3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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|
6 |
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o AIM: use true log-P extrapolation for near surface temp (= as in |
7 |
|
F.Molteni paper) ; update aim.5l_cs output. |
8 |
|
|
9 |
|
checkpoint50g_post |
10 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
11 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
12 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
13 |
|
made the default because of faster convergence than ADI |
14 |
|
|
15 |
|
checkpoint50f_post |
16 |
|
o exf totally restructured |
17 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
18 |
|
and made sure it's still differentiable |
19 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
20 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
21 |
|
- updated adjoint/makefile and relevant verif. accordingly |
22 |
|
|
23 |
|
checkpoint50f_pre |
24 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
25 |
|
+ change Evap over land. (update aim.5l_cs output) |
26 |
|
o added missing .cvsignores and made uniform across expts |
27 |
|
o changed configuration of tidal_basin_2d expt |
28 |
|
o added pkg/debug functions for tracing code in fatal crashes |
29 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
30 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
31 |
|
o removed lots of single quotes from comments |
32 |
|
|
33 |
|
checkpoint50e_post |
34 |
|
o make KPP work with PTRACERS |
35 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
36 |
|
nearly a copy of kpp_transport_s |
37 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
38 |
|
gPtr(of the surface layer) instead |
39 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
40 |
|
checkpoint50e_pre |
41 |
|
|
42 |
|
checkpoint50d_post |
43 |
|
o change kpp output from multiple-record state files to single-record state |
44 |
|
files analogous to write_state.F |
45 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
46 |
|
analogous to the cg2d-related output. |
47 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
48 |
|
so that writing to internal file fn (with length 512) fails. |
49 |
|
checkpoint50d_pre |
50 |
|
|
51 |
|
checkpoint50c_post |
52 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
53 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
54 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
55 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
56 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
57 |
|
|
58 |
|
checkpoint50c_pre |
59 |
|
Merging from release1_p13: |
60 |
|
o bug fix for pkg/seaice dynamic solver |
61 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
62 |
|
|
63 |
|
checkpoint50b_post |
64 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
65 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
66 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
67 |
|
to timestep.F |
68 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
69 |
|
o re-generate output for highly sensitive test-exp: |
70 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
71 |
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|
72 |
|
checkpoint50b_pre |
73 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
74 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
75 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
76 |
|
|
77 |
|
checkpoint50a_post |
78 |
|
o Bug fix for merging between c50 and KPP. |
79 |
|
ikey was passed from thermodynamics to kpp_calc via |
80 |
|
common block rather than being recomputed in kpp_calc, |
81 |
|
in contradiction with new key itdkey. |
82 |
|
New key ikppkey created, and tamc.h headers updated. |
83 |
|
|
84 |
|
checkpoint50 |
85 |
|
- 2nd step of merge with ecco-branch: |
86 |
|
merge changes in ecco-branch back into main trunk |
87 |
|
- bug fix in find_alpha |
88 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
89 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
90 |
|
- merged some sliced AD support routines |
91 |
|
|
92 |
|
checkpoint49 |
93 |
|
merged from ecco-branch: |
94 |
|
o exf: |
95 |
|
- Enable initialisation of forcing fields to constant |
96 |
|
(runtime) values. |
97 |
|
- in exf_getffields.F |
98 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
99 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
100 |
|
with bulf formulae. |
101 |
|
- exf_init.F modify #ifdef for exf_init_evap |
102 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
103 |
|
The following INT-usages are not safe: |
104 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
105 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
106 |
|
and were modified. |
107 |
|
o autodiff: checkpoint_lev... |
108 |
|
- updated storing for bulk formulae (some arrays were missing) |
109 |
|
- added state for seaice package |
110 |
|
- synchronized with main branch |
111 |
|
o DIVA: |
112 |
|
Modif.s in |
113 |
|
- the_main_loop.F |
114 |
|
- the_model_main.F |
115 |
|
and added cost_final_restore.F cost_final_store.F |
116 |
|
o With these changes, it is possible to fully separate |
117 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
118 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
119 |
|
into separate model executions. |
120 |
|
This enables better tuning of DIVA to given queue sizes. |
121 |
|
o Loss of cost function value in consecutive DIVA runs is |
122 |
|
fixed by storing to 'costfinal' file. |
123 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
124 |
|
beginning/end of adjoint integration is accounted for. |
125 |
|
The current changes apply to TAF-1.4.26. |
126 |
|
TAF has one remaining bug, requiring one manual change |
127 |
|
(see MITgcm manual). |
128 |
|
o cal: synchronized between MAIN and ecco-branch |
129 |
|
|
130 |
|
checkpoint48i_post |
131 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
132 |
|
(mostly adding new routines to make list and replacing |
133 |
|
pressure by totPhiHyd). |
134 |
|
o Updated and merged grdchk package |
135 |
|
- has both ADM and TLM checks |
136 |
|
- works for single- and multi-proc. |
137 |
|
- output cleaned |
138 |
|
- worked successfully for parallel DIVA |
139 |
|
o genmake: |
140 |
|
- Adding -platform=SP4 |
141 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
142 |
|
o Modif. for DIVA: |
143 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
144 |
|
(similar thing would apply for active files such as |
145 |
|
tbar, sbar, psbar, which should not be reinitialised; |
146 |
|
only relevant for ecco-branch) |
147 |
|
|
148 |
|
checkpoint48h_post |
149 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
150 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
151 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
