3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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|
6 |
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checkpoint57e_post |
7 |
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o Adding eddy stress controls a la Ferreira et al. |
8 |
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checkpoint57e_pre |
9 |
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|
10 |
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o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
11 |
|
update output.txt of exp. fizhi-gridalt-hs |
12 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
13 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
14 |
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o parameter calendarDumps: when set, approximate months (30-31 days) and years |
15 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
16 |
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KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
17 |
|
months and years. Requires pkg/cal. |
18 |
|
o diagnostics: add pickup functionality |
19 |
|
- off by default for backwards compatibility |
20 |
|
- current version only uses MDSIO -- MNC will be added |
21 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
22 |
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o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
23 |
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|
24 |
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checkpoint57d_post |
25 |
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o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
26 |
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o modify verification/ideal_2D_oce so that it tests the creation of mnc |
27 |
|
output from the diagnostics package |
28 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
29 |
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o make genmake2 more portable by using ".$FS" instead of ".f" for more |
30 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
31 |
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o add coordinate variables to the MNC output from the diagnostics package |
32 |
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o change MNC-flags default value: true when useMNC=TRUE |
33 |
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o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
34 |
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the ability (off by default) to read the grid information using MNC |
35 |
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o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
36 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
37 |
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o do snap-shot diagnostics at the middle of the time-interval (instead of |
38 |
|
at the end). |
39 |
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o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
40 |
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new test for AIM with thSIce + slab-ocean |
41 |
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o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
42 |
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o move state variable diagnostics to the beginning of the time step ; |
43 |
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(note: still needs some work specially for snap-shot diagnostics) |
44 |
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duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
45 |
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|
46 |
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checkpoint57c_post |
47 |
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o Change testing option (-ieee) to get closer agreement between g77 & ifort |
48 |
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o generate new output.txt files on faulks with g77 & the new -ieee option |
49 |
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checkpoint57c_pre |
50 |
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|
51 |
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o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
52 |
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update output.txt of exp. global_ocean.90x40x15 |
53 |
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o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
54 |
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results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
55 |
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o add saltFlux(+File) forcing capability with periodicExternalForcing |
56 |
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o allow to use pkg diagnostics for GM-Redi & ThSIce output |
57 |
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o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
58 |
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o improvements for the MNC output from DIAGNOSTICS: |
59 |
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- correct handling of the unlimitied dimension |
60 |
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- all dims now have associated coordinate variables |
61 |
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- variables located at U, V, and Corner ("Z") points are now written |
62 |
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with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
63 |
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*all* data points are output |
64 |
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o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
65 |
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o added pkg/seaice/seaice_monitor.F |
66 |
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o mdsio_readfield.F can now read files visible only to master MPI process. |
67 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
68 |
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o exf_getffields interpolation defaults to bilinear for all scalar forcing |
69 |
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fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
70 |
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spurious negative numbers for precipitation and humidity. Will cause |
71 |
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some small numerical differences for integrations using pkg/exf/exf_interp.F. |
72 |
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o pkg/ctrl/ |
73 |
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* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
74 |
