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revision 1.128 by heimbach, Thu Feb 6 22:43:09 2003 UTC revision 1.195 by edhill, Fri Oct 24 05:29:35 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o undid all of cp51 pending some cleanups and discussion
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  checkpoint48c_post
406  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
407  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.

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