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revision 1.128 by heimbach, Thu Feb 6 22:43:09 2003 UTC revision 1.192 by dimitri, Wed Oct 22 16:35:47 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    untagged
7    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
8    
9    checkpoint51m_post
10    o incorporating changes to get TAMC/TAF working in genmake2
11      - added new TAMC/TAF targets to the Makefile
12      - various cleanups related to package handling
13      - these changes should have no impact on the forward model
14    
15    checkpoint51l_post
16    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
17     - faster algorithm for cal_addtime.F
18     - higher precision arithmetic, where needed
19     - pkg/exf *startdate variables changed from calendar date to
20       model integration time
21    
22    checkpoint51l_pre
23    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
24    o enable to apply restoring on S & T only in a latitude band.
25    o update output (external_forcing_surf modif. change truncation errors)
26       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
27    
28    checkpoint51k_post
29    o change default to: useNHMTerms=.FALSE.
30     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
31       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
32     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
33        exp1, ideal_2D_oce
34     - change data file of oceanic exp (leave the results unchanged for now)
35       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
36    o set gravitySign automatically according to the vertical coordinate used
37      (and change sign: back to "logical" value: +1 when R increases downward)
38    o added an include barrier to the default CPP_OPTIONS.h and
39      removed the #include "PACKAGES_CONFIG.h" from it
40    o fix a bug in mom_fluxform (from chk51j_post)
41    
42    checkpoint51j_post
43    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
44    o adjusted some flow directives (dynamics, thermodynamics)
45    o added cubed-sphere case to test cost function
46    o heckpoint_lev?_directives.h now include
47      pkg-specific directives, whenever those are enabled.
48    o Moving pkg-specific flow directives to corresponding pkg
49      Moving pkg-specific differentiation list to corresponding pkg
50      Moving pkg-specific checkpoint-lev storing to corresponding pkg
51      ---> conventions are
52           - pkg_ad.flow
53           - pkg_ad_diff.list
54           - pkg_ad_check_lev?_dir.h
55    
56    checkpoint51i_post
57    o merge of the branch-genmake2
58      - knowingly breaks the older genmake
59      - automatic generation of all ALLOW_${PKG_NAME} defines
60      - new testreport supersedes older testscript
61    o large number of package inclusion and header cleanups
62    checkpoint51i_pre
63    
64    o new output for adjoin of global ocean vector invariant
65    o fix for checkpoint of thermodynamic seaice and bulk_force
66    o Steph gchem various cleanups
67    
68    checkpoint 51h_pre
69    o fixed some single quotes
70    o modify gchem pkg to be more versatile
71    o modifications to clean up dic pkg
72    o add pkg/cfc
73    
74    checkpoint51g_post
75    o provide links for ARPACK and ADM*TLM
76    o start removing verification/vero/
77    o update AD-related stuff
78      (in particular some IF-statements in model/src/ routines)
79    o adding to verification/global_ocean.90x40x15/ adjoint of
80      vector invariant setup
81    
82    checkpoint51f_post
83    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
84    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
85      of tracer Green's fucntions for ocean inversion project.
86    
87    checkpoint51f_pre
88    o Added on-the-fly spatial interpolation capability
89        "USE_EXF_INTERPOLATION" to pkg/exf.
90      - This is a temporary Cartesian-grid hack until
91        the super-duper ESMF coupler becomes available.
92      - See verification/global_with_exf/README for usage example.
93      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
94        flags and modified pkg/seaice accordingly.
95    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
96        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
97        non-local transport term.
98    
99    checkpoint51e_post
100    o pkg/mom_vecinv:
101      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
102      - add time-ave diagnostic of vorticity advection.
103    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
104    o atmospheric geopotential: - include water vapor effect;
105                                - use p^kappa in p* scaling.
106    o land pkg: read initial state from files.
107    o AIM : add stratospheric drag in the upper level
108    
109    checkpoint51d_post
110    o change function ILNBLNK (=> last non-blank char.) to return zero
111      (instead of the string length) when the string. char is empty
112    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
113    o modif's to restore TAMC compatibility
114      - avoid "_d" constructs in PARAMETER declarations
115      - avoid interrupting lines by comment lines
116    o Use cluster local disks for purely local I/O
117      vs. globally visible disks needed for ctrl stuff
118      (merged from ecco-branch)
119      - new active_file_loc... and mdsio_..._loc routines
120      - affected packages: autodiff, ctrl, grdchk, mdsio
121    
122    checkpoint51c_post
123    o introducing integer flag debugLevel
124      - debLevZero: suppress all output
125      - debLevA: standard
126      - debLevB: equivalent to current debugMode=.TRUE.