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May be enabled via doPackDiag |
75 |
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* introduce z-scaling of |
76 |
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+ gradient (doZscalePack) and |
77 |
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+ control (doZscaleUnpack) |
78 |
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o pkg/mdsio/ |
79 |
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* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
80 |
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* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
81 |
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|
82 |
|
checkpoint57b_post |
83 |
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o simplify options in diagnostics_fill arguments (remove weird combinations) |
84 |
|
o fix MNC coordinate variables so that they now contain per-face index |
85 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
86 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
87 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
88 |
|
o Implement instantaneous output within pkg diagnostics: |
89 |
|
setting a negative frequency in data.diagnostics produces |
90 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
91 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
92 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
93 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
94 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
95 |
|
becomes the coordinate variable for the 'T' dimension |
96 |
|
o add CF-style coordinate variables to MNC |
97 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
98 |
|
missing along the T axis but otherwise it works! |
99 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
100 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
101 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
102 |
|
this is based directly on what the model compute, so that the content of |
103 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
104 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
105 |
|
o clean up build options files for SunOS, in particular |
106 |
|
- remove -traditional from xmakedepend |
107 |
|
- change -xarch=v9 to -xarch=native for f77 |
108 |
|
- restore use of make (not gmake) |
109 |
|
- add CC=gcc if using g77 |
110 |
|
o changes per discussion of AM, JMC, & EH3 today: |
111 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
112 |
|
creating proper CF-style coordinate variables and in recognition |
113 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
114 |
|
the grid files into any of the other NetCDF files |
115 |
|
- *always* output grid variables with MDSIO (this will eventually be |
116 |
|
changed) |
117 |
|
- output MNC grid file if useMNC is true |
118 |
|
o every instance of _END_MASTER() has been found and replaced with |
119 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
120 |
|
preprocessors |
121 |
|
o re-arrange diagnostics pkg initialisation: |
122 |
|
- allow each package to extend the available diagnostics list |
123 |
|
- add some checking and fix small problems (multi-threaded, ...) |
124 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
125 |
|
look through the short list of active diag. (instead of the long list) |
126 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
127 |
|
|
128 |
|
checkpoint57a_post |
129 |
|
o this set of changes restores TAMC compatibility |
130 |
|
tested for global_ocean.90x40x15 adjoint on trough |
131 |
|
(what a pain) |
132 |
|
|
133 |
|
checkpoint57a_pre |
134 |
|
o some modifs in tools/build_options for sunos |
135 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
136 |
|
|
137 |
|
checkpoint57 |
138 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
139 |
|
- new parameter viscA4W (defaults to viscA4) |
140 |
|
- affects only non-hydrostatic code |
141 |
|
- to be done: no-slip lateral boundary conditions |
142 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
143 |
|
o implement Implicit Vertical advection for pTracers |
144 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
145 |
|
(implemented also for implicit vertical diffusion & advection) |
146 |
|
o OBCS: extend application of tracer open boundary conditions |
147 |
|
to a strip beyond the boundary of width Olx/Oly |
148 |
|
o add call monitor to TAF set of required calls (flow directives) |
149 |
|
and include in natl_box_adjoint |
150 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
151 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
152 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
153 |
|
(theta2, salt2 in ecco_cost_weights) |
154 |
|
|
155 |
|
checkpoint56c_post |
156 |
|
o OBCS as control variables |
157 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
158 |
|
- remove balance of obcs controls from default |
159 |
|
- fix index bug nobcs in ctrl_init |
160 |
|
- fix dummy fields filen in ctrl_pack |
161 |
|
- add dummy weights for obcs |
162 |
|
o lsopt: comment out fort.94 output |
163 |
|
o optim: |
164 |
|
- remove unnecessary header files |
165 |
|
- adjusted namelists |
166 |
|
- add xerbla.F to Makefile |
167 |
|
o exf: |
168 |
|
- multiple modifications of exf_check_range |
169 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
170 |
|
o mdsio: |
171 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
172 |
|
|
173 |
|
checkpoint56b_post |
174 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
175 |
|
is called from DO_THE_MODEL_IO |
176 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
177 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
178 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
179 |
|
o add another verification experiment that tests both the cfc-pkg and |
180 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
181 |
|
reactive tendencies treated inline with regular timestepping |
182 |
|
o testreport previously did a lousy job of comparing small numbers, so |
183 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
184 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
185 |
|
testreport. |
186 |
|
o ptracers_monitor: bug fix for MPI |
187 |
|
|
188 |
|
checkpoint56a_post |
189 |
|
o GCHEM: finish reorganizating the package |
190 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
191 |
|
(introduces another 3D-array for each passive tracer, but only if |
192 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
193 |
|
gchemTendency is not needed because the timestep is done separately) |
194 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
195 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
196 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
