3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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|
6 |
|
o mnc-ifying the seaice package |
7 |
|
o introduced an alternative length scale calculation for use in the limiting |
8 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
9 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
10 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
11 |
|
as well as grad(vort3). Made it compatible with both approximate form |
12 |
|
for the cubed sphere and full form of these gradients. Added flag |
13 |
|
useFullLeith to select between approximate and full form. |
14 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
15 |
|
update output.txt of exp. fizhi-gridalt-hs |
16 |
|
o change port_rand funtion to allow to set the seed. |
17 |
|
o fix obscure MNC bug involving conversion between reals and integers |
18 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
19 |
|
new version is now more standards-compliant |
20 |
|
|
21 |
|
checkpoint57e_post |
22 |
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o Adding eddy stress controls a la Ferreira et al. |
23 |
|
checkpoint57e_pre |
24 |
|
|
25 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
26 |
|
update output.txt of exp. fizhi-gridalt-hs |
27 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
28 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
29 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
30 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
31 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
32 |
|
months and years. Requires pkg/cal. |
33 |
|
o diagnostics: add pickup functionality |
34 |
|
- off by default for backwards compatibility |
35 |
|
- current version only uses MDSIO -- MNC will be added |
36 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
37 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
38 |
|
|
39 |
|
checkpoint57d_post |
40 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
41 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
42 |
|
output from the diagnostics package |
43 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
44 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
45 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
46 |
|
o add coordinate variables to the MNC output from the diagnostics package |
47 |
|
o change MNC-flags default value: true when useMNC=TRUE |
48 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
49 |
|
the ability (off by default) to read the grid information using MNC |
50 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
51 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
52 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
53 |
|
at the end). |
54 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
55 |
|
new test for AIM with thSIce + slab-ocean |
56 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
57 |
|
o move state variable diagnostics to the beginning of the time step ; |
58 |
|
(note: still needs some work specially for snap-shot diagnostics) |
59 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
60 |
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|
61 |
|
checkpoint57c_post |
62 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
63 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
64 |
|
checkpoint57c_pre |
65 |
|
|
66 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
67 |
|
update output.txt of exp. global_ocean.90x40x15 |
68 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
69 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
70 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
71 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
72 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
73 |
|
o improvements for the MNC output from DIAGNOSTICS: |
74 |
|
- correct handling of the unlimitied dimension |
75 |
|
- all dims now have associated coordinate variables |
76 |
|
- variables located at U, V, and Corner ("Z") points are now written |
77 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
78 |
|
*all* data points are output |
79 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
80 |
|
o added pkg/seaice/seaice_monitor.F |
81 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
82 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
83 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
84 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
85 |
|
spurious negative numbers for precipitation and humidity. Will cause |
86 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
87 |
|
o pkg/ctrl/ |
88 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
89 |
|
May be enabled via doPackDiag |
90 |
|
* introduce z-scaling of |
91 |
|
+ gradient (doZscalePack) and |
92 |
|
+ control (doZscaleUnpack) |
93 |
|
o pkg/mdsio/ |
94 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
95 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
96 |
|
|
97 |
|
checkpoint57b_post |
98 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
99 |
|
o fix MNC coordinate variables so that they now contain per-face index |
100 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
101 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
102 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
103 |
|
o Implement instantaneous output within pkg diagnostics: |
104 |
|
setting a negative frequency in data.diagnostics produces |
105 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
106 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
107 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
108 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
109 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
110 |
|
becomes the coordinate variable for the 'T' dimension |
111 |
|
o add CF-style coordinate variables to MNC |
112 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
113 |
|
missing along the T axis but otherwise it works! |
114 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
115 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
116 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
117 |
|
this is based directly on what the model compute, so that the content of |
118 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
119 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
120 |
|
o clean up build options files for SunOS, in particular |
121 |
|
- remove -traditional from xmakedepend |
122 |
|
- change -xarch=v9 to -xarch=native for f77 |
123 |
|
- restore use of make (not gmake) |
124 |
|
- add CC=gcc if using g77 |
125 |
|
o changes per discussion of AM, JMC, & EH3 today: |
126 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
127 |
|
creating proper CF-style coordinate variables and in recognition |
128 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
129 |
|
the grid files into any of the other NetCDF files |
130 |
|
- *always* output grid variables with MDSIO (this will eventually be |
131 |
|
changed) |
132 |
|
- output MNC grid file if useMNC is true |
133 |
|
o every instance of _END_MASTER() has been found and replaced with |
134 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
135 |
|
preprocessors |
136 |
|
o re-arrange diagnostics pkg initialisation: |
137 |
|
- allow each package to extend the available diagnostics list |
138 |
|
- add some checking and fix small problems (multi-threaded, ...) |
139 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
140 |
|
look through the short list of active diag. (instead of the long list) |
141 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
142 |
|
|
143 |
|
checkpoint57a_post |
144 |
|
o this set of changes restores TAMC compatibility |
145 |
|
tested for global_ocean.90x40x15 adjoint on trough |
146 |
|
(what a pain) |
147 |
|
|
148 |
|
checkpoint57a_pre |
149 |
|
o some modifs in tools/build_options for sunos |
150 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
151 |
|
|
152 |
|
checkpoint57 |
153 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
154 |
|
- new parameter viscA4W (defaults to viscA4) |
155 |
|
- affects only non-hydrostatic code |
156 |
|
- to be done: no-slip lateral boundary conditions |
157 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
158 |
|
o implement Implicit Vertical advection for pTracers |
159 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
160 |
|
(implemented also for implicit vertical diffusion & advection) |
161 |
|
o OBCS: extend application of tracer open boundary conditions |
162 |
|
to a strip beyond the boundary of width Olx/Oly |
163 |
|
o add call monitor to TAF set of required calls (flow directives) |
164 |
|
and include in natl_box_adjoint |
165 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
166 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
167 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
168 |
|
(theta2, salt2 in ecco_cost_weights) |
169 |
|
|
170 |
|
checkpoint56c_post |
171 |
|
o OBCS as control variables |
172 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
173 |
|
- remove balance of obcs controls from default |
174 |
|
- fix index bug nobcs in ctrl_init |
175 |
|
- fix dummy fields filen in ctrl_pack |
176 |
|
- add dummy weights for obcs |
177 |
|
o lsopt: comment out fort.94 output |
178 |
|
o optim: |
179 |
|
- remove unnecessary header files |
180 |
|
- adjusted namelists |
181 |
|
- add xerbla.F to Makefile |
182 |
|
o exf: |
183 |
|
- multiple modifications of exf_check_range |
184 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
185 |
|
o mdsio: |
186 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
187 |
|
|
188 |
|
checkpoint56b_post |
189 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
190 |
|
is called from DO_THE_MODEL_IO |
191 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
192 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
193 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
194 |
|
o add another verification experiment that tests both the cfc-pkg and |
195 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
196 |
|
reactive tendencies treated inline with regular timestepping |
197 |
|
o testreport previously did a lousy job of comparing small numbers, so |
198 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
199 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
200 |
|
testreport. |
201 |
|
o ptracers_monitor: bug fix for MPI |
202 |
|
|
203 |
|
checkpoint56a_post |
204 |
|
o GCHEM: finish reorganizating the package |
205 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
206 |
|
(introduces another 3D-array for each passive tracer, but only if |
207 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
208 |
|
gchemTendency is not needed because the timestep is done separately) |
209 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
210 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
211 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
212 |
|
so clear to me how that should be done in a general way. |
213 |
|
o CFC: improve formatting of output in CFC_ATMOS |
214 |
|
o PTRACERS: |
215 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
216 |
|
that ALL experiments with ptracers enable can be checked. This makes |
217 |
|
GCHEM_MONITOR obsolete. |
218 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
219 |
|
monitorFreq |
220 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
221 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
222 |
|
o exf_check_range: |
223 |
|
* default changed to .TRUE. |
224 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
225 |
|
* STOP in exf_check_range if 'out of range' |
226 |
|
* range chosen generous to allow for potential extema |
227 |
|
TBD: a version with stricter range |
228 |
|
