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$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.534 2005/08/19 23:49:45 heimbach Exp $ |
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$Name: $ |
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|
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Notes on tags used in MITgcmUV |
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============================== |
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|
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o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
8 |
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
9 |
|
10 |
checkpoint57q_post |
11 |
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
12 |
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
13 |
- bug was reported by Jean-Michel and Ian Fenty |
14 |
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
15 |
update exp. cpl_aim+ocn output. |
16 |
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
17 |
Needed for high-res. runs with large global files |
18 |
to be able to limit tapelev size |
19 |
o Changed some tests for adjoint: |
20 |
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
21 |
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
22 |
* global_ocean.90x40x15/ back to default 3-level checkpointing |
23 |
o Modifications to enable scripted COMMON to MODULE conversion |
24 |
* verification/OpenAD/code/ has necessary scripts and description; |
25 |
* converts, compiles and runs successfully; |
26 |
|
27 |
checkpoint57p_post |
28 |
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
29 |
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
30 |
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
31 |
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
32 |
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
33 |
(was already the case for dissipation with mom_vecinv, |
34 |
and also the case for grad.PhiHyd when staggered-timeStep) |
35 |
This will allow to put dissipation out-off the AB time-stepping. |
36 |
Unfortunately, affects truncation error. Update output of exp. that "fails" |
37 |
(cg2d matching number) and leave the others for later: front_relax(10), |
38 |
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
39 |
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
40 |
|
41 |
checkpoint57o_post |
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o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
43 |
(2) its ready to be documented during the 20050801 DocFest |
44 |
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
45 |
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
46 |
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
47 |
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
48 |
(worth another tag) |
49 |
|
50 |
checkpoint57n_post |
51 |
o adding precip control xx_precip 32 |
52 |
o adding swflux control xx_swflux 33 |
53 |
o Replacing 10 forcing penalty cost routines by 1 generic. |
54 |
o Implementing partitioning in time-mean and variable adjustment |
55 |
for atmos. state. |
56 |
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
57 |
o in natl_box_adjoint: |
58 |
* updated exp 1 to 10 |
59 |
(but does not have time-mean vs. variable split results yet) |
60 |
o updated global1x1/*_seaice_adj/ |
61 |
to incorporate latest changes |
62 |
o enable useSingleCpuIO for mdsio vector routines |
63 |
(applies in particular to tapelev I/O) |
64 |
o removed inefficient K-loop in all active_file*control*.F |
65 |
|
66 |
checkpoint57m_post |
67 |
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
68 |
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
69 |
o pkg/exch2: filling of face-corner halo regions is optional |
70 |
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
71 |
|
72 |
checkpoint57l_post |
73 |
tag before updating tutorials (pre-release-2) |
74 |
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
75 |
for output and interpolation of input fields onto model grid) |
76 |
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
77 |
Affects results of exp. rotating_tank ; update output.txt. |
78 |
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
79 |
and taking the square quantity and/or using a fraction-weight field. |
80 |
o fix aim_diagnostics_init.F mate numbers. |
81 |
o add mnc output capability to diagnostics/diagstat and update |
82 |
our cvsignore files for the ACSII output generated |
83 |
|
84 |
checkpoint57k_post |
85 |
o lab_sea now uses diagnostics package and provides a suite of |
86 |
new EXF diagnostics output. |
87 |
|
88 |
checkpoint57j_post |
89 |
o exf |
90 |
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
91 |
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
92 |
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
93 |
* extended diagnostics output |
94 |
- now includes all EXF variables |
95 |
- hs, hl moved to common block |
96 |
- separate S/R for diagnostics, called after ctrl vector is added |
97 |
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
98 |
- EXFqnet contains true Qnet (i.e. includes qsw) |
99 |
* updated verif. lab_sea, global_with_exf |
100 |
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
101 |
to ensure that diagnostics sees a true EXFqnet |
102 |
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
103 |
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
104 |
several times with different frequencies. |
105 |
o mnc-ify the thsice package as requested by Daniel Enderton |
106 |
- the monitor--MNC output needs work |
107 |
- many attributes need to be added (most are currently blank) |
108 |
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
109 |
- many attributes need to be added (most are currently blank) |
110 |
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
111 |
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
112 |
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
113 |
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
114 |
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
115 |
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
116 |
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
117 |
|
118 |
checkpoint57i_post |
119 |
o Diagnostics package was changed: diagnostic allocation is now deactivated |
120 |
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
121 |
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
122 |
add 1rst Order upwind vertical Shear. |
123 |
o add a quick fix for A/B checkpointing in OFFLINE mode |
124 |
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
125 |
end-run around the C/Fortran linking horror in eesup/src/timers.F |
126 |
o added pkg/runclock: allows user to terminate run based on wall clock |
127 |
o added non-hydrostatic scaling parameter: nh_am2 |
128 |
o pkg/my82: futile attempt to make results compiler-independent by adding |
129 |
some "_d 0", etc. no effect. |
130 |
o for mnc output, fill the 'T' coordinate var with myTime and create a |
131 |
separate 'iter' variable for iteration count |
132 |
o pkg/diagnostics: |
133 |
add new capability: output of Global/Regional & per-level statistics ; |
134 |
tested against monitor output (including land & thSIce) on various exp. |
135 |
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
136 |
|
137 |
checkpoint57h_done |
138 |
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
139 |
data.diagnostics, data.gchem, data.ptracers) is done. |
140 |
|
141 |
o pkg/diagnostics: prepare for Global/Regional statistics. |
142 |
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
143 |
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
144 |
and rename it: DIFFERENT_MULTIPLE |
145 |
|
146 |
checkpoint57h_post |
147 |
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
148 |
o pkg/diagnostics: change output frequency, now in seconds (instead |
149 |
of Nb of iterations). This requires to change data.diagnostics. |
150 |
checkpoint57h_pre |
151 |
|
152 |
o in mnc, let the user create the output dir if both mnc_outdir_date |
153 |
and mnc_outdir_num are false |
154 |
o add fflags() to pkg/diagnostics which allows one to specify, on a |
155 |
per-file basis, the file precision [default behavior is unchanged] |
156 |
o added diagnostics to pkg/kpp, including computation of mixed layer |
157 |
depth based on a temperature/density criterion |
158 |
o updated verification/natl_box to test the new pkg/kpp diagnostics |
159 |
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
160 |
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
161 |
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
162 |
not mnc -- this mistake was found by JMC and is now corrected |
163 |
|
164 |
checkpoint57g_post |
165 |
o add Adams-Bashforth 3rd Order time stepping: |
166 |
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
167 |
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
168 |
checkpoint57g_pre |
169 |
|
170 |
o make lambda[Theta,Salt]ClimRelax spatially varying |
171 |
(default remains spatially uniform constant based on tau) |
172 |
o added new control variables |
173 |
* init. uVel, vVel, etanN |
174 |
* lambda[Theta,Salt]ClimRelax |
175 |
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
176 |
(suggested by G. Forget) |
177 |
|
178 |
checkpoint57f_post |
179 |
o add parameter "baseTime" = model base time = time at iteration zero |
180 |
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
181 |
account for baseTime shift |
182 |
o move Coriolis arrays from PARAMS.h to GRID.h |
183 |
checkpoint57f_pre |
184 |
|
185 |
o mnc-ifying the seaice package |
186 |
o introduced an alternative length scale calculation for use in the limiting |
187 |
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
188 |
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
189 |
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
190 |
as well as grad(vort3). Made it compatible with both approximate form |
191 |
for the cubed sphere and full form of these gradients. Added flag |
192 |
useFullLeith to select between approximate and full form. |
193 |
o add "d0" in getcon.F to reduce differences between compilers/platforms |
194 |
update output.txt of exp. fizhi-gridalt-hs |
195 |
o change port_rand funtion to allow to set the seed. |
196 |
o fix obscure MNC bug involving conversion between reals and integers |
197 |
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
198 |
new version is now more standards-compliant |
199 |
o adjoint-related modifications |
200 |
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
201 |
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
202 |
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
203 |
|
204 |
checkpoint57e_post |
205 |
o Adding eddy stress controls a la Ferreira et al. |
206 |
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
207 |
|
208 |
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
209 |
update output.txt of exp. fizhi-gridalt-hs |
210 |
o add more "Z" dimensions and associated coordinate vars to MNC |
211 |
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
212 |
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
213 |
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
214 |
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
215 |
months and years. Requires pkg/cal. |
216 |
o diagnostics: add pickup functionality |
217 |
- off by default for backwards compatibility |
218 |
- current version only uses MDSIO -- MNC will be added |
219 |
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
220 |
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
221 |
|
222 |
checkpoint57d_post |
223 |
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
224 |
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
225 |
output from the diagnostics package |
226 |
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
227 |
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
228 |
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
229 |
o add coordinate variables to the MNC output from the diagnostics package |
230 |
o change MNC-flags default value: true when useMNC=TRUE |
231 |
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
232 |
the ability (off by default) to read the grid information using MNC |
233 |
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
234 |
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
235 |
o do snap-shot diagnostics at the middle of the time-interval (instead of |
236 |
at the end). |
237 |
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
238 |
new test for AIM with thSIce + slab-ocean |
239 |
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
240 |
o move state variable diagnostics to the beginning of the time step ; |
241 |
(note: still needs some work specially for snap-shot diagnostics) |
242 |
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
243 |
|
244 |
checkpoint57c_post |
245 |
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
246 |
o generate new output.txt files on faulks with g77 & the new -ieee option |
247 |
checkpoint57c_pre |
248 |
|
249 |
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
250 |
update output.txt of exp. global_ocean.90x40x15 |
251 |
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
252 |
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
253 |
o add saltFlux(+File) forcing capability with periodicExternalForcing |
254 |
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
255 |
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
256 |
o improvements for the MNC output from DIAGNOSTICS: |
257 |
- correct handling of the unlimitied dimension |
258 |
- all dims now have associated coordinate variables |
259 |
- variables located at U, V, and Corner ("Z") points are now written |
260 |
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
261 |
*all* data points are output |
262 |
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
263 |
o added pkg/seaice/seaice_monitor.F |
264 |
o mdsio_readfield.F can now read files visible only to master MPI process. |
265 |
o pkg/seaice: some test code for ice-modified ocean stress |
266 |
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
267 |
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
268 |
spurious negative numbers for precipitation and humidity. Will cause |
269 |
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
270 |
o pkg/ctrl/ |
271 |
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
272 |
May be enabled via doPackDiag |
273 |
* introduce z-scaling of |
274 |
+ gradient (doZscalePack) and |
275 |
+ control (doZscaleUnpack) |
276 |
o pkg/mdsio/ |
277 |
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
278 |
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
279 |
|
280 |
checkpoint57b_post |
281 |
o simplify options in diagnostics_fill arguments (remove weird combinations) |
282 |
o fix MNC coordinate variables so that they now contain per-face index |
283 |
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
284 |
general, EXCH2 grids are only aligned to a "local" coordinate system |
285 |
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
286 |
o Implement instantaneous output within pkg diagnostics: |
287 |
setting a negative frequency in data.diagnostics produces |
288 |
"snap-shot" output (as opposed to time-average if freq > 0) |
289 |
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
290 |
NOTE: change ptracer diagnostics name: use 2 characters to work with |
291 |
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
292 |
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
293 |
becomes the coordinate variable for the 'T' dimension |
294 |
o add CF-style coordinate variables to MNC |
295 |
- just a first cut: numbers are meaningless on the cubesphere and |
296 |
missing along the T axis but otherwise it works! |
297 |
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
298 |
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
299 |
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
300 |
this is based directly on what the model compute, so that the content of |
301 |
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
302 |
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
303 |
o clean up build options files for SunOS, in particular |
304 |
- remove -traditional from xmakedepend |
305 |
- change -xarch=v9 to -xarch=native for f77 |
306 |
- restore use of make (not gmake) |
307 |
- add CC=gcc if using g77 |
308 |
o changes per discussion of AM, JMC, & EH3 today: |
309 |
- move redundant "grid" variables out of "state" -- in preparation of |
310 |
creating proper CF-style coordinate variables and in recognition |
311 |
that any/all grid variables can be easily copied (eg. w/NCO) from |
312 |
the grid files into any of the other NetCDF files |
313 |
- *always* output grid variables with MDSIO (this will eventually be |
314 |
changed) |
315 |
- output MNC grid file if useMNC is true |
316 |
o every instance of _END_MASTER() has been found and replaced with |
317 |
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
318 |
preprocessors |
319 |
o re-arrange diagnostics pkg initialisation: |
320 |
- allow each package to extend the available diagnostics list |
321 |
- add some checking and fix small problems (multi-threaded, ...) |
322 |
- new S/R diagnostics_fill (replace fill_diagnostics): |
323 |
look through the short list of active diag. (instead of the long list) |
324 |
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
325 |
|
326 |
checkpoint57a_post |
327 |
o this set of changes restores TAMC compatibility |
328 |
tested for global_ocean.90x40x15 adjoint on trough |
329 |
(what a pain) |
330 |
|
331 |
checkpoint57a_pre |
332 |
o some modifs in tools/build_options for sunos |
333 |
o call ctrl_pack for ctrl at end for optimcycle=0 |
334 |
|
335 |
checkpoint57 |
336 |
o add horizontal bi-harmonic viscosity for vertical velocity |
337 |
- new parameter viscA4W (defaults to viscA4) |
338 |
- affects only non-hydrostatic code |
339 |
- to be done: no-slip lateral boundary conditions |
340 |
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
341 |
o implement Implicit Vertical advection for pTracers |
342 |
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
343 |
(implemented also for implicit vertical diffusion & advection) |
344 |
o OBCS: extend application of tracer open boundary conditions |
345 |
to a strip beyond the boundary of width Olx/Oly |
346 |
o add call monitor to TAF set of required calls (flow directives) |
347 |
and include in natl_box_adjoint |
348 |
o untangle a few ifdefs related to cost, ctrl, autodiff |
349 |
untangel a few ALLOW_ECCO_OPTIMIZATION |
350 |
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
351 |
(theta2, salt2 in ecco_cost_weights) |
352 |
|
353 |
checkpoint56c_post |
354 |
o OBCS as control variables |
355 |
- update ctrl_ad_diff.list, obcs_ad_diff.list |
356 |
- remove balance of obcs controls from default |
357 |
- fix index bug nobcs in ctrl_init |
358 |
- fix dummy fields filen in ctrl_pack |
359 |
- add dummy weights for obcs |
360 |
o lsopt: comment out fort.94 output |
361 |
o optim: |
362 |
- remove unnecessary header files |
363 |
- adjusted namelists |
364 |
- add xerbla.F to Makefile |
365 |
o exf: |
366 |
- multiple modifications of exf_check_range |
367 |
- unit change in exf_init_runoff from [m/year] to [m/s] |
368 |
o mdsio: |
369 |
- i/o-vector change debugLevel from debLevA to debLevB |
370 |
|
371 |
checkpoint56b_post |
372 |
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
373 |
is called from DO_THE_MODEL_IO |
374 |
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
375 |
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
376 |
- clean up PTRACERS_WRITE_TIMEAVE a little |
377 |
o add another verification experiment that tests both the cfc-pkg and |
378 |
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
379 |
reactive tendencies treated inline with regular timestepping |
380 |
o testreport previously did a lousy job of comparing small numbers, so |
381 |
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
382 |
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
383 |
testreport. |
384 |
o ptracers_monitor: bug fix for MPI |
385 |
|
386 |
checkpoint56a_post |
387 |
o GCHEM: finish reorganizating the package |
388 |
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
389 |
(introduces another 3D-array for each passive tracer, but only if |
390 |
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
391 |
gchemTendency is not needed because the timestep is done separately) |
392 |
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
393 |
- GCHEM is now---more or less cleanly---separate from PTRACERS |
394 |
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
395 |
so clear to me how that should be done in a general way. |
396 |
o CFC: improve formatting of output in CFC_ATMOS |
397 |
o PTRACERS: |
398 |
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
399 |
that ALL experiments with ptracers enable can be checked. This makes |
400 |
GCHEM_MONITOR obsolete. |
401 |
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
402 |
monitorFreq |
403 |
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
404 |
o add PTRACERS (PTR0[1-5]) to testreport output |
405 |
o exf_check_range: |
406 |
* default changed to .TRUE. |
407 |
* will check values for niter0 if debLevA, every timestep if debLevB |
408 |
* STOP in exf_check_range if 'out of range' |
409 |
* range chosen generous to allow for potential extema |
410 |
TBD: a version with stricter range |
411 |
permitted range would be runtime parameters |
412 |
o GMredi: |
413 |
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
414 |
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
415 |
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
416 |
o GCHEM: |
417 |
- move call to GCHEM_FORCING_SEP, so that it is now called before |
418 |
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
419 |
- introduced a useGCHEM runtime flag and applied it everywhere. |
420 |
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
421 |
this flag is now only visible within GCHEM-pkg routines. |
422 |
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
423 |
be replaced by a 3D array that is computed before thermodynamics; for |
424 |
this, the tracer ID iTracer had to be included into the parameter list |
425 |
of ptracers_forcing |
426 |
- set up forward_step to call gchem_forcing, that will replace |
427 |
gchem_forcing_int in ptracers_forcing |
428 |
- cleaning up |
429 |
o small cleaning of exch2: remove files that are also in eesupp/src |
430 |
|
431 |
checkpoint56 |
432 |
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
433 |
o mnc: cleanup "full" files--fixes out-of-memory problem |
434 |
o ECCO-GODAE |
435 |
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
436 |
* fully merged and updated from SIO code |
437 |
windstress sign change affects |
438 |
- exf_inscal_[u/v]stress |
439 |
- sign of xx_tau[u/v] adjustments |
440 |
- signs in cost_scat |
441 |
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
442 |
* natl_box_adjoint updated and compressed |
443 |
* 2-level checkpoint switch added |
444 |
(tested in EXP. 1 of natl_box_adjoint) |
445 |
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
446 |
o SVD |
447 |
* first complete, non-hacked version for SVD calculations |
448 |
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
449 |
performed via direct access files admtlm_vector.it???? |
450 |
(via ctrl_[un]pack) |
451 |
* optimcycle is used for ARPACK iteration counter |
452 |
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
453 |
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
454 |
and add linear transforms where necessary |
455 |
* controls are initial/final SST, SSS (can be extended; need to check |
456 |
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
457 |
o mdsio: filename info to both stderr, stdout |
458 |
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
459 |
from sign change |
460 |
|
461 |
checkpoint55j_post |
462 |
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
463 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
464 |
o add consistent build directories and .cvsignore files to verification |
465 |
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
466 |
o make all subroutines 30 or less characters in length for certain older |
467 |
compilers to work (a thorough search only turns up two routines in |
468 |
pkg/ptracers) |
469 |
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
470 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
471 |
|
472 |
checkpoint55i_post |
473 |
o change arrays for total vertical diffusivity (2.D if explicit, |
474 |
3.D if implicit) ; each ptracer uses its own background value. |
475 |
o added mnc/NetCDF output capability to ocn_compon_interf |
476 |
- added bits to verification/cpl_aim+ocn so that it can run on |
477 |
ITRDA and other clusters without the mpirun "-wd" option |
478 |
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
479 |
configuration |
480 |
o give MNC the ability to create additional files rather than |
481 |
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
482 |
- the default is just less than 2GB which is a practical limit |
483 |
on many systems |
484 |
o Compute the non-local term using either KPP vertical diffusivity (=default) |
485 |
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
486 |
|
487 |
checkpoint55h_post |
488 |
o add verification test "vermix" |
489 |
o remove all the *_ioinc flags and replace with the single global |
490 |
outputTypesInclusive flag |
491 |
o allow to set a vertical profile of vertical diffusivity for T & S |
492 |
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
493 |
o useMNC moved from data.mnc to data.pkg |
494 |
|
495 |
checkpoint55g_post |
496 |
o Renaming carbon AD experiments to comply with testreport conventions |
497 |
o Updating adjoint of Held-Suarez hs94.1x64x5 |
498 |
o Fixing directives for non-ECCO forward_step, after ECCO directives |
499 |
have been fixed to avoid recomp. of do_oceanic_phys |
500 |
Works well for global_ocean.90x40x15, |
501 |
but recomp. issue remains for carbon |
502 |
o Updating adjoint output for natl_box_adjoint after |
503 |
pkg/ecco has been modified (see taga c55d_post) |
504 |
|
505 |
checkpoint55f_post |
506 |
o rename to timeave_init_fixed |
507 |
|
508 |
checkpoint55e_post |
509 |
o some delicate re-shuffle of store directives to avoid one |
510 |
extra call of do_oceanic_physics |
511 |
affects ecco_the_main_loop.F, do_oceanic_physics.F |
512 |
checkpoint_lev1_directives.h |
513 |
o NB: this may break global_ocean adjoint temporarily, |
514 |
but it is clear how to fix it. Will do later, need this now. |
515 |
|
516 |
checkpoint55d_post |
517 |
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
518 |
o ecco_cost_weights is modified to 1x1 runs |
519 |
o modifs to allow observations to be read in as |
520 |
single file or yearly files |
521 |
o enable to read exf forcing fields as either |
522 |
single file or yearly files (flag useExfYearlyFields) |
523 |
checkpoint55d_pre |
524 |
|
525 |
o switch between 2-level and 3-level checkpointing |
526 |
o add ability of MNC to write local and "partial" (eg. 2D slices where |
527 |
the full 3D field is never actually stored) arrays to NetCDF files |
528 |
with the correct (that is, the complete multi-dimensional) set of |
529 |
array indicies |
530 |
- used in mom_vecinv() to write the diagFreq output |
531 |
- tested (demonstrated) in verification/aim.5l_cs |
532 |
o further mnc-ification |
533 |
- add verification/lab_sea to the list with mnc setups |
534 |
- fix undefined mnc v-names in cd_code |
535 |
- add kpp to mnc output (both snapshot and timeave) |
536 |
o non-hydrostatic code |
537 |
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
538 |
in calc_gw.F |
539 |
- defaults to viscAh |
540 |
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
541 |
friction or Leith) in non-hydrostatic mode, as long as there is |
542 |
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
543 |
o pkg/cost |
544 |
extend simple cost functions to treat time mean quantities |
545 |
(T,U,V) via cost_accumulate_state from cost_tile |
546 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
547 |
be 2 times larger than the minimum size the advection scheme requires. |
548 |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
549 |
o GGL90 (Gaspar's TKE mixed layer) |
550 |
- add horizontal diffusion of TKE, requires exchanges in |
551 |
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
552 |
default. In OPA there is no horizontal diffusion of TKE but the |
553 |
mixing coefficients are computed from a horizontal average of TKE of |
554 |
6 points or so. I think that diffusion has a little more physical |
555 |
justification. |
556 |
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
557 |
was in vain) |
558 |
- mask tke-variable in ggl90_init |
559 |
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
560 |
o fix biharmonic diffusion on CS-grid. |
561 |
o more obcs stuff |
562 |
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
563 |
for reading boundary values. This routine is called from |
564 |
obcs_prescribe_read |
565 |
- updated obcs_check |
566 |
- changed sponge layer relaxation parameter units for days to seconds |
567 |
- turned off sponge layer by default |
568 |
- changed argument list of OBCS_CALC to myTime+deltaTclock |
569 |
- fixed about 35 bugs in obcs_external_fields_load |
570 |
|
571 |
checkpoint55c_post |
572 |
o obcs stuff |
573 |
- new runtime flags useOBCSprescribe, useOBCSbalance |
574 |
- re-arranged obcs_calc |
575 |
- moved exf_getobcs to obcs_prescibe_read |
576 |
obcs_prescibe_read is called after ORLANSKI stuff |
577 |
and independent of it (executable can contain all). |
578 |
- updated obcs_check |
579 |
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
580 |
These may be necessary only if tangential velocities are |
581 |
prescribed at OB, not sure, needs testing. |
582 |
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
583 |
which simplifies the calls and passes the ifc check-bounds test |
584 |
|
585 |
checkpoint55b_post |
586 |
o add a 2D scalar, Z location, exchange_2 routine. |
587 |
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
588 |
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
589 |
affects advect_cs results (for the wrong reason): update output.txt |
590 |
o use a more standard discretization for biharmonic viscosity ; |
591 |
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
592 |
affects results of dome set-up: update output.txt |
593 |
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
594 |
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
595 |
|
596 |
checkpoint55a_post |
597 |
o merged code to |
598 |
* prescribe/read time-dependent open boundaries |
599 |
(works in conjunction with exf, cal) |
600 |
* sponge layer code for open boundaries |
601 |
* each boundary N/S/E/W now has its own CPP option |
602 |
(healthy for the adjoint) |
603 |
|
604 |
checkpoint55 |
605 |
o up-to-date adjoint of previous breaks |
606 |
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
607 |
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
608 |
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
609 |
- carbon: * remove tr1-related adjoint verification |
610 |
* add ptracer as control variable |
611 |
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
612 |
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
613 |
|
614 |
checkpoint54f_post |
615 |
o in verification/carbin/ remove experiment related to |
616 |
ALLOW_PASSIVE_TRACER (array tr1 etc) |
617 |
code_ad/ input_ad/ results_ad |
618 |
|
619 |
o add two new packages |
620 |
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
621 |
+ subject to optimization (memory) |
622 |
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
623 |
+ subject to reordering (many GOTOs in the original code) |
624 |
+ so far opps is called for every (i,j) point, and then operates in |
625 |
the vertical; one may want to reorder the scheme in order operate in |
626 |
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
627 |
fields) |
628 |
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
629 |
- all verification tests compile and run with linux_ia32_g77 |
630 |
- defaults are compatible with current input files--nothing |
631 |
should change if you were not previously using MNC |
632 |
- MNC output has been added in numerous places (eg. timeave) |
633 |
but there are still a few writes not yet do-able with MNC |
634 |
(this is in progress) |
635 |
- flags now allow for either/or/both use of MDSIO and MNC and |
636 |
documentation will soon follow |
637 |
- numerous small formatting cleanups for ProTeX |
638 |
o add version info (via BUILD_INFO.h) to MNC and stdout |
639 |
|
640 |
checkpoint54e_post |
641 |
o add two new packages |
642 |
- pp81 (Packanowski and Philander, 1981), Richardson number and |
643 |
stratification dependent mixing |
644 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
645 |
- these scheme operate in a similar manner as KPP (without ghat, of |
646 |
course), however there is only one diffusivity that is used for both |
647 |
temperature and salinity (and passive tracers)ç |
648 |
o add offline package |
649 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
650 |
provided by Stephanie Dutkiewicz |
651 |
o genmake2: add ability to search for C compilers and cleanup test output |
652 |
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
653 |
|
654 |
checkpoint54d_post |
655 |
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
656 |
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
657 |
leading to additional shift by 5 days each year of integration |
658 |
(i.e. leading to considerable offset over the years) |
659 |
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
660 |
o start with no AB and no initial filtering (staggerTimeStep): |
661 |
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
662 |
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
663 |
(external loading & cpl import/export stay in forward_step.F) |
664 |
o update coupling interface to work with new staggerTimeStep |
665 |
o change MDSIO ptracers_pickup. |
666 |
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
667 |
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
668 |
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
669 |
|
670 |
checkpoint54c_post |
671 |
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
672 |
this affects (truncation error) output.txt of test-exp: |
673 |
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
674 |
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
675 |
o change Qnet to always be the net heat flux, (+upward). |
676 |
affects (truncation error) output of natl_box exp.: updated |
677 |
o define the max number of passive tracers in PTRACERS_SIZE.h |
678 |
o start to test mnc routinely in exp0 |
679 |
o add sea-ice loading (sIceLoad) as a new forcing field. |
680 |
|
681 |
checkpoint54b_post |
682 |
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
683 |
impressive on Altix and Opteron systems) |
684 |
o diagnostics can now write NetCDF files through the mnc package |
685 |
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
686 |
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
687 |
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
688 |
affects (truncation error) output of lab_sea & natl_box exp.: updated |
689 |
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
690 |
|
691 |
checkpoint54a_post |
692 |
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
693 |
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
694 |
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
695 |
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
696 |
+ internal_wave (shift in writing cg2d_ini_res) |
697 |
checkpoint54a_pre |
698 |
|
699 |
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
700 |
- modified verification/lab_sea and natl_box_adjoint accordingly |
701 |
|
702 |
checkpoint54 |
703 |
checkpoint53g_post |
704 |
o prepare splitting of thermodynamics: store convect.counter in common block |
705 |
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
706 |
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
707 |
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
708 |
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
709 |
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
710 |
o restore adjointability |
711 |
|
712 |
checkpoint53f_post |
713 |
o modifications that affect AIM experiment results (update output.txt): |
714 |
- no advection of S at top interface Nr (pkg/generic_advdiff) |
715 |
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
716 |
o AIM pkg: |
717 |
- include stability function into surf.Flux derivative relative to Tsurf |
718 |
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
719 |
|
720 |
checkpoint53e_post |
721 |
o merged cylindrical coord configuration |
722 |
o added rotating_tank experiment |
723 |
checkpoint53e_pre |
724 |
|
725 |
checkpoint53d_post |
726 |
o faulks upgraded: re-generate output.txt that have changed: |
727 |
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
728 |
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
729 |
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
730 |
o added Sadourny discretization of Coriolis |
731 |
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
732 |
- re-enabled use of omega3 (useAbsVorticity) |
733 |
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
734 |
vector-invariant equations |
735 |
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
736 |
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
737 |
hopefully without new bugs |
738 |
- still to do: biharmonic friction for non-hydrostatic w |
739 |
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
740 |
o regenerated output for global_ocean_ebm (using -ieee) |
741 |
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
742 |
of mom_common/ |
743 |
- simple re-arrangement of instructions within computing loop |
744 |
checkpoint53d_pre |
745 |
|
746 |
checkpoint53c_post |
747 |
o new version of coupler for AIM+thSIce and Ocean models |
748 |
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
749 |
- land: change Evaporation of snow |
750 |
- aim with thSIce: fix bug in snow-precip. |
751 |
o changes to calc_gw.F |
752 |
- bug fix for w^2 term near the bottom boundary |
753 |
- (hopefully) improve the lateral slip boundary condtions for use with |
754 |
partial/looped cells |
755 |
- because the bug fix changes two verification experiments anyway (exp5 |
756 |
and plume on slope), change the lateral boundary condition from half slip |
757 |
to the value of no_slip_sides |
758 |
o ebm package wasnt quite up to the parallel task. Fixed that. |
759 |
o Adjoint of EBM package + verification |
760 |
* TLM OK |
761 |
* ADM not sufficient accuracy yet (needs further testing) |
762 |
|
763 |
checkpoint53b_post |
764 |
o Commiting new energy balance model to repository |
765 |
* package is pkg/ebm |
766 |
* verif. is verification/global_ocean_ebm |
767 |
* references are in ebm_driver.F |
768 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
769 |
C Global thermohaline circulation. Part I: |
770 |
C Sensitivity to atmospheric moisture transport. |
771 |
C J. Climate 12(1), 71-82 |
772 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
773 |
C Global thermohaline circulation. Part II: |
774 |
C Sensitivity with interactive transport. |
775 |
C J. Climate 12(1), 83-91 |
776 |
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
777 |
C Destabilization of the thermohaline circulation |
778 |
C by atmospheric eddy transports. |
779 |
C J. Climate 7(12), 1870-1882 |
780 |
o Will need long integration testing. |
781 |
checkpoint53b_pre |
782 |
|
783 |
o created pkg/mom_common in preparation for variable viscosity code |
784 |
o renamed and split ini_mnc_io |
785 |
o pkg/land: only liquid water can diffuse or run-off |
786 |
o AIM using land: soil wetness availability account for snow |
787 |
o added printMapIncludesZeros to EEPARMS namelist |
788 |
|
789 |
checkpoint53a_post |
790 |
o restore TAMC compatiility for exf_constants.h |
791 |
(no usage of _d in .h) |
792 |
o Additional storing in KPP in an attempt to fix |
793 |
TAMC problem with adjoint of KPP code. |
794 |
(no success...) |
795 |
Identical code works fine with TAF. |
796 |
o Fixed verification/natl_box_adjoint experiments. |
797 |
Initial conditions for Experiments 4 and 5 are now |
798 |
set to "SEAICE_initialHEFF=0", which is more reasonable, |
799 |
and hence gives results closer to that of Experiment 2. |
800 |
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
801 |
|
802 |
checkpoint53 |
803 |
o stable checkpoint with up to date adjoint |
804 |
TLM tests only run for 1st grdchk at the moment. Its unclear if |
805 |
this is a code problem or a problem with resetting code for g_ |
806 |
variables that is being autogenerated wrong. |
807 |
Otherwise: |
808 |
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
809 |
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
810 |
are both still in chaos following their security messes. |
811 |
|
812 |
checkpoint52n_post |
813 |
o various build (mostly genmake2) changes including: |
814 |
- ability to build/run more easily within Cygwin and MacOS X |
815 |
- more complicated Makefiles with a stronger dependence on Gnu Make |
816 |
o pkg/seaice modifications |
817 |
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
818 |
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
819 |
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
820 |
- changed proxy for geostrophic velocity and updated |
821 |
verification/lab_sea/results/* accordingly |
822 |
- removed ADI dynamic solver from pkg/seaice |
823 |
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
824 |
they caused a segmentation fault under certain circumstances |
825 |
- removed unused field WATR |
826 |
o bug fix in exf-package: |
827 |
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
828 |
now reflect that. |
829 |
o small fixes in the cal-package: |
830 |
- set reference date to first of January for the 'model'-calendar |
831 |
- failing of cal_CheckDate in cal_FullDate now actually results in a |
832 |
warning |
833 |
o small modifications in exf-package to increase flexibility: |
834 |
- change climtempfreeze from a constant to a runtime parameter that |
835 |
is specified in data.exf_clim (default = -1.9) |
836 |
- introduce runtime parameter windstressmax (default = 2.0) that is |
837 |
specified in data.exf |
838 |
o fix in pkg/thsice: |
839 |
- update Evap (Tsf changes) to be consistent with Latent heat flux |
840 |
- maintain snow precipitation unchanged (even if Tsf >=0). |
841 |
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
842 |
|
843 |
checkpoint52m_post |
844 |
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
845 |
this does not change any of the results, because myIter=0 in swfrac always |
846 |
lead to jwtype=2 (the default anyway), but the call makes little sense |
847 |
as a default |
848 |
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
849 |
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
850 |
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
851 |
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
852 |
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
853 |
o extending useSingleCpuIO option to work with new exch2 I/O format |
854 |
- old-style, missing-tile I/O is still accessible by defining CPP |
855 |
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
856 |
o monitor package can write to NetCDF files and/or STDOUT |
857 |
o fix re-definition bug in MNC_GRID_INIT_ALL() |
858 |
o doc/api_reference added |
859 |
- a framework for building an API Reference Manual using all |
860 |
the "protex" comments embedded in the code |
861 |
- see pkg/generic_advdiff, pkg/mnc for examples |
862 |
o MNC: |
863 |
- make myThid the last argument for all subroutines |
864 |
- new default for the grid files: NO halos |
865 |
- add useMNC and other run-time flags |
866 |
- separate per-file-group handling of the unlimited dimension |
867 |
- early initialization of MNC w/ flags read at the eeboot stage |
868 |
and lookup tables set in initialize_fixed |
869 |
- write all MNC output to a freshly-created directory |
870 |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
871 |
o test exp. advect_cs: use the standard cs32 grid ; update output. |
872 |
o Added functionality to grdchk: |
873 |
pick global i,j,k position (or nearest wet) where to perform check. |
874 |
|
875 |
checkpoint52l_post |
876 |
o new land formulation: |
877 |
a) use ground enthalpy as prognostic variable to ensure exact |
878 |
energy conservation. |
879 |
b) account for water temperature and for latent heat of freezing |
880 |
in all processes (rain, run-off, ground storage) |
881 |
c) compute surface and ground temperature implicitly. |
882 |
o aim_v23 modification for new land model: |
883 |
a) Treat separately land / ocean / sea-ice surface fluxes |
884 |
to allow implicit computation of land & sea-ice surface temp. |
885 |
b) add snow precipitation. |
886 |
checkpoint52l_pre |
887 |
|
888 |
o fix problem (when 1 tile is empty) in min/max monitor. |
889 |
o fix bug in timeAve (u,vZetatave in common block) |
890 |
o no restoring terms under ice for pkg/seaice |
891 |
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
892 |
o bug fix for pkg/seaice pickups |
893 |
o change MNC call locations and add coordinate attributes |
894 |
o mask vorticity at the corner ; affects global_ocean.cs output |
895 |
o fix ini_curvilinear_grid ; test CS experiments with mpi |
896 |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
897 |
o exf: Adding simple range check routine for exf fields after read |
898 |
|
899 |
checkpoint52k_post |
900 |
o removed top-level directory "diags" |
901 |
- we migrated these functions to pkg/timeave a long time ago |
902 |
o fixed bug introduced in pkg/monitor |
903 |
o accuracy ctrlprec = 32 insuffient for gradient checks using |
904 |
averaged fields (I/O via cost_averages) |
905 |
-> use ctrl.h in active_file*.F to control I/O precision. |
906 |
o paramter list of CALL ADTHE_MAIN_LOOP |
907 |
o added initial do_the_model_io to ecco |
908 |
o set all ...Freq to zero after cost_final |
909 |
taveFreq, dumpFreq, pChkptFreq |
910 |
o MAIN and ECCO differentiability restored |
911 |
|
912 |
checkpoint52j_post |
913 |
o fix nchklev in tamc.h for global_ocean... |
914 |
o Bringing flow and store directives up-to-date |
915 |
o Really weird thing! |
916 |
call do_the_model_io from the_main_loop with parameters |
917 |
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
918 |
TAF places a faulty re-call of initialise_varia |
919 |
after cost_final call which should not be there! |
920 |
checkpoint52j_pre |
921 |
|
922 |
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
923 |
error messages |
924 |
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
925 |
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
926 |
debug output |
927 |
o modfied mdsio_writefield.F to handle non-global files under exch2 |
928 |
o update AIM Cubed-Sphere exp (aim.5l_cs): |
929 |
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
930 |
o update AIM Equatorial Channel exp: |
931 |
use standard aim_v23 pkg and change the SST fields to be more realistic. |
932 |
o globalFile now works with exch2 |
933 |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
934 |
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
935 |
o limit timeave output for hi-res integrations |
936 |
|
937 |
checkpoint52i_post |
938 |
o removed CPP_EEOPTIONS.h from verification/*/code |
939 |
o updated the tiling for global_ocean_pressure |
940 |
checkpoint52i_pre |
941 |
|
942 |
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
943 |
the old pkg/aim). |
944 |
|
945 |
checkpoint52h_pre |
946 |
o shortened offending lines in exch2_send_rx?.template |
947 |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
948 |
o genmake2: add build & execute test for NetCDF code |
949 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
950 |
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
951 |
o added useSingleCPUIO flag to monitor.F and mon_out.F |
952 |
o added temporary hack for sea-ice dynamics on the cube: |
953 |
metric terms are ignored and it is assumed that |
954 |
there is no sea-ice on cube faces 1, 2, 4, and 5. |
955 |
|
956 |
checkpoint52f_post |
957 |
o added exch2 cube routines to pkg/exch2 |
958 |
o modified hs94.cs-32x32x5 to use it |
959 |
o added new grid files to hs94.cs-32x32x5 |
960 |
checkpoint52f_pre |
961 |
|
962 |
checkpoint52e_post |
963 |
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
964 |
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
965 |
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
966 |
to work with implicit vertical advection and AB ; |
967 |
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
968 |
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
969 |
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
970 |
checkpoint52e_pre |
971 |
|
972 |
o fix bug in impldiff when Nr=1 or Nr=2. |
973 |
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
974 |
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
975 |
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
976 |
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
977 |
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
978 |
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
979 |
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
980 |
|
981 |
checkpoint52d_post |
982 |
o re-tiled many expts to allow comparison in multi-processor mode |
983 |
- updated output accordingly |
984 |
- changed hs94.128x64x5 to use intial T from file rather than use the |
985 |
random number generator |
986 |
o add infrastructure in model routines for fizhi and gridalt packages |
987 |
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
988 |
o changes to permit hi-res, cubed-sphere, configuration |
989 |
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
990 |
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
991 |
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
992 |
of surface winds for the cube |
993 |
(A verification experiment, based on global_ocean.cs32x15, but with |
994 |
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
995 |
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
996 |
complete with example surface forcing files and matlab scripts to look |
997 |
at the output and compare it with that of global_ocean.cs32x15.) |
998 |
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
999 |
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
1000 |
to conform to the common rule. |
1001 |
o check-in the first version of the coupler + interfaces for multi-components |
1002 |
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
1003 |
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
1004 |
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
1005 |
- ocean and atmos. share the same horizontal grid (no interpolation). |
1006 |
- exchanges between component and coupler is done in forward_step |
1007 |
o new verification experiment, cpl_aim+ocn: |
1008 |
coupled ocean - AIM atmosphere on cs32 grid. |
1009 |
|
1010 |
checkpoint52d_pre |
1011 |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
1012 |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
1013 |
|
1014 |
checkpoint52c_post |
1015 |
o Fixing OPTIONS files for use of exf: |
1016 |
- ALLOW_ECCO not needed |
1017 |
- ECCO_CPPOPTIONS.h should not be included from |
1018 |
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
1019 |
as has been the case in the past |
1020 |
- All cal/exf related options are currently set in |
1021 |
single header file. Should remain so until we |
1022 |
agree on a consistent new policy. |
1023 |
o Removed all CPP options for cal package. |
1024 |
cal has no more CPP options. |
1025 |
o modified STOREs in GAD_ADVECTION |
1026 |
o corrected key comp. for passkey |
1027 |
|
1028 |
checkpoint52b_post |
1029 |
o new version: "thsice" of thermodynamic sea-ice pkg: |
1030 |
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
1031 |
- modify fluxes but do not change theta directly; |
1032 |
- light cleaning of bulk_force pkg (still needed with thsice). |
1033 |
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
1034 |
+ output_thsice.txt to test thsice & bulk_force pkgs. |
1035 |
o put back grid & coriolis monitor output. |
1036 |
checkpoint52b_pre |
1037 |
|
1038 |
o call "do_the_model_io" at the beginning (=> dump initial state) |
1039 |
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
1040 |
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
1041 |
(need info on NUMBER_OF_PTRACERS) |
1042 |
o missing PTRACERS headers in some routines |
1043 |
o default tamc.h in pkg/autodiff supposed to crash |
1044 |
to ensure proper customization |
1045 |
|
1046 |
checkpoint52a_post |
1047 |
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
1048 |
- moved surfaceTendencyTice from pkg/seaice to main code |
1049 |
- subroutine FREEZE_SURFACE now limits only surface temperature |
1050 |
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
1051 |
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
1052 |
- keep the old version of FREEZE for backward compatibility; |
1053 |
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
1054 |
- corresponding modifs for TAF directives |
1055 |
o added surface flux output variables to TIMEAVE_STATVARS |
1056 |
o time-averaged output for pkg/ptracers |
1057 |
o fix problem with ECCO-related divided adjoint |
1058 |
snapshot file was missing some ad-variables, |
1059 |
but no warning issued by TAF |
1060 |
|
1061 |
checkpoint52a_pre |
1062 |
o some bug fixes for #undef REAL4_IS_SLOW |
1063 |
|
1064 |
checkpoint52 = ecco_c52_e35 |
1065 |
o after testing adjoints of checkpoint51u_post |
1066 |
|
1067 |
checkpoint51u_post |
1068 |
o this is the post-merge tag of the ecco-branch |
1069 |
(needs another clean checkout and re-testing) |
1070 |
o various natl_box_adjoint configs and results |
1071 |
but no input fields |
1072 |
o obcs adjoint not yet merged! |
1073 |
o adding ECCO global 1x1 and 2x2 degree configs |
1074 |
o updated/extended some store directives for seaice |
1075 |
o pkg/ecco now containes ecco-specific part of cost function |
1076 |
o top level routines the_main_loop, forward_step |
1077 |
supersede those in model/src/ |
1078 |
previous input data.cost now in data.ecco |
1079 |
(new namelist ecco_cost_nml) |
1080 |
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
1081 |
|
1082 |
checkpoint51t_post |
1083 |
o this is the pre-merge tag of the ecco-branch |
1084 |
|
1085 |
checkpoint51s_post |
1086 |
o cleanup: removed various obsolete #define-s |
1087 |
o pkg/grdchk |
1088 |
- renamed 'ph-grd 3' to 'grad-res' |
1089 |
- merged from ecco-branch |
1090 |
(remaining bug fixes for obcs gradient checks) |
1091 |
- additional high-precision output for testreport |
1092 |
(grep for 'precision_grdchk_result') |
1093 |
|
1094 |
checkpoint51r_post |
1095 |
o cleaned up or removed CPP_OPTIONS.h files |
1096 |
o updated results for some of the tests to reflect the new |
1097 |
optfiles (-ieee: -O0 instead of -O3) |
1098 |
|
1099 |
checkpoint51q_post |
1100 |
o cd_code: |
1101 |
- moved cd_scheme.F -> cd_code_scheme.F |
1102 |
- separate read_checkpoint from cd_code_ini_vars.F |
1103 |
- separated cd_code part from write_checkpoint |
1104 |
- updated AD_SOURCE, generated .flow |
1105 |
- added CD_CODE_VARS.h to the_main_loop |
1106 |
- Moving cd_code specific store dir.s to pkg/cd_code |
1107 |
o ctrl package totally restructured |
1108 |
- pack/unpack now optional and decoupled from |
1109 |
xx_/adxx_ I/O |
1110 |
- ctrl_pack/unpack cleaned |
1111 |
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
1112 |
- confined inclusion of AD_CONFIG.h to where necessary. |
1113 |
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
1114 |
|
1115 |
checkpoint51p_post |
1116 |
o create initial cd_code package |
1117 |
- WARNING: the initialization of fields within packages |
1118 |
is broken because INI_FIELDS (where READ_CHECKPOINT is |
1119 |
called) is called *before* PACKAGES_INIT_VARIABLES. |
1120 |
This seems to be backwards since |
1121 |
1) its important to initially zero the entire field including |
1122 |
the "halo" region |
1123 |
2) zeroing needs to be done *before* reading pickup info |
1124 |
and the pickup call might or might not happen in any |
1125 |
particular run |
1126 |
- this needs an overhaul for R2 |
1127 |
o cleanup verification/*/code/GMREDI_OPTIONS.h |
1128 |
o cleanup testreport |
1129 |
|
1130 |
checkpoint51o_post |
1131 |
o bringing AD-related verif's up to date with genmake2 |
1132 |
- carbon/ |
1133 |
- global_ocean.90x40x15/ |
1134 |
- hs.94.1x64x5/ |
1135 |
- (front_relax/ ) |
1136 |
o (more) consistent directory structure for AD-related verif.'s |
1137 |
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
1138 |
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
1139 |
o bug fix in find_alpha.F for MDJWF: |
1140 |
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
1141 |
change rho -> rho-rhoConst |
1142 |
- replace call find_rho to find_rhonum |
1143 |
o initialisation of rFlx extended to full array (required by TAF) |
1144 |
and shifted to thermodynamics |
1145 |
o removed PTRACERS.h in ptracers routine |
1146 |
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
1147 |
o Correcting initialisations for fVerU, fVerV. |
1148 |
o helping TAF to recognize dependency on kUp for |
1149 |
fVerU, fVerV |
1150 |
o Replacing delZ by delR in pkg/ctrl/ |
1151 |
checkpoint51o_pre |
1152 |
|
1153 |
o undid all of cp51 pending some cleanups and discussion |
1154 |
o added the [#include "AD_CONFIG.h"] statement to all files that need |
1155 |
it for adjoint/tl #defines |
1156 |
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
1157 |
o removed tools/genmake since it no longer works |
1158 |
|
1159 |
checkpoint51n_post |
1160 |
o modifications to make FREEZE flux visible to pkg/kpp |
1161 |
- moved surfaceTendencyTice from pkg/seaice to main code |
1162 |
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
1163 |
- subroutine FREEZE now limits only surface temperature |
1164 |
(this means new output.txt for global_ocean.90x40x15, |
1165 |
global_ocean.cs32x15, and global_with_exf) |
1166 |
o added surface flux output variables to TIMEAVE_STATVARS |
1167 |
|
1168 |
checkpoint51n_pre |
1169 |
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
1170 |
o added [#include "AD_CONFIG.h"] to all files that use the following |
1171 |
defines: |
1172 |
- ALLOW_ADJOINT_RUN |
1173 |
- ALLOW_TANGENTLINEAR_RUN |
1174 |
- ALLOW_ECCO_OPTIMIZATION |
1175 |
|
1176 |
checkpoint51m_post |
1177 |
o incorporating changes to get TAMC/TAF working in genmake2 |
1178 |
- added new TAMC/TAF targets to the Makefile |
1179 |
- various cleanups related to package handling |
1180 |
- these changes should have no impact on the forward model |
1181 |
|
1182 |
checkpoint51l_post |
1183 |
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
1184 |
- faster algorithm for cal_addtime.F |
1185 |
- higher precision arithmetic, where needed |
1186 |
- pkg/exf *startdate variables changed from calendar date to |
1187 |
model integration time |
1188 |
|
1189 |
checkpoint51l_pre |
1190 |
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
1191 |
o enable to apply restoring on S & T only in a latitude band. |
1192 |
o update output (external_forcing_surf modif. change truncation errors) |
1193 |
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
1194 |
|
1195 |
checkpoint51k_post |
1196 |
o change default to: useNHMTerms=.FALSE. |
1197 |
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
1198 |
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
1199 |
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
1200 |
exp1, ideal_2D_oce |
1201 |
- change data file of oceanic exp (leave the results unchanged for now) |
1202 |
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
1203 |
o set gravitySign automatically according to the vertical coordinate used |
1204 |
(and change sign: back to "logical" value: +1 when R increases downward) |
1205 |
o added an include barrier to the default CPP_OPTIONS.h and |
1206 |
removed the #include "PACKAGES_CONFIG.h" from it |
1207 |
o fix a bug in mom_fluxform (from chk51j_post) |
1208 |
|
1209 |
checkpoint51j_post |
1210 |
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
1211 |
o adjusted some flow directives (dynamics, thermodynamics) |
1212 |
o added cubed-sphere case to test cost function |
1213 |
o heckpoint_lev?_directives.h now include |
1214 |
pkg-specific directives, whenever those are enabled. |
1215 |
o Moving pkg-specific flow directives to corresponding pkg |
1216 |
Moving pkg-specific differentiation list to corresponding pkg |
1217 |
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
1218 |
---> conventions are |
1219 |
- pkg_ad.flow |
1220 |
- pkg_ad_diff.list |
1221 |
- pkg_ad_check_lev?_dir.h |
1222 |
|
1223 |
checkpoint51i_post |
1224 |
o merge of the branch-genmake2 |
1225 |
- knowingly breaks the older genmake |
1226 |
- automatic generation of all ALLOW_${PKG_NAME} defines |
1227 |
- new testreport supersedes older testscript |
1228 |
o large number of package inclusion and header cleanups |
1229 |
checkpoint51i_pre |
1230 |
|
1231 |
o new output for adjoin of global ocean vector invariant |
1232 |
o fix for checkpoint of thermodynamic seaice and bulk_force |
1233 |
o Steph gchem various cleanups |
1234 |
|
1235 |
checkpoint 51h_pre |
1236 |
o fixed some single quotes |
1237 |
o modify gchem pkg to be more versatile |
1238 |
o modifications to clean up dic pkg |
1239 |
o add pkg/cfc |
1240 |
|
1241 |
checkpoint51g_post |
1242 |
o provide links for ARPACK and ADM*TLM |
1243 |
o start removing verification/vero/ |
1244 |
o update AD-related stuff |
1245 |
(in particular some IF-statements in model/src/ routines) |
1246 |
o adding to verification/global_ocean.90x40x15/ adjoint of |
1247 |
vector invariant setup |
1248 |
|
1249 |
checkpoint51f_post |
1250 |
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
1251 |
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
1252 |
of tracer Green's fucntions for ocean inversion project. |
1253 |
|
1254 |
checkpoint51f_pre |
1255 |
o Added on-the-fly spatial interpolation capability |
1256 |
"USE_EXF_INTERPOLATION" to pkg/exf. |
1257 |
- This is a temporary Cartesian-grid hack until |
1258 |
the super-duper ESMF coupler becomes available. |
1259 |
- See verification/global_with_exf/README for usage example. |
1260 |
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
1261 |
flags and modified pkg/seaice accordingly. |
1262 |
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
1263 |
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
1264 |
non-local transport term. |
1265 |
|
1266 |
checkpoint51e_post |
1267 |
o pkg/mom_vecinv: |
1268 |
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
1269 |
- add time-ave diagnostic of vorticity advection. |
1270 |
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
1271 |
o atmospheric geopotential: - include water vapor effect; |
1272 |
- use p^kappa in p* scaling. |
1273 |
o land pkg: read initial state from files. |
1274 |
o AIM : add stratospheric drag in the upper level |
1275 |
|
1276 |
checkpoint51d_post |
1277 |
o change function ILNBLNK (=> last non-blank char.) to return zero |
1278 |
(instead of the string length) when the string. char is empty |
1279 |
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
1280 |
o modif's to restore TAMC compatibility |
1281 |
- avoid "_d" constructs in PARAMETER declarations |
1282 |
- avoid interrupting lines by comment lines |
1283 |
o Use cluster local disks for purely local I/O |
1284 |
vs. globally visible disks needed for ctrl stuff |
1285 |
(merged from ecco-branch) |
1286 |
- new active_file_loc... and mdsio_..._loc routines |
1287 |
- affected packages: autodiff, ctrl, grdchk, mdsio |
1288 |
|
1289 |
checkpoint51c_post |
1290 |
o introducing integer flag debugLevel |
1291 |
- debLevZero: suppress all output |
1292 |
- debLevA: standard |
1293 |
- debLevB: equivalent to current debugMode=.TRUE. |
1294 |
o introducing pathname variable mdsioLocalDir for mdsio |
1295 |
that can be specified at runtime |
1296 |
(relevant for cluster I/O to local disk) |
1297 |
` |
1298 |
>>>checkpoint51b_post |
1299 |
adjoint of ptracers |
1300 |
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
1301 |
o extended state in checkpoint_lev?, etc. |
1302 |
o alternative ctrl/cost with tr1 or ptracer |
1303 |
o new comlev1_bibj_ptracers |
1304 |
o new ptracers.flow |
1305 |
o made ptracers_forcing same as external_forcing_s |
1306 |
o added verification for adjoint with ptracers |
1307 |
- adm. grdchk fail so far |
1308 |
- tlm. grdchk OK |
1309 |
- checked tapelev/comlev recomputations: OK |
1310 |
<<<checkpoint51b_pre |
1311 |
|
1312 |
checkpoint51a_post |
1313 |
o added code for biogeochemistry package |
1314 |
- new pkgs: dic, gchem |
1315 |
- new subroutine in ptracers |
1316 |
o modify code for biogeo packages |
1317 |
- in model/src and pkg/ptracers |
1318 |
|
1319 |
checkpoint51 |
1320 |
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
1321 |
- autodiff, ctrl, exf, grdchk, seaice |
1322 |
kept separate packages |
1323 |
- cost, ecco, obcs |
1324 |
o updating verification/internal_wave, verification/lab_sea |
1325 |
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
1326 |
|
1327 |
checkpoint50i_post |
1328 |
o Preparing next differentiable checkpoint and sync |
1329 |
of MAIN vs. ecco-branch |
1330 |
- 1st step: this one is differentiable |
1331 |
- 2nd step: next(! not this) checkpoint will have updated packages |
1332 |
from ecco-branch) |
1333 |
|
1334 |
checkpoint50h_post |
1335 |
o new package "land": provide surface BC for AIM. |
1336 |
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
1337 |
o AIM: use true log-P extrapolation for near surface temp (= as in |
1338 |
F.Molteni paper) ; update aim.5l_cs output. |
1339 |
o New variable in PARM03 for more flexible pickups |
1340 |
o somewhat cleaned package initialisation sequence for |
1341 |
ctrl/ cost/ ecco/ in packages_... routines |
1342 |
|
1343 |
checkpoint50g_post |
1344 |
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
1345 |
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
1346 |
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
1347 |
made the default because of faster convergence than ADI |
1348 |
|
1349 |
checkpoint50f_post |
1350 |
o exf totally restructured |
1351 |
- replaced all exf_set_ routines by one generic exf_set_gen.F |
1352 |
and made sure it's still differentiable |
1353 |
- split exf_getffields.F into new exf_bulkformulae.F |
1354 |
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
1355 |
- updated adjoint/makefile and relevant verif. accordingly |
1356 |
|
1357 |
checkpoint50f_pre |
1358 |
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
1359 |
+ change Evap over land. (update aim.5l_cs output) |
1360 |
o added missing .cvsignores and made uniform across expts |
1361 |
o changed configuration of tidal_basin_2d expt |
1362 |
o added pkg/debug functions for tracing code in fatal crashes |
1363 |
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
1364 |
o new fn in pkg/monitor to stop model if solution grows too big |
1365 |
o removed lots of single quotes from comments |
1366 |
|
1367 |
checkpoint50e_post |
1368 |
o make KPP work with PTRACERS |
1369 |
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
1370 |
nearly a copy of kpp_transport_s |
1371 |
- there is no analogue to SurfaceTendencyS, so I have to use |
1372 |
gPtr(of the surface layer) instead |
1373 |
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
1374 |
checkpoint50e_pre |
1375 |
|
1376 |
checkpoint50d_post |
1377 |
o change kpp output from multiple-record state files to single-record state |
1378 |
files analogous to write_state.F |
1379 |
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
1380 |
analogous to the cg2d-related output. |
1381 |
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
1382 |
so that writing to internal file fn (with length 512) fails. |
1383 |
checkpoint50d_pre |
1384 |
|
1385 |
checkpoint50c_post |
1386 |
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
1387 |
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
1388 |
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
1389 |
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
1390 |
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
1391 |
|
1392 |
checkpoint50c_pre |
1393 |
Merging from release1_p13: |
1394 |
o bug fix for pkg/seaice dynamic solver |
1395 |
o Added SEAICE_initialHEFF to pkg/seaice |
1396 |
|
1397 |
checkpoint50b_post |
1398 |
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
1399 |
o in order to put the momForcing out of the Adams-Bashforth: |
1400 |
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
1401 |
to timestep.F |
1402 |
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
1403 |
o re-generate output for highly sensitive test-exp: |
1404 |
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
1405 |
|
1406 |
checkpoint50b_pre |
1407 |
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
1408 |
o corrected CPP option mismatch in exf_Bulk... functions for case |
1409 |
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
1410 |
|
1411 |
checkpoint50a_post |
1412 |
o Bug fix for merging between c50 and KPP. |
1413 |
ikey was passed from thermodynamics to kpp_calc via |
1414 |
common block rather than being recomputed in kpp_calc, |
1415 |
in contradiction with new key itdkey. |
1416 |
New key ikppkey created, and tamc.h headers updated. |
1417 |
|
1418 |
checkpoint50 |
1419 |
- 2nd step of merge with ecco-branch: |
1420 |
merge changes in ecco-branch back into main trunk |
1421 |
- bug fix in find_alpha |
1422 |
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
1423 |
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
1424 |
- merged some sliced AD support routines |
1425 |
|
1426 |
checkpoint49 |
1427 |
merged from ecco-branch: |
1428 |
o exf: |
1429 |
- Enable initialisation of forcing fields to constant |
1430 |
(runtime) values. |
1431 |
- in exf_getffields.F |
1432 |
Reduce i-/j-loop to interior domain, discarding overlaps. |
1433 |
That also fixes wrong TAF-key computations for key_1, key_2 |
1434 |
with bulf formulae. |
1435 |
- exf_init.F modify #ifdef for exf_init_evap |
1436 |
- exf_getffieldrec.F, ctrl_getrec.F |
1437 |
The following INT-usages are not safe: |
1438 |
fldsecs = int(fldsecs/fldperiod)*fldperiod |
1439 |
fldcount = int(fldsecs/fldperiod) + 1 |
1440 |
and were modified. |
1441 |
o autodiff: checkpoint_lev... |
1442 |
- updated storing for bulk formulae (some arrays were missing) |
1443 |
- added state for seaice package |
1444 |
- synchronized with main branch |
1445 |
o DIVA: |
1446 |
Modif.s in |
1447 |
- the_main_loop.F |
1448 |
- the_model_main.F |
1449 |
and added cost_final_restore.F cost_final_store.F |
1450 |
o With these changes, it is possible to fully separate |
1451 |
the first forward run to compute the cost function (mdthe_main_loop) |
1452 |
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
1453 |
into separate model executions. |
1454 |
This enables better tuning of DIVA to given queue sizes. |
1455 |
o Loss of cost function value in consecutive DIVA runs is |
1456 |
fixed by storing to 'costfinal' file. |
1457 |
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
1458 |
beginning/end of adjoint integration is accounted for. |
1459 |
The current changes apply to TAF-1.4.26. |
1460 |
TAF has one remaining bug, requiring one manual change |
1461 |
(see MITgcm manual). |
1462 |
o cal: synchronized between MAIN and ecco-branch |
1463 |
|
1464 |
checkpoint48i_post |
1465 |
o Changes to restore differentiability of code w.r.t. previous tag |
1466 |
(mostly adding new routines to make list and replacing |
1467 |
pressure by totPhiHyd). |
1468 |
o Updated and merged grdchk package |
1469 |
- has both ADM and TLM checks |
1470 |
- works for single- and multi-proc. |
1471 |
- output cleaned |
1472 |
- worked successfully for parallel DIVA |
1473 |
o genmake: |
1474 |
- Adding -platform=SP4 |
1475 |
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
1476 |
o Modif. for DIVA: |
1477 |
ctrl_unpack should not be called in intermediate DIVA interval. |
1478 |
(similar thing would apply for active files such as |
1479 |
tbar, sbar, psbar, which should not be reinitialised; |
1480 |
only relevant for ecco-branch) |
1481 |
|
1482 |
checkpoint48h_post |
1483 |
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
1484 |
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
1485 |
o Added SEAICE_initialHEFF to pkg/seaice |
1486 |
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
1487 |
|
1488 |
checkpoint48g_post |
1489 |
--- EOS: |
1490 |
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
1491 |
store total Potential in totPhyHyd for diagnostics & EOS. |
1492 |
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
1493 |
--- Pressure/geopotential gradient: |
1494 |
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
1495 |
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
1496 |
( changes results of global_ocean_pressure ) |
1497 |
o NLFS + z-coord.: add eta*Rho' contribution. |
1498 |
o accurate phiHyd when using interface-W at the middle between 2 centers |
1499 |
( changes results of ideal_2D_oce ) |
1500 |
o includes r* 2nd term in potential gradient. |
1501 |
|
1502 |
checkpoint48f_post |
1503 |
Merging from release1_p12: |
1504 |
o Modifications for using pkg/exf with pkg/seaice |
1505 |
- improved description of the various forcing configurations |
1506 |
- added basic radiation bulk formulae to pkg/exf |
1507 |
- units/sign fix for evap computation in exf_getffields.F |
1508 |
- updated verification/global_with_exf/results/output.txt |
1509 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
1510 |
(SBO) core products, including oceanic mass, center-of-mass, |
1511 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
1512 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
1513 |
to avoid negative values in shallow regions. |
1514 |
- updated verification/natl_box/results/output.txt |
1515 |
- updated verification/lab_sea/results/output.txt |
1516 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
1517 |
o Added useSingleCpuIO option (see PARAMS.h). |
1518 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
1519 |
work with multi-field files, e.g., for single-file pickup. |
1520 |
o pkg/seaice: |
1521 |
- bug fix in growth.F: QNET for no shortwave case |
1522 |
- added HeffFile for specifying initial sea-ice thickness |
1523 |
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
1524 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
1525 |
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
1526 |
o pkg/seaice: |
1527 |
- adjoint-friendly modifications |
1528 |
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
1529 |
|
1530 |
checkpoint48e_post |
1531 |
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
1532 |
o dynamics: change definition of computational domain & adapt mom_fluxform |
1533 |
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
1534 |
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
1535 |
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
1536 |
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
1537 |
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
1538 |
inverted_barometer solid-body.cs-32x32x1 |
1539 |
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
1540 |
|
1541 |
checkpoint48d_post |
1542 |
o in preparation for r*: |
1543 |
a) use pre-computed gradient of hydrostatic potential: |
1544 |
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
1545 |
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
1546 |
=> affects results of glob_oce_pressure (different truncation error) |
1547 |
update output.txt of ideal_2D_oce & global_ocean_pressure |
1548 |
|
1549 |
checkpoint48d_pre |
1550 |
o in preparation for r*: |
1551 |
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
1552 |
pass the 2 comp. of the grad. as arguments to momentum S/R. |
1553 |
but for the moment, only used if it does not change the results. |
1554 |
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
1555 |
|
1556 |
checkpoint48c_post |
1557 |
Modifications in treatment of initial flux forcing controls |
1558 |
to avoid extra storing of flux fields. |
1559 |
|
1560 |
checkpoint48c_pre |
1561 |
o Added tidal_basin_2d experiment (currently 1D!) |
1562 |
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
1563 |
|
1564 |
checkpoint48b_post |
1565 |
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
1566 |
(modification to pressure gradient not yet implemented) |
1567 |
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
1568 |
(for U & V) that are used for vertical advection of momentum. |
1569 |
|
1570 |
checkpoint48a_post |
1571 |
o In preparation for r*, use temp. array to compute vertical transport |
1572 |
in flux-form momentum pkg. => change results of few test-exp. |
1573 |
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
1574 |
lab_sea, natl_box & plume_on_slope |
1575 |
|
1576 |
checkpoint48 |
1577 |
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
1578 |
|
1579 |
checkpoint47j_post |
1580 |
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
1581 |
o moved adexch from forward_step to addummy_in_stepping |
1582 |
o added exch in ctrl_map_... |
1583 |
o aveFreq.=0. at end of cost_final to avoid overwrite in |
1584 |
reverse checkpointing loop |
1585 |
o Yet more changes in gmredi: |
1586 |
* adgmredi_calc_tensor |
1587 |
avoiding all recomputation of gmredi_slope_limit |
1588 |
* adgmredi_x/y/rtransport |
1589 |
added flag for excessive storing to avoid recomp. of |
1590 |
u/v/rtans, dTdx/y/z |
1591 |
-> this is not really necessary and very memory-consuming |
1592 |
* adgmredi_slope_psi: |
1593 |
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
1594 |
* gmredi_slope_limit |
1595 |
re-activated full calculation of taperfct for case 'ac02' |
1596 |
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
1597 |
|
1598 |
checkpoint47i_post |
1599 |
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
1600 |
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
1601 |
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
1602 |
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
1603 |
o gmredi: fix few bugs. |
1604 |
|
1605 |
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
1606 |
This will be a good checkpoint to plug into the ecco-branch. |
1607 |
o few modif.'s to get latest version adjointed |
1608 |
(mainly kick out code in ini_linear_phisurf) |
1609 |
o modif's to run adjoint with exactConserv |
1610 |
o case GM_BOLUS_ADVEC should be cleaned |
1611 |
S/R gmredi_slope_psi should be cleaned |
1612 |
o verification/carbon now has exactConserv=.TRUE. |
1613 |
|
1614 |
checkpoint47g_post |
1615 |
o time-average AIM output: becomes independent from statvars time-average |
1616 |
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
1617 |
o After TAF bug fix: |
1618 |
Tested adjoint of gmredi package. |
1619 |
Tests were done with checkpoint47 rather than with latest |
1620 |
checkpoint47f_post since the latter is broken for the adjoint |
1621 |
verification/carbon/ contains both ADM and TLM gradient checks. |
1622 |
Here they are, before they get changed/lost/stolen. |
1623 |
Mostly modif.'s to fix numerical sensitivities. |
1624 |
Gradient checks OK for |
1625 |
- GM_taper_scheme: |
1626 |
* clipping |
1627 |
* ac02 |
1628 |
* linear |
1629 |
* glw91 |
1630 |
* dm95 |
1631 |
* ldd97 |
1632 |
- GMREDI_OPTIONS: |
1633 |
* GM_VISBECK_VARIABLE_K |
1634 |
* GM_NON_UNITY_DIAGONAL |
1635 |
* GM_EXTRA_DIAGONAL |
1636 |
* GM_BOLUS_ADVEC |
1637 |
in conjunction with data.gmredi parameters to be checked in |
1638 |
in a few minutes under verification/carbon/code/ |
1639 |
|
1640 |
checkpoint47f_post |
1641 |
Merging from release1_p10: |
1642 |
o modifications for using pkg/exf with pkg/seaice |
1643 |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
1644 |
and SEAICE_EXTERNAL_FLUXES |
1645 |
- pkg/exf CPP options EXF_READ_EVAP and |
1646 |
EXF_NO_BULK_COMPUTATIONS |
1647 |
- usage examples are Experiments 8 and 9 in |
1648 |
verification/lab_sea/README |
1649 |
- verification/lab_sea default experiment now uses |
1650 |
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
1651 |
|
1652 |
checkpoint47e_post |
1653 |
o created a tag prior to creating a branch |
1654 |
|
1655 |
checkpoint47d_post |
1656 |
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
1657 |
at the bottom boundary had an erroneous half slip boundary condition |
1658 |
o added bottom drag and no slip boundary condition capabilities to |
1659 |
oceanic pressure coordinates code |
1660 |
o added new verification experiment global_ocean_pressure, this experiment is |
1661 |
also described in the tutorial section of the manual |
1662 |
checkpoint47d_pre |
1663 |
|
1664 |
checkpoint47c_post |
1665 |
o Added a verification experiment for a global cubed-sphere ocean run |
1666 |
- verification/global_ocean.cubed32x32x30 |
1667 |
- uses pkg/therm_seaice and pkg/bulk_forcing |
1668 |
|
1669 |
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
1670 |
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
1671 |
when using P-coordinate; only implemented for atmospheric config. |
1672 |
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
1673 |
NOTES: requires option NONLIN_FRSURF to be "#define". |
1674 |
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
1675 |
|
1676 |
checkpoint47b_post |
1677 |
Merging from release1_p9: |
1678 |
o pkg/seaice |
1679 |
- removed GOTO's and added taf directives |
1680 |
- double precision constants to reduce the g77 (Linux) |
1681 |
to F77 (SGI) differences reported in release1_p8 |
1682 |
o tools/genmake |
1683 |
- added SGI options |
1684 |
o verification/testscript |
1685 |
- updated to that of checkpoint47a_post |
1686 |
o verification/global_ocean.90x40x15/input/eedata |
1687 |
- modified for SGI f77 compatibility |
1688 |
o verification/lab_sea |
1689 |
- added description of sea-ice model |
1690 |
- added missing matlab routines |
1691 |
- added test of thermodynamics parallelization |
1692 |
|
1693 |
checkpoint47a_post |
1694 |
o new pkg: aim_v23 |
1695 |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
1696 |
for now, keep the same surface forcing as before. |
1697 |
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
1698 |
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
1699 |
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
1700 |
o add diagnostic of surface correction term in monitor output |
1701 |
|
1702 |
o bulk_force and therm_seaice |
1703 |
- Two packages: bulk_force (Bulk forcing) |
1704 |
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
1705 |
- Earlier integration from Stephaine Dutkiewicz |
1706 |
and Patrick Heimbach. |
1707 |
- Two ifdef statements for compile time, |
1708 |
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
1709 |
|
1710 |
checkpoint47 |
1711 |
differentiable version of checkpoint46n_post |
1712 |
o bug fix in quasihydrostaticterms |
1713 |
o * "clean" adjoint code (in terms of extensive recomputations) |
1714 |
can now be obtained for all GMREDI options (i.e. for |
1715 |
- GM_VISBECK_VARIABLE_K |
1716 |
- GM_NON_UNITY_DIAGONAL |
1717 |
- GM_EXTRA_DIAGONAL |
1718 |
- GM_BOLUS_ADVEC ) |
1719 |
* However, wrong gradient check problem remains unsolved. |
1720 |
* New CPP options have been introduced for different |
1721 |
tapering schemes |
1722 |
o external_fields_load now part of differentiation list |
1723 |
o pressure needs multiple storing; |
1724 |
would be nice to have store_pressure at beginning or |
1725 |
end of forward_step, e.g. by having phiHyd global (5-dim.) |
1726 |
(NB: pressure is needed for certain cases in find_rho, |
1727 |
which is also invoked through convective_adjustment). |
1728 |
o recomputations in find_rho for cases |
1729 |
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
1730 |
o #define ATMOSPHERIC_LOADING should be differentiable |
1731 |
o ini_forcing shifted to begining of initialise_varia |
1732 |
o Incorporating QNVS line search routines into MITgcm |
1733 |
(this is separate code, and therefore not under pkg) |
1734 |
lsopt/, optim/ |
1735 |
o Updated verification/carbon/ |
1736 |
- #define GM_VISBECK_VARIABLE_K |
1737 |
- GM_taper_scheme = 'ldd97' |
1738 |
|
1739 |
checkpoint46n_post |
1740 |
Merging from release1_p8: |
1741 |
o verification/natl_box: |
1742 |
updating new external_fields_load routine |
1743 |
o New package: pkg/seaice |
1744 |
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
1745 |
The sea-ice code is based on Hibler (1979-1980). |
1746 |
Two sea-ice dynamic solvers, ADI and LSR, are included. |
1747 |
In addition to computing prognostic sea-ice variables and diagnosing |
1748 |
the forcing/external data fields that drive the ocean model, |
1749 |
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
1750 |
The implied surface heat flux is then stored in variable |
1751 |
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
1752 |
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
1753 |
non-local transport term. Because this call precedes model |
1754 |
thermodynamics, temperature under sea-ice may not be "exactly" at |
1755 |
the freezing point by the time theta is dumped or time-averaged. |
1756 |
N.B.: fairly large differences in accuracy occur across |
1757 |
different platforms/compilers; comparison between |
1758 |
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
1759 |
generated output gives: |
1760 |
T S U V |
1761 |
C D M c m s m s m s m s |
1762 |
n p a R g m m e . m m e . m m e . m m e . |
1763 |
f n k u 2 i a a d i a a d i a a d i a a d |
1764 |
g d e n d n x n . n x n . n x n . n x n . |
1765 |
|
1766 |
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
1767 |
o GAD: |
1768 |
- generated new common blocks to account for call of |
1769 |
same gad routines with differing traceridentities |
1770 |
(needed to modify tracerIdentity indices in GAD.h) |
1771 |
- generated separate common blocks for case useCubedSphereExchange |
1772 |
(Department of Futurology) |
1773 |
- parameter lists to gmredi_?transport: added tracerIdentity |
1774 |
- added new key indices to tamc.h |
1775 |
o external_fields_load: |
1776 |
- added this routine to TAF list |
1777 |
- needed to make some common blocks global and additional storing |
1778 |
along the same lines as exf package (checkpoint_lev?_directives.h) |
1779 |
o exf: |
1780 |
updated external forcing package |
1781 |
- bug fixes carried over from ecco-branch |
1782 |
(missing OBCS_OPTIONS.h in two routines) |
1783 |
- enable easy to use "no forcing". |
1784 |
- added exf I/O for atmospheric loading |
1785 |
- added exf I/O for runoff data |
1786 |
- transfered scaling between exf <-> MITgcm to exf namelist |
1787 |
o Adding new verification experiment global_with_exf. |
1788 |
This verification experiment is almost identical to the |
1789 |
global_ocean.90x40x15 experiment, except that it uses |
1790 |
the exf (and cal) package instead of the |
1791 |
external_fields_load routine (cf README file). |
1792 |
|
1793 |
checkpoint46m_post |
1794 |
o modified testscript to return -- when there are no lines of "%MON" output |
1795 |
o added new flag "quasiHydrostatic" for QH mode |
1796 |
and new routine quasihydrostaticterms() |
1797 |
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
1798 |
New routine: mom_u_coriolis_nh() |
1799 |
o fixed sign of non-hydrostatic metric terms in u and v equations. |
1800 |
Depend on correct sign of gravitySign. |
1801 |
o added work.pc* to .cvsignore in aim directories using ifc |
1802 |
o introduced flag for controllin non-hydrostatic metric terms |
1803 |
o removed gravitySign from PARM04 |
1804 |
o switched to g77/ifc from pgf77 in aim experiments |
1805 |
|
1806 |
checkpoint46l_post |
1807 |
o made convective adjustment work with pressure coordinates: |
1808 |
- changed the direction of k-loop in convective_adjustment.F for the |
1809 |
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
1810 |
- adjusted the reference pressure k-index in convective_adjustment.F |
1811 |
- adjusted the convection condition in convect.F (in analogy to |
1812 |
calc_ivdc.F) |
1813 |
- convective_adjustment no longer computes anything on the halos |
1814 |
- removed the warnings about negative salinity from find_rho.F and |
1815 |
find_alpha.F; instead the new routine look_for_neg_salinity, called |
1816 |
at the beginning of find_rho, find_alpha, and find_beta, does a |
1817 |
check of the entire slice, if CPP-option |
1818 |
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
1819 |
checkpoint46l_pre |
1820 |
|
1821 |
checkpoint46k_post |
1822 |
o fixed the verification/global_ocean.90x40x15 experiment: |
1823 |
- new bathymetry (the world according to A., JMC, and M.) |
1824 |
- new initial fields and forcing fields (*.bin files) |
1825 |
- new POLY3.COEFFS (for the next release one should switch to a full |
1826 |
equation of state: JMD95P or MDJWF) |
1827 |
- fixed several errors and redundancies in the data file |
1828 |
- experiment uses looped cells |
1829 |
- added matlab directory with diagnostic scripts for plotting of output |
1830 |
|
1831 |
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
1832 |
- read AIM physics parameters from a file (data.aimphys) |
1833 |
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
1834 |
|
1835 |
checkpoint46j_post |
1836 |
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
1837 |
o move wVel computation at the end of the time step, in S/R integr_continuity |
1838 |
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
1839 |
o update timeave pkg for wVel diagnostic. |
1840 |
checkpoint46j_pre |
1841 |
|
1842 |
checkpoint46i_post |
1843 |
o Clean up AIM package (and keep the results unchanged): |
1844 |
include CPP_OPTION and use IMPLICT NONE in all routines ; |
1845 |
declare all the variables _RL ; use _d 0 for all numerical constants. |
1846 |
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
1847 |
|
1848 |
checkpoint46h_post |
1849 |
o cleaned up the use of rhoNil and rhoConst. |
1850 |
- rhoNil should only appear in the LINEAR equation of state, everywhere |
1851 |
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
1852 |
and the dynamical equations are all divided by rhoConst |
1853 |
o introduced new parameter rhoConstFresh, a reference density of fresh |
1854 |
water, to remove the fresh water flux's dependence on rhoNil. The default |
1855 |
value is 999.8 kg/m^3 |
1856 |
o cleanup up external_forcing.F and external_forcing_surf.F |
1857 |
- can now be used by both OCEANIC and OCEANICP |
1858 |
checkpoint46h_pre |
1859 |
|
1860 |
Added code to convert surface volume flux (fresh water) into |
1861 |
a mass flux when using P coordinates in the ocean (OCEANICP). |
1862 |
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
1863 |
|
1864 |
checkpoint46g_post |
1865 |
o Include a new diagnostic variable phiHydLow for the ocean model |
1866 |
- in z-coordinates, it is the bottom pressure anomaly |
1867 |
- in p-coordinates, it is the sea surface elevation |
1868 |
- in both cases, these variable have global drift, reflecting the mass |
1869 |
drift in z-coordinates and the volume drift in p-coordinates |
1870 |
- included time averaging for phiHydLow, be aware of the drift! |
1871 |
o depth-dependent computation of Bo_surf for pressure coordinates |
1872 |
in the ocean (buoyancyRelation='OCEANICP') |
1873 |
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
1874 |
Theta, Salinity, and Pressure in the parameter list. This routine is |
1875 |
presently contained in find_rho.F. This routine does not give the |
1876 |
correct density for 'POLY3', which would be a z-dependent reference |
1877 |
density. |
1878 |
o cleaned up find_rho |
1879 |
- removed obsolete 'eqn' from the parameter list. |
1880 |
o added two new verification experiments: gop and goz |
1881 |
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
1882 |
checkpoint46g_pre |
1883 |
|
1884 |
checkpoint46f_post |
1885 |
o Enable tangent linear (forward mode) gradient checks: |
1886 |
- extended active file handling to g_... files |
1887 |
- added TANGENT_SIMULATION to theSimulationMode |
1888 |
- extended grdchk package accordingly |
1889 |
o added tangent linear setup in verification/carbon/code_ftl |
1890 |
o added adjoint setup in verification/front_relax/code_ad |
1891 |
|
1892 |
checkpoint46e_post |
1893 |
o Added new equation of state -> MDJWF |
1894 |
- EOS of McDougall et al., 2002, JAOT, submitted |
1895 |
- caveat: the equation of state is only valid for a smaller (more |
1896 |
realistic?) range of values than JMD95P/Z and UNESCO |
1897 |
- added masks to the calculation of pressure in store_pressure |
1898 |
- added more check values for density in check_eos (ini_eos.F), some of |
1899 |
the old check values are out of the range of the MDJWF-eos, so don't |
1900 |
expect perfect matches for those |
1901 |
checkpoint46e_pre |
1902 |
|
1903 |
checkpoint46d_post |
1904 |
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
1905 |
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
1906 |
case of pressure coordinates. eosType='JMD95Z' in |
1907 |
combination with buoyancyRelation='OCEANICP' now causes an error. |
1908 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1909 |
in find_alpha/beta. |
1910 |
checkpoint46d_pre |
1911 |
|
1912 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1913 |
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
1914 |
|
1915 |
checkpoint46c_post |
1916 |
o Changes necessary for ocean in p-coordinates |
1917 |
- Added new buoyancy relation = 'OCEANICP' |
1918 |
- Added new parameters = gravitySign (this used to be contained inside |
1919 |
the factor dRdZ which I added when we first switched to R coordinates). |
1920 |
X GM/Redi is not compatible (yet) |
1921 |
X bottom drag and no-slip need to be debugged. |
1922 |
checkpoint46c_pre |
1923 |
|
1924 |
checkpoint46b_post |
1925 |
o Added new equation of state -> JMD95Z and JMD95P |
1926 |
- EOS of Jackett and McDougall, 1995, JAOT |
1927 |
- moved all EOS parameters into EOS.h |
1928 |
- new routines ini_eos.F, store_pressure.F |
1929 |
o Added UNESCO EOS, but not recommended because it requires |
1930 |
in-situ temperature (see JMD95) |
1931 |
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
1932 |
unesco.f to be used with POLY3 |
1933 |
checkpoint46b_pre |
1934 |
|
1935 |
checkpoint46a_post |
1936 |
o Added (atmospheric) pressure loading |
1937 |
- new field in FFIELDS.h, etc... |
1938 |
- new cpp flag ATMOSPHERIC_LOADING |
1939 |
o Changed hFacC to _hFacC in calc_phi_hyd.F |
1940 |
o Added SHORTWAVE_HEATING to some files for consistency |
1941 |
checkpoint46a_pre |
1942 |
|
1943 |
checkpoint46 |
1944 |
further merges from release1_p5 |
1945 |
o new ctrl package |
1946 |
- adopted from ECCO environment to enable optimization |
1947 |
- added Eliassen Palm fluxes to controls |
1948 |
o added Eliassen Palm flux controls to gradient check package |
1949 |
o cost package |
1950 |
- Compatible with new ctrl package |
1951 |
- added Eliassen Palm cost hooks |
1952 |
- modif's of existing cost functions |
1953 |
o Adjoint-related bug fixes in kpp: |
1954 |
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
1955 |
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
1956 |
o autodiff package |
1957 |
- flow directives: |
1958 |
+ new for S/R do_the_model_io |
1959 |
+ enhanced for S/R checkpoint |
1960 |
+ new gmredi.flow |
1961 |
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
1962 |
disable adcommon.h/g_common.h by default. |
1963 |
- fixed problem for adjoint of global_max |
1964 |
o modified verification/carbon/ |
1965 |
o New setup for adjoint of global_ocean |
1966 |
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
1967 |
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
1968 |
o incorporated hooks for sponge layer code (external_forcing.F) |
1969 |
|
1970 |
checkpoint45d_post |
1971 |
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
1972 |
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
1973 |
(affects plume_on_slope "cg2d" output) |
1974 |
o add new parameter deltaTfreesurf for free-surface time stepping |
1975 |
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
1976 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
1977 |
o change phiMin in exp1 (to agree with documentation) |
1978 |
o add new flags: |
1979 |
- T,S forcing inside/outside Adams-Bashforth |
1980 |
- turn off temp,salt advection and/or forcing |
1981 |
- for each tracer, define internal flag for multiDimAdvection & A-B |
1982 |
o monitor: change definition of KE to check conservation of Energy |
1983 |
|
1984 |
checkpoint45c_post |
1985 |
o Removed f90 comments ("!") |
1986 |
o Modified initialisations to enable exf package for MITgcm |
1987 |
(without invoking ECCO_PACKAGE). |
1988 |
o modifications to gradient check package (Martin Losch) |
1989 |
- enable centered differences |
1990 |
- modified format of standard output |
1991 |
|
1992 |
checkpoint45b_post |
1993 |
o cleaned exchange calls in cg2d |
1994 |
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
1995 |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
1996 |
to configure barotropic setup (Martin Losch) |
1997 |
o moved some initialisations within bi,bj loop in dynamics |
1998 |
(TAF flow dependency) |
1999 |
o in initialise_varia, moved call packages_init_variables |
2000 |
before convective_adjustment_init |
2001 |
(corresponding adjustment of TAF tape initialisation). |
2002 |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
2003 |
|
2004 |
checkpoint45a_post |
2005 |
o compute Rho over the whole domain (extend iMin,jMin indices) |
2006 |
o specific exchange for X-slice domain (case Ny=1) |
2007 |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
2008 |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
2009 |
|
2010 |
checkpoint44h_post = checkpoint45 |
2011 |
o Fix to restore differentiability: |
2012 |
place at which packages_init_variables is called in |
2013 |
initialise_varia is crucial for reverse control flow. |
2014 |
o modifications in GMRedi to enable stable adjoint |
2015 |
(corresponding modif's in thermodynamics, dynamics) |
2016 |
o added missing hook for sponge layer code in external_forcing |
2017 |
o modified test cost functions |
2018 |
o storing in gad_advection (plus removal of write(0,*)! |
2019 |
o missing headers TR1.h added in convective_adjustment routines |
2020 |
o errorMessageUnit set non-equal zero in eeboot |
2021 |
(conflict on some platforms, e.g. IBM SP3) |
2022 |
o modified carbon verif. |
2023 |
|
2024 |
checkpoint44h_pre |
2025 |
o vertical grid option: allow to put the Interface at the middle between |
2026 |
2 cell-centers ; replace delZ in pkg/kpp by drF. |
2027 |
o GM Advective form: Tracers are advected using the residual transport (= |
2028 |
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
2029 |
|
2030 |
checkpoint44g_post |
2031 |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
2032 |
results) ; ifdef missing in thermodynamics.F |
2033 |
|
2034 |
checkpoint44f_pre,checkpoint44f_post |
2035 |
o added PTRACERS package |
2036 |
This allows an arbitrary number of passive tracers to be integrated |
2037 |
forward simultaneously with the dynamicaly model. |
2038 |
+ Implemented so far: |
2039 |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
2040 |
- I/O and checkpointing |
2041 |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
2042 |
+ Not implemented so far: |
2043 |
- KPP |
2044 |
- OBCS |
2045 |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
2046 |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
2047 |
line in data.pkg. |
2048 |
+ This package is disabled by default since it increases storage. |
2049 |
|
2050 |
|
2051 |
o testscript: added -cleanup option |
2052 |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
2053 |
b) enable to filter 2D fields. |
2054 |
|
2055 |
checkpoint44e_pre,post |
2056 |
o re-wrote convective adjustment to use pre-calculated weights |
2057 |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
2058 |
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
2059 |
Original calls to convect() still in place. |
2060 |
|
2061 |
chkpt44d_pre,post |
2062 |
o added missing EXCLUDE_MONITOR flags |
2063 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
2064 |
(incompatible typ in MIN/MAX expressions caused problems |
2065 |
on IBM SP3) |
2066 |
o in genmake added variable MAKEDEPEND |
2067 |
plus resetting for case SunOS |
2068 |
o added timer_stats.c routine for IBM SP3 |
2069 |
o removed variables in dynamics |
2070 |
!!! I forgot to create tag chkpt44d_pre !!! |
2071 |
!!! But chkpt44d_pre = chkpt44c_post !!! |
2072 |
|
2073 |
o real fresh water flux implemented with non-linear free-surface. |
2074 |
|
2075 |
chkpt44c_pre,post |
2076 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
2077 |
USE_NATURAL_BCS in solve_for_P); |
2078 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
2079 |
|
2080 |
checkpoint44b_pre/_post |
2081 |
o merge of relevant stuff from the ecco-branch: |
2082 |
- genmake: removed $S64 overwrite for case SunOS |
2083 |
- pkg/exf: update and corrections for field swapping and obcs |
2084 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
2085 |
harmonized between ECCO and MITgcm |
2086 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
2087 |
updated checkpointing_lev... lists for obcs |
2088 |
- model/src: minor changes in forward_step, plot_field |
2089 |
added directive for divided adjoint in the_main_loop |
2090 |
- pkg/mdsio: added mdsio_gl_slice |
2091 |
|
2092 |
o check parameters & config (chkpt44a_pre,post) |
2093 |
o OBC and NonLin_FrSurf. |
2094 |
|
2095 |
checkpoint44 |
2096 |
o fix bug in mom_vi_del2uv |
2097 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
2098 |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
2099 |
o update AIM experiments (NCEP input files) |
2100 |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
2101 |
o added some stuff for AD |
2102 |
|
2103 |
checkpoint43 |
2104 |
o added two new advection tests |
2105 |
o added global 4x4 degree ocean test |
2106 |
o added test of H&S94 with free surface on cube |
2107 |
o some final mods for gradient check, adjoint,... |
2108 |
|
2109 |
checkpoint42 |
2110 |
Fixed AD-related problems: |
2111 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
2112 |
(mainly thermodynamics.F) |
2113 |
o New store directives for multi-dim. advection schemes |
2114 |
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
2115 |
* new common block and key passkey |
2116 |
(mainly gad_advection.F) |
2117 |
o Modified store directives for split of dynamics/thermodynamics |
2118 |
for the case ALLOW_KPP |
2119 |
o Cleaned argument list for timestep_tracer.F |
2120 |
|
2121 |
checkpoint41 |
2122 |
o re-formatted/added comments in prologues of key subroutines |
2123 |
to work with protex |
2124 |
|
2125 |
checkpoint40 |
2126 |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
2127 |
o added FLT (floats) package from Arne along with demo. experiment |
2128 |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
2129 |
implementation of forward-in-time forcing terms |
2130 |
o more mods for non-linear free-surface including new variable |
2131 |
o modified multi-dim method to work on cube |
2132 |
o bug fix in KPP (from DM) |
2133 |
|
2134 |
checkpoint40pre9 |
2135 |
o added DST advection schemes |
2136 |
o fix MPI bug on SGI's |
2137 |
o modifications for non-linear free-surface |
2138 |
o fixed conditionals for fixed flow/passive tracer only mode |
2139 |
o added tension/strain form of stress tensor |
2140 |
o changes to commenting of arguments for TAF/TAMC |
2141 |
o added/updated many matlab scripts |
2142 |
o added multi-dimensional advection method for tracers |
2143 |
|
2144 |
checkpoint40pre8 |
2145 |
o new package rw/ |
2146 |
Added method for dumping intermediate local arrays: |
2147 |
mdsio_writetile - same as mdsio_writefield except works from inside |
2148 |
bi,bj loop |
2149 |
mdsio_writelocal - same as mdsio_writetile except works for local |
2150 |
arrays |
2151 |
write_local_r? - higher-level wrapper for mdsio_writelocal |
2152 |
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
2153 |
Example given at end of mom_vecinv.F that dumps some local arrays. |
2154 |
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
2155 |
control flux-form versus vector invariant code. |
2156 |
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
2157 |
or genmake -DISABLE ... |
2158 |
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
2159 |
(additional storing is now needed for case vecinv; |
2160 |
currently nothing implemented to switch this storing off |
2161 |
in case fluxform is used since no CPP flag available). |
2162 |
|
2163 |
checkpoint40pre7 |
2164 |
o bug fix in dynamics.F |
2165 |
calc_viscosity called before k=1,Nr loop. |
2166 |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
2167 |
o cleaned initialisations in ctrl_map_ini |
2168 |
related to TAF |
2169 |
|
2170 |
checkpoint40pre6 |
2171 |
o split dynamics into thermodynamics & dynamics |
2172 |
o corresponding split of calc_diffusivity into |
2173 |
calc_diffusivity, calc_viscosity |
2174 |
(kpp_calc_diff, kpp_calc_visc). |
2175 |
o Added diffkr, kapgm to control variables |
2176 |
o bug fix in gmredi_slope_limit for ldd97 |
2177 |
|
2178 |
checkpoint40pre5 |
2179 |
o proper initialization of Adams-Bashforth time stepping |
2180 |
+ uses forward step for very first step of model (iter=0) |
2181 |
o re-generated *all* output since almost all output is modified by this |
2182 |
change (sorry but we've been putting this one off for about 2 years) |
2183 |
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
2184 |
*not* regenerated since they are already out of date and I don't |
2185 |
want to create the impression that they are suddenly working. |
2186 |
o removed KAP stuff for DEC's |
2187 |
o modified/added many .cvsignore files in */code and */input |
2188 |
o added new expt "solid-body.cs-32x32x1" |
2189 |
+ this uses an alternative form of ini_curvilinear_grid.F which |
2190 |
is not necessarily any better than the current one... |
2191 |
|
2192 |
checkpoint40pre4 |
2193 |
o added re-initialisations of utrans,vtrans,rtrans in |
2194 |
calc_common_factors which are crucial for TAF. |
2195 |
o extended iMin,jMin range for calc_common_factors, |
2196 |
calc_diffusivity |
2197 |
o added option ALLOW_PASSIVE_TRACER |
2198 |
o a few minor updates and fixes |
2199 |
|
2200 |
checkpoint40pre3 |
2201 |
o created calc_gtr1.F for gad package |
2202 |
o split the_main_loop and re-introduced forward_step |
2203 |
o some recomputations of nIter0 for TAMC |
2204 |
|
2205 |
checkpoint40pre2 |
2206 |
o Updated to latest branch of AJA, JMC |
2207 |
o Added gradient check package |
2208 |
o Added routines for passive tracer handling |
2209 |
o Added carbon sequestration sensitivity experiment |
2210 |
|
2211 |
checkpoint39 |
2212 |
o Modifications and fixes to support TAMC |
2213 |
(mainly missing or wrong directives) |
2214 |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
2215 |
in addummy_in_stepping |
2216 |
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
2217 |
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
2218 |
o Included following packages: |
2219 |
cal: calendar |
2220 |
exf: external forcing |
2221 |
ecco: essential routines to control use of cal, exf |
2222 |
(NB: this is not the full ECCO environment) |
2223 |
o disabled some packages by default in genmake |
2224 |
|
2225 |
checkpoint38 |
2226 |
o see notes_c37_adj.txt |
2227 |
o corrected wrong layer index in external_forcing_t |
2228 |
o replaced the_main_loop/forward_step by the_main_loop |
2229 |
o removed forceoutput from write_state |
2230 |
(replaced criteria for initial/final state) |
2231 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
2232 |
|
2233 |
checkpoint37 |
2234 |
o mdsio.F routine split and packaged in pkg/mdsio |
2235 |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
2236 |
used unless genmake -disable=mdsio) |
2237 |
o allow a more precise surface-geopotential gradient for the atmosphere |
2238 |
taking into account the change in space of Alpha (=1/rho) at the surface. |
2239 |
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
2240 |
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
2241 |
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
2242 |
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
2243 |
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
2244 |
o Time-Average diagnostics defined as a pseudo package "timeave". |
2245 |
o pickup files : old pickup (before c35) did not work with new code (c35 |
2246 |
and after) unless activating 2 commented lines in initialise-varia. |
2247 |
o Non-Hydrostatic pickup file Pb fixed. |
2248 |
o bug with Rigid-lid version (since c35) fixed. |
2249 |
|
2250 |
checkpoint36 |
2251 |
o implement Crank-Nickelson barotropic time-stepping |
2252 |
o recover Time-Average diagnostics |
2253 |
o fix Pb in checkpoint (PR#19) |
2254 |
o AIM become a standard package ; clean unused CPP_kees |
2255 |
|
2256 |
checkpoint35 |
2257 |
o subtantial rewrite of dynamics.f |
2258 |
o allows staggered time-stepping |
2259 |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
2260 |
o added bottom drag (linear + quadratic) |
2261 |
|
2262 |
checkpoint34 |
2263 |
o Modified exchange routines for correct reverse simulation. |
2264 |
o Added verification output to comply with bug fix in impldiff.F |
2265 |
as of c33 (exp2, natl_box). |
2266 |
o Corrected store directives in dynamics.F |
2267 |
o Corrected array boundaries in impldiff.F |
2268 |
o Corrected array dimensions in gmredi. |
2269 |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
2270 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
2271 |
o Added mdsio_gl.F for ECCO purposes. |
2272 |
|
2273 |
checkpoint33 |
2274 |
o Fixed bug in lower BC in impldiff.F |
2275 |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
2276 |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
2277 |
- Removed verification/natl_box/code/external_fields_scale.F |
2278 |
(did not differ from that in model/src) |
2279 |
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
2280 |
(see FFIELDS.h for description) |
2281 |
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
2282 |
kpp_calc.F and kpp_transport_t.F |
2283 |
- Removed model/src/external_fields_scale.F and calls to it |
2284 |
- verification/natl_box uses flux data with "atmospheric" sign so |
2285 |
a special version of external_fields_load.F is used to |
2286 |
change the data as it's read in. This way, the arrays |
2287 |
have the right units and signs at all times tha a user could |
2288 |
possibly use them. |
2289 |
o Corrected genmake to delete a temporary file during configuration |
2290 |
|
2291 |
checkpoint32 |
2292 |
o Scaling of forcing fields moved from external_forcing.F to |
2293 |
external_fields_scale.F, called directly after loading fields. |
2294 |
o Surface relaxation terms added to surface tendency fields in |
2295 |
extra subroutine. |
2296 |
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
2297 |
fields. |
2298 |
o Changes in GMRedi to comply with packaging structure. |
2299 |
o Modifications and bug fixes in KPP package. |
2300 |
o Verification experiment for KPP added (verification/nat_box/) |
2301 |
|
2302 |
checkpoint31 |
2303 |
o Packages interface brought in line with defined standard |
2304 |
-> new routines packages_...F |
2305 |
-> changes in initialise_fixed.F, initialise_varia.F |
2306 |
-> enables initialisation interface for ECCO package |
2307 |
o Rescaling of external forcing fields immediately after read |
2308 |
(removed from external_forcing.F) |
2309 |
-> new: surface_fields_scale.F |
2310 |
-> affects ini_foorcing.F, external_fields_load.F |
2311 |
o Computation of surface tendencies before tendency updates. |
2312 |
-> new: external_forcing_surf.F |
2313 |
o Change of variable names useGMRedi, useKPP, useECCO |
2314 |
o Further changes in dynamics.F, impldiff.F for TAMC |
2315 |
o Tested for experiments 0, 2, 4. |
2316 |
- not yet tested for GMRedi. |
2317 |
- not yet tested for KPP. |
2318 |
|
2319 |
checkpoint30 |
2320 |
o Updates for OBCs |
2321 |
o New experiment for test OBCs (internal_wave) |
2322 |
o New output.txt in verification/exp4/results/ |
2323 |
o Updates for KPP: calculation of viscosity corrected, new variables |
2324 |
kpp_dumpFreq and kpp_taveFreq |
2325 |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
2326 |
and entry for T90 in genmake |
2327 |
|
2328 |
checkpoint29 |
2329 |
o packaged KPP and GM/Redi |
2330 |
|
2331 |
checkpoint28 |
2332 |
o Corrected initialization of hFacMin for difference vertical coordinates |
2333 |
o Modified calculation of partial cell thickness to more robust algorithm |
2334 |
o config_summary.F: replaced write_1D_... by write_0D_... |
2335 |
read_write.F: added subroutines write_0D_... |
2336 |
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
2337 |
included some initialisations required for TAMC. |
2338 |
o routine calc_isoslopes: modified sqrt computation to make it |
2339 |
differentiable for zero argument. |
2340 |
o routines dynamics, impldiff: |
2341 |
included store directives and tape key computations required for TAMC. |
2342 |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
2343 |
|
2344 |
checkpoint27 |
2345 |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
2346 |
formulation works properly with variable resolution. |
2347 |
o restructured the calling tree between the_model_main() and dynamics() |
2348 |
o split initialise() into initialise_fixed() and initialise_varia() |
2349 |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
2350 |
in new routine ini_psurf() |
2351 |
|
2352 |
checkpoint26 |
2353 |
o moved some #ifdef in optional routines to encompass everything |
2354 |
except the argument declarations. This was using up some memory. |
2355 |
o fixed macros like _ADT to work with both versions of Linux cpp |
2356 |
o cleaned up some unused and uninitialized variables |
2357 |
(helps when debugging with strict compile options) |
2358 |
o split up CPP_EEOPTIONS.h into options and macros |
2359 |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
2360 |
o patch for 2 processor JAM mode |
2361 |
|
2362 |
checkpoint25 |
2363 |
o updates for OBCs and NH |
2364 |
o dramatically reduced memory usage |
2365 |
o added "JAM" routines for use on Artic network |
2366 |
o parameterization of convection by implicit vertical diffusion |
2367 |
o added a diagnostic of convective index |
2368 |
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
2369 |
(this is was partly for OBCs and NH but also in anticipation of |
2370 |
an explicit free-surface option) |
2371 |
o initial state input files for U and V |
2372 |
|
2373 |
checkpoint24 |
2374 |
o Removed some spurious "REAL"s |
2375 |
o Updated KPP to latest version from JPL |
2376 |
o Added a COS(latitude) in horizontal viscosity |
2377 |
|
2378 |
checkpoint23 |
2379 |
o Added del^4 diffusion for salt and temperature |
2380 |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
2381 |
|
2382 |
checkpoint22 |
2383 |
o Made many small changes: implicit none, format(i5), etc... |
2384 |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
2385 |
|
2386 |
checkpoint21 |
2387 |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
2388 |
o Split-up mid-level I/O routines |
2389 |
o Updated input data for experiments 0,1,2,4 and 5 |
2390 |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
2391 |
|
2392 |
checkpoint20 |
2393 |
o Tidied up open-boundaries some more |
2394 |
o Added non-hydrostatic code |
2395 |
o Fixed some input data |
2396 |
o Modified MPI start-up to work in "coupled" context. |
2397 |
|
2398 |
checkpoint19 |
2399 |
o Tidied up directory structure for verification experiments. |
2400 |
o Added new code for open boundaries. |
2401 |
o Corrected advective terms near boundaries. |
2402 |
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
2403 |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
2404 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
2405 |
|
2406 |
checkpoint18 |
2407 |
o Further changes for optional code generation with |
2408 |
CPP - ugh! |
2409 |
|
2410 |
checkpoint17 |
2411 |
o Beginning to incorporating modularity |
2412 |
for supporting atmos. and ocean configs. |
2413 |
o Small changes for TAMC complinace |
2414 |
o New ultra simple test case. Barotropic box |
2415 |
configuration "exp0". |
2416 |
|
2417 |
checkpoint16 |
2418 |
o Minor changes to exchange routines to support |
2419 |
accumulation in reverse mode. Adjoint of an |
2420 |
assignment is an addition. |
2421 |
o Changes to support compilation by TAMC (LR(1) |
2422 |
syntax) and by g77 under Linux ( 72 character |
2423 |
limit ). |
2424 |
|
2425 |
checkpoint15 |
2426 |
Rewrote exchange routines to allow |
2427 |
o General tile <-> tile connectivity. |
2428 |
o TAMC reverse mode flag ( is this really needed? ) |
2429 |
o Variable width overlap and exchange region widths. |
2430 |
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
2431 |
shmput/shmget, VIA, SYSV shmem and every other cool |
2432 |
communication method. |
2433 |
|
2434 |
checkpoint14 |
2435 |
Consistent isomorphism chages made. These allow dynamical core |
2436 |
to support both pressure and meters as a vertical coordinate. |
2437 |
|
2438 |
checkpoint13 |
2439 |
Release which corrects global_max problem and a couple |
2440 |
of KGM time-averaging diagnostic errors. Also contains |
2441 |
a double-gyre experiment setup as well as the baseline |
2442 |
4 degree global template. The double gyre template is |
2443 |
organised to allow it to be applied automatically to |
2444 |
the baseline configuration. |
2445 |
|
2446 |
branch-point-rdot |
2447 |
A few tidy-ups have been made bt the real point of this |
2448 |
check-point (excuse the pun) is to allow a branch to be |
2449 |
made for the purposes of adding the rDot alterations. |
2450 |
I don't want to commit the rDot to the main-trunk until |
2451 |
we've actually tested it... |
2452 |
|
2453 |
checkpoint12 |
2454 |
Tidy up and added generic genmake script (formerly |
2455 |
configure script). |
2456 |
Released to testers. |
2457 |
|
2458 |
checkpoint11 |
2459 |
Re-arranged initialise() and introduced ini_vertical_grid() |
2460 |
and ini_masks_etc(). |
2461 |
|
2462 |
checkpoint10 |
2463 |
Introduced the configure script. |
2464 |
Separated out the diags package. |
2465 |
Added template for writing time-averages of tile/intermediate quantities. |
2466 |
Updated SIZE.h in exp2 and made the data big-endian. |
2467 |
|
2468 |
checkpoint9 |
2469 |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
2470 |
General tidy-up. |
2471 |
SST.bin SSS.bin added to verification/exp2 |
2472 |
|
2473 |
checkpoint8 |
2474 |
Inludes time-dependant forcing and time-averaging. |
2475 |
Works at 4x4 and 2.8125x2.8125 global |
2476 |
|
2477 |
checkpoint7-4degree-ref |
2478 |
Branch from checkpoint7. Released for application to |
2479 |
global modeling and general modeling - process studies, regional |
2480 |
model etc.. |
2481 |
Configured for verification/exp2 - 4 degree global, two process. |
2482 |
|
2483 |
checkpoint7 |
2484 |
Created by cnh |
2485 |
Simple 4 degree global simulation |
2486 |
configuration. |
2487 |
Includes climatological wind, |
2488 |
hydrography, bathymetry etc |
2489 |
Does not include Heat Flux and E-P |
2490 |
|
2491 |
checkpoint6 |
2492 |
Created by cnh |
2493 |
merged checkpoint5 with CD and |
2494 |
spherical polar code. |
2495 |
Still some problems with GM Redi |
2496 |
abd full topography. |
2497 |
|
2498 |
checkpoint5 |
2499 |
Created by AJA |
2500 |
contains updates to GM Redi |
2501 |
and reordered timestepping loop |
2502 |
for Implicit Diffusion. |
2503 |
|
2504 |
checkpoint4 |
2505 |
Created by cnh |
2506 |
Contains memory saving macros ( _rdxc etc..) for when |
2507 |
grid variations are limited. |
2508 |
Contains polynomial coeffs for EOS and knudsen program |
2509 |
for generation. |
2510 |
|
2511 |
checkpoint3 |
2512 |
Created by cnh |
2513 |
Added extra flags for runtime options |
2514 |
Added this file |
2515 |
Added implicit free-surface |
2516 |
Added pre-conditioner |
2517 |
Put compare01 into repository ( compare01/... ) |
2518 |
Put data and eedata into repository ( verification/exp1 ) |
2519 |
|
2520 |
checkpoint2 |
2521 |
Created by AJA |
2522 |
Added GM/Redi |
2523 |
|
2524 |
checkpoint1 |
2525 |
Created by AJA |
2526 |
Restructured kloop in dynamics.F |
2527 |
Added non-linear EOS |
2528 |
|
2529 |
baseline |
2530 |
Original checked in code |