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revision 1.162 by adcroft, Thu Jun 5 16:16:00 2003 UTC revision 1.237 by afe, Fri Jan 9 21:29:24 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint52f_pre
7    o added exch2 cube routines to pkg/exch2
8    o modified hs94.cs-32x32x5 to use it
9    o added new grid files to hs94.cs-32x32x5
10    checkpoint52f_post
11    
12    checkpoint52e_post
13    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
14      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
15    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
16      to work with implicit vertical advection and AB ;
17    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
18    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
19     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
20    checkpoint52e_pre
21    
22    o fix bug in impldiff when Nr=1 or Nr=2.
23    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
24    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
25    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
26      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
27    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
28    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
29    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
30    
31    checkpoint52d_post
32    o re-tiled many expts to allow comparison in multi-processor mode
33      - updated output accordingly
34      - changed hs94.128x64x5 to use intial T from file rather than use the
35        random number generator
36    o add infrastructure in model routines for fizhi and gridalt packages
37    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
38    o changes to permit hi-res, cubed-sphere, configuration
39      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
40      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
41      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
42        of surface winds for the cube
43      (A verification experiment, based on global_ocean.cs32x15, but with
44       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
45       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
46       complete with example surface forcing files and matlab scripts to look
47       at the output and compare it with that of global_ocean.cs32x15.)
48    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
49       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
50       to conform to the common rule.
51    o check-in the first version of the coupler + interfaces for multi-components
52       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
53       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
54       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
55       - ocean and atmos. share the same horizontal grid (no interpolation).
56       - exchanges between component and coupler is done in forward_step
57    o new verification experiment, cpl_aim+ocn:
58       coupled ocean - AIM atmosphere on cs32 grid.
59    
60    checkpoint52d_pre
61    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
62    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
63    
64    checkpoint52c_post
65    o Fixing OPTIONS files for use of exf:
66      - ALLOW_ECCO not needed
67      - ECCO_CPPOPTIONS.h should not be included from
68        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
69        as has been the case in the past
70      - All cal/exf related options are currently set in
71        single header file. Should remain so until we
72        agree on a consistent new policy.
73    o Removed all CPP options for cal package.
74      cal has no more CPP options.
75    o modified STOREs in GAD_ADVECTION
76    o corrected key comp. for passkey
77    
78    checkpoint52b_post
79    o new version: "thsice" of thermodynamic sea-ice pkg:
80     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
81     - modify fluxes but do not change theta directly;
82     - light cleaning of bulk_force pkg (still needed with thsice).
83     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
84       + output_thsice.txt to test thsice & bulk_force pkgs.
85    o put back grid & coriolis monitor output.
86    checkpoint52b_pre
87    
88    o call "do_the_model_io" at the beginning (=> dump initial state)
89    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
90    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
91      (need info on NUMBER_OF_PTRACERS)
92    o missing PTRACERS headers in some routines
93    o default tamc.h in pkg/autodiff supposed to crash
94      to ensure proper customization
95    
96    checkpoint52a_post
97    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
98      - moved surfaceTendencyTice from pkg/seaice to main code
99      - subroutine FREEZE_SURFACE now limits only surface temperature
100        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
101        => new output.txt for global_ocean.cs32x15 & global_with_exf
102      - keep the old version of FREEZE for backward compatibility;
103        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
104      - corresponding modifs for TAF directives
105    o added surface flux output variables to TIMEAVE_STATVARS
106    o time-averaged output for pkg/ptracers
107    o fix problem with ECCO-related divided adjoint
108      snapshot file was missing some ad-variables,
109      but no warning issued by TAF
110    
111    checkpoint52a_pre
112    o some bug fixes for #undef REAL4_IS_SLOW
113    
114    checkpoint52 = ecco_c52_e35
115    o after testing adjoints of checkpoint51u_post
116    
117    checkpoint51u_post
118    o this is the post-merge tag of the ecco-branch
119      (needs another clean checkout and re-testing)
120    o various natl_box_adjoint configs and results
121      but no input fields
122    o obcs adjoint not yet merged!