permitted range would be runtime parameters |
229 |
|
o GMredi: |
230 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
231 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
232 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
233 |
|
o GCHEM: |
234 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
235 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
236 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
237 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
238 |
|
this flag is now only visible within GCHEM-pkg routines. |
239 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
240 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
241 |
|
this, the tracer ID iTracer had to be included into the parameter list |
242 |
|
of ptracers_forcing |
243 |
|
- set up forward_step to call gchem_forcing, that will replace |
244 |
|
gchem_forcing_int in ptracers_forcing |
245 |
|
- cleaning up |
246 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
247 |
|
|
248 |
|
checkpoint56 |
249 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
250 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
251 |
|
o ECCO-GODAE |
252 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
253 |
|
* fully merged and updated from SIO code |
254 |
|
windstress sign change affects |
255 |
|
- exf_inscal_[u/v]stress |
256 |
|
- sign of xx_tau[u/v] adjustments |
257 |
|
- signs in cost_scat |
258 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
259 |
|
* natl_box_adjoint updated and compressed |
260 |
|
* 2-level checkpoint switch added |
261 |
|
(tested in EXP. 1 of natl_box_adjoint) |
262 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
263 |
|
o SVD |
264 |
|
* first complete, non-hacked version for SVD calculations |
265 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
266 |
|
performed via direct access files admtlm_vector.it???? |
267 |
|
(via ctrl_[un]pack) |
268 |
|
* optimcycle is used for ARPACK iteration counter |
269 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
270 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
271 |
|
and add linear transforms where necessary |
272 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
273 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
274 |
|
o mdsio: filename info to both stderr, stdout |
275 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
276 |
|
from sign change |
277 |
|
|
278 |
|
checkpoint55j_post |
279 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
280 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
281 |
|
o add consistent build directories and .cvsignore files to verification |
282 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
283 |
|
o make all subroutines 30 or less characters in length for certain older |
284 |
|
compilers to work (a thorough search only turns up two routines in |
285 |
|
pkg/ptracers) |
286 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
287 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
288 |
|
|
289 |
|
checkpoint55i_post |
290 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
291 |
|
3.D if implicit) ; each ptracer uses its own background value. |
292 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
293 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
294 |
|
ITRDA and other clusters without the mpirun "-wd" option |
295 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
296 |
|
configuration |
297 |
|
o give MNC the ability to create additional files rather than |
298 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
299 |
|
- the default is just less than 2GB which is a practical limit |
300 |
|
on many systems |
301 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
302 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
303 |
|
|
304 |
|
checkpoint55h_post |
305 |
|
o add verification test "vermix" |
306 |
|
o remove all the *_ioinc flags and replace with the single global |
307 |
|
outputTypesInclusive flag |
308 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
309 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
310 |
|
o useMNC moved from data.mnc to data.pkg |
311 |
|
|
312 |
|
checkpoint55g_post |
313 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
314 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
315 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
316 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
317 |
|
Works well for global_ocean.90x40x15, |
318 |
|
but recomp. issue remains for carbon |
319 |
|
o Updating adjoint output for natl_box_adjoint after |
320 |
|
pkg/ecco has been modified (see taga c55d_post) |
321 |
|
|
322 |
|
checkpoint55f_post |
323 |
|
o rename to timeave_init_fixed |
324 |
|
|
325 |
|
checkpoint55e_post |
326 |
|
o some delicate re-shuffle of store directives to avoid one |
327 |
|
extra call of do_oceanic_physics |
328 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
329 |
|
checkpoint_lev1_directives.h |
330 |
|
o NB: this may break global_ocean adjoint temporarily, |
331 |
|
but it is clear how to fix it. Will do later, need this now. |
332 |
|
|
333 |
|
checkpoint55d_post |
334 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
335 |
|
o ecco_cost_weights is modified to 1x1 runs |
336 |
|
o modifs to allow observations to be read in as |
337 |
|
single file or yearly files |
338 |
|
o enable to read exf forcing fields as either |
339 |
|
single file or yearly files (flag useExfYearlyFields) |
340 |
|
checkpoint55d_pre |
341 |
|
|
342 |
|
o switch between 2-level and 3-level checkpointing |
343 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
344 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
345 |
|
with the correct (that is, the complete multi-dimensional) set of |
346 |
|
array indicies |
347 |
|
- used in mom_vecinv() to write the diagFreq output |
348 |
|
- tested (demonstrated) in verification/aim.5l_cs |
349 |
|
o further mnc-ification |
350 |
|
- add verification/lab_sea to the list with mnc setups |
351 |
|
- fix undefined mnc v-names in cd_code |
352 |
|
- add kpp to mnc output (both snapshot and timeave) |
353 |
|
o non-hydrostatic code |
354 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
355 |
|
in calc_gw.F |
356 |
|
- defaults to viscAh |
357 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
358 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
359 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
360 |
|
o pkg/cost |
361 |
|
extend simple cost functions to treat time mean quantities |
362 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
363 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
364 |
|
be 2 times larger than the minimum size the advection scheme requires. |
365 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
366 |
|
o GGL90 (Gaspar's TKE mixed layer) |
367 |
|
- add horizontal diffusion of TKE, requires exchanges in |
368 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
369 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
370 |
|
mixing coefficients are computed from a horizontal average of TKE of |
371 |
|
6 points or so. I think that diffusion has a little more physical |
372 |
|
justification. |
373 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
374 |
|
was in vain) |
375 |
|
- mask tke-variable in ggl90_init |
376 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
377 |
|
o fix biharmonic diffusion on CS-grid. |
378 |
|
o more obcs stuff |
379 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
380 |
|
for reading boundary values. This routine is called from |
381 |
|
obcs_prescribe_read |
382 |
|
- updated obcs_check |
383 |
|
- changed sponge layer relaxation parameter units for days to seconds |
384 |
|
- turned off sponge layer by default |
385 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
386 |
|
- fixed about 35 bugs in obcs_external_fields_load |
387 |
|
|
388 |
|
checkpoint55c_post |
389 |
|
o obcs stuff |
390 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
391 |
|
- re-arranged obcs_calc |
392 |
|
- moved exf_getobcs to obcs_prescibe_read |
393 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
394 |
|
and independent of it (executable can contain all). |
395 |
|
- updated obcs_check |
396 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
397 |
|
These may be necessary only if tangential velocities are |
398 |
|
prescribed at OB, not sure, needs testing. |
399 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
400 |
|
which simplifies the calls and passes the ifc check-bounds test |
401 |
|
|
402 |
|
checkpoint55b_post |
403 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
404 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
405 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
406 |
|
affects advect_cs results (for the wrong reason): update output.txt |
407 |
|
o use a more standard discretization for biharmonic viscosity ; |
408 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
409 |
|
affects results of dome set-up: update output.txt |
410 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
411 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
412 |
|
|
413 |
|
checkpoint55a_post |
414 |
|
o merged code to |
415 |
|
* prescribe/read time-dependent open boundaries |
416 |
|
(works in conjunction with exf, cal) |
417 |
|
* sponge layer code for open boundaries |
418 |
|
* each boundary N/S/E/W now has its own CPP option |
419 |
|
(healthy for the adjoint) |
420 |
|
|
421 |
|
checkpoint55 |
422 |
|
o up-to-date adjoint of previous breaks |
423 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
424 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
425 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
426 |
|
- carbon: * remove tr1-related adjoint verification |
427 |
|
* add ptracer as control variable |
428 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
429 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
430 |
|
|
431 |
|
checkpoint54f_post |
432 |
|
o in verification/carbin/ remove experiment related to |
433 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
434 |
|
code_ad/ input_ad/ results_ad |
435 |
|
|
436 |
|
o add two new packages |
437 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
438 |
|
+ subject to optimization (memory) |
439 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
440 |
|
+ subject to reordering (many GOTOs in the original code) |
441 |
|
+ so far opps is called for every (i,j) point, and then operates in |
442 |
|
the vertical; one may want to reorder the scheme in order operate in |
443 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
444 |
|
fields) |
445 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
446 |
|
- all verification tests compile and run with linux_ia32_g77 |
447 |
|
- defaults are compatible with current input files--nothing |
448 |
|
should change if you were not previously using MNC |
449 |
|
- MNC output has been added in numerous places (eg. timeave) |
450 |
|
but there are still a few writes not yet do-able with MNC |
451 |
|
(this is in progress) |
452 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
453 |
|
documentation will soon follow |
454 |
|
- numerous small formatting cleanups for ProTeX |
455 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
456 |
|
|
457 |
|
checkpoint54e_post |
458 |
|
o add two new packages |
459 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
460 |
|
stratification dependent mixing |
461 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
462 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
463 |
|
course), however there is only one diffusivity that is used for both |
464 |
|
temperature and salinity (and passive tracers)ç |
465 |
|
o add offline package |
466 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
467 |
|
provided by Stephanie Dutkiewicz |
468 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
469 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
470 |
|
|
471 |
|
checkpoint54d_post |
472 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
473 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
474 |
|
leading to additional shift by 5 days each year of integration |
475 |
|
(i.e. leading to considerable offset over the years) |
476 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
477 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
478 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
479 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
480 |
|
(external loading & cpl import/export stay in forward_step.F) |
481 |
|
o update coupling interface to work with new staggerTimeStep |
482 |
|
o change MDSIO ptracers_pickup. |
483 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
484 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
485 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
486 |
|
|
487 |
|
checkpoint54c_post |
488 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
489 |
|
this affects (truncation error) output.txt of test-exp: |
490 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
491 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
492 |
|
o change Qnet to always be the net heat flux, (+upward). |
493 |
|
affects (truncation error) output of natl_box exp.: updated |
494 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
495 |
|
o start to test mnc routinely in exp0 |
496 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
497 |
|
|
498 |
|
checkpoint54b_post |
499 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
500 |
|
impressive on Altix and Opteron systems) |
501 |
|
o diagnostics can now write NetCDF files through the mnc package |
502 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
503 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
504 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
505 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
506 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
507 |
|
|
508 |
|
checkpoint54a_post |
509 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
510 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
511 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
512 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
513 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
514 |
|
checkpoint54a_pre |
515 |
|
|
516 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
517 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
518 |
|
|
519 |
|
checkpoint54 |
520 |
|
checkpoint53g_post |
521 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
522 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
523 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
524 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
525 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
526 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
527 |
|
o restore adjointability |
528 |
|
|
529 |
|
checkpoint53f_post |
530 |
|
o modifications that affect AIM experiment results (update output.txt): |
531 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
532 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
533 |
|
o AIM pkg: |
534 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
535 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
536 |
|
|
537 |
|
checkpoint53e_post |
538 |
|
o merged cylindrical coord configuration |
539 |
|
o added rotating_tank experiment |
540 |
|
checkpoint53e_pre |
541 |
|
|
542 |
|
checkpoint53d_post |
543 |
|
o faulks upgraded: re-generate output.txt that have changed: |
544 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
545 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
546 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
547 |
|
o added Sadourny discretization of Coriolis |
548 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
549 |
|
- re-enabled use of omega3 (useAbsVorticity) |
550 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
551 |
|
vector-invariant equations |
552 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
553 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
554 |
|
hopefully without new bugs |
555 |
|
- still to do: biharmonic friction for non-hydrostatic w |
556 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
557 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
558 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
559 |
|
of mom_common/ |
560 |
|
- simple re-arrangement of instructions within computing loop |
561 |
|
checkpoint53d_pre |
562 |
|
|
563 |
|
checkpoint53c_post |
564 |
|
o new version of coupler for AIM+thSIce and Ocean models |
565 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
566 |
|
- land: change Evaporation of snow |
567 |
|
- aim with thSIce: fix bug in snow-precip. |
568 |
|
o changes to calc_gw.F |
569 |
|
- bug fix for w^2 term near the bottom boundary |
570 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
571 |
|
partial/looped cells |
572 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
573 |
|
and plume on slope), change the lateral boundary condition from half slip |
574 |
|
to the value of no_slip_sides |
575 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
576 |
|
o Adjoint of EBM package + verification |
577 |
|
* TLM OK |
578 |
|
* ADM not sufficient accuracy yet (needs further testing) |
579 |
|
|
580 |
|
checkpoint53b_post |
581 |
|
o Commiting new energy balance model to repository |
582 |
|
* package is pkg/ebm |
583 |
|
* verif. is verification/global_ocean_ebm |
584 |
|
* references are in ebm_driver.F |
585 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
586 |
|
C Global thermohaline circulation. Part I: |
587 |
|
C Sensitivity to atmospheric moisture transport. |
588 |
|
C J. Climate 12(1), 71-82 |
589 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
590 |
|
C Global thermohaline circulation. Part II: |
591 |
|
C Sensitivity with interactive transport. |
592 |
|
C J. Climate 12(1), 83-91 |
593 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
594 |
|
C Destabilization of the thermohaline circulation |
595 |
|
C by atmospheric eddy transports. |
596 |
|
C J. Climate 7(12), 1870-1882 |
597 |
|
o Will need long integration testing. |
598 |
|
checkpoint53b_pre |
599 |
|
|
600 |
|
o created pkg/mom_common in preparation for variable viscosity code |
601 |
|
o renamed and split ini_mnc_io |
602 |
|
o pkg/land: only liquid water can diffuse or run-off |
603 |
|
o AIM using land: soil wetness availability account for snow |
604 |
|
o added printMapIncludesZeros to EEPARMS namelist |
605 |
|
|
606 |
|
checkpoint53a_post |
607 |
|
o restore TAMC compatiility for exf_constants.h |
608 |
|
(no usage of _d in .h) |
609 |
|
o Additional storing in KPP in an attempt to fix |
610 |
|
TAMC problem with adjoint of KPP code. |
611 |
|
(no success...) |
612 |
|
Identical code works fine with TAF. |
613 |
|
o Fixed verification/natl_box_adjoint experiments. |
614 |
|
Initial conditions for Experiments 4 and 5 are now |
615 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
616 |
|
and hence gives results closer to that of Experiment 2. |
617 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
618 |
|
|
619 |
|
checkpoint53 |
620 |
|
o stable checkpoint with up to date adjoint |
621 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
622 |
|
this is a code problem or a problem with resetting code for g_ |
623 |
|
variables that is being autogenerated wrong. |
624 |
|
Otherwise: |
625 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
626 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
627 |
|
are both still in chaos following their security messes. |
628 |
|
|
629 |
|
checkpoint52n_post |
630 |
|
o various build (mostly genmake2) changes including: |
631 |
|
- ability to build/run more easily within Cygwin and MacOS X |
632 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
633 |
|
o pkg/seaice modifications |
634 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
635 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
636 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
637 |
|
- changed proxy for geostrophic velocity and updated |
638 |
|
verification/lab_sea/results/* accordingly |
639 |
|
- removed ADI dynamic solver from pkg/seaice |
640 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
641 |
|
they caused a segmentation fault under certain circumstances |
642 |
|
- removed unused field WATR |
643 |
|
o bug fix in exf-package: |
644 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
645 |
|
now reflect that. |
646 |
|
o small fixes in the cal-package: |
647 |
|
- set reference date to first of January for the 'model'-calendar |
648 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
649 |
|
warning |
650 |
|
o small modifications in exf-package to increase flexibility: |
651 |
|
- change climtempfreeze from a constant to a runtime parameter that |
652 |
|
is specified in data.exf_clim (default = -1.9) |
653 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
654 |
|
specified in data.exf |
655 |
|
o fix in pkg/thsice: |
656 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
657 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
658 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
659 |
|
|
660 |
|
checkpoint52m_post |
661 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
662 |
|
this does not change any of the results, because myIter=0 in swfrac always |
663 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
664 |
|
as a default |
665 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
666 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
667 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
668 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
669 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
670 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
671 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
672 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
673 |
|
o monitor package can write to NetCDF files and/or STDOUT |
674 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
675 |
|
o doc/api_reference added |
676 |
|
- a framework for building an API Reference Manual using all |
677 |
|
the "protex" comments embedded in the code |
678 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
679 |
|
o MNC: |
680 |
|
- make myThid the last argument for all subroutines |
681 |
|
- new default for the grid files: NO halos |
682 |
|
- add useMNC and other run-time flags |
683 |
|
- separate per-file-group handling of the unlimited dimension |
684 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
685 |
|
and lookup tables set in initialize_fixed |
686 |
|
- write all MNC output to a freshly-created directory |
687 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
688 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
689 |
|
o Added functionality to grdchk: |
690 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
691 |
|
|
692 |
|
checkpoint52l_post |
693 |
|
o new land formulation: |
694 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
695 |
|
energy conservation. |
696 |
|
b) account for water temperature and for latent heat of freezing |
697 |
|
in all processes (rain, run-off, ground storage) |
698 |
|
c) compute surface and ground temperature implicitly. |
699 |
|
o aim_v23 modification for new land model: |
700 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
701 |
|
to allow implicit computation of land & sea-ice surface temp. |
702 |
|