152 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
153 |
|
|
154 |
|
checkpoint48g_post |
155 |
|
--- EOS: |
156 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
157 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
158 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
159 |
|
--- Pressure/geopotential gradient: |
160 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
161 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
162 |
|
( changes results of global_ocean_pressure ) |
163 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
164 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
165 |
|
( changes results of ideal_2D_oce ) |
166 |
|
o includes r* 2nd term in potential gradient. |
167 |
|
|
168 |
|
checkpoint48f_post |
169 |
|
Merging from release1_p12: |
170 |
|
o Modifications for using pkg/exf with pkg/seaice |
171 |
|
- improved description of the various forcing configurations |
172 |
|
- added basic radiation bulk formulae to pkg/exf |
173 |
|
- units/sign fix for evap computation in exf_getffields.F |
174 |
|
- updated verification/global_with_exf/results/output.txt |
175 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
176 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
177 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
178 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
179 |
|
to avoid negative values in shallow regions. |
180 |
|
- updated verification/natl_box/results/output.txt |
181 |
|
- updated verification/lab_sea/results/output.txt |
182 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
183 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
184 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
185 |
|
work with multi-field files, e.g., for single-file pickup. |
186 |
|
o pkg/seaice: |
187 |
|
- bug fix in growth.F: QNET for no shortwave case |
188 |
|
- added HeffFile for specifying initial sea-ice thickness |
189 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
190 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
191 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
192 |
|
o pkg/seaice: |
193 |
|
- adjoint-friendly modifications |
194 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
195 |
|
|
196 |
|
checkpoint48e_post |
197 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
198 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
199 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
200 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
201 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
202 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
203 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
204 |
|
inverted_barometer solid-body.cs-32x32x1 |
205 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
206 |
|
|
207 |
|
checkpoint48d_post |
208 |
|
o in preparation for r*: |
209 |
|
a) use pre-computed gradient of hydrostatic potential: |
210 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
211 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
212 |
|
=> affects results of glob_oce_pressure (different truncation error) |
213 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
214 |
|
|
215 |
|
checkpoint48d_pre |
216 |
|
o in preparation for r*: |
217 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
218 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
219 |
|
but for the moment, only used if it does not change the results. |
220 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
221 |
|
|
222 |
|
checkpoint48c_post |
223 |
|
Modifications in treatment of initial flux forcing controls |
224 |
|
to avoid extra storing of flux fields. |
225 |
|
|
226 |
|
checkpoint48c_pre |
227 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
228 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
229 |
|
|
230 |
|
checkpoint48b_post |
231 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
232 |
|
(modification to pressure gradient not yet implemented) |
233 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
234 |
|
(for U & V) that are used for vertical advection of momentum. |
235 |
|
|
236 |
|
checkpoint48a_post |
237 |
|
o In preparation for r*, use temp. array to compute vertical transport |
238 |
|
in flux-form momentum pkg. => change results of few test-exp. |
239 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
240 |
|
lab_sea, natl_box & plume_on_slope |
241 |
|
|
242 |
|
checkpoint48 |
243 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
244 |
|
|
245 |
|
checkpoint47j_post |
246 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
247 |
|
o moved adexch from forward_step to addummy_in_stepping |
248 |
|
o added exch in ctrl_map_... |
249 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
250 |
|
reverse checkpointing loop |
251 |
|
o Yet more changes in gmredi: |
252 |
|
* adgmredi_calc_tensor |
253 |
|
avoiding all recomputation of gmredi_slope_limit |
254 |
|
* adgmredi_x/y/rtransport |
255 |
|
added flag for excessive storing to avoid recomp. of |
256 |
|
u/v/rtans, dTdx/y/z |
257 |
|
-> this is not really necessary and very memory-consuming |
258 |
|
* adgmredi_slope_psi: |
259 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
260 |
|
* gmredi_slope_limit |
261 |
|
re-activated full calculation of taperfct for case 'ac02' |
262 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
263 |
|
|
264 |
|
checkpoint47i_post |
265 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
266 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
267 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
268 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
269 |
|
o gmredi: fix few bugs. |
270 |
|
|
271 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
272 |
|
This will be a good checkpoint to plug into the ecco-branch. |
273 |
|
o few modif.'s to get latest version adjointed |
274 |
|
(mainly kick out code in ini_linear_phisurf) |
275 |
|
o modif's to run adjoint with exactConserv |
276 |
|
o case GM_BOLUS_ADVEC should be cleaned |
277 |
|
S/R gmredi_slope_psi should be cleaned |
278 |
|
o verification/carbon now has exactConserv=.TRUE. |
279 |
|
|
280 |
|
checkpoint47g_post |
281 |
|
o time-average AIM output: becomes independent from statvars time-average |
282 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
283 |
|
o After TAF bug fix: |
284 |
|
Tested adjoint of gmredi package. |
285 |
|
Tests were done with checkpoint47 rather than with latest |
286 |
|
checkpoint47f_post since the latter is broken for the adjoint |
287 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
288 |
|
Here they are, before they get changed/lost/stolen. |
289 |
|
Mostly modif.'s to fix numerical sensitivities. |
290 |
|
Gradient checks OK for |
291 |
|
- GM_taper_scheme: |
292 |
|
* clipping |
293 |
|
