1 |
dimitri |
1.426 |
$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.425 2004/12/20 23:32:52 dimitri Exp $ |
2 |
cnh |
1.1 |
|
3 |
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Notes on tags used in MITgcmUV |
4 |
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============================== |
5 |
edhill |
1.412 |
|
6 |
dimitri |
1.426 |
o pkg/seaice: some test code for ice-modified ocean stress |
7 |
dimitri |
1.425 |
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
8 |
|
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
9 |
|
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spurious negative numbers for precipitation and humidity. Will cause |
10 |
|
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some small numerical differences for integrations using pkg/exf/exf_interp.F. |
11 |
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|
12 |
jmc |
1.424 |
checkpoint57b_post |
13 |
|
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o simplify options in diagnostics_fill arguments (remove weird combinations) |
14 |
edhill |
1.423 |
o fix MNC coordinate variables so that they now contain per-face index |
15 |
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|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
16 |
|
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
17 |
jmc |
1.422 |
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
18 |
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o Implement instantaneous output within pkg diagnostics: |
19 |
|
|
setting a negative frequency in data.diagnostics produces |
20 |
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|
"snap-shot" output (as opposed to time-average if freq > 0) |
21 |
jmc |
1.421 |
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
22 |
|
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NOTE: change ptracer diagnostics name: use 2 characters to work with |
23 |
|
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
24 |
edhill |
1.420 |
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
25 |
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|
becomes the coordinate variable for the 'T' dimension |
26 |
edhill |
1.419 |
o add CF-style coordinate variables to MNC |
27 |
|
|
- just a first cut: numbers are meaningless on the cubesphere and |
28 |
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|
missing along the T axis but otherwise it works! |
29 |
dimitri |
1.418 |
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
30 |
jmc |
1.417 |
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
31 |
jmc |
1.416 |
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
32 |
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|
this is based directly on what the model compute, so that the content of |
33 |
|
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
34 |
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o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
35 |
mlosch |
1.415 |
o clean up build options files for SunOS, in particular |
36 |
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- remove -traditional from xmakedepend |
37 |
|
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- change -xarch=v9 to -xarch=native for f77 |
38 |
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- restore use of make (not gmake) |
39 |
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- add CC=gcc if using g77 |
40 |
edhill |
1.413 |
o changes per discussion of AM, JMC, & EH3 today: |
41 |
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- move redundant "grid" variables out of "state" -- in preparation of |
42 |
|
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creating proper CF-style coordinate variables and in recognition |
43 |
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that any/all grid variables can be easily copied (eg. w/NCO) from |
44 |
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the grid files into any of the other NetCDF files |
45 |
|
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- *always* output grid variables with MDSIO (this will eventually be |
46 |
|
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changed) |
47 |
|
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- output MNC grid file if useMNC is true |
48 |
edhill |
1.412 |
o every instance of _END_MASTER() has been found and replaced with |
49 |
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_END_MASTER( myThid ) in order to satisfy certain picky Sun |
50 |
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preprocessors |
51 |
jmc |
1.411 |
o re-arrange diagnostics pkg initialisation: |
52 |
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- allow each package to extend the available diagnostics list |
53 |
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- add some checking and fix small problems (multi-threaded, ...) |
54 |
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- new S/R diagnostics_fill (replace fill_diagnostics): |
55 |
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look through the short list of active diag. (instead of the long list) |
56 |
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create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
57 |
edhill |
1.381 |
|
58 |
heimbach |
1.410 |
checkpoint57a_post |
59 |
|
|
o this set of changes restores TAMC compatibility |
60 |
|
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tested for global_ocean.90x40x15 adjoint on trough |
61 |
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(what a pain) |
62 |
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|
63 |
heimbach |
1.409 |
checkpoint57a_pre |
64 |
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o some modifs in tools/build_options for sunos |
65 |
|
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o call ctrl_pack for ctrl at end for optimcycle=0 |
66 |
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|
67 |
jmc |
1.408 |
checkpoint57 |
68 |
mlosch |
1.406 |
o add horizontal bi-harmonic viscosity for vertical velocity |
69 |
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- new parameter viscA4W (defaults to viscA4) |
70 |
|
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- affects only non-hydrostatic code |
71 |
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- to be done: no-slip lateral boundary conditions |
72 |
dimitri |
1.405 |
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
73 |
jmc |
1.404 |
o implement Implicit Vertical advection for pTracers |
74 |
jmc |
1.401 |
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
75 |
jmc |
1.402 |
(implemented also for implicit vertical diffusion & advection) |
76 |
mlosch |
1.400 |
o OBCS: extend application of tracer open boundary conditions |
77 |
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to a strip beyond the boundary of width Olx/Oly |
78 |
heimbach |
1.403 |
o add call monitor to TAF set of required calls (flow directives) |
79 |
|
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and include in natl_box_adjoint |
80 |
|
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o untangle a few ifdefs related to cost, ctrl, autodiff |
81 |
|
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
82 |
heimbach |
1.407 |
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
83 |
|
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(theta2, salt2 in ecco_cost_weights) |
84 |
mlosch |
1.400 |
|
85 |
mlosch |
1.399 |
checkpoint56c_post |
86 |
|
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o OBCS as control variables |
87 |
|
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
88 |
|
|
- remove balance of obcs controls from default |
89 |
|
|
- fix index bug nobcs in ctrl_init |
90 |
|
|
- fix dummy fields filen in ctrl_pack |
91 |
|
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- add dummy weights for obcs |
92 |
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o lsopt: comment out fort.94 output |
93 |
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o optim: |
94 |
|
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- remove unnecessary header files |
95 |
|
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- adjusted namelists |
96 |
|
|
- add xerbla.F to Makefile |
97 |
|
|
o exf: |
98 |
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- multiple modifications of exf_check_range |
99 |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
100 |
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o mdsio: |
101 |
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- i/o-vector change debugLevel from debLevA to debLevB |
102 |
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|
103 |
mlosch |
1.398 |
checkpoint56b_post |
104 |
mlosch |
1.397 |
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
105 |
|
|
is called from DO_THE_MODEL_IO |
106 |
|
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
107 |
|
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
108 |
|
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- clean up PTRACERS_WRITE_TIMEAVE a little |
109 |
mlosch |
1.396 |
o add another verification experiment that tests both the cfc-pkg and |
110 |
|
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
111 |
|
|
reactive tendencies treated inline with regular timestepping |
112 |
mlosch |
1.395 |
o testreport previously did a lousy job of comparing small numbers, so |
113 |
|
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
114 |
|
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
115 |
|
|
testreport. |
116 |
|
|
o ptracers_monitor: bug fix for MPI |
117 |
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|
118 |
mlosch |
1.394 |
checkpoint56a_post |
119 |
|
|
o GCHEM: finish reorganizating the package |
120 |
|
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
121 |
|
|
(introduces another 3D-array for each passive tracer, but only if |
122 |
|
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
123 |
|
|
gchemTendency is not needed because the timestep is done separately) |
124 |
|
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
125 |
|
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
126 |
|
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
127 |
|
|
so clear to me how that should be done in a general way. |
128 |
|
|
o CFC: improve formatting of output in CFC_ATMOS |
129 |
|
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o PTRACERS: |
130 |
|
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- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
131 |
|
|
that ALL experiments with ptracers enable can be checked. This makes |
132 |
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GCHEM_MONITOR obsolete. |
133 |
|
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- include a runtime parameter PTRACERS_monitorFreq that defaults to |
134 |
|
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monitorFreq |
135 |
|
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
136 |
edhill |
1.393 |
o add PTRACERS (PTR0[1-5]) to testreport output |
137 |
heimbach |
1.391 |
o exf_check_range: |
138 |
|
|
* default changed to .TRUE. |
139 |
|
|
* will check values for niter0 if debLevA, every timestep if debLevB |
140 |
|
|
* STOP in exf_check_range if 'out of range' |
141 |
|
|
* range chosen generous to allow for potential extema |
142 |
|
|
TBD: a version with stricter range |
143 |
|
|
permitted range would be runtime parameters |
144 |
jmc |
1.390 |
o GMredi: |
145 |
|
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
146 |
|
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
147 |
|
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- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
148 |
mlosch |
1.388 |
o GCHEM: |
149 |
|
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
150 |
|
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
151 |
|
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
152 |
mlosch |
1.392 |
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
153 |
|
|
this flag is now only visible within GCHEM-pkg routines. |
154 |
|
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
155 |
|
|
be replaced by a 3D array that is computed before thermodynamics; for |
156 |
|
|
this, the tracer ID iTracer had to be included into the parameter list |
157 |
|
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of ptracers_forcing |
158 |
mlosch |
1.394 |
- set up forward_step to call gchem_forcing, that will replace |
159 |
mlosch |
1.392 |
gchem_forcing_int in ptracers_forcing |
160 |
|
|
- cleaning up |
161 |
jmc |
1.389 |
o small cleaning of exch2: remove files that are also in eesupp/src |
162 |
mlosch |
1.387 |
|
163 |
heimbach |
1.386 |
checkpoint56 |
164 |
jmc |
1.385 |
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
165 |
edhill |
1.384 |
o mnc: cleanup "full" files--fixes out-of-memory problem |
166 |
heimbach |
1.386 |
o ECCO-GODAE |
167 |
|
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
168 |
|
|
* fully merged and updated from SIO code |
169 |
|
|
windstress sign change affects |
170 |
|
|
- exf_inscal_[u/v]stress |
171 |
|
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- sign of xx_tau[u/v] adjustments |
172 |
|
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- signs in cost_scat |
173 |
|
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* ctrl_get_gen: avoid update of tau[u/v] for first few days |
174 |
|
|
* natl_box_adjoint updated and compressed |
175 |
|
|
* 2-level checkpoint switch added |
176 |
|
|
(tested in EXP. 1 of natl_box_adjoint) |
177 |
|
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
178 |
|
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o SVD |
179 |
|
|
* first complete, non-hacked version for SVD calculations |
180 |
|
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
181 |
|
|
performed via direct access files admtlm_vector.it???? |
182 |
|
|
(via ctrl_[un]pack) |
183 |
|
|
* optimcycle is used for ARPACK iteration counter |
184 |
|
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
185 |
|
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
186 |
|
|
and add linear transforms where necessary |
187 |
|
|
* controls are initial/final SST, SSS (can be extended; need to check |
188 |
|
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
189 |
|
|
o mdsio: filename info to both stderr, stdout |
190 |
|
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
191 |
|
|
from sign change |
192 |
edhill |
1.384 |
|
193 |
jmc |
1.383 |
checkpoint55j_post |
194 |
jmc |
1.382 |
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
195 |
|
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
196 |
edhill |
1.381 |
o add consistent build directories and .cvsignore files to verification |
197 |
dimitri |
1.380 |
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
198 |
edhill |
1.379 |
o make all subroutines 30 or less characters in length for certain older |
199 |
|
|
compilers to work (a thorough search only turns up two routines in |
200 |
|
|
pkg/ptracers) |
201 |
jmc |
1.378 |
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
202 |
|
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
203 |
|
|
|
204 |
jmc |
1.377 |
checkpoint55i_post |
205 |
jmc |
1.376 |
o change arrays for total vertical diffusivity (2.D if explicit, |
206 |
|
|
3.D if implicit) ; each ptracer uses its own background value. |
207 |
edhill |
1.375 |
o added mnc/NetCDF output capability to ocn_compon_interf |
208 |
|
|
- added bits to verification/cpl_aim+ocn so that it can run on |
209 |
|
|
ITRDA and other clusters without the mpirun "-wd" option |
210 |
afe |
1.374 |