b) add snow precipitation. |
703 |
|
checkpoint52l_pre |
704 |
|
|
705 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
706 |
|
o fix bug in timeAve (u,vZetatave in common block) |
707 |
|
o no restoring terms under ice for pkg/seaice |
708 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
709 |
|
o bug fix for pkg/seaice pickups |
710 |
|
o change MNC call locations and add coordinate attributes |
711 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
712 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
713 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
714 |
|
o exf: Adding simple range check routine for exf fields after read |
715 |
|
|
716 |
|
checkpoint52k_post |
717 |
|
o removed top-level directory "diags" |
718 |
|
- we migrated these functions to pkg/timeave a long time ago |
719 |
|
o fixed bug introduced in pkg/monitor |
720 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
721 |
|
averaged fields (I/O via cost_averages) |
722 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
723 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
724 |
|
o added initial do_the_model_io to ecco |
725 |
|
o set all ...Freq to zero after cost_final |
726 |
|
taveFreq, dumpFreq, pChkptFreq |
727 |
|
o MAIN and ECCO differentiability restored |
728 |
|
|
729 |
|
checkpoint52j_post |
730 |
|
o fix nchklev in tamc.h for global_ocean... |
731 |
|
o Bringing flow and store directives up-to-date |
732 |
|
o Really weird thing! |
733 |
|
call do_the_model_io from the_main_loop with parameters |
734 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
735 |
|
TAF places a faulty re-call of initialise_varia |
736 |
|
after cost_final call which should not be there! |
737 |
|
checkpoint52j_pre |
738 |
|
|
739 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
740 |
|
error messages |
741 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
742 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
743 |
|
debug output |
744 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
745 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
746 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
747 |
|
o update AIM Equatorial Channel exp: |
748 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
749 |
|
o globalFile now works with exch2 |
750 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
751 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
752 |
|
o limit timeave output for hi-res integrations |
753 |
|
|
754 |
|
checkpoint52i_post |
755 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
756 |
|
o updated the tiling for global_ocean_pressure |
757 |
|
checkpoint52i_pre |
758 |
|
|
759 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
760 |
|
the old pkg/aim). |
761 |
|
|
762 |
|
checkpoint52h_pre |
763 |
|
o shortened offending lines in exch2_send_rx?.template |
764 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
765 |
|
o genmake2: add build & execute test for NetCDF code |
766 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
767 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
768 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
769 |
|
o added temporary hack for sea-ice dynamics on the cube: |
770 |
|
metric terms are ignored and it is assumed that |
771 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
772 |
|
|
773 |
|
checkpoint52f_post |
774 |
|
o added exch2 cube routines to pkg/exch2 |
775 |
|
o modified hs94.cs-32x32x5 to use it |
776 |
|
o added new grid files to hs94.cs-32x32x5 |
777 |
|
checkpoint52f_pre |
778 |
|
|
779 |
|
checkpoint52e_post |
780 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
781 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
782 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
783 |
|
to work with implicit vertical advection and AB ; |
784 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
785 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
786 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
787 |
|
checkpoint52e_pre |
788 |
|
|
789 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
790 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
791 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
792 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
793 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
794 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
795 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
796 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
797 |
|
|
798 |
|
checkpoint52d_post |
799 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
800 |
|
- updated output accordingly |
801 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
802 |
|
random number generator |
803 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
804 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
805 |
|
o changes to permit hi-res, cubed-sphere, configuration |
806 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
807 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
808 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
809 |
|
of surface winds for the cube |
810 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
811 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
812 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
813 |
|
complete with example surface forcing files and matlab scripts to look |
814 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
815 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
816 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
817 |
|
to conform to the common rule. |
818 |
|
o check-in the first version of the coupler + interfaces for multi-components |
819 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
820 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
821 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
822 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
823 |
|
- exchanges between component and coupler is done in forward_step |
824 |
|
o new verification experiment, cpl_aim+ocn: |
825 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
826 |
|
|
827 |
|
checkpoint52d_pre |
828 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
829 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
830 |
|
|
831 |
|
checkpoint52c_post |
832 |
|
o Fixing OPTIONS files for use of exf: |
833 |
|
- ALLOW_ECCO not needed |
834 |
|
- ECCO_CPPOPTIONS.h should not be included from |
835 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
836 |
|
as has been the case in the past |
837 |
|
- All cal/exf related options are currently set in |
838 |
|
single header file. Should remain so until we |
839 |
|
agree on a consistent new policy. |
840 |
|
o Removed all CPP options for cal package. |
841 |
|
cal has no more CPP options. |
842 |
|
o modified STOREs in GAD_ADVECTION |
843 |
|
o corrected key comp. for passkey |
844 |
|
|
845 |
|
checkpoint52b_post |
846 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
847 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
848 |
|
- modify fluxes but do not change theta directly; |
849 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
850 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
851 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
852 |
|
o put back grid & coriolis monitor output. |
853 |
|
checkpoint52b_pre |
854 |
|
|
855 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
856 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
857 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
858 |
|
(need info on NUMBER_OF_PTRACERS) |
859 |
|
o missing PTRACERS headers in some routines |
860 |
|
o default tamc.h in pkg/autodiff supposed to crash |
861 |
|
to ensure proper customization |
862 |
|
|
863 |
|
checkpoint52a_post |
864 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
865 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
866 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
867 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
868 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
869 |
|
- keep the old version of FREEZE for backward compatibility; |
870 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
871 |
|
- corresponding modifs for TAF directives |
872 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
873 |
|
o time-averaged output for pkg/ptracers |
874 |
|
o fix problem with ECCO-related divided adjoint |
875 |
|
snapshot file was missing some ad-variables, |
876 |
|
but no warning issued by TAF |
877 |
|
|
878 |
|
checkpoint52a_pre |
879 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
880 |
|
|
881 |
|
checkpoint52 = ecco_c52_e35 |
882 |
|
o after testing adjoints of checkpoint51u_post |
883 |
|
|
884 |
|
checkpoint51u_post |
885 |
|
o this is the post-merge tag of the ecco-branch |
886 |
|
(needs another clean checkout and re-testing) |
887 |
|
o various natl_box_adjoint configs and results |
888 |
|
but no input fields |
889 |
|
o obcs adjoint not yet merged! |
890 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
891 |
|
o updated/extended some store directives for seaice |
892 |
|
o pkg/ecco now containes ecco-specific part of cost function |
893 |
|
o top level routines the_main_loop, forward_step |
894 |
|
supersede those in model/src/ |
895 |
|
previous input data.cost now in data.ecco |
896 |
|
(new namelist ecco_cost_nml) |
897 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
898 |
|
|
899 |
|
checkpoint51t_post |
900 |
|
o this is the pre-merge tag of the ecco-branch |
901 |
|
|
902 |
|
checkpoint51s_post |
903 |
|
o cleanup: removed various obsolete #define-s |
904 |
|
o pkg/grdchk |
905 |
|
- renamed 'ph-grd 3' to 'grad-res' |
906 |
|
- merged from ecco-branch |
907 |
|
(remaining bug fixes for obcs gradient checks) |
908 |
|
- additional high-precision output for testreport |
909 |
|
(grep for 'precision_grdchk_result') |
910 |
|
|
911 |
|
checkpoint51r_post |
912 |
|
o cleaned up or removed CPP_OPTIONS.h files |
913 |
|
o updated results for some of the tests to reflect the new |
914 |
|
optfiles (-ieee: -O0 instead of -O3) |
915 |
|
|
916 |
|
checkpoint51q_post |
917 |
|
o cd_code: |
918 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
919 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
920 |
|
- separated cd_code part from write_checkpoint |
921 |
|
- updated AD_SOURCE, generated .flow |
922 |
|
- added CD_CODE_VARS.h to the_main_loop |
923 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
924 |
|
o ctrl package totally restructured |
925 |
|
- pack/unpack now optional and decoupled from |
926 |
|
xx_/adxx_ I/O |
927 |
|
- ctrl_pack/unpack cleaned |
928 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
929 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
930 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
931 |
|
|
932 |
|
checkpoint51p_post |
933 |
|
o create initial cd_code package |
934 |
|
- WARNING: the initialization of fields within packages |
935 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
936 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
937 |
|
This seems to be backwards since |
938 |
|
1) its important to initially zero the entire field including |
939 |
|
the "halo" region |
940 |
|
2) zeroing needs to be done *before* reading pickup info |
941 |
|
and the pickup call might or might not happen in any |
942 |
|
particular run |
943 |
|
- this needs an overhaul for R2 |
944 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
945 |
|
o cleanup testreport |
946 |
|
|
947 |
|
checkpoint51o_post |
948 |
|
o bringing AD-related verif's up to date with genmake2 |
949 |
|
- carbon/ |
950 |
|
- global_ocean.90x40x15/ |
951 |
|
- hs.94.1x64x5/ |
952 |
|
- (front_relax/ ) |
953 |
|
