3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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|
6 |
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checkpoint52h_pre |
7 |
|
o shortened offending lines in exch2_send_rx?.template |
8 |
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o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
9 |
|
o genmake2: add build & execute test for NetCDF code |
10 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
11 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
12 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
13 |
|
o added temporary hack for sea-ice dynamics on the cube: |
14 |
|
metric terms are ignored and it is assumed that |
15 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
16 |
|
|
17 |
|
checkpoint52f_post |
18 |
|
o added exch2 cube routines to pkg/exch2 |
19 |
|
o modified hs94.cs-32x32x5 to use it |
20 |
|
o added new grid files to hs94.cs-32x32x5 |
21 |
|
checkpoint52f_pre |
22 |
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|
23 |
|
checkpoint52e_post |
24 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
25 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
26 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
27 |
|
to work with implicit vertical advection and AB ; |
28 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
29 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
30 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
31 |
|
checkpoint52e_pre |
32 |
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|
33 |
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o fix bug in impldiff when Nr=1 or Nr=2. |
34 |
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o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
35 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
36 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
37 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
38 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
39 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
40 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
41 |
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|
42 |
|
checkpoint52d_post |
43 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
44 |
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- updated output accordingly |
45 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
46 |
|
random number generator |
47 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
48 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
49 |
|
o changes to permit hi-res, cubed-sphere, configuration |
50 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
51 |
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- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
52 |
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- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
53 |
|
of surface winds for the cube |
54 |
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(A verification experiment, based on global_ocean.cs32x15, but with |
55 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
56 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
57 |
|
complete with example surface forcing files and matlab scripts to look |
58 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
59 |
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o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
60 |
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but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
61 |
|
to conform to the common rule. |
62 |
|
o check-in the first version of the coupler + interfaces for multi-components |
63 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
64 |
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- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
65 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
66 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
67 |
|
- exchanges between component and coupler is done in forward_step |
68 |
|
o new verification experiment, cpl_aim+ocn: |
69 |
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coupled ocean - AIM atmosphere on cs32 grid. |
70 |
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|
71 |
|
checkpoint52d_pre |
72 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
73 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
74 |
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|
75 |
|
checkpoint52c_post |
76 |
|
o Fixing OPTIONS files for use of exf: |
77 |
|
- ALLOW_ECCO not needed |
78 |
|
- ECCO_CPPOPTIONS.h should not be included from |
79 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
80 |
|
as has been the case in the past |
81 |
|
- All cal/exf related options are currently set in |
82 |
|
single header file. Should remain so until we |
83 |
|
agree on a consistent new policy. |
84 |
|
o Removed all CPP options for cal package. |
85 |
|
cal has no more CPP options. |
86 |
|
o modified STOREs in GAD_ADVECTION |
87 |
|
o corrected key comp. for passkey |
88 |
|
|
89 |
|
checkpoint52b_post |
90 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
91 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
92 |
|
- modify fluxes but do not change theta directly; |
93 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
94 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
95 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
96 |
|
o put back grid & coriolis monitor output. |
97 |
|
checkpoint52b_pre |
98 |