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
211 |
|
|
configuration |
212 |
edhill |
1.373 |
o give MNC the ability to create additional files rather than |
213 |
|
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
214 |
|
|
- the default is just less than 2GB which is a practical limit |
215 |
|
|
on many systems |
216 |
jmc |
1.372 |
o Compute the non-local term using either KPP vertical diffusivity (=default) |
217 |
|
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
218 |
jmc |
1.349 |
|
219 |
jmc |
1.371 |
checkpoint55h_post |
220 |
|
|
o add verification test "vermix" |
221 |
edhill |
1.370 |
o remove all the *_ioinc flags and replace with the single global |
222 |
|
|
outputTypesInclusive flag |
223 |
jmc |
1.369 |
o allow to set a vertical profile of vertical diffusivity for T & S |
224 |
jmc |
1.371 |
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
225 |
|
|
o useMNC moved from data.mnc to data.pkg |
226 |
jmc |
1.369 |
|
227 |
heimbach |
1.368 |
checkpoint55g_post |
228 |
|
|
o Renaming carbon AD experiments to comply with testreport conventions |
229 |
|
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
230 |
|
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
231 |
|
|
have been fixed to avoid recomp. of do_oceanic_phys |
232 |
|
|
Works well for global_ocean.90x40x15, |
233 |
|
|
but recomp. issue remains for carbon |
234 |
|
|
o Updating adjoint output for natl_box_adjoint after |
235 |
|
|
pkg/ecco has been modified (see taga c55d_post) |
236 |
|
|
|
237 |
edhill |
1.367 |
checkpoint55f_post |
238 |
|
|
o rename to timeave_init_fixed |
239 |
|
|
|
240 |
heimbach |
1.366 |
checkpoint55e_post |
241 |
|
|
o some delicate re-shuffle of store directives to avoid one |
242 |
|
|
extra call of do_oceanic_physics |
243 |
|
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
244 |
|
|
checkpoint_lev1_directives.h |
245 |
|
|
o NB: this may break global_ocean adjoint temporarily, |
246 |
|
|
but it is clear how to fix it. Will do later, need this now. |
247 |
|
|
|
248 |
heimbach |
1.365 |
checkpoint55d_post |
249 |
|
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
250 |
|
|
o ecco_cost_weights is modified to 1x1 runs |
251 |
|
|
o modifs to allow observations to be read in as |
252 |
|
|
single file or yearly files |
253 |
|
|
o enable to read exf forcing fields as either |
254 |
|
|
single file or yearly files (flag useExfYearlyFields) |
255 |
|
|
checkpoint55d_pre |
256 |
|
|
|
257 |
|
|
o switch between 2-level and 3-level checkpointing |
258 |
edhill |
1.364 |
o add ability of MNC to write local and "partial" (eg. 2D slices where |
259 |
|
|
the full 3D field is never actually stored) arrays to NetCDF files |
260 |
|
|
with the correct (that is, the complete multi-dimensional) set of |
261 |
|
|
array indicies |
262 |
|
|
- used in mom_vecinv() to write the diagFreq output |
263 |
|
|
- tested (demonstrated) in verification/aim.5l_cs |
264 |
edhill |
1.363 |
o further mnc-ification |
265 |
|
|
- add verification/lab_sea to the list with mnc setups |
266 |
|
|
- fix undefined mnc v-names in cd_code |
267 |
|
|
- add kpp to mnc output (both snapshot and timeave) |
268 |
mlosch |
1.362 |
o non-hydrostatic code |
269 |
|
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
270 |
|
|
in calc_gw.F |
271 |
|
|
- defaults to viscAh |
272 |
|
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
273 |
|
|
friction or Leith) in non-hydrostatic mode, as long as there is |
274 |
|
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
275 |
heimbach |
1.360 |
o pkg/cost |
276 |
|
|
extend simple cost functions to treat time mean quantities |
277 |
|
|
(T,U,V) via cost_accumulate_state from cost_tile |
278 |
jmc |
1.358 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
279 |
|
|
be 2 times larger than the minimum size the advection scheme requires. |
280 |
|
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
281 |
mlosch |
1.356 |
o GGL90 (Gaspar's TKE mixed layer) |
282 |
|
|
- add horizontal diffusion of TKE, requires exchanges in |
283 |
|
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
284 |
|
|
default. In OPA there is no horizontal diffusion of TKE but the |
285 |
|
|
mixing coefficients are computed from a horizontal average of TKE of |
286 |
|
|
6 points or so. I think that diffusion has a little more physical |
287 |
|
|
justification. |
288 |
|
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
289 |
|
|
was in vain) |
290 |
|
|
- mask tke-variable in ggl90_init |
291 |
jmc |
1.355 |
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
292 |
|
|
o fix biharmonic diffusion on CS-grid. |
293 |
mlosch |
1.354 |
o more obcs stuff |
294 |
|
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
295 |
|
|
for reading boundary values. This routine is called from |
296 |
|
|
obcs_prescribe_read |
297 |
|
|
- updated obcs_check |
298 |
mlosch |
1.357 |
- changed sponge layer relaxation parameter units for days to seconds |
299 |
|
|
- turned off sponge layer by default |
300 |
heimbach |
1.359 |
- changed argument list of OBCS_CALC to myTime+deltaTclock |
301 |
mlosch |
1.361 |
- fixed about 35 bugs in obcs_external_fields_load |
302 |
mlosch |
1.354 |
|
303 |
heimbach |
1.353 |
checkpoint55c_post |
304 |
heimbach |
1.352 |
o obcs stuff |
305 |
|
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
306 |
|
|
- re-arranged obcs_calc |
307 |
|
|
- moved exf_getobcs to obcs_prescibe_read |
308 |
|
|
obcs_prescibe_read is called after ORLANSKI stuff |
309 |
|
|
and independent of it (executable can contain all). |
310 |
|
|
- updated obcs_check |
311 |
heimbach |
1.353 |
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
312 |
|
|
These may be necessary only if tangential velocities are |
313 |
|
|
prescribed at OB, not sure, needs testing. |
314 |
edhill |
1.351 |
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
315 |
|
|
which simplifies the calls and passes the ifc check-bounds test |
316 |
|
|
|
317 |
jmc |
1.350 |
checkpoint55b_post |
318 |
|
|
o add a 2D scalar, Z location, exchange_2 routine. |
319 |
jmc |
1.349 |
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
320 |
|
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
321 |
|
|
affects advect_cs results (for the wrong reason): update output.txt |
322 |
jmc |
1.348 |
o use a more standard discretization for biharmonic viscosity ; |
323 |
|
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
324 |
|
|
affects results of dome set-up: update output.txt |
325 |
|
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
326 |
|
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
327 |
mlosch |
1.341 |
|
328 |
heimbach |
1.347 |
checkpoint55a_post |
329 |
|
|
o merged code to |
330 |
|
|
* prescribe/read time-dependent open boundaries |
331 |
|
|
(works in conjunction with exf, cal) |
332 |
|
|
* sponge layer code for open boundaries |
333 |
|
|
* each boundary N/S/E/W now has its own CPP option |
334 |
|
|
(healthy for the adjoint) |
335 |
|
|
|
336 |
heimbach |
1.346 |
checkpoint55 |
337 |
|
|
o up-to-date adjoint of previous breaks |
338 |
|
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
339 |
|
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
340 |
|
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
341 |
|
|
- carbon: * remove tr1-related adjoint verification |
342 |
|
|
* add ptracer as control variable |
343 |
|
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
344 |
|
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
345 |
|
|
|
346 |
heimbach |
1.345 |
checkpoint54f_post |
347 |
|
|
o in verification/carbin/ remove experiment related to |
348 |
|
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
349 |
|
|
code_ad/ input_ad/ results_ad |
350 |
|
|
|
351 |
mlosch |
1.344 |
o add two new packages |
352 |
|
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
353 |
|
|
+ subject to optimization (memory) |
354 |
|
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
355 |
|
|
+ subject to reordering (many GOTOs in the original code) |
356 |
|
|
+ so far opps is called for every (i,j) point, and then operates in |
357 |
|
|
the vertical; one may want to reorder the scheme in order operate in |
358 |
|
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
359 |
|
|
fields) |
360 |
edhill |
1.343 |
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
361 |
|
|
- all verification tests compile and run with linux_ia32_g77 |
362 |
|
|
- defaults are compatible with current input files--nothing |
363 |
|
|
should change if you were not previously using MNC |
364 |
|
|
- MNC output has been added in numerous places (eg. timeave) |
365 |
|
|
but there are still a few writes not yet do-able with MNC |
366 |
|
|
(this is in progress) |
367 |
|
|
- flags now allow for either/or/both use of MDSIO and MNC and |
368 |
|
|
documentation will soon follow |
369 |
|
|
- numerous small formatting cleanups for ProTeX |
370 |
edhill |
1.342 |
o add version info (via BUILD_INFO.h) to MNC and stdout |
371 |
|
|
|
372 |
mlosch |
1.341 |
checkpoint54e_post |
373 |
|
|
o add two new packages |
374 |
|
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
375 |
|
|
stratification dependent mixing |
376 |
|
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
377 |
|
|
- these scheme operate in a similar manner as KPP (without ghat, of |
378 |
|
|
course), however there is only one diffusivity that is used for both |
379 |
|
|
temperature and salinity (and passive tracers)ç |
380 |
stephd |
1.340 |
o add offline package |
381 |
edhill |
1.339 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
382 |
|
|
provided by Stephanie Dutkiewicz |
383 |
edhill |
1.338 |
o genmake2: add ability to search for C compilers and cleanup test output |
384 |
|
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
385 |
|
|
|
386 |
jmc |
1.337 |
checkpoint54d_post |
387 |
adcroft |
1.336 |
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
388 |
jmc |
1.337 |
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
389 |
|
|
leading to additional shift by 5 days each year of integration |
390 |
|
|
(i.e. leading to considerable offset over the years) |
391 |
jmc |
1.335 |
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
392 |
|
|
o start with no AB and no initial filtering (staggerTimeStep): |
393 |
|
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
394 |
|
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
395 |
|
|
(external loading & cpl import/export stay in forward_step.F) |
396 |
|
|
o update coupling interface to work with new staggerTimeStep |
397 |
|
|
o change MDSIO ptracers_pickup. |
398 |
jmc |
1.334 |
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
399 |
edhill |
1.333 |
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
400 |
jmc |
1.334 |
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
401 |
edhill |
1.333 |
|
402 |
jmc |
1.332 |
checkpoint54c_post |
403 |
jmc |
1.331 |
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
404 |
|
|
this affects (truncation error) output.txt of test-exp: |
405 |
|
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
406 |
|
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
407 |
jmc |
1.330 |
o change Qnet to always be the net heat flux, (+upward). |
408 |
|
|
affects (truncation error) output of natl_box exp.: updated |
409 |
jmc |
1.329 |
o define the max number of passive tracers in PTRACERS_SIZE.h |
410 |
|
|
o start to test mnc routinely in exp0 |
411 |
|
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
412 |
|
|
|
413 |
jmc |
1.328 |
checkpoint54b_post |
414 |
edhill |
1.327 |
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
415 |
|
|
impressive on Altix and Opteron systems) |
416 |
edhill |
1.326 |
o diagnostics can now write NetCDF files through the mnc package |
417 |
jmc |
1.325 |
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
418 |
jmc |
1.324 |
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
419 |
jmc |
1.323 |
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
420 |
|
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
421 |
|
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
422 |
|
|
|
423 |
jmc |
1.322 |
checkpoint54a_post |
424 |
|
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
425 |
|
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
426 |
|
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
427 |
|
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
428 |
|
|
+ internal_wave (shift in writing cg2d_ini_res) |
429 |
jmc |
1.321 |
checkpoint54a_pre |
430 |
|
|
|
431 |
dimitri |
1.320 |
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
432 |
|
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
433 |
|
|
|
434 |
heimbach |
1.319 |
checkpoint54 |
435 |
heimbach |
1.318 |
checkpoint53g_post |
436 |
jmc |
1.317 |
o prepare splitting of thermodynamics: store convect.counter in common block |
437 |
jmc |
1.316 |
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
438 |
|
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
439 |
dimitri |
1.315 |
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
440 |
jmc |
1.314 |
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
441 |
|
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
442 |
heimbach |
1.318 |
o restore adjointability |
443 |
jmc |
1.314 |
|
444 |
jmc |
1.313 |
checkpoint53f_post |
445 |
|
|
o modifications that affect AIM experiment results (update output.txt): |
446 |
|
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
447 |
|
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
448 |
jmc |
1.312 |
o AIM pkg: |
449 |
|
|
- include stability function into surf.Flux derivative relative to Tsurf |
450 |
|
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
451 |
jmc |
1.313 |
|
452 |
afe |
1.311 |
checkpoint53e_post |
453 |
|
|
o merged cylindrical coord configuration |
454 |
|
|
o added rotating_tank experiment |
455 |
afe |
1.310 |
checkpoint53e_pre |
456 |
|
|
|
457 |
jmc |
1.309 |
checkpoint53d_post |
458 |
jmc |
1.308 |
o faulks upgraded: re-generate output.txt that have changed: |
459 |
|
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
460 |
adcroft |
1.307 |
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
461 |
jmc |
1.306 |
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
462 |
adcroft |
1.305 |
o added Sadourny discretization of Coriolis |
463 |
|
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
464 |
|
|
- re-enabled use of omega3 (useAbsVorticity) |
465 |
adcroft |
1.304 |
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
466 |
jmc |
1.309 |
vector-invariant equations |
467 |
adcroft |
1.304 |
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
468 |
mlosch |
1.303 |
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
469 |
|
|
hopefully without new bugs |
470 |
|
|
- still to do: biharmonic friction for non-hydrostatic w |
471 |
adcroft |
1.302 |
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
472 |
|
|
o regenerated output for global_ocean_ebm (using -ieee) |
473 |
adcroft |
1.301 |
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
474 |
|
|
of mom_common/ |
475 |
|
|
- simple re-arrangement of instructions within computing loop |
476 |
|
|
checkpoint53d_pre |
477 |
mlosch |
1.297 |
|
478 |
heimbach |
1.300 |
checkpoint53c_post |
479 |
jmc |
1.299 |
o new version of coupler for AIM+thSIce and Ocean models |
480 |
|
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
481 |
|
|
- land: change Evaporation of snow |
482 |
|
|
- aim with thSIce: fix bug in snow-precip. |
483 |
mlosch |
1.297 |
o changes to calc_gw.F |
484 |
|
|
- bug fix for w^2 term near the bottom boundary |
485 |
|
|
