3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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|
6 |
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checkpoint52j_post |
7 |
|
o fix nchklev in tamc.h for global_ocean... |
8 |
|
o Bringing flow and store directives up-to-date |
9 |
|
o Really weird thing! |
10 |
|
call do_the_model_io from the_main_loop with parameters |
11 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
12 |
|
TAF places a faulty re-call of initialise_varia |
13 |
|
after cost_final call which should not be there! |
14 |
|
checkpoint52j_pre |
15 |
|
|
16 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
17 |
|
error messages |
18 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
19 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
20 |
|
debug output |
21 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
22 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
23 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
24 |
|
o update AIM Equatorial Channel exp: |
25 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
26 |
|
o globalFile now works with exch2 |
27 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
28 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
29 |
|
o limit timeave output for hi-res integrations |
30 |
|
|
31 |
|
checkpoint52i_post |
32 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
33 |
|
o updated the tiling for global_ocean_pressure |
34 |
|
checkpoint52i_pre |
35 |
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|
36 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
37 |
|
the old pkg/aim). |
38 |
|
|
39 |
|
checkpoint52h_pre |
40 |
|
o shortened offending lines in exch2_send_rx?.template |
41 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
42 |
|
o genmake2: add build & execute test for NetCDF code |
43 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
44 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
45 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
46 |
|
o added temporary hack for sea-ice dynamics on the cube: |
47 |
|
metric terms are ignored and it is assumed that |
48 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
49 |
|
|
50 |
|
checkpoint52f_post |
51 |
|
o added exch2 cube routines to pkg/exch2 |
52 |
|
o modified hs94.cs-32x32x5 to use it |
53 |
|
o added new grid files to hs94.cs-32x32x5 |
54 |
|
checkpoint52f_pre |
55 |
|
|
56 |
|
checkpoint52e_post |
57 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
58 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
59 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
60 |
|
to work with implicit vertical advection and AB ; |
61 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
62 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
63 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
64 |
|
checkpoint52e_pre |
65 |
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|
66 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
67 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
68 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
69 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
70 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
71 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
72 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
73 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
74 |
|
|
75 |
|
checkpoint52d_post |
76 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
77 |
|
- updated output accordingly |
78 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
79 |
|
random number generator |
80 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
81 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
82 |
|
o changes to permit hi-res, cubed-sphere, configuration |
83 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
84 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
85 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
86 |
|
of surface winds for the cube |
87 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
88 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
89 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
90 |
|
complete with example surface forcing files and matlab scripts to look |
91 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
92 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
93 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
94 |
|
to conform to the common rule. |
95 |
|
o check-in the first version of the coupler + interfaces for multi-components |
96 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
97 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
98 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
99 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
100 |
|
- exchanges between component and coupler is done in forward_step |
101 |
|
o new verification experiment, cpl_aim+ocn: |
102 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
103 |
|
|
104 |
|
checkpoint52d_pre |
105 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
106 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
107 |
|
|
108 |
|
checkpoint52c_post |
109 |
|
o Fixing OPTIONS files for use of exf: |
110 |
|
- ALLOW_ECCO not needed |
111 |
|
- ECCO_CPPOPTIONS.h should not be included from |
112 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
113 |
|
as has been the case in the past |
114 |
|
- All cal/exf related options are currently set in |
115 |
|
single header file. Should remain so until we |
116 |
|
agree on a consistent new policy. |
117 |
|
o Removed all CPP options for cal package. |
118 |
|
cal has no more CPP options. |
119 |
|
o modified STOREs in GAD_ADVECTION |
120 |
|
o corrected key comp. for passkey |
121 |
|
|
122 |
|
checkpoint52b_post |
123 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
124 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
125 |
|
- modify fluxes but do not change theta directly; |
126 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
127 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
128 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
129 |
|
o put back grid & coriolis monitor output. |
130 |
|
checkpoint52b_pre |
131 |
|
|
132 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
133 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
134 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
135 |
|
(need info on NUMBER_OF_PTRACERS) |
136 |
|
o missing PTRACERS headers in some routines |
137 |
|
o default tamc.h in pkg/autodiff supposed to crash |
138 |
|
to ensure proper customization |
139 |
|
|
140 |
|
checkpoint52a_post |
141 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
142 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
143 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
144 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
145 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
146 |
|
- keep the old version of FREEZE for backward compatibility; |
147 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
148 |
|
- corresponding modifs for TAF directives |
149 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
150 |
|
o time-averaged output for pkg/ptracers |
151 |
|
o fix problem with ECCO-related divided adjoint |
152 |
|
snapshot file was missing some ad-variables, |
153 |
|
but no warning issued by TAF |
154 |
|
|
155 |
|
checkpoint52a_pre |
156 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
157 |
|
|
158 |
|
checkpoint52 = ecco_c52_e35 |
159 |
|
o after testing adjoints of checkpoint51u_post |
160 |
|
|
161 |
|
checkpoint51u_post |
162 |
|
o this is the post-merge tag of the ecco-branch |
163 |
|
(needs another clean checkout and re-testing) |
164 |
|
o various natl_box_adjoint configs and results |
165 |
|
but no input fields |
166 |
|
o obcs adjoint not yet merged! |
167 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
168 |
|
o updated/extended some store directives for seaice |
169 |
|
o pkg/ecco now containes ecco-specific part of cost function |
170 |
|
o top level routines the_main_loop, forward_step |
171 |
|
supersede those in model/src/ |
172 |
|
previous input data.cost now in data.ecco |
173 |
|
(new namelist ecco_cost_nml) |
174 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
175 |
|
|
176 |
|
checkpoint51t_post |
177 |
|
o this is the pre-merge tag of the ecco-branch |
178 |
|
|
179 |
|
checkpoint51s_post |
180 |
|
o cleanup: removed various obsolete #define-s |
181 |
|
o pkg/grdchk |
182 |
|
- renamed 'ph-grd 3' to 'grad-res' |
183 |
|
- merged from ecco-branch |
184 |
|
(remaining bug fixes for obcs gradient checks) |
185 |
|
- additional high-precision output for testreport |
186 |
|
(grep for 'precision_grdchk_result') |
187 |
|
|
188 |
|
checkpoint51r_post |
189 |
|
o cleaned up or removed CPP_OPTIONS.h files |
190 |
|
o updated results for some of the tests to reflect the new |
191 |
|
optfiles (-ieee: -O0 instead of -O3) |
192 |
|
|
193 |
|
checkpoint51q_post |
194 |
|
o cd_code: |
195 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
196 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
197 |
|
- separated cd_code part from write_checkpoint |
198 |
|
- updated AD_SOURCE, generated .flow |
199 |
|
- added CD_CODE_VARS.h to the_main_loop |