127    o introducing pathname variable mdsioLocalDir for mdsio
128      that can be specified at runtime
129      (relevant for cluster I/O to local disk)
130    `
131    >>>checkpoint51b_post
132    adjoint of ptracers
133    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
134    o extended state in checkpoint_lev?, etc.
135    o alternative ctrl/cost with tr1 or ptracer
136    o new comlev1_bibj_ptracers
137    o new ptracers.flow
138    o made ptracers_forcing same as external_forcing_s
139    o added verification for adjoint with ptracers
140      - adm. grdchk fail so far
141      - tlm. grdchk OK
142      - checked tapelev/comlev recomputations: OK
143    <<<checkpoint51b_pre
144    
145    checkpoint51a_post
146    o added code for biogeochemistry package
147      - new pkgs: dic, gchem
148      - new subroutine in ptracers
149    o modify code for biogeo packages
150      - in model/src and pkg/ptracers
151    
152    checkpoint51
153    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
154      - autodiff, ctrl, exf, grdchk, seaice
155      kept separate packages
156      - cost, ecco, obcs
157    o updating verification/internal_wave, verification/lab_sea
158      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
159    
160    checkpoint50i_post
161    o Preparing next differentiable checkpoint and sync
162      of MAIN vs. ecco-branch
163      - 1st step: this one is differentiable
164      - 2nd step: next(! not this) checkpoint will have updated packages
165                  from ecco-branch)
166    
167    checkpoint50h_post
168    o new package "land": provide surface BC for AIM.
169    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
170    o AIM: use true log-P extrapolation for near surface temp (= as in
171        F.Molteni paper) ; update aim.5l_cs output.
172    o New variable in PARM03 for more flexible pickups
173    o somewhat cleaned package initialisation sequence for
174      ctrl/ cost/ ecco/ in packages_... routines
175    
176    checkpoint50g_post
177    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
178      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
179      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
180        made the default because of faster convergence than ADI
181    
182    checkpoint50f_post
183    o exf totally restructured
184      - replaced all exf_set_ routines by one generic exf_set_gen.F
185        and made sure it's still differentiable
186      - split exf_getffields.F into new exf_bulkformulae.F
187      - exf_inscal_/exf_outscal_ suffixes consistent with field names
188      - updated adjoint/makefile and relevant verif. accordingly
189    
190    checkpoint50f_pre
191     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
192          + change Evap over land. (update aim.5l_cs output)
193     o added missing .cvsignores and made uniform across expts
194     o changed configuration of tidal_basin_2d expt
195     o added pkg/debug functions for tracing code in fatal crashes
196     o tidied pkg/monitor to use MONITOR_OPTIONS.h
197     o new fn in pkg/monitor to stop model if solution grows too big
198     o removed lots of single quotes from comments
199    
200    checkpoint50e_post
201    o make KPP work with PTRACERS
202     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
203       nearly a copy of kpp_transport_s
204     - there is no analogue to SurfaceTendencyS, so I have to use
205       gPtr(of the surface layer) instead
206    o add a new platform SunFire+mpi (SunFire 15000) to genmake
207    checkpoint50e_pre
208    
209    checkpoint50d_post
210    o change kpp output from multiple-record state files to single-record state
211      files analogous to write_state.F
212    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
213      analogous to the cg2d-related output.
214    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
215      so that writing to internal file fn (with length 512) fails.
216    checkpoint50d_pre
217    
218    checkpoint50c_post
219    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
220    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
221    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
222    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
223    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
224    
225    checkpoint50c_pre
226    Merging from release1_p13:
227    o bug fix for pkg/seaice dynamic solver
228    o Added SEAICE_initialHEFF to pkg/seaice
229    
230    checkpoint50b_post
231    o store u*,v* in gU,V instead of in guNm1,gvNm1
232    o in order to put the momForcing out of the Adams-Bashforth:
233      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
234      to timestep.F
235    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
236    o re-generate output for highly sensitive test-exp:
237       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
238    
239    checkpoint50b_pre
240    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
241    o corrected CPP option mismatch in exf_Bulk... functions for case
242      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
243    
244    checkpoint50a_post
245    o Bug fix for merging between c50 and KPP.
246      ikey was passed from thermodynamics to kpp_calc via
247      common block rather than being recomputed in kpp_calc,
248      in contradiction with new key itdkey.
249      New key ikppkey created, and tamc.h headers updated.
250    
251    checkpoint50
252    - 2nd step of merge with ecco-branch:
253      merge changes in ecco-branch back into main trunk
254    - bug fix in find_alpha
255    - more storing in gmredi_calc_tensor.F, kpp_routines.F
256    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
257    - merged some sliced AD support routines
258    
259    checkpoint49
260    merged from ecco-branch:
261    o exf:
262      - Enable initialisation of forcing fields to constant
263        (runtime) values.