* ac02 |
294 |
|
* linear |
295 |
|
* glw91 |
296 |
|
* dm95 |
297 |
|
* ldd97 |
298 |
|
- GMREDI_OPTIONS: |
299 |
|
* GM_VISBECK_VARIABLE_K |
300 |
|
* GM_NON_UNITY_DIAGONAL |
301 |
|
* GM_EXTRA_DIAGONAL |
302 |
|
* GM_BOLUS_ADVEC |
303 |
|
in conjunction with data.gmredi parameters to be checked in |
304 |
|
in a few minutes under verification/carbon/code/ |
305 |
|
|
306 |
|
checkpoint47f_post |
307 |
|
Merging from release1_p10: |
308 |
|
o modifications for using pkg/exf with pkg/seaice |
309 |
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
310 |
|
and SEAICE_EXTERNAL_FLUXES |
311 |
|
- pkg/exf CPP options EXF_READ_EVAP and |
312 |
|
EXF_NO_BULK_COMPUTATIONS |
313 |
|
- usage examples are Experiments 8 and 9 in |
314 |
|
verification/lab_sea/README |
315 |
|
- verification/lab_sea default experiment now uses |
316 |
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
317 |
|
|
318 |
|
checkpoint47e_post |
319 |
|
o created a tag prior to creating a branch |
320 |
|
|
321 |
|
checkpoint47d_post |
322 |
|
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
323 |
|
at the bottom boundary had an erroneous half slip boundary condition |
324 |
|
o added bottom drag and no slip boundary condition capabilities to |
325 |
|
oceanic pressure coordinates code |
326 |
|
o added new verification experiment global_ocean_pressure, this experiment is |
327 |
|
also described in the tutorial section of the manual |
328 |
|
checkpoint47d_pre |
329 |
|
|
330 |
|
checkpoint47c_post |
331 |
|
o Added a verification experiment for a global cubed-sphere ocean run |
332 |
|
- verification/global_ocean.cubed32x32x30 |
333 |
|
- uses pkg/therm_seaice and pkg/bulk_forcing |
334 |
|
|
335 |
|
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
336 |
|
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
337 |
|
when using P-coordinate; only implemented for atmospheric config. |
338 |
|
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
339 |
|
NOTES: requires option NONLIN_FRSURF to be "#define". |
340 |
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
341 |
|
|
342 |
|
checkpoint47b_post |
343 |
|
Merging from release1_p9: |
344 |
|
o pkg/seaice |
345 |
|
- removed GOTO's and added taf directives |
346 |
|
- double precision constants to reduce the g77 (Linux) |
347 |
|
to F77 (SGI) differences reported in release1_p8 |
348 |
|
o tools/genmake |
349 |
|
- added SGI options |
350 |
|
o verification/testscript |
351 |
|
- updated to that of checkpoint47a_post |
352 |
|
o verification/global_ocean.90x40x15/input/eedata |
353 |
|
- modified for SGI f77 compatibility |
354 |
|
o verification/lab_sea |
355 |
|
- added description of sea-ice model |
356 |
|
- added missing matlab routines |
357 |
|
- added test of thermodynamics parallelization |
358 |
|
|
359 |
|
checkpoint47a_post |
360 |
|
o new pkg: aim_v23 |
361 |
|
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
362 |
|
for now, keep the same surface forcing as before. |
363 |
|
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
364 |
|
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
365 |
|
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
366 |
|
o add diagnostic of surface correction term in monitor output |
367 |
|
|
368 |
|
o bulk_force and therm_seaice |
369 |
|
- Two packages: bulk_force (Bulk forcing) |
370 |
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
371 |
|
- Earlier integration from Stephaine Dutkiewicz |
372 |
|
and Patrick Heimbach. |
373 |
|
- Two ifdef statements for compile time, |
374 |
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
375 |
|
|
376 |
|
checkpoint47 |
377 |
|
differentiable version of checkpoint46n_post |
378 |
|
o bug fix in quasihydrostaticterms |
379 |
|
o * "clean" adjoint code (in terms of extensive recomputations) |
380 |
|
can now be obtained for all GMREDI options (i.e. for |
381 |
|
- GM_VISBECK_VARIABLE_K |
382 |
|
- GM_NON_UNITY_DIAGONAL |
383 |
|
- GM_EXTRA_DIAGONAL |
384 |
|
- GM_BOLUS_ADVEC ) |
385 |
|
* However, wrong gradient check problem remains unsolved. |
386 |
|
* New CPP options have been introduced for different |
387 |
|
tapering schemes |
388 |
|
o external_fields_load now part of differentiation list |
389 |
|
o pressure needs multiple storing; |
390 |
|
would be nice to have store_pressure at beginning or |
391 |
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
392 |
|
(NB: pressure is needed for certain cases in find_rho, |
393 |
|
which is also invoked through convective_adjustment). |
394 |
|
o recomputations in find_rho for cases |
395 |
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
396 |
|
o #define ATMOSPHERIC_LOADING should be differentiable |
397 |
|
o ini_forcing shifted to begining of initialise_varia |
398 |
|
o Incorporating QNVS line search routines into MITgcm |
399 |
|
(this is separate code, and therefore not under pkg) |
400 |
|
lsopt/, optim/ |
401 |
|
o Updated verification/carbon/ |
402 |
|
- #define GM_VISBECK_VARIABLE_K |
403 |
|
- GM_taper_scheme = 'ldd97' |
404 |
|
|
405 |
|
checkpoint46n_post |
406 |
|
Merging from release1_p8: |
407 |
|
o verification/natl_box: |
408 |
|
updating new external_fields_load routine |
409 |
|
o New package: pkg/seaice |
410 |
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
411 |
|
The sea-ice code is based on Hibler (1979-1980). |
412 |
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
413 |
|
In addition to computing prognostic sea-ice variables and diagnosing |
414 |
|
the forcing/external data fields that drive the ocean model, |
415 |
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
416 |
|
The implied surface heat flux is then stored in variable |
417 |
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
418 |
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
419 |
|
non-local transport term. Because this call precedes model |
420 |
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
421 |
|
the freezing point by the time theta is dumped or time-averaged. |
422 |
|
N.B.: fairly large differences in accuracy occur across |
423 |
|
different platforms/compilers; comparison between |
424 |
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
425 |
|
generated output gives: |
426 |
|
T S U V |
427 |
|
C D M c m s m s m s m s |
428 |
|
n p a R g m m e . m m e . m m e . m m e . |
429 |
|
f n k u 2 i a a d i a a d i a a d i a a d |
430 |
|
g d e n d n x n . n x n . n x n . n x n . |
431 |
|
|
432 |
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
433 |
|
o GAD: |
434 |
|
- generated new common blocks to account for call of |
435 |
|
same gad routines with differing traceridentities |
436 |
|
(needed to modify tracerIdentity indices in GAD.h) |
437 |
|
- generated separate common blocks for case useCubedSphereExchange |
