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revision 1.1 by cnh, Tue May 26 14:38:05 1998 UTC revision 1.58 by heimbach, Thu Feb 7 20:00:09 2002 UTC
# Line 2  $Header$ Line 2  $Header$
2    
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint44b_pre/_post
7    o merge of relevant stuff from the ecco-branch:
8      - genmake: removed $S64 overwrite for case SunOS
9      - pkg/exf: update and corrections for field swapping and obcs
10      - pkg/ecco: parameter lists for the_model_main, the_main_loop
11                  harmonized between ECCO and MITgcm
12      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
13                      updated checkpointing_lev... lists for obcs
14      - model/src: minor changes in forward_step, plot_field
15                   added directive for divided adjoint in the_main_loop
16      - pkg/mdsio: added mdsio_gl_slice
17    
18    next checkpoint:
19    o check parameters & config (chkpt44a_pre,post)
20    o OBC and NonLin_FrSurf.
21    
22    checkpoint44
23    o fix bug in mom_vi_del2uv
24    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
25    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
26    o update AIM experiments (NCEP input files)
27    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
28    o added some stuff for AD
29    
30    checkpoint43
31    o added two new advection tests
32    o added global 4x4 degree ocean test
33    o added test of H&S94 with free surface on cube
34    o some final mods for gradient check, adjoint,...
35    
36    checkpoint42
37      Fixed AD-related problems:
38    o Store directives up-to-date with re-arranged Adams-Bashforth
39      (mainly thermodynamics.F)
40    o New store directives for multi-dim. advection schemes
41      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
42      * new common block and key passkey
43      (mainly gad_advection.F)
44    o Modified store directives for split of dynamics/thermodynamics
45      for the case ALLOW_KPP
46    o Cleaned argument list for timestep_tracer.F
47    
48    checkpoint41
49    o re-formatted/added comments in prologues of key subroutines
50      to work with protex
51    
52    checkpoint40
53    o moved calc_gs, calc_gt and calc_tr1 back to model/src
54    o added FLT (floats) package from Arne along with demo. experiment
55    o re-arranged Adams-Bashforth scheme for tracers to allow easier
56      implementation of forward-in-time forcing terms
57    o more mods for non-linear free-surface including new variable
58    o modified multi-dim method to work on cube
59    o bug fix in KPP (from DM)
60    
61    checkpoint40pre9
62    o added DST advection schemes
63    o fix MPI bug on SGI's
64    o modifications for non-linear free-surface
65    o fixed conditionals for fixed flow/passive tracer only mode
66    o added tension/strain form of stress tensor
67    o changes to commenting of arguments for TAF/TAMC
68    o added/updated many matlab scripts
69    o added multi-dimensional advection method for tracers
70      
71    checkpoint40pre8
72    o new package rw/
73      Added method for dumping intermediate local arrays:
74      mdsio_writetile - same as mdsio_writefield except works from inside
75                        bi,bj loop
76      mdsio_writelocal - same as mdsio_writetile except works for local
77                         arrays
78      write_local_r? - higher-level wrapper for mdsio_writelocal
79      Controlled by diagFreq. Defaults to zero (ie. no dumps)
80      Example given at end of mom_vecinv.F that dumps some local arrays.
81    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
82      control flux-form versus vector invariant code.
83      Switch is runtime flag vectorInvariantMomentum (defaults to false)
84      or genmake -DISABLE ...
85    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
86      (additional storing is now needed for case vecinv;
87      currently nothing implemented to switch this storing off
88      in case fluxform is used since no CPP flag available).
89    
90    checkpoint40pre7
91    o bug fix in dynamics.F
92      calc_viscosity called before k=1,Nr loop.
93    o added some #ifdef's ALLOW_PASSIVE_TRACER
94    o cleaned initialisations in ctrl_map_ini
95      related to TAF
96    
97    checkpoint40pre6
98    o split dynamics into thermodynamics & dynamics
99    o corresponding split of calc_diffusivity into
100      calc_diffusivity, calc_viscosity
101      (kpp_calc_diff, kpp_calc_visc).
