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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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checkpoint57o_post |
8 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
9 |
|
(2) its ready to be documented during the 20050801 DocFest |
10 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
11 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
12 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
13 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
14 |
|
(worth another tag) |
15 |
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|
16 |
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checkpoint57n_post |
17 |
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o adding precip control xx_precip 32 |
18 |
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o adding swflux control xx_swflux 33 |
19 |
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o Replacing 10 forcing penalty cost routines by 1 generic. |
20 |
|
o Implementing partitioning in time-mean and variable adjustment |
21 |
|
for atmos. state. |
22 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
23 |
|
o in natl_box_adjoint: |
24 |
|
* updated exp 1 to 10 |
25 |
|
(but does not have time-mean vs. variable split results yet) |
26 |
|
o updated global1x1/*_seaice_adj/ |
27 |
|
to incorporate latest changes |
28 |
|
o enable useSingleCpuIO for mdsio vector routines |
29 |
|
(applies in particular to tapelev I/O) |
30 |
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o removed inefficient K-loop in all active_file*control*.F |
31 |
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|
32 |
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checkpoint57m_post |
33 |
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o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
34 |
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and advect_cs (use EXCH-2 and standard cs-32 grid files). |
35 |
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o pkg/exch2: filling of face-corner halo regions is optional |
36 |
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(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
37 |
|
|
38 |
|
checkpoint57l_post |
39 |
|
tag before updating tutorials (pre-release-2) |
40 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
41 |
|
for output and interpolation of input fields onto model grid) |
42 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
43 |
|
Affects results of exp. rotating_tank ; update output.txt. |
44 |
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o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
45 |
|
and taking the square quantity and/or using a fraction-weight field. |
46 |
|
o fix aim_diagnostics_init.F mate numbers. |
47 |
|
o add mnc output capability to diagnostics/diagstat and update |
48 |
|
our cvsignore files for the ACSII output generated |
49 |
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|
50 |
|
checkpoint57k_post |
51 |
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o lab_sea now uses diagnostics package and provides a suite of |
52 |
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new EXF diagnostics output. |
53 |
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|
54 |
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checkpoint57j_post |
55 |
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o exf |
56 |
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* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
57 |
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Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
58 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
59 |
|
* extended diagnostics output |
60 |
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- now includes all EXF variables |
61 |
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- hs, hl moved to common block |
62 |
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- separate S/R for diagnostics, called after ctrl vector is added |
63 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
64 |
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- EXFqnet contains true Qnet (i.e. includes qsw) |
65 |
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* updated verif. lab_sea, global_with_exf |
66 |
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* Rearranging hflux (exf_mapfields -> exf_getforcing) |
67 |
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to ensure that diagnostics sees a true EXFqnet |
68 |
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o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
69 |
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o diagnostics pkg: change pointers so that 1 diagnostic can be used |
70 |
|
several times with different frequencies. |
71 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
72 |
|
- the monitor--MNC output needs work |
73 |
|
- many attributes need to be added (most are currently blank) |
74 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
75 |
|
- many attributes need to be added (most are currently blank) |
76 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
77 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
78 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
79 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
80 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
81 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
82 |
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(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
83 |
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|
84 |
|
checkpoint57i_post |
85 |
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o Diagnostics package was changed: diagnostic allocation is now deactivated |
86 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
87 |
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o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
88 |
|
add 1rst Order upwind vertical Shear. |
89 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
90 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
91 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
92 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
93 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