438 |
|
(Department of Futurology) |
439 |
|
- parameter lists to gmredi_?transport: added tracerIdentity |
440 |
|
- added new key indices to tamc.h |
441 |
|
o external_fields_load: |
442 |
|
- added this routine to TAF list |
443 |
|
- needed to make some common blocks global and additional storing |
444 |
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
445 |
|
o exf: |
446 |
|
updated external forcing package |
447 |
|
- bug fixes carried over from ecco-branch |
448 |
|
(missing OBCS_OPTIONS.h in two routines) |
449 |
|
- enable easy to use "no forcing". |
450 |
|
- added exf I/O for atmospheric loading |
451 |
|
- added exf I/O for runoff data |
452 |
|
- transfered scaling between exf <-> MITgcm to exf namelist |
453 |
|
o Adding new verification experiment global_with_exf. |
454 |
|
This verification experiment is almost identical to the |
455 |
|
global_ocean.90x40x15 experiment, except that it uses |
456 |
|
the exf (and cal) package instead of the |
457 |
|
external_fields_load routine (cf README file). |
458 |
|
|
459 |
|
checkpoint46m_post |
460 |
|
o modified testscript to return -- when there are no lines of "%MON" output |
461 |
|
o added new flag "quasiHydrostatic" for QH mode |
462 |
|
and new routine quasihydrostaticterms() |
463 |
|
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
464 |
|
New routine: mom_u_coriolis_nh() |
465 |
|
o fixed sign of non-hydrostatic metric terms in u and v equations. |
466 |
|
Depend on correct sign of gravitySign. |
467 |
|
o added work.pc* to .cvsignore in aim directories using ifc |
468 |
|
o introduced flag for controllin non-hydrostatic metric terms |
469 |
|
o removed gravitySign from PARM04 |
470 |
|
o switched to g77/ifc from pgf77 in aim experiments |
471 |
|
|
472 |
|
checkpoint46l_post |
473 |
|
o made convective adjustment work with pressure coordinates: |
474 |
|
- changed the direction of k-loop in convective_adjustment.F for the |
475 |
|
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
476 |
|
- adjusted the reference pressure k-index in convective_adjustment.F |
477 |
|
- adjusted the convection condition in convect.F (in analogy to |
478 |
|
calc_ivdc.F) |
479 |
|
- convective_adjustment no longer computes anything on the halos |
480 |
|
- removed the warnings about negative salinity from find_rho.F and |
481 |
|
find_alpha.F; instead the new routine look_for_neg_salinity, called |
482 |
|
at the beginning of find_rho, find_alpha, and find_beta, does a |
483 |
|
check of the entire slice, if CPP-option |
484 |
|
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
485 |
|
checkpoint46l_pre |
486 |
|
|
487 |
|
checkpoint46k_post |
488 |
|
o fixed the verification/global_ocean.90x40x15 experiment: |
489 |
|
- new bathymetry (the world according to A., JMC, and M.) |
490 |
|
- new initial fields and forcing fields (*.bin files) |
491 |
|
- new POLY3.COEFFS (for the next release one should switch to a full |
492 |
|
equation of state: JMD95P or MDJWF) |
493 |
|
- fixed several errors and redundancies in the data file |
494 |
|
- experiment uses looped cells |
495 |
|
- added matlab directory with diagnostic scripts for plotting of output |
496 |
|
|
497 |
|
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
498 |
|
- read AIM physics parameters from a file (data.aimphys) |
499 |
|
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
500 |
|
|
501 |
|
checkpoint46j_post |
502 |
|
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
503 |
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
504 |
|
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
505 |
|
o update timeave pkg for wVel diagnostic. |
506 |
|
checkpoint46j_pre |
507 |
|
|
508 |
|
checkpoint46i_post |
509 |
|
o Clean up AIM package (and keep the results unchanged): |
510 |
|
include CPP_OPTION and use IMPLICT NONE in all routines ; |
511 |
|
declare all the variables _RL ; use _d 0 for all numerical constants. |
512 |
|
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
513 |
|
|
514 |
|
checkpoint46h_post |
515 |
|
o cleaned up the use of rhoNil and rhoConst. |
516 |
|
- rhoNil should only appear in the LINEAR equation of state, everywhere |
517 |
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
518 |
|
and the dynamical equations are all divided by rhoConst |
519 |
|
o introduced new parameter rhoConstFresh, a reference density of fresh |
520 |
|
water, to remove the fresh water flux's dependence on rhoNil. The default |
521 |
|
value is 999.8 kg/m^3 |
522 |
|
o cleanup up external_forcing.F and external_forcing_surf.F |
523 |
|
- can now be used by both OCEANIC and OCEANICP |
524 |
|
checkpoint46h_pre |
525 |
|
|
526 |
|
Added code to convert surface volume flux (fresh water) into |
527 |
|
a mass flux when using P coordinates in the ocean (OCEANICP). |
528 |
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
529 |
|
|
530 |
|
checkpoint46g_post |
531 |
|
o Include a new diagnostic variable phiHydLow for the ocean model |
532 |
|
- in z-coordinates, it is the bottom pressure anomaly |
533 |
|
- in p-coordinates, it is the sea surface elevation |
534 |
|
- in both cases, these variable have global drift, reflecting the mass |
535 |
|
drift in z-coordinates and the volume drift in p-coordinates |
536 |
|
- included time averaging for phiHydLow, be aware of the drift! |
537 |
|
o depth-dependent computation of Bo_surf for pressure coordinates |
538 |
|
in the ocean (buoyancyRelation='OCEANICP') |
539 |
|
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
540 |
|
Theta, Salinity, and Pressure in the parameter list. This routine is |
541 |
|
presently contained in find_rho.F. This routine does not give the |
542 |
|
correct density for 'POLY3', which would be a z-dependent reference |
543 |
|
density. |
544 |
|
o cleaned up find_rho |
545 |
|
- removed obsolete 'eqn' from the parameter list. |
546 |
|
o added two new verification experiments: gop and goz |
547 |
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
548 |
|
checkpoint46g_pre |
549 |
|
|
550 |
|
checkpoint46f_post |
551 |
|
o Enable tangent linear (forward mode) gradient checks: |
552 |
|
- extended active file handling to g_... files |
553 |
|
- added TANGENT_SIMULATION to theSimulationMode |
554 |
|
- extended grdchk package accordingly |
555 |
|
o added tangent linear setup in verification/carbon/code_ftl |
556 |
|
o added adjoint setup in verification/front_relax/code_ad |
557 |
|
|
558 |
|
checkpoint46e_post |
559 |
|
o Added new equation of state -> MDJWF |
560 |
|
- EOS of McDougall et al., 2002, JAOT, submitted |
561 |
|
- caveat: the equation of state is only valid for a smaller (more |
562 |
|
realistic?) range of values than JMD95P/Z and UNESCO |
563 |
|
- added masks to the calculation of pressure in store_pressure |