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|
99 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
100 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
101 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
102 |
|
(need info on NUMBER_OF_PTRACERS) |
103 |
|
o missing PTRACERS headers in some routines |
104 |
|
o default tamc.h in pkg/autodiff supposed to crash |
105 |
|
to ensure proper customization |
106 |
|
|
107 |
|
checkpoint52a_post |
108 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
109 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
110 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
111 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
112 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
113 |
|
- keep the old version of FREEZE for backward compatibility; |
114 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
115 |
|
- corresponding modifs for TAF directives |
116 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
117 |
|
o time-averaged output for pkg/ptracers |
118 |
|
o fix problem with ECCO-related divided adjoint |
119 |
|
snapshot file was missing some ad-variables, |
120 |
|
but no warning issued by TAF |
121 |
|
|
122 |
|
checkpoint52a_pre |
123 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
124 |
|
|
125 |
|
checkpoint52 = ecco_c52_e35 |
126 |
|
o after testing adjoints of checkpoint51u_post |
127 |
|
|
128 |
|
checkpoint51u_post |
129 |
|
o this is the post-merge tag of the ecco-branch |
130 |
|
(needs another clean checkout and re-testing) |
131 |
|
o various natl_box_adjoint configs and results |
132 |
|
but no input fields |
133 |
|
o obcs adjoint not yet merged! |
134 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
135 |
|
o updated/extended some store directives for seaice |
136 |
|
o pkg/ecco now containes ecco-specific part of cost function |
137 |
|
o top level routines the_main_loop, forward_step |
138 |
|
supersede those in model/src/ |
139 |
|
previous input data.cost now in data.ecco |
140 |
|
(new namelist ecco_cost_nml) |
141 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
142 |
|
|
143 |
|
checkpoint51t_post |
144 |
|
o this is the pre-merge tag of the ecco-branch |
145 |
|
|
146 |
|
checkpoint51s_post |
147 |
|
o cleanup: removed various obsolete #define-s |
148 |
|
o pkg/grdchk |
149 |
|
- renamed 'ph-grd 3' to 'grad-res' |
150 |
|
- merged from ecco-branch |
151 |
|
(remaining bug fixes for obcs gradient checks) |
152 |
|
- additional high-precision output for testreport |
153 |
|
(grep for 'precision_grdchk_result') |
154 |
|
|
155 |
|
checkpoint51r_post |
156 |
|
o cleaned up or removed CPP_OPTIONS.h files |
157 |
|
o updated results for some of the tests to reflect the new |
158 |
|
optfiles (-ieee: -O0 instead of -O3) |
159 |
|
|
160 |
|
checkpoint51q_post |
161 |
|
o cd_code: |
162 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
163 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
164 |
|
- separated cd_code part from write_checkpoint |
165 |
|
- updated AD_SOURCE, generated .flow |
166 |
|
- added CD_CODE_VARS.h to the_main_loop |
167 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
168 |
|
o ctrl package totally restructured |
169 |
|
- pack/unpack now optional and decoupled from |
170 |
|
xx_/adxx_ I/O |
171 |
|
- ctrl_pack/unpack cleaned |
172 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
173 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
174 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
175 |
|
|
176 |
|
checkpoint51p_post |
177 |
|
o create initial cd_code package |
178 |
|
- WARNING: the initialization of fields within packages |
179 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
180 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
181 |
|
This seems to be backwards since |
182 |
|
1) its important to initially zero the entire field including |
183 |
|
the "halo" region |
184 |
|
2) zeroing needs to be done *before* reading pickup info |
185 |
|
and the pickup call might or might not happen in any |
186 |
|
particular run |
187 |
|
- this needs an overhaul for R2 |
188 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
189 |
|
o cleanup testreport |
190 |
|
|
191 |
|
checkpoint51o_post |
192 |
|
o bringing AD-related verif's up to date with genmake2 |
193 |
|
- carbon/ |
194 |
|
- global_ocean.90x40x15/ |
195 |
|
- hs.94.1x64x5/ |
196 |
|
- (front_relax/ ) |
197 |
|
o (more) consistent directory structure for AD-related verif.'s |
198 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
199 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
200 |
|
o bug fix in find_alpha.F for MDJWF: |
201 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
202 |
|
change rho -> rho-rhoConst |
203 |
|
- replace call find_rho to find_rhonum |
204 |
|
o initialisation of rFlx extended to full array (required by TAF) |
205 |
|
and shifted to thermodynamics |
206 |
|
o removed PTRACERS.h in ptracers routine |
207 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
208 |
|
o Correcting initialisations for fVerU, fVerV. |
209 |
|
o helping TAF to recognize dependency on kUp for |
210 |
|
fVerU, fVerV |
211 |
|
o Replacing delZ by delR in pkg/ctrl/ |
212 |
|
checkpoint51o_pre |
213 |
|
|
214 |
|
o undid all of cp51 pending some cleanups and discussion |
215 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
216 |
|
it for adjoint/tl #defines |
217 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
218 |
|
o removed tools/genmake since it no longer works |
219 |
|
|