264      - in exf_getffields.F
265        Reduce i-/j-loop to interior domain, discarding overlaps.
266        That also fixes wrong TAF-key computations for key_1, key_2
267        with bulf formulae.
268      - exf_init.F modify #ifdef for exf_init_evap
269      - exf_getffieldrec.F, ctrl_getrec.F
270        The following INT-usages are not safe:
271          fldsecs  = int(fldsecs/fldperiod)*fldperiod
272          fldcount = int(fldsecs/fldperiod) + 1
273        and were modified.
274    o autodiff: checkpoint_lev...
275      - updated storing for bulk formulae (some arrays were missing)
276      - added state for seaice package
277      - synchronized with main branch
278    o DIVA:
279      Modif.s in
280      - the_main_loop.F
281      - the_model_main.F
282      and added cost_final_restore.F cost_final_store.F
283      o With these changes, it is possible to fully separate
284        the first forward run to compute the cost function (mdthe_main_loop)
285        and adjoint runs over individual DIVA intervals (adthe_main_loop)
286        into separate model executions.
287        This enables better tuning of DIVA to given queue sizes.
288      o Loss of cost function value in consecutive DIVA runs is
289        fixed by storing to 'costfinal' file.
290      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
291        beginning/end of adjoint integration is accounted for.
292      The current changes apply to TAF-1.4.26.
293      TAF has one remaining bug, requiring one manual change
294      (see MITgcm manual).
295    o cal: synchronized between MAIN and ecco-branch
296    
297    checkpoint48i_post
298    o Changes to restore differentiability of code w.r.t. previous tag
299      (mostly adding new routines to make list and replacing
300      pressure by totPhiHyd).
301    o Updated and merged grdchk package
302      - has both ADM and TLM checks
303      - works for single- and multi-proc.
304      - output cleaned
305      - worked successfully for parallel DIVA
306    o genmake:
307      - Adding -platform=SP4
308      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
309    o Modif. for DIVA:
310      ctrl_unpack should not be called in intermediate DIVA interval.
311      (similar thing would apply for active files such as
312      tbar, sbar, psbar, which should not be reinitialised;
313      only relevant for ecco-branch)
314    
315    checkpoint48h_post
316    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
317    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
318    o Added SEAICE_initialHEFF to pkg/seaice
319    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
320    
321    checkpoint48g_post
322    --- EOS:
323    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
324      store total Potential in totPhyHyd for diagnostics & EOS.
325    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
326    --- Pressure/geopotential gradient:
327    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
328    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
329      ( changes results of global_ocean_pressure )
330    o NLFS + z-coord.: add eta*Rho' contribution.
331    o accurate phiHyd when using interface-W at the middle between 2 centers
332     ( changes results of ideal_2D_oce )
333    o includes r* 2nd term in potential gradient.
334    
335    checkpoint48f_post
336    Merging from release1_p12:
337    o Modifications for using pkg/exf with pkg/seaice
338      - improved description of the various forcing configurations
339      - added basic radiation bulk formulae to pkg/exf
340      - units/sign fix for evap computation in exf_getffields.F
341      - updated verification/global_with_exf/results/output.txt
342    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
343      (SBO) core products, including oceanic mass, center-of-mass,
344      angular, and bottom pressure (see pkg/sbo/README.sbo).
345    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
346      to avoid negative values in shallow regions.
347      - updated verification/natl_box/results/output.txt
348      - updated verification/lab_sea/results/output.txt
349    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
350    o Added useSingleCpuIO option (see PARAMS.h).
351    o Updated useSingleCpuIO option in mdsio_writefield.F to
352      work with multi-field files, e.g., for single-file pickup.
353    o pkg/seaice:
354      - bug fix in growth.F: QNET for no shortwave case
355      - added HeffFile for specifying initial sea-ice thickness
356      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
357    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
358      kpp_transport_t.F, forward_step.F, and the_main_loop.F
359    o pkg/seaice:
360      - adjoint-friendly modifications
361      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
362    
363    checkpoint48e_post
364    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
365    o dynamics: change definition of computational domain & adapt mom_fluxform
366      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
367    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
368        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
369        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
370        global_ocean.90x40x15 global_with_exf global_ocean_pressure
371        inverted_barometer solid-body.cs-32x32x1
372      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
373    
374    checkpoint48d_post
375    o in preparation for r*:
376     a) use pre-computed gradient of hydrostatic potential:
377        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
378     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
379        => affects results of glob_oce_pressure (different truncation error)  
380      update output.txt of ideal_2D_oce & global_ocean_pressure
381    
382    checkpoint48d_pre
383    o in preparation for r*:
384      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
385      pass the 2 comp. of the grad. as arguments to momentum S/R.
386      but for the moment, only used if it does not change the results.
387    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
388    
389  checkpoint48c_post  checkpoint48c_post
390  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
391  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.

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