102    o Added diffkr, kapgm to control variables
103    o bug fix in gmredi_slope_limit for ldd97
104    
105    checkpoint40pre5
106    o proper initialization of Adams-Bashforth time stepping
107      + uses forward step for very first step of model (iter=0)
108    o re-generated *all* output since almost all output is modified by this
109      change (sorry but we've been putting this one off for about 2 years)
110      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
111        *not* regenerated since they are already out of date and I don't
112        want to create the impression that they are suddenly working.
113    o removed KAP stuff for DEC's
114    o modified/added many .cvsignore files in */code and */input
115    o added new expt "solid-body.cs-32x32x1"
116      + this uses an alternative form of ini_curvilinear_grid.F which
117        is not necessarily any better than the current one...
118    
119    checkpoint40pre4
120    o added re-initialisations of utrans,vtrans,rtrans in
121      calc_common_factors which are crucial for TAF.
122    o extended iMin,jMin range for calc_common_factors,
123      calc_diffusivity
124    o added option ALLOW_PASSIVE_TRACER
125    o a few minor updates and fixes
126    
127    checkpoint40pre3
128    o created calc_gtr1.F for gad package
129    o split the_main_loop and re-introduced forward_step
130    o some recomputations of nIter0 for TAMC
131    
132    checkpoint40pre2
133    o Updated to latest branch of AJA, JMC
134    o Added gradient check package
135    o Added routines for passive tracer handling
136    o Added carbon sequestration sensitivity experiment
137    
138    checkpoint39
139     o Modifications and fixes to support TAMC
140       (mainly missing or wrong directives)
141     o Corrected common blocks when fooling TAMC to produce adjoint I/O
142       in addummy_in_stepping
143     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
144     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
145     o Included following packages:
146       cal: calendar
147       exf: external forcing
148       ecco: essential routines to control use of cal, exf
149             (NB: this is not the full ECCO environment)
150     o disabled some packages by default in genmake
151    
152    checkpoint38
153     o see notes_c37_adj.txt
154     o corrected wrong layer index in external_forcing_t
155     o replaced the_main_loop/forward_step by the_main_loop
156     o removed forceoutput from write_state
157       (replaced criteria for initial/final state)
158     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
159    
160    checkpoint37
161     o mdsio.F routine split and packaged in pkg/mdsio
162       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
163        used unless genmake -disable=mdsio)
164     o allow a more precise surface-geopotential gradient for the atmosphere
165       taking into account the change in space of Alpha (=1/rho) at the surface.
166     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
167       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
168     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
169       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
170       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
171     o Time-Average diagnostics defined as a pseudo package "timeave".
172     o pickup files : old pickup (before c35) did not work with new code (c35
173       and after) unless activating 2 commented lines in initialise-varia.
174     o Non-Hydrostatic pickup file Pb fixed.
175     o bug with Rigid-lid version (since c35) fixed.  
176    
177    checkpoint36
178     o implement Crank-Nickelson barotropic time-stepping
179     o recover Time-Average diagnostics
180     o fix Pb in checkpoint (PR#19)
181     o AIM become a standard package ; clean unused CPP_kees
182    
183    checkpoint35
184     o subtantial rewrite of dynamics.f
185     o allows staggered time-stepping
186     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
187     o added bottom drag (linear + quadratic)
188    
189    checkpoint34
190     o Modified exchange routines for correct reverse simulation.
191     o Added verification output to comply with bug fix in impldiff.F
192       as of c33 (exp2, natl_box).
193     o Corrected store directives in dynamics.F
194     o Corrected array boundaries in impldiff.F
195     o Corrected array dimensions in gmredi.
196       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
197     o Added routine GLOBAL_SUM_INT to global_sum.F
198     o Added mdsio_gl.F for ECCO purposes.
199    
200    checkpoint33
201     o Fixed bug in lower BC in impldiff.F
202     o Fixed confusion about units of forcing arrays in FFIELDS.h
203       namely Fu,Fv,Qnet,Qsw,EmPmR:
204       - Removed verification/natl_box/code/external_fields_scale.F
205         (did not differ from that in model/src)
206       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
207         (see FFIELDS.h for description)
208       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
209         kpp_calc.F and kpp_transport_t.F
210       - Removed model/src/external_fields_scale.F and calls to it
211       - verification/natl_box uses flux data with "atmospheric" sign so
212         a special version of external_fields_load.F is used to
213         change the data as it's read in. This way, the arrays
214         have the right units and signs at all times tha a user could
215         possibly use them.