220 |
|
checkpoint51n_post |
221 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
222 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
223 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
224 |
|
- subroutine FREEZE now limits only surface temperature |
225 |
|
(this means new output.txt for global_ocean.90x40x15, |
226 |
|
global_ocean.cs32x15, and global_with_exf) |
227 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
228 |
|
|
229 |
|
checkpoint51n_pre |
230 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
231 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
232 |
|
defines: |
233 |
|
- ALLOW_ADJOINT_RUN |
234 |
|
- ALLOW_TANGENTLINEAR_RUN |
235 |
|
- ALLOW_ECCO_OPTIMIZATION |
236 |
|
|
237 |
|
checkpoint51m_post |
238 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
239 |
|
- added new TAMC/TAF targets to the Makefile |
240 |
|
- various cleanups related to package handling |
241 |
|
- these changes should have no impact on the forward model |
242 |
|
|
243 |
|
checkpoint51l_post |
244 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
245 |
|
- faster algorithm for cal_addtime.F |
246 |
|
- higher precision arithmetic, where needed |
247 |
|
- pkg/exf *startdate variables changed from calendar date to |
248 |
|
model integration time |
249 |
|
|
250 |
|
checkpoint51l_pre |
251 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
252 |
|
o enable to apply restoring on S & T only in a latitude band. |
253 |
|
o update output (external_forcing_surf modif. change truncation errors) |
254 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
255 |
|
|
256 |
|
checkpoint51k_post |
257 |
|
o change default to: useNHMTerms=.FALSE. |
258 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
259 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
260 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
261 |
|
exp1, ideal_2D_oce |
262 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
263 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
264 |
|
o set gravitySign automatically according to the vertical coordinate used |
265 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
266 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
267 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
268 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
269 |
|
|
270 |
|
checkpoint51j_post |
271 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
272 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
273 |
|
o added cubed-sphere case to test cost function |
274 |
|
o heckpoint_lev?_directives.h now include |
275 |
|
pkg-specific directives, whenever those are enabled. |
276 |
|
o Moving pkg-specific flow directives to corresponding pkg |
277 |
|
Moving pkg-specific differentiation list to corresponding pkg |
278 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
279 |
|
---> conventions are |
280 |
|
- pkg_ad.flow |
281 |
|
- pkg_ad_diff.list |
282 |
|
- pkg_ad_check_lev?_dir.h |
283 |
|
|
284 |
|
checkpoint51i_post |
285 |
|
o merge of the branch-genmake2 |
286 |
|
- knowingly breaks the older genmake |
287 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
288 |
|
- new testreport supersedes older testscript |
289 |
|
o large number of package inclusion and header cleanups |
290 |
|
checkpoint51i_pre |
291 |
|
|
292 |
|
o new output for adjoin of global ocean vector invariant |
293 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
294 |
|
o Steph gchem various cleanups |
295 |
|
|
296 |
|
checkpoint 51h_pre |
297 |
|
o fixed some single quotes |
298 |
|
o modify gchem pkg to be more versatile |
299 |
|
o modifications to clean up dic pkg |
300 |
|
o add pkg/cfc |
301 |
|
|
302 |
|
checkpoint51g_post |
303 |
|
o provide links for ARPACK and ADM*TLM |
304 |
|
o start removing verification/vero/ |
305 |
|
o update AD-related stuff |
306 |
|
(in particular some IF-statements in model/src/ routines) |
307 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
308 |
|
vector invariant setup |
309 |
|
|
310 |
|
checkpoint51f_post |
311 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
312 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
313 |
|
of tracer Green's fucntions for ocean inversion project. |
314 |
|
|
315 |
|
checkpoint51f_pre |
316 |
|
o Added on-the-fly spatial interpolation capability |
317 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
318 |
|
- This is a temporary Cartesian-grid hack until |
319 |
|
the super-duper ESMF coupler becomes available. |
320 |
|
- See verification/global_with_exf/README for usage example. |
321 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
322 |
|
flags and modified pkg/seaice accordingly. |
323 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
324 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
325 |
|
non-local transport term. |
326 |
|
|
327 |
|
checkpoint51e_post |
328 |
|
o pkg/mom_vecinv: |
329 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
330 |
|
- add time-ave diagnostic of vorticity advection. |
331 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
332 |
|
o atmospheric geopotential: - include water vapor effect; |
333 |
|
- use p^kappa in p* scaling. |
334 |
|
o land pkg: read initial state from files. |
335 |
|
o AIM : add stratospheric drag in the upper level |
336 |
|
|
337 |
|
checkpoint51d_post |
338 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
339 |
|
(instead of the string length) when the string. char is empty |
340 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