o (more) consistent directory structure for AD-related verif.'s |
954 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
955 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
956 |
|
o bug fix in find_alpha.F for MDJWF: |
957 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
958 |
|
change rho -> rho-rhoConst |
959 |
|
- replace call find_rho to find_rhonum |
960 |
|
o initialisation of rFlx extended to full array (required by TAF) |
961 |
|
and shifted to thermodynamics |
962 |
|
o removed PTRACERS.h in ptracers routine |
963 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
964 |
|
o Correcting initialisations for fVerU, fVerV. |
965 |
|
o helping TAF to recognize dependency on kUp for |
966 |
|
fVerU, fVerV |
967 |
|
o Replacing delZ by delR in pkg/ctrl/ |
968 |
|
checkpoint51o_pre |
969 |
|
|
970 |
|
o undid all of cp51 pending some cleanups and discussion |
971 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
972 |
|
it for adjoint/tl #defines |
973 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
974 |
|
o removed tools/genmake since it no longer works |
975 |
|
|
976 |
|
checkpoint51n_post |
977 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
978 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
979 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
980 |
|
- subroutine FREEZE now limits only surface temperature |
981 |
|
(this means new output.txt for global_ocean.90x40x15, |
982 |
|
global_ocean.cs32x15, and global_with_exf) |
983 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
984 |
|
|
985 |
|
checkpoint51n_pre |
986 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
987 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
988 |
|
defines: |
989 |
|
- ALLOW_ADJOINT_RUN |
990 |
|
- ALLOW_TANGENTLINEAR_RUN |
991 |
|
- ALLOW_ECCO_OPTIMIZATION |
992 |
|
|
993 |
|
checkpoint51m_post |
994 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
995 |
|
- added new TAMC/TAF targets to the Makefile |
996 |
|
- various cleanups related to package handling |
997 |
|
- these changes should have no impact on the forward model |
998 |
|
|
999 |
|
checkpoint51l_post |
1000 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
1001 |
|
- faster algorithm for cal_addtime.F |
1002 |
|
- higher precision arithmetic, where needed |
1003 |
|
- pkg/exf *startdate variables changed from calendar date to |
1004 |
|
model integration time |
1005 |
|
|
1006 |
|
checkpoint51l_pre |
1007 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
1008 |
|
o enable to apply restoring on S & T only in a latitude band. |
1009 |
|
o update output (external_forcing_surf modif. change truncation errors) |
1010 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
1011 |
|
|
1012 |
|
checkpoint51k_post |
1013 |
|
o change default to: useNHMTerms=.FALSE. |
1014 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
1015 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
1016 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
1017 |
|
exp1, ideal_2D_oce |
1018 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
1019 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
1020 |
|
o set gravitySign automatically according to the vertical coordinate used |
1021 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
1022 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
1023 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
1024 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
1025 |
|
|
1026 |
|
checkpoint51j_post |
1027 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
1028 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
1029 |
|
o added cubed-sphere case to test cost function |
1030 |
|
o heckpoint_lev?_directives.h now include |
1031 |
|
pkg-specific directives, whenever those are enabled. |
1032 |
|
o Moving pkg-specific flow directives to corresponding pkg |
1033 |
|
Moving pkg-specific differentiation list to corresponding pkg |
1034 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
1035 |
|
---> conventions are |
1036 |
|
- pkg_ad.flow |
1037 |
|
- pkg_ad_diff.list |
1038 |
|
- pkg_ad_check_lev?_dir.h |
1039 |
|
|
1040 |
|
checkpoint51i_post |
1041 |
|
o merge of the branch-genmake2 |
1042 |
|
- knowingly breaks the older genmake |
1043 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
1044 |
|
- new testreport supersedes older testscript |
1045 |
|
o large number of package inclusion and header cleanups |
1046 |
|
checkpoint51i_pre |
1047 |
|
|
1048 |
|
o new output for adjoin of global ocean vector invariant |
1049 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
1050 |
|
o Steph gchem various cleanups |
1051 |
|
|
1052 |
|
checkpoint 51h_pre |
1053 |
|
o fixed some single quotes |
1054 |
|
o modify gchem pkg to be more versatile |
1055 |
|
o modifications to clean up dic pkg |
1056 |
|
o add pkg/cfc |
1057 |
|
|
1058 |
|
checkpoint51g_post |
1059 |
|
o provide links for ARPACK and ADM*TLM |
1060 |
|
o start removing verification/vero/ |
1061 |
|
o update AD-related stuff |
1062 |
|
(in particular some IF-statements in model/src/ routines) |
1063 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
1064 |
|
vector invariant setup |
1065 |
|
|
1066 |
|
checkpoint51f_post |
1067 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
1068 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
1069 |
|
of tracer Green's fucntions for ocean inversion project. |
1070 |
|
|
1071 |
|
checkpoint51f_pre |
1072 |
|
o Added on-the-fly spatial interpolation capability |
1073 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
1074 |
|
- This is a temporary Cartesian-grid hack until |
1075 |
|
the super-duper ESMF coupler becomes available. |
1076 |
|
- See verification/global_with_exf/README for usage example. |
1077 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
1078 |
|
flags and modified pkg/seaice accordingly. |
1079 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
1080 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
1081 |
|
non-local transport term. |
1082 |
|
|
1083 |
|
checkpoint51e_post |
1084 |
|
o pkg/mom_vecinv: |
1085 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
1086 |
|
- add time-ave diagnostic of vorticity advection. |
1087 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
1088 |
|
o atmospheric geopotential: - include water vapor effect; |
1089 |
|
- use p^kappa in p* scaling. |
1090 |
|
o land pkg: read initial state from files. |
1091 |
|
o AIM : add stratospheric drag in the upper level |
1092 |
|
|
1093 |
|
checkpoint51d_post |
1094 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
1095 |
|
(instead of the string length) when the string. char is empty |
1096 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
1097 |
|
o modif's to restore TAMC compatibility |
1098 |
|
- avoid "_d" constructs in PARAMETER declarations |
1099 |
|
- avoid interrupting lines by comment lines |
1100 |
|
o Use cluster local disks for purely local I/O |
1101 |
|
vs. globally visible disks needed for ctrl stuff |
1102 |
|
(merged from ecco-branch) |
1103 |
|
- new active_file_loc... and mdsio_..._loc routines |
1104 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
1105 |
|
|
1106 |
|
checkpoint51c_post |
1107 |
|
o introducing integer flag debugLevel |
1108 |
|
- debLevZero: suppress all output |
1109 |
|
- debLevA: standard |
1110 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
1111 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
1112 |
|
that can be specified at runtime |
1113 |
|
(relevant for cluster I/O to local disk) |
1114 |
|
` |
1115 |
|
>>>checkpoint51b_post |
1116 |
|
adjoint of ptracers |
1117 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
1118 |
|
o extended state in checkpoint_lev?, etc. |
1119 |
|
o alternative ctrl/cost with tr1 or ptracer |
1120 |
|
o new comlev1_bibj_ptracers |
1121 |
|
o new ptracers.flow |
1122 |
|
o made ptracers_forcing same as external_forcing_s |
1123 |
|
o added verification for adjoint with ptracers |
1124 |
|
- adm. grdchk fail so far |
1125 |
|
- tlm. grdchk OK |
1126 |
|
- checked tapelev/comlev recomputations: OK |
1127 |
|
<<<checkpoint51b_pre |
1128 |
|
|
1129 |
|
checkpoint51a_post |
1130 |
|
o added code for biogeochemistry package |
1131 |
|
- new pkgs: dic, gchem |
1132 |
|
- new subroutine in ptracers |
1133 |
|
o modify code for biogeo packages |
1134 |
|
- in model/src and pkg/ptracers |
1135 |
|
|
1136 |
|
checkpoint51 |
1137 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
1138 |
|
- autodiff, ctrl, exf, grdchk, seaice |
1139 |
|
kept separate packages |
1140 |
|
- cost, ecco, obcs |
1141 |
|
o updating verification/internal_wave, verification/lab_sea |
1142 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
1143 |
|
|
1144 |
|
checkpoint50i_post |
1145 |
|
o Preparing next differentiable checkpoint and sync |
1146 |
|
of MAIN vs. ecco-branch |
1147 |
|
- 1st step: this one is differentiable |
1148 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
1149 |
|
from ecco-branch) |
1150 |
|
|
1151 |
|
checkpoint50h_post |
1152 |
|
o new package "land": provide surface BC for AIM. |
1153 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
1154 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
1155 |
|
F.Molteni paper) ; update aim.5l_cs output. |
1156 |
|
o New variable in PARM03 for more flexible pickups |
1157 |
|
o somewhat cleaned package initialisation sequence for |
1158 |
|
ctrl/ cost/ ecco/ in packages_... routines |
1159 |
|
|
1160 |
|
checkpoint50g_post |
1161 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
1162 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
1163 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
1164 |
|
made the default because of faster convergence than ADI |
1165 |
|
|
1166 |
|
checkpoint50f_post |
1167 |
|
o exf totally restructured |
1168 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
1169 |
|
and made sure it's still differentiable |
1170 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
1171 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
1172 |
|
- updated adjoint/makefile and relevant verif. accordingly |
1173 |
|
|
1174 |
|
checkpoint50f_pre |
1175 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
1176 |
|
+ change Evap over land. (update aim.5l_cs output) |
1177 |
|
o added missing .cvsignores and made uniform across expts |
1178 |
|
o changed configuration of tidal_basin_2d expt |
1179 |
|
o added pkg/debug functions for tracing code in fatal crashes |
1180 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
1181 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
1182 |
|
o removed lots of single quotes from comments |
1183 |
|
|
1184 |
|
checkpoint50e_post |
1185 |
|
o make KPP work with PTRACERS |
1186 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
1187 |
|
nearly a copy of kpp_transport_s |
1188 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
1189 |
|
gPtr(of the surface layer) instead |
1190 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
1191 |
|
checkpoint50e_pre |
1192 |
|
|
1193 |
|
checkpoint50d_post |
1194 |
|
o change kpp output from multiple-record state files to single-record state |
1195 |
|
files analogous to write_state.F |
1196 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
1197 |
|
analogous to the cg2d-related output. |
1198 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
1199 |
|
so that writing to internal file fn (with length 512) fails. |
1200 |
|
checkpoint50d_pre |
1201 |
|
|
1202 |
|
checkpoint50c_post |
1203 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
1204 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
1205 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
