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revision 1.146 by heimbach, Tue Mar 25 22:48:11 2003 UTC revision 1.221 by dimitri, Mon Dec 8 02:13:59 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 change global_ocean.cs32x15 because of Pb with GM on CS-grid.
7    o added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
8    
9    checkpoint52d_pre
10    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
11    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
12    
13    checkpoint52c_post
14    o Fixing OPTIONS files for use of exf:
15      - ALLOW_ECCO not needed
16      - ECCO_CPPOPTIONS.h should not be included from
17        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
18        as has been the case in the past
19      - All cal/exf related options are currently set in
20        single header file. Should remain so until we
21        agree on a consistent new policy.
22    o Removed all CPP options for cal package.
23      cal has no more CPP options.
24    o modified STOREs in GAD_ADVECTION
25    o corrected key comp. for passkey
26    
27    checkpoint52b_post
28    o new version: "thsice" of thermodynamic sea-ice pkg:
29     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
30     - modify fluxes but do not change theta directly;
31     - light cleaning of bulk_force pkg (still needed with thsice).
32     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
33       + output_thsice.txt to test thsice & bulk_force pkgs.
34    o put back grid & coriolis monitor output.
35    checkpoint52b_pre
36    
37    o call "do_the_model_io" at the beginning (=> dump initial state)
38    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
39    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
40      (need info on NUMBER_OF_PTRACERS)
41    o missing PTRACERS headers in some routines
42    o default tamc.h in pkg/autodiff supposed to crash
43      to ensure proper customization
44    
45    checkpoint52a_post
46    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
47      - moved surfaceTendencyTice from pkg/seaice to main code
48      - subroutine FREEZE_SURFACE now limits only surface temperature
49        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
50        => new output.txt for global_ocean.cs32x15 & global_with_exf
51      - keep the old version of FREEZE for backward compatibility;
52        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
53      - corresponding modifs for TAF directives
54    o added surface flux output variables to TIMEAVE_STATVARS
55    o time-averaged output for pkg/ptracers
56    o fix problem with ECCO-related divided adjoint
57      snapshot file was missing some ad-variables,
58      but no warning issued by TAF
59    
60    checkpoint52a_pre
61    o some bug fixes for #undef REAL4_IS_SLOW
62    
63    checkpoint52 = ecco_c52_e35
64    o after testing adjoints of checkpoint51u_post
65    
66    checkpoint51u_post
67    o this is the post-merge tag of the ecco-branch
68      (needs another clean checkout and re-testing)
69    o various natl_box_adjoint configs and results
70      but no input fields
71    o obcs adjoint not yet merged!
72    o adding ECCO global 1x1 and 2x2 degree configs
73    o updated/extended some store directives for seaice
74    o pkg/ecco now containes ecco-specific part of cost function
75    o top level routines the_main_loop, forward_step
76      supersede those in model/src/
77      previous input data.cost now in data.ecco
78      (new namelist ecco_cost_nml)
79    o in ctrl/ cleaned some cross-dependencies and updated CPP options
80    
81    checkpoint51t_post
82    o this is the pre-merge tag of the ecco-branch
83    
84    checkpoint51s_post
85    o cleanup: removed various obsolete #define-s
86    o pkg/grdchk
87      - renamed 'ph-grd 3' to 'grad-res'
88      - merged from ecco-branch
89        (remaining bug fixes for obcs gradient checks)
90      - additional high-precision output for testreport
91        (grep for 'precision_grdchk_result')
92    
93    checkpoint51r_post
94    o cleaned up or removed CPP_OPTIONS.h files
95    o updated results for some of the tests to reflect the new
96      optfiles (-ieee: -O0 instead of -O3)
97    
98    checkpoint51q_post
99    o cd_code:
100      - moved cd_scheme.F -> cd_code_scheme.F
101      - separate read_checkpoint from cd_code_ini_vars.F
102      - separated cd_code part from write_checkpoint
103      - updated AD_SOURCE, generated .flow
104      - added CD_CODE_VARS.h to the_main_loop
105      - Moving cd_code specific store dir.s to pkg/cd_code
106    o ctrl package totally restructured
107      - pack/unpack now optional and decoupled from
108        xx_/adxx_ I/O
109      - ctrl_pack/unpack cleaned
110        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
111      - confined inclusion of AD_CONFIG.h to where necessary.
112    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
113    
114    checkpoint51p_post
115    o create initial cd_code package
116      - WARNING: the initialization of fields within packages
117        is broken because INI_FIELDS (where READ_CHECKPOINT is
118        called) is called *before* PACKAGES_INIT_VARIABLES.
