3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
|
|
6 |
|
o OBCS: extend application of tracer open boundary conditions |
7 |
|
to a strip beyond the boundary of width Olx/Oly |
8 |
|
|
9 |
|
checkpoint56c_post |
10 |
|
o OBCS as control variables |
11 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
12 |
|
- remove balance of obcs controls from default |
13 |
|
- fix index bug nobcs in ctrl_init |
14 |
|
- fix dummy fields filen in ctrl_pack |
15 |
|
- add dummy weights for obcs |
16 |
|
o lsopt: comment out fort.94 output |
17 |
|
o optim: |
18 |
|
- remove unnecessary header files |
19 |
|
- adjusted namelists |
20 |
|
- add xerbla.F to Makefile |
21 |
|
o exf: |
22 |
|
- multiple modifications of exf_check_range |
23 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
24 |
|
o mdsio: |
25 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
26 |
|
|
27 |
|
checkpoint56b_post |
28 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
29 |
|
is called from DO_THE_MODEL_IO |
30 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
31 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
32 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
33 |
|
o add another verification experiment that tests both the cfc-pkg and |
34 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
35 |
|
reactive tendencies treated inline with regular timestepping |
36 |
|
o testreport previously did a lousy job of comparing small numbers, so |
37 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
38 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
39 |
|
testreport. |
40 |
|
o ptracers_monitor: bug fix for MPI |
41 |
|
|
42 |
|
checkpoint56a_post |
43 |
|
o GCHEM: finish reorganizating the package |
44 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
45 |
|
(introduces another 3D-array for each passive tracer, but only if |
46 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
47 |
|
gchemTendency is not needed because the timestep is done separately) |
48 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
49 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
50 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
51 |
|
so clear to me how that should be done in a general way. |
52 |
|
o CFC: improve formatting of output in CFC_ATMOS |
53 |
|
o PTRACERS: |
54 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
55 |
|
that ALL experiments with ptracers enable can be checked. This makes |
56 |
|
GCHEM_MONITOR obsolete. |
57 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
58 |
|
monitorFreq |
59 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
60 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
61 |
|
o exf_check_range: |
62 |
|
* default changed to .TRUE. |
63 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
64 |
|
* STOP in exf_check_range if 'out of range' |
65 |
|
* range chosen generous to allow for potential extema |
66 |
|
TBD: a version with stricter range |
67 |
|
permitted range would be runtime parameters |
68 |
|
o GMredi: |
69 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
70 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
71 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
72 |
|
o GCHEM: |
73 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
74 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
75 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
76 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
77 |
|
this flag is now only visible within GCHEM-pkg routines. |
78 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
79 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
80 |
|
this, the tracer ID iTracer had to be included into the parameter list |
81 |
|
of ptracers_forcing |
82 |
|
- set up forward_step to call gchem_forcing, that will replace |
83 |
|
gchem_forcing_int in ptracers_forcing |
84 |
|
- cleaning up |
85 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
86 |
|
|
87 |
|
checkpoint56 |
88 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
89 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
90 |
|
o ECCO-GODAE |
91 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
92 |
|
* fully merged and updated from SIO code |
93 |
|
windstress sign change affects |
94 |
|
- exf_inscal_[u/v]stress |
95 |
|
- sign of xx_tau[u/v] adjustments |
96 |
|
- signs in cost_scat |
97 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
98 |
|
* natl_box_adjoint updated and compressed |
99 |
|
* 2-level checkpoint switch added |
100 |
|
(tested in EXP. 1 of natl_box_adjoint) |
101 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
102 |
|
o SVD |
103 |
|
* first complete, non-hacked version for SVD calculations |
104 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
105 |
|
performed via direct access files admtlm_vector.it???? |
106 |
|
(via ctrl_[un]pack) |
107 |
|
* optimcycle is used for ARPACK iteration counter |
108 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
109 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
110 |
|
and add linear transforms where necessary |
111 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
112 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
113 |
|
o mdsio: filename info to both stderr, stdout |
114 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
115 |
|
from sign change |
116 |
|
|
117 |
|
checkpoint55j_post |
118 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