123    o adding ECCO global 1x1 and 2x2 degree configs
124    o updated/extended some store directives for seaice
125    o pkg/ecco now containes ecco-specific part of cost function
126    o top level routines the_main_loop, forward_step
127      supersede those in model/src/
128      previous input data.cost now in data.ecco
129      (new namelist ecco_cost_nml)
130    o in ctrl/ cleaned some cross-dependencies and updated CPP options
131    
132    checkpoint51t_post
133    o this is the pre-merge tag of the ecco-branch
134    
135    checkpoint51s_post
136    o cleanup: removed various obsolete #define-s
137    o pkg/grdchk
138      - renamed 'ph-grd 3' to 'grad-res'
139      - merged from ecco-branch
140        (remaining bug fixes for obcs gradient checks)
141      - additional high-precision output for testreport
142        (grep for 'precision_grdchk_result')
143    
144    checkpoint51r_post
145    o cleaned up or removed CPP_OPTIONS.h files
146    o updated results for some of the tests to reflect the new
147      optfiles (-ieee: -O0 instead of -O3)
148    
149    checkpoint51q_post
150    o cd_code:
151      - moved cd_scheme.F -> cd_code_scheme.F
152      - separate read_checkpoint from cd_code_ini_vars.F
153      - separated cd_code part from write_checkpoint
154      - updated AD_SOURCE, generated .flow
155      - added CD_CODE_VARS.h to the_main_loop
156      - Moving cd_code specific store dir.s to pkg/cd_code
157    o ctrl package totally restructured
158      - pack/unpack now optional and decoupled from
159        xx_/adxx_ I/O
160      - ctrl_pack/unpack cleaned
161        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
162      - confined inclusion of AD_CONFIG.h to where necessary.
163    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
164    
165    checkpoint51p_post
166    o create initial cd_code package
167      - WARNING: the initialization of fields within packages
168        is broken because INI_FIELDS (where READ_CHECKPOINT is
169        called) is called *before* PACKAGES_INIT_VARIABLES.
170        This seems to be backwards since
171        1) its important to initially zero the entire field including
172           the "halo" region
173        2) zeroing needs to be done *before* reading pickup info
174           and the pickup call might or might not happen in any
175           particular run
176      - this needs an overhaul for R2
177    o cleanup verification/*/code/GMREDI_OPTIONS.h
178    o cleanup testreport
179    
180    checkpoint51o_post
181    o bringing AD-related verif's up to date with genmake2
182      - carbon/
183      - global_ocean.90x40x15/
184      - hs.94.1x64x5/
185      - (front_relax/ )
186    o (more) consistent directory structure for AD-related verif.'s
187    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
188    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
189    o bug fix in find_alpha.F for MDJWF:
190      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
191        change rho -> rho-rhoConst
192      - replace call find_rho to find_rhonum
193    o initialisation of rFlx extended to full array (required by TAF)
194      and shifted to thermodynamics
195    o removed PTRACERS.h in ptracers routine
196    o added surfacetendencyPtr to S/R parameter list pracers_forcing
197    o Correcting initialisations for fVerU, fVerV.
198    o helping TAF to recognize dependency on kUp for
199      fVerU, fVerV
200    o Replacing delZ by delR in pkg/ctrl/
201    checkpoint51o_pre
202    
203    o undid all of cp51 pending some cleanups and discussion
204    o added the [#include "AD_CONFIG.h"] statement to all files that need
205       it for adjoint/tl #defines
206     o re-worked the build logic in genmake2 to support AD_CONFIG.h
207     o removed tools/genmake since it no longer works
208    
209    checkpoint51n_post
210    o modifications to make FREEZE flux visible to pkg/kpp
211      - moved surfaceTendencyTice from pkg/seaice to main code
212      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
213      - subroutine FREEZE now limits only surface temperature
214        (this means new output.txt for global_ocean.90x40x15,
215         global_ocean.cs32x15, and global_with_exf)
216    o added surface flux output variables to TIMEAVE_STATVARS
217    
218    checkpoint51n_pre
219    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
220    o added [#include "AD_CONFIG.h"] to all files that use the following
221      defines:
222      - ALLOW_ADJOINT_RUN
223      - ALLOW_TANGENTLINEAR_RUN
224      - ALLOW_ECCO_OPTIMIZATION
225    
226    checkpoint51m_post
227    o incorporating changes to get TAMC/TAF working in genmake2
228      - added new TAMC/TAF targets to the Makefile
229      - various cleanups related to package handling
230      - these changes should have no impact on the forward model
231    
232    checkpoint51l_post
233    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
234     - faster algorithm for cal_addtime.F
235     - higher precision arithmetic, where needed
236     - pkg/exf *startdate variables changed from calendar date to
237       model integration time
238    
239    checkpoint51l_pre
240    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
241    o enable to apply restoring on S & T only in a latitude band.
242    o update output (external_forcing_surf modif. change truncation errors)
243       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
244    
245    checkpoint51k_post
246    o change default to: useNHMTerms=.FALSE.
247     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
248       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
249     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
250        exp1, ideal_2D_oce
251     - change data file of oceanic exp (leave the results unchanged for now)
252       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
253    o set gravitySign automatically according to the vertical coordinate used
254      (and change sign: back to "logical" value: +1 when R increases downward)
255    o added an include barrier to the default CPP_OPTIONS.h and
256      removed the #include "PACKAGES_CONFIG.h" from it
257    o fix a bug in mom_fluxform (from chk51j_post)
258    
259    checkpoint51j_post
260    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
261    o adjusted some flow directives (dynamics, thermodynamics)
262    o added cubed-sphere case to test cost function
263    o heckpoint_lev?_directives.h now include
264      pkg-specific directives, whenever those are enabled.