564 |
|
- added more check values for density in check_eos (ini_eos.F), some of |
565 |
|
the old check values are out of the range of the MDJWF-eos, so don't |
566 |
|
expect perfect matches for those |
567 |
|
checkpoint46e_pre |
568 |
|
|
569 |
|
checkpoint46d_post |
570 |
|
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
571 |
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
572 |
|
case of pressure coordinates. eosType='JMD95Z' in |
573 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
574 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
575 |
|
in find_alpha/beta. |
576 |
|
checkpoint46d_pre |
577 |
|
|
578 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
579 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
580 |
|
|
581 |
|
checkpoint46c_post |
582 |
|
o Changes necessary for ocean in p-coordinates |
583 |
|
- Added new buoyancy relation = 'OCEANICP' |
584 |
|
- Added new parameters = gravitySign (this used to be contained inside |
585 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
586 |
|
X GM/Redi is not compatible (yet) |
587 |
|
X bottom drag and no-slip need to be debugged. |
588 |
|
checkpoint46c_pre |
589 |
|
|
590 |
|
checkpoint46b_post |
591 |
|
o Added new equation of state -> JMD95Z and JMD95P |
592 |
|
- EOS of Jackett and McDougall, 1995, JAOT |
593 |
|
- moved all EOS parameters into EOS.h |
594 |
|
- new routines ini_eos.F, store_pressure.F |
595 |
|
o Added UNESCO EOS, but not recommended because it requires |
596 |
|
in-situ temperature (see JMD95) |
597 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
598 |
|
unesco.f to be used with POLY3 |
599 |
|
checkpoint46b_pre |
600 |
|
|
601 |
|
checkpoint46a_post |
602 |
|
o Added (atmospheric) pressure loading |
603 |
|
- new field in FFIELDS.h, etc... |
604 |
|
- new cpp flag ATMOSPHERIC_LOADING |
605 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
606 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
607 |
|
checkpoint46a_pre |
608 |
|
|
609 |
|
checkpoint46 |
610 |
|
further merges from release1_p5 |
611 |
|
o new ctrl package |
612 |
|
- adopted from ECCO environment to enable optimization |
613 |
|
- added Eliassen Palm fluxes to controls |
614 |
|
o added Eliassen Palm flux controls to gradient check package |
615 |
|
o cost package |
616 |
|
- Compatible with new ctrl package |
617 |
|
- added Eliassen Palm cost hooks |
618 |
|
- modif's of existing cost functions |
619 |
|
o Adjoint-related bug fixes in kpp: |
620 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
621 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
622 |
|
o autodiff package |
623 |
|
- flow directives: |
624 |
|
+ new for S/R do_the_model_io |
625 |
|
+ enhanced for S/R checkpoint |
626 |
|
+ new gmredi.flow |
627 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
628 |
|
disable adcommon.h/g_common.h by default. |
629 |
|
- fixed problem for adjoint of global_max |
630 |
|
o modified verification/carbon/ |
631 |
|
o New setup for adjoint of global_ocean |
632 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
633 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
634 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
635 |
|
|
636 |
|
checkpoint45d_post |
637 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
638 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
639 |
|
(affects plume_on_slope "cg2d" output) |
640 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
641 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
642 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
643 |
|
o change phiMin in exp1 (to agree with documentation) |
644 |
|
o add new flags: |
645 |
|
- T,S forcing inside/outside Adams-Bashforth |
646 |
|
- turn off temp,salt advection and/or forcing |
647 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
648 |
|
o monitor: change definition of KE to check conservation of Energy |
649 |
|
|
650 |
|
checkpoint45c_post |
651 |
|
o Removed f90 comments ("!") |
652 |
|
o Modified initialisations to enable exf package for MITgcm |
653 |
|
(without invoking ECCO_PACKAGE). |
654 |
|
o modifications to gradient check package (Martin Losch) |
655 |
|
- enable centered differences |
656 |
|
- modified format of standard output |
657 |
|
|
658 |
|
checkpoint45b_post |
659 |
|
o cleaned exchange calls in cg2d |
660 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
661 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
662 |
|
to configure barotropic setup (Martin Losch) |
663 |
|
o moved some initialisations within bi,bj loop in dynamics |
664 |
|
(TAF flow dependency) |
665 |
|
o in initialise_varia, moved call packages_init_variables |
666 |
|
before convective_adjustment_init |
667 |
|
(corresponding adjustment of TAF tape initialisation). |
668 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
669 |
|
|
670 |
|
checkpoint45a_post |
671 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
672 |
|
o specific exchange for X-slice domain (case Ny=1) |
673 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
674 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
675 |
|
|
676 |
|
checkpoint44h_post = checkpoint45 |
677 |
|
o Fix to restore differentiability: |
678 |
|
place at which packages_init_variables is called in |
679 |
|
initialise_varia is crucial for reverse control flow. |
680 |
|
o modifications in GMRedi to enable stable adjoint |
681 |
|
(corresponding modif's in thermodynamics, dynamics) |
682 |
|
o added missing hook for sponge layer code in external_forcing |
683 |
|
o modified test cost functions |
684 |
|
o storing in gad_advection (plus removal of write(0,*)! |
685 |
|
o missing headers TR1.h added in convective_adjustment routines |
686 |
|
o errorMessageUnit set non-equal zero in eeboot |
687 |
|
(conflict on some platforms, e.g. IBM SP3) |
688 |
|
o modified carbon verif. |
689 |
|
|
690 |
|
checkpoint44h_pre |
691 |
|
o vertical grid option: allow to put the Interface at the middle between |
692 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
693 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
694 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
695 |
|
|
696 |
|
checkpoint44g_post |
697 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
698 |
|
results) ; ifdef missing in thermodynamics.F |
699 |
|
|
700 |
|
checkpoint44f_pre,checkpoint44f_post |
701 |
|
o added PTRACERS package |
702 |
|
This allows an arbitrary number of passive tracers to be integrated |
703 |
|
forward simultaneously with the dynamicaly model. |
704 |
|
+ Implemented so far: |
705 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
706 |
|
- I/O and checkpointing |
707 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
708 |
|
+ Not implemented so far: |
709 |
|
- KPP |