119 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
120 |
|
o add consistent build directories and .cvsignore files to verification |
121 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
122 |
|
o make all subroutines 30 or less characters in length for certain older |
123 |
|
compilers to work (a thorough search only turns up two routines in |
124 |
|
pkg/ptracers) |
125 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
126 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
127 |
|
|
128 |
|
checkpoint55i_post |
129 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
130 |
|
3.D if implicit) ; each ptracer uses its own background value. |
131 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
132 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
133 |
|
ITRDA and other clusters without the mpirun "-wd" option |
134 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
135 |
|
configuration |
136 |
|
o give MNC the ability to create additional files rather than |
137 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
138 |
|
- the default is just less than 2GB which is a practical limit |
139 |
|
on many systems |
140 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
141 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
142 |
|
|
143 |
|
checkpoint55h_post |
144 |
|
o add verification test "vermix" |
145 |
|
o remove all the *_ioinc flags and replace with the single global |
146 |
|
outputTypesInclusive flag |
147 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
148 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
149 |
|
o useMNC moved from data.mnc to data.pkg |
150 |
|
|
151 |
|
checkpoint55g_post |
152 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
153 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
154 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
155 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
156 |
|
Works well for global_ocean.90x40x15, |
157 |
|
but recomp. issue remains for carbon |
158 |
|
o Updating adjoint output for natl_box_adjoint after |
159 |
|
pkg/ecco has been modified (see taga c55d_post) |
160 |
|
|
161 |
|
checkpoint55f_post |
162 |
|
o rename to timeave_init_fixed |
163 |
|
|
164 |
|
checkpoint55e_post |
165 |
|
o some delicate re-shuffle of store directives to avoid one |
166 |
|
extra call of do_oceanic_physics |
167 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
168 |
|
checkpoint_lev1_directives.h |
169 |
|
o NB: this may break global_ocean adjoint temporarily, |
170 |
|
but it is clear how to fix it. Will do later, need this now. |
171 |
|
|
172 |
|
checkpoint55d_post |
173 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
174 |
|
o ecco_cost_weights is modified to 1x1 runs |
175 |
|
o modifs to allow observations to be read in as |
176 |
|
single file or yearly files |
177 |
|
o enable to read exf forcing fields as either |
178 |
|
single file or yearly files (flag useExfYearlyFields) |
179 |
|
checkpoint55d_pre |
180 |
|
|
181 |
|
o switch between 2-level and 3-level checkpointing |
182 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
183 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
184 |
|
with the correct (that is, the complete multi-dimensional) set of |
185 |
|
array indicies |
186 |
|
- used in mom_vecinv() to write the diagFreq output |
187 |
|
- tested (demonstrated) in verification/aim.5l_cs |
188 |
|
o further mnc-ification |
189 |
|
- add verification/lab_sea to the list with mnc setups |
190 |
|
- fix undefined mnc v-names in cd_code |
191 |
|
- add kpp to mnc output (both snapshot and timeave) |
192 |
|
o non-hydrostatic code |
193 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
194 |
|
in calc_gw.F |
195 |
|
- defaults to viscAh |
196 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
197 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
198 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
199 |
|
o pkg/cost |
200 |
|
extend simple cost functions to treat time mean quantities |
201 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
202 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
203 |
|
be 2 times larger than the minimum size the advection scheme requires. |
204 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
205 |
|
o GGL90 (Gaspar's TKE mixed layer) |
206 |
|
- add horizontal diffusion of TKE, requires exchanges in |
207 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
208 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
209 |
|
mixing coefficients are computed from a horizontal average of TKE of |
210 |
|
6 points or so. I think that diffusion has a little more physical |
211 |
|
justification. |
212 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
213 |
|
was in vain) |
214 |
|
- mask tke-variable in ggl90_init |
215 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
216 |
|
o fix biharmonic diffusion on CS-grid. |
217 |
|
o more obcs stuff |
218 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
219 |
|
for reading boundary values. This routine is called from |
220 |
|
obcs_prescribe_read |
221 |
|
- updated obcs_check |
222 |
|
- changed sponge layer relaxation parameter units for days to seconds |
223 |
|
- turned off sponge layer by default |
224 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
225 |
|
- fixed about 35 bugs in obcs_external_fields_load |
226 |
|
|
227 |
|
checkpoint55c_post |
228 |
|
o obcs stuff |