1206 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
1207 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
1208 |
|
|
1209 |
|
checkpoint50c_pre |
1210 |
|
Merging from release1_p13: |
1211 |
|
o bug fix for pkg/seaice dynamic solver |
1212 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
1213 |
|
|
1214 |
|
checkpoint50b_post |
1215 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
1216 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
1217 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
1218 |
|
to timestep.F |
1219 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
1220 |
|
o re-generate output for highly sensitive test-exp: |
1221 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
1222 |
|
|
1223 |
|
checkpoint50b_pre |
1224 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
1225 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
1226 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
1227 |
|
|
1228 |
|
checkpoint50a_post |
1229 |
|
o Bug fix for merging between c50 and KPP. |
1230 |
|
ikey was passed from thermodynamics to kpp_calc via |
1231 |
|
common block rather than being recomputed in kpp_calc, |
1232 |
|
in contradiction with new key itdkey. |
1233 |
|
New key ikppkey created, and tamc.h headers updated. |
1234 |
|
|
1235 |
|
checkpoint50 |
1236 |
|
- 2nd step of merge with ecco-branch: |
1237 |
|
merge changes in ecco-branch back into main trunk |
1238 |
|
- bug fix in find_alpha |
1239 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
1240 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
1241 |
|
- merged some sliced AD support routines |
1242 |
|
|
1243 |
|
checkpoint49 |
1244 |
|
merged from ecco-branch: |
1245 |
|
o exf: |
1246 |
|
- Enable initialisation of forcing fields to constant |
1247 |
|
(runtime) values. |
1248 |
|
- in exf_getffields.F |
1249 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
1250 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
1251 |
|
with bulf formulae. |
1252 |
|
- exf_init.F modify #ifdef for exf_init_evap |
1253 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
1254 |
|
The following INT-usages are not safe: |
1255 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
1256 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
1257 |
|
and were modified. |
1258 |
|
o autodiff: checkpoint_lev... |
1259 |
|
- updated storing for bulk formulae (some arrays were missing) |
1260 |
|
- added state for seaice package |
1261 |
|
- synchronized with main branch |
1262 |
|
o DIVA: |
1263 |
|
Modif.s in |
1264 |
|
- the_main_loop.F |
1265 |
|
- the_model_main.F |
1266 |
|
and added cost_final_restore.F cost_final_store.F |
1267 |
|
o With these changes, it is possible to fully separate |
1268 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
1269 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
1270 |
|
into separate model executions. |
1271 |
|
This enables better tuning of DIVA to given queue sizes. |
1272 |
|
o Loss of cost function value in consecutive DIVA runs is |
1273 |
|
fixed by storing to 'costfinal' file. |
1274 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
1275 |
|
beginning/end of adjoint integration is accounted for. |
1276 |
|
The current changes apply to TAF-1.4.26. |
1277 |
|
TAF has one remaining bug, requiring one manual change |
1278 |
|
(see MITgcm manual). |
1279 |
|
o cal: synchronized between MAIN and ecco-branch |
1280 |
|
|
1281 |
|
checkpoint48i_post |
1282 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
1283 |
|
(mostly adding new routines to make list and replacing |
1284 |
|
pressure by totPhiHyd). |
1285 |
|
o Updated and merged grdchk package |
1286 |
|
- has both ADM and TLM checks |
1287 |
|
- works for single- and multi-proc. |
1288 |
|
- output cleaned |
1289 |
|
- worked successfully for parallel DIVA |
1290 |
|
o genmake: |
1291 |
|
- Adding -platform=SP4 |
1292 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
1293 |
|
o Modif. for DIVA: |
1294 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
1295 |
|
(similar thing would apply for active files such as |
1296 |
|
tbar, sbar, psbar, which should not be reinitialised; |
1297 |
|
only relevant for ecco-branch) |
1298 |
|
|
1299 |
|
checkpoint48h_post |
1300 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
1301 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
1302 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
1303 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
1304 |
|
|
1305 |
|
checkpoint48g_post |
1306 |
|
--- EOS: |
1307 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
1308 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
1309 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
1310 |
|
--- Pressure/geopotential gradient: |
1311 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
1312 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
1313 |
|
( changes results of global_ocean_pressure ) |
1314 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
1315 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
1316 |
|
( changes results of ideal_2D_oce ) |
1317 |
|
o includes r* 2nd term in potential gradient. |
1318 |
|
|
1319 |
|
checkpoint48f_post |
1320 |
|
Merging from release1_p12: |
1321 |
|
o Modifications for using pkg/exf with pkg/seaice |
1322 |
|
- improved description of the various forcing configurations |
1323 |
|
- added basic radiation bulk formulae to pkg/exf |
1324 |
|
- units/sign fix for evap computation in exf_getffields.F |
1325 |
|
- updated verification/global_with_exf/results/output.txt |
1326 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
1327 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
1328 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
1329 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
1330 |
|
to avoid negative values in shallow regions. |
1331 |
|
- updated verification/natl_box/results/output.txt |
1332 |
|
- updated verification/lab_sea/results/output.txt |
1333 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
1334 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
1335 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
1336 |
|
work with multi-field files, e.g., for single-file pickup. |
1337 |
|
o pkg/seaice: |
1338 |
|
- bug fix in growth.F: QNET for no shortwave case |
1339 |
|
- added HeffFile for specifying initial sea-ice thickness |
1340 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
1341 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
1342 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
1343 |
|
o pkg/seaice: |
1344 |
|
- adjoint-friendly modifications |
1345 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
1346 |
|
|
1347 |
|
checkpoint48e_post |
1348 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
1349 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
1350 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
1351 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
1352 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
1353 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
1354 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
1355 |
|
inverted_barometer solid-body.cs-32x32x1 |
1356 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
1357 |
|
|
1358 |
|
checkpoint48d_post |
1359 |
|
o in preparation for r*: |
1360 |
|
a) use pre-computed gradient of hydrostatic potential: |
1361 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
1362 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
1363 |
|
=> affects results of glob_oce_pressure (different truncation error) |
1364 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
1365 |
|
|
1366 |
|
checkpoint48d_pre |
1367 |
|
o in preparation for r*: |
1368 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
1369 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
1370 |
|
but for the moment, only used if it does not change the results. |
1371 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
1372 |
|
|
1373 |
|
checkpoint48c_post |
1374 |
|
Modifications in treatment of initial flux forcing controls |
1375 |
|
to avoid extra storing of flux fields. |
1376 |
|
|
1377 |
|
checkpoint48c_pre |
1378 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
1379 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
1380 |
|
|
1381 |
|
checkpoint48b_post |
1382 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
1383 |
|
(modification to pressure gradient not yet implemented) |
1384 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
1385 |
|
(for U & V) that are used for vertical advection of momentum. |
1386 |
|
|
1387 |
|
checkpoint48a_post |
1388 |
|
o In preparation for r*, use temp. array to compute vertical transport |
1389 |
|
in flux-form momentum pkg. => change results of few test-exp. |
1390 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
1391 |
|
lab_sea, natl_box & plume_on_slope |
1392 |
|
|
1393 |
|
checkpoint48 |
1394 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
1395 |
|
|
1396 |
|
checkpoint47j_post |
1397 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
1398 |
|
o moved adexch from forward_step to addummy_in_stepping |
1399 |
|
o added exch in ctrl_map_... |
1400 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
1401 |
|
reverse checkpointing loop |
1402 |
|
o Yet more changes in gmredi: |
1403 |
|
* adgmredi_calc_tensor |
1404 |
|
avoiding all recomputation of gmredi_slope_limit |
1405 |
|
* adgmredi_x/y/rtransport |
1406 |
|
added flag for excessive storing to avoid recomp. of |
1407 |
|
u/v/rtans, dTdx/y/z |
1408 |
|
-> this is not really necessary and very memory-consuming |
1409 |
|
* adgmredi_slope_psi: |
1410 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
1411 |
|
* gmredi_slope_limit |
1412 |
|
re-activated full calculation of taperfct for case 'ac02' |
1413 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
1414 |
|
|
1415 |
|
checkpoint47i_post |
1416 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
1417 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
1418 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
1419 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
1420 |
|
o gmredi: fix few bugs. |
1421 |
|
|
1422 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
1423 |
|
This will be a good checkpoint to plug into the ecco-branch. |
1424 |
|
o few modif.'s to get latest version adjointed |
1425 |
|
(mainly kick out code in ini_linear_phisurf) |
1426 |
|
o modif's to run adjoint with exactConserv |
1427 |
|
o case GM_BOLUS_ADVEC should be cleaned |
1428 |
|
S/R gmredi_slope_psi should be cleaned |
1429 |
|
o verification/carbon now has exactConserv=.TRUE. |
1430 |
|
|
1431 |
|
checkpoint47g_post |
1432 |
|
o time-average AIM output: becomes independent from statvars time-average |
1433 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
1434 |
|
o After TAF bug fix: |
1435 |
|
Tested adjoint of gmredi package. |
1436 |
|
Tests were done with checkpoint47 rather than with latest |
1437 |
|
checkpoint47f_post since the latter is broken for the adjoint |
1438 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
1439 |
|
Here they are, before they get changed/lost/stolen. |
1440 |
|
Mostly modif.'s to fix numerical sensitivities. |
1441 |
|
Gradient checks OK for |
1442 |
|
- GM_taper_scheme: |
1443 |
|
* clipping |
1444 |
|
* ac02 |
1445 |
|
* linear |
1446 |
|
* glw91 |
1447 |
|
* dm95 |
1448 |
|
* ldd97 |
1449 |
|
- GMREDI_OPTIONS: |
1450 |
|
* GM_VISBECK_VARIABLE_K |
1451 |
|
* GM_NON_UNITY_DIAGONAL |
1452 |
|
* GM_EXTRA_DIAGONAL |
1453 |
|
* GM_BOLUS_ADVEC |
1454 |
|
in conjunction with data.gmredi parameters to be checked in |
1455 |
|
in a few minutes under verification/carbon/code/ |
1456 |
|
|
1457 |