197 |
|
so clear to me how that should be done in a general way. |
198 |
|
o CFC: improve formatting of output in CFC_ATMOS |
199 |
|
o PTRACERS: |
200 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
201 |
|
that ALL experiments with ptracers enable can be checked. This makes |
202 |
|
GCHEM_MONITOR obsolete. |
203 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
204 |
|
monitorFreq |
205 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
206 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
207 |
|
o exf_check_range: |
208 |
|
* default changed to .TRUE. |
209 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
210 |
|
* STOP in exf_check_range if 'out of range' |
211 |
|
* range chosen generous to allow for potential extema |
212 |
|
TBD: a version with stricter range |
213 |
|
permitted range would be runtime parameters |
214 |
|
o GMredi: |
215 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
216 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
217 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
218 |
|
o GCHEM: |
219 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
220 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
221 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
222 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
223 |
|
this flag is now only visible within GCHEM-pkg routines. |
224 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
225 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
226 |
|
this, the tracer ID iTracer had to be included into the parameter list |
227 |
|
of ptracers_forcing |
228 |
|
- set up forward_step to call gchem_forcing, that will replace |
229 |
|
gchem_forcing_int in ptracers_forcing |
230 |
|
- cleaning up |
231 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
232 |
|
|
233 |
|
checkpoint56 |
234 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
235 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
236 |
|
o ECCO-GODAE |
237 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
238 |
|
* fully merged and updated from SIO code |
239 |
|
windstress sign change affects |
240 |
|
- exf_inscal_[u/v]stress |
241 |
|
- sign of xx_tau[u/v] adjustments |
242 |
|
- signs in cost_scat |
243 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
244 |
|
* natl_box_adjoint updated and compressed |
245 |
|
* 2-level checkpoint switch added |
246 |
|
(tested in EXP. 1 of natl_box_adjoint) |
247 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
248 |
|
o SVD |
249 |
|
* first complete, non-hacked version for SVD calculations |
250 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
251 |
|
performed via direct access files admtlm_vector.it???? |
252 |
|
(via ctrl_[un]pack) |
253 |
|
* optimcycle is used for ARPACK iteration counter |
254 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
255 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
256 |
|
and add linear transforms where necessary |
257 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
258 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
259 |
|
o mdsio: filename info to both stderr, stdout |
260 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
261 |
|
from sign change |
262 |
|
|
263 |
|
checkpoint55j_post |
264 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
265 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
266 |
|
o add consistent build directories and .cvsignore files to verification |
267 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
268 |
|
o make all subroutines 30 or less characters in length for certain older |
269 |
|
compilers to work (a thorough search only turns up two routines in |
270 |
|
pkg/ptracers) |
271 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
272 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
273 |
|
|
274 |
|
checkpoint55i_post |
275 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
276 |
|
3.D if implicit) ; each ptracer uses its own background value. |
277 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
278 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
279 |
|
ITRDA and other clusters without the mpirun "-wd" option |
280 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
281 |
|
configuration |
282 |
|
o give MNC the ability to create additional files rather than |
283 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
284 |
|
- the default is just less than 2GB which is a practical limit |
285 |
|
on many systems |
286 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
287 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
288 |
|
|
289 |
|
checkpoint55h_post |
290 |
|
o add verification test "vermix" |
291 |
|
o remove all the *_ioinc flags and replace with the single global |
292 |
|
outputTypesInclusive flag |
293 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
294 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
295 |
|
o useMNC moved from data.mnc to data.pkg |
296 |
|
|
297 |
|
checkpoint55g_post |
298 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
299 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
300 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
301 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
302 |
|
Works well for global_ocean.90x40x15, |
303 |
|
but recomp. issue remains for carbon |
304 |
|
o Updating adjoint output for natl_box_adjoint after |
305 |
|
pkg/ecco has been modified (see taga c55d_post) |
306 |
|
|
307 |
|
checkpoint55f_post |
308 |
|
o rename to timeave_init_fixed |
309 |
|
|
310 |
|
checkpoint55e_post |
311 |
|
o some delicate re-shuffle of store directives to avoid one |
312 |
|
extra call of do_oceanic_physics |
313 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
314 |
|
checkpoint_lev1_directives.h |
315 |
|
o NB: this may break global_ocean adjoint temporarily, |
316 |
|
but it is clear how to fix it. Will do later, need this now. |
317 |
|
|
318 |
|
checkpoint55d_post |
319 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
320 |
|
o ecco_cost_weights is modified to 1x1 runs |
321 |
|
o modifs to allow observations to be read in as |
322 |
|
single file or yearly files |
323 |
|
o enable to read exf forcing fields as either |
324 |
|
single file or yearly files (flag useExfYearlyFields) |
325 |
|
checkpoint55d_pre |
326 |
|
|
327 |
|
o switch between 2-level and 3-level checkpointing |
328 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
329 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
330 |
|
with the correct (that is, the complete multi-dimensional) set of |
331 |
|
array indicies |
332 |
|
- used in mom_vecinv() to write the diagFreq output |
333 |
|
- tested (demonstrated) in verification/aim.5l_cs |