229 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
230 |
|
- re-arranged obcs_calc |
231 |
|
- moved exf_getobcs to obcs_prescibe_read |
232 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
233 |
|
and independent of it (executable can contain all). |
234 |
|
- updated obcs_check |
235 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
236 |
|
These may be necessary only if tangential velocities are |
237 |
|
prescribed at OB, not sure, needs testing. |
238 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
239 |
|
which simplifies the calls and passes the ifc check-bounds test |
240 |
|
|
241 |
|
checkpoint55b_post |
242 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
243 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
244 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
245 |
|
affects advect_cs results (for the wrong reason): update output.txt |
246 |
|
o use a more standard discretization for biharmonic viscosity ; |
247 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
248 |
|
affects results of dome set-up: update output.txt |
249 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
250 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
251 |
|
|
252 |
|
checkpoint55a_post |
253 |
|
o merged code to |
254 |
|
* prescribe/read time-dependent open boundaries |
255 |
|
(works in conjunction with exf, cal) |
256 |
|
* sponge layer code for open boundaries |
257 |
|
* each boundary N/S/E/W now has its own CPP option |
258 |
|
(healthy for the adjoint) |
259 |
|
|
260 |
|
checkpoint55 |
261 |
|
o up-to-date adjoint of previous breaks |
262 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
263 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
264 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
265 |
|
- carbon: * remove tr1-related adjoint verification |
266 |
|
* add ptracer as control variable |
267 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
268 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
269 |
|
|
270 |
|
checkpoint54f_post |
271 |
|
o in verification/carbin/ remove experiment related to |
272 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
273 |
|
code_ad/ input_ad/ results_ad |
274 |
|
|
275 |
|
o add two new packages |
276 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
277 |
|
+ subject to optimization (memory) |
278 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
279 |
|
+ subject to reordering (many GOTOs in the original code) |
280 |
|
+ so far opps is called for every (i,j) point, and then operates in |
281 |
|
the vertical; one may want to reorder the scheme in order operate in |
282 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
283 |
|
fields) |
284 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
285 |
|
- all verification tests compile and run with linux_ia32_g77 |
286 |
|
- defaults are compatible with current input files--nothing |
287 |
|
should change if you were not previously using MNC |
288 |
|
- MNC output has been added in numerous places (eg. timeave) |
289 |
|
but there are still a few writes not yet do-able with MNC |
290 |
|
(this is in progress) |
291 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
292 |
|
documentation will soon follow |
293 |
|
- numerous small formatting cleanups for ProTeX |
294 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
295 |
|
|
296 |
|
checkpoint54e_post |
297 |
|
o add two new packages |
298 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
299 |
|
stratification dependent mixing |
300 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
301 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
302 |
|
course), however there is only one diffusivity that is used for both |
303 |
|
temperature and salinity (and passive tracers)ç |
304 |
|
o add offline package |
305 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
306 |
|
provided by Stephanie Dutkiewicz |
307 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
308 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
309 |
|
|
310 |
|
checkpoint54d_post |
311 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
312 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
313 |
|
leading to additional shift by 5 days each year of integration |
314 |
|
(i.e. leading to considerable offset over the years) |
315 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
316 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
317 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
318 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
319 |
|
(external loading & cpl import/export stay in forward_step.F) |
320 |
|
o update coupling interface to work with new staggerTimeStep |
321 |
|
o change MDSIO ptracers_pickup. |
322 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
323 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
324 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
325 |
|
|
326 |
|
checkpoint54c_post |
327 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
328 |
|
this affects (truncation error) output.txt of test-exp: |
329 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
330 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
331 |
|
o change Qnet to always be the net heat flux, (+upward). |
332 |
|
affects (truncation error) output of natl_box exp.: updated |
333 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
334 |
|
o start to test mnc routinely in exp0 |
335 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