200 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
201 |
|
o ctrl package totally restructured |
202 |
|
- pack/unpack now optional and decoupled from |
203 |
|
xx_/adxx_ I/O |
204 |
|
- ctrl_pack/unpack cleaned |
205 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
206 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
207 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
208 |
|
|
209 |
|
checkpoint51p_post |
210 |
|
o create initial cd_code package |
211 |
|
- WARNING: the initialization of fields within packages |
212 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
213 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
214 |
|
This seems to be backwards since |
215 |
|
1) its important to initially zero the entire field including |
216 |
|
the "halo" region |
217 |
|
2) zeroing needs to be done *before* reading pickup info |
218 |
|
and the pickup call might or might not happen in any |
219 |
|
particular run |
220 |
|
- this needs an overhaul for R2 |
221 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
222 |
|
o cleanup testreport |
223 |
|
|
224 |
|
checkpoint51o_post |
225 |
|
o bringing AD-related verif's up to date with genmake2 |
226 |
|
- carbon/ |
227 |
|
- global_ocean.90x40x15/ |
228 |
|
- hs.94.1x64x5/ |
229 |
|
- (front_relax/ ) |
230 |
|
o (more) consistent directory structure for AD-related verif.'s |
231 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
232 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
233 |
|
o bug fix in find_alpha.F for MDJWF: |
234 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
235 |
|
change rho -> rho-rhoConst |
236 |
|
- replace call find_rho to find_rhonum |
237 |
|
o initialisation of rFlx extended to full array (required by TAF) |
238 |
|
and shifted to thermodynamics |
239 |
|
o removed PTRACERS.h in ptracers routine |
240 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
241 |
|
o Correcting initialisations for fVerU, fVerV. |
242 |
|
o helping TAF to recognize dependency on kUp for |
243 |
|
fVerU, fVerV |
244 |
|
o Replacing delZ by delR in pkg/ctrl/ |
245 |
|
checkpoint51o_pre |
246 |
|
|
247 |
|
o undid all of cp51 pending some cleanups and discussion |
248 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
249 |
|
it for adjoint/tl #defines |
250 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
251 |
|
o removed tools/genmake since it no longer works |
252 |
|
|
253 |
|
checkpoint51n_post |
254 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
255 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
256 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
257 |
|
- subroutine FREEZE now limits only surface temperature |
258 |
|
(this means new output.txt for global_ocean.90x40x15, |
259 |
|
global_ocean.cs32x15, and global_with_exf) |
260 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
261 |
|
|
262 |
|
checkpoint51n_pre |
263 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
264 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
265 |
|
defines: |
266 |
|
- ALLOW_ADJOINT_RUN |
267 |
|
- ALLOW_TANGENTLINEAR_RUN |
268 |
|
- ALLOW_ECCO_OPTIMIZATION |
269 |
|
|
270 |
|
checkpoint51m_post |
271 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
272 |
|
- added new TAMC/TAF targets to the Makefile |
273 |
|
- various cleanups related to package handling |
274 |
|
- these changes should have no impact on the forward model |
275 |
|
|
276 |
|
checkpoint51l_post |
277 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
278 |
|
- faster algorithm for cal_addtime.F |
279 |
|
- higher precision arithmetic, where needed |
280 |
|
- pkg/exf *startdate variables changed from calendar date to |
281 |
|
model integration time |
282 |
|
|
283 |
|
checkpoint51l_pre |
284 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
285 |
|
o enable to apply restoring on S & T only in a latitude band. |
286 |
|
o update output (external_forcing_surf modif. change truncation errors) |
287 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
288 |
|
|
289 |
|
checkpoint51k_post |
290 |
|
o change default to: useNHMTerms=.FALSE. |
291 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
292 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
293 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
294 |
|
exp1, ideal_2D_oce |
295 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
296 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
297 |
|
o set gravitySign automatically according to the vertical coordinate used |
298 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
299 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
300 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
301 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
302 |
|
|
303 |
|
checkpoint51j_post |
304 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
305 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
306 |
|
o added cubed-sphere case to test cost function |
307 |
|
o heckpoint_lev?_directives.h now include |
308 |
|
pkg-specific directives, whenever those are enabled. |
309 |
|
o Moving pkg-specific flow directives to corresponding pkg |
310 |
|
Moving pkg-specific differentiation list to corresponding pkg |
311 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
312 |
|
---> conventions are |
313 |
|
- pkg_ad.flow |
314 |
|
- pkg_ad_diff.list |
315 |
|
- pkg_ad_check_lev?_dir.h |
316 |
|
|
317 |
|
checkpoint51i_post |
318 |
|
o merge of the branch-genmake2 |
319 |
|
- knowingly breaks the older genmake |
320 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
321 |
|
- new testreport supersedes older testscript |
322 |
|
o large number of package inclusion and header cleanups |
323 |
|
checkpoint51i_pre |
324 |
|
|
325 |
|
o new output for adjoin of global ocean vector invariant |
326 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
327 |
|
o Steph gchem various cleanups |
328 |
|
|
329 |
|
checkpoint 51h_pre |
330 |
|
o fixed some single quotes |
331 |
|
o modify gchem pkg to be more versatile |
332 |
|
o modifications to clean up dic pkg |
333 |
|
o add pkg/cfc |
334 |
|
|
335 |
|
checkpoint51g_post |
336 |
|
o provide links for ARPACK and ADM*TLM |
337 |
|
o start removing verification/vero/ |
338 |
|
o update AD-related stuff |
339 |
|
(in particular some IF-statements in model/src/ routines) |
340 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
341 |
|
vector invariant setup |
342 |
|
|
343 |
|
checkpoint51f_post |
344 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
345 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
346 |
|
of tracer Green's fucntions for ocean inversion project. |
347 |
|
|
348 |
|
checkpoint51f_pre |
349 |
|
o Added on-the-fly spatial interpolation capability |
350 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
351 |
|
- This is a temporary Cartesian-grid hack until |
352 |
|
the super-duper ESMF coupler becomes available. |
353 |
|
- See verification/global_with_exf/README for usage example. |
354 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
355 |
|
flags and modified pkg/seaice accordingly. |
356 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
357 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
358 |
|
non-local transport term. |
359 |
|
|
360 |
|
checkpoint51e_post |
361 |
|
o pkg/mom_vecinv: |
362 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
363 |
|
- add time-ave diagnostic of vorticity advection. |
364 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
365 |
|
o atmospheric geopotential: - include water vapor effect; |
366 |
|
- use p^kappa in p* scaling. |
367 |
|
o land pkg: read initial state from files. |
368 |
|
o AIM : add stratospheric drag in the upper level |
369 |
|
|
370 |
|
checkpoint51d_post |
371 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
372 |
|
(instead of the string length) when the string. char is empty |
373 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
374 |
|
o modif's to restore TAMC compatibility |
375 |
|
- avoid "_d" constructs in PARAMETER declarations |
376 |
|
- avoid interrupting lines by comment lines |
377 |
|
o Use cluster local disks for purely local I/O |
378 |
|
vs. globally visible disks needed for ctrl stuff |
379 |
|
(merged from ecco-branch) |
380 |
|
- new active_file_loc... and mdsio_..._loc routines |
381 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
382 |
|
|
383 |
|
checkpoint51c_post |
384 |
|
o introducing integer flag debugLevel |
385 |
|
- debLevZero: suppress all output |
386 |
|
- debLevA: standard |
387 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
388 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
389 |
|
that can be specified at runtime |
390 |
|
(relevant for cluster I/O to local disk) |
391 |
|
` |
392 |
|
>>>checkpoint51b_post |
393 |
|
adjoint of ptracers |
394 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
395 |
|
o extended state in checkpoint_lev?, etc. |
396 |
|
o alternative ctrl/cost with tr1 or ptracer |
397 |
|
o new comlev1_bibj_ptracers |
398 |
|
o new ptracers.flow |
399 |
|
o made ptracers_forcing same as external_forcing_s |
400 |
|
o added verification for adjoint with ptracers |
401 |
|
- adm. grdchk fail so far |
402 |
|
- tlm. grdchk OK |
403 |
|
- checked tapelev/comlev recomputations: OK |
