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revision 1.125 by jmc, Mon Jan 27 21:42:19 2003 UTC revision 1.194 by dimitri, Thu Oct 23 07:14:48 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    
7    
8    checkpoint51n_post
9    o modifications to make FREEZE flux visible to pkg/kpp
10      - moved surfaceTendencyTice from pkg/seaice to main code
11      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
12      - subroutine FREEZE now limits only surface temperature
13        (this means new output.txt for global_ocean.90x40x15,
14         global_ocean.cs32x15, and global_with_exf)
15    o added surface flux output variables to TIMEAVE_STATVARS
16    
17    checkpoint51n_pre
18    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
19    o added [#include "AD_CONFIG.h"] to all files that use the following
20      defines:
21      - ALLOW_ADJOINT_RUN
22      - ALLOW_TANGENTLINEAR_RUN
23      - ALLOW_ECCO_OPTIMIZATION
24    
25    checkpoint51m_post
26    o incorporating changes to get TAMC/TAF working in genmake2
27      - added new TAMC/TAF targets to the Makefile
28      - various cleanups related to package handling
29      - these changes should have no impact on the forward model
30    
31    checkpoint51l_post
32    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
33     - faster algorithm for cal_addtime.F
34     - higher precision arithmetic, where needed
35     - pkg/exf *startdate variables changed from calendar date to
36       model integration time
37    
38    checkpoint51l_pre
39    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
40    o enable to apply restoring on S & T only in a latitude band.
41    o update output (external_forcing_surf modif. change truncation errors)
42       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
43    
44    checkpoint51k_post
45    o change default to: useNHMTerms=.FALSE.
46     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
47       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
48     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
49        exp1, ideal_2D_oce
50     - change data file of oceanic exp (leave the results unchanged for now)
51       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
52    o set gravitySign automatically according to the vertical coordinate used
53      (and change sign: back to "logical" value: +1 when R increases downward)
54    o added an include barrier to the default CPP_OPTIONS.h and
55      removed the #include "PACKAGES_CONFIG.h" from it
56    o fix a bug in mom_fluxform (from chk51j_post)
57    
58    checkpoint51j_post
59    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
60    o adjusted some flow directives (dynamics, thermodynamics)
61    o added cubed-sphere case to test cost function
62    o heckpoint_lev?_directives.h now include
63      pkg-specific directives, whenever those are enabled.
64    o Moving pkg-specific flow directives to corresponding pkg
65      Moving pkg-specific differentiation list to corresponding pkg
66      Moving pkg-specific checkpoint-lev storing to corresponding pkg
67      ---> conventions are
68           - pkg_ad.flow
69           - pkg_ad_diff.list
70           - pkg_ad_check_lev?_dir.h
71    
72    checkpoint51i_post
73    o merge of the branch-genmake2
74      - knowingly breaks the older genmake
75      - automatic generation of all ALLOW_${PKG_NAME} defines
76      - new testreport supersedes older testscript
77    o large number of package inclusion and header cleanups
78    checkpoint51i_pre
79    
80    o new output for adjoin of global ocean vector invariant
81    o fix for checkpoint of thermodynamic seaice and bulk_force
82    o Steph gchem various cleanups
83    
84    checkpoint 51h_pre
85    o fixed some single quotes
86    o modify gchem pkg to be more versatile
87    o modifications to clean up dic pkg
88    o add pkg/cfc
89    
90    checkpoint51g_post
91    o provide links for ARPACK and ADM*TLM
92    o start removing verification/vero/
93    o update AD-related stuff
94      (in particular some IF-statements in model/src/ routines)
95    o adding to verification/global_ocean.90x40x15/ adjoint of
96      vector invariant setup
97    
98    checkpoint51f_post
99    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
100    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
101      of tracer Green's fucntions for ocean inversion project.
102    
103    checkpoint51f_pre
104    o Added on-the-fly spatial interpolation capability
105        "USE_EXF_INTERPOLATION" to pkg/exf.
106      - This is a temporary Cartesian-grid hack until
107        the super-duper ESMF coupler becomes available.
108      - See verification/global_with_exf/README for usage example.
109      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
110        flags and modified pkg/seaice accordingly.
111    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
112        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
113        non-local transport term.
114    
115    checkpoint51e_post
116    o pkg/mom_vecinv:
117      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
118      - add time-ave diagnostic of vorticity advection.
119    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
120    o atmospheric geopotential: - include water vapor effect;
121                                - use p^kappa in p* scaling.
122    o land pkg: read initial state from files.
123    o AIM : add stratospheric drag in the upper level
124    
125    checkpoint51d_post
126    o change function ILNBLNK (=> last non-blank char.) to return zero
127      (instead of the string length) when the string. char is empty
128    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
129    o modif's to restore TAMC compatibility
130      - avoid "_d" constructs in PARAMETER declarations
131      - avoid interrupting lines by comment lines
132    o Use cluster local disks for purely local I/O
133      vs. globally visible disks needed for ctrl stuff
134      (merged from ecco-branch)
135      - new active_file_loc... and mdsio_..._loc routines
136      - affected packages: autodiff, ctrl, grdchk, mdsio
137    
138    checkpoint51c_post
139    o introducing integer flag debugLevel
140      - debLevZero: suppress all output
141      - debLevA: standard
142      - debLevB: equivalent to current debugMode=.TRUE.