336 |
|
|
337 |
|
checkpoint54b_post |
338 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
339 |
|
impressive on Altix and Opteron systems) |
340 |
|
o diagnostics can now write NetCDF files through the mnc package |
341 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
342 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
343 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
344 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
345 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
346 |
|
|
347 |
|
checkpoint54a_post |
348 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
349 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
350 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
351 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
352 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
353 |
|
checkpoint54a_pre |
354 |
|
|
355 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
356 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
357 |
|
|
358 |
|
checkpoint54 |
359 |
|
checkpoint53g_post |
360 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
361 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
362 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
363 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
364 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
365 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
366 |
|
o restore adjointability |
367 |
|
|
368 |
|
checkpoint53f_post |
369 |
|
o modifications that affect AIM experiment results (update output.txt): |
370 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
371 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
372 |
|
o AIM pkg: |
373 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
374 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
375 |
|
|
376 |
|
checkpoint53e_post |
377 |
|
o merged cylindrical coord configuration |
378 |
|
o added rotating_tank experiment |
379 |
|
checkpoint53e_pre |
380 |
|
|
381 |
|
checkpoint53d_post |
382 |
|
o faulks upgraded: re-generate output.txt that have changed: |
383 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
384 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
385 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
386 |
|
o added Sadourny discretization of Coriolis |
387 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
388 |
|
- re-enabled use of omega3 (useAbsVorticity) |
389 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
390 |
|
vector-invariant equations |
391 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
392 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
393 |
|
hopefully without new bugs |
394 |
|
- still to do: biharmonic friction for non-hydrostatic w |
395 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
396 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
397 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
398 |
|
of mom_common/ |
399 |
|
- simple re-arrangement of instructions within computing loop |
400 |
|
checkpoint53d_pre |
401 |
|
|
402 |
|
checkpoint53c_post |
403 |
|
o new version of coupler for AIM+thSIce and Ocean models |
404 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
405 |
|
- land: change Evaporation of snow |
406 |
|
- aim with thSIce: fix bug in snow-precip. |
407 |
|
o changes to calc_gw.F |
408 |
|
- bug fix for w^2 term near the bottom boundary |
409 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
410 |
|
partial/looped cells |
411 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
412 |
|
and plume on slope), change the lateral boundary condition from half slip |
413 |
|
to the value of no_slip_sides |
414 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
415 |
|
o Adjoint of EBM package + verification |
416 |
|
* TLM OK |
417 |
|
* ADM not sufficient accuracy yet (needs further testing) |
418 |
|
|
419 |
|
checkpoint53b_post |
420 |
|
o Commiting new energy balance model to repository |
421 |
|
* package is pkg/ebm |
422 |
|
* verif. is verification/global_ocean_ebm |
423 |
|
* references are in ebm_driver.F |
424 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
425 |
|
C Global thermohaline circulation. Part I: |
426 |
|
C Sensitivity to atmospheric moisture transport. |
427 |
|
C J. Climate 12(1), 71-82 |
428 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
429 |
|
C Global thermohaline circulation. Part II: |
430 |
|
C Sensitivity with interactive transport. |
431 |
|
C J. Climate 12(1), 83-91 |
432 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
433 |
|
C Destabilization of the thermohaline circulation |
434 |
|
C by atmospheric eddy transports. |
435 |
|
C J. Climate 7(12), 1870-1882 |
436 |
|
o Will need long integration testing. |
437 |
|
checkpoint53b_pre |
438 |
|
|
439 |
|
o created pkg/mom_common in preparation for variable viscosity code |
440 |
|
o renamed and split ini_mnc_io |
441 |
|
o pkg/land: only liquid water can diffuse or run-off |
442 |
|
o AIM using land: soil wetness availability account for snow |
443 |
|
o added printMapIncludesZeros to EEPARMS namelist |
444 |
|
|
445 |
|
checkpoint53a_post |
446 |
|
o restore TAMC compatiility for exf_constants.h |
447 |
|
(no usage of _d in .h) |
448 |
|
o Additional storing in KPP in an attempt to fix |
449 |
|
TAMC problem with adjoint of KPP code. |
450 |
|
(no success...) |
451 |
|
Identical code works fine with TAF. |
452 |
|
o Fixed verification/natl_box_adjoint experiments. |
453 |
|
Initial conditions for Experiments 4 and 5 are now |
454 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
455 |
|
and hence gives results closer to that of Experiment 2. |
456 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
457 |
|
|
458 |
|
checkpoint53 |
459 |
|
o stable checkpoint with up to date adjoint |
460 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
461 |
|
this is a code problem or a problem with resetting code for g_ |
462 |
|
variables that is being autogenerated wrong. |
463 |
|
Otherwise: |
464 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
465 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
466 |
|
are both still in chaos following their security messes. |
467 |
|
|
468 |
|
checkpoint52n_post |
469 |
|
o various build (mostly genmake2) changes including: |
470 |
|
- ability to build/run more easily within Cygwin and MacOS X |
471 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
472 |
|
o pkg/seaice modifications |
473 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
474 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
475 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
476 |
|
- changed proxy for geostrophic velocity and updated |
477 |
|
verification/lab_sea/results/* accordingly |
478 |
|
- removed ADI dynamic solver from pkg/seaice |
479 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
480 |
|
they caused a segmentation fault under certain circumstances |
481 |
|
- removed unused field WATR |
482 |
|
o bug fix in exf-package: |
483 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
484 |
|
now reflect that. |
485 |
|
o small fixes in the cal-package: |
486 |
|
- set reference date to first of January for the 'model'-calendar |
487 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
488 |
|
warning |
489 |
|
o small modifications in exf-package to increase flexibility: |
490 |
|
- change climtempfreeze from a constant to a runtime parameter that |
491 |
|
is specified in data.exf_clim (default = -1.9) |
492 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
493 |
|
specified in data.exf |
494 |
|
o fix in pkg/thsice: |
495 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
496 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
497 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
498 |
|
|
499 |
|
checkpoint52m_post |
500 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
501 |
|
this does not change any of the results, because myIter=0 in swfrac always |
502 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
503 |
|
as a default |
504 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
505 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
506 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
507 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
508 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
509 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
510 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
511 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
512 |
|
o monitor package can write to NetCDF files and/or STDOUT |
513 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
514 |
|
o doc/api_reference added |
515 |
|
- a framework for building an API Reference Manual using all |
516 |
|
the "protex" comments embedded in the code |
517 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
518 |
|
o MNC: |
519 |
|
- make myThid the last argument for all subroutines |
520 |
|
- new default for the grid files: NO halos |
521 |
|
- add useMNC and other run-time flags |
522 |
|
- separate per-file-group handling of the unlimited dimension |
523 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
524 |
|
and lookup tables set in initialize_fixed |
525 |
|
- write all MNC output to a freshly-created directory |
526 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
527 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
528 |
|
o Added functionality to grdchk: |
529 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
530 |
|
|
531 |
|
checkpoint52l_post |
532 |
|
o new land formulation: |
533 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
534 |
|
energy conservation. |
535 |
|
b) account for water temperature and for latent heat of freezing |
536 |
|
in all processes (rain, run-off, ground storage) |
537 |
|
c) compute surface and ground temperature implicitly. |
538 |
|
o aim_v23 modification for new land model: |
539 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
540 |
|
to allow implicit computation of land & sea-ice surface temp. |
541 |
|
b) add snow precipitation. |
542 |
|
checkpoint52l_pre |
543 |
|
|
544 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
545 |
|
o fix bug in timeAve (u,vZetatave in common block) |
546 |
|
o no restoring terms under ice for pkg/seaice |
547 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
548 |
|
o bug fix for pkg/seaice pickups |
549 |
|
o change MNC call locations and add coordinate attributes |
550 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
551 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
552 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
553 |
|
o exf: Adding simple range check routine for exf fields after read |
554 |
|
|
555 |
|
checkpoint52k_post |
556 |
|
o removed top-level directory "diags" |
557 |
|
- we migrated these functions to pkg/timeave a long time ago |
558 |
|
o fixed bug introduced in pkg/monitor |
559 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
560 |
|
averaged fields (I/O via cost_averages) |
561 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
562 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
563 |
|
o added initial do_the_model_io to ecco |
564 |
|
o set all ...Freq to zero after cost_final |
565 |
|
taveFreq, dumpFreq, pChkptFreq |
566 |
|
o MAIN and ECCO differentiability restored |
567 |
|
|
568 |
|
checkpoint52j_post |
569 |
|
o fix nchklev in tamc.h for global_ocean... |
570 |
|
o Bringing flow and store directives up-to-date |
571 |
|
o Really weird thing! |
572 |
|
call do_the_model_io from the_main_loop with parameters |
573 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
574 |
|
TAF places a faulty re-call of initialise_varia |
575 |
|
after cost_final call which should not be there! |
576 |
|
checkpoint52j_pre |
577 |
|
|
578 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
579 |
|
error messages |
580 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
581 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
582 |
|
debug output |
583 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
584 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
585 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
586 |
|
o update AIM Equatorial Channel exp: |
587 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
588 |
|
o globalFile now works with exch2 |
589 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
590 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
591 |
|
o limit timeave output for hi-res integrations |
592 |
|
|
593 |
|
checkpoint52i_post |
594 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
595 |
|
o updated the tiling for global_ocean_pressure |
596 |
|
checkpoint52i_pre |
597 |
|
|
598 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
599 |
|
the old pkg/aim). |
600 |
|
|
601 |
|
checkpoint52h_pre |
602 |
|
o shortened offending lines in exch2_send_rx?.template |
603 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
604 |
|
o genmake2: add build & execute test for NetCDF code |
605 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
606 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
607 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
608 |
|
o added temporary hack for sea-ice dynamics on the cube: |
609 |
|
metric terms are ignored and it is assumed that |
610 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
611 |
|
|
612 |
|
checkpoint52f_post |
613 |
|
o added exch2 cube routines to pkg/exch2 |
614 |
|
o modified hs94.cs-32x32x5 to use it |
615 |
|
o added new grid files to hs94.cs-32x32x5 |
616 |
|
checkpoint52f_pre |
617 |
|
|
618 |
|
checkpoint52e_post |
619 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
620 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
621 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
622 |
|
to work with implicit vertical advection and AB ; |
623 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
624 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
625 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
626 |
|
checkpoint52e_pre |
627 |
|
|
628 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
629 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
630 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
631 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
632 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
633 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
634 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
635 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
636 |
|
|
637 |
|
checkpoint52d_post |
638 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
639 |
|
- updated output accordingly |
640 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
641 |
|
random number generator |
642 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
643 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
644 |
|
o changes to permit hi-res, cubed-sphere, configuration |
645 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
646 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
647 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
648 |
|
of surface winds for the cube |
649 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
650 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
651 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
652 |
|
complete with example surface forcing files and matlab scripts to look |
653 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
654 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
655 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
656 |
|
to conform to the common rule. |
657 |
|
o check-in the first version of the coupler + interfaces for multi-components |
658 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
659 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
660 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
661 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
662 |
|
- exchanges between component and coupler is done in forward_step |
663 |
|
o new verification experiment, cpl_aim+ocn: |
664 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
665 |
|
|
666 |
|
checkpoint52d_pre |
667 |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
668 |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
669 |
|
|