265    o Moving pkg-specific flow directives to corresponding pkg
266      Moving pkg-specific differentiation list to corresponding pkg
267      Moving pkg-specific checkpoint-lev storing to corresponding pkg
268      ---> conventions are
269           - pkg_ad.flow
270           - pkg_ad_diff.list
271           - pkg_ad_check_lev?_dir.h
272    
273    checkpoint51i_post
274    o merge of the branch-genmake2
275      - knowingly breaks the older genmake
276      - automatic generation of all ALLOW_${PKG_NAME} defines
277      - new testreport supersedes older testscript
278    o large number of package inclusion and header cleanups
279    checkpoint51i_pre
280    
281    o new output for adjoin of global ocean vector invariant
282    o fix for checkpoint of thermodynamic seaice and bulk_force
283    o Steph gchem various cleanups
284    
285    checkpoint 51h_pre
286    o fixed some single quotes
287    o modify gchem pkg to be more versatile
288    o modifications to clean up dic pkg
289    o add pkg/cfc
290    
291    checkpoint51g_post
292    o provide links for ARPACK and ADM*TLM
293    o start removing verification/vero/
294    o update AD-related stuff
295      (in particular some IF-statements in model/src/ routines)
296    o adding to verification/global_ocean.90x40x15/ adjoint of
297      vector invariant setup
298    
299    checkpoint51f_post
300    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
301    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
302      of tracer Green's fucntions for ocean inversion project.
303    
304    checkpoint51f_pre
305    o Added on-the-fly spatial interpolation capability
306        "USE_EXF_INTERPOLATION" to pkg/exf.
307      - This is a temporary Cartesian-grid hack until
308        the super-duper ESMF coupler becomes available.
309      - See verification/global_with_exf/README for usage example.
310      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
311        flags and modified pkg/seaice accordingly.
312    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
313        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
314        non-local transport term.
315    
316    checkpoint51e_post
317    o pkg/mom_vecinv:
318      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
319      - add time-ave diagnostic of vorticity advection.
320    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
321    o atmospheric geopotential: - include water vapor effect;
322                                - use p^kappa in p* scaling.
323    o land pkg: read initial state from files.
324    o AIM : add stratospheric drag in the upper level
325    
326    checkpoint51d_post
327    o change function ILNBLNK (=> last non-blank char.) to return zero
328      (instead of the string length) when the string. char is empty
329    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
330    o modif's to restore TAMC compatibility
331      - avoid "_d" constructs in PARAMETER declarations
332      - avoid interrupting lines by comment lines
333    o Use cluster local disks for purely local I/O
334      vs. globally visible disks needed for ctrl stuff
335      (merged from ecco-branch)
336      - new active_file_loc... and mdsio_..._loc routines
337      - affected packages: autodiff, ctrl, grdchk, mdsio
338    
339    checkpoint51c_post
340    o introducing integer flag debugLevel
341      - debLevZero: suppress all output
342      - debLevA: standard
343      - debLevB: equivalent to current debugMode=.TRUE.
344    o introducing pathname variable mdsioLocalDir for mdsio
345      that can be specified at runtime
346      (relevant for cluster I/O to local disk)
347    `
348    >>>checkpoint51b_post
349    adjoint of ptracers
350    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
351    o extended state in checkpoint_lev?, etc.
352    o alternative ctrl/cost with tr1 or ptracer
353    o new comlev1_bibj_ptracers
354    o new ptracers.flow
355    o made ptracers_forcing same as external_forcing_s
356    o added verification for adjoint with ptracers
357      - adm. grdchk fail so far
358      - tlm. grdchk OK
359      - checked tapelev/comlev recomputations: OK
360    <<<checkpoint51b_pre
361    
362    checkpoint51a_post
363    o added code for biogeochemistry package
364      - new pkgs: dic, gchem
365      - new subroutine in ptracers
366    o modify code for biogeo packages
367      - in model/src and pkg/ptracers
368    
369    checkpoint51
370    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
371      - autodiff, ctrl, exf, grdchk, seaice
372      kept separate packages
373      - cost, ecco, obcs
374    o updating verification/internal_wave, verification/lab_sea
375      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
376    
377    checkpoint50i_post
378    o Preparing next differentiable checkpoint and sync
379      of MAIN vs. ecco-branch
380      - 1st step: this one is differentiable
381      - 2nd step: next(! not this) checkpoint will have updated packages
382                  from ecco-branch)
383    
384    checkpoint50h_post
385    o new package "land": provide surface BC for AIM.
386    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
387  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
388      F.Molteni paper) ; update aim.5l_cs output.      F.Molteni paper) ; update aim.5l_cs output.
389  o New variable in PARM03 for more flexible pickups  o New variable in PARM03 for more flexible pickups
390    o somewhat cleaned package initialisation sequence for
391      ctrl/ cost/ ecco/ in packages_... routines
392    
393  checkpoint50g_post  checkpoint50g_post
394  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)

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