334 |
|
o further mnc-ification |
335 |
|
- add verification/lab_sea to the list with mnc setups |
336 |
|
- fix undefined mnc v-names in cd_code |
337 |
|
- add kpp to mnc output (both snapshot and timeave) |
338 |
|
o non-hydrostatic code |
339 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
340 |
|
in calc_gw.F |
341 |
|
- defaults to viscAh |
342 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
343 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
344 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
345 |
|
o pkg/cost |
346 |
|
extend simple cost functions to treat time mean quantities |
347 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
348 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
349 |
|
be 2 times larger than the minimum size the advection scheme requires. |
350 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
351 |
|
o GGL90 (Gaspar's TKE mixed layer) |
352 |
|
- add horizontal diffusion of TKE, requires exchanges in |
353 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
354 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
355 |
|
mixing coefficients are computed from a horizontal average of TKE of |
356 |
|
6 points or so. I think that diffusion has a little more physical |
357 |
|
justification. |
358 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
359 |
|
was in vain) |
360 |
|
- mask tke-variable in ggl90_init |
361 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
362 |
|
o fix biharmonic diffusion on CS-grid. |
363 |
|
o more obcs stuff |
364 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
365 |
|
for reading boundary values. This routine is called from |
366 |
|
obcs_prescribe_read |
367 |
|
- updated obcs_check |
368 |
|
- changed sponge layer relaxation parameter units for days to seconds |
369 |
|
- turned off sponge layer by default |
370 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
371 |
|
- fixed about 35 bugs in obcs_external_fields_load |
372 |
|
|
373 |
|
checkpoint55c_post |
374 |
|
o obcs stuff |
375 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
376 |
|
- re-arranged obcs_calc |
377 |
|
- moved exf_getobcs to obcs_prescibe_read |
378 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
379 |
|
and independent of it (executable can contain all). |
380 |
|
- updated obcs_check |
381 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
382 |
|
These may be necessary only if tangential velocities are |
383 |
|
prescribed at OB, not sure, needs testing. |
384 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
385 |
|
which simplifies the calls and passes the ifc check-bounds test |
386 |
|
|
387 |
|
checkpoint55b_post |
388 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
389 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
390 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
391 |
|
affects advect_cs results (for the wrong reason): update output.txt |
392 |
|
o use a more standard discretization for biharmonic viscosity ; |
393 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
394 |
|
affects results of dome set-up: update output.txt |
395 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
396 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
397 |
|
|
398 |
|
checkpoint55a_post |
399 |
|
o merged code to |
400 |
|
* prescribe/read time-dependent open boundaries |
401 |
|
(works in conjunction with exf, cal) |
402 |
|
* sponge layer code for open boundaries |
403 |
|
* each boundary N/S/E/W now has its own CPP option |
404 |
|
(healthy for the adjoint) |
405 |
|
|
406 |
|
checkpoint55 |
407 |
|
o up-to-date adjoint of previous breaks |
408 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
409 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
410 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
411 |
|
- carbon: * remove tr1-related adjoint verification |
412 |
|
* add ptracer as control variable |
413 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
414 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
415 |
|
|
416 |
|
checkpoint54f_post |
417 |
|
o in verification/carbin/ remove experiment related to |
418 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
419 |
|
code_ad/ input_ad/ results_ad |
420 |
|
|
421 |
|
o add two new packages |
422 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
423 |
|
+ subject to optimization (memory) |
424 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
425 |
|
+ subject to reordering (many GOTOs in the original code) |
426 |
|
+ so far opps is called for every (i,j) point, and then operates in |
427 |
|
the vertical; one may want to reorder the scheme in order operate in |
428 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
429 |
|
fields) |
430 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
431 |
|
- all verification tests compile and run with linux_ia32_g77 |
432 |
|
- defaults are compatible with current input files--nothing |
433 |
|
should change if you were not previously using MNC |
434 |
|
- MNC output has been added in numerous places (eg. timeave) |
435 |
|
but there are still a few writes not yet do-able with MNC |
436 |
|
(this is in progress) |
437 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
438 |
|
documentation will soon follow |
439 |
|
- numerous small formatting cleanups for ProTeX |
440 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
441 |
|
|
442 |
|
checkpoint54e_post |
443 |
|
o add two new packages |
444 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
445 |
|
stratification dependent mixing |
446 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
447 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
448 |
|
course), however there is only one diffusivity that is used for both |
449 |
|
temperature and salinity (and passive tracers)ç |
450 |
|
o add offline package |
451 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
452 |
|
provided by Stephanie Dutkiewicz |
453 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
454 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
455 |
|
|
456 |
|
checkpoint54d_post |
457 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
458 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
459 |
|
leading to additional shift by 5 days each year of integration |
460 |
|
(i.e. leading to considerable offset over the years) |
461 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
462 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
463 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
464 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
465 |
|
(external loading & cpl import/export stay in forward_step.F) |
466 |
|
o update coupling interface to work with new staggerTimeStep |