710 |
|
- OBCS |
711 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
712 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
713 |
|
line in data.pkg. |
714 |
|
+ This package is disabled by default since it increases storage. |
715 |
|
|
716 |
|
|
717 |
|
o testscript: added -cleanup option |
718 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
719 |
|
b) enable to filter 2D fields. |
720 |
|
|
721 |
|
checkpoint44e_pre,post |
722 |
|
o re-wrote convective adjustment to use pre-calculated weights |
723 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
724 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
725 |
|
Original calls to convect() still in place. |
726 |
|
|
727 |
|
chkpt44d_pre,post |
728 |
|
o added missing EXCLUDE_MONITOR flags |
729 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
730 |
|
(incompatible typ in MIN/MAX expressions caused problems |
731 |
|
on IBM SP3) |
732 |
|
o in genmake added variable MAKEDEPEND |
733 |
|
plus resetting for case SunOS |
734 |
|
o added timer_stats.c routine for IBM SP3 |
735 |
|
o removed variables in dynamics |
736 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
737 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
738 |
|
|
739 |
|
o real fresh water flux implemented with non-linear free-surface. |
740 |
|
|
741 |
|
chkpt44c_pre,post |
742 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
743 |
|
USE_NATURAL_BCS in solve_for_P); |
744 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
745 |
|
|
746 |
|
checkpoint44b_pre/_post |
747 |
|
o merge of relevant stuff from the ecco-branch: |
748 |
|
- genmake: removed $S64 overwrite for case SunOS |
749 |
|
- pkg/exf: update and corrections for field swapping and obcs |
750 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
751 |
|
harmonized between ECCO and MITgcm |
752 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
753 |
|
updated checkpointing_lev... lists for obcs |
754 |
|
- model/src: minor changes in forward_step, plot_field |
755 |
|
added directive for divided adjoint in the_main_loop |
756 |
|
- pkg/mdsio: added mdsio_gl_slice |
757 |
|
|
758 |
|
o check parameters & config (chkpt44a_pre,post) |
759 |
|
o OBC and NonLin_FrSurf. |
760 |
|
|
761 |
|
checkpoint44 |
762 |
|
o fix bug in mom_vi_del2uv |
763 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
764 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
765 |
|
o update AIM experiments (NCEP input files) |
766 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
767 |
|
o added some stuff for AD |
768 |
|
|
769 |
|
checkpoint43 |
770 |
|
o added two new advection tests |
771 |
|
o added global 4x4 degree ocean test |
772 |
|
o added test of H&S94 with free surface on cube |
773 |
|
o some final mods for gradient check, adjoint,... |
774 |
|
|
775 |
|
checkpoint42 |
776 |
|
Fixed AD-related problems: |
777 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
778 |
|
(mainly thermodynamics.F) |
779 |
|
o New store directives for multi-dim. advection schemes |
780 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
781 |
|
* new common block and key passkey |
782 |
|
(mainly gad_advection.F) |
783 |
|
o Modified store directives for split of dynamics/thermodynamics |
784 |
|
for the case ALLOW_KPP |
785 |
|
o Cleaned argument list for timestep_tracer.F |
786 |
|
|
787 |
|
checkpoint41 |
788 |
|
o re-formatted/added comments in prologues of key subroutines |
789 |
|
to work with protex |
790 |
|
|
791 |
|
checkpoint40 |
792 |
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
793 |
|
o added FLT (floats) package from Arne along with demo. experiment |
794 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
795 |
|
implementation of forward-in-time forcing terms |
796 |
|
o more mods for non-linear free-surface including new variable |
797 |
|
o modified multi-dim method to work on cube |
798 |
|
o bug fix in KPP (from DM) |
799 |
|
|
800 |
|
checkpoint40pre9 |
801 |
|
o added DST advection schemes |
802 |
|
o fix MPI bug on SGI's |
803 |
|
o modifications for non-linear free-surface |
804 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
805 |
|
o added tension/strain form of stress tensor |
806 |
|
o changes to commenting of arguments for TAF/TAMC |
807 |
|
o added/updated many matlab scripts |
808 |
|
o added multi-dimensional advection method for tracers |
809 |
|
|
810 |
|
checkpoint40pre8 |
811 |
|
o new package rw/ |
812 |
|
Added method for dumping intermediate local arrays: |
813 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
814 |
|
bi,bj loop |
815 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
816 |
|
arrays |
817 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
818 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
819 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
820 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
821 |
|
control flux-form versus vector invariant code. |
822 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
823 |
|
or genmake -DISABLE ... |
824 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
825 |
|
(additional storing is now needed for case vecinv; |
826 |
|
currently nothing implemented to switch this storing off |
827 |
|
in case fluxform is used since no CPP flag available). |
828 |
|
|
829 |
|
checkpoint40pre7 |
830 |
|
o bug fix in dynamics.F |
831 |
|
calc_viscosity called before k=1,Nr loop. |
832 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
833 |
|
o cleaned initialisations in ctrl_map_ini |
834 |
|
related to TAF |
835 |
|
|
836 |
|
checkpoint40pre6 |
837 |
|
o split dynamics into thermodynamics & dynamics |
838 |
|
o corresponding split of calc_diffusivity into |
839 |
|
calc_diffusivity, calc_viscosity |
840 |
|
(kpp_calc_diff, kpp_calc_visc). |
841 |
|
o Added diffkr, kapgm to control variables |
842 |
|
o bug fix in gmredi_slope_limit for ldd97 |
843 |
|
|
844 |
|
checkpoint40pre5 |
845 |
|
o proper initialization of Adams-Bashforth time stepping |
846 |
|
+ uses forward step for very first step of model (iter=0) |
847 |
|
o re-generated *all* output since almost all output is modified by this |
848 |
|
change (sorry but we've been putting this one off for about 2 years) |
849 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
850 |
|
*not* regenerated since they are already out of date and I don't |
851 |
|
want to create the impression that they are suddenly working. |
852 |
|
o removed KAP stuff for DEC's |
853 |
|
o modified/added many .cvsignore files in */code and */input |
854 |
|
o added new expt "solid-body.cs-32x32x1" |
855 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
856 |
|
is not necessarily any better than the current one... |
857 |
|
|
858 |
|
checkpoint40pre4 |
859 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