|
checkpoint47f_post |
1458 |
|
Merging from release1_p10: |
1459 |
|
o modifications for using pkg/exf with pkg/seaice |
1460 |
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
1461 |
|
and SEAICE_EXTERNAL_FLUXES |
1462 |
|
- pkg/exf CPP options EXF_READ_EVAP and |
1463 |
|
EXF_NO_BULK_COMPUTATIONS |
1464 |
|
- usage examples are Experiments 8 and 9 in |
1465 |
|
verification/lab_sea/README |
1466 |
|
- verification/lab_sea default experiment now uses |
1467 |
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
1468 |
|
|
1469 |
|
checkpoint47e_post |
1470 |
|
o created a tag prior to creating a branch |
1471 |
|
|
1472 |
|
checkpoint47d_post |
1473 |
|
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
1474 |
|
at the bottom boundary had an erroneous half slip boundary condition |
1475 |
|
o added bottom drag and no slip boundary condition capabilities to |
1476 |
|
oceanic pressure coordinates code |
1477 |
|
o added new verification experiment global_ocean_pressure, this experiment is |
1478 |
|
also described in the tutorial section of the manual |
1479 |
|
checkpoint47d_pre |
1480 |
|
|
1481 |
|
checkpoint47c_post |
1482 |
|
o Added a verification experiment for a global cubed-sphere ocean run |
1483 |
|
- verification/global_ocean.cubed32x32x30 |
1484 |
|
- uses pkg/therm_seaice and pkg/bulk_forcing |
1485 |
|
|
1486 |
|
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
1487 |
|
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
1488 |
|
when using P-coordinate; only implemented for atmospheric config. |
1489 |
|
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
1490 |
|
NOTES: requires option NONLIN_FRSURF to be "#define". |
1491 |
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
1492 |
|
|
1493 |
|
checkpoint47b_post |
1494 |
|
Merging from release1_p9: |
1495 |
|
o pkg/seaice |
1496 |
|
- removed GOTO's and added taf directives |
1497 |
|
- double precision constants to reduce the g77 (Linux) |
1498 |
|
to F77 (SGI) differences reported in release1_p8 |
1499 |
|
o tools/genmake |
1500 |
|
- added SGI options |
1501 |
|
o verification/testscript |
1502 |
|
- updated to that of checkpoint47a_post |
1503 |
|
o verification/global_ocean.90x40x15/input/eedata |
1504 |
|
- modified for SGI f77 compatibility |
1505 |
|
o verification/lab_sea |
1506 |
|
- added description of sea-ice model |
1507 |
|
- added missing matlab routines |
1508 |
|
- added test of thermodynamics parallelization |
1509 |
|
|
1510 |
|
checkpoint47a_post |
1511 |
|
o new pkg: aim_v23 |
1512 |
|
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
1513 |
|
for now, keep the same surface forcing as before. |
1514 |
|
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
1515 |
|
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
1516 |
|
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
1517 |
|
o add diagnostic of surface correction term in monitor output |
1518 |
|
|
1519 |
|
o bulk_force and therm_seaice |
1520 |
|
- Two packages: bulk_force (Bulk forcing) |
1521 |
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
1522 |
|
- Earlier integration from Stephaine Dutkiewicz |
1523 |
|
and Patrick Heimbach. |
1524 |
|
- Two ifdef statements for compile time, |
1525 |
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
1526 |
|
|
1527 |
|
checkpoint47 |
1528 |
|
differentiable version of checkpoint46n_post |
1529 |
|
o bug fix in quasihydrostaticterms |
1530 |
|
o * "clean" adjoint code (in terms of extensive recomputations) |
1531 |
|
can now be obtained for all GMREDI options (i.e. for |
1532 |
|
- GM_VISBECK_VARIABLE_K |
1533 |
|
- GM_NON_UNITY_DIAGONAL |
1534 |
|
- GM_EXTRA_DIAGONAL |
1535 |
|
- GM_BOLUS_ADVEC ) |
1536 |
|
* However, wrong gradient check problem remains unsolved. |
1537 |
|
* New CPP options have been introduced for different |
1538 |
|
tapering schemes |
1539 |
|
o external_fields_load now part of differentiation list |
1540 |
|
o pressure needs multiple storing; |
1541 |
|
would be nice to have store_pressure at beginning or |
1542 |
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
1543 |
|
(NB: pressure is needed for certain cases in find_rho, |
1544 |
|
which is also invoked through convective_adjustment). |
1545 |
|
o recomputations in find_rho for cases |
1546 |
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
1547 |
|
o #define ATMOSPHERIC_LOADING should be differentiable |
1548 |
|
o ini_forcing shifted to begining of initialise_varia |
1549 |
|
o Incorporating QNVS line search routines into MITgcm |
1550 |
|
(this is separate code, and therefore not under pkg) |
1551 |
|
lsopt/, optim/ |
1552 |
|
o Updated verification/carbon/ |
1553 |
|
- #define GM_VISBECK_VARIABLE_K |
1554 |
|
- GM_taper_scheme = 'ldd97' |
1555 |
|
|
1556 |
|
checkpoint46n_post |
1557 |
|
Merging from release1_p8: |
1558 |
|
o verification/natl_box: |
1559 |
|
updating new external_fields_load routine |
1560 |
|
o New package: pkg/seaice |
1561 |
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
1562 |
|
The sea-ice code is based on Hibler (1979-1980). |
1563 |
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
1564 |
|
In addition to computing prognostic sea-ice variables and diagnosing |
1565 |
|
the forcing/external data fields that drive the ocean model, |
1566 |
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
1567 |
|
The implied surface heat flux is then stored in variable |
1568 |
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
1569 |
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
1570 |
|
non-local transport term. Because this call precedes model |
1571 |
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
1572 |
|
the freezing point by the time theta is dumped or time-averaged. |
1573 |
|
N.B.: fairly large differences in accuracy occur across |
1574 |
|
different platforms/compilers; comparison between |
1575 |
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
1576 |
|
generated output gives: |
1577 |
|
T S U V |
1578 |
|
C D M c m s m s m s m s |
1579 |
|
n p a R g m m e . m m e . m m e . m m e . |
1580 |
|
f n k u 2 i a a d i a a d i a a d i a a d |
1581 |
|
g d e n d n x n . n x n . n x n . n x n . |
1582 |
|
|
1583 |
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
1584 |
|
o GAD: |
1585 |
|
- generated new common blocks to account for call of |
1586 |
|
same gad routines with differing traceridentities |
1587 |
|
(needed to modify tracerIdentity indices in GAD.h) |
1588 |
|
- generated separate common blocks for case useCubedSphereExchange |
1589 |
|
(Department of Futurology) |
1590 |
|
- parameter lists to gmredi_?transport: added tracerIdentity |
1591 |
|
- added new key indices to tamc.h |
1592 |
|
o external_fields_load: |
1593 |
|
- added this routine to TAF list |
1594 |
|
- needed to make some common blocks global and additional storing |
1595 |
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
1596 |
|
o exf: |
1597 |
|
updated external forcing package |
1598 |
|
- bug fixes carried over from ecco-branch |
1599 |
|
(missing OBCS_OPTIONS.h in two routines) |
1600 |
|
- enable easy to use "no forcing". |
1601 |
|
- added exf I/O for atmospheric loading |
1602 |
|
- added exf I/O for runoff data |
1603 |
|
- transfered scaling between exf <-> MITgcm to exf namelist |
1604 |
|
o Adding new verification experiment global_with_exf. |
1605 |
|
This verification experiment is almost identical to the |
1606 |
|
global_ocean.90x40x15 experiment, except that it uses |
1607 |
|
the exf (and cal) package instead of the |
1608 |
|
external_fields_load routine (cf README file). |
1609 |
|
|
1610 |
|
checkpoint46m_post |
1611 |
|
o modified testscript to return -- when there are no lines of "%MON" output |
1612 |
|
o added new flag "quasiHydrostatic" for QH mode |
1613 |
|
and new routine quasihydrostaticterms() |
1614 |
|
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
1615 |
|
New routine: mom_u_coriolis_nh() |
1616 |
|
o fixed sign of non-hydrostatic metric terms in u and v equations. |
1617 |
|
Depend on correct sign of gravitySign. |
1618 |
|
o added work.pc* to .cvsignore in aim directories using ifc |
1619 |
|
o introduced flag for controllin non-hydrostatic metric terms |
1620 |
|
o removed gravitySign from PARM04 |
1621 |
|
o switched to g77/ifc from pgf77 in aim experiments |
1622 |
|
|
1623 |
|
checkpoint46l_post |
1624 |
|
o made convective adjustment work with pressure coordinates: |
1625 |
|
- changed the direction of k-loop in convective_adjustment.F for the |
1626 |
|
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
1627 |
|
- adjusted the reference pressure k-index in convective_adjustment.F |
1628 |
|
- adjusted the convection condition in convect.F (in analogy to |
1629 |
|
calc_ivdc.F) |
1630 |
|
- convective_adjustment no longer computes anything on the halos |
1631 |
|
- removed the warnings about negative salinity from find_rho.F and |
1632 |
|
find_alpha.F; instead the new routine look_for_neg_salinity, called |
1633 |
|
at the beginning of find_rho, find_alpha, and find_beta, does a |
1634 |
|
check of the entire slice, if CPP-option |
1635 |
|
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
1636 |
|
checkpoint46l_pre |
1637 |
|
|
1638 |
|
checkpoint46k_post |
1639 |
|
o fixed the verification/global_ocean.90x40x15 experiment: |
1640 |
|
- new bathymetry (the world according to A., JMC, and M.) |
1641 |
|
- new initial fields and forcing fields (*.bin files) |
1642 |
|
- new POLY3.COEFFS (for the next release one should switch to a full |
1643 |
|
equation of state: JMD95P or MDJWF) |
1644 |
|
- fixed several errors and redundancies in the data file |
1645 |
|
- experiment uses looped cells |
1646 |
|
- added matlab directory with diagnostic scripts for plotting of output |
1647 |
|
|
1648 |
|
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
1649 |
|
- read AIM physics parameters from a file (data.aimphys) |
1650 |
|
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
1651 |
|
|
1652 |
|
checkpoint46j_post |
1653 |
|
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
1654 |
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
1655 |
|
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
1656 |
|
o update timeave pkg for wVel diagnostic. |
1657 |
|
checkpoint46j_pre |
1658 |
|
|
1659 |
|
checkpoint46i_post |
1660 |
|
o Clean up AIM package (and keep the results unchanged): |
1661 |
|
include CPP_OPTION and use IMPLICT NONE in all routines ; |
1662 |
|
declare all the variables _RL ; use _d 0 for all numerical constants. |
1663 |
|
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
1664 |
|
|
1665 |
|
checkpoint46h_post |
1666 |
|
o cleaned up the use of rhoNil and rhoConst. |
1667 |
|
- rhoNil should only appear in the LINEAR equation of state, everywhere |
1668 |
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
1669 |
|
and the dynamical equations are all divided by rhoConst |
1670 |
|
o introduced new parameter rhoConstFresh, a reference density of fresh |
1671 |
|
water, to remove the fresh water flux's dependence on rhoNil. The default |
1672 |
|
value is 999.8 kg/m^3 |
1673 |
|
o cleanup up external_forcing.F and external_forcing_surf.F |
1674 |
|
- can now be used by both OCEANIC and OCEANICP |
1675 |
|
checkpoint46h_pre |
1676 |
|
|
1677 |
|
Added code to convert surface volume flux (fresh water) into |
1678 |
|
a mass flux when using P coordinates in the ocean (OCEANICP). |
1679 |
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
1680 |
|
|
1681 |
|
checkpoint46g_post |
1682 |
|
o Include a new diagnostic variable phiHydLow for the ocean model |
1683 |
|
- in z-coordinates, it is the bottom pressure anomaly |
1684 |
|
- in p-coordinates, it is the sea surface elevation |