143    o introducing pathname variable mdsioLocalDir for mdsio
144      that can be specified at runtime
145      (relevant for cluster I/O to local disk)
146    `
147    >>>checkpoint51b_post
148    adjoint of ptracers
149    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
150    o extended state in checkpoint_lev?, etc.
151    o alternative ctrl/cost with tr1 or ptracer
152    o new comlev1_bibj_ptracers
153    o new ptracers.flow
154    o made ptracers_forcing same as external_forcing_s
155    o added verification for adjoint with ptracers
156      - adm. grdchk fail so far
157      - tlm. grdchk OK
158      - checked tapelev/comlev recomputations: OK
159    <<<checkpoint51b_pre
160    
161    checkpoint51a_post
162    o added code for biogeochemistry package
163      - new pkgs: dic, gchem
164      - new subroutine in ptracers
165    o modify code for biogeo packages
166      - in model/src and pkg/ptracers
167    
168    checkpoint51
169    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
170      - autodiff, ctrl, exf, grdchk, seaice
171      kept separate packages
172      - cost, ecco, obcs
173    o updating verification/internal_wave, verification/lab_sea
174      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
175    
176    checkpoint50i_post
177    o Preparing next differentiable checkpoint and sync
178      of MAIN vs. ecco-branch
179      - 1st step: this one is differentiable
180      - 2nd step: next(! not this) checkpoint will have updated packages
181                  from ecco-branch)
182    
183    checkpoint50h_post
184    o new package "land": provide surface BC for AIM.
185    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
186    o AIM: use true log-P extrapolation for near surface temp (= as in
187        F.Molteni paper) ; update aim.5l_cs output.
188    o New variable in PARM03 for more flexible pickups
189    o somewhat cleaned package initialisation sequence for
190      ctrl/ cost/ ecco/ in packages_... routines
191    
192    checkpoint50g_post
193    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
194      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
195      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
196        made the default because of faster convergence than ADI
197    
198    checkpoint50f_post
199    o exf totally restructured
200      - replaced all exf_set_ routines by one generic exf_set_gen.F
201        and made sure it's still differentiable
202      - split exf_getffields.F into new exf_bulkformulae.F
203      - exf_inscal_/exf_outscal_ suffixes consistent with field names
204      - updated adjoint/makefile and relevant verif. accordingly
205    
206    checkpoint50f_pre
207     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
208          + change Evap over land. (update aim.5l_cs output)
209     o added missing .cvsignores and made uniform across expts
210     o changed configuration of tidal_basin_2d expt
211     o added pkg/debug functions for tracing code in fatal crashes
212     o tidied pkg/monitor to use MONITOR_OPTIONS.h
213     o new fn in pkg/monitor to stop model if solution grows too big
214     o removed lots of single quotes from comments
215    
216    checkpoint50e_post
217    o make KPP work with PTRACERS
218     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
219       nearly a copy of kpp_transport_s
220     - there is no analogue to SurfaceTendencyS, so I have to use
221       gPtr(of the surface layer) instead
222    o add a new platform SunFire+mpi (SunFire 15000) to genmake
223    checkpoint50e_pre
224    
225    checkpoint50d_post
226    o change kpp output from multiple-record state files to single-record state
227      files analogous to write_state.F
228    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
229      analogous to the cg2d-related output.
230    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
231      so that writing to internal file fn (with length 512) fails.
232    checkpoint50d_pre
233    
234    checkpoint50c_post
235    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
236    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
237    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
238    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
239    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
240    
241    checkpoint50c_pre
242    Merging from release1_p13:
243    o bug fix for pkg/seaice dynamic solver
244    o Added SEAICE_initialHEFF to pkg/seaice
245    
246    checkpoint50b_post
247    o store u*,v* in gU,V instead of in guNm1,gvNm1
248    o in order to put the momForcing out of the Adams-Bashforth:
249      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
250      to timestep.F
251    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
252    o re-generate output for highly sensitive test-exp:
253       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
254    
255    checkpoint50b_pre
256    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
257    o corrected CPP option mismatch in exf_Bulk... functions for case
258      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
259    
260    checkpoint50a_post
261    o Bug fix for merging between c50 and KPP.
262      ikey was passed from thermodynamics to kpp_calc via
263      common block rather than being recomputed in kpp_calc,
264      in contradiction with new key itdkey.
265      New key ikppkey created, and tamc.h headers updated.
266    
267    checkpoint50
268    - 2nd step of merge with ecco-branch:
269      merge changes in ecco-branch back into main trunk
270    - bug fix in find_alpha
271    - more storing in gmredi_calc_tensor.F, kpp_routines.F
272    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
273    - merged some sliced AD support routines
274    
275    checkpoint49
276    merged from ecco-branch:
277    o exf:
278      - Enable initialisation of forcing fields to constant
279        (runtime) values.
280      - in exf_getffields.F
281        Reduce i-/j-loop to interior domain, discarding overlaps.
282        That also fixes wrong TAF-key computations for key_1, key_2
283        with bulf formulae.
284      - exf_init.F modify #ifdef for exf_init_evap
285      - exf_getffieldrec.F, ctrl_getrec.F
286        The following INT-usages are not safe:
287          fldsecs  = int(fldsecs/fldperiod)*fldperiod
288          fldcount = int(fldsecs/fldperiod) + 1
289        and were modified.
290    o autodiff: checkpoint_lev...
291      - updated storing for bulk formulae (some arrays were missing)
292      - added state for seaice package
293      - synchronized with main branch
294    o DIVA:
295      Modif.s in
296      - the_main_loop.F
297      - the_model_main.F
298      and added cost_final_restore.F cost_final_store.F
299      o With these changes, it is possible to fully separate
300        the first forward run to compute the cost function (mdthe_main_loop)
301        and adjoint runs over individual DIVA intervals (adthe_main_loop)
302        into separate model executions.
303        This enables better tuning of DIVA to given queue sizes.
304      o Loss of cost function value in consecutive DIVA runs is
305        fixed by storing to 'costfinal' file.
306      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
307        beginning/end of adjoint integration is accounted for.
308      The current changes apply to TAF-1.4.26.
309      TAF has one remaining bug, requiring one manual change
310      (see MITgcm manual).
311    o cal: synchronized between MAIN and ecco-branch
312    
313    checkpoint48i_post
314    o Changes to restore differentiability of code w.r.t. previous tag
315      (mostly adding new routines to make list and replacing
316      pressure by totPhiHyd).
317    o Updated and merged grdchk package
318      - has both ADM and TLM checks
319      - works for single- and multi-proc.
320      - output cleaned
321      - worked successfully for parallel DIVA
322    o genmake:
323      - Adding -platform=SP4
324      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
325    o Modif. for DIVA:
326      ctrl_unpack should not be called in intermediate DIVA interval.
327      (similar thing would apply for active files such as
328      tbar, sbar, psbar, which should not be reinitialised;
329      only relevant for ecco-branch)
330    
331    checkpoint48h_post
332    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
333    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
334    o Added SEAICE_initialHEFF to pkg/seaice
335    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
336    
337    checkpoint48g_post
338    --- EOS:
339    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
340      store total Potential in totPhyHyd for diagnostics & EOS.
341    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
342    --- Pressure/geopotential gradient:
343    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
344    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
345      ( changes results of global_ocean_pressure )
346    o NLFS + z-coord.: add eta*Rho' contribution.
347    o accurate phiHyd when using interface-W at the middle between 2 centers
348     ( changes results of ideal_2D_oce )
349    o includes r* 2nd term in potential gradient.
350    
351    checkpoint48f_post
352    Merging from release1_p12:
353    o Modifications for using pkg/exf with pkg/seaice
354      - improved description of the various forcing configurations
355      - added basic radiation bulk formulae to pkg/exf
356      - units/sign fix for evap computation in exf_getffields.F
357      - updated verification/global_with_exf/results/output.txt
358    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
359      (SBO) core products, including oceanic mass, center-of-mass,
360      angular, and bottom pressure (see pkg/sbo/README.sbo).
361    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
362      to avoid negative values in shallow regions.
363      - updated verification/natl_box/results/output.txt
364      - updated verification/lab_sea/results/output.txt
365    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
366    o Added useSingleCpuIO option (see PARAMS.h).
367    o Updated useSingleCpuIO option in mdsio_writefield.F to
368      work with multi-field files, e.g., for single-file pickup.
369    o pkg/seaice:
370      - bug fix in growth.F: QNET for no shortwave case
371      - added HeffFile for specifying initial sea-ice thickness
372      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
373    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
374      kpp_transport_t.F, forward_step.F, and the_main_loop.F
375    o pkg/seaice:
376      - adjoint-friendly modifications
377      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
378    
379    checkpoint48e_post
380    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
381    o dynamics: change definition of computational domain & adapt mom_fluxform
382      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
383    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
384        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
385        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
386        global_ocean.90x40x15 global_with_exf global_ocean_pressure
387        inverted_barometer solid-body.cs-32x32x1
388      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
389    
390    checkpoint48d_post
391    o in preparation for r*:
392     a) use pre-computed gradient of hydrostatic potential:
393        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
394     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
395        => affects results of glob_oce_pressure (different truncation error)  
396      update output.txt of ideal_2D_oce & global_ocean_pressure
397    
398    checkpoint48d_pre
399    o in preparation for r*:
400      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
401      pass the 2 comp. of the grad. as arguments to momentum S/R.
402      but for the moment, only used if it does not change the results.
403    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
404    
405    checkpoint48c_post
406    Modifications in treatment of initial flux forcing controls
407    to avoid extra storing of flux fields.
408    
409    checkpoint48c_pre
410    o Added tidal_basin_2d experiment (currently 1D!)
411    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
412    
413  checkpoint48b_post  checkpoint48b_post
414  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
415   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)

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