216     o Corrected genmake to delete a temporary file during configuration
217    
218    checkpoint32
219     o Scaling of forcing fields moved from external_forcing.F to
220       external_fields_scale.F, called directly after loading fields.
221     o Surface relaxation terms added to surface tendency fields in
222       extra subroutine.
223     o impldiff.F changed to avoid storing by TAMC of huge intermediate
224       fields.
225     o Changes in GMRedi to comply with packaging structure.
226     o Modifications and bug fixes in KPP package.
227     o Verification experiment for KPP added (verification/nat_box/)
228    
229    checkpoint31
230     o Packages interface brought in line with defined standard
231       -> new routines packages_...F
232       -> changes in initialise_fixed.F, initialise_varia.F
233       -> enables initialisation interface for ECCO package
234     o Rescaling of external forcing fields immediately after read
235       (removed from external_forcing.F)
236       -> new: surface_fields_scale.F
237       -> affects ini_foorcing.F, external_fields_load.F
238     o Computation of surface tendencies before tendency updates.
239       -> new: external_forcing_surf.F
240     o Change of variable names useGMRedi, useKPP, useECCO
241     o Further changes in dynamics.F, impldiff.F for TAMC
242     o Tested for experiments 0, 2, 4.
243       - not yet tested for GMRedi.
244       - not yet tested for KPP.
245    
246    checkpoint30
247     o Updates for OBCs
248     o New experiment for test OBCs (internal_wave)
249     o New output.txt in verification/exp4/results/
250     o Updates for KPP: calculation of viscosity corrected, new variables
251       kpp_dumpFreq and kpp_taveFreq
252     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
253       and entry for T90 in genmake
254    
255    checkpoint29
256     o packaged KPP and GM/Redi
257    
258    checkpoint28
259     o Corrected initialization of hFacMin for difference vertical coordinates
260     o Modified calculation of partial cell thickness to more robust algorithm
261     o config_summary.F: replaced write_1D_... by write_0D_...
262       read_write.F: added subroutines write_0D_...
263     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
264       included some initialisations required for TAMC.
265     o routine calc_isoslopes: modified sqrt computation to make it
266       differentiable for zero argument.
267     o routines dynamics, impldiff:
268       included store directives and tape key computations required for TAMC.
269     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
270    
271    checkpoint27
272     o fixed calc_isoslopes() to so that cancellation of terms in tensor
273       formulation works properly with variable resolution.
274     o restructured the calling tree between the_model_main() and dynamics()
275     o split initialise() into initialise_fixed() and initialise_varia()
276     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
277       in new routine ini_psurf()
278    
279    checkpoint26
280     o moved some #ifdef in optional routines to encompass everything
281       except the argument declarations. This was using up some memory.
282     o fixed macros like _ADT to work with both versions of Linux cpp
283     o cleaned up some unused and uninitialized variables
284       (helps when debugging with strict compile options)
285     o split up CPP_EEOPTIONS.h into options and macros
286       (macros are now in eesupp/inc/CPP_EEMACROS.h)
287     o patch for 2 processor JAM mode
288    
289    checkpoint25
290     o updates for OBCs and NH
291     o dramatically reduced memory usage
292     o added "JAM" routines for use on Artic network
293     o parameterization of convection by implicit vertical diffusion
294     o added a diagnostic of convective index
295     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
296       (this is was partly for OBCs and NH but also in anticipation of
297        an explicit free-surface option)
298     o initial state input files for U and V
299    
300    checkpoint24
301     o Removed some spurious "REAL"s
302     o Updated KPP to latest version from JPL
303     o Added a COS(latitude) in horizontal viscosity
304    
305    checkpoint23
306     o Added del^4 diffusion for salt and temperature
307     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
308    
309    checkpoint22
310     o Made many small changes: implicit none, format(i5), etc...
311     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
312    
313    checkpoint21
314     o Introduced new I/O package that supports direct-access records (mdsio.F)
315     o Split-up mid-level I/O routines
316     o Updated input data for experiments 0,1,2,4 and 5
317     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
318    
319    checkpoint20
320     o Tidied up open-boundaries some more
321     o Added non-hydrostatic code
322     o Fixed some input data
323     o Modified MPI start-up to work in "coupled" context.