1685 |
|
- in both cases, these variable have global drift, reflecting the mass |
1686 |
|
drift in z-coordinates and the volume drift in p-coordinates |
1687 |
|
- included time averaging for phiHydLow, be aware of the drift! |
1688 |
|
o depth-dependent computation of Bo_surf for pressure coordinates |
1689 |
|
in the ocean (buoyancyRelation='OCEANICP') |
1690 |
|
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
1691 |
|
Theta, Salinity, and Pressure in the parameter list. This routine is |
1692 |
|
presently contained in find_rho.F. This routine does not give the |
1693 |
|
correct density for 'POLY3', which would be a z-dependent reference |
1694 |
|
density. |
1695 |
|
o cleaned up find_rho |
1696 |
|
- removed obsolete 'eqn' from the parameter list. |
1697 |
|
o added two new verification experiments: gop and goz |
1698 |
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
1699 |
|
checkpoint46g_pre |
1700 |
|
|
1701 |
|
checkpoint46f_post |
1702 |
|
o Enable tangent linear (forward mode) gradient checks: |
1703 |
|
- extended active file handling to g_... files |
1704 |
|
- added TANGENT_SIMULATION to theSimulationMode |
1705 |
|
- extended grdchk package accordingly |
1706 |
|
o added tangent linear setup in verification/carbon/code_ftl |
1707 |
|
o added adjoint setup in verification/front_relax/code_ad |
1708 |
|
|
1709 |
|
checkpoint46e_post |
1710 |
|
o Added new equation of state -> MDJWF |
1711 |
|
- EOS of McDougall et al., 2002, JAOT, submitted |
1712 |
|
- caveat: the equation of state is only valid for a smaller (more |
1713 |
|
realistic?) range of values than JMD95P/Z and UNESCO |
1714 |
|
- added masks to the calculation of pressure in store_pressure |
1715 |
|
- added more check values for density in check_eos (ini_eos.F), some of |
1716 |
|
the old check values are out of the range of the MDJWF-eos, so don't |
1717 |
|
expect perfect matches for those |
1718 |
|
checkpoint46e_pre |
1719 |
|
|
1720 |
|
checkpoint46d_post |
1721 |
|
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
1722 |
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
1723 |
|
case of pressure coordinates. eosType='JMD95Z' in |
1724 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
1725 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1726 |
|
in find_alpha/beta. |
1727 |
|
checkpoint46d_pre |
1728 |
|
|
1729 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1730 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
1731 |
|
|
1732 |
|
checkpoint46c_post |
1733 |
|
o Changes necessary for ocean in p-coordinates |
1734 |
|
- Added new buoyancy relation = 'OCEANICP' |
1735 |
|
- Added new parameters = gravitySign (this used to be contained inside |
1736 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
1737 |
|
X GM/Redi is not compatible (yet) |
1738 |
|
X bottom drag and no-slip need to be debugged. |
1739 |
|
checkpoint46c_pre |
1740 |
|
|
1741 |
|
checkpoint46b_post |
1742 |
|
o Added new equation of state -> JMD95Z and JMD95P |
1743 |
|
- EOS of Jackett and McDougall, 1995, JAOT |
1744 |
|
- moved all EOS parameters into EOS.h |
1745 |
|
- new routines ini_eos.F, store_pressure.F |
1746 |
|
o Added UNESCO EOS, but not recommended because it requires |
1747 |
|
in-situ temperature (see JMD95) |
1748 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
1749 |
|
unesco.f to be used with POLY3 |
1750 |
|
checkpoint46b_pre |
1751 |
|
|
1752 |
|
checkpoint46a_post |
1753 |
|
o Added (atmospheric) pressure loading |
1754 |
|
- new field in FFIELDS.h, etc... |
1755 |
|
- new cpp flag ATMOSPHERIC_LOADING |
1756 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
1757 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
1758 |
|
checkpoint46a_pre |
1759 |
|
|
1760 |
|
checkpoint46 |
1761 |
|
further merges from release1_p5 |
1762 |
|
o new ctrl package |
1763 |
|
- adopted from ECCO environment to enable optimization |
1764 |
|
- added Eliassen Palm fluxes to controls |
1765 |
|
o added Eliassen Palm flux controls to gradient check package |
1766 |
|
o cost package |
1767 |
|
- Compatible with new ctrl package |
1768 |
|
- added Eliassen Palm cost hooks |
1769 |
|
- modif's of existing cost functions |
1770 |
|
o Adjoint-related bug fixes in kpp: |
1771 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
1772 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
1773 |
|
o autodiff package |
1774 |
|
- flow directives: |
1775 |
|
+ new for S/R do_the_model_io |
1776 |
|
+ enhanced for S/R checkpoint |
1777 |
|
+ new gmredi.flow |
1778 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
1779 |
|
disable adcommon.h/g_common.h by default. |
1780 |
|
- fixed problem for adjoint of global_max |
1781 |
|
o modified verification/carbon/ |
1782 |
|
o New setup for adjoint of global_ocean |
1783 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
1784 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
1785 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
1786 |
|
|
1787 |
|
checkpoint45d_post |
1788 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
1789 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
1790 |
|
(affects plume_on_slope "cg2d" output) |
1791 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
1792 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
1793 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
1794 |
|
o change phiMin in exp1 (to agree with documentation) |
1795 |
|
o add new flags: |
1796 |
|
- T,S forcing inside/outside Adams-Bashforth |
1797 |
|
- turn off temp,salt advection and/or forcing |
1798 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
1799 |
|
o monitor: change definition of KE to check conservation of Energy |
1800 |
|
|
1801 |
|
checkpoint45c_post |
1802 |
|
o Removed f90 comments ("!") |
1803 |
|
o Modified initialisations to enable exf package for MITgcm |
1804 |
|
(without invoking ECCO_PACKAGE). |
1805 |
|
o modifications to gradient check package (Martin Losch) |
1806 |
|
- enable centered differences |
1807 |
|
- modified format of standard output |
1808 |
|
|
1809 |
|
checkpoint45b_post |
1810 |
|
o cleaned exchange calls in cg2d |
1811 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
1812 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
1813 |
|
to configure barotropic setup (Martin Losch) |
1814 |
|
o moved some initialisations within bi,bj loop in dynamics |
1815 |
|
(TAF flow dependency) |
1816 |
|
o in initialise_varia, moved call packages_init_variables |
1817 |
|
before convective_adjustment_init |
1818 |
|
(corresponding adjustment of TAF tape initialisation). |
1819 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
1820 |
|
|
1821 |
|
checkpoint45a_post |
1822 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
1823 |
|
o specific exchange for X-slice domain (case Ny=1) |
1824 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
1825 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
1826 |
|
|
1827 |
|
checkpoint44h_post = checkpoint45 |
1828 |
|
o Fix to restore differentiability: |
1829 |
|
place at which packages_init_variables is called in |
1830 |
|
initialise_varia is crucial for reverse control flow. |
1831 |
|
o modifications in GMRedi to enable stable adjoint |
1832 |
|
(corresponding modif's in thermodynamics, dynamics) |
1833 |
|
o added missing hook for sponge layer code in external_forcing |
1834 |
|
o modified test cost functions |
1835 |
|
o storing in gad_advection (plus removal of write(0,*)! |
1836 |
|
o missing headers TR1.h added in convective_adjustment routines |
1837 |
|
o errorMessageUnit set non-equal zero in eeboot |
1838 |
|
(conflict on some platforms, e.g. IBM SP3) |
1839 |
|
o modified carbon verif. |
1840 |
|
|
1841 |
|
checkpoint44h_pre |
1842 |
|
o vertical grid option: allow to put the Interface at the middle between |
1843 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
1844 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
1845 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
1846 |
|
|
1847 |
|
checkpoint44g_post |
1848 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
1849 |
|
results) ; ifdef missing in thermodynamics.F |
1850 |
|
|
1851 |
|
checkpoint44f_pre,checkpoint44f_post |
1852 |
|
o added PTRACERS package |
1853 |
|
This allows an arbitrary number of passive tracers to be integrated |
1854 |
|
forward simultaneously with the dynamicaly model. |
1855 |
|
+ Implemented so far: |
1856 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
1857 |
|
- I/O and checkpointing |
1858 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
1859 |
|
+ Not implemented so far: |
1860 |
|
- KPP |
1861 |
|
- OBCS |
1862 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
1863 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
1864 |
|
line in data.pkg. |
1865 |
|
+ This package is disabled by default since it increases storage. |
1866 |
|
|
1867 |
|
|
1868 |
|
o testscript: added -cleanup option |
1869 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
1870 |
|
b) enable to filter 2D fields. |
1871 |
|
|
1872 |
|
checkpoint44e_pre,post |
1873 |
|
o re-wrote convective adjustment to use pre-calculated weights |
1874 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
1875 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
1876 |
|
Original calls to convect() still in place. |
1877 |
|
|
1878 |
|
chkpt44d_pre,post |
1879 |
|
o added missing EXCLUDE_MONITOR flags |
1880 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
1881 |
|
(incompatible typ in MIN/MAX expressions caused problems |
1882 |
|
on IBM SP3) |
1883 |
|
o in genmake added variable MAKEDEPEND |
1884 |
|
plus resetting for case SunOS |
1885 |
|
o added timer_stats.c routine for IBM SP3 |
1886 |
|
o removed variables in dynamics |
1887 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
1888 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
1889 |
|
|
1890 |
|
o real fresh water flux implemented with non-linear free-surface. |
1891 |
|
|
1892 |
|
chkpt44c_pre,post |
1893 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
1894 |
|
USE_NATURAL_BCS in solve_for_P); |
1895 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
1896 |
|
|
1897 |
|
checkpoint44b_pre/_post |
1898 |
|
o merge of relevant stuff from the ecco-branch: |
1899 |
|
- genmake: removed $S64 overwrite for case SunOS |
1900 |
|
- pkg/exf: update and corrections for field swapping and obcs |
1901 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
1902 |
|
harmonized between ECCO and MITgcm |
1903 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
1904 |
|
updated checkpointing_lev... lists for obcs |
1905 |
|
- model/src: minor changes in forward_step, plot_field |
1906 |
|
added directive for divided adjoint in the_main_loop |
1907 |
|
- pkg/mdsio: added mdsio_gl_slice |
1908 |
|
|
1909 |
|
o check parameters & config (chkpt44a_pre,post) |
1910 |
|
o OBC and NonLin_FrSurf. |
1911 |
|
|
1912 |
|
checkpoint44 |
1913 |
|
o fix bug in mom_vi_del2uv |
1914 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
1915 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
1916 |
|
o update AIM experiments (NCEP input files) |
1917 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
1918 |
|
o added some stuff for AD |
1919 |
|
|
1920 |
|
checkpoint43 |
1921 |
|
o added two new advection tests |
1922 |
|
o added global 4x4 degree ocean test |
1923 |
|
o added test of H&S94 with free surface on cube |
1924 |
|
o some final mods for gradient check, adjoint,... |
1925 |
|
|
1926 |
checkpoint42 |
checkpoint42 |
1927 |
Fixed AD-related problems: |
Fixed AD-related problems: |
1928 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
o Store directives up-to-date with re-arranged Adams-Bashforth |