404 |
|
<<<checkpoint51b_pre |
405 |
|
|
406 |
|
checkpoint51a_post |
407 |
|
o added code for biogeochemistry package |
408 |
|
- new pkgs: dic, gchem |
409 |
|
- new subroutine in ptracers |
410 |
|
o modify code for biogeo packages |
411 |
|
- in model/src and pkg/ptracers |
412 |
|
|
413 |
|
checkpoint51 |
414 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
415 |
|
- autodiff, ctrl, exf, grdchk, seaice |
416 |
|
kept separate packages |
417 |
|
- cost, ecco, obcs |
418 |
|
o updating verification/internal_wave, verification/lab_sea |
419 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
420 |
|
|
421 |
|
checkpoint50i_post |
422 |
|
o Preparing next differentiable checkpoint and sync |
423 |
|
of MAIN vs. ecco-branch |
424 |
|
- 1st step: this one is differentiable |
425 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
426 |
|
from ecco-branch) |
427 |
|
|
428 |
|
checkpoint50h_post |
429 |
|
o new package "land": provide surface BC for AIM. |
430 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
431 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
432 |
|
F.Molteni paper) ; update aim.5l_cs output. |
433 |
|
o New variable in PARM03 for more flexible pickups |
434 |
|
o somewhat cleaned package initialisation sequence for |
435 |
|
ctrl/ cost/ ecco/ in packages_... routines |
436 |
|
|
437 |
|
checkpoint50g_post |
438 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
439 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
440 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
441 |
|
made the default because of faster convergence than ADI |
442 |
|
|
443 |
|
checkpoint50f_post |
444 |
|
o exf totally restructured |
445 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
446 |
|
and made sure it's still differentiable |
447 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
448 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
449 |
|
- updated adjoint/makefile and relevant verif. accordingly |
450 |
|
|
451 |
|
checkpoint50f_pre |
452 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
453 |
|
+ change Evap over land. (update aim.5l_cs output) |
454 |
|
o added missing .cvsignores and made uniform across expts |
455 |
|
o changed configuration of tidal_basin_2d expt |
456 |
|
o added pkg/debug functions for tracing code in fatal crashes |
457 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
458 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
459 |
|
o removed lots of single quotes from comments |
460 |
|
|
461 |
|
checkpoint50e_post |
462 |
|
o make KPP work with PTRACERS |
463 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
464 |
|
nearly a copy of kpp_transport_s |
465 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
466 |
|
gPtr(of the surface layer) instead |
467 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
468 |
|
checkpoint50e_pre |
469 |
|
|
470 |
|
checkpoint50d_post |
471 |
|
o change kpp output from multiple-record state files to single-record state |
472 |
|
files analogous to write_state.F |
473 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
474 |
|
analogous to the cg2d-related output. |
475 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
476 |
|
so that writing to internal file fn (with length 512) fails. |
477 |
|
checkpoint50d_pre |
478 |
|
|
479 |
|
checkpoint50c_post |
480 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
481 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
482 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
483 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
484 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
485 |
|
|
486 |
|
checkpoint50c_pre |
487 |
|
Merging from release1_p13: |
488 |
|
o bug fix for pkg/seaice dynamic solver |
489 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
490 |
|
|
491 |
|
checkpoint50b_post |
492 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
493 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
494 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
495 |
|
to timestep.F |
496 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
497 |
|
o re-generate output for highly sensitive test-exp: |
498 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
499 |
|
|
500 |
|
checkpoint50b_pre |
501 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
502 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
503 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
504 |
|
|
505 |
|
checkpoint50a_post |
506 |
|
o Bug fix for merging between c50 and KPP. |
507 |
|
ikey was passed from thermodynamics to kpp_calc via |
508 |
|
common block rather than being recomputed in kpp_calc, |
509 |
|
in contradiction with new key itdkey. |
510 |
|
New key ikppkey created, and tamc.h headers updated. |
511 |
|
|
512 |
|
checkpoint50 |
513 |
|
- 2nd step of merge with ecco-branch: |
514 |
|
merge changes in ecco-branch back into main trunk |
515 |
|
- bug fix in find_alpha |
516 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
517 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
518 |
|
- merged some sliced AD support routines |
519 |
|
|
520 |
|
checkpoint49 |
521 |
|
merged from ecco-branch: |
522 |
|
o exf: |
523 |
|
- Enable initialisation of forcing fields to constant |
524 |
|
(runtime) values. |
525 |
|
- in exf_getffields.F |
526 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
527 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
528 |
|
with bulf formulae. |
529 |
|
- exf_init.F modify #ifdef for exf_init_evap |
530 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
531 |
|
The following INT-usages are not safe: |
532 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
533 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
534 |
|
and were modified. |
535 |
|
o autodiff: checkpoint_lev... |
536 |
|
- updated storing for bulk formulae (some arrays were missing) |
537 |
|
- added state for seaice package |
538 |
|
- synchronized with main branch |
539 |
|
o DIVA: |
540 |
|
Modif.s in |
541 |
|
- the_main_loop.F |
542 |
|
- the_model_main.F |
543 |
|
and added cost_final_restore.F cost_final_store.F |
544 |
|
o With these changes, it is possible to fully separate |
545 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
546 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
547 |
|
into separate model executions. |
548 |
|
This enables better tuning of DIVA to given queue sizes. |
549 |
|
o Loss of cost function value in consecutive DIVA runs is |
550 |
|
fixed by storing to 'costfinal' file. |
551 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
552 |
|
beginning/end of adjoint integration is accounted for. |
553 |
|
The current changes apply to TAF-1.4.26. |
554 |
|
TAF has one remaining bug, requiring one manual change |
555 |
|
(see MITgcm manual). |
556 |
|
o cal: synchronized between MAIN and ecco-branch |
557 |
|
|
558 |
|
checkpoint48i_post |
559 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
560 |
|
(mostly adding new routines to make list and replacing |
561 |
|
pressure by totPhiHyd). |
562 |
|
o Updated and merged grdchk package |
563 |
|
- has both ADM and TLM checks |
564 |
|
- works for single- and multi-proc. |
565 |
|
- output cleaned |
566 |
|
- worked successfully for parallel DIVA |
567 |
|
o genmake: |
568 |
|
- Adding -platform=SP4 |
569 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
570 |
|
o Modif. for DIVA: |
571 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
572 |
|
(similar thing would apply for active files such as |
573 |
|
tbar, sbar, psbar, which should not be reinitialised; |
574 |
|
only relevant for ecco-branch) |
575 |
|
|
576 |
|
checkpoint48h_post |
577 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
578 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
579 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
580 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
581 |
|
|
582 |
|
checkpoint48g_post |
583 |
|
--- EOS: |
584 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
585 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
586 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
587 |
|
--- Pressure/geopotential gradient: |
588 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
589 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
590 |
|
( changes results of global_ocean_pressure ) |
591 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
592 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
593 |
|
( changes results of ideal_2D_oce ) |
594 |
|
o includes r* 2nd term in potential gradient. |
595 |
|
|
596 |
|
checkpoint48f_post |
597 |
|
Merging from release1_p12: |
598 |
|
o Modifications for using pkg/exf with pkg/seaice |
599 |
|
- improved description of the various forcing configurations |
600 |
|
- added basic radiation bulk formulae to pkg/exf |
601 |
|
- units/sign fix for evap computation in exf_getffields.F |
602 |
|
- updated verification/global_with_exf/results/output.txt |
603 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
604 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
605 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
606 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
607 |
|
to avoid negative values in shallow regions. |
608 |
|