341 |
|
o modif's to restore TAMC compatibility |
342 |
|
- avoid "_d" constructs in PARAMETER declarations |
343 |
|
- avoid interrupting lines by comment lines |
344 |
|
o Use cluster local disks for purely local I/O |
345 |
|
vs. globally visible disks needed for ctrl stuff |
346 |
|
(merged from ecco-branch) |
347 |
|
- new active_file_loc... and mdsio_..._loc routines |
348 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
349 |
|
|
350 |
|
checkpoint51c_post |
351 |
|
o introducing integer flag debugLevel |
352 |
|
- debLevZero: suppress all output |
353 |
|
- debLevA: standard |
354 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
355 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
356 |
|
that can be specified at runtime |
357 |
|
(relevant for cluster I/O to local disk) |
358 |
|
` |
359 |
|
>>>checkpoint51b_post |
360 |
|
adjoint of ptracers |
361 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
362 |
|
o extended state in checkpoint_lev?, etc. |
363 |
|
o alternative ctrl/cost with tr1 or ptracer |
364 |
|
o new comlev1_bibj_ptracers |
365 |
|
o new ptracers.flow |
366 |
|
o made ptracers_forcing same as external_forcing_s |
367 |
|
o added verification for adjoint with ptracers |
368 |
|
- adm. grdchk fail so far |
369 |
|
- tlm. grdchk OK |
370 |
|
- checked tapelev/comlev recomputations: OK |
371 |
|
<<<checkpoint51b_pre |
372 |
|
|
373 |
|
checkpoint51a_post |
374 |
|
o added code for biogeochemistry package |
375 |
|
- new pkgs: dic, gchem |
376 |
|
- new subroutine in ptracers |
377 |
|
o modify code for biogeo packages |
378 |
|
- in model/src and pkg/ptracers |
379 |
|
|
380 |
|
checkpoint51 |
381 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
382 |
|
- autodiff, ctrl, exf, grdchk, seaice |
383 |
|
kept separate packages |
384 |
|
- cost, ecco, obcs |
385 |
|
o updating verification/internal_wave, verification/lab_sea |
386 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
387 |
|
|
388 |
|
checkpoint50i_post |
389 |
|
o Preparing next differentiable checkpoint and sync |
390 |
|
of MAIN vs. ecco-branch |
391 |
|
- 1st step: this one is differentiable |
392 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
393 |
|
from ecco-branch) |
394 |
|
|
395 |
|
checkpoint50h_post |
396 |
|
o new package "land": provide surface BC for AIM. |
397 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
398 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
399 |
|
F.Molteni paper) ; update aim.5l_cs output. |
400 |
|
o New variable in PARM03 for more flexible pickups |
401 |
|
o somewhat cleaned package initialisation sequence for |
402 |
|
ctrl/ cost/ ecco/ in packages_... routines |
403 |
|
|
404 |
|
checkpoint50g_post |
405 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
406 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
407 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
408 |
|
made the default because of faster convergence than ADI |
409 |
|
|
410 |
|
checkpoint50f_post |
411 |
|
o exf totally restructured |
412 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
413 |
|
and made sure it's still differentiable |
414 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
415 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
416 |
|
- updated adjoint/makefile and relevant verif. accordingly |
417 |
|
|
418 |
|
checkpoint50f_pre |
419 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
420 |
|
+ change Evap over land. (update aim.5l_cs output) |
421 |
|
o added missing .cvsignores and made uniform across expts |
422 |
|
o changed configuration of tidal_basin_2d expt |
423 |
|
o added pkg/debug functions for tracing code in fatal crashes |
424 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
425 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
426 |
|
o removed lots of single quotes from comments |
427 |
|
|
428 |
|
checkpoint50e_post |
429 |
|
o make KPP work with PTRACERS |
430 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
431 |
|
nearly a copy of kpp_transport_s |
432 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
433 |
|
gPtr(of the surface layer) instead |
434 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
435 |
|
checkpoint50e_pre |
436 |
|
|
437 |
|
checkpoint50d_post |
438 |
|
o change kpp output from multiple-record state files to single-record state |
439 |
|
files analogous to write_state.F |
440 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
441 |
|
analogous to the cg2d-related output. |
442 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
443 |
|
so that writing to internal file fn (with length 512) fails. |
444 |
|
checkpoint50d_pre |
445 |
|
|
446 |
|
checkpoint50c_post |
447 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
448 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
449 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
450 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
451 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
452 |
|
|
453 |
|
checkpoint50c_pre |
454 |
|
Merging from release1_p13: |
455 |
|
o bug fix for pkg/seaice dynamic solver |
456 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
457 |
|
|
458 |
|
checkpoint50b_post |
459 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
460 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
461 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
462 |
|
to timestep.F |
463 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
464 |
|
o re-generate output for highly sensitive test-exp: |