- (hopefully) improve the lateral slip boundary condtions for use with |
486 |
|
|
partial/looped cells |
487 |
|
|
- because the bug fix changes two verification experiments anyway (exp5 |
488 |
|
|
and plume on slope), change the lateral boundary condition from half slip |
489 |
|
|
to the value of no_slip_sides |
490 |
heimbach |
1.298 |
o ebm package wasnt quite up to the parallel task. Fixed that. |
491 |
heimbach |
1.300 |
o Adjoint of EBM package + verification |
492 |
|
|
* TLM OK |
493 |
|
|
* ADM not sufficient accuracy yet (needs further testing) |
494 |
heimbach |
1.295 |
|
495 |
heimbach |
1.296 |
checkpoint53b_post |
496 |
|
|
o Commiting new energy balance model to repository |
497 |
|
|
* package is pkg/ebm |
498 |
|
|
* verif. is verification/global_ocean_ebm |
499 |
|
|
* references are in ebm_driver.F |
500 |
|
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
501 |
|
|
C Global thermohaline circulation. Part I: |
502 |
|
|
C Sensitivity to atmospheric moisture transport. |
503 |
|
|
C J. Climate 12(1), 71-82 |
504 |
|
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
505 |
|
|
C Global thermohaline circulation. Part II: |
506 |
|
|
C Sensitivity with interactive transport. |
507 |
|
|
C J. Climate 12(1), 83-91 |
508 |
|
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
509 |
|
|
C Destabilization of the thermohaline circulation |
510 |
|
|
C by atmospheric eddy transports. |
511 |
|
|
C J. Climate 7(12), 1870-1882 |
512 |
|
|
o Will need long integration testing. |
513 |
heimbach |
1.295 |
checkpoint53b_pre |
514 |
dimitri |
1.292 |
|
515 |
adcroft |
1.294 |
o created pkg/mom_common in preparation for variable viscosity code |
516 |
|
|
o renamed and split ini_mnc_io |
517 |
jmc |
1.293 |
o pkg/land: only liquid water can diffuse or run-off |
518 |
|
|
o AIM using land: soil wetness availability account for snow |
519 |
dimitri |
1.292 |
o added printMapIncludesZeros to EEPARMS namelist |
520 |
heimbach |
1.290 |
|
521 |
|
|
checkpoint53a_post |
522 |
|
|
o restore TAMC compatiility for exf_constants.h |
523 |
|
|
(no usage of _d in .h) |
524 |
|
|
o Additional storing in KPP in an attempt to fix |
525 |
|
|
TAMC problem with adjoint of KPP code. |
526 |
|
|
(no success...) |
527 |
|
|
Identical code works fine with TAF. |
528 |
dimitri |
1.291 |
o Fixed verification/natl_box_adjoint experiments. |
529 |
|
|
Initial conditions for Experiments 4 and 5 are now |
530 |
|
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
531 |
|
|
and hence gives results closer to that of Experiment 2. |
532 |
|
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
533 |
cnh |
1.289 |
|
534 |
|
|
checkpoint53 |
535 |
|
|
o stable checkpoint with up to date adjoint |
536 |
|
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
537 |
|
|
this is a code problem or a problem with resetting code for g_ |
538 |
|
|
variables that is being autogenerated wrong. |
539 |
|
|
Otherwise: |
540 |
|
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
541 |
|
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
542 |
|
|
are both still in chaos following their security messes. |
543 |
jmc |
1.279 |
|
544 |
edhill |
1.288 |
checkpoint52n_post |
545 |
|
|
o various build (mostly genmake2) changes including: |
546 |
|
|
- ability to build/run more easily within Cygwin and MacOS X |
547 |
|
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
548 |
dimitri |
1.285 |
o pkg/seaice modifications |
549 |
dimitri |
1.287 |
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
550 |
|
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
551 |
|
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
552 |
dimitri |
1.285 |
- changed proxy for geostrophic velocity and updated |
553 |
dimitri |
1.286 |
verification/lab_sea/results/* accordingly |
554 |
dimitri |
1.285 |
- removed ADI dynamic solver from pkg/seaice |
555 |
|
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
556 |
|
|
they caused a segmentation fault under certain circumstances |
557 |
mlosch |
1.283 |
- removed unused field WATR |
558 |
mlosch |
1.282 |
o bug fix in exf-package: |
559 |
|
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
560 |
|
|
now reflect that. |
561 |
mlosch |
1.281 |
o small fixes in the cal-package: |
562 |
|
|
- set reference date to first of January for the 'model'-calendar |
563 |
|
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
564 |
|
|
warning |
565 |
mlosch |
1.280 |
o small modifications in exf-package to increase flexibility: |
566 |
|
|
- change climtempfreeze from a constant to a runtime parameter that |
567 |
|
|
is specified in data.exf_clim (default = -1.9) |
568 |
|
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
569 |
|
|
specified in data.exf |
570 |
jmc |
1.279 |
o fix in pkg/thsice: |
571 |
|
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
572 |
|
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
573 |
|
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
574 |
edhill |
1.272 |
|
575 |
jmc |
1.278 |
checkpoint52m_post |
576 |
mlosch |
1.277 |
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
577 |
|
|
this does not change any of the results, because myIter=0 in swfrac always |
578 |
|
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
579 |
|
|
as a default |
580 |
jmc |
1.276 |
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
581 |
jmc |
1.275 |
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
582 |
|
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
583 |
|
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
584 |
|
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
585 |
dimitri |
1.274 |
o extending useSingleCpuIO option to work with new exch2 I/O format |
586 |
|
|
- old-style, missing-tile I/O is still accessible by defining CPP |
587 |
|
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
588 |
edhill |
1.273 |
o monitor package can write to NetCDF files and/or STDOUT |
589 |
|
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
590 |
edhill |
1.272 |
o doc/api_reference added |
591 |
|
|
- a framework for building an API Reference Manual using all |
592 |
|
|
the "protex" comments embedded in the code |
593 |
|
|
- see pkg/generic_advdiff, pkg/mnc for examples |
594 |
edhill |
1.269 |
o MNC: |
595 |
|
|
- make myThid the last argument for all subroutines |
596 |
|
|
- new default for the grid files: NO halos |
597 |
edhill |
1.270 |
- add useMNC and other run-time flags |
598 |
|
|
- separate per-file-group handling of the unlimited dimension |
599 |
|
|
- early initialization of MNC w/ flags read at the eeboot stage |
600 |
|
|
and lookup tables set in initialize_fixed |
601 |
|
|
- write all MNC output to a freshly-created directory |
602 |
jmc |
1.268 |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
603 |
|
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
604 |
heimbach |
1.271 |
o Added functionality to grdchk: |
605 |
|
|
pick global i,j,k position (or nearest wet) where to perform check. |
606 |
jmc |
1.266 |
|
607 |
jmc |
1.267 |
checkpoint52l_post |
608 |
|
|
o new land formulation: |
609 |
|
|
a) use ground enthalpy as prognostic variable to ensure exact |
610 |
|
|
energy conservation. |
611 |
|
|
b) account for water temperature and for latent heat of freezing |
612 |
|
|
in all processes (rain, run-off, ground storage) |
613 |
|
|
c) compute surface and ground temperature implicitly. |
614 |
|
|
o aim_v23 modification for new land model: |
615 |
|
|
a) Treat separately land / ocean / sea-ice surface fluxes |
616 |
|
|
to allow implicit computation of land & sea-ice surface temp. |
617 |
|
|
b) add snow precipitation. |
618 |
jmc |
1.266 |
checkpoint52l_pre |
619 |
|
|
|
620 |
jmc |
1.265 |
o fix problem (when 1 tile is empty) in min/max monitor. |
621 |
|
|
o fix bug in timeAve (u,vZetatave in common block) |
622 |
dimitri |
1.264 |
o no restoring terms under ice for pkg/seaice |
623 |
dimitri |
1.263 |
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
624 |
|
|
o bug fix for pkg/seaice pickups |
625 |
edhill |
1.262 |
o change MNC call locations and add coordinate attributes |
626 |
jmc |
1.260 |
o mask vorticity at the corner ; affects global_ocean.cs output |
627 |
|
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
628 |
jmc |
1.259 |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
629 |
heimbach |
1.261 |
o exf: Adding simple range check routine for exf fields after read |
630 |
adcroft |
1.256 |
|
631 |
heimbach |
1.257 |
checkpoint52k_post |
632 |
adcroft |
1.256 |
o removed top-level directory "diags" |
633 |
|
|
- we migrated these functions to pkg/timeave a long time ago |
634 |
|
|
o fixed bug introduced in pkg/monitor |
635 |
heimbach |
1.257 |
o accuracy ctrlprec = 32 insuffient for gradient checks using |
636 |
|
|
averaged fields (I/O via cost_averages) |
637 |
|
|
-> use ctrl.h in active_file*.F to control I/O precision. |
638 |
|
|
o paramter list of CALL ADTHE_MAIN_LOOP |
639 |
|
|
o added initial do_the_model_io to ecco |
640 |
|
|
o set all ...Freq to zero after cost_final |
641 |
|
|
taveFreq, dumpFreq, pChkptFreq |
642 |
heimbach |
1.258 |
o MAIN and ECCO differentiability restored |
643 |
heimbach |
1.255 |
|
644 |
|
|
checkpoint52j_post |
645 |
|
|
o fix nchklev in tamc.h for global_ocean... |
646 |
|
|
o Bringing flow and store directives up-to-date |
647 |
|
|
o Really weird thing! |
648 |
|
|
call do_the_model_io from the_main_loop with parameters |
649 |
|
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
650 |
|
|
TAF places a faulty re-call of initialise_varia |
651 |
|
|
after cost_final call which should not be there! |
652 |
|
|
checkpoint52j_pre |
653 |
jmc |
1.253 |
|
654 |
afe |
1.254 |
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
655 |
|
|
error messages |
656 |
jmc |
1.253 |
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
657 |
afe |
1.252 |
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
658 |
|
|
debug output |
659 |
afe |
1.251 |
o modfied mdsio_writefield.F to handle non-global files under exch2 |
660 |
jmc |
1.250 |
o update AIM Cubed-Sphere exp (aim.5l_cs): |
661 |
|
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
662 |
|
|
o update AIM Equatorial Channel exp: |
663 |
|
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
664 |
afe |
1.248 |
o globalFile now works with exch2 |
665 |
afe |
1.247 |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
666 |
jmc |
1.253 |
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
667 |
dimitri |
1.249 |
o limit timeave output for hi-res integrations |
668 |
adcroft |
1.245 |
|
669 |
|
|
checkpoint52i_post |
670 |
|
|
o removed CPP_EEOPTIONS.h from verification/*/code |
671 |
|
|
o updated the tiling for global_ocean_pressure |
672 |
|
|
checkpoint52i_pre |
673 |
jmc |
1.246 |
|
674 |
|
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
675 |
|
|
the old pkg/aim). |
676 |
afe |
1.239 |
|
677 |
dimitri |
1.244 |
checkpoint52h_pre |
678 |
afe |
1.243 |
o shortened offending lines in exch2_send_rx?.template |
679 |
afe |
1.242 |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
680 |
edhill |
1.240 |
o genmake2: add build & execute test for NetCDF code |
681 |
afe |
1.239 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
682 |
|
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
683 |
dimitri |
1.238 |
o added useSingleCPUIO flag to monitor.F and mon_out.F |
684 |
dimitri |
1.241 |
o added temporary hack for sea-ice dynamics on the cube: |
685 |
|
|
metric terms are ignored and it is assumed that |
686 |
|
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
687 |
dimitri |
1.238 |
|
688 |
|
|
checkpoint52f_post |
689 |
afe |
1.236 |
o added exch2 cube routines to pkg/exch2 |
690 |
|
|
o modified hs94.cs-32x32x5 to use it |
691 |
|
|
o added new grid files to hs94.cs-32x32x5 |
692 |
dimitri |
1.238 |
checkpoint52f_pre |
693 |
dimitri |
1.228 |
|
694 |
jmc |
1.235 |
checkpoint52e_post |
695 |
jmc |
1.234 |
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
696 |
|
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
697 |
jmc |
1.235 |
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
698 |
|
|
to work with implicit vertical advection and AB ; |
699 |
|
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
700 |
|
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
701 |
|
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
702 |
jmc |
1.233 |
checkpoint52e_pre |
703 |
|
|
|
704 |
|
|
o fix bug in impldiff when Nr=1 or Nr=2. |
705 |
jmc |
1.232 |
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
706 |
|
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
707 |
jmc |
1.229 |
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
708 |
|
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
709 |
dimitri |
1.228 |
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
710 |
dimitri |
1.231 |
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
711 |
|
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
712 |
jmc |
1.220 |
|
713 |
jmc |
1.226 |
checkpoint52d_post |
714 |
adcroft |
1.230 |
o re-tiled many expts to allow comparison in multi-processor mode |
715 |
|
|
- updated output accordingly |
716 |
|
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
717 |
|
|
random number generator |
718 |
molod |
1.227 |
o add infrastructure in model routines for fizhi and gridalt packages |
719 |
jmc |
1.220 |
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
720 |
dimitri |
1.222 |
o changes to permit hi-res, cubed-sphere, configuration |
721 |
|
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
722 |
|
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
723 |
|
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
724 |
|
|
of surface winds for the cube |
725 |
|
|
(A verification experiment, based on global_ocean.cs32x15, but with |
726 |
|
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
727 |
|
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
728 |
|
|
complete with example surface forcing files and matlab scripts to look |
729 |
|
|
at the output and compare it with that of global_ocean.cs32x15.) |
730 |
jmc |
1.223 |
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
731 |
|
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
732 |
|
|
to conform to the common rule. |
733 |
jmc |
1.224 |
o check-in the first version of the coupler + interfaces for multi-components |
734 |
|
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
735 |
|
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
736 |
|
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
737 |
|
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
738 |
|
|
- exchanges between component and coupler is done in forward_step |
739 |
jmc |
1.225 |
o new verification experiment, cpl_aim+ocn: |
740 |
|
|
coupled ocean - AIM atmosphere on cs32 grid. |
741 |
jmc |
1.217 |
|
742 |
dimitri |
1.219 |
checkpoint52d_pre |
743 |
jmc |
1.217 |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
744 |
jmc |
1.218 |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
745 |
heimbach |
1.213 |
|
746 |
heimbach |
1.216 |
checkpoint52c_post |
747 |
heimbach |
1.213 |
o Fixing OPTIONS files for use of exf: |
748 |
|
|
- ALLOW_ECCO not needed |
749 |
|
|
- ECCO_CPPOPTIONS.h should not be included from |
750 |
|
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
751 |
|
|
as has been the case in the past |
752 |
|
|
- All cal/exf related options are currently set in |
753 |
|
|
single header file. Should remain so until we |
754 |
|
|
agree on a consistent new policy. |
755 |
heimbach |
1.214 |
o Removed all CPP options for cal package. |
756 |
|
|