- updated verification/natl_box/results/output.txt |
609 |
|
- updated verification/lab_sea/results/output.txt |
610 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
611 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
612 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
613 |
|
work with multi-field files, e.g., for single-file pickup. |
614 |
|
o pkg/seaice: |
615 |
|
- bug fix in growth.F: QNET for no shortwave case |
616 |
|
- added HeffFile for specifying initial sea-ice thickness |
617 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
618 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
619 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
620 |
|
o pkg/seaice: |
621 |
|
- adjoint-friendly modifications |
622 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
623 |
|
|
624 |
|
checkpoint48e_post |
625 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
626 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
627 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
628 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
629 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
630 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
631 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
632 |
|
inverted_barometer solid-body.cs-32x32x1 |
633 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
634 |
|
|
635 |
|
checkpoint48d_post |
636 |
|
o in preparation for r*: |
637 |
|
a) use pre-computed gradient of hydrostatic potential: |
638 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
639 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
640 |
|
=> affects results of glob_oce_pressure (different truncation error) |
641 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
642 |
|
|
643 |
|
checkpoint48d_pre |
644 |
|
o in preparation for r*: |
645 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
646 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
647 |
|
but for the moment, only used if it does not change the results. |
648 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
649 |
|
|
650 |
|
checkpoint48c_post |
651 |
|
Modifications in treatment of initial flux forcing controls |
652 |
|
to avoid extra storing of flux fields. |
653 |
|
|
654 |
|
checkpoint48c_pre |
655 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
656 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
657 |
|
|
658 |
|
checkpoint48b_post |
659 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
660 |
|
(modification to pressure gradient not yet implemented) |
661 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
662 |
|
(for U & V) that are used for vertical advection of momentum. |
663 |
|
|
664 |
|
checkpoint48a_post |
665 |
|
o In preparation for r*, use temp. array to compute vertical transport |
666 |
|
in flux-form momentum pkg. => change results of few test-exp. |
667 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
668 |
|
lab_sea, natl_box & plume_on_slope |
669 |
|
|
670 |
|
checkpoint48 |
671 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
672 |
|
|
673 |
|
checkpoint47j_post |
674 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
675 |
|
o moved adexch from forward_step to addummy_in_stepping |
676 |
|
o added exch in ctrl_map_... |
677 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
678 |
|
reverse checkpointing loop |
679 |
|
o Yet more changes in gmredi: |
680 |
|
* adgmredi_calc_tensor |
681 |
|
avoiding all recomputation of gmredi_slope_limit |
682 |
|
* adgmredi_x/y/rtransport |
683 |
|
added flag for excessive storing to avoid recomp. of |
684 |
|
u/v/rtans, dTdx/y/z |
685 |
|
-> this is not really necessary and very memory-consuming |
686 |
|
* adgmredi_slope_psi: |
687 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
688 |
|
* gmredi_slope_limit |
689 |
|
re-activated full calculation of taperfct for case 'ac02' |
690 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
691 |
|
|
692 |
|
checkpoint47i_post |
693 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
694 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
695 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
696 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
697 |
|
o gmredi: fix few bugs. |
698 |
|
|
699 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
700 |
|
This will be a good checkpoint to plug into the ecco-branch. |
701 |
|
o few modif.'s to get latest version adjointed |
702 |
|
(mainly kick out code in ini_linear_phisurf) |
703 |
|
o modif's to run adjoint with exactConserv |
704 |
|
o case GM_BOLUS_ADVEC should be cleaned |
705 |
|
S/R gmredi_slope_psi should be cleaned |
706 |
|
o verification/carbon now has exactConserv=.TRUE. |
707 |
|
|
708 |
|
checkpoint47g_post |
709 |
|
o time-average AIM output: becomes independent from statvars time-average |
710 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
711 |
|
o After TAF bug fix: |
712 |
|
Tested adjoint of gmredi package. |
713 |
|
Tests were done with checkpoint47 rather than with latest |
714 |
|
checkpoint47f_post since the latter is broken for the adjoint |
715 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
716 |
|
Here they are, before they get changed/lost/stolen. |
717 |
|
Mostly modif.'s to fix numerical sensitivities. |
718 |
|
Gradient checks OK for |
719 |
|
- GM_taper_scheme: |
720 |
|
* clipping |
721 |
|
* ac02 |
722 |
|
* linear |
723 |
|
* glw91 |
724 |
|
* dm95 |
725 |
|
* ldd97 |
726 |
|
- GMREDI_OPTIONS: |
727 |
|
* GM_VISBECK_VARIABLE_K |
728 |
|
* GM_NON_UNITY_DIAGONAL |
729 |
|
* GM_EXTRA_DIAGONAL |
730 |
|
* GM_BOLUS_ADVEC |
731 |
|
in conjunction with data.gmredi parameters to be checked in |
732 |
|
in a few minutes under verification/carbon/code/ |
733 |
|
|
734 |
|
checkpoint47f_post |
735 |
|
Merging from release1_p10: |
736 |
|
o modifications for using pkg/exf with pkg/seaice |
737 |
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
738 |
|
and SEAICE_EXTERNAL_FLUXES |
739 |
|
- pkg/exf CPP options EXF_READ_EVAP and |
740 |
|
EXF_NO_BULK_COMPUTATIONS |
741 |
|
- usage examples are Experiments 8 and 9 in |
742 |
|
verification/lab_sea/README |
743 |
|
- verification/lab_sea default experiment now uses |
744 |
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
745 |
|
|
746 |
|
checkpoint47e_post |
747 |
|
o created a tag prior to creating a branch |
748 |
|
|
749 |
|
checkpoint47d_post |
750 |
|
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
751 |
|
at the bottom boundary had an erroneous half slip boundary condition |
752 |
|
o added bottom drag and no slip boundary condition capabilities to |
753 |
|
oceanic pressure coordinates code |
754 |
|
o added new verification experiment global_ocean_pressure, this experiment is |
755 |
|
also described in the tutorial section of the manual |
756 |
|
checkpoint47d_pre |
757 |
|
|
758 |
|
checkpoint47c_post |
759 |
|
o Added a verification experiment for a global cubed-sphere ocean run |
760 |
|
- verification/global_ocean.cubed32x32x30 |
761 |
|
- uses pkg/therm_seaice and pkg/bulk_forcing |
762 |
|
|
763 |
|
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
764 |
|
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
765 |
|
when using P-coordinate; only implemented for atmospheric config. |
766 |
|
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
767 |
|
NOTES: requires option NONLIN_FRSURF to be "#define". |
768 |
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
769 |
|
|
770 |
|
checkpoint47b_post |
771 |
|
Merging from release1_p9: |
772 |
|
o pkg/seaice |
773 |
|
- removed GOTO's and added taf directives |
774 |
|
- double precision constants to reduce the g77 (Linux) |
775 |
|
to F77 (SGI) differences reported in release1_p8 |
776 |
|
o tools/genmake |
777 |
|
- added SGI options |
778 |
|
o verification/testscript |
779 |
|
- updated to that of checkpoint47a_post |
780 |
|
o verification/global_ocean.90x40x15/input/eedata |
781 |
|
- modified for SGI f77 compatibility |
782 |
|
o verification/lab_sea |
783 |
|
- added description of sea-ice model |
784 |
|
- added missing matlab routines |
785 |
|
- added test of thermodynamics parallelization |
786 |
|
|
787 |
|
checkpoint47a_post |
788 |
|
o new pkg: aim_v23 |
789 |
|
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
790 |
|
for now, keep the same surface forcing as before. |
791 |
|
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
792 |
|
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
793 |
|
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
794 |
|
o add diagnostic of surface correction term in monitor output |
795 |
|
|
796 |
|
o bulk_force and therm_seaice |
797 |
|
- Two packages: bulk_force (Bulk forcing) |
798 |
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
799 |
|
- Earlier integration from Stephaine Dutkiewicz |
800 |
|
and Patrick Heimbach. |
801 |
|
- Two ifdef statements for compile time, |
802 |
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
803 |
|
|
804 |
|
checkpoint47 |
805 |
|
differentiable version of checkpoint46n_post |
806 |
|
o bug fix in quasihydrostaticterms |
807 |
|
o * "clean" adjoint code (in terms of extensive recomputations) |
808 |
|
can now be obtained for all GMREDI options (i.e. for |
809 |
|
- GM_VISBECK_VARIABLE_K |
810 |
|
- GM_NON_UNITY_DIAGONAL |