467 |
|
o change MDSIO ptracers_pickup. |
468 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
469 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
470 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
471 |
|
|
472 |
|
checkpoint54c_post |
473 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
474 |
|
this affects (truncation error) output.txt of test-exp: |
475 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
476 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
477 |
|
o change Qnet to always be the net heat flux, (+upward). |
478 |
|
affects (truncation error) output of natl_box exp.: updated |
479 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
480 |
|
o start to test mnc routinely in exp0 |
481 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
482 |
|
|
483 |
|
checkpoint54b_post |
484 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
485 |
|
impressive on Altix and Opteron systems) |
486 |
|
o diagnostics can now write NetCDF files through the mnc package |
487 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
488 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
489 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
490 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
491 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
492 |
|
|
493 |
|
checkpoint54a_post |
494 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
495 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
496 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
497 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
498 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
499 |
|
checkpoint54a_pre |
500 |
|
|
501 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
502 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
503 |
|
|
504 |
|
checkpoint54 |
505 |
|
checkpoint53g_post |
506 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
507 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
508 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
509 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
510 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
511 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
512 |
|
o restore adjointability |
513 |
|
|
514 |
|
checkpoint53f_post |
515 |
|
o modifications that affect AIM experiment results (update output.txt): |
516 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
517 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
518 |
|
o AIM pkg: |
519 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
520 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
521 |
|
|
522 |
|
checkpoint53e_post |
523 |
|
o merged cylindrical coord configuration |
524 |
|
o added rotating_tank experiment |
525 |
|
checkpoint53e_pre |
526 |
|
|
527 |
|
checkpoint53d_post |
528 |
|
o faulks upgraded: re-generate output.txt that have changed: |
529 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
530 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
531 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
532 |
|
o added Sadourny discretization of Coriolis |
533 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
534 |
|
- re-enabled use of omega3 (useAbsVorticity) |
535 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
536 |
|
vector-invariant equations |
537 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
538 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
539 |
|
hopefully without new bugs |
540 |
|
- still to do: biharmonic friction for non-hydrostatic w |
541 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
542 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
543 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
544 |
|
of mom_common/ |
545 |
|
- simple re-arrangement of instructions within computing loop |
546 |
|
checkpoint53d_pre |
547 |
|
|
548 |
|
checkpoint53c_post |
549 |
|
o new version of coupler for AIM+thSIce and Ocean models |
550 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
551 |
|
- land: change Evaporation of snow |
552 |
|
- aim with thSIce: fix bug in snow-precip. |
553 |
|
o changes to calc_gw.F |
554 |
|
- bug fix for w^2 term near the bottom boundary |
555 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
556 |
|
partial/looped cells |
557 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
558 |
|
and plume on slope), change the lateral boundary condition from half slip |
559 |
|
to the value of no_slip_sides |
560 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
561 |
|
o Adjoint of EBM package + verification |
562 |
|
* TLM OK |
563 |
|
* ADM not sufficient accuracy yet (needs further testing) |
564 |
|
|
565 |
|
checkpoint53b_post |
566 |
|
o Commiting new energy balance model to repository |
567 |
|
* package is pkg/ebm |
568 |
|
* verif. is verification/global_ocean_ebm |
569 |
|
* references are in ebm_driver.F |
570 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
571 |
|
C Global thermohaline circulation. Part I: |
572 |
|
C Sensitivity to atmospheric moisture transport. |
573 |
|
C J. Climate 12(1), 71-82 |
574 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
575 |
|
C Global thermohaline circulation. Part II: |
576 |
|
C Sensitivity with interactive transport. |
577 |
|
C J. Climate 12(1), 83-91 |
578 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
579 |
|
C Destabilization of the thermohaline circulation |
580 |
|
C by atmospheric eddy transports. |
581 |
|
C J. Climate 7(12), 1870-1882 |
582 |
|
o Will need long integration testing. |
583 |
|
checkpoint53b_pre |
584 |
|
|
585 |
|
o created pkg/mom_common in preparation for variable viscosity code |
586 |
|
o renamed and split ini_mnc_io |
587 |
|
o pkg/land: only liquid water can diffuse or run-off |
588 |
|
o AIM using land: soil wetness availability account for snow |
589 |
|
o added printMapIncludesZeros to EEPARMS namelist |
590 |
|
|
591 |
|
checkpoint53a_post |
592 |
|
o restore TAMC compatiility for exf_constants.h |
593 |
|
(no usage of _d in .h) |
594 |
|
o Additional storing in KPP in an attempt to fix |
595 |
|
TAMC problem with adjoint of KPP code. |
596 |
|
(no success...) |
597 |
|
Identical code works fine with TAF. |
598 |
|
o Fixed verification/natl_box_adjoint experiments. |
599 |
|
Initial conditions for Experiments 4 and 5 are now |
600 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
601 |
|
and hence gives results closer to that of Experiment 2. |
602 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
603 |
|
|
604 |
|
checkpoint53 |
605 |
|
o stable checkpoint with up to date adjoint |
606 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
607 |
|
this is a code problem or a problem with resetting code for g_ |