cal has no more CPP options. |
757 |
heimbach |
1.215 |
o modified STOREs in GAD_ADVECTION |
758 |
|
|
o corrected key comp. for passkey |
759 |
heimbach |
1.210 |
|
760 |
jmc |
1.212 |
checkpoint52b_post |
761 |
|
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
762 |
|
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
763 |
|
|
- modify fluxes but do not change theta directly; |
764 |
|
|
- light cleaning of bulk_force pkg (still needed with thsice). |
765 |
|
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
766 |
|
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
767 |
|
|
o put back grid & coriolis monitor output. |
768 |
jmc |
1.211 |
checkpoint52b_pre |
769 |
|
|
|
770 |
|
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
771 |
|
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
772 |
heimbach |
1.210 |
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
773 |
|
|
(need info on NUMBER_OF_PTRACERS) |
774 |
|
|
o missing PTRACERS headers in some routines |
775 |
|
|
o default tamc.h in pkg/autodiff supposed to crash |
776 |
|
|
to ensure proper customization |
777 |
dimitri |
1.206 |
|
778 |
heimbach |
1.209 |
checkpoint52a_post |
779 |
jmc |
1.208 |
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
780 |
dimitri |
1.207 |
- moved surfaceTendencyTice from pkg/seaice to main code |
781 |
jmc |
1.208 |
- subroutine FREEZE_SURFACE now limits only surface temperature |
782 |
|
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
783 |
|
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
784 |
|
|
- keep the old version of FREEZE for backward compatibility; |
785 |
|
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
786 |
heimbach |
1.209 |
- corresponding modifs for TAF directives |
787 |
dimitri |
1.207 |
o added surface flux output variables to TIMEAVE_STATVARS |
788 |
|
|
o time-averaged output for pkg/ptracers |
789 |
heimbach |
1.209 |
o fix problem with ECCO-related divided adjoint |
790 |
|
|
snapshot file was missing some ad-variables, |
791 |
|
|
but no warning issued by TAF |
792 |
dimitri |
1.206 |
|
793 |
dimitri |
1.207 |
checkpoint52a_pre |
794 |
dimitri |
1.206 |
o some bug fixes for #undef REAL4_IS_SLOW |
795 |
heimbach |
1.205 |
|
796 |
|
|
checkpoint52 = ecco_c52_e35 |
797 |
|
|
o after testing adjoints of checkpoint51u_post |
798 |
edhill |
1.203 |
|
799 |
heimbach |
1.204 |
checkpoint51u_post |
800 |
|
|
o this is the post-merge tag of the ecco-branch |
801 |
|
|
(needs another clean checkout and re-testing) |
802 |
|
|
o various natl_box_adjoint configs and results |
803 |
|
|
but no input fields |
804 |
|
|
o obcs adjoint not yet merged! |
805 |
|
|
o adding ECCO global 1x1 and 2x2 degree configs |
806 |
|
|
o updated/extended some store directives for seaice |
807 |
|
|
o pkg/ecco now containes ecco-specific part of cost function |
808 |
|
|
o top level routines the_main_loop, forward_step |
809 |
|
|
supersede those in model/src/ |
810 |
|
|
previous input data.cost now in data.ecco |
811 |
|
|
(new namelist ecco_cost_nml) |
812 |
|
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
813 |
|
|
|
814 |
|
|
checkpoint51t_post |
815 |
|
|
o this is the pre-merge tag of the ecco-branch |
816 |
|
|
|
817 |
edhill |
1.203 |
checkpoint51s_post |
818 |
|
|
o cleanup: removed various obsolete #define-s |
819 |
heimbach |
1.204 |
o pkg/grdchk |
820 |
|
|
- renamed 'ph-grd 3' to 'grad-res' |
821 |
|
|
- merged from ecco-branch |
822 |
|
|
(remaining bug fixes for obcs gradient checks) |
823 |
|
|
- additional high-precision output for testreport |
824 |
|
|
(grep for 'precision_grdchk_result') |
825 |
edhill |
1.202 |
|
826 |
|
|
checkpoint51r_post |
827 |
|
|
o cleaned up or removed CPP_OPTIONS.h files |
828 |
|
|
o updated results for some of the tests to reflect the new |
829 |
|
|
optfiles (-ieee: -O0 instead of -O3) |
830 |
heimbach |
1.201 |
|
831 |
|
|
checkpoint51q_post |
832 |
|
|
o cd_code: |
833 |
|
|
- moved cd_scheme.F -> cd_code_scheme.F |
834 |
|
|
- separate read_checkpoint from cd_code_ini_vars.F |
835 |
|
|
- separated cd_code part from write_checkpoint |
836 |
|
|
- updated AD_SOURCE, generated .flow |
837 |
|
|
- added CD_CODE_VARS.h to the_main_loop |
838 |
|
|
- Moving cd_code specific store dir.s to pkg/cd_code |
839 |
|
|
o ctrl package totally restructured |
840 |
|
|
- pack/unpack now optional and decoupled from |
841 |
|
|
xx_/adxx_ I/O |
842 |
|
|
- ctrl_pack/unpack cleaned |
843 |
|
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
844 |
|
|
- confined inclusion of AD_CONFIG.h to where necessary. |
845 |
|
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
846 |
edhill |
1.198 |
|
847 |
edhill |
1.200 |
checkpoint51p_post |
848 |
edhill |
1.198 |
o create initial cd_code package |
849 |
edhill |
1.199 |
- WARNING: the initialization of fields within packages |
850 |
|
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
851 |
|
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
852 |
|
|
This seems to be backwards since |
853 |
|
|
1) its important to initially zero the entire field including |
854 |
|
|
the "halo" region |
855 |
|
|
2) zeroing needs to be done *before* reading pickup info |
856 |
|
|
and the pickup call might or might not happen in any |
857 |
|
|
particular run |
858 |
|
|
- this needs an overhaul for R2 |
859 |
edhill |
1.198 |
o cleanup verification/*/code/GMREDI_OPTIONS.h |
860 |
|
|
o cleanup testreport |
861 |
heimbach |
1.196 |
|
862 |
|
|
checkpoint51o_post |
863 |
|
|
o bringing AD-related verif's up to date with genmake2 |
864 |
|
|
- carbon/ |
865 |
|
|
- global_ocean.90x40x15/ |
866 |
|
|
- hs.94.1x64x5/ |
867 |
|
|
- (front_relax/ ) |
868 |
|
|
o (more) consistent directory structure for AD-related verif.'s |
869 |
|
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
870 |
|
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
871 |
|
|
o bug fix in find_alpha.F for MDJWF: |
872 |
|
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
873 |
|
|
change rho -> rho-rhoConst |
874 |
|
|
- replace call find_rho to find_rhonum |
875 |
|
|
o initialisation of rFlx extended to full array (required by TAF) |
876 |
|
|
and shifted to thermodynamics |
877 |
|
|
o removed PTRACERS.h in ptracers routine |
878 |
|
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
879 |
|
|
o Correcting initialisations for fVerU, fVerV. |
880 |
|
|
o helping TAF to recognize dependency on kUp for |
881 |
|
|
fVerU, fVerV |
882 |
|
|
o Replacing delZ by delR in pkg/ctrl/ |
883 |
|
|
checkpoint51o_pre |
884 |
dimitri |
1.192 |
|
885 |
edhill |
1.195 |
o undid all of cp51 pending some cleanups and discussion |
886 |
heimbach |
1.197 |
o added the [#include "AD_CONFIG.h"] statement to all files that need |
887 |
|
|
it for adjoint/tl #defines |
888 |
|
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
889 |
|
|
o removed tools/genmake since it no longer works |
890 |
dimitri |
1.194 |
|
891 |
|
|
checkpoint51n_post |
892 |
|
|
o modifications to make FREEZE flux visible to pkg/kpp |
893 |
|
|
- moved surfaceTendencyTice from pkg/seaice to main code |
894 |
|
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
895 |
|
|
- subroutine FREEZE now limits only surface temperature |
896 |
|
|
(this means new output.txt for global_ocean.90x40x15, |
897 |
|
|
global_ocean.cs32x15, and global_with_exf) |
898 |
|
|
o added surface flux output variables to TIMEAVE_STATVARS |
899 |
|
|
|
900 |
|
|
checkpoint51n_pre |
901 |
dimitri |
1.192 |
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
902 |
edhill |
1.193 |
o added [#include "AD_CONFIG.h"] to all files that use the following |
903 |
|
|
defines: |
904 |
|
|
- ALLOW_ADJOINT_RUN |
905 |
|
|
- ALLOW_TANGENTLINEAR_RUN |
906 |
|
|
- ALLOW_ECCO_OPTIMIZATION |
907 |
edhill |
1.190 |
|
908 |
edhill |
1.191 |
checkpoint51m_post |
909 |
edhill |
1.190 |
o incorporating changes to get TAMC/TAF working in genmake2 |
910 |
|
|
- added new TAMC/TAF targets to the Makefile |
911 |
|
|
- various cleanups related to package handling |
912 |
edhill |
1.191 |
- these changes should have no impact on the forward model |
913 |
dimitri |
1.189 |
|
914 |
|
|
checkpoint51l_post |
915 |
|
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
916 |
|
|
- faster algorithm for cal_addtime.F |
917 |
|
|
- higher precision arithmetic, where needed |
918 |
|
|
- pkg/exf *startdate variables changed from calendar date to |
919 |
|
|
model integration time |
920 |
|
|
|
921 |
|
|
checkpoint51l_pre |
922 |
jmc |
1.188 |
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
923 |
|
|
o enable to apply restoring on S & T only in a latitude band. |
924 |
|
|
o update output (external_forcing_surf modif. change truncation errors) |
925 |
|
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
926 |
edhill |
1.186 |
|
927 |
jmc |
1.187 |
checkpoint51k_post |
928 |
|
|
o change default to: useNHMTerms=.FALSE. |
929 |
|
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
930 |
|
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
931 |
|
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
932 |
|
|
exp1, ideal_2D_oce |
933 |
|
|
- change data file of oceanic exp (leave the results unchanged for now) |
934 |
|
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
935 |
|
|
o set gravitySign automatically according to the vertical coordinate used |
936 |
|
|
(and change sign: back to "logical" value: +1 when R increases downward) |
937 |
edhill |
1.186 |
o added an include barrier to the default CPP_OPTIONS.h and |
938 |
|
|
removed the #include "PACKAGES_CONFIG.h" from it |
939 |
jmc |
1.187 |
o fix a bug in mom_fluxform (from chk51j_post) |
940 |
heimbach |
1.185 |
|
941 |
|
|
checkpoint51j_post |
942 |
|
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
943 |
|
|
o adjusted some flow directives (dynamics, thermodynamics) |
944 |
|
|
o added cubed-sphere case to test cost function |
945 |
|
|
o heckpoint_lev?_directives.h now include |
946 |
|
|
pkg-specific directives, whenever those are enabled. |
947 |
|
|
o Moving pkg-specific flow directives to corresponding pkg |
948 |
|
|
Moving pkg-specific differentiation list to corresponding pkg |
949 |
|
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
950 |
|
|
---> conventions are |
951 |
|
|
- pkg_ad.flow |
952 |
|
|
- pkg_ad_diff.list |
953 |
|
|
- pkg_ad_check_lev?_dir.h |
954 |
stephd |
1.181 |
|
955 |
edhill |
1.184 |
checkpoint51i_post |
956 |
|
|
o merge of the branch-genmake2 |
957 |
|
|
- knowingly breaks the older genmake |
958 |
|
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
959 |
|
|
- new testreport supersedes older testscript |
960 |
|
|
o large number of package inclusion and header cleanups |
961 |
|
|
checkpoint51i_pre |
962 |
|
|
|
963 |
edhill |
1.183 |
o new output for adjoin of global ocean vector invariant |
964 |
|
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
965 |
|
|
o Steph gchem various cleanups |
966 |
|
|
|
967 |
stephd |
1.181 |
checkpoint 51h_pre |
968 |
edhill |
1.183 |
o fixed some single quotes |
969 |
stephd |
1.181 |
o modify gchem pkg to be more versatile |
970 |
|
|
o modifications to clean up dic pkg |
971 |
|
|
o add pkg/cfc |
972 |
heimbach |
1.182 |
|
973 |
|
|
checkpoint51g_post |
974 |
|
|
o provide links for ARPACK and ADM*TLM |
975 |
|
|
o start removing verification/vero/ |
976 |
|
|
o update AD-related stuff |
977 |
|
|
(in particular some IF-statements in model/src/ routines) |
978 |
|
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
979 |
|
|
vector invariant setup |
980 |
dimitri |
1.177 |
|
981 |
heimbach |
1.180 |
checkpoint51f_post |
982 |
jmc |
1.179 |
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
983 |
dimitri |
1.178 |
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
984 |
dimitri |
1.177 |
of tracer Green's fucntions for ocean inversion project. |
985 |
dimitri |
1.175 |
|
986 |
dimitri |
1.176 |
checkpoint51f_pre |
987 |
dimitri |
1.175 |
o Added on-the-fly spatial interpolation capability |
988 |
|
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
989 |
dimitri |
1.176 |
- This is a temporary Cartesian-grid hack until |
990 |
dimitri |
1.175 |
the super-duper ESMF coupler becomes available. |
991 |
dimitri |
1.176 |
- See verification/global_with_exf/README for usage example. |
992 |
|
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
993 |
|
|
flags and modified pkg/seaice accordingly. |
994 |
dimitri |
1.175 |
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
995 |
|
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
996 |
|
|
non-local transport term. |
997 |
heimbach |
1.172 |
|
998 |
jmc |
1.174 |
checkpoint51e_post |
999 |
|
|
o pkg/mom_vecinv: |
1000 |
|
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
1001 |
|
|
- add time-ave diagnostic of vorticity advection. |
1002 |
|
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
1003 |
|
|
o atmospheric geopotential: - include water vapor effect; |
1004 |
|
|
- use p^kappa in p* scaling. |
1005 |
jmc |
1.173 |
o land pkg: read initial state from files. |
1006 |
|
|
o AIM : add stratospheric drag in the upper level |
1007 |
|
|
|
1008 |
heimbach |
1.172 |
checkpoint51d_post |
1009 |
jmc |
1.173 |
o change function ILNBLNK (=> last non-blank char.) to return zero |
1010 |
|
|
(instead of the string length) when the string. char is empty |
1011 |
jmc |
1.171 |
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
1012 |
heimbach |
1.172 |
o modif's to restore TAMC compatibility |
1013 |
|
|
- avoid "_d" constructs in PARAMETER declarations |
1014 |
|
|
- avoid interrupting lines by comment lines |
1015 |
|
|
o Use cluster local disks for purely local I/O |
1016 |
|
|
vs. globally visible disks needed for ctrl stuff |
1017 |
|
|
(merged from ecco-branch) |
1018 |
|
|
- new active_file_loc... and mdsio_..._loc routines |
1019 |
|
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
1020 |
heimbach |
1.169 |
|
1021 |
heimbach |
1.170 |
checkpoint51c_post |
1022 |
|
|
o introducing integer flag debugLevel |
1023 |
|
|
- debLevZero: suppress all output |
1024 |
|
|
- debLevA: standard |
1025 |
|
|
- debLevB: equivalent to current debugMode=.TRUE. |
1026 |
|
|
o introducing pathname variable mdsioLocalDir for mdsio |
1027 |
|
|
that can be specified at runtime |
1028 |
|
|
(relevant for cluster I/O to local disk) |
1029 |
|
|
` |
1030 |
heimbach |
1.169 |
>>>checkpoint51b_post |
1031 |
|
|
adjoint of ptracers |
1032 |
|
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
1033 |
|
|
o extended state in checkpoint_lev?, etc. |
1034 |
|
|
o alternative ctrl/cost with tr1 or ptracer |
1035 |
|
|
o new comlev1_bibj_ptracers |
1036 |
|
|
o new ptracers.flow |
1037 |
|
|
o made ptracers_forcing same as external_forcing_s |
1038 |
|
|
o added verification for adjoint with ptracers |
1039 |
|
|
- adm. grdchk fail so far |
1040 |
|
|
- tlm. grdchk OK |
1041 |
|
|
- checked tapelev/comlev recomputations: OK |
1042 |
|
|
<<<checkpoint51b_pre |
1043 |
stephd |
1.168 |
|
1044 |
|
|
checkpoint51a_post |
1045 |
|
|
o added code for biogeochemistry package |
1046 |
|
|
- new pkgs: dic, gchem |
1047 |
|
|
- new subroutine in ptracers |
1048 |
|
|
o modify code for biogeo packages |
1049 |
|
|
- in model/src and pkg/ptracers |
1050 |
heimbach |
1.166 |
|
1051 |
|
|
checkpoint51 |
1052 |
|
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
1053 |
|
|
- autodiff, ctrl, exf, grdchk, seaice |
1054 |
|
|
kept separate packages |
1055 |
|
|
- cost, ecco, obcs |
1056 |
heimbach |
1.167 |
o updating verification/internal_wave, verification/lab_sea |
1057 |
|
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
1058 |
heimbach |
1.165 |
|
1059 |
|
|
checkpoint50i_post |