811 |
|
- GM_EXTRA_DIAGONAL |
812 |
|
- GM_BOLUS_ADVEC ) |
813 |
|
* However, wrong gradient check problem remains unsolved. |
814 |
|
* New CPP options have been introduced for different |
815 |
|
tapering schemes |
816 |
|
o external_fields_load now part of differentiation list |
817 |
|
o pressure needs multiple storing; |
818 |
|
would be nice to have store_pressure at beginning or |
819 |
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
820 |
|
(NB: pressure is needed for certain cases in find_rho, |
821 |
|
which is also invoked through convective_adjustment). |
822 |
|
o recomputations in find_rho for cases |
823 |
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
824 |
|
o #define ATMOSPHERIC_LOADING should be differentiable |
825 |
|
o ini_forcing shifted to begining of initialise_varia |
826 |
|
o Incorporating QNVS line search routines into MITgcm |
827 |
|
(this is separate code, and therefore not under pkg) |
828 |
|
lsopt/, optim/ |
829 |
|
o Updated verification/carbon/ |
830 |
|
- #define GM_VISBECK_VARIABLE_K |
831 |
|
- GM_taper_scheme = 'ldd97' |
832 |
|
|
833 |
|
checkpoint46n_post |
834 |
|
Merging from release1_p8: |
835 |
|
o verification/natl_box: |
836 |
|
updating new external_fields_load routine |
837 |
|
o New package: pkg/seaice |
838 |
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
839 |
|
The sea-ice code is based on Hibler (1979-1980). |
840 |
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
841 |
|
In addition to computing prognostic sea-ice variables and diagnosing |
842 |
|
the forcing/external data fields that drive the ocean model, |
843 |
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
844 |
|
The implied surface heat flux is then stored in variable |
845 |
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
846 |
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
847 |
|
non-local transport term. Because this call precedes model |
848 |
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
849 |
|
the freezing point by the time theta is dumped or time-averaged. |
850 |
|
N.B.: fairly large differences in accuracy occur across |
851 |
|
different platforms/compilers; comparison between |
852 |
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
853 |
|
generated output gives: |
854 |
|
T S U V |
855 |
|
C D M c m s m s m s m s |
856 |
|
n p a R g m m e . m m e . m m e . m m e . |
857 |
|
f n k u 2 i a a d i a a d i a a d i a a d |
858 |
|
g d e n d n x n . n x n . n x n . n x n . |
859 |
|
|
860 |
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
861 |
|
o GAD: |
862 |
|
- generated new common blocks to account for call of |
863 |
|
same gad routines with differing traceridentities |
864 |
|
(needed to modify tracerIdentity indices in GAD.h) |
865 |
|
- generated separate common blocks for case useCubedSphereExchange |
866 |
|
(Department of Futurology) |
867 |
|
- parameter lists to gmredi_?transport: added tracerIdentity |
868 |
|
- added new key indices to tamc.h |
869 |
|
o external_fields_load: |
870 |
|
- added this routine to TAF list |
871 |
|
- needed to make some common blocks global and additional storing |
872 |
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
873 |
|
o exf: |
874 |
|
updated external forcing package |
875 |
|
- bug fixes carried over from ecco-branch |
876 |
|
(missing OBCS_OPTIONS.h in two routines) |
877 |
|
- enable easy to use "no forcing". |
878 |
|
- added exf I/O for atmospheric loading |
879 |
|
- added exf I/O for runoff data |
880 |
|
- transfered scaling between exf <-> MITgcm to exf namelist |
881 |
|
o Adding new verification experiment global_with_exf. |
882 |
|
This verification experiment is almost identical to the |
883 |
|
global_ocean.90x40x15 experiment, except that it uses |
884 |
|
the exf (and cal) package instead of the |
885 |
|
external_fields_load routine (cf README file). |
886 |
|
|
887 |
|
checkpoint46m_post |
888 |
|
o modified testscript to return -- when there are no lines of "%MON" output |
889 |
|
o added new flag "quasiHydrostatic" for QH mode |
890 |
|
and new routine quasihydrostaticterms() |
891 |
|
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
892 |
|
New routine: mom_u_coriolis_nh() |
893 |
|
o fixed sign of non-hydrostatic metric terms in u and v equations. |
894 |
|
Depend on correct sign of gravitySign. |
895 |
|
o added work.pc* to .cvsignore in aim directories using ifc |
896 |
|
o introduced flag for controllin non-hydrostatic metric terms |
897 |
|
o removed gravitySign from PARM04 |
898 |
|
o switched to g77/ifc from pgf77 in aim experiments |
899 |
|
|
900 |
|
checkpoint46l_post |
901 |
|
o made convective adjustment work with pressure coordinates: |
902 |
|
- changed the direction of k-loop in convective_adjustment.F for the |
903 |
|
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
904 |
|
- adjusted the reference pressure k-index in convective_adjustment.F |
905 |
|
- adjusted the convection condition in convect.F (in analogy to |
906 |
|
calc_ivdc.F) |
907 |
|
- convective_adjustment no longer computes anything on the halos |
908 |
|
- removed the warnings about negative salinity from find_rho.F and |
909 |
|
find_alpha.F; instead the new routine look_for_neg_salinity, called |
910 |
|
at the beginning of find_rho, find_alpha, and find_beta, does a |
911 |
|
check of the entire slice, if CPP-option |
912 |
|
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
913 |
|
checkpoint46l_pre |
914 |
|
|
915 |
|
checkpoint46k_post |
916 |
|
o fixed the verification/global_ocean.90x40x15 experiment: |
917 |
|
- new bathymetry (the world according to A., JMC, and M.) |
918 |
|
- new initial fields and forcing fields (*.bin files) |
919 |
|
- new POLY3.COEFFS (for the next release one should switch to a full |
920 |
|
equation of state: JMD95P or MDJWF) |
921 |
|
- fixed several errors and redundancies in the data file |
922 |
|
- experiment uses looped cells |
923 |
|
- added matlab directory with diagnostic scripts for plotting of output |
924 |
|
|
925 |
|
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
926 |
|
- read AIM physics parameters from a file (data.aimphys) |
927 |
|
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
928 |
|
|
929 |
|
checkpoint46j_post |
930 |
|
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
931 |
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
932 |
|
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
933 |
|
o update timeave pkg for wVel diagnostic. |
934 |
|
checkpoint46j_pre |
935 |
|
|
936 |
|
checkpoint46i_post |
937 |
|
o Clean up AIM package (and keep the results unchanged): |
938 |
|
include CPP_OPTION and use IMPLICT NONE in all routines ; |
939 |
|
declare all the variables _RL ; use _d 0 for all numerical constants. |
940 |
|
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
941 |
|
|
942 |
|
checkpoint46h_post |
943 |
|
o cleaned up the use of rhoNil and rhoConst. |
944 |
|
- rhoNil should only appear in the LINEAR equation of state, everywhere |
945 |
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
946 |
|
and the dynamical equations are all divided by rhoConst |
947 |
|
o introduced new parameter rhoConstFresh, a reference density of fresh |
948 |
|
water, to remove the fresh water flux's dependence on rhoNil. The default |
949 |
|
value is 999.8 kg/m^3 |
950 |
|
o cleanup up external_forcing.F and external_forcing_surf.F |
951 |
|
- can now be used by both OCEANIC and OCEANICP |
952 |
|
checkpoint46h_pre |
953 |
|
|
954 |
|
Added code to convert surface volume flux (fresh water) into |
955 |
|
a mass flux when using P coordinates in the ocean (OCEANICP). |
956 |
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
957 |
|
|
958 |
|
checkpoint46g_post |
959 |
|
o Include a new diagnostic variable phiHydLow for the ocean model |
960 |
|
- in z-coordinates, it is the bottom pressure anomaly |
961 |
|
- in p-coordinates, it is the sea surface elevation |
962 |
|
- in both cases, these variable have global drift, reflecting the mass |
963 |
|
drift in z-coordinates and the volume drift in p-coordinates |
964 |
|
- included time averaging for phiHydLow, be aware of the drift! |
965 |
|
o depth-dependent computation of Bo_surf for pressure coordinates |
966 |
|
in the ocean (buoyancyRelation='OCEANICP') |
967 |
|
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
968 |
|
Theta, Salinity, and Pressure in the parameter list. This routine is |
969 |
|
presently contained in find_rho.F. This routine does not give the |
970 |
|
correct density for 'POLY3', which would be a z-dependent reference |
971 |
|
density. |
972 |
|
o cleaned up find_rho |
973 |
|
- removed obsolete 'eqn' from the parameter list. |
974 |
|
o added two new verification experiments: gop and goz |
975 |
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
976 |
|
checkpoint46g_pre |
977 |
|
|
978 |
|
checkpoint46f_post |
979 |
|
o Enable tangent linear (forward mode) gradient checks: |
980 |
|
- extended active file handling to g_... files |
981 |
|
- added TANGENT_SIMULATION to theSimulationMode |
982 |
|
- extended grdchk package accordingly |
983 |
|
o added tangent linear setup in verification/carbon/code_ftl |
984 |
|
o added adjoint setup in verification/front_relax/code_ad |
985 |
|
|
986 |
|