608 |
|
variables that is being autogenerated wrong. |
609 |
|
Otherwise: |
610 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
611 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
612 |
|
are both still in chaos following their security messes. |
613 |
|
|
614 |
|
checkpoint52n_post |
615 |
|
o various build (mostly genmake2) changes including: |
616 |
|
- ability to build/run more easily within Cygwin and MacOS X |
617 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
618 |
|
o pkg/seaice modifications |
619 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
620 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
621 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
622 |
|
- changed proxy for geostrophic velocity and updated |
623 |
|
verification/lab_sea/results/* accordingly |
624 |
|
- removed ADI dynamic solver from pkg/seaice |
625 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
626 |
|
they caused a segmentation fault under certain circumstances |
627 |
|
- removed unused field WATR |
628 |
|
o bug fix in exf-package: |
629 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
630 |
|
now reflect that. |
631 |
|
o small fixes in the cal-package: |
632 |
|
- set reference date to first of January for the 'model'-calendar |
633 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
634 |
|
warning |
635 |
|
o small modifications in exf-package to increase flexibility: |
636 |
|
- change climtempfreeze from a constant to a runtime parameter that |
637 |
|
is specified in data.exf_clim (default = -1.9) |
638 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
639 |
|
specified in data.exf |
640 |
|
o fix in pkg/thsice: |
641 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
642 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
643 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
644 |
|
|
645 |
|
checkpoint52m_post |
646 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
647 |
|
this does not change any of the results, because myIter=0 in swfrac always |
648 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
649 |
|
as a default |
650 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
651 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
652 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
653 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
654 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
655 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
656 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
657 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
658 |
|
o monitor package can write to NetCDF files and/or STDOUT |
659 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
660 |
|
o doc/api_reference added |
661 |
|
- a framework for building an API Reference Manual using all |
662 |
|
the "protex" comments embedded in the code |
663 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
664 |
|
o MNC: |
665 |
|
- make myThid the last argument for all subroutines |
666 |
|
- new default for the grid files: NO halos |
667 |
|
- add useMNC and other run-time flags |
668 |
|
- separate per-file-group handling of the unlimited dimension |
669 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
670 |
|
and lookup tables set in initialize_fixed |
671 |
|
- write all MNC output to a freshly-created directory |
672 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
673 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
674 |
|
o Added functionality to grdchk: |
675 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
676 |
|
|
677 |
|
checkpoint52l_post |
678 |
|
o new land formulation: |
679 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
680 |
|
energy conservation. |
681 |
|
b) account for water temperature and for latent heat of freezing |
682 |
|
in all processes (rain, run-off, ground storage) |
683 |
|
c) compute surface and ground temperature implicitly. |
684 |
|
o aim_v23 modification for new land model: |
685 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
686 |
|
to allow implicit computation of land & sea-ice surface temp. |
687 |
|
b) add snow precipitation. |
688 |
|
checkpoint52l_pre |
689 |
|
|
690 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
691 |
|
o fix bug in timeAve (u,vZetatave in common block) |
692 |
|
o no restoring terms under ice for pkg/seaice |
693 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
694 |
|
o bug fix for pkg/seaice pickups |
695 |
|
o change MNC call locations and add coordinate attributes |
696 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
697 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
698 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
699 |
|
o exf: Adding simple range check routine for exf fields after read |
700 |
|
|
701 |
|
checkpoint52k_post |
702 |
|
o removed top-level directory "diags" |
703 |
|
- we migrated these functions to pkg/timeave a long time ago |
704 |
|
o fixed bug introduced in pkg/monitor |
705 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
706 |
|
averaged fields (I/O via cost_averages) |
707 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
708 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
709 |
|
o added initial do_the_model_io to ecco |
710 |
|
o set all ...Freq to zero after cost_final |
711 |
|
taveFreq, dumpFreq, pChkptFreq |
712 |
|
o MAIN and ECCO differentiability restored |
713 |
|
|
714 |
|
checkpoint52j_post |
715 |
|
o fix nchklev in tamc.h for global_ocean... |
716 |
|
o Bringing flow and store directives up-to-date |
717 |
|
o Really weird thing! |
718 |
|
call do_the_model_io from the_main_loop with parameters |
719 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
720 |
|
TAF places a faulty re-call of initialise_varia |
721 |
|
after cost_final call which should not be there! |
722 |
|
checkpoint52j_pre |
723 |
|
|
724 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
725 |
|
error messages |
726 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
727 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
728 |
|
debug output |
729 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
730 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
731 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
732 |
|
o update AIM Equatorial Channel exp: |
733 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
734 |
|
o globalFile now works with exch2 |
735 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
736 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
737 |
|
o limit timeave output for hi-res integrations |
738 |
|
|
739 |
|
checkpoint52i_post |
740 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
741 |
|
o updated the tiling for global_ocean_pressure |