119        This seems to be backwards since
120        1) its important to initially zero the entire field including
121           the "halo" region
122        2) zeroing needs to be done *before* reading pickup info
123           and the pickup call might or might not happen in any
124           particular run
125      - this needs an overhaul for R2
126    o cleanup verification/*/code/GMREDI_OPTIONS.h
127    o cleanup testreport
128    
129    checkpoint51o_post
130    o bringing AD-related verif's up to date with genmake2
131      - carbon/
132      - global_ocean.90x40x15/
133      - hs.94.1x64x5/
134      - (front_relax/ )
135    o (more) consistent directory structure for AD-related verif.'s
136    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
137    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
138    o bug fix in find_alpha.F for MDJWF:
139      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
140        change rho -> rho-rhoConst
141      - replace call find_rho to find_rhonum
142    o initialisation of rFlx extended to full array (required by TAF)
143      and shifted to thermodynamics
144    o removed PTRACERS.h in ptracers routine
145    o added surfacetendencyPtr to S/R parameter list pracers_forcing
146    o Correcting initialisations for fVerU, fVerV.
147    o helping TAF to recognize dependency on kUp for
148      fVerU, fVerV
149    o Replacing delZ by delR in pkg/ctrl/
150    checkpoint51o_pre
151    
152    o undid all of cp51 pending some cleanups and discussion
153    o added the [#include "AD_CONFIG.h"] statement to all files that need
154       it for adjoint/tl #defines
155     o re-worked the build logic in genmake2 to support AD_CONFIG.h
156     o removed tools/genmake since it no longer works
157    
158    checkpoint51n_post
159    o modifications to make FREEZE flux visible to pkg/kpp
160      - moved surfaceTendencyTice from pkg/seaice to main code
161      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
162      - subroutine FREEZE now limits only surface temperature
163        (this means new output.txt for global_ocean.90x40x15,
164         global_ocean.cs32x15, and global_with_exf)
165    o added surface flux output variables to TIMEAVE_STATVARS
166    
167    checkpoint51n_pre
168    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
169    o added [#include "AD_CONFIG.h"] to all files that use the following
170      defines:
171      - ALLOW_ADJOINT_RUN
172      - ALLOW_TANGENTLINEAR_RUN
173      - ALLOW_ECCO_OPTIMIZATION
174    
175    checkpoint51m_post
176    o incorporating changes to get TAMC/TAF working in genmake2
177      - added new TAMC/TAF targets to the Makefile
178      - various cleanups related to package handling
179      - these changes should have no impact on the forward model
180    
181    checkpoint51l_post
182    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
183     - faster algorithm for cal_addtime.F
184     - higher precision arithmetic, where needed
185     - pkg/exf *startdate variables changed from calendar date to
186       model integration time
187    
188    checkpoint51l_pre
189    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
190    o enable to apply restoring on S & T only in a latitude band.
191    o update output (external_forcing_surf modif. change truncation errors)
192       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
193    
194    checkpoint51k_post
195    o change default to: useNHMTerms=.FALSE.
196     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
197       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
198     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
199        exp1, ideal_2D_oce
200     - change data file of oceanic exp (leave the results unchanged for now)
201       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
202    o set gravitySign automatically according to the vertical coordinate used
203      (and change sign: back to "logical" value: +1 when R increases downward)
204    o added an include barrier to the default CPP_OPTIONS.h and
205      removed the #include "PACKAGES_CONFIG.h" from it
206    o fix a bug in mom_fluxform (from chk51j_post)
207    
208    checkpoint51j_post
209    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
210    o adjusted some flow directives (dynamics, thermodynamics)
211    o added cubed-sphere case to test cost function
212    o heckpoint_lev?_directives.h now include
213      pkg-specific directives, whenever those are enabled.
214    o Moving pkg-specific flow directives to corresponding pkg
215      Moving pkg-specific differentiation list to corresponding pkg
216      Moving pkg-specific checkpoint-lev storing to corresponding pkg
217      ---> conventions are
218           - pkg_ad.flow
219           - pkg_ad_diff.list
220           - pkg_ad_check_lev?_dir.h
221    
222    checkpoint51i_post
223    o merge of the branch-genmake2
224      - knowingly breaks the older genmake
225      - automatic generation of all ALLOW_${PKG_NAME} defines
226      - new testreport supersedes older testscript
227    o large number of package inclusion and header cleanups
228    checkpoint51i_pre
229    
230    o new output for adjoin of global ocean vector invariant
231    o fix for checkpoint of thermodynamic seaice and bulk_force
232    o Steph gchem various cleanups
233    
234    checkpoint 51h_pre
235    o fixed some single quotes
236    o modify gchem pkg to be more versatile
237    o modifications to clean up dic pkg
238    o add pkg/cfc
239    
240    checkpoint51g_post
241    o provide links for ARPACK and ADM*TLM
242    o start removing verification/vero/
243    o update AD-related stuff
244      (in particular some IF-statements in model/src/ routines)
245    o adding to verification/global_ocean.90x40x15/ adjoint of
246      vector invariant setup
247    
248    checkpoint51f_post
249    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
250    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
251      of tracer Green's fucntions for ocean inversion project.
252    
253    checkpoint51f_pre
254    o Added on-the-fly spatial interpolation capability
255        "USE_EXF_INTERPOLATION" to pkg/exf.
256      - This is a temporary Cartesian-grid hack until
257        the super-duper ESMF coupler becomes available.
258      - See verification/global_with_exf/README for usage example.
259      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
260        flags and modified pkg/seaice accordingly.
261    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
262        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
263        non-local transport term.