checkpoint46e_post |
987 |
|
o Added new equation of state -> MDJWF |
988 |
|
- EOS of McDougall et al., 2002, JAOT, submitted |
989 |
|
- caveat: the equation of state is only valid for a smaller (more |
990 |
|
realistic?) range of values than JMD95P/Z and UNESCO |
991 |
|
- added masks to the calculation of pressure in store_pressure |
992 |
|
- added more check values for density in check_eos (ini_eos.F), some of |
993 |
|
the old check values are out of the range of the MDJWF-eos, so don't |
994 |
|
expect perfect matches for those |
995 |
|
checkpoint46e_pre |
996 |
|
|
997 |
|
checkpoint46d_post |
998 |
|
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
999 |
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
1000 |
|
case of pressure coordinates. eosType='JMD95Z' in |
1001 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
1002 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1003 |
|
in find_alpha/beta. |
1004 |
|
checkpoint46d_pre |
1005 |
|
|
1006 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1007 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
1008 |
|
|
1009 |
|
checkpoint46c_post |
1010 |
|
o Changes necessary for ocean in p-coordinates |
1011 |
|
- Added new buoyancy relation = 'OCEANICP' |
1012 |
|
- Added new parameters = gravitySign (this used to be contained inside |
1013 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
1014 |
|
X GM/Redi is not compatible (yet) |
1015 |
|
X bottom drag and no-slip need to be debugged. |
1016 |
|
checkpoint46c_pre |
1017 |
|
|
1018 |
|
checkpoint46b_post |
1019 |
|
o Added new equation of state -> JMD95Z and JMD95P |
1020 |
|
- EOS of Jackett and McDougall, 1995, JAOT |
1021 |
|
- moved all EOS parameters into EOS.h |
1022 |
|
- new routines ini_eos.F, store_pressure.F |
1023 |
|
o Added UNESCO EOS, but not recommended because it requires |
1024 |
|
in-situ temperature (see JMD95) |
1025 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
1026 |
|
unesco.f to be used with POLY3 |
1027 |
|
checkpoint46b_pre |
1028 |
|
|
1029 |
|
checkpoint46a_post |
1030 |
|
o Added (atmospheric) pressure loading |
1031 |
|
- new field in FFIELDS.h, etc... |
1032 |
|
- new cpp flag ATMOSPHERIC_LOADING |
1033 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
1034 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
1035 |
|
checkpoint46a_pre |
1036 |
|
|
1037 |
|
checkpoint46 |
1038 |
|
further merges from release1_p5 |
1039 |
|
o new ctrl package |
1040 |
|
- adopted from ECCO environment to enable optimization |
1041 |
|
- added Eliassen Palm fluxes to controls |
1042 |
|
o added Eliassen Palm flux controls to gradient check package |
1043 |
|
o cost package |
1044 |
|
- Compatible with new ctrl package |
1045 |
|
- added Eliassen Palm cost hooks |
1046 |
|
- modif's of existing cost functions |
1047 |
|
o Adjoint-related bug fixes in kpp: |
1048 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
1049 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
1050 |
|
o autodiff package |
1051 |
|
- flow directives: |
1052 |
|
+ new for S/R do_the_model_io |
1053 |
|
+ enhanced for S/R checkpoint |
1054 |
|
+ new gmredi.flow |
1055 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
1056 |
|
disable adcommon.h/g_common.h by default. |
1057 |
|
- fixed problem for adjoint of global_max |
1058 |
|
o modified verification/carbon/ |
1059 |
|
o New setup for adjoint of global_ocean |
1060 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
1061 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
1062 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
1063 |
|
|
1064 |
|
checkpoint45d_post |
1065 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
1066 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
1067 |
|
(affects plume_on_slope "cg2d" output) |
1068 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
1069 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
1070 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
1071 |
|
o change phiMin in exp1 (to agree with documentation) |
1072 |
|
o add new flags: |
1073 |
|
- T,S forcing inside/outside Adams-Bashforth |
1074 |
|
- turn off temp,salt advection and/or forcing |
1075 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
1076 |
|
o monitor: change definition of KE to check conservation of Energy |
1077 |
|
|
1078 |
|
checkpoint45c_post |
1079 |
|
o Removed f90 comments ("!") |
1080 |
|
o Modified initialisations to enable exf package for MITgcm |
1081 |
|
(without invoking ECCO_PACKAGE). |
1082 |
|
o modifications to gradient check package (Martin Losch) |
1083 |
|
- enable centered differences |
1084 |
|
- modified format of standard output |
1085 |
|
|
1086 |
|
checkpoint45b_post |
1087 |
|
o cleaned exchange calls in cg2d |
1088 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
1089 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
1090 |
|
to configure barotropic setup (Martin Losch) |
1091 |
|
o moved some initialisations within bi,bj loop in dynamics |
1092 |
|
(TAF flow dependency) |
1093 |
|
o in initialise_varia, moved call packages_init_variables |
1094 |
|
before convective_adjustment_init |
1095 |
|
(corresponding adjustment of TAF tape initialisation). |
1096 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
1097 |
|
|
1098 |
|
checkpoint45a_post |
1099 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
1100 |
|
o specific exchange for X-slice domain (case Ny=1) |
1101 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
1102 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
1103 |
|
|
1104 |
|
checkpoint44h_post = checkpoint45 |
1105 |
|
o Fix to restore differentiability: |
1106 |
|
place at which packages_init_variables is called in |
1107 |
|
initialise_varia is crucial for reverse control flow. |
1108 |
|
o modifications in GMRedi to enable stable adjoint |
1109 |
|
(corresponding modif's in thermodynamics, dynamics) |
1110 |
|
o added missing hook for sponge layer code in external_forcing |
1111 |
|
o modified test cost functions |
1112 |
|
o storing in gad_advection (plus removal of write(0,*)! |
1113 |
|
o missing headers TR1.h added in convective_adjustment routines |
1114 |
|
o errorMessageUnit set non-equal zero in eeboot |
1115 |
|
(conflict on some platforms, e.g. IBM SP3) |
1116 |
|
o modified carbon verif. |
1117 |
|
|
1118 |
|
checkpoint44h_pre |
1119 |
|
o vertical grid option: allow to put the Interface at the middle between |
1120 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
1121 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
1122 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
1123 |
|
|
1124 |
|
checkpoint44g_post |
1125 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
1126 |
|
results) ; ifdef missing in thermodynamics.F |
1127 |
|
|
1128 |
|
checkpoint44f_pre,checkpoint44f_post |
1129 |
|
o added PTRACERS package |
1130 |
|
This allows an arbitrary number of passive tracers to be integrated |
1131 |
|
forward simultaneously with the dynamicaly model. |
1132 |
|
+ Implemented so far: |
1133 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
1134 |
|
- I/O and checkpointing |
1135 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
1136 |
|
+ Not implemented so far: |
1137 |
|
- KPP |
1138 |
|
- OBCS |
1139 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
1140 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
1141 |
|
line in data.pkg. |
1142 |
|
+ This package is disabled by default since it increases storage. |
1143 |
|
|
1144 |
|
|
1145 |
|
o testscript: added -cleanup option |
1146 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
1147 |
|
b) enable to filter 2D fields. |
1148 |
|
|
1149 |
|
checkpoint44e_pre,post |
1150 |
|
o re-wrote convective adjustment to use pre-calculated weights |
1151 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
1152 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
1153 |
|
Original calls to convect() still in place. |
1154 |
|
|
1155 |
|
chkpt44d_pre,post |
1156 |
|
o added missing EXCLUDE_MONITOR flags |
1157 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
1158 |
|
(incompatible typ in MIN/MAX expressions caused problems |
1159 |
|
on IBM SP3) |
1160 |
|
o in genmake added variable MAKEDEPEND |
1161 |
|
plus resetting for case SunOS |
1162 |
|
o added timer_stats.c routine for IBM SP3 |
1163 |
|
o removed variables in dynamics |
1164 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
1165 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
1166 |
|
|
1167 |
|
o real fresh water flux implemented with non-linear free-surface. |
1168 |
|
|
1169 |
|
chkpt44c_pre,post |
1170 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
1171 |
|
USE_NATURAL_BCS in solve_for_P); |
1172 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
1173 |
|
|
1174 |
|
checkpoint44b_pre/_post |
1175 |
|
o merge of relevant stuff from the ecco-branch: |
1176 |
|
- genmake: removed $S64 overwrite for case SunOS |
1177 |
|
- pkg/exf: update and corrections for field swapping and obcs |
1178 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
1179 |
|
harmonized between ECCO and MITgcm |
1180 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
1181 |
|
updated checkpointing_lev... lists for obcs |
1182 |
|
- model/src: minor changes in forward_step, plot_field |