465 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
466 |
|
|
467 |
|
checkpoint50b_pre |
468 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
469 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
470 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
471 |
|
|
472 |
|
checkpoint50a_post |
473 |
|
o Bug fix for merging between c50 and KPP. |
474 |
|
ikey was passed from thermodynamics to kpp_calc via |
475 |
|
common block rather than being recomputed in kpp_calc, |
476 |
|
in contradiction with new key itdkey. |
477 |
|
New key ikppkey created, and tamc.h headers updated. |
478 |
|
|
479 |
|
checkpoint50 |
480 |
|
- 2nd step of merge with ecco-branch: |
481 |
|
merge changes in ecco-branch back into main trunk |
482 |
|
- bug fix in find_alpha |
483 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
484 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
485 |
|
- merged some sliced AD support routines |
486 |
|
|
487 |
|
checkpoint49 |
488 |
|
merged from ecco-branch: |
489 |
|
o exf: |
490 |
|
- Enable initialisation of forcing fields to constant |
491 |
|
(runtime) values. |
492 |
|
- in exf_getffields.F |
493 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
494 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
495 |
|
with bulf formulae. |
496 |
|
- exf_init.F modify #ifdef for exf_init_evap |
497 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
498 |
|
The following INT-usages are not safe: |
499 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
500 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
501 |
|
and were modified. |
502 |
|
o autodiff: checkpoint_lev... |
503 |
|
- updated storing for bulk formulae (some arrays were missing) |
504 |
|
- added state for seaice package |
505 |
|
- synchronized with main branch |
506 |
|
o DIVA: |
507 |
|
Modif.s in |
508 |
|
- the_main_loop.F |
509 |
|
- the_model_main.F |
510 |
|
and added cost_final_restore.F cost_final_store.F |
511 |
|
o With these changes, it is possible to fully separate |
512 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
513 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
514 |
|
into separate model executions. |
515 |
|
This enables better tuning of DIVA to given queue sizes. |
516 |
|
o Loss of cost function value in consecutive DIVA runs is |
517 |
|
fixed by storing to 'costfinal' file. |
518 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
519 |
|
beginning/end of adjoint integration is accounted for. |
520 |
|
The current changes apply to TAF-1.4.26. |
521 |
|
TAF has one remaining bug, requiring one manual change |
522 |
|
(see MITgcm manual). |
523 |
|
o cal: synchronized between MAIN and ecco-branch |
524 |
|
|
525 |
|
checkpoint48i_post |
526 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
527 |
|
(mostly adding new routines to make list and replacing |
528 |
|
pressure by totPhiHyd). |
529 |
|
o Updated and merged grdchk package |
530 |
|
- has both ADM and TLM checks |
531 |
|
- works for single- and multi-proc. |
532 |
|
- output cleaned |
533 |
|
- worked successfully for parallel DIVA |
534 |
|
o genmake: |
535 |
|
- Adding -platform=SP4 |
536 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
537 |
|
o Modif. for DIVA: |
538 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
539 |
|
(similar thing would apply for active files such as |
540 |
|
tbar, sbar, psbar, which should not be reinitialised; |
541 |
|
only relevant for ecco-branch) |
542 |
|
|
543 |
|
checkpoint48h_post |
544 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
545 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
546 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
547 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
548 |
|
|
549 |
|
checkpoint48g_post |
550 |
|
--- EOS: |
551 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
552 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
553 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
554 |
|
--- Pressure/geopotential gradient: |
555 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
556 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
557 |
|
( changes results of global_ocean_pressure ) |
558 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
559 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
560 |
|
( changes results of ideal_2D_oce ) |
561 |
|
o includes r* 2nd term in potential gradient. |
562 |
|
|
563 |
|
checkpoint48f_post |
564 |
|
Merging from release1_p12: |
565 |
|
o Modifications for using pkg/exf with pkg/seaice |
566 |
|
- improved description of the various forcing configurations |
567 |
|
- added basic radiation bulk formulae to pkg/exf |
568 |
|
- units/sign fix for evap computation in exf_getffields.F |
569 |
|
- updated verification/global_with_exf/results/output.txt |
570 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
571 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
572 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
573 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
574 |
|
to avoid negative values in shallow regions. |
575 |
|
- updated verification/natl_box/results/output.txt |
576 |
|
- updated verification/lab_sea/results/output.txt |
577 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
578 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
579 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
580 |
|
work with multi-field files, e.g., for single-file pickup. |
581 |
|
o pkg/seaice: |
582 |
|
- bug fix in growth.F: QNET for no shortwave case |