1060 |
|
|
o Preparing next differentiable checkpoint and sync |
1061 |
|
|
of MAIN vs. ecco-branch |
1062 |
|
|
- 1st step: this one is differentiable |
1063 |
|
|
- 2nd step: next(! not this) checkpoint will have updated packages |
1064 |
|
|
from ecco-branch) |
1065 |
jmc |
1.161 |
|
1066 |
heimbach |
1.164 |
checkpoint50h_post |
1067 |
jmc |
1.163 |
o new package "land": provide surface BC for AIM. |
1068 |
|
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
1069 |
jmc |
1.161 |
o AIM: use true log-P extrapolation for near surface temp (= as in |
1070 |
|
|
F.Molteni paper) ; update aim.5l_cs output. |
1071 |
adcroft |
1.162 |
o New variable in PARM03 for more flexible pickups |
1072 |
heimbach |
1.164 |
o somewhat cleaned package initialisation sequence for |
1073 |
|
|
ctrl/ cost/ ecco/ in packages_... routines |
1074 |
dimitri |
1.160 |
|
1075 |
|
|
checkpoint50g_post |
1076 |
|
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
1077 |
|
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
1078 |
|
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
1079 |
|
|
made the default because of faster convergence than ADI |
1080 |
heimbach |
1.159 |
|
1081 |
|
|
checkpoint50f_post |
1082 |
|
|
o exf totally restructured |
1083 |
|
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
1084 |
|
|
and made sure it's still differentiable |
1085 |
|
|
- split exf_getffields.F into new exf_bulkformulae.F |
1086 |
|
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
1087 |
|
|
- updated adjoint/makefile and relevant verif. accordingly |
1088 |
adcroft |
1.156 |
|
1089 |
heimbach |
1.158 |
checkpoint50f_pre |
1090 |
jmc |
1.157 |
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
1091 |
|
|
+ change Evap over land. (update aim.5l_cs output) |
1092 |
adcroft |
1.156 |
o added missing .cvsignores and made uniform across expts |
1093 |
|
|
o changed configuration of tidal_basin_2d expt |
1094 |
|
|
o added pkg/debug functions for tracing code in fatal crashes |
1095 |
|
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
1096 |
|
|
o new fn in pkg/monitor to stop model if solution grows too big |
1097 |
|
|
o removed lots of single quotes from comments |
1098 |
|
|
|
1099 |
mlosch |
1.155 |
checkpoint50e_post |
1100 |
|
|
o make KPP work with PTRACERS |
1101 |
|
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
1102 |
|
|
nearly a copy of kpp_transport_s |
1103 |
|
|
- there is no analogue to SurfaceTendencyS, so I have to use |
1104 |
|
|
gPtr(of the surface layer) instead |
1105 |
|
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
1106 |
|
|
checkpoint50e_pre |
1107 |
|
|
|
1108 |
|
|
checkpoint50d_post |
1109 |
mlosch |
1.154 |
o change kpp output from multiple-record state files to single-record state |
1110 |
|
|
files analogous to write_state.F |
1111 |
|
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
1112 |
|
|
analogous to the cg2d-related output. |
1113 |
mlosch |
1.155 |
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
1114 |
|
|
so that writing to internal file fn (with length 512) fails. |
1115 |
mlosch |
1.154 |
checkpoint50d_pre |
1116 |
jmc |
1.151 |
|
1117 |
jmc |
1.153 |
checkpoint50c_post |
1118 |
|
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
1119 |
jmc |
1.152 |
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
1120 |
jmc |
1.151 |
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
1121 |
|
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
1122 |
|
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
1123 |
dimitri |
1.150 |
|
1124 |
|
|
checkpoint50c_pre |
1125 |
|
|
Merging from release1_p13: |
1126 |
|
|
o bug fix for pkg/seaice dynamic solver |
1127 |
|
|
o Added SEAICE_initialHEFF to pkg/seaice |
1128 |
jmc |
1.149 |
|
1129 |
|
|
checkpoint50b_post |
1130 |
|
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
1131 |
|
|
o in order to put the momForcing out of the Adams-Bashforth: |
1132 |
|
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
1133 |
|
|
to timestep.F |
1134 |
|
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
1135 |
|
|
o re-generate output for highly sensitive test-exp: |
1136 |
|
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
1137 |
heimbach |
1.146 |
|
1138 |
jmc |
1.148 |
checkpoint50b_pre |
1139 |
jmc |
1.147 |
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
1140 |
heimbach |
1.146 |
o corrected CPP option mismatch in exf_Bulk... functions for case |
1141 |
|
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
1142 |
heimbach |
1.145 |
|
1143 |
|
|
checkpoint50a_post |
1144 |
|
|
o Bug fix for merging between c50 and KPP. |
1145 |
|
|
ikey was passed from thermodynamics to kpp_calc via |
1146 |
|
|
common block rather than being recomputed in kpp_calc, |
1147 |
|
|
in contradiction with new key itdkey. |
1148 |
|
|
New key ikppkey created, and tamc.h headers updated. |
1149 |
heimbach |
1.143 |
|
1150 |
heimbach |
1.144 |
checkpoint50 |
1151 |
|
|
- 2nd step of merge with ecco-branch: |
1152 |
|
|
merge changes in ecco-branch back into main trunk |
1153 |
|
|
- bug fix in find_alpha |
1154 |
|
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
1155 |
|
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
1156 |
|
|
- merged some sliced AD support routines |
1157 |
|
|
|
1158 |
heimbach |
1.143 |
checkpoint49 |
1159 |
|
|
merged from ecco-branch: |
1160 |
|
|
o exf: |
1161 |
|
|
- Enable initialisation of forcing fields to constant |
1162 |
|
|
(runtime) values. |
1163 |
|
|
- in exf_getffields.F |
1164 |
|
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
1165 |
|
|
That also fixes wrong TAF-key computations for key_1, key_2 |
1166 |
|
|
with bulf formulae. |
1167 |
|
|
- exf_init.F modify #ifdef for exf_init_evap |
1168 |
|
|
- exf_getffieldrec.F, ctrl_getrec.F |
1169 |
|
|
The following INT-usages are not safe: |
1170 |
|
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
1171 |
|
|
fldcount = int(fldsecs/fldperiod) + 1 |
1172 |
|
|
and were modified. |
1173 |
|
|
o autodiff: checkpoint_lev... |
1174 |
|
|
- updated storing for bulk formulae (some arrays were missing) |
1175 |
|
|
- added state for seaice package |
1176 |
|
|
- synchronized with main branch |
1177 |
|
|
o DIVA: |
1178 |
|
|
Modif.s in |
1179 |
heimbach |
1.144 |
- the_main_loop.F |
1180 |
|
|
- the_model_main.F |
1181 |
heimbach |
1.143 |
and added cost_final_restore.F cost_final_store.F |
1182 |
|
|
o With these changes, it is possible to fully separate |
1183 |
|
|
the first forward run to compute the cost function (mdthe_main_loop) |
1184 |
|
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
1185 |
|
|
into separate model executions. |
1186 |
|
|
This enables better tuning of DIVA to given queue sizes. |
1187 |
|
|
o Loss of cost function value in consecutive DIVA runs is |
1188 |
|
|
fixed by storing to 'costfinal' file. |
1189 |
|
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
1190 |
|
|
beginning/end of adjoint integration is accounted for. |
1191 |
|
|
The current changes apply to TAF-1.4.26. |
1192 |
|
|
TAF has one remaining bug, requiring one manual change |
1193 |
|
|
(see MITgcm manual). |
1194 |
|
|
o cal: synchronized between MAIN and ecco-branch |
1195 |
heimbach |
1.141 |
|
1196 |
heimbach |
1.142 |
checkpoint48i_post |
1197 |
heimbach |
1.141 |
o Changes to restore differentiability of code w.r.t. previous tag |
1198 |
|
|
(mostly adding new routines to make list and replacing |
1199 |
|
|
pressure by totPhiHyd). |
1200 |
|
|
o Updated and merged grdchk package |
1201 |
|
|
- has both ADM and TLM checks |
1202 |
|
|
- works for single- and multi-proc. |
1203 |
|
|
- output cleaned |
1204 |
|
|
- worked successfully for parallel DIVA |
1205 |
|
|
o genmake: |
1206 |
|
|
- Adding -platform=SP4 |
1207 |
|
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
1208 |
|
|
o Modif. for DIVA: |
1209 |
|
|
ctrl_unpack should not be called in intermediate DIVA interval. |
1210 |
|
|
(similar thing would apply for active files such as |
1211 |
|
|
tbar, sbar, psbar, which should not be reinitialised; |
1212 |
|
|
only relevant for ecco-branch) |
1213 |
dimitri |
1.136 |
|
1214 |
heimbach |
1.140 |
checkpoint48h_post |
1215 |
jmc |
1.137 |
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
1216 |
dimitri |
1.136 |
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
1217 |
|
|
o Added SEAICE_initialHEFF to pkg/seaice |
1218 |
dimitri |
1.139 |
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
1219 |
jmc |
1.135 |
|
1220 |
|
|
checkpoint48g_post |
1221 |
|
|
--- EOS: |
1222 |
|
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
1223 |
|
|
store total Potential in totPhyHyd for diagnostics & EOS. |
1224 |
|
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
1225 |
|
|
--- Pressure/geopotential gradient: |
1226 |
|
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
1227 |
|
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
1228 |
|
|
( changes results of global_ocean_pressure ) |
1229 |
|
|
o NLFS + z-coord.: add eta*Rho' contribution. |
1230 |
|
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
1231 |
|
|
( changes results of ideal_2D_oce ) |
1232 |
|
|
o includes r* 2nd term in potential gradient. |
1233 |
dimitri |
1.134 |
|
1234 |
|
|
checkpoint48f_post |
1235 |
|
|
Merging from release1_p12: |
1236 |
|
|
o Modifications for using pkg/exf with pkg/seaice |
1237 |
|
|
- improved description of the various forcing configurations |
1238 |
|
|
- added basic radiation bulk formulae to pkg/exf |
1239 |
|
|
- units/sign fix for evap computation in exf_getffields.F |
1240 |
|
|
- updated verification/global_with_exf/results/output.txt |
1241 |
|
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
1242 |
|
|
(SBO) core products, including oceanic mass, center-of-mass, |
1243 |
|
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
1244 |
|
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
1245 |
|
|
to avoid negative values in shallow regions. |
1246 |
|
|
- updated verification/natl_box/results/output.txt |
1247 |
|
|
- updated verification/lab_sea/results/output.txt |
1248 |
|
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
1249 |
|
|
o Added useSingleCpuIO option (see PARAMS.h). |
1250 |
|
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
1251 |
|
|
work with multi-field files, e.g., for single-file pickup. |
1252 |
|
|
o pkg/seaice: |
1253 |
|
|
- bug fix in growth.F: QNET for no shortwave case |
1254 |
|
|
- added HeffFile for specifying initial sea-ice thickness |
1255 |
|
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
1256 |
|
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
1257 |
|
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
1258 |
|
|
o pkg/seaice: |
1259 |
|
|
- adjoint-friendly modifications |
1260 |
|
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
1261 |
jmc |
1.131 |
|
1262 |
jmc |
1.133 |
checkpoint48e_post |
1263 |
jmc |
1.131 |
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
1264 |
jmc |
1.132 |
o dynamics: change definition of computational domain & adapt mom_fluxform |
1265 |
|
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
1266 |
|
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
1267 |
|
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
1268 |
jmc |
1.133 |
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
1269 |
jmc |
1.132 |
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
1270 |
|
|
inverted_barometer solid-body.cs-32x32x1 |
1271 |
|
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
1272 |
jmc |
1.130 |
|
1273 |
|
|
checkpoint48d_post |
1274 |
|
|
o in preparation for r*: |
1275 |
|
|
a) use pre-computed gradient of hydrostatic potential: |
1276 |
|
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
1277 |
|
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
1278 |
|
|
=> affects results of glob_oce_pressure (different truncation error) |
1279 |
|
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
1280 |
jmc |
1.129 |
|
1281 |
|
|
checkpoint48d_pre |
1282 |
|
|
o in preparation for r*: |
1283 |
|
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
1284 |
|
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
1285 |
|
|
but for the moment, only used if it does not change the results. |
1286 |
|
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
1287 |
jmc |
1.126 |
|
1288 |
heimbach |
1.128 |
checkpoint48c_post |
1289 |
|
|
Modifications in treatment of initial flux forcing controls |
1290 |
|
|
to avoid extra storing of flux fields. |
1291 |
|
|
|
1292 |
|
|
checkpoint48c_pre |
1293 |
adcroft |
1.127 |
o Added tidal_basin_2d experiment (currently 1D!) |
1294 |
jmc |
1.126 |
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
1295 |
jmc |
1.124 |
|
1296 |
jmc |
1.125 |
checkpoint48b_post |
1297 |
jmc |
1.124 |
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
1298 |
|
|
(modification to pressure gradient not yet implemented) |
1299 |
|
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
1300 |
|
|
(for U & V) that are used for vertical advection of momentum. |
1301 |
jmc |
1.123 |
|
1302 |
|
|
checkpoint48a_post |
1303 |
|
|
o In preparation for r*, use temp. array to compute vertical transport |
1304 |
|
|
in flux-form momentum pkg. => change results of few test-exp. |
1305 |
|
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
1306 |
|
|
lab_sea, natl_box & plume_on_slope |
1307 |
jmc |
1.122 |
|
1308 |
|
|
checkpoint48 |
1309 |
|
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
1310 |
heimbach |
1.121 |
|
1311 |
|
|
checkpoint47j_post |
1312 |
jmc |
1.120 |
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
1313 |
heimbach |
1.121 |
o moved adexch from forward_step to addummy_in_stepping |
1314 |
|
|
o added exch in ctrl_map_... |
1315 |
|
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
1316 |
|
|
reverse checkpointing loop |
1317 |
|
|
o Yet more changes in gmredi: |
1318 |
|
|
* adgmredi_calc_tensor |
1319 |
|
|
avoiding all recomputation of gmredi_slope_limit |
1320 |
|
|
* adgmredi_x/y/rtransport |
1321 |
|
|
added flag for excessive storing to avoid recomp. of |
1322 |
|
|
u/v/rtans, dTdx/y/z |
1323 |
|
|
-> this is not really necessary and very memory-consuming |
1324 |
|
|
* adgmredi_slope_psi: |
1325 |
|
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
1326 |
|
|
* gmredi_slope_limit |
1327 |
|
|
re-activated full calculation of taperfct for case 'ac02' |
1328 |
|
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
1329 |
heimbach |
1.116 |
|
1330 |
jmc |
1.119 |
checkpoint47i_post |
1331 |
|
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
1332 |
|
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
1333 |
|
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
1334 |
|
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
1335 |
|
|
o gmredi: fix few bugs. |
1336 |
|
|
|
1337 |
adcroft |
1.118 |
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
1338 |
heimbach |
1.116 |
This will be a good checkpoint to plug into the ecco-branch. |
1339 |
|
|
o few modif.'s to get latest version adjointed |
1340 |
|
|
(mainly kick out code in ini_linear_phisurf) |
1341 |
|
|
o modif's to run adjoint with exactConserv |
1342 |
|
|
o case GM_BOLUS_ADVEC should be cleaned |
1343 |
|
|
S/R gmredi_slope_psi should be cleaned |
1344 |
|
|
o verification/carbon now has exactConserv=.TRUE. |
1345 |
jmc |
1.114 |
|
1346 |
heimbach |
1.115 |
checkpoint47g_post |
1347 |
jmc |
1.114 |
o time-average AIM output: becomes independent from statvars time-average |
1348 |
|
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
1349 |
heimbach |
1.115 |
o After TAF bug fix: |
1350 |
|
|