1183 |
|
added directive for divided adjoint in the_main_loop |
1184 |
|
- pkg/mdsio: added mdsio_gl_slice |
1185 |
|
|
1186 |
|
o check parameters & config (chkpt44a_pre,post) |
1187 |
|
o OBC and NonLin_FrSurf. |
1188 |
|
|
1189 |
|
checkpoint44 |
1190 |
|
o fix bug in mom_vi_del2uv |
1191 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
1192 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
1193 |
|
o update AIM experiments (NCEP input files) |
1194 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
1195 |
|
o added some stuff for AD |
1196 |
|
|
1197 |
|
checkpoint43 |
1198 |
|
o added two new advection tests |
1199 |
|
o added global 4x4 degree ocean test |
1200 |
|
o added test of H&S94 with free surface on cube |
1201 |
|
o some final mods for gradient check, adjoint,... |
1202 |
|
|
1203 |
|
checkpoint42 |
1204 |
|
Fixed AD-related problems: |
1205 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
1206 |
|
(mainly thermodynamics.F) |
1207 |
|
o New store directives for multi-dim. advection schemes |
1208 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
1209 |
|
* new common block and key passkey |
1210 |
|
(mainly gad_advection.F) |
1211 |
|
o Modified store directives for split of dynamics/thermodynamics |
1212 |
|
for the case ALLOW_KPP |
1213 |
|
o Cleaned argument list for timestep_tracer.F |
1214 |
|
|
1215 |
|
checkpoint41 |
1216 |
|
o re-formatted/added comments in prologues of key subroutines |
1217 |
|
to work with protex |
1218 |
|
|
1219 |
|
checkpoint40 |
1220 |
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
1221 |
|
o added FLT (floats) package from Arne along with demo. experiment |
1222 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
1223 |
|
implementation of forward-in-time forcing terms |
1224 |
|
o more mods for non-linear free-surface including new variable |
1225 |
|
o modified multi-dim method to work on cube |
1226 |
|
o bug fix in KPP (from DM) |
1227 |
|
|
1228 |
|
checkpoint40pre9 |
1229 |
|
o added DST advection schemes |
1230 |
|
o fix MPI bug on SGI's |
1231 |
|
o modifications for non-linear free-surface |
1232 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
1233 |
|
o added tension/strain form of stress tensor |
1234 |
|
o changes to commenting of arguments for TAF/TAMC |
1235 |
|
o added/updated many matlab scripts |
1236 |
|
o added multi-dimensional advection method for tracers |
1237 |
|
|
1238 |
|
checkpoint40pre8 |
1239 |
|
o new package rw/ |
1240 |
|
Added method for dumping intermediate local arrays: |
1241 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
1242 |
|
bi,bj loop |
1243 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
1244 |
|
arrays |
1245 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
1246 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
1247 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
1248 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
1249 |
|
control flux-form versus vector invariant code. |
1250 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
1251 |
|
or genmake -DISABLE ... |
1252 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
1253 |
|
(additional storing is now needed for case vecinv; |
1254 |
|
currently nothing implemented to switch this storing off |
1255 |
|
in case fluxform is used since no CPP flag available). |
1256 |
|
|
1257 |
|
checkpoint40pre7 |
1258 |
|
o bug fix in dynamics.F |
1259 |
|
calc_viscosity called before k=1,Nr loop. |
1260 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
1261 |
|
o cleaned initialisations in ctrl_map_ini |
1262 |
|
related to TAF |
1263 |
|
|
1264 |
|
checkpoint40pre6 |
1265 |
|
o split dynamics into thermodynamics & dynamics |
1266 |
|
o corresponding split of calc_diffusivity into |
1267 |
|
calc_diffusivity, calc_viscosity |
1268 |
|
(kpp_calc_diff, kpp_calc_visc). |
1269 |
|
o Added diffkr, kapgm to control variables |
1270 |
|
o bug fix in gmredi_slope_limit for ldd97 |
1271 |
|
|
1272 |
|
checkpoint40pre5 |
1273 |
|
o proper initialization of Adams-Bashforth time stepping |
1274 |
|
+ uses forward step for very first step of model (iter=0) |
1275 |
|
o re-generated *all* output since almost all output is modified by this |
1276 |
|
change (sorry but we've been putting this one off for about 2 years) |
1277 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
1278 |
|
*not* regenerated since they are already out of date and I don't |
1279 |
|
want to create the impression that they are suddenly working. |
1280 |
|
o removed KAP stuff for DEC's |
1281 |
|
o modified/added many .cvsignore files in */code and */input |
1282 |
|
o added new expt "solid-body.cs-32x32x1" |
1283 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
1284 |
|
is not necessarily any better than the current one... |
1285 |
|
|
1286 |
|
checkpoint40pre4 |
1287 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
1288 |
|
calc_common_factors which are crucial for TAF. |
1289 |
|
o extended iMin,jMin range for calc_common_factors, |
1290 |
|
calc_diffusivity |
1291 |
|
o added option ALLOW_PASSIVE_TRACER |
1292 |
|
o a few minor updates and fixes |
1293 |
|
|
1294 |
|
checkpoint40pre3 |
1295 |
|
o created calc_gtr1.F for gad package |
1296 |
|
o split the_main_loop and re-introduced forward_step |
1297 |
|
o some recomputations of nIter0 for TAMC |
1298 |
|
|
1299 |
|
checkpoint40pre2 |
1300 |
|
o Updated to latest branch of AJA, JMC |
1301 |
|
o Added gradient check package |
1302 |
|
o Added routines for passive tracer handling |
1303 |
|
o Added carbon sequestration sensitivity experiment |
1304 |
|
|
1305 |
|
checkpoint39 |
1306 |
|
o Modifications and fixes to support TAMC |
1307 |
|
(mainly missing or wrong directives) |
1308 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
1309 |
|
in addummy_in_stepping |
1310 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
1311 |
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
1312 |
|
o Included following packages: |
1313 |
|
cal: calendar |
1314 |
|
exf: external forcing |
1315 |
|
ecco: essential routines to control use of cal, exf |
1316 |
|
(NB: this is not the full ECCO environment) |
1317 |
|
o disabled some packages by default in genmake |
1318 |
|
|
1319 |
|
checkpoint38 |
1320 |
|
o see notes_c37_adj.txt |
1321 |
|
o corrected wrong layer index in external_forcing_t |
1322 |
|
o replaced the_main_loop/forward_step by the_main_loop |
1323 |
|
o removed forceoutput from write_state |
1324 |
|
(replaced criteria for initial/final state) |
1325 |
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
1326 |
|
|
1327 |
|
checkpoint37 |
1328 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
1329 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
1330 |
|
used unless genmake -disable=mdsio) |
1331 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
1332 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
1333 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
1334 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
1335 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
1336 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
1337 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
1338 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
1339 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
1340 |
|
and after) unless activating 2 commented lines in initialise-varia. |
1341 |
|
o Non-Hydrostatic pickup file Pb fixed. |
1342 |
|
o bug with Rigid-lid version (since c35) fixed. |
1343 |
|
|
1344 |
|
checkpoint36 |
1345 |
|
o implement Crank-Nickelson barotropic time-stepping |
1346 |
|
o recover Time-Average diagnostics |
1347 |
|
o fix Pb in checkpoint (PR#19) |
1348 |
|
o AIM become a standard package ; clean unused CPP_kees |
1349 |
|
|
1350 |
|
checkpoint35 |
1351 |
|
o subtantial rewrite of dynamics.f |
1352 |
|
o allows staggered time-stepping |
1353 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
1354 |
|
o added bottom drag (linear + quadratic) |
1355 |
|
|
1356 |
|
checkpoint34 |
1357 |
|
o Modified exchange routines for correct reverse simulation. |
1358 |
|
o Added verification output to comply with bug fix in impldiff.F |
1359 |
|
as of c33 (exp2, natl_box). |
1360 |
|
o Corrected store directives in dynamics.F |
1361 |
|
o Corrected array boundaries in impldiff.F |
1362 |
|
o Corrected array dimensions in gmredi. |
1363 |
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
1364 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
1365 |
|
o Added mdsio_gl.F for ECCO purposes. |
1366 |
|
|
1367 |
|
checkpoint33 |
1368 |
|
o Fixed bug in lower BC in impldiff.F |
1369 |
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
1370 |
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
1371 |
|
- Removed verification/natl_box/code/external_fields_scale.F |
1372 |
|
(did not differ from that in model/src) |
1373 |
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
1374 |
|
(see FFIELDS.h for description) |
1375 |
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
1376 |
|
kpp_calc.F and kpp_transport_t.F |
1377 |
|
- Removed model/src/external_fields_scale.F and calls to it |
1378 |
|
- verification/natl_box uses flux data with "atmospheric" sign so |
1379 |
|
a special version of external_fields_load.F is used to |