860 |
|
calc_common_factors which are crucial for TAF. |
861 |
|
o extended iMin,jMin range for calc_common_factors, |
862 |
|
calc_diffusivity |
863 |
|
o added option ALLOW_PASSIVE_TRACER |
864 |
|
o a few minor updates and fixes |
865 |
|
|
866 |
|
checkpoint40pre3 |
867 |
|
o created calc_gtr1.F for gad package |
868 |
|
o split the_main_loop and re-introduced forward_step |
869 |
|
o some recomputations of nIter0 for TAMC |
870 |
|
|
871 |
|
checkpoint40pre2 |
872 |
|
o Updated to latest branch of AJA, JMC |
873 |
|
o Added gradient check package |
874 |
|
o Added routines for passive tracer handling |
875 |
|
o Added carbon sequestration sensitivity experiment |
876 |
|
|
877 |
|
checkpoint39 |
878 |
|
o Modifications and fixes to support TAMC |
879 |
|
(mainly missing or wrong directives) |
880 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
881 |
|
in addummy_in_stepping |
882 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
883 |
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
884 |
|
o Included following packages: |
885 |
|
cal: calendar |
886 |
|
exf: external forcing |
887 |
|
ecco: essential routines to control use of cal, exf |
888 |
|
(NB: this is not the full ECCO environment) |
889 |
|
o disabled some packages by default in genmake |
890 |
|
|
891 |
|
checkpoint38 |
892 |
|
o see notes_c37_adj.txt |
893 |
|
o corrected wrong layer index in external_forcing_t |
894 |
|
o replaced the_main_loop/forward_step by the_main_loop |
895 |
|
o removed forceoutput from write_state |
896 |
|
(replaced criteria for initial/final state) |
897 |
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
898 |
|
|
899 |
|
checkpoint37 |
900 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
901 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
902 |
|
used unless genmake -disable=mdsio) |
903 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
904 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
905 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
906 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
907 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
908 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
909 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
910 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
911 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
912 |
|
and after) unless activating 2 commented lines in initialise-varia. |
913 |
|
o Non-Hydrostatic pickup file Pb fixed. |
914 |
|
o bug with Rigid-lid version (since c35) fixed. |
915 |
|
|
916 |
|
checkpoint36 |
917 |
|
o implement Crank-Nickelson barotropic time-stepping |
918 |
|
o recover Time-Average diagnostics |
919 |
|
o fix Pb in checkpoint (PR#19) |
920 |
|
o AIM become a standard package ; clean unused CPP_kees |
921 |
|
|
922 |
|
checkpoint35 |
923 |
|
o subtantial rewrite of dynamics.f |
924 |
|
o allows staggered time-stepping |
925 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
926 |
|
o added bottom drag (linear + quadratic) |
927 |
|
|
928 |
|
checkpoint34 |
929 |
|
o Modified exchange routines for correct reverse simulation. |
930 |
|
o Added verification output to comply with bug fix in impldiff.F |
931 |
|
as of c33 (exp2, natl_box). |
932 |
|
o Corrected store directives in dynamics.F |
933 |
|
o Corrected array boundaries in impldiff.F |
934 |
|
o Corrected array dimensions in gmredi. |
935 |
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
936 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
937 |
|
o Added mdsio_gl.F for ECCO purposes. |
938 |
|
|
939 |
|
checkpoint33 |
940 |
|
o Fixed bug in lower BC in impldiff.F |
941 |
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
942 |
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
943 |
|
- Removed verification/natl_box/code/external_fields_scale.F |
944 |
|
(did not differ from that in model/src) |
945 |
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
946 |
|
(see FFIELDS.h for description) |
947 |
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
948 |
|
kpp_calc.F and kpp_transport_t.F |
949 |
|
- Removed model/src/external_fields_scale.F and calls to it |
950 |
|
- verification/natl_box uses flux data with "atmospheric" sign so |
951 |
|
a special version of external_fields_load.F is used to |
952 |
|
change the data as it's read in. This way, the arrays |
953 |
|
have the right units and signs at all times tha a user could |
954 |
|
possibly use them. |
955 |
|
o Corrected genmake to delete a temporary file during configuration |
956 |
|
|
957 |
|
checkpoint32 |
958 |
|
o Scaling of forcing fields moved from external_forcing.F to |
959 |
|
external_fields_scale.F, called directly after loading fields. |
960 |
|
o Surface relaxation terms added to surface tendency fields in |
961 |
|
extra subroutine. |
962 |
|
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
963 |
|
fields. |
964 |
|
o Changes in GMRedi to comply with packaging structure. |
965 |
|
o Modifications and bug fixes in KPP package. |
966 |
|
o Verification experiment for KPP added (verification/nat_box/) |
967 |
|
|
968 |
|
checkpoint31 |
969 |
|
o Packages interface brought in line with defined standard |
970 |
|
-> new routines packages_...F |
971 |
|
-> changes in initialise_fixed.F, initialise_varia.F |
972 |
|
-> enables initialisation interface for ECCO package |
973 |
|
o Rescaling of external forcing fields immediately after read |
974 |
|
(removed from external_forcing.F) |
975 |
|
-> new: surface_fields_scale.F |
976 |
|
-> affects ini_foorcing.F, external_fields_load.F |
977 |
|
o Computation of surface tendencies before tendency updates. |
978 |
|
-> new: external_forcing_surf.F |
979 |
|
o Change of variable names useGMRedi, useKPP, useECCO |
980 |
|
o Further changes in dynamics.F, impldiff.F for TAMC |
981 |
|
o Tested for experiments 0, 2, 4. |
982 |
|
- not yet tested for GMRedi. |
983 |
|
- not yet tested for KPP. |
984 |
|
|
985 |
|
checkpoint30 |
986 |
|
o Updates for OBCs |
987 |
|
o New experiment for test OBCs (internal_wave) |
988 |
|
o New output.txt in verification/exp4/results/ |
989 |
|
o Updates for KPP: calculation of viscosity corrected, new variables |
990 |
|
kpp_dumpFreq and kpp_taveFreq |
991 |
|
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
992 |
|
and entry for T90 in genmake |
993 |
|
|
994 |
|
checkpoint29 |
995 |
|
o packaged KPP and GM/Redi |
996 |
|
|
997 |
|
checkpoint28 |
998 |
|
o Corrected initialization of hFacMin for difference vertical coordinates |
999 |
|
o Modified calculation of partial cell thickness to more robust algorithm |
1000 |
|
o config_summary.F: replaced write_1D_... by write_0D_... |
1001 |
|
read_write.F: added subroutines write_0D_... |
1002 |
|