Tested adjoint of gmredi package. |
1351 |
|
|
Tests were done with checkpoint47 rather than with latest |
1352 |
|
|
checkpoint47f_post since the latter is broken for the adjoint |
1353 |
|
|
verification/carbon/ contains both ADM and TLM gradient checks. |
1354 |
|
|
Here they are, before they get changed/lost/stolen. |
1355 |
|
|
Mostly modif.'s to fix numerical sensitivities. |
1356 |
|
|
Gradient checks OK for |
1357 |
|
|
- GM_taper_scheme: |
1358 |
|
|
* clipping |
1359 |
|
|
* ac02 |
1360 |
|
|
* linear |
1361 |
|
|
* glw91 |
1362 |
|
|
* dm95 |
1363 |
|
|
* ldd97 |
1364 |
|
|
- GMREDI_OPTIONS: |
1365 |
|
|
* GM_VISBECK_VARIABLE_K |
1366 |
|
|
* GM_NON_UNITY_DIAGONAL |
1367 |
|
|
* GM_EXTRA_DIAGONAL |
1368 |
|
|
* GM_BOLUS_ADVEC |
1369 |
|
|
in conjunction with data.gmredi parameters to be checked in |
1370 |
|
|
in a few minutes under verification/carbon/code/ |
1371 |
cheisey |
1.112 |
|
1372 |
dimitri |
1.113 |
checkpoint47f_post |
1373 |
|
|
Merging from release1_p10: |
1374 |
|
|
o modifications for using pkg/exf with pkg/seaice |
1375 |
|
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
1376 |
|
|
and SEAICE_EXTERNAL_FLUXES |
1377 |
|
|
- pkg/exf CPP options EXF_READ_EVAP and |
1378 |
|
|
EXF_NO_BULK_COMPUTATIONS |
1379 |
|
|
- usage examples are Experiments 8 and 9 in |
1380 |
|
|
verification/lab_sea/README |
1381 |
|
|
- verification/lab_sea default experiment now uses |
1382 |
|
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
1383 |
|
|
|
1384 |
cheisey |
1.112 |
checkpoint47e_post |
1385 |
|
|
o created a tag prior to creating a branch |
1386 |
|
|
|
1387 |
mlosch |
1.111 |
checkpoint47d_post |
1388 |
|
|
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
1389 |
|
|
at the bottom boundary had an erroneous half slip boundary condition |
1390 |
|
|
o added bottom drag and no slip boundary condition capabilities to |
1391 |
|
|
oceanic pressure coordinates code |
1392 |
|
|
o added new verification experiment global_ocean_pressure, this experiment is |
1393 |
|
|
also described in the tutorial section of the manual |
1394 |
|
|
checkpoint47d_pre |
1395 |
cheisey |
1.110 |
|
1396 |
|
|
checkpoint47c_post |
1397 |
|
|
o Added a verification experiment for a global cubed-sphere ocean run |
1398 |
|
|
- verification/global_ocean.cubed32x32x30 |
1399 |
|
|
- uses pkg/therm_seaice and pkg/bulk_forcing |
1400 |
jmc |
1.109 |
|
1401 |
|
|
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
1402 |
|
|
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
1403 |
|
|
when using P-coordinate; only implemented for atmospheric config. |
1404 |
|
|
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
1405 |
|
|
NOTES: requires option NONLIN_FRSURF to be "#define". |
1406 |
|
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
1407 |
dimitri |
1.108 |
|
1408 |
|
|
checkpoint47b_post |
1409 |
|
|
Merging from release1_p9: |
1410 |
|
|
o pkg/seaice |
1411 |
|
|
- removed GOTO's and added taf directives |
1412 |
|
|
- double precision constants to reduce the g77 (Linux) |
1413 |
|
|
to F77 (SGI) differences reported in release1_p8 |
1414 |
|
|
o tools/genmake |
1415 |
|
|
- added SGI options |
1416 |
|
|
o verification/testscript |
1417 |
|
|
- updated to that of checkpoint47a_post |
1418 |
|
|
o verification/global_ocean.90x40x15/input/eedata |
1419 |
|
|
- modified for SGI f77 compatibility |
1420 |
|
|
o verification/lab_sea |
1421 |
|
|
- added description of sea-ice model |
1422 |
|
|
- added missing matlab routines |
1423 |
|
|
- added test of thermodynamics parallelization |
1424 |
jmc |
1.105 |
|
1425 |
jmc |
1.106 |
checkpoint47a_post |
1426 |
jmc |
1.105 |
o new pkg: aim_v23 |
1427 |
|
|
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
1428 |
|
|
for now, keep the same surface forcing as before. |
1429 |
|
|
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
1430 |
|
|
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
1431 |
|
|
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
1432 |
|
|
o add diagnostic of surface correction term in monitor output |
1433 |
jmc |
1.106 |
|
1434 |
|
|
o bulk_force and therm_seaice |
1435 |
cheisey |
1.107 |
- Two packages: bulk_force (Bulk forcing) |
1436 |
|
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
1437 |
|
|
- Earlier integration from Stephaine Dutkiewicz |
1438 |
|
|
and Patrick Heimbach. |
1439 |
|
|
- Two ifdef statements for compile time, |
1440 |
|
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
1441 |
heimbach |
1.104 |
|
1442 |
|
|
checkpoint47 |
1443 |
|
|
differentiable version of checkpoint46n_post |
1444 |
|
|
o bug fix in quasihydrostaticterms |
1445 |
|
|
o * "clean" adjoint code (in terms of extensive recomputations) |
1446 |
|
|
can now be obtained for all GMREDI options (i.e. for |
1447 |
|
|
- GM_VISBECK_VARIABLE_K |
1448 |
|
|
- GM_NON_UNITY_DIAGONAL |
1449 |
|
|
- GM_EXTRA_DIAGONAL |
1450 |
|
|
- GM_BOLUS_ADVEC ) |
1451 |
|
|
* However, wrong gradient check problem remains unsolved. |
1452 |
|
|
* New CPP options have been introduced for different |
1453 |
|
|
tapering schemes |
1454 |
|
|
o external_fields_load now part of differentiation list |
1455 |
|
|
o pressure needs multiple storing; |
1456 |
|
|
would be nice to have store_pressure at beginning or |
1457 |
|
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
1458 |
|
|
(NB: pressure is needed for certain cases in find_rho, |
1459 |
|
|
which is also invoked through convective_adjustment). |
1460 |
|
|
o recomputations in find_rho for cases |
1461 |
|
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
1462 |
|
|
o #define ATMOSPHERIC_LOADING should be differentiable |
1463 |
|
|
o ini_forcing shifted to begining of initialise_varia |
1464 |
|
|
o Incorporating QNVS line search routines into MITgcm |
1465 |
|
|
(this is separate code, and therefore not under pkg) |
1466 |
|
|
lsopt/, optim/ |
1467 |
|
|
o Updated verification/carbon/ |
1468 |
|
|
- #define GM_VISBECK_VARIABLE_K |
1469 |
|
|
- GM_taper_scheme = 'ldd97' |
1470 |
heimbach |
1.103 |
|
1471 |
|
|
checkpoint46n_post |
1472 |
|
|
Merging from release1_p8: |
1473 |
|
|
o verification/natl_box: |
1474 |
|
|
updating new external_fields_load routine |
1475 |
|
|
o New package: pkg/seaice |
1476 |
|
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
1477 |
|
|
The sea-ice code is based on Hibler (1979-1980). |
1478 |
|
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
1479 |
|
|
In addition to computing prognostic sea-ice variables and diagnosing |
1480 |
|
|
the forcing/external data fields that drive the ocean model, |
1481 |
|
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
1482 |
|
|
The implied surface heat flux is then stored in variable |
1483 |
|
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
1484 |
|
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
1485 |
|
|
non-local transport term. Because this call precedes model |
1486 |
|
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
1487 |
|
|
the freezing point by the time theta is dumped or time-averaged. |
1488 |
|
|
N.B.: fairly large differences in accuracy occur across |
1489 |
|
|
different platforms/compilers; comparison between |
1490 |
|
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
1491 |
|
|
generated output gives: |
1492 |
|
|
T S U V |
1493 |
|
|
C D M c m s m s m s m s |
1494 |
|
|
n p a R g m m e . m m e . m m e . m m e . |
1495 |
|
|
f n k u 2 i a a d i a a d i a a d i a a d |
1496 |
|
|
g d e n d n x n . n x n . n x n . n x n . |
1497 |
|
|
|
1498 |
|
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
1499 |
|
|
o GAD: |
1500 |
|
|
- generated new common blocks to account for call of |
1501 |
|
|
same gad routines with differing traceridentities |
1502 |
|
|
(needed to modify tracerIdentity indices in GAD.h) |
1503 |
|
|
- generated separate common blocks for case useCubedSphereExchange |
1504 |
|
|
(Department of Futurology) |
1505 |
|
|
- parameter lists to gmredi_?transport: added tracerIdentity |
1506 |
|
|
- added new key indices to tamc.h |
1507 |
|
|
o external_fields_load: |
1508 |
|
|
- added this routine to TAF list |
1509 |
|
|
- needed to make some common blocks global and additional storing |
1510 |
|
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
1511 |
|
|
o exf: |
1512 |
|
|
updated external forcing package |
1513 |
|
|
- bug fixes carried over from ecco-branch |
1514 |
|
|
(missing OBCS_OPTIONS.h in two routines) |
1515 |
|
|
- enable easy to use "no forcing". |
1516 |
|
|
- added exf I/O for atmospheric loading |
1517 |
|
|
- added exf I/O for runoff data |
1518 |
|
|
- transfered scaling between exf <-> MITgcm to exf namelist |
1519 |
|
|
o Adding new verification experiment global_with_exf. |
1520 |
|
|
This verification experiment is almost identical to the |
1521 |
|
|
global_ocean.90x40x15 experiment, except that it uses |
1522 |
|
|
the exf (and cal) package instead of the |
1523 |
|
|
external_fields_load routine (cf README file). |
1524 |
adcroft |
1.94 |
|
1525 |
adcroft |
1.102 |
checkpoint46m_post |
1526 |
adcroft |
1.101 |
o modified testscript to return -- when there are no lines of "%MON" output |
1527 |
adcroft |
1.100 |
o added new flag "quasiHydrostatic" for QH mode |
1528 |
|
|
and new routine quasihydrostaticterms() |
1529 |
adcroft |
1.99 |
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
1530 |
|
|
New routine: mom_u_coriolis_nh() |
1531 |
adcroft |
1.98 |
o fixed sign of non-hydrostatic metric terms in u and v equations. |
1532 |
|
|
Depend on correct sign of gravitySign. |
1533 |
adcroft |
1.97 |
o added work.pc* to .cvsignore in aim directories using ifc |
1534 |
adcroft |
1.96 |
o introduced flag for controllin non-hydrostatic metric terms |
1535 |
adcroft |
1.95 |
o removed gravitySign from PARM04 |
1536 |
adcroft |
1.94 |
o switched to g77/ifc from pgf77 in aim experiments |
1537 |
mlosch |
1.93 |
|
1538 |
|
|
checkpoint46l_post |
1539 |
|
|
o made convective adjustment work with pressure coordinates: |
1540 |
|
|
- changed the direction of k-loop in convective_adjustment.F for the |
1541 |
|
|
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
1542 |
|
|
- adjusted the reference pressure k-index in convective_adjustment.F |
1543 |
|
|
- adjusted the convection condition in convect.F (in analogy to |
1544 |
|
|
calc_ivdc.F) |
1545 |
|
|
- convective_adjustment no longer computes anything on the halos |
1546 |
|
|
- removed the warnings about negative salinity from find_rho.F and |
1547 |
|
|
find_alpha.F; instead the new routine look_for_neg_salinity, called |
1548 |
|
|
at the beginning of find_rho, find_alpha, and find_beta, does a |
1549 |
|
|
check of the entire slice, if CPP-option |
1550 |
|
|
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
1551 |
|
|
checkpoint46l_pre |
1552 |
mlosch |
1.91 |
|
1553 |
mlosch |
1.92 |
checkpoint46k_post |
1554 |
mlosch |
1.91 |
o fixed the verification/global_ocean.90x40x15 experiment: |
1555 |
|
|
- new bathymetry (the world according to A., JMC, and M.) |
1556 |
|
|
- new initial fields and forcing fields (*.bin files) |
1557 |
|
|
- new POLY3.COEFFS (for the next release one should switch to a full |
1558 |
|
|
equation of state: JMD95P or MDJWF) |
1559 |
|
|
- fixed several errors and redundancies in the data file |
1560 |
|
|
- experiment uses looped cells |
1561 |
|
|
- added matlab directory with diagnostic scripts for plotting of output |
1562 |
jmc |
1.90 |
|
1563 |
|
|
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
1564 |
|
|
- read AIM physics parameters from a file (data.aimphys) |
1565 |
|
|
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
1566 |
jmc |
1.89 |
|
1567 |
|
|
checkpoint46j_post |
1568 |
|
|
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
1569 |
|
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
1570 |
|
|
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
1571 |
|
|
o update timeave pkg for wVel diagnostic. |
1572 |
|
|
checkpoint46j_pre |
1573 |
mlosch |
1.87 |
|
1574 |
jmc |
1.88 |
checkpoint46i_post |
1575 |
|
|
o Clean up AIM package (and keep the results unchanged): |
1576 |
|
|
include CPP_OPTION and use IMPLICT NONE in all routines ; |
1577 |
|
|
declare all the variables _RL ; use _d 0 for all numerical constants. |
1578 |
|
|
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
1579 |
mlosch |
1.87 |
|
1580 |
|
|
checkpoint46h_post |
1581 |
|
|
o cleaned up the use of rhoNil and rhoConst. |
1582 |
|
|
- rhoNil should only appear in the LINEAR equation of state, everywhere |
1583 |
|
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
1584 |
|
|
and the dynamical equations are all divided by rhoConst |
1585 |
|
|
o introduced new parameter rhoConstFresh, a reference density of fresh |
1586 |
|
|
water, to remove the fresh water flux's dependence on rhoNil. The default |
1587 |
|
|
value is 999.8 kg/m^3 |
1588 |
|
|
o cleanup up external_forcing.F and external_forcing_surf.F |
1589 |
|
|
- can now be used by both OCEANIC and OCEANICP |
1590 |
|
|
checkpoint46h_pre |
1591 |
|
|
|
1592 |
|
|
Added code to convert surface volume flux (fresh water) into |
1593 |
|
|
a mass flux when using P coordinates in the ocean (OCEANICP). |
1594 |
|
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
1595 |
mlosch |
1.86 |
|
1596 |
|
|
checkpoint46g_post |
1597 |
|
|
o Include a new diagnostic variable phiHydLow for the ocean model |
1598 |
|
|
- in z-coordinates, it is the bottom pressure anomaly |
1599 |
|
|
- in p-coordinates, it is the sea surface elevation |
1600 |
|
|
- in both cases, these variable have global drift, reflecting the mass |
1601 |
|
|
drift in z-coordinates and the volume drift in p-coordinates |
1602 |
|
|
- included time averaging for phiHydLow, be aware of the drift! |
1603 |
|
|
o depth-dependent computation of Bo_surf for pressure coordinates |
1604 |
|
|
in the ocean (buoyancyRelation='OCEANICP') |
1605 |
|
|
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
1606 |
|
|
Theta, Salinity, and Pressure in the parameter list. This routine is |
1607 |
|
|
presently contained in find_rho.F. This routine does not give the |
1608 |
|
|
correct density for 'POLY3', which would be a z-dependent reference |
1609 |
|
|
density. |
1610 |
|
|
o cleaned up find_rho |
1611 |
|
|
- removed obsolete 'eqn' from the parameter list. |
1612 |
|
|
o added two new verification experiments: gop and goz |
1613 |
|
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
1614 |
|
|
checkpoint46g_pre |
1615 |
heimbach |
1.85 |
|
1616 |
|
|
checkpoint46f_post |
1617 |
|
|
o Enable tangent linear (forward mode) gradient checks: |
1618 |
|
|
- extended active file handling to g_... files |
1619 |
|
|
- added TANGENT_SIMULATION to theSimulationMode |
1620 |
|
|
- extended grdchk package accordingly |
1621 |
|
|
o added tangent linear setup in verification/carbon/code_ftl |
1622 |
|
|
o added adjoint setup in verification/front_relax/code_ad |
1623 |
mlosch |
1.82 |
|
1624 |
cnh |
1.84 |
checkpoint46e_post |
1625 |
mlosch |
1.83 |
o Added new equation of state -> MDJWF |
1626 |
|
|
- EOS of McDougall et al., 2002, JAOT, submitted |
1627 |
|
|
- caveat: the equation of state is only valid for a smaller (more |
1628 |
|
|
realistic?) range of values than JMD95P/Z and UNESCO |
1629 |
|
|
- added masks to the calculation of pressure in store_pressure |
1630 |
|
|
- added more check values for density in check_eos (ini_eos.F), some of |
1631 |
|
|
the old check values are out of the range of the MDJWF-eos, so don't |
1632 |
|
|
expect perfect matches for those |
1633 |
cnh |
1.84 |
checkpoint46e_pre |
1634 |
mlosch |
1.83 |
|
1635 |
mlosch |
1.82 |
checkpoint46d_post |
1636 |
|
|