264    
265    checkpoint51e_post
266    o pkg/mom_vecinv:
267      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
268      - add time-ave diagnostic of vorticity advection.
269    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
270    o atmospheric geopotential: - include water vapor effect;
271                                - use p^kappa in p* scaling.
272    o land pkg: read initial state from files.
273    o AIM : add stratospheric drag in the upper level
274    
275    checkpoint51d_post
276    o change function ILNBLNK (=> last non-blank char.) to return zero
277      (instead of the string length) when the string. char is empty
278    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
279    o modif's to restore TAMC compatibility
280      - avoid "_d" constructs in PARAMETER declarations
281      - avoid interrupting lines by comment lines
282    o Use cluster local disks for purely local I/O
283      vs. globally visible disks needed for ctrl stuff
284      (merged from ecco-branch)
285      - new active_file_loc... and mdsio_..._loc routines
286      - affected packages: autodiff, ctrl, grdchk, mdsio
287    
288    checkpoint51c_post
289    o introducing integer flag debugLevel
290      - debLevZero: suppress all output
291      - debLevA: standard
292      - debLevB: equivalent to current debugMode=.TRUE.
293    o introducing pathname variable mdsioLocalDir for mdsio
294      that can be specified at runtime
295      (relevant for cluster I/O to local disk)
296    `
297    >>>checkpoint51b_post
298    adjoint of ptracers
299    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
300    o extended state in checkpoint_lev?, etc.
301    o alternative ctrl/cost with tr1 or ptracer
302    o new comlev1_bibj_ptracers
303    o new ptracers.flow
304    o made ptracers_forcing same as external_forcing_s
305    o added verification for adjoint with ptracers
306      - adm. grdchk fail so far
307      - tlm. grdchk OK
308      - checked tapelev/comlev recomputations: OK
309    <<<checkpoint51b_pre
310    
311    checkpoint51a_post
312    o added code for biogeochemistry package
313      - new pkgs: dic, gchem
314      - new subroutine in ptracers
315    o modify code for biogeo packages
316      - in model/src and pkg/ptracers
317    
318    checkpoint51
319    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
320      - autodiff, ctrl, exf, grdchk, seaice
321      kept separate packages
322      - cost, ecco, obcs
323    o updating verification/internal_wave, verification/lab_sea
324      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
325    
326    checkpoint50i_post
327    o Preparing next differentiable checkpoint and sync
328      of MAIN vs. ecco-branch
329      - 1st step: this one is differentiable
330      - 2nd step: next(! not this) checkpoint will have updated packages
331                  from ecco-branch)
332    
333    checkpoint50h_post
334    o new package "land": provide surface BC for AIM.
335    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
336    o AIM: use true log-P extrapolation for near surface temp (= as in
337        F.Molteni paper) ; update aim.5l_cs output.
338    o New variable in PARM03 for more flexible pickups
339    o somewhat cleaned package initialisation sequence for
340      ctrl/ cost/ ecco/ in packages_... routines
341    
342    checkpoint50g_post
343    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
344      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
345      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
346        made the default because of faster convergence than ADI
347    
348    checkpoint50f_post
349    o exf totally restructured
350      - replaced all exf_set_ routines by one generic exf_set_gen.F
351        and made sure it's still differentiable
352      - split exf_getffields.F into new exf_bulkformulae.F
353      - exf_inscal_/exf_outscal_ suffixes consistent with field names
354      - updated adjoint/makefile and relevant verif. accordingly
355    
356    checkpoint50f_pre
357     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
358          + change Evap over land. (update aim.5l_cs output)
359     o added missing .cvsignores and made uniform across expts
360     o changed configuration of tidal_basin_2d expt
361     o added pkg/debug functions for tracing code in fatal crashes
362     o tidied pkg/monitor to use MONITOR_OPTIONS.h
363     o new fn in pkg/monitor to stop model if solution grows too big
364     o removed lots of single quotes from comments
365    
366    checkpoint50e_post
367    o make KPP work with PTRACERS
368     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
369       nearly a copy of kpp_transport_s
370     - there is no analogue to SurfaceTendencyS, so I have to use
371       gPtr(of the surface layer) instead
372    o add a new platform SunFire+mpi (SunFire 15000) to genmake
373    checkpoint50e_pre
374    
375    checkpoint50d_post
376    o change kpp output from multiple-record state files to single-record state
377      files analogous to write_state.F
378    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
379      analogous to the cg2d-related output.
380    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
381      so that writing to internal file fn (with length 512) fails.
382    checkpoint50d_pre
383    
384    checkpoint50c_post
385    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
386    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
387    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
388    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
389    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
390    
391    checkpoint50c_pre
392    Merging from release1_p13:
393    o bug fix for pkg/seaice dynamic solver
394    o Added SEAICE_initialHEFF to pkg/seaice
395    
396    checkpoint50b_post
397    o store u*,v* in gU,V instead of in guNm1,gvNm1
398    o in order to put the momForcing out of the Adams-Bashforth:
399      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
400      to timestep.F
401    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
402    o re-generate output for highly sensitive test-exp:
403       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
404    
405    checkpoint50b_pre
406    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
407  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
408    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
409    

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