1380 |
|
change the data as it's read in. This way, the arrays |
1381 |
|
have the right units and signs at all times tha a user could |
1382 |
|
possibly use them. |
1383 |
|
o Corrected genmake to delete a temporary file during configuration |
1384 |
|
|
1385 |
|
checkpoint32 |
1386 |
|
o Scaling of forcing fields moved from external_forcing.F to |
1387 |
|
external_fields_scale.F, called directly after loading fields. |
1388 |
|
o Surface relaxation terms added to surface tendency fields in |
1389 |
|
extra subroutine. |
1390 |
|
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
1391 |
|
fields. |
1392 |
|
o Changes in GMRedi to comply with packaging structure. |
1393 |
|
o Modifications and bug fixes in KPP package. |
1394 |
|
o Verification experiment for KPP added (verification/nat_box/) |
1395 |
|
|
1396 |
|
checkpoint31 |
1397 |
|
o Packages interface brought in line with defined standard |
1398 |
|
-> new routines packages_...F |
1399 |
|
-> changes in initialise_fixed.F, initialise_varia.F |
1400 |
|
-> enables initialisation interface for ECCO package |
1401 |
|
o Rescaling of external forcing fields immediately after read |
1402 |
|
(removed from external_forcing.F) |
1403 |
|
-> new: surface_fields_scale.F |
1404 |
|
-> affects ini_foorcing.F, external_fields_load.F |
1405 |
|
o Computation of surface tendencies before tendency updates. |
1406 |
|
-> new: external_forcing_surf.F |
1407 |
|
o Change of variable names useGMRedi, useKPP, useECCO |
1408 |
|
o Further changes in dynamics.F, impldiff.F for TAMC |
1409 |
|
o Tested for experiments 0, 2, 4. |
1410 |
|
- not yet tested for GMRedi. |
1411 |
|
- not yet tested for KPP. |
1412 |
|
|
1413 |
|
checkpoint30 |
1414 |
|
o Updates for OBCs |
1415 |
|
o New experiment for test OBCs (internal_wave) |
1416 |
|
o New output.txt in verification/exp4/results/ |
1417 |
|
o Updates for KPP: calculation of viscosity corrected, new variables |
1418 |
|
kpp_dumpFreq and kpp_taveFreq |
1419 |
|
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
1420 |
|
and entry for T90 in genmake |
1421 |
|
|
1422 |
|
checkpoint29 |
1423 |
|
o packaged KPP and GM/Redi |
1424 |
|
|
1425 |
|
checkpoint28 |
1426 |
|
o Corrected initialization of hFacMin for difference vertical coordinates |
1427 |
|
o Modified calculation of partial cell thickness to more robust algorithm |
1428 |
|
o config_summary.F: replaced write_1D_... by write_0D_... |
1429 |
|
read_write.F: added subroutines write_0D_... |
1430 |
|
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
1431 |
|
included some initialisations required for TAMC. |
1432 |
|
o routine calc_isoslopes: modified sqrt computation to make it |
1433 |
|
differentiable for zero argument. |
1434 |
|
o routines dynamics, impldiff: |
1435 |
|
included store directives and tape key computations required for TAMC. |
1436 |
|
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
1437 |
|
|
1438 |
|
checkpoint27 |
1439 |
|
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
1440 |
|
formulation works properly with variable resolution. |
1441 |
|
o restructured the calling tree between the_model_main() and dynamics() |
1442 |
|
o split initialise() into initialise_fixed() and initialise_varia() |
1443 |
|
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
1444 |
|
in new routine ini_psurf() |
1445 |
|
|
1446 |
|
checkpoint26 |
1447 |
|
o moved some #ifdef in optional routines to encompass everything |
1448 |
|
except the argument declarations. This was using up some memory. |
1449 |
|
o fixed macros like _ADT to work with both versions of Linux cpp |
1450 |
|
o cleaned up some unused and uninitialized variables |
1451 |
|
(helps when debugging with strict compile options) |
1452 |
|
o split up CPP_EEOPTIONS.h into options and macros |
1453 |
|
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
1454 |
|
o patch for 2 processor JAM mode |
1455 |
|
|
1456 |
|
checkpoint25 |
1457 |
|
o updates for OBCs and NH |
1458 |
|
o dramatically reduced memory usage |
1459 |
|
o added "JAM" routines for use on Artic network |
1460 |
|
o parameterization of convection by implicit vertical diffusion |
1461 |
|
o added a diagnostic of convective index |
1462 |
|
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
1463 |
|
(this is was partly for OBCs and NH but also in anticipation of |
1464 |
|
an explicit free-surface option) |
1465 |
|
o initial state input files for U and V |
1466 |
|
|
1467 |
|
checkpoint24 |
1468 |
|
o Removed some spurious "REAL"s |
1469 |
|
o Updated KPP to latest version from JPL |
1470 |
|
o Added a COS(latitude) in horizontal viscosity |
1471 |
|
|
1472 |
|
checkpoint23 |
1473 |
|
o Added del^4 diffusion for salt and temperature |
1474 |
|
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
1475 |
|
|
1476 |
|
checkpoint22 |
1477 |
|
o Made many small changes: implicit none, format(i5), etc... |
1478 |
|
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
1479 |
|
|
1480 |
|
checkpoint21 |
1481 |
|
o Introduced new I/O package that supports direct-access records (mdsio.F) |
1482 |
|
o Split-up mid-level I/O routines |
1483 |
|
o Updated input data for experiments 0,1,2,4 and 5 |
1484 |
|
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
1485 |
|
|
1486 |
|
checkpoint20 |
1487 |
|
o Tidied up open-boundaries some more |
1488 |
|
o Added non-hydrostatic code |
1489 |
|
o Fixed some input data |
1490 |
|
o Modified MPI start-up to work in "coupled" context. |
1491 |
|
|
1492 |
|
checkpoint19 |
1493 |
|
o Tidied up directory structure for verification experiments. |
1494 |
|
o Added new code for open boundaries. |
1495 |
|
o Corrected advective terms near boundaries. |
1496 |
|
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
1497 |
|
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
1498 |
|
o Split default parameters out of ini_parms.F into set_defaults.F. |
1499 |
|
|
1500 |
|
checkpoint18 |
1501 |
|
o Further changes for optional code generation with |
1502 |
|
CPP - ugh! |
1503 |
|
|
1504 |
|
checkpoint17 |
1505 |
|
o Beginning to incorporating modularity |
1506 |
|
for supporting atmos. and ocean configs. |
1507 |
|
o Small changes for TAMC complinace |
1508 |
|
o New ultra simple test case. Barotropic box |
1509 |
|
configuration "exp0". |
1510 |
|
|
1511 |
|
checkpoint16 |
1512 |
|
o Minor changes to exchange routines to support |
1513 |
|
accumulation in reverse mode. Adjoint of an |
1514 |
|
assignment is an addition. |
1515 |
|
o Changes to support compilation by TAMC (LR(1) |
1516 |
|
syntax) and by g77 under Linux ( 72 character |
1517 |
|
limit ). |
1518 |
|
|
1519 |
|
checkpoint15 |
1520 |
|
Rewrote exchange routines to allow |
1521 |
|
o General tile <-> tile connectivity. |
1522 |
|
o TAMC reverse mode flag ( is this really needed? ) |
1523 |
|
o Variable width overlap and exchange region widths. |
1524 |
|
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
1525 |
|
shmput/shmget, VIA, SYSV shmem and every other cool |
1526 |
|
communication method. |
1527 |
|
|
1528 |
|
checkpoint14 |
1529 |
|
Consistent isomorphism chages made. These allow dynamical core |
1530 |
|
to support both pressure and meters as a vertical coordinate. |
1531 |
|
|
1532 |
|
checkpoint13 |
1533 |
|
Release which corrects global_max problem and a couple |
1534 |
|
of KGM time-averaging diagnostic errors. Also contains |
1535 |
|
a double-gyre experiment setup as well as the baseline |
1536 |
|
4 degree global template. The double gyre template is |
1537 |
|
organised to allow it to be applied automatically to |
1538 |
|
the baseline configuration. |
1539 |
|
|
1540 |
|
branch-point-rdot |
1541 |
|
A few tidy-ups have been made bt the real point of this |
1542 |
|
check-point (excuse the pun) is to allow a branch to be |
1543 |
|
made for the purposes of adding the rDot alterations. |
1544 |
|
I don't want to commit the rDot to the main-trunk until |
1545 |
|
we've actually tested it... |
1546 |
|
|
1547 |
|
checkpoint12 |
1548 |
|
Tidy up and added generic genmake script (formerly |
1549 |
|
configure script). |
1550 |
|
Released to testers. |
1551 |
|
|
1552 |
|
checkpoint11 |
1553 |
|
Re-arranged initialise() and introduced ini_vertical_grid() |
1554 |
|
and ini_masks_etc(). |
1555 |
|
|
1556 |
|
checkpoint10 |
1557 |
|
Introduced the configure script. |
1558 |
|
Separated out the diags package. |
1559 |
|
Added template for writing time-averages of tile/intermediate quantities. |
1560 |
|
Updated SIZE.h in exp2 and made the data big-endian. |
1561 |
|
|
1562 |
|
checkpoint9 |
1563 |
|
MPI fix. Filename changes (meta/data). salbin*y stuff. |
1564 |
|
General tidy-up. |
1565 |
|
SST.bin SSS.bin added to verification/exp2 |
1566 |
|
|
1567 |
|
checkpoint8 |
1568 |
|
Inludes time-dependant forcing and time-averaging. |
1569 |
|
Works at 4x4 and 2.8125x2.8125 global |
1570 |
|
|
1571 |
|
checkpoint7-4degree-ref |
1572 |
|
Branch from checkpoint7. Released for application to |
1573 |
|
global modeling and general modeling - process studies, regional |
1574 |
|
model etc.. |
1575 |
|
Configured for verification/exp2 - 4 degree global, two process. |
1576 |
|
|
1577 |
checkpoint7 |
checkpoint7 |
1578 |
Created by cnh |
Created by cnh |
1579 |
Simple 4 degree global simulation |
Simple 4 degree global simulation |