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
1637 |
|
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
1638 |
|
|
case of pressure coordinates. eosType='JMD95Z' in |
1639 |
|
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
1640 |
|
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1641 |
|
|
in find_alpha/beta. |
1642 |
|
|
checkpoint46d_pre |
1643 |
|
|
|
1644 |
|
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1645 |
|
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
1646 |
adcroft |
1.81 |
|
1647 |
|
|
checkpoint46c_post |
1648 |
|
|
o Changes necessary for ocean in p-coordinates |
1649 |
|
|
- Added new buoyancy relation = 'OCEANICP' |
1650 |
|
|
- Added new parameters = gravitySign (this used to be contained inside |
1651 |
|
|
the factor dRdZ which I added when we first switched to R coordinates). |
1652 |
|
|
X GM/Redi is not compatible (yet) |
1653 |
|
|
X bottom drag and no-slip need to be debugged. |
1654 |
|
|
checkpoint46c_pre |
1655 |
mlosch |
1.80 |
|
1656 |
|
|
checkpoint46b_post |
1657 |
|
|
o Added new equation of state -> JMD95Z and JMD95P |
1658 |
mlosch |
1.83 |
- EOS of Jackett and McDougall, 1995, JAOT |
1659 |
mlosch |
1.80 |
- moved all EOS parameters into EOS.h |
1660 |
|
|
- new routines ini_eos.F, store_pressure.F |
1661 |
|
|
o Added UNESCO EOS, but not recommended because it requires |
1662 |
|
|
in-situ temperature (see JMD95) |
1663 |
|
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
1664 |
|
|
unesco.f to be used with POLY3 |
1665 |
|
|
checkpoint46b_pre |
1666 |
mlosch |
1.79 |
|
1667 |
|
|
checkpoint46a_post |
1668 |
|
|
o Added (atmospheric) pressure loading |
1669 |
|
|
- new field in FFIELDS.h, etc... |
1670 |
|
|
- new cpp flag ATMOSPHERIC_LOADING |
1671 |
|
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
1672 |
|
|
o Added SHORTWAVE_HEATING to some files for consistency |
1673 |
|
|
checkpoint46a_pre |
1674 |
heimbach |
1.78 |
|
1675 |
|
|
checkpoint46 |
1676 |
|
|
further merges from release1_p5 |
1677 |
|
|
o new ctrl package |
1678 |
|
|
- adopted from ECCO environment to enable optimization |
1679 |
|
|
- added Eliassen Palm fluxes to controls |
1680 |
|
|
o added Eliassen Palm flux controls to gradient check package |
1681 |
|
|
o cost package |
1682 |
|
|
- Compatible with new ctrl package |
1683 |
|
|
- added Eliassen Palm cost hooks |
1684 |
|
|
- modif's of existing cost functions |
1685 |
|
|
o Adjoint-related bug fixes in kpp: |
1686 |
|
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
1687 |
|
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
1688 |
|
|
o autodiff package |
1689 |
|
|
- flow directives: |
1690 |
|
|
+ new for S/R do_the_model_io |
1691 |
|
|
+ enhanced for S/R checkpoint |
1692 |
|
|
+ new gmredi.flow |
1693 |
|
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
1694 |
|
|
disable adcommon.h/g_common.h by default. |
1695 |
|
|
- fixed problem for adjoint of global_max |
1696 |
|
|
o modified verification/carbon/ |
1697 |
|
|
o New setup for adjoint of global_ocean |
1698 |
|
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
1699 |
|
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
1700 |
|
|
o incorporated hooks for sponge layer code (external_forcing.F) |
1701 |
|
|
|
1702 |
jmc |
1.77 |
checkpoint45d_post |
1703 |
|
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
1704 |
jmc |
1.76 |
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
1705 |
|
|
(affects plume_on_slope "cg2d" output) |
1706 |
jmc |
1.77 |
o add new parameter deltaTfreesurf for free-surface time stepping |
1707 |
|
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
1708 |
jmc |
1.75 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
1709 |
jmc |
1.74 |
o change phiMin in exp1 (to agree with documentation) |
1710 |
|
|
o add new flags: |
1711 |
|
|
- T,S forcing inside/outside Adams-Bashforth |
1712 |
|
|
- turn off temp,salt advection and/or forcing |
1713 |
|
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
1714 |
|
|
o monitor: change definition of KE to check conservation of Energy |
1715 |
heimbach |
1.73 |
|
1716 |
|
|
checkpoint45c_post |
1717 |
|
|
o Removed f90 comments ("!") |
1718 |
|
|
o Modified initialisations to enable exf package for MITgcm |
1719 |
|
|
(without invoking ECCO_PACKAGE). |
1720 |
|
|
o modifications to gradient check package (Martin Losch) |
1721 |
|
|
- enable centered differences |
1722 |
|
|
- modified format of standard output |
1723 |
heimbach |
1.72 |
|
1724 |
|
|
checkpoint45b_post |
1725 |
|
|
o cleaned exchange calls in cg2d |
1726 |
|
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
1727 |
|
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
1728 |
|
|
to configure barotropic setup (Martin Losch) |
1729 |
|
|
o moved some initialisations within bi,bj loop in dynamics |
1730 |
|
|
(TAF flow dependency) |
1731 |
|
|
o in initialise_varia, moved call packages_init_variables |
1732 |
|
|
before convective_adjustment_init |
1733 |
|
|
(corresponding adjustment of TAF tape initialisation). |
1734 |
|
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
1735 |
jmc |
1.70 |
|
1736 |
jmc |
1.71 |
checkpoint45a_post |
1737 |
|
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
1738 |
|
|
o specific exchange for X-slice domain (case Ny=1) |
1739 |
jmc |
1.70 |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
1740 |
|
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
1741 |
jmc |
1.67 |
|
1742 |
heimbach |
1.69 |
checkpoint44h_post = checkpoint45 |
1743 |
|
|
o Fix to restore differentiability: |
1744 |
|
|
place at which packages_init_variables is called in |
1745 |
|
|
initialise_varia is crucial for reverse control flow. |
1746 |
|
|
o modifications in GMRedi to enable stable adjoint |
1747 |
|
|
(corresponding modif's in thermodynamics, dynamics) |
1748 |
|
|
o added missing hook for sponge layer code in external_forcing |
1749 |
|
|
o modified test cost functions |
1750 |
|
|
o storing in gad_advection (plus removal of write(0,*)! |
1751 |
|
|
o missing headers TR1.h added in convective_adjustment routines |
1752 |
|
|
o errorMessageUnit set non-equal zero in eeboot |
1753 |
|
|
(conflict on some platforms, e.g. IBM SP3) |
1754 |
|
|
o modified carbon verif. |
1755 |
|
|
|
1756 |
|
|
checkpoint44h_pre |
1757 |
jmc |
1.68 |
o vertical grid option: allow to put the Interface at the middle between |
1758 |
|
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
1759 |
jmc |
1.67 |
o GM Advective form: Tracers are advected using the residual transport (= |
1760 |
|
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
1761 |
jmc |
1.66 |
|
1762 |
|
|
checkpoint44g_post |
1763 |
|
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
1764 |
|
|
results) ; ifdef missing in thermodynamics.F |
1765 |
adcroft |
1.65 |
|
1766 |
|
|
checkpoint44f_pre,checkpoint44f_post |
1767 |
|
|
o added PTRACERS package |
1768 |
|
|
This allows an arbitrary number of passive tracers to be integrated |
1769 |
|
|
forward simultaneously with the dynamicaly model. |
1770 |
|
|
+ Implemented so far: |
1771 |
|
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
1772 |
|
|
- I/O and checkpointing |
1773 |
|
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
1774 |
|
|
+ Not implemented so far: |
1775 |
|
|
- KPP |
1776 |
|
|
- OBCS |
1777 |
|
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
1778 |
|
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
1779 |
|
|
line in data.pkg. |
1780 |
|
|
+ This package is disabled by default since it increases storage. |
1781 |
|
|
|
1782 |
jmc |
1.60 |
|
1783 |
adcroft |
1.64 |
o testscript: added -cleanup option |
1784 |
jmc |
1.63 |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
1785 |
|
|
b) enable to filter 2D fields. |
1786 |
adcroft |
1.62 |
|
1787 |
|
|
checkpoint44e_pre,post |
1788 |
|
|
o re-wrote convective adjustment to use pre-calculated weights |
1789 |
|
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
1790 |
|
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
1791 |
|
|
Original calls to convect() still in place. |
1792 |
heimbach |
1.61 |
|
1793 |
|
|
chkpt44d_pre,post |
1794 |
|
|
o added missing EXCLUDE_MONITOR flags |
1795 |
|
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
1796 |
|
|
(incompatible typ in MIN/MAX expressions caused problems |
1797 |
|
|
on IBM SP3) |
1798 |
|
|
o in genmake added variable MAKEDEPEND |
1799 |
|
|
plus resetting for case SunOS |
1800 |
|
|
o added timer_stats.c routine for IBM SP3 |
1801 |
|
|
o removed variables in dynamics |
1802 |
|
|
!!! I forgot to create tag chkpt44d_pre !!! |
1803 |
|
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
1804 |
jmc |
1.63 |
|
1805 |
|
|
o real fresh water flux implemented with non-linear free-surface. |
1806 |
heimbach |
1.58 |
|
1807 |
jmc |
1.59 |
chkpt44c_pre,post |
1808 |
|
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
1809 |
|
|
USE_NATURAL_BCS in solve_for_P); |
1810 |
|
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
1811 |
|
|
|
1812 |
heimbach |
1.58 |
checkpoint44b_pre/_post |
1813 |
|
|
o merge of relevant stuff from the ecco-branch: |
1814 |
|
|
- genmake: removed $S64 overwrite for case SunOS |
1815 |
|
|
- pkg/exf: update and corrections for field swapping and obcs |
1816 |
|
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
1817 |
|
|
harmonized between ECCO and MITgcm |
1818 |
|
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
1819 |
|
|
updated checkpointing_lev... lists for obcs |
1820 |
|
|
- model/src: minor changes in forward_step, plot_field |
1821 |
|
|
added directive for divided adjoint in the_main_loop |
1822 |
|
|
- pkg/mdsio: added mdsio_gl_slice |
1823 |
jmc |
1.57 |
|
1824 |
|
|
o check parameters & config (chkpt44a_pre,post) |
1825 |
jmc |
1.56 |
o OBC and NonLin_FrSurf. |
1826 |
|
|
|
1827 |
heimbach |
1.55 |
checkpoint44 |
1828 |
jmc |
1.54 |
o fix bug in mom_vi_del2uv |
1829 |
jmc |
1.56 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
1830 |
|
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
1831 |
|
|
o update AIM experiments (NCEP input files) |
1832 |
|
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
1833 |
heimbach |
1.55 |
o added some stuff for AD |
1834 |
adcroft |
1.53 |
|
1835 |
|
|
checkpoint43 |
1836 |
|
|
o added two new advection tests |
1837 |
|
|
o added global 4x4 degree ocean test |
1838 |
|
|
o added test of H&S94 with free surface on cube |
1839 |
|
|
o some final mods for gradient check, adjoint,... |
1840 |
heimbach |
1.52 |
|
1841 |
|
|
checkpoint42 |
1842 |
|
|
Fixed AD-related problems: |
1843 |
|
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
1844 |
|
|
(mainly thermodynamics.F) |
1845 |
|
|
o New store directives for multi-dim. advection schemes |
1846 |
|
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
1847 |
|
|
* new common block and key passkey |
1848 |
|
|
(mainly gad_advection.F) |
1849 |
|
|
o Modified store directives for split of dynamics/thermodynamics |
1850 |
|
|
for the case ALLOW_KPP |
1851 |
|
|
o Cleaned argument list for timestep_tracer.F |
1852 |
adcroft |
1.51 |
|
1853 |
|
|
checkpoint41 |
1854 |
|
|
o re-formatted/added comments in prologues of key subroutines |
1855 |
|
|
to work with protex |
1856 |
heimbach |
1.47 |
|
1857 |
adcroft |
1.50 |
checkpoint40 |
1858 |
|
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
1859 |
|
|
o added FLT (floats) package from Arne along with demo. experiment |
1860 |
|
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
1861 |
|
|
implementation of forward-in-time forcing terms |
1862 |
|
|
o more mods for non-linear free-surface including new variable |
1863 |
|
|
o modified multi-dim method to work on cube |
1864 |
|
|
o bug fix in KPP (from DM) |
1865 |
|
|
|
1866 |
adcroft |
1.49 |
checkpoint40pre9 |
1867 |
|
|
o added DST advection schemes |
1868 |
|
|
o fix MPI bug on SGI's |
1869 |
|
|
o modifications for non-linear free-surface |
1870 |
|
|
o fixed conditionals for fixed flow/passive tracer only mode |
1871 |
|
|
o added tension/strain form of stress tensor |
1872 |
|
|
o changes to commenting of arguments for TAF/TAMC |
1873 |
|
|
o added/updated many matlab scripts |
1874 |
adcroft |
1.50 |
o added multi-dimensional advection method for tracers |
1875 |
adcroft |
1.49 |
|
1876 |
adcroft |
1.48 |
checkpoint40pre8 |
1877 |
heimbach |
1.47 |
o new package rw/ |
1878 |
|
|
Added method for dumping intermediate local arrays: |
1879 |
|
|
mdsio_writetile - same as mdsio_writefield except works from inside |
1880 |
|
|
bi,bj loop |
1881 |
|
|
mdsio_writelocal - same as mdsio_writetile except works for local |
1882 |
|
|
arrays |
1883 |
|
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
1884 |
|
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
1885 |
|
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
1886 |
|
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
1887 |
|
|
control flux-form versus vector invariant code. |
1888 |
|
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
1889 |
|
|
or genmake -DISABLE ... |
1890 |
|
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
1891 |
|
|
(additional storing is now needed for case vecinv; |
1892 |
|
|
currently nothing implemented to switch this storing off |
1893 |
|
|
in case fluxform is used since no CPP flag available). |
1894 |
heimbach |
1.46 |
|
1895 |
|
|
checkpoint40pre7 |
1896 |
|
|
o bug fix in dynamics.F |
1897 |
|
|
calc_viscosity called before k=1,Nr loop. |
1898 |
|
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
1899 |
|
|
o cleaned initialisations in ctrl_map_ini |
1900 |
|
|
related to TAF |
1901 |
heimbach |
1.45 |
|
1902 |
|
|
checkpoint40pre6 |
1903 |
|
|
o split dynamics into thermodynamics & dynamics |
1904 |
|
|
o corresponding split of calc_diffusivity into |
1905 |
|
|
calc_diffusivity, calc_viscosity |
1906 |
|
|
(kpp_calc_diff, kpp_calc_visc). |
1907 |
|
|
o Added diffkr, kapgm to control variables |
1908 |
|
|
o bug fix in gmredi_slope_limit for ldd97 |
1909 |
adcroft |
1.44 |
|
1910 |
|
|
checkpoint40pre5 |
1911 |
|
|
o proper initialization of Adams-Bashforth time stepping |
1912 |
|
|
+ uses forward step for very first step of model (iter=0) |
1913 |
|
|
o re-generated *all* output since almost all output is modified by this |
1914 |
|
|
change (sorry but we've been putting this one off for about 2 years) |
1915 |
|
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
1916 |
|
|
*not* regenerated since they are already out of date and I don't |
1917 |
|
|
want to create the impression that they are suddenly working. |
1918 |
|
|
o removed KAP stuff for DEC's |
1919 |
|
|
o modified/added many .cvsignore files in */code and */input |
1920 |
|
|
o added new expt "solid-body.cs-32x32x1" |
1921 |
|
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
1922 |
|
|
is not necessarily any better than the current one... |
1923 |
heimbach |
1.43 |
|
1924 |
|
|
checkpoint40pre4 |
1925 |
|
|
o added re-initialisations of utrans,vtrans,rtrans in |
1926 |
|
|
calc_common_factors which are crucial for TAF. |
1927 |
|
|
o extended iMin,jMin range for calc_common_factors, |
1928 |
|
|
calc_diffusivity |
1929 |
|
|
o added option ALLOW_PASSIVE_TRACER |
1930 |
|
|
o a few minor updates and fixes |
1931 |
|
|
|
1932 |
heimbach |
1.42 |
checkpoint40pre3 |
1933 |
|
|
o created calc_gtr1.F for gad package |
1934 |
|
|
o split the_main_loop and re-introduced forward_step |
1935 |
|
|
o some recomputations of nIter0 for TAMC |
1936 |
|
|
|
1937 |
heimbach |
1.41 |
checkpoint40pre2 |
1938 |
|
|
o Updated to latest branch of AJA, JMC |
1939 |
|
|
o Added gradient check package |
1940 |
|
|
o Added routines for passive tracer handling |
1941 |
|
|
o Added carbon sequestration sensitivity experiment |
1942 |
|
|
|
1943 |
heimbach |
1.39 |
checkpoint39 |
1944 |
|
|
o Modifications and fixes to support TAMC |
1945 |
|
|
(mainly missing or wrong directives) |
1946 |
|
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
1947 |
|
|
in addummy_in_stepping |
1948 |
|
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
1949 |
|
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
1950 |
|
|
o Included following packages: |
1951 |
|
|
cal: calendar |
1952 |
|
|
exf: external forcing |
1953 |
|
|
ecco: essential routines to control use of cal, exf |
1954 |
|
|
(NB: this is not the full ECCO environment) |
1955 |
heimbach |
1.40 |
o disabled some packages by default in genmake |
1956 |
heimbach |
1.39 |
|
1957 |
heimbach |
1.38 |
checkpoint38 |
1958 |
|
|
o see notes_c37_adj.txt |
1959 |
|
|
o corrected wrong layer index in external_forcing_t |
1960 |
|
|
o replaced the_main_loop/forward_step by the_main_loop |
1961 |
|
|
o removed forceoutput from write_state |
1962 |
|
|
(replaced criteria for initial/final state) |
1963 |
|
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
1964 |
jmc |
1.36 |
|
1965 |
jmc |
1.37 |
checkpoint37 |
1966 |
|
|
o mdsio.F routine split and packaged in pkg/mdsio |
1967 |
|
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
1968 |
|
|
used unless genmake -disable=mdsio) |
1969 |
|
|
o allow a more precise surface-geopotential gradient for the atmosphere |
1970 |
|
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
1971 |
|
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
1972 |
|
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
1973 |
|
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
1974 |
|
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
1975 |
|
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
1976 |
|
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
1977 |
|
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
1978 |
|
|
and after) unless activating 2 commented lines in initialise-varia. |
1979 |
|
|
o Non-Hydrostatic pickup file Pb fixed. |
1980 |
|
|
o bug with Rigid-lid version (since c35) fixed. |
1981 |
|
|
|
1982 |
jmc |
1.36 |
checkpoint36 |
1983 |
jmc |
1.37 |
o implement Crank-Nickelson barotropic time-stepping |
1984 |
jmc |
1.36 |
o recover Time-Average diagnostics |
1985 |
|
|
o fix Pb in checkpoint (PR#19) |
1986 |
|
|
o AIM become a standard package ; clean unused CPP_kees |
1987 |
jmc |
1.35 |
|
1988 |
|
|
checkpoint35 |
1989 |
|
|
o subtantial rewrite of dynamics.f |
1990 |
|
|
o allows staggered time-stepping |
1991 |
|
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
1992 |
|
|
o added bottom drag (linear + quadratic) |
1993 |
heimbach |
1.33 |
|
1994 |
|
|
checkpoint34 |
1995 |
|
|
o Modified exchange routines for correct reverse simulation. |
1996 |
|
|
o Added verification output to comply with bug fix in impldiff.F |
1997 |
|
|
as of c33 (exp2, natl_box). |
1998 |
|
|
o Corrected store directives in dynamics.F |
1999 |
|
|
o Corrected array boundaries in impldiff.F |
2000 |
|
|
o Corrected array dimensions in gmredi. |
2001 |
|
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
2002 |
heimbach |
1.34 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
2003 |
heimbach |
1.33 |
o Added mdsio_gl.F for ECCO purposes. |
2004 |
adcroft |
1.32 |
|
2005 |
|
|
checkpoint33 |
2006 |
|
|
o Fixed bug in lower BC in impldiff.F |
2007 |
|
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
2008 |
|
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
2009 |
|
|
- Removed verification/natl_box/code/external_fields_scale.F |
2010 |
|
|
(did not differ from that in model/src) |
2011 |
|
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
2012 |
|
|
(see FFIELDS.h for description) |
2013 |
|
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
2014 |
|
|
kpp_calc.F and kpp_transport_t.F |
2015 |
|
|
- Removed model/src/external_fields_scale.F and calls to it |
2016 |
|
|
- verification/natl_box uses flux data with "atmospheric" sign so |
2017 |
|
|
a special version of external_fields_load.F is used to |
2018 |
|
|
change the data as it's read in. This way, the arrays |
2019 |
|
|
have the right units and signs at all times tha a user could |
2020 |
|
|
possibly use them. |
2021 |
|
|
o Corrected genmake to delete a temporary file during configuration |
2022 |
heimbach |
1.31 |
|
2023 |
|
|
checkpoint32 |
2024 |
|
|
o Scaling of forcing fields moved from external_forcing.F to |
2025 |
|
|
external_fields_scale.F, called directly after loading fields. |
2026 |
|
|
o Surface relaxation terms added to surface tendency fields in |
2027 |
|
|
extra subroutine. |
2028 |
|
|
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
2029 |
|
|
fields. |
2030 |
|
|
o Changes in GMRedi to comply with packaging structure. |
2031 |
|
|
o Modifications and bug fixes in KPP package. |
2032 |
|
|
o Verification experiment for KPP added (verification/nat_box/) |
2033 |
heimbach |
1.30 |
|
2034 |
|
|
checkpoint31 |
2035 |
|
|
o Packages interface brought in line with defined standard |
2036 |
|
|
-> new routines packages_...F |
2037 |
|
|
-> changes in initialise_fixed.F, initialise_varia.F |
2038 |
|
|
-> enables initialisation interface for ECCO package |
2039 |
|
|
o Rescaling of external forcing fields immediately after read |
2040 |
|
|
(removed from external_forcing.F) |
2041 |
|
|
-> new: surface_fields_scale.F |
2042 |
|
|
-> affects ini_foorcing.F, external_fields_load.F |
2043 |
|
|
o Computation of surface tendencies before tendency updates. |
2044 |
|
|
-> new: external_forcing_surf.F |
2045 |
|
|
o Change of variable names useGMRedi, useKPP, useECCO |
2046 |
|
|
o Further changes in dynamics.F, impldiff.F for TAMC |
2047 |
|
|
o Tested for experiments 0, 2, 4. |
2048 |
|
|
- not yet tested for GMRedi. |
2049 |
|
|
- not yet tested for KPP. |
2050 |
adcroft |
1.29 |
|
2051 |
|
|
checkpoint30 |
2052 |
|
|
o Updates for OBCs |
2053 |
|
|
o New experiment for test OBCs (internal_wave) |
2054 |
|
|
o New output.txt in verification/exp4/results/ |
2055 |
|
|
o Updates for KPP: calculation of viscosity corrected, new variables |
2056 |
|
|
kpp_dumpFreq and kpp_taveFreq |
2057 |
|
|
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
2058 |
|
|
and entry for T90 in genmake |
2059 |
adcroft |
1.28 |
|
2060 |
|
|
checkpoint29 |
2061 |
|
|
o packaged KPP and GM/Redi |
2062 |
heimbach |
1.27 |
|
2063 |
|
|
checkpoint28 |
2064 |
|
|
o Corrected initialization of hFacMin for difference vertical coordinates |
2065 |
|
|
o Modified calculation of partial cell thickness to more robust algorithm |
2066 |
|
|
o config_summary.F: replaced write_1D_... by write_0D_... |
2067 |
|
|
read_write.F: added subroutines write_0D_... |
2068 |
|
|
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
2069 |
|
|
included some initialisations required for TAMC. |
2070 |
|
|
o routine calc_isoslopes: modified sqrt computation to make it |
2071 |
|
|
differentiable for zero argument. |
2072 |
|
|
o routines dynamics, impldiff: |
2073 |
|
|
included store directives and tape key computations required for TAMC. |
2074 |
|
|
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
2075 |
adcroft |
1.26 |
|
2076 |
|
|
checkpoint27 |
2077 |
|
|
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
2078 |
|
|
formulation works properly with variable resolution. |
2079 |
|
|
o restructured the calling tree between the_model_main() and dynamics() |
2080 |
|
|
o split initialise() into initialise_fixed() and initialise_varia() |
2081 |
|
|
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
2082 |
|
|
in new routine ini_psurf() |
2083 |
adcroft |
1.25 |
|
2084 |
|
|
checkpoint26 |
2085 |
|
|
o moved some #ifdef in optional routines to encompass everything |
2086 |
|
|
except the argument declarations. This was using up some memory. |
2087 |
|
|
o fixed macros like _ADT to work with both versions of Linux cpp |
2088 |
|
|
o cleaned up some unused and uninitialized variables |
2089 |
|
|
(helps when debugging with strict compile options) |
2090 |
|
|
o split up CPP_EEOPTIONS.h into options and macros |
2091 |
|
|
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
2092 |
|
|
o patch for 2 processor JAM mode |
2093 |
adcroft |
1.24 |
|
2094 |
|
|
checkpoint25 |
2095 |
|
|
o updates for OBCs and NH |
2096 |
|
|
o dramatically reduced memory usage |
2097 |
|
|
o added "JAM" routines for use on Artic network |
2098 |
|
|
o parameterization of convection by implicit vertical diffusion |
2099 |
|
|
o added a diagnostic of convective index |
2100 |
|
|
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
2101 |
|
|
(this is was partly for OBCs and NH but also in anticipation of |
2102 |
|
|
an explicit free-surface option) |
2103 |
|
|
o initial state input files for U and V |
2104 |
adcroft |
1.23 |
|
2105 |
|
|
checkpoint24 |
2106 |
|
|
o Removed some spurious "REAL"s |
2107 |
|
|
o Updated KPP to latest version from JPL |
2108 |
|
|
o Added a COS(latitude) in horizontal viscosity |
2109 |
adcroft |
1.22 |
|
2110 |
|
|
checkpoint23 |
2111 |
|
|
o Added del^4 diffusion for salt and temperature |
2112 |
|
|
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
2113 |
adcroft |
1.21 |
|
2114 |
|
|
checkpoint22 |
2115 |
|
|
o Made many small changes: implicit none, format(i5), etc... |
2116 |
|
|
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
2117 |
adcroft |
1.20 |
|
2118 |
|
|
checkpoint21 |
2119 |
|
|
o Introduced new I/O package that supports direct-access records (mdsio.F) |
2120 |
|
|
o Split-up mid-level I/O routines |
2121 |
|
|
o Updated input data for experiments 0,1,2,4 and 5 |
2122 |
|
|
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
2123 |
adcroft |
1.18 |
|
2124 |
adcroft |
1.19 |
checkpoint20 |
2125 |
|
|
o Tidied up open-boundaries some more |
2126 |
|
|
o Added non-hydrostatic code |
2127 |
|
|
o Fixed some input data |
2128 |
|
|
o Modified MPI start-up to work in "coupled" context. |
2129 |
|
|
|
2130 |
adcroft |
1.18 |
checkpoint19 |
2131 |
|
|
o Tidied up directory structure for verification experiments. |
2132 |
|
|
o Added new code for open boundaries. |
2133 |
|
|
o Corrected advective terms near boundaries. |
2134 |
|
|
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
2135 |
|
|
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
2136 |
adcroft |
1.19 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
2137 |
cnh |
1.17 |
|
2138 |
|
|
checkpoint18 |
2139 |
|
|
o Further changes for optional code generation with |
2140 |
|
|
CPP - ugh! |
2141 |
cnh |
1.16 |
|
2142 |
|
|
checkpoint17 |
2143 |
|
|
o Beginning to incorporating modularity |
2144 |
|
|
for supporting atmos. and ocean configs. |
2145 |
|
|
o Small changes for TAMC complinace |
2146 |
|
|
o New ultra simple test case. Barotropic box |
2147 |
|
|
configuration "exp0". |
2148 |
cnh |
1.15 |
|
2149 |
|
|
checkpoint16 |
2150 |
|
|
o Minor changes to exchange routines to support |
2151 |
|
|
accumulation in reverse mode. Adjoint of an |
2152 |
|
|
assignment is an addition. |
2153 |
|
|
o Changes to support compilation by TAMC (LR(1) |
2154 |
|
|
syntax) and by g77 under Linux ( 72 character |
2155 |
|
|
limit ). |
2156 |
cnh |
1.14 |
|
2157 |
|
|
checkpoint15 |
2158 |
|
|
Rewrote exchange routines to allow |
2159 |
|
|
o General tile <-> tile connectivity. |
2160 |
|
|
o TAMC reverse mode flag ( is this really needed? ) |
2161 |
|
|
o Variable width overlap and exchange region widths. |
2162 |
|
|
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
2163 |
|
|
shmput/shmget, VIA, SYSV shmem and every other cool |
2164 |
|
|
communication method. |
2165 |
cnh |
1.13 |
|
2166 |
|
|
checkpoint14 |
2167 |
|
|
Consistent isomorphism chages made. These allow dynamical core |
2168 |
|
|
to support both pressure and meters as a vertical coordinate. |
2169 |
cnh |
1.12 |
|
2170 |
|
|
checkpoint13 |
2171 |
|
|
Release which corrects global_max problem and a couple |
2172 |
|
|
of KGM time-averaging diagnostic errors. Also contains |
2173 |
|
|
a double-gyre experiment setup as well as the baseline |
2174 |
|
|
4 degree global template. The double gyre template is |
2175 |
|
|
organised to allow it to be applied automatically to |
2176 |
|
|
the baseline configuration. |
2177 |
adcroft |
1.11 |
|
2178 |
|
|
branch-point-rdot |
2179 |
|
|
A few tidy-ups have been made bt the real point of this |
2180 |
|
|
check-point (excuse the pun) is to allow a branch to be |
2181 |
|
|
made for the purposes of adding the rDot alterations. |
2182 |
|
|
I don't want to commit the rDot to the main-trunk until |
2183 |
|
|
we've actually tested it... |
2184 |
cnh |
1.10 |
|
2185 |
|
|
checkpoint12 |
2186 |
|
|
Tidy up and added generic genmake script (formerly |
2187 |
|
|
configure script). |
2188 |
|
|
Released to testers. |
2189 |
adcroft |
1.9 |
|
2190 |
|
|
checkpoint11 |
2191 |
|
|
Re-arranged initialise() and introduced ini_vertical_grid() |
2192 |
|
|
and ini_masks_etc(). |
2193 |
adcroft |
1.8 |
|
2194 |
|
|
checkpoint10 |
2195 |
|
|
Introduced the configure script. |
2196 |
|
|
Separated out the diags package. |
2197 |
|
|
Added template for writing time-averages of tile/intermediate quantities. |
2198 |
|
|
Updated SIZE.h in exp2 and made the data big-endian. |
2199 |
adcroft |
1.7 |
|
2200 |
|
|
checkpoint9 |
2201 |
|
|
MPI fix. Filename changes (meta/data). salbin*y stuff. |
2202 |
|
|
General tidy-up. |
2203 |
|
|
SST.bin SSS.bin added to verification/exp2 |
2204 |
adcroft |
1.6 |
|
2205 |
|
|
checkpoint8 |
2206 |
|
|
Inludes time-dependant forcing and time-averaging. |
2207 |
|
|
Works at 4x4 and 2.8125x2.8125 global |
2208 |
|
|
|
2209 |
|
|
checkpoint7-4degree-ref |
2210 |
|
|
Branch from checkpoint7. Released for application to |
2211 |
|
|
global modeling and general modeling - process studies, regional |
2212 |
|
|
model etc.. |
2213 |
|
|
Configured for verification/exp2 - 4 degree global, two process. |
2214 |
cnh |
1.5 |
|
2215 |
|
|
checkpoint7 |
2216 |
|
|
Created by cnh |
2217 |
|
|
Simple 4 degree global simulation |
2218 |
|
|
configuration. |
2219 |
|
|
Includes climatological wind, |
2220 |
|
|
hydrography, bathymetry etc |
2221 |
|
|
Does not include Heat Flux and E-P |
2222 |
cnh |
1.4 |
|
2223 |
|
|
checkpoint6 |
2224 |
|
|
Created by cnh |
2225 |
|
|
merged checkpoint5 with CD and |
2226 |
|
|
spherical polar code. |
2227 |
|
|
Still some problems with GM Redi |
2228 |
|
|
abd full topography. |
2229 |
cnh |
1.3 |
|
2230 |
|
|
checkpoint5 |
2231 |
|
|
Created by AJA |
2232 |
|
|
contains updates to GM Redi |
2233 |
|
|
and reordered timestepping loop |
2234 |
|
|
for Implicit Diffusion. |
2235 |
cnh |
1.2 |
|
2236 |
|
|
checkpoint4 |
2237 |
|
|
Created by cnh |
2238 |
|
|
Contains memory saving macros ( _rdxc etc..) for when |
2239 |
|
|
grid variations are limited. |
2240 |
|
|
Contains polynomial coeffs for EOS and knudsen program |
2241 |
|
|
for generation. |
2242 |
|
|
|
2243 |
cnh |
1.1 |
checkpoint3 |
2244 |
|
|
Created by cnh |
2245 |
|
|
Added extra flags for runtime options |
2246 |
|
|
Added this file |
2247 |
|
|
Added implicit free-surface |
2248 |
|
|
Added pre-conditioner |
2249 |
|
|
Put compare01 into repository ( compare01/... ) |
2250 |
|
|
Put data and eedata into repository ( verification/exp1 ) |
2251 |
|
|
|
2252 |
|
|
checkpoint2 |
2253 |
|
|
Created by AJA |
2254 |
|
|
Added GM/Redi |
2255 |
|
|
|
2256 |
|
|
checkpoint1 |
2257 |
|
|
Created by AJA |
2258 |
|
|
Restructured kloop in dynamics.F |
2259 |
|
|
Added non-linear EOS |
2260 |
|
|
|
2261 |
cnh |
1.2 |
baseline |
2262 |
|
|
Original checked in code |
2263 |
cnh |
1.1 |
|