583 |
|
- added HeffFile for specifying initial sea-ice thickness |
584 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
585 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
586 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
587 |
|
o pkg/seaice: |
588 |
|
- adjoint-friendly modifications |
589 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
590 |
|
|
591 |
|
checkpoint48e_post |
592 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
593 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
594 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
595 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
596 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
597 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
598 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
599 |
|
inverted_barometer solid-body.cs-32x32x1 |
600 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
601 |
|
|
602 |
|
checkpoint48d_post |
603 |
|
o in preparation for r*: |
604 |
|
a) use pre-computed gradient of hydrostatic potential: |
605 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
606 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
607 |
|
=> affects results of glob_oce_pressure (different truncation error) |
608 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
609 |
|
|
610 |
|
checkpoint48d_pre |
611 |
|
o in preparation for r*: |
612 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
613 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
614 |
|
but for the moment, only used if it does not change the results. |
615 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
616 |
|
|
617 |
|
checkpoint48c_post |
618 |
|
Modifications in treatment of initial flux forcing controls |
619 |
|
to avoid extra storing of flux fields. |
620 |
|
|
621 |
|
checkpoint48c_pre |
622 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
623 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
624 |
|
|
625 |
|
checkpoint48b_post |
626 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
627 |
|
(modification to pressure gradient not yet implemented) |
628 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
629 |
|
(for U & V) that are used for vertical advection of momentum. |
630 |
|
|
631 |
|
checkpoint48a_post |
632 |
|
o In preparation for r*, use temp. array to compute vertical transport |
633 |
|
in flux-form momentum pkg. => change results of few test-exp. |
634 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
635 |
|
lab_sea, natl_box & plume_on_slope |
636 |
|
|
637 |
|
checkpoint48 |
638 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
639 |
|
|
640 |
|
checkpoint47j_post |
641 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
642 |
|
o moved adexch from forward_step to addummy_in_stepping |
643 |
|
o added exch in ctrl_map_... |
644 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
645 |
|
reverse checkpointing loop |
646 |
|
o Yet more changes in gmredi: |
647 |
|
* adgmredi_calc_tensor |
648 |
|
avoiding all recomputation of gmredi_slope_limit |
649 |
|
* adgmredi_x/y/rtransport |
650 |
|
added flag for excessive storing to avoid recomp. of |
651 |
|
u/v/rtans, dTdx/y/z |
652 |
|
-> this is not really necessary and very memory-consuming |
653 |
|
* adgmredi_slope_psi: |
654 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
655 |
|
* gmredi_slope_limit |
656 |
|
re-activated full calculation of taperfct for case 'ac02' |
657 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
658 |
|
|
659 |
|
checkpoint47i_post |
660 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
661 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
662 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
663 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
664 |
|
o gmredi: fix few bugs. |
665 |
|
|
666 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
667 |
|
This will be a good checkpoint to plug into the ecco-branch. |
668 |
|
o few modif.'s to get latest version adjointed |
669 |
|
(mainly kick out code in ini_linear_phisurf) |
670 |
|
o modif's to run adjoint with exactConserv |
671 |
|
o case GM_BOLUS_ADVEC should be cleaned |
672 |
|
S/R gmredi_slope_psi should be cleaned |
673 |
|
o verification/carbon now has exactConserv=.TRUE. |
674 |
|
|
675 |
|
checkpoint47g_post |
676 |
|
o time-average AIM output: becomes independent from statvars time-average |
677 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
678 |
|
o After TAF bug fix: |
679 |
|
Tested adjoint of gmredi package. |
680 |
|
Tests were done with checkpoint47 rather than with latest |
681 |
|
checkpoint47f_post since the latter is broken for the adjoint |
682 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
683 |
|
Here they are, before they get changed/lost/stolen. |
684 |
|
Mostly modif.'s to fix numerical sensitivities. |
685 |
|
Gradient checks OK for |
686 |
|
- GM_taper_scheme: |
687 |
|
* clipping |
688 |
|
* ac02 |
689 |
|
* linear |
690 |
|
* glw91 |
691 |
|
* dm95 |
692 |
|
* ldd97 |
693 |
|
- GMREDI_OPTIONS: |
694 |
|
* GM_VISBECK_VARIABLE_K |
695 |
|
* GM_NON_UNITY_DIAGONAL |
696 |
|
* GM_EXTRA_DIAGONAL |
697 |
|
* GM_BOLUS_ADVEC |
698 |
|
in conjunction with data.gmredi parameters to be checked in |
699 |
|
in a few minutes under verification/carbon/code/ |
700 |
|
|
701 |
checkpoint47f_post |
checkpoint47f_post |
702 |
Merging from release1_p10: |
Merging from release1_p10: |
703 |
o modifications for using pkg/exf with pkg/seaice |
o modifications for using pkg/exf with pkg/seaice |