742 |
|
checkpoint52i_pre |
743 |
|
|
744 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
745 |
|
the old pkg/aim). |
746 |
|
|
747 |
|
checkpoint52h_pre |
748 |
|
o shortened offending lines in exch2_send_rx?.template |
749 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
750 |
|
o genmake2: add build & execute test for NetCDF code |
751 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
752 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
753 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
754 |
|
o added temporary hack for sea-ice dynamics on the cube: |
755 |
|
metric terms are ignored and it is assumed that |
756 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
757 |
|
|
758 |
|
checkpoint52f_post |
759 |
|
o added exch2 cube routines to pkg/exch2 |
760 |
|
o modified hs94.cs-32x32x5 to use it |
761 |
|
o added new grid files to hs94.cs-32x32x5 |
762 |
|
checkpoint52f_pre |
763 |
|
|
764 |
|
checkpoint52e_post |
765 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
766 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
767 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
768 |
|
to work with implicit vertical advection and AB ; |
769 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
770 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
771 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
772 |
|
checkpoint52e_pre |
773 |
|
|
774 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
775 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
776 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
777 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
778 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
779 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
780 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
781 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
782 |
|
|
783 |
|
checkpoint52d_post |
784 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
785 |
|
- updated output accordingly |
786 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
787 |
|
random number generator |
788 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
789 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
790 |
|
o changes to permit hi-res, cubed-sphere, configuration |
791 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
792 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
793 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
794 |
|
of surface winds for the cube |
795 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
796 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
797 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
798 |
|
complete with example surface forcing files and matlab scripts to look |
799 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
800 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
801 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
802 |
|
to conform to the common rule. |
803 |
|
o check-in the first version of the coupler + interfaces for multi-components |
804 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
805 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
806 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
807 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
808 |
|
- exchanges between component and coupler is done in forward_step |
809 |
|
o new verification experiment, cpl_aim+ocn: |
810 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
811 |
|
|
812 |
|
checkpoint52d_pre |
813 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
814 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
815 |
|
|
816 |
|
checkpoint52c_post |
817 |
|
o Fixing OPTIONS files for use of exf: |
818 |
|
- ALLOW_ECCO not needed |
819 |
|
- ECCO_CPPOPTIONS.h should not be included from |
820 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
821 |
|
as has been the case in the past |
822 |
|
- All cal/exf related options are currently set in |
823 |
|
single header file. Should remain so until we |
824 |
|
agree on a consistent new policy. |
825 |
|
o Removed all CPP options for cal package. |
826 |
|
cal has no more CPP options. |
827 |
|
o modified STOREs in GAD_ADVECTION |
828 |
|
o corrected key comp. for passkey |
829 |
|
|
830 |
|
checkpoint52b_post |
831 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
832 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
833 |
|
- modify fluxes but do not change theta directly; |
834 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
835 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
836 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
837 |
|
o put back grid & coriolis monitor output. |
838 |
|
checkpoint52b_pre |
839 |
|
|
840 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
841 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
842 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
843 |
|
(need info on NUMBER_OF_PTRACERS) |
844 |
|
o missing PTRACERS headers in some routines |
845 |
|
o default tamc.h in pkg/autodiff supposed to crash |
846 |
|
to ensure proper customization |
847 |
|
|
848 |
|
checkpoint52a_post |
849 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
850 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
851 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
852 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
853 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
854 |
|
- keep the old version of FREEZE for backward compatibility; |
855 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
856 |
|
- corresponding modifs for TAF directives |
857 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
858 |
|
o time-averaged output for pkg/ptracers |
859 |
|
o fix problem with ECCO-related divided adjoint |
860 |
|
snapshot file was missing some ad-variables, |
861 |
|
but no warning issued by TAF |
862 |
|
|
863 |
|
checkpoint52a_pre |
864 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
865 |
|
|
866 |
|
checkpoint52 = ecco_c52_e35 |
867 |
|
o after testing adjoints of checkpoint51u_post |
868 |
|
|
869 |
|
checkpoint51u_post |
870 |
|
o this is the post-merge tag of the ecco-branch |
871 |
|
(needs another clean checkout and re-testing) |
872 |
|
o various natl_box_adjoint configs and results |
873 |
|
but no input fields |
874 |
|
o obcs adjoint not yet merged! |
875 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
876 |
|
o updated/extended some store directives for seaice |
877 |
|
o pkg/ecco now containes ecco-specific part of cost function |
878 |
|
o top level routines the_main_loop, forward_step |
879 |
|
supersede those in model/src/ |
880 |
|
previous input data.cost now in data.ecco |
881 |
|