94 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
95 |
|
some "_d 0", etc. no effect. |
96 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
97 |
|
separate 'iter' variable for iteration count |
98 |
|
o pkg/diagnostics: |
99 |
|
add new capability: output of Global/Regional & per-level statistics ; |
100 |
|
tested against monitor output (including land & thSIce) on various exp. |
101 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
102 |
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|
103 |
|
checkpoint57h_done |
104 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
105 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
106 |
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|
107 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
108 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
109 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
110 |
|
and rename it: DIFFERENT_MULTIPLE |
111 |
|
|
112 |
|
checkpoint57h_post |
113 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
114 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
115 |
|
of Nb of iterations). This requires to change data.diagnostics. |
116 |
|
checkpoint57h_pre |
117 |
|
|
118 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
119 |
|
and mnc_outdir_num are false |
120 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
121 |
|
per-file basis, the file precision [default behavior is unchanged] |
122 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
123 |
|
depth based on a temperature/density criterion |
124 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
125 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
126 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
127 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
128 |
|
not mnc -- this mistake was found by JMC and is now corrected |
129 |
|
|
130 |
|
checkpoint57g_post |
131 |
|
o add Adams-Bashforth 3rd Order time stepping: |
132 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
133 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
134 |
|
checkpoint57g_pre |
135 |
|
|
136 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
137 |
|
(default remains spatially uniform constant based on tau) |
138 |
|
o added new control variables |
139 |
|
* init. uVel, vVel, etanN |
140 |
|
* lambda[Theta,Salt]ClimRelax |
141 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
142 |
|
(suggested by G. Forget) |
143 |
|
|
144 |
|
checkpoint57f_post |
145 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
146 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
147 |
|
account for baseTime shift |
148 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
149 |
|
checkpoint57f_pre |
150 |
|
|
151 |
|
o mnc-ifying the seaice package |
152 |
|
o introduced an alternative length scale calculation for use in the limiting |
153 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
154 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
155 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
156 |
|
as well as grad(vort3). Made it compatible with both approximate form |
157 |
|
for the cubed sphere and full form of these gradients. Added flag |
158 |
|
useFullLeith to select between approximate and full form. |
159 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
160 |
|
update output.txt of exp. fizhi-gridalt-hs |
161 |
|
o change port_rand funtion to allow to set the seed. |
162 |
|
o fix obscure MNC bug involving conversion between reals and integers |
163 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
164 |
|
new version is now more standards-compliant |
165 |
|
o adjoint-related modifications |
166 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
167 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
168 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
169 |
|
|
170 |
|
checkpoint57e_post |
171 |
|
o Adding eddy stress controls a la Ferreira et al. |
172 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
173 |
|
|
174 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
175 |
|
update output.txt of exp. fizhi-gridalt-hs |
176 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
177 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
178 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
179 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
180 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
181 |
|
months and years. Requires pkg/cal. |
182 |
|
o diagnostics: add pickup functionality |
183 |
|
- off by default for backwards compatibility |
184 |
|
- current version only uses MDSIO -- MNC will be added |
185 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
186 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
187 |
|
|
188 |
|
checkpoint57d_post |
189 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
190 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
191 |
|
output from the diagnostics package |
192 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
193 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
194 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
195 |
|
o add coordinate variables to the MNC output from the diagnostics package |
196 |
|
o change MNC-flags default value: true when useMNC=TRUE |
197 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
198 |
|
the ability (off by default) to read the grid information using MNC |
199 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
200 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
201 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
202 |
|
at the end). |
203 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
204 |
|
new test for AIM with thSIce + slab-ocean |
205 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
206 |
|
o move state variable diagnostics to the beginning of the time step ; |
207 |
|
(note: still needs some work specially for snap-shot diagnostics) |
208 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
209 |
|
|
210 |
|
checkpoint57c_post |
211 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
212 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
213 |
|
checkpoint57c_pre |
214 |
|
|
215 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
216 |
|
update output.txt of exp. global_ocean.90x40x15 |
217 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