324    
325    checkpoint19
326     o Tidied up directory structure for verification experiments.
327     o Added new code for open boundaries.
328     o Corrected advective terms near boundaries.
329     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
330     o Implemented free-slip/no-slip BCs and del^4 dissipation.
331     o Split default parameters out of ini_parms.F into set_defaults.F.
332    
333    checkpoint18
334     o Further changes for optional code generation with
335       CPP - ugh!
336    
337    checkpoint17
338     o Beginning to incorporating modularity
339       for supporting atmos. and ocean configs.
340     o Small changes for TAMC complinace
341     o New ultra simple test case. Barotropic box
342       configuration "exp0".
343    
344    checkpoint16
345     o Minor changes to exchange routines to support
346       accumulation in reverse mode. Adjoint of an
347       assignment is an addition.
348     o Changes to support compilation by TAMC (LR(1)
349       syntax) and by g77 under Linux ( 72 character
350       limit ).
351    
352    checkpoint15
353     Rewrote exchange routines to allow
354     o General tile <-> tile connectivity.
355     o TAMC reverse mode flag ( is this really needed? )
356     o Variable width overlap and exchange region widths.
357     o Hooks for sharing data via DMA, Arctic, Memory Channel,
358       shmput/shmget, VIA, SYSV shmem and every other cool
359       communication method.
360    
361    checkpoint14
362     Consistent isomorphism chages made. These allow dynamical core
363     to support both pressure and meters as a vertical coordinate.
364    
365    checkpoint13
366     Release which corrects global_max problem and a couple
367     of KGM time-averaging diagnostic errors. Also contains
368     a double-gyre experiment setup as well as the baseline
369     4 degree global template. The double gyre template is
370     organised to allow it to be applied automatically to
371     the baseline configuration.
372    
373    branch-point-rdot
374     A few tidy-ups have been made bt the real point of this
375     check-point (excuse the pun) is to allow a branch to be
376     made for the purposes of adding the rDot alterations.
377     I don't want to commit the rDot to the main-trunk until
378     we've actually tested it...
379    
380    checkpoint12
381     Tidy up and added generic genmake script (formerly
382     configure script).
383     Released to testers.
384    
385    checkpoint11
386     Re-arranged initialise() and introduced ini_vertical_grid()
387     and ini_masks_etc().
388    
389    checkpoint10
390     Introduced the configure script.
391     Separated out the diags package.
392     Added template for writing time-averages of tile/intermediate quantities.
393     Updated SIZE.h in exp2 and made the data big-endian.
394    
395    checkpoint9
396     MPI fix. Filename changes (meta/data). salbin*y stuff.
397     General tidy-up.
398     SST.bin SSS.bin added to verification/exp2
399    
400    checkpoint8
401     Inludes time-dependant forcing and time-averaging.
402     Works at 4x4 and 2.8125x2.8125 global
403    
404    checkpoint7-4degree-ref
405     Branch from checkpoint7. Released for application to
406     global modeling and general modeling - process studies, regional
407     model etc..
408     Configured for verification/exp2 - 4 degree global, two process.
409    
410    checkpoint7
411     Created by cnh
412     Simple 4 degree global simulation
413     configuration.
414     Includes climatological wind,
415     hydrography, bathymetry etc
416     Does not include Heat Flux and E-P
417    
418    checkpoint6
419     Created by cnh
420     merged checkpoint5 with CD and
421     spherical polar code.
422     Still some problems with GM Redi
423     abd full topography.
424    
425    checkpoint5
426     Created by AJA
427     contains updates to GM Redi
428     and reordered timestepping loop
429     for Implicit Diffusion.
430    
431    checkpoint4
432     Created by cnh
433     Contains memory saving macros ( _rdxc etc..) for when
434     grid variations are limited.
435     Contains polynomial coeffs for EOS and knudsen program
436     for generation.
437    
438  checkpoint3  checkpoint3
439   Created by cnh   Created by cnh
440   Added extra flags for runtime options   Added extra flags for runtime options
# Line 20  checkpoint1 Line 453  checkpoint1
453   Restructured kloop in dynamics.F   Restructured kloop in dynamics.F
454   Added non-linear EOS   Added non-linear EOS
455    
456  baseline - Original checked in code  baseline
457     Original checked in code
458    

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