(new namelist ecco_cost_nml) |
882 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
883 |
|
|
884 |
|
checkpoint51t_post |
885 |
|
o this is the pre-merge tag of the ecco-branch |
886 |
|
|
887 |
|
checkpoint51s_post |
888 |
|
o cleanup: removed various obsolete #define-s |
889 |
|
o pkg/grdchk |
890 |
|
- renamed 'ph-grd 3' to 'grad-res' |
891 |
|
- merged from ecco-branch |
892 |
|
(remaining bug fixes for obcs gradient checks) |
893 |
|
- additional high-precision output for testreport |
894 |
|
(grep for 'precision_grdchk_result') |
895 |
|
|
896 |
|
checkpoint51r_post |
897 |
|
o cleaned up or removed CPP_OPTIONS.h files |
898 |
|
o updated results for some of the tests to reflect the new |
899 |
|
optfiles (-ieee: -O0 instead of -O3) |
900 |
|
|
901 |
|
checkpoint51q_post |
902 |
|
o cd_code: |
903 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
904 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
905 |
|
- separated cd_code part from write_checkpoint |
906 |
|
- updated AD_SOURCE, generated .flow |
907 |
|
- added CD_CODE_VARS.h to the_main_loop |
908 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
909 |
|
o ctrl package totally restructured |
910 |
|
- pack/unpack now optional and decoupled from |
911 |
|
xx_/adxx_ I/O |
912 |
|
- ctrl_pack/unpack cleaned |
913 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
914 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
915 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
916 |
|
|
917 |
|
checkpoint51p_post |
918 |
|
o create initial cd_code package |
919 |
|
- WARNING: the initialization of fields within packages |
920 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
921 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
922 |
|
This seems to be backwards since |
923 |
|
1) its important to initially zero the entire field including |
924 |
|
the "halo" region |
925 |
|
2) zeroing needs to be done *before* reading pickup info |
926 |
|
and the pickup call might or might not happen in any |
927 |
|
particular run |
928 |
|
- this needs an overhaul for R2 |
929 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
930 |
|
o cleanup testreport |
931 |
|
|
932 |
|
checkpoint51o_post |
933 |
|
o bringing AD-related verif's up to date with genmake2 |
934 |
|
- carbon/ |
935 |
|
- global_ocean.90x40x15/ |
936 |
|
- hs.94.1x64x5/ |
937 |
|
- (front_relax/ ) |
938 |
|
o (more) consistent directory structure for AD-related verif.'s |
939 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
940 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
941 |
|
o bug fix in find_alpha.F for MDJWF: |
942 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
943 |
|
change rho -> rho-rhoConst |
944 |
|
- replace call find_rho to find_rhonum |
945 |
|
o initialisation of rFlx extended to full array (required by TAF) |
946 |
|
and shifted to thermodynamics |
947 |
|
o removed PTRACERS.h in ptracers routine |
948 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
949 |
|
o Correcting initialisations for fVerU, fVerV. |
950 |
|
o helping TAF to recognize dependency on kUp for |
951 |
|
fVerU, fVerV |
952 |
|
o Replacing delZ by delR in pkg/ctrl/ |
953 |
|
checkpoint51o_pre |
954 |
|
|
955 |
|
o undid all of cp51 pending some cleanups and discussion |
956 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
957 |
|
it for adjoint/tl #defines |
958 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
959 |
|
o removed tools/genmake since it no longer works |
960 |
|
|
961 |
|
checkpoint51n_post |
962 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
963 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
964 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
965 |
|
- subroutine FREEZE now limits only surface temperature |
966 |
|
(this means new output.txt for global_ocean.90x40x15, |
967 |
|
global_ocean.cs32x15, and global_with_exf) |
968 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
969 |
|
|
970 |
|
checkpoint51n_pre |
971 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
972 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
973 |
|
defines: |
974 |
|
- ALLOW_ADJOINT_RUN |
975 |
|
- ALLOW_TANGENTLINEAR_RUN |
976 |
|
- ALLOW_ECCO_OPTIMIZATION |
977 |
|
|
978 |
|
checkpoint51m_post |
979 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
980 |
|
- added new TAMC/TAF targets to the Makefile |
981 |
|
- various cleanups related to package handling |
982 |
|
- these changes should have no impact on the forward model |
983 |
|
|
984 |
|
checkpoint51l_post |
985 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
986 |
|
- faster algorithm for cal_addtime.F |
987 |
|
- higher precision arithmetic, where needed |
988 |
|
- pkg/exf *startdate variables changed from calendar date to |
989 |
|
model integration time |
990 |
|
|
991 |
|
checkpoint51l_pre |
992 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
993 |
|
o enable to apply restoring on S & T only in a latitude band. |
994 |
|
o update output (external_forcing_surf modif. change truncation errors) |
995 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
996 |
|
|
997 |
|
checkpoint51k_post |
998 |
|
o change default to: useNHMTerms=.FALSE. |
999 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
1000 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
1001 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
1002 |
|
exp1, ideal_2D_oce |
1003 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
1004 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
1005 |
|
o set gravitySign automatically according to the vertical coordinate used |
1006 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
1007 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
1008 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
1009 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
1010 |
|
|
1011 |
|
checkpoint51j_post |
1012 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
1013 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
1014 |
|
o added cubed-sphere case to test cost function |
1015 |
|
o heckpoint_lev?_directives.h now include |
1016 |
|
pkg-specific directives, whenever those are enabled. |
1017 |
|
o Moving pkg-specific flow directives to corresponding pkg |
1018 |
|
Moving pkg-specific differentiation list to corresponding pkg |
1019 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
1020 |
|
---> conventions are |
1021 |
|
- pkg_ad.flow |
1022 |
|
- pkg_ad_diff.list |
1023 |
|
- pkg_ad_check_lev?_dir.h |
1024 |
|
|
1025 |
checkpoint51i_post |
checkpoint51i_post |
1026 |
o merge of the branch-genmake2 |
o merge of the branch-genmake2 |
1027 |
- knowingly breaks the older genmake |
- knowingly breaks the older genmake |