218 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
219 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
220 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
221 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
222 |
|
o improvements for the MNC output from DIAGNOSTICS: |
223 |
|
- correct handling of the unlimitied dimension |
224 |
|
- all dims now have associated coordinate variables |
225 |
|
- variables located at U, V, and Corner ("Z") points are now written |
226 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
227 |
|
*all* data points are output |
228 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
229 |
|
o added pkg/seaice/seaice_monitor.F |
230 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
231 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
232 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
233 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
234 |
|
spurious negative numbers for precipitation and humidity. Will cause |
235 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
236 |
|
o pkg/ctrl/ |
237 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
238 |
|
May be enabled via doPackDiag |
239 |
|
* introduce z-scaling of |
240 |
|
+ gradient (doZscalePack) and |
241 |
|
+ control (doZscaleUnpack) |
242 |
|
o pkg/mdsio/ |
243 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
244 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
245 |
|
|
246 |
|
checkpoint57b_post |
247 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
248 |
|
o fix MNC coordinate variables so that they now contain per-face index |
249 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
250 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
251 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
252 |
|
o Implement instantaneous output within pkg diagnostics: |
253 |
|
setting a negative frequency in data.diagnostics produces |
254 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
255 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
256 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
257 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
258 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
259 |
|
becomes the coordinate variable for the 'T' dimension |
260 |
|
o add CF-style coordinate variables to MNC |
261 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
262 |
|
missing along the T axis but otherwise it works! |
263 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
264 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
265 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
266 |
|
this is based directly on what the model compute, so that the content of |
267 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
268 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
269 |
|
o clean up build options files for SunOS, in particular |
270 |
|
- remove -traditional from xmakedepend |
271 |
|
- change -xarch=v9 to -xarch=native for f77 |
272 |
|
- restore use of make (not gmake) |
273 |
|
- add CC=gcc if using g77 |
274 |
|
o changes per discussion of AM, JMC, & EH3 today: |
275 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
276 |
|
creating proper CF-style coordinate variables and in recognition |
277 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
278 |
|
the grid files into any of the other NetCDF files |
279 |
|
- *always* output grid variables with MDSIO (this will eventually be |
280 |
|
changed) |
281 |
|
- output MNC grid file if useMNC is true |
282 |
|
o every instance of _END_MASTER() has been found and replaced with |
283 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
284 |
|
preprocessors |
285 |
|
o re-arrange diagnostics pkg initialisation: |
286 |
|
- allow each package to extend the available diagnostics list |
287 |
|
- add some checking and fix small problems (multi-threaded, ...) |
288 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
289 |
|
look through the short list of active diag. (instead of the long list) |
290 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
291 |
|
|
292 |
|
checkpoint57a_post |
293 |
|
o this set of changes restores TAMC compatibility |
294 |
|
tested for global_ocean.90x40x15 adjoint on trough |
295 |
|
(what a pain) |
296 |
|
|
297 |
|
checkpoint57a_pre |
298 |
|
o some modifs in tools/build_options for sunos |
299 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
300 |
|
|
301 |
|
checkpoint57 |
302 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
303 |
|
- new parameter viscA4W (defaults to viscA4) |
304 |
|
- affects only non-hydrostatic code |
305 |
|
- to be done: no-slip lateral boundary conditions |
306 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
307 |
|
o implement Implicit Vertical advection for pTracers |
308 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
309 |
|
(implemented also for implicit vertical diffusion & advection) |
310 |
|
o OBCS: extend application of tracer open boundary conditions |
311 |
|
to a strip beyond the boundary of width Olx/Oly |
312 |
|
o add call monitor to TAF set of required calls (flow directives) |
313 |
|
and include in natl_box_adjoint |
314 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
315 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
316 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
317 |
|
(theta2, salt2 in ecco_cost_weights) |
318 |
|
|
319 |
|
checkpoint56c_post |
320 |
|
o OBCS as control variables |
321 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
322 |
|
- remove balance of obcs controls from default |
323 |
|
- fix index bug nobcs in ctrl_init |
324 |
|
- fix dummy fields filen in ctrl_pack |
325 |
|
- add dummy weights for obcs |
326 |
|
o lsopt: comment out fort.94 output |
327 |
|
o optim: |
328 |
|
- remove unnecessary header files |
329 |
|
- adjusted namelists |
330 |
|
- add xerbla.F to Makefile |
331 |
|
o exf: |
332 |
|
- multiple modifications of exf_check_range |
333 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
334 |
|
o mdsio: |
335 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
336 |
|
|
337 |
|
checkpoint56b_post |
338 |
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
339 |
is called from DO_THE_MODEL_IO |
is called from DO_THE_MODEL_IO |
340 |
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |