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$Header$ |
$Header$ |
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$Name$ |
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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
6 |
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7 |
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checkpoint57h_post |
8 |
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o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
9 |
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o pkg/diagnostics: change output frequency, now in seconds (instead |
10 |
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of Nb of iterations). This requires to change data.diagnostics. |
11 |
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checkpoint57h_pre |
12 |
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|
13 |
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o in mnc, let the user create the output dir if both mnc_outdir_date |
14 |
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and mnc_outdir_num are false |
15 |
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o add fflags() to pkg/diagnostics which allows one to specify, on a |
16 |
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per-file basis, the file precision [default behavior is unchanged] |
17 |
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o added diagnostics to pkg/kpp, including computation of mixed layer |
18 |
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depth based on a temperature/density criterion |
19 |
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o updated verification/natl_box to test the new pkg/kpp diagnostics |
20 |
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o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
21 |
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o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
22 |
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o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
23 |
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not mnc -- this mistake was found by JMC and is now corrected |
24 |
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|
25 |
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checkpoint57g_post |
26 |
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o add Adams-Bashforth 3rd Order time stepping: |
27 |
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- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
28 |
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- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
29 |
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checkpoint57g_pre |
30 |
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|
31 |
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o make lambda[Theta,Salt]ClimRelax spatially varying |
32 |
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(default remains spatially uniform constant based on tau) |
33 |
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o added new control variables |
34 |
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* init. uVel, vVel, etanN |
35 |
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* lambda[Theta,Salt]ClimRelax |
36 |
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o separate masks used for ctrl_pack/unpack 'from write_grid' output |
37 |
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(suggested by G. Forget) |
38 |
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|
39 |
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checkpoint57f_post |
40 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
41 |
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new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
42 |
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account for baseTime shift |
43 |
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o move Coriolis arrays from PARAMS.h to GRID.h |
44 |
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checkpoint57f_pre |
45 |
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|
46 |
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o mnc-ifying the seaice package |
47 |
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o introduced an alternative length scale calculation for use in the limiting |
48 |
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maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
49 |
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o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
50 |
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o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
51 |
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as well as grad(vort3). Made it compatible with both approximate form |
52 |
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for the cubed sphere and full form of these gradients. Added flag |
53 |
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useFullLeith to select between approximate and full form. |
54 |
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o add "d0" in getcon.F to reduce differences between compilers/platforms |
55 |
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update output.txt of exp. fizhi-gridalt-hs |
56 |
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o change port_rand funtion to allow to set the seed. |
57 |
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o fix obscure MNC bug involving conversion between reals and integers |
58 |
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- it caused no problems with certain (eg. gcc, ifc) compilers but the |
59 |
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new version is now more standards-compliant |
60 |
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o adjoint-related modifications |
61 |
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* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
62 |
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* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
63 |
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* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
64 |
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|
65 |
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checkpoint57e_post |
66 |
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o Adding eddy stress controls a la Ferreira et al. |
67 |
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checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
68 |
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|
69 |
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o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
70 |
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update output.txt of exp. fizhi-gridalt-hs |
71 |
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o add more "Z" dimensions and associated coordinate vars to MNC |
72 |
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o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
73 |
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o parameter calendarDumps: when set, approximate months (30-31 days) and years |
74 |
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(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
75 |
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KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
76 |
|
months and years. Requires pkg/cal. |
77 |
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o diagnostics: add pickup functionality |
78 |
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- off by default for backwards compatibility |
79 |
|
- current version only uses MDSIO -- MNC will be added |
80 |
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o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
81 |
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o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
82 |
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|
83 |
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checkpoint57d_post |
84 |
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o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
85 |
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o modify verification/ideal_2D_oce so that it tests the creation of mnc |
86 |
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output from the diagnostics package |
87 |
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o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
88 |
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o make genmake2 more portable by using ".$FS" instead of ".f" for more |
89 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
90 |
|
o add coordinate variables to the MNC output from the diagnostics package |
91 |
|
o change MNC-flags default value: true when useMNC=TRUE |
92 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
93 |
|
the ability (off by default) to read the grid information using MNC |
94 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
95 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
96 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
97 |
|
at the end). |
98 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
99 |
|
new test for AIM with thSIce + slab-ocean |
100 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
101 |
|
o move state variable diagnostics to the beginning of the time step ; |
102 |
|
(note: still needs some work specially for snap-shot diagnostics) |
103 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
104 |
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|
105 |
|
checkpoint57c_post |
106 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
107 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
108 |
|
checkpoint57c_pre |
109 |
|
|
110 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
111 |
|
update output.txt of exp. global_ocean.90x40x15 |
112 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
113 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
114 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
115 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
116 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
117 |
|
o improvements for the MNC output from DIAGNOSTICS: |
118 |
|
- correct handling of the unlimitied dimension |
119 |
|
- all dims now have associated coordinate variables |
120 |
|
- variables located at U, V, and Corner ("Z") points are now written |
121 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
122 |
|
*all* data points are output |
123 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
124 |
|
o added pkg/seaice/seaice_monitor.F |
125 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
126 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
127 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
128 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
129 |
|
spurious negative numbers for precipitation and humidity. Will cause |
130 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
131 |
|
o pkg/ctrl/ |
132 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
133 |
|
May be enabled via doPackDiag |
134 |
|
* introduce z-scaling of |
135 |
|
+ gradient (doZscalePack) and |
136 |
|
+ control (doZscaleUnpack) |
137 |
|
o pkg/mdsio/ |
138 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
139 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
140 |
|
|
141 |
|
checkpoint57b_post |
142 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
143 |
|
o fix MNC coordinate variables so that they now contain per-face index |
144 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
145 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
146 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
147 |
|
o Implement instantaneous output within pkg diagnostics: |
148 |
|
setting a negative frequency in data.diagnostics produces |
149 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
150 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
151 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
152 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
153 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
154 |
|
becomes the coordinate variable for the 'T' dimension |
155 |
|
o add CF-style coordinate variables to MNC |
156 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
157 |
|
missing along the T axis but otherwise it works! |
158 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
159 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
160 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
161 |
|
this is based directly on what the model compute, so that the content of |
162 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
163 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
164 |
|
o clean up build options files for SunOS, in particular |
165 |
|
- remove -traditional from xmakedepend |
166 |
|
- change -xarch=v9 to -xarch=native for f77 |
167 |
|
- restore use of make (not gmake) |
168 |
|
- add CC=gcc if using g77 |
169 |
|
o changes per discussion of AM, JMC, & EH3 today: |
170 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
171 |
|
creating proper CF-style coordinate variables and in recognition |
172 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
173 |
|
the grid files into any of the other NetCDF files |
174 |
|
- *always* output grid variables with MDSIO (this will eventually be |
175 |
|
changed) |
176 |
|
- output MNC grid file if useMNC is true |
177 |
|
o every instance of _END_MASTER() has been found and replaced with |
178 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
179 |
|
preprocessors |
180 |
|
o re-arrange diagnostics pkg initialisation: |
181 |
|
- allow each package to extend the available diagnostics list |
182 |
|
- add some checking and fix small problems (multi-threaded, ...) |
183 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
184 |
|
look through the short list of active diag. (instead of the long list) |
185 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
186 |
|
|
187 |
|
checkpoint57a_post |
188 |
|
o this set of changes restores TAMC compatibility |
189 |
|
tested for global_ocean.90x40x15 adjoint on trough |
190 |
|
(what a pain) |
191 |
|
|
192 |
|
checkpoint57a_pre |
193 |
|
o some modifs in tools/build_options for sunos |
194 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
195 |
|
|
196 |
|
checkpoint57 |
197 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
198 |
|
- new parameter viscA4W (defaults to viscA4) |
199 |
|
- affects only non-hydrostatic code |
200 |
|
- to be done: no-slip lateral boundary conditions |
201 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
202 |
|
o implement Implicit Vertical advection for pTracers |
203 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
204 |
|
(implemented also for implicit vertical diffusion & advection) |
205 |
|
o OBCS: extend application of tracer open boundary conditions |
206 |
|
to a strip beyond the boundary of width Olx/Oly |
207 |
|
o add call monitor to TAF set of required calls (flow directives) |
208 |
|
and include in natl_box_adjoint |
209 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
210 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
211 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
212 |
|
(theta2, salt2 in ecco_cost_weights) |
213 |
|
|
214 |
|
checkpoint56c_post |
215 |
|
o OBCS as control variables |
216 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
217 |
|
- remove balance of obcs controls from default |
218 |
|
- fix index bug nobcs in ctrl_init |
219 |
|
- fix dummy fields filen in ctrl_pack |
220 |
|
- add dummy weights for obcs |
221 |
|
o lsopt: comment out fort.94 output |
222 |
|
o optim: |
223 |
|
- remove unnecessary header files |
224 |
|
- adjusted namelists |
225 |
|
- add xerbla.F to Makefile |
226 |
|
o exf: |
227 |
|
- multiple modifications of exf_check_range |
228 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
229 |
|
o mdsio: |
230 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
231 |
|
|
232 |
|
checkpoint56b_post |
233 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
234 |
|
is called from DO_THE_MODEL_IO |
235 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
236 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
237 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
238 |
|
o add another verification experiment that tests both the cfc-pkg and |
239 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
240 |
|
reactive tendencies treated inline with regular timestepping |
241 |
|
o testreport previously did a lousy job of comparing small numbers, so |
242 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
243 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
244 |
|
testreport. |
245 |
|
o ptracers_monitor: bug fix for MPI |
246 |
|
|
247 |
|
checkpoint56a_post |
248 |
|
o GCHEM: finish reorganizating the package |
249 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
250 |
|
(introduces another 3D-array for each passive tracer, but only if |
251 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
252 |
|
gchemTendency is not needed because the timestep is done separately) |
253 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
254 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
255 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
256 |
|
so clear to me how that should be done in a general way. |
257 |
|
o CFC: improve formatting of output in CFC_ATMOS |
258 |
|
o PTRACERS: |
259 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
260 |
|
that ALL experiments with ptracers enable can be checked. This makes |
261 |
|
GCHEM_MONITOR obsolete. |
262 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
263 |
|
monitorFreq |
264 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
265 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
266 |
|
o exf_check_range: |
267 |
|
* default changed to .TRUE. |
268 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
269 |
|
* STOP in exf_check_range if 'out of range' |
270 |
|
* range chosen generous to allow for potential extema |
271 |
|
TBD: a version with stricter range |
272 |
|
permitted range would be runtime parameters |
273 |
|
o GMredi: |
274 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
275 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
276 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
277 |
|
o GCHEM: |
278 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
279 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
280 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
281 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
282 |
|
this flag is now only visible within GCHEM-pkg routines. |
283 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
284 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
285 |
|
this, the tracer ID iTracer had to be included into the parameter list |
286 |
|
of ptracers_forcing |
287 |
|
- set up forward_step to call gchem_forcing, that will replace |
288 |
|
gchem_forcing_int in ptracers_forcing |
289 |
|
- cleaning up |
290 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
291 |
|
|
292 |
|
checkpoint56 |
293 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
294 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
295 |
|
o ECCO-GODAE |
296 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
297 |
|
* fully merged and updated from SIO code |
298 |
|
windstress sign change affects |
299 |
|
- exf_inscal_[u/v]stress |
300 |
|
- sign of xx_tau[u/v] adjustments |
301 |
|
- signs in cost_scat |
302 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
303 |
|
* natl_box_adjoint updated and compressed |
304 |
|
* 2-level checkpoint switch added |
305 |
|
(tested in EXP. 1 of natl_box_adjoint) |
306 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
307 |
|
o SVD |
308 |
|
* first complete, non-hacked version for SVD calculations |
309 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
310 |
|
performed via direct access files admtlm_vector.it???? |
311 |
|
(via ctrl_[un]pack) |
312 |
|
* optimcycle is used for ARPACK iteration counter |
313 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
314 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
315 |
|
and add linear transforms where necessary |
316 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
317 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
318 |
|
o mdsio: filename info to both stderr, stdout |
319 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
320 |
|
from sign change |
321 |
|
|
322 |
|
checkpoint55j_post |
323 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
324 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
325 |
|
o add consistent build directories and .cvsignore files to verification |
326 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
327 |
|
o make all subroutines 30 or less characters in length for certain older |
328 |
|
compilers to work (a thorough search only turns up two routines in |
329 |
|
pkg/ptracers) |
330 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
331 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
332 |
|
|
333 |
|
checkpoint55i_post |
334 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
335 |
|
3.D if implicit) ; each ptracer uses its own background value. |
336 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
337 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
338 |
|
ITRDA and other clusters without the mpirun "-wd" option |
339 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
340 |
|
configuration |
341 |
|
o give MNC the ability to create additional files rather than |
342 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
343 |
|
- the default is just less than 2GB which is a practical limit |
344 |
|
on many systems |
345 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
346 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
347 |
|
|
348 |
|
checkpoint55h_post |
349 |
|
o add verification test "vermix" |
350 |
|
o remove all the *_ioinc flags and replace with the single global |
351 |
|
outputTypesInclusive flag |
352 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
353 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
354 |
|
o useMNC moved from data.mnc to data.pkg |
355 |
|
|
356 |
|
checkpoint55g_post |
357 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
358 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
359 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
360 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
361 |
|
Works well for global_ocean.90x40x15, |
362 |
|
but recomp. issue remains for carbon |
363 |
|
o Updating adjoint output for natl_box_adjoint after |
364 |
|
pkg/ecco has been modified (see taga c55d_post) |
365 |
|
|
366 |
|
checkpoint55f_post |
367 |
|
o rename to timeave_init_fixed |
368 |
|
|
369 |
|
checkpoint55e_post |
370 |
|
o some delicate re-shuffle of store directives to avoid one |
371 |
|
extra call of do_oceanic_physics |
372 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
373 |
|
checkpoint_lev1_directives.h |
374 |
|
o NB: this may break global_ocean adjoint temporarily, |
375 |
|
but it is clear how to fix it. Will do later, need this now. |
376 |
|
|
377 |
|
checkpoint55d_post |
378 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
379 |
|
o ecco_cost_weights is modified to 1x1 runs |
380 |
|
o modifs to allow observations to be read in as |
381 |
|
single file or yearly files |
382 |
|
o enable to read exf forcing fields as either |
383 |
|
single file or yearly files (flag useExfYearlyFields) |
384 |
|
checkpoint55d_pre |
385 |
|
|
386 |
|
o switch between 2-level and 3-level checkpointing |
387 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
388 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
389 |
|
with the correct (that is, the complete multi-dimensional) set of |
390 |
|
array indicies |
391 |
|
- used in mom_vecinv() to write the diagFreq output |
392 |
|
- tested (demonstrated) in verification/aim.5l_cs |
393 |
|
o further mnc-ification |
394 |
|
- add verification/lab_sea to the list with mnc setups |
395 |
|
- fix undefined mnc v-names in cd_code |
396 |
|
- add kpp to mnc output (both snapshot and timeave) |
397 |
|
o non-hydrostatic code |
398 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
399 |
|
in calc_gw.F |
400 |
|
- defaults to viscAh |
401 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
402 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
403 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
404 |
|
o pkg/cost |
405 |
|
extend simple cost functions to treat time mean quantities |
406 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
407 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
408 |
|
be 2 times larger than the minimum size the advection scheme requires. |
409 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
410 |
|
o GGL90 (Gaspar's TKE mixed layer) |
411 |
|
- add horizontal diffusion of TKE, requires exchanges in |
412 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
413 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
414 |
|
mixing coefficients are computed from a horizontal average of TKE of |
415 |
|
6 points or so. I think that diffusion has a little more physical |
416 |
|
justification. |
417 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
418 |
|
was in vain) |
419 |
|
- mask tke-variable in ggl90_init |
420 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
421 |
|
o fix biharmonic diffusion on CS-grid. |
422 |
|
o more obcs stuff |
423 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
424 |
|
for reading boundary values. This routine is called from |
425 |
|
obcs_prescribe_read |
426 |
|
- updated obcs_check |
427 |
|
- changed sponge layer relaxation parameter units for days to seconds |
428 |
|
- turned off sponge layer by default |
429 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
430 |
|
- fixed about 35 bugs in obcs_external_fields_load |
431 |
|
|
432 |
|
checkpoint55c_post |
433 |
|
o obcs stuff |
434 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
435 |
|
- re-arranged obcs_calc |
436 |
|
- moved exf_getobcs to obcs_prescibe_read |
437 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
438 |
|
and independent of it (executable can contain all). |
439 |
|
- updated obcs_check |
440 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
441 |
|
These may be necessary only if tangential velocities are |
442 |
|
prescribed at OB, not sure, needs testing. |
443 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
444 |
|
which simplifies the calls and passes the ifc check-bounds test |
445 |
|
|
446 |
|
checkpoint55b_post |
447 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
448 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
449 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
450 |
|
affects advect_cs results (for the wrong reason): update output.txt |
451 |
|
o use a more standard discretization for biharmonic viscosity ; |
452 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
453 |
|
affects results of dome set-up: update output.txt |
454 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
455 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
456 |
|
|
457 |
|
checkpoint55a_post |
458 |
|
o merged code to |
459 |
|
* prescribe/read time-dependent open boundaries |
460 |
|
(works in conjunction with exf, cal) |
461 |
|
* sponge layer code for open boundaries |
462 |
|
* each boundary N/S/E/W now has its own CPP option |
463 |
|
(healthy for the adjoint) |
464 |
|
|
465 |
|
checkpoint55 |
466 |
|
o up-to-date adjoint of previous breaks |
467 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
468 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
469 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
470 |
|
- carbon: * remove tr1-related adjoint verification |
471 |
|
* add ptracer as control variable |
472 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
473 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
474 |
|
|
475 |
|
checkpoint54f_post |
476 |
|
o in verification/carbin/ remove experiment related to |
477 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
478 |
|
code_ad/ input_ad/ results_ad |
479 |
|
|
480 |
|
o add two new packages |
481 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
482 |
|
+ subject to optimization (memory) |
483 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
484 |
|
+ subject to reordering (many GOTOs in the original code) |
485 |
|
+ so far opps is called for every (i,j) point, and then operates in |
486 |
|
the vertical; one may want to reorder the scheme in order operate in |
487 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
488 |
|
fields) |
489 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
490 |
|
- all verification tests compile and run with linux_ia32_g77 |
491 |
|
- defaults are compatible with current input files--nothing |
492 |
|
should change if you were not previously using MNC |
493 |
|
- MNC output has been added in numerous places (eg. timeave) |
494 |
|
but there are still a few writes not yet do-able with MNC |
495 |
|
(this is in progress) |
496 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
497 |
|
documentation will soon follow |
498 |
|
- numerous small formatting cleanups for ProTeX |
499 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
500 |
|
|
501 |
|
checkpoint54e_post |
502 |
|
o add two new packages |
503 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
504 |
|
stratification dependent mixing |
505 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
506 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
507 |
|
course), however there is only one diffusivity that is used for both |
508 |
|
temperature and salinity (and passive tracers)ç |
509 |
|
o add offline package |
510 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
511 |
|
provided by Stephanie Dutkiewicz |
512 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
513 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
514 |
|
|
515 |
|
checkpoint54d_post |
516 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
517 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
518 |
|
leading to additional shift by 5 days each year of integration |
519 |
|
(i.e. leading to considerable offset over the years) |
520 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
521 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
522 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
523 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
524 |
|
(external loading & cpl import/export stay in forward_step.F) |
525 |
|
o update coupling interface to work with new staggerTimeStep |
526 |
|
o change MDSIO ptracers_pickup. |
527 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
528 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
529 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
530 |
|
|
531 |
|
checkpoint54c_post |
532 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
533 |
|
this affects (truncation error) output.txt of test-exp: |
534 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
535 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
536 |
|
o change Qnet to always be the net heat flux, (+upward). |
537 |
|
affects (truncation error) output of natl_box exp.: updated |
538 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
539 |
|
o start to test mnc routinely in exp0 |
540 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
541 |
|
|
542 |
|
checkpoint54b_post |
543 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
544 |
|
impressive on Altix and Opteron systems) |
545 |
|
o diagnostics can now write NetCDF files through the mnc package |
546 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
547 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
548 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
549 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
550 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
551 |
|
|
552 |
|
checkpoint54a_post |
553 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
554 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
555 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
556 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
557 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
558 |
|
checkpoint54a_pre |
559 |
|
|
560 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
561 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
562 |
|
|
563 |
|
checkpoint54 |
564 |
|
checkpoint53g_post |
565 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
566 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
567 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
568 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
569 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
570 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
571 |
|
o restore adjointability |
572 |
|
|
573 |
|
checkpoint53f_post |
574 |
|
o modifications that affect AIM experiment results (update output.txt): |
575 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
576 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
577 |
|
o AIM pkg: |
578 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
579 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
580 |
|
|
581 |
|
checkpoint53e_post |
582 |
|
o merged cylindrical coord configuration |
583 |
|
o added rotating_tank experiment |
584 |
|
checkpoint53e_pre |
585 |
|
|
586 |
|
checkpoint53d_post |
587 |
|
o faulks upgraded: re-generate output.txt that have changed: |
588 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
589 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
590 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
591 |
|
o added Sadourny discretization of Coriolis |
592 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
593 |
|
- re-enabled use of omega3 (useAbsVorticity) |
594 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
595 |
|
vector-invariant equations |
596 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
597 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
598 |
|
hopefully without new bugs |
599 |
|
- still to do: biharmonic friction for non-hydrostatic w |
600 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
601 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
602 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
603 |
|
of mom_common/ |
604 |
|
- simple re-arrangement of instructions within computing loop |
605 |
|
checkpoint53d_pre |
606 |
|
|
607 |
|
checkpoint53c_post |
608 |
|
o new version of coupler for AIM+thSIce and Ocean models |
609 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
610 |
|
- land: change Evaporation of snow |
611 |
|
- aim with thSIce: fix bug in snow-precip. |
612 |
|
o changes to calc_gw.F |
613 |
|
- bug fix for w^2 term near the bottom boundary |
614 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
615 |
|
partial/looped cells |
616 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
617 |
|
and plume on slope), change the lateral boundary condition from half slip |
618 |
|
to the value of no_slip_sides |
619 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
620 |
|
o Adjoint of EBM package + verification |
621 |
|
* TLM OK |
622 |
|
* ADM not sufficient accuracy yet (needs further testing) |
623 |
|
|
624 |
|
checkpoint53b_post |
625 |
|
o Commiting new energy balance model to repository |
626 |
|
* package is pkg/ebm |
627 |
|
* verif. is verification/global_ocean_ebm |
628 |
|
* references are in ebm_driver.F |
629 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
630 |
|
C Global thermohaline circulation. Part I: |
631 |
|
C Sensitivity to atmospheric moisture transport. |
632 |
|
C J. Climate 12(1), 71-82 |
633 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
634 |
|
C Global thermohaline circulation. Part II: |
635 |
|
C Sensitivity with interactive transport. |
636 |
|
C J. Climate 12(1), 83-91 |
637 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
638 |
|
C Destabilization of the thermohaline circulation |
639 |
|
C by atmospheric eddy transports. |
640 |
|
C J. Climate 7(12), 1870-1882 |
641 |
|
o Will need long integration testing. |
642 |
|
checkpoint53b_pre |
643 |
|
|
644 |
|
o created pkg/mom_common in preparation for variable viscosity code |
645 |
|
o renamed and split ini_mnc_io |
646 |
|
o pkg/land: only liquid water can diffuse or run-off |
647 |
|
o AIM using land: soil wetness availability account for snow |
648 |
|
o added printMapIncludesZeros to EEPARMS namelist |
649 |
|
|
650 |
|
checkpoint53a_post |
651 |
|
o restore TAMC compatiility for exf_constants.h |
652 |
|
(no usage of _d in .h) |
653 |
|
o Additional storing in KPP in an attempt to fix |
654 |
|
TAMC problem with adjoint of KPP code. |
655 |
|
(no success...) |
656 |
|
Identical code works fine with TAF. |
657 |
|
o Fixed verification/natl_box_adjoint experiments. |
658 |
|
Initial conditions for Experiments 4 and 5 are now |
659 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
660 |
|
and hence gives results closer to that of Experiment 2. |
661 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
662 |
|
|
663 |
|
checkpoint53 |
664 |
|
o stable checkpoint with up to date adjoint |
665 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
666 |
|
this is a code problem or a problem with resetting code for g_ |
667 |
|
variables that is being autogenerated wrong. |
668 |
|
Otherwise: |
669 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
670 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
671 |
|
are both still in chaos following their security messes. |
672 |
|
|
673 |
|
checkpoint52n_post |
674 |
|
o various build (mostly genmake2) changes including: |
675 |
|
- ability to build/run more easily within Cygwin and MacOS X |
676 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
677 |
|
o pkg/seaice modifications |
678 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
679 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
680 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
681 |
|
- changed proxy for geostrophic velocity and updated |
682 |
|
verification/lab_sea/results/* accordingly |
683 |
|
- removed ADI dynamic solver from pkg/seaice |
684 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
685 |
|
they caused a segmentation fault under certain circumstances |
686 |
|
- removed unused field WATR |
687 |
|
o bug fix in exf-package: |
688 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
689 |
|
now reflect that. |
690 |
|
o small fixes in the cal-package: |
691 |
|
- set reference date to first of January for the 'model'-calendar |
692 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
693 |
|
warning |
694 |
|
o small modifications in exf-package to increase flexibility: |
695 |
|
- change climtempfreeze from a constant to a runtime parameter that |
696 |
|
is specified in data.exf_clim (default = -1.9) |
697 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
698 |
|
specified in data.exf |
699 |
|
o fix in pkg/thsice: |
700 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
701 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
702 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
703 |
|
|
704 |
|
checkpoint52m_post |
705 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
706 |
|
this does not change any of the results, because myIter=0 in swfrac always |
707 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
708 |
|
as a default |
709 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
710 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
711 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
712 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
713 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
714 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
715 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
716 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
717 |
|
o monitor package can write to NetCDF files and/or STDOUT |
718 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
719 |
|
o doc/api_reference added |
720 |
|
- a framework for building an API Reference Manual using all |
721 |
|
the "protex" comments embedded in the code |
722 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
723 |
|
o MNC: |
724 |
|
- make myThid the last argument for all subroutines |
725 |
|
- new default for the grid files: NO halos |
726 |
|
- add useMNC and other run-time flags |
727 |
|
- separate per-file-group handling of the unlimited dimension |
728 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
729 |
|
and lookup tables set in initialize_fixed |
730 |
|
- write all MNC output to a freshly-created directory |
731 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
732 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
733 |
|
o Added functionality to grdchk: |
734 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
735 |
|
|
736 |
|
checkpoint52l_post |
737 |
|
o new land formulation: |
738 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
739 |
|
energy conservation. |
740 |
|
b) account for water temperature and for latent heat of freezing |
741 |
|
in all processes (rain, run-off, ground storage) |
742 |
|
c) compute surface and ground temperature implicitly. |
743 |
|
o aim_v23 modification for new land model: |
744 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
745 |
|
to allow implicit computation of land & sea-ice surface temp. |
746 |
|
b) add snow precipitation. |
747 |
|
checkpoint52l_pre |
748 |
|
|
749 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
750 |
|
o fix bug in timeAve (u,vZetatave in common block) |
751 |
|
o no restoring terms under ice for pkg/seaice |
752 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
753 |
|
o bug fix for pkg/seaice pickups |
754 |
|
o change MNC call locations and add coordinate attributes |
755 |
o mask vorticity at the corner ; affects global_ocean.cs output |
o mask vorticity at the corner ; affects global_ocean.cs output |
756 |
o fix ini_curvilinear_grid ; test CS experiments with mpi |
o fix ini_curvilinear_grid ; test CS experiments with mpi |
757 |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
758 |
|
o exf: Adding simple range check routine for exf fields after read |
759 |
|
|
760 |
checkpoint52k_post |
checkpoint52k_post |
761 |
o removed top-level directory "diags" |
o removed top-level directory "diags" |