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
1003 |
|
included some initialisations required for TAMC. |
1004 |
|
o routine calc_isoslopes: modified sqrt computation to make it |
1005 |
|
differentiable for zero argument. |
1006 |
|
o routines dynamics, impldiff: |
1007 |
|
included store directives and tape key computations required for TAMC. |
1008 |
|
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
1009 |
|
|
1010 |
|
checkpoint27 |
1011 |
|
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
1012 |
|
formulation works properly with variable resolution. |
1013 |
|
o restructured the calling tree between the_model_main() and dynamics() |
1014 |
|
o split initialise() into initialise_fixed() and initialise_varia() |
1015 |
|
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
1016 |
|
in new routine ini_psurf() |
1017 |
|
|
1018 |
|
checkpoint26 |
1019 |
|
o moved some #ifdef in optional routines to encompass everything |
1020 |
|
except the argument declarations. This was using up some memory. |
1021 |
|
o fixed macros like _ADT to work with both versions of Linux cpp |
1022 |
|
o cleaned up some unused and uninitialized variables |
1023 |
|
(helps when debugging with strict compile options) |
1024 |
|
o split up CPP_EEOPTIONS.h into options and macros |
1025 |
|
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
1026 |
|
o patch for 2 processor JAM mode |
1027 |
|
|
1028 |
|
checkpoint25 |
1029 |
|
o updates for OBCs and NH |
1030 |
|
o dramatically reduced memory usage |
1031 |
|
o added "JAM" routines for use on Artic network |
1032 |
|
o parameterization of convection by implicit vertical diffusion |
1033 |
|
o added a diagnostic of convective index |
1034 |
|
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
1035 |
|
(this is was partly for OBCs and NH but also in anticipation of |
1036 |
|
an explicit free-surface option) |
1037 |
|
o initial state input files for U and V |
1038 |
|
|
1039 |
|
checkpoint24 |
1040 |
|
o Removed some spurious "REAL"s |
1041 |
|
o Updated KPP to latest version from JPL |
1042 |
|
o Added a COS(latitude) in horizontal viscosity |
1043 |
|
|
1044 |
|
checkpoint23 |
1045 |
|
o Added del^4 diffusion for salt and temperature |
1046 |
|
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
1047 |
|
|
1048 |
|
checkpoint22 |
1049 |
|
o Made many small changes: implicit none, format(i5), etc... |
1050 |
|
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
1051 |
|
|
1052 |
|
checkpoint21 |
1053 |
|
o Introduced new I/O package that supports direct-access records (mdsio.F) |
1054 |
|
o Split-up mid-level I/O routines |
1055 |
|
o Updated input data for experiments 0,1,2,4 and 5 |
1056 |
|
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
1057 |
|
|
1058 |
|
checkpoint20 |
1059 |
|
o Tidied up open-boundaries some more |
1060 |
|
o Added non-hydrostatic code |
1061 |
|
o Fixed some input data |
1062 |
|
o Modified MPI start-up to work in "coupled" context. |
1063 |
|
|
1064 |
|
checkpoint19 |
1065 |
|
o Tidied up directory structure for verification experiments. |
1066 |
|
o Added new code for open boundaries. |
1067 |
|
o Corrected advective terms near boundaries. |
1068 |
|
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
1069 |
|
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
1070 |
|
o Split default parameters out of ini_parms.F into set_defaults.F. |
1071 |
|
|
1072 |
|
checkpoint18 |
1073 |
|
o Further changes for optional code generation with |
1074 |
|
CPP - ugh! |
1075 |
|
|
1076 |
|
checkpoint17 |
1077 |
|
o Beginning to incorporating modularity |
1078 |
|
for supporting atmos. and ocean configs. |
1079 |
|
o Small changes for TAMC complinace |
1080 |
|
o New ultra simple test case. Barotropic box |
1081 |
|
configuration "exp0". |
1082 |
|
|
1083 |
|
checkpoint16 |
1084 |
|
o Minor changes to exchange routines to support |
1085 |
|
accumulation in reverse mode. Adjoint of an |
1086 |
|
assignment is an addition. |
1087 |
|
o Changes to support compilation by TAMC (LR(1) |
1088 |
|
syntax) and by g77 under Linux ( 72 character |
1089 |
|
limit ). |
1090 |
|
|
1091 |
|
checkpoint15 |
1092 |
|
Rewrote exchange routines to allow |
1093 |
|
o General tile <-> tile connectivity. |
1094 |
|
o TAMC reverse mode flag ( is this really needed? ) |
1095 |
|
o Variable width overlap and exchange region widths. |
1096 |
|
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
1097 |
|
shmput/shmget, VIA, SYSV shmem and every other cool |
1098 |
|
communication method. |
1099 |
|
|
1100 |
|
checkpoint14 |
1101 |
|
Consistent isomorphism chages made. These allow dynamical core |
1102 |
|
to support both pressure and meters as a vertical coordinate. |
1103 |
|
|
1104 |
|
checkpoint13 |
1105 |
|
Release which corrects global_max problem and a couple |
1106 |
|
of KGM time-averaging diagnostic errors. Also contains |
1107 |
|
a double-gyre experiment setup as well as the baseline |
1108 |
|
4 degree global template. The double gyre template is |
1109 |
|
organised to allow it to be applied automatically to |
1110 |
|
the baseline configuration. |
1111 |
|
|
1112 |
|
branch-point-rdot |
1113 |
|
A few tidy-ups have been made bt the real point of this |
1114 |
|
check-point (excuse the pun) is to allow a branch to be |
1115 |
|
made for the purposes of adding the rDot alterations. |
1116 |
|
I don't want to commit the rDot to the main-trunk until |
1117 |
|
we've actually tested it... |
1118 |
|
|
1119 |
|
checkpoint12 |
1120 |
|
Tidy up and added generic genmake script (formerly |
1121 |
|
configure script). |
1122 |
|
Released to testers. |
1123 |
|
|
1124 |
|
checkpoint11 |
1125 |
|
Re-arranged initialise() and introduced ini_vertical_grid() |
1126 |
|
and ini_masks_etc(). |
1127 |
|
|
1128 |
|
checkpoint10 |
1129 |
|
Introduced the configure script. |
1130 |
|
Separated out the diags package. |
1131 |
|
Added template for writing time-averages of tile/intermediate quantities. |
1132 |
|
Updated SIZE.h in exp2 and made the data big-endian. |
1133 |
|
|
1134 |
|
checkpoint9 |
1135 |
|
MPI fix. Filename changes (meta/data). salbin*y stuff. |
1136 |
|
General tidy-up. |
1137 |
|
SST.bin SSS.bin added to verification/exp2 |
1138 |
|
|
1139 |
|
checkpoint8 |
1140 |
|
Inludes time-dependant forcing and time-averaging. |
1141 |
|
Works at 4x4 and 2.8125x2.8125 global |
1142 |
|
|
1143 |
|
checkpoint7-4degree-ref |
1144 |
|
Branch from checkpoint7. Released for application to |
1145 |
|
global modeling and general modeling - process studies, regional |
1146 |
|
model etc.. |
1147 |
|
Configured for verification/exp2 - 4 degree global, two process. |
1148 |
|
|
1149 |
checkpoint7 |
checkpoint7 |
1150 |
Created by cnh |
Created by cnh |
1151 |
Simple 4 degree global simulation |
Simple 4 degree global simulation |