)
1007     o patch for 2 processor JAM mode
1008 adcroft 1.24
1009     checkpoint25
1010     o updates for OBCs and NH
1011     o dramatically reduced memory usage
1012     o added "JAM" routines for use on Artic network
1013     o parameterization of convection by implicit vertical diffusion
1014     o added a diagnostic of convective index
1015     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1016     (this is was partly for OBCs and NH but also in anticipation of
1017     an explicit free-surface option)
1018     o initial state input files for U and V
1019 adcroft 1.23
1020     checkpoint24
1021     o Removed some spurious "REAL"s
1022     o Updated KPP to latest version from JPL
1023     o Added a COS(latitude) in horizontal viscosity
1024 adcroft 1.22
1025     checkpoint23
1026     o Added del^4 diffusion for salt and temperature
1027     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1028 adcroft 1.21
1029     checkpoint22
1030     o Made many small changes: implicit none, format(i5), etc...
1031     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1032 adcroft 1.20
1033     checkpoint21
1034     o Introduced new I/O package that supports direct-access records (mdsio.F)
1035     o Split-up mid-level I/O routines
1036     o Updated input data for experiments 0,1,2,4 and 5
1037     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1038 adcroft 1.18
1039 adcroft 1.19 checkpoint20
1040     o Tidied up open-boundaries some more
1041     o Added non-hydrostatic code
1042     o Fixed some input data
1043     o Modified MPI start-up to work in "coupled" context.
1044    
1045 adcroft 1.18 checkpoint19
1046     o Tidied up directory structure for verification experiments.
1047     o Added new code for open boundaries.
1048     o Corrected advective terms near boundaries.
1049     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1050     o Implemented free-slip/no-slip BCs and del^4 dissipation.
1051 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
1052 cnh 1.17
1053     checkpoint18
1054     o Further changes for optional code generation with
1055     CPP - ugh!
1056 cnh 1.16
1057     checkpoint17
1058     o Beginning to incorporating modularity
1059     for supporting atmos. and ocean configs.
1060     o Small changes for TAMC complinace
1061     o New ultra simple test case. Barotropic box
1062     configuration "exp0".
1063 cnh 1.15
1064     checkpoint16
1065     o Minor changes to exchange routines to support
1066     accumulation in reverse mode. Adjoint of an
1067     assignment is an addition.
1068     o Changes to support compilation by TAMC (LR(1)
1069     syntax) and by g77 under Linux ( 72 character
1070     limit ).
1071 cnh 1.14
1072     checkpoint15
1073     Rewrote exchange routines to allow
1074     o General tile <-> tile connectivity.
1075     o TAMC reverse mode flag ( is this really needed? )
1076     o Variable width overlap and exchange region widths.
1077     o Hooks for sharing data via DMA, Arctic, Memory Channel,
1078     shmput/shmget, VIA, SYSV shmem and every other cool
1079     communication method.
1080 cnh 1.13
1081     checkpoint14
1082     Consistent isomorphism chages made. These allow dynamical core
1083     to support both pressure and meters as a vertical coordinate.
1084 cnh 1.12
1085     checkpoint13
1086     Release which corrects global_max problem and a couple
1087     of KGM time-averaging diagnostic errors. Also contains
1088     a double-gyre experiment setup as well as the baseline
1089     4 degree global template. The double gyre template is
1090     organised to allow it to be applied automatically to
1091     the baseline configuration.
1092 adcroft 1.11
1093     branch-point-rdot
1094     A few tidy-ups have been made bt the real point of this
1095     check-point (excuse the pun) is to allow a branch to be
1096     made for the purposes of adding the rDot alterations.
1097     I don't want to commit the rDot to the main-trunk until
1098     we've actually tested it...
1099 cnh 1.10
1100     checkpoint12
1101     Tidy up and added generic genmake script (formerly
1102     configure script).
1103     Released to testers.
1104 adcroft 1.9
1105     checkpoint11
1106     Re-arranged initialise() and introduced ini_vertical_grid()
1107     and ini_masks_etc().
1108 adcroft 1.8
1109     checkpoint10
1110     Introduced the configure script.
1111     Separated out the diags package.
1112     Added template for writing time-averages of tile/intermediate quantities.
1113     Updated SIZE.h in exp2 and made the data big-endian.
1114 adcroft 1.7
1115     checkpoint9
1116     MPI fix. Filename changes (meta/data). salbin*y stuff.
1117     General tidy-up.
1118     SST.bin SSS.bin added to verification/exp2
1119 adcroft 1.6
1120     checkpoint8
1121     Inludes time-dependant forcing and time-averaging.
1122     Works at 4x4 and 2.8125x2.8125 global
1123    
1124     checkpoint7-4degree-ref
1125     Branch from checkpoint7. Released for application to
1126     global modeling and general modeling - process studies, regional
1127     model etc..
1128     Configured for verification/exp2 - 4 degree global, two process.
1129 cnh 1.5
1130     checkpoint7
1131     Created by cnh
1132     Simple 4 degree global simulation
1133     configuration.
1134     Includes climatological wind,
1135     hydrography, bathymetry etc
1136     Does not include Heat Flux and E-P
1137 cnh 1.4
1138     checkpoint6
1139     Created by cnh
1140     merged checkpoint5 with CD and
1141     spherical polar code.
1142     Still some problems with GM Redi
1143     abd full topography.
1144 cnh 1.3
1145     checkpoint5
1146     Created by AJA
1147     contains updates to GM Redi
1148     and reordered timestepping loop
1149     for Implicit Diffusion.
1150 cnh 1.2
1151     checkpoint4
1152     Created by cnh
1153     Contains memory saving macros ( _rdxc etc..) for when
1154     grid variations are limited.
1155     Contains polynomial coeffs for EOS and knudsen program
1156     for generation.
1157    
1158 cnh 1.1 checkpoint3
1159     Created by cnh
1160     Added extra flags for runtime options
1161     Added this file
1162     Added implicit free-surface
1163     Added pre-conditioner
1164     Put compare01 into repository ( compare01/... )
1165     Put data and eedata into repository ( verification/exp1 )
1166    
1167     checkpoint2
1168     Created by AJA
1169     Added GM/Redi
1170    
1171     checkpoint1
1172     Created by AJA
1173     Restructured kloop in dynamics.F
1174     Added non-linear EOS
1175    
1176 cnh 1.2 baseline
1177     Original checked in code
1178 cnh 1.1

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