3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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|
6 |
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o mnc: cleanup "full" files--fixes out-of-memory problem |
7 |
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|
8 |
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checkpoint55j_post |
9 |
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o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
10 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
11 |
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o add consistent build directories and .cvsignore files to verification |
12 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
13 |
|
o make all subroutines 30 or less characters in length for certain older |
14 |
|
compilers to work (a thorough search only turns up two routines in |
15 |
|
pkg/ptracers) |
16 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
17 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
18 |
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|
19 |
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checkpoint55i_post |
20 |
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o change arrays for total vertical diffusivity (2.D if explicit, |
21 |
|
3.D if implicit) ; each ptracer uses its own background value. |
22 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
23 |
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- added bits to verification/cpl_aim+ocn so that it can run on |
24 |
|
ITRDA and other clusters without the mpirun "-wd" option |
25 |
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o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
26 |
|
configuration |
27 |
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o give MNC the ability to create additional files rather than |
28 |
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exceeding a specified file size limit "MNC_MAX_FILESIZE" |
29 |
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- the default is just less than 2GB which is a practical limit |
30 |
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on many systems |
31 |
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o Compute the non-local term using either KPP vertical diffusivity (=default) |
32 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
33 |
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|
34 |
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checkpoint55h_post |
35 |
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o add verification test "vermix" |
36 |
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o remove all the *_ioinc flags and replace with the single global |
37 |
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outputTypesInclusive flag |
38 |
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o allow to set a vertical profile of vertical diffusivity for T & S |
39 |
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o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
40 |
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o useMNC moved from data.mnc to data.pkg |
41 |
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|
42 |
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checkpoint55g_post |
43 |
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o Renaming carbon AD experiments to comply with testreport conventions |
44 |
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o Updating adjoint of Held-Suarez hs94.1x64x5 |
45 |
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o Fixing directives for non-ECCO forward_step, after ECCO directives |
46 |
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have been fixed to avoid recomp. of do_oceanic_phys |
47 |
|
Works well for global_ocean.90x40x15, |
48 |
|
but recomp. issue remains for carbon |
49 |
|
o Updating adjoint output for natl_box_adjoint after |
50 |
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pkg/ecco has been modified (see taga c55d_post) |
51 |
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|
52 |
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checkpoint55f_post |
53 |
|
o rename to timeave_init_fixed |
54 |
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|
55 |
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checkpoint55e_post |
56 |
|
o some delicate re-shuffle of store directives to avoid one |
57 |
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extra call of do_oceanic_physics |
58 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
59 |
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checkpoint_lev1_directives.h |
60 |
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o NB: this may break global_ocean adjoint temporarily, |
61 |
|
but it is clear how to fix it. Will do later, need this now. |
62 |
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|
63 |
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checkpoint55d_post |
64 |
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o ECCO specific cost function terms (up-to-date with 1x1 runs) |
65 |
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o ecco_cost_weights is modified to 1x1 runs |
66 |
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o modifs to allow observations to be read in as |
67 |
|
single file or yearly files |
68 |
|
o enable to read exf forcing fields as either |
69 |
|
single file or yearly files (flag useExfYearlyFields) |
70 |
|
checkpoint55d_pre |
71 |
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|
72 |
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o switch between 2-level and 3-level checkpointing |
73 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
74 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
75 |
|
with the correct (that is, the complete multi-dimensional) set of |
76 |
|
array indicies |
77 |
|
- used in mom_vecinv() to write the diagFreq output |
78 |
|
- tested (demonstrated) in verification/aim.5l_cs |
79 |
|
o further mnc-ification |
80 |
|
- add verification/lab_sea to the list with mnc setups |
81 |
|
- fix undefined mnc v-names in cd_code |
82 |
|
- add kpp to mnc output (both snapshot and timeave) |
83 |
|
o non-hydrostatic code |
84 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
85 |
|
in calc_gw.F |
86 |
|
- defaults to viscAh |
87 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
88 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
89 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
90 |
|
o pkg/cost |
91 |
|
extend simple cost functions to treat time mean quantities |
92 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
93 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
94 |
|
be 2 times larger than the minimum size the advection scheme requires. |
95 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
96 |
|
o GGL90 (Gaspar's TKE mixed layer) |
97 |
|
- add horizontal diffusion of TKE, requires exchanges in |
98 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
99 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
100 |
|
mixing coefficients are computed from a horizontal average of TKE of |
101 |
|
6 points or so. I think that diffusion has a little more physical |
102 |
|
justification. |
103 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
104 |
|
was in vain) |
105 |
|
- mask tke-variable in ggl90_init |
106 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
107 |
|
o fix biharmonic diffusion on CS-grid. |
108 |
|
o more obcs stuff |
109 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
110 |
|
for reading boundary values. This routine is called from |
111 |
|
obcs_prescribe_read |
112 |
|
- updated obcs_check |
113 |
|
- changed sponge layer relaxation parameter units for days to seconds |
114 |
|
- turned off sponge layer by default |
115 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
116 |
|
- fixed about 35 bugs in obcs_external_fields_load |
117 |
|
|
118 |
|
checkpoint55c_post |
119 |
|
o obcs stuff |
120 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
121 |
|
- re-arranged obcs_calc |
122 |
|
- moved exf_getobcs to obcs_prescibe_read |
123 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
124 |
|
and independent of it (executable can contain all). |
125 |
|
- updated obcs_check |
126 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
127 |
|
These may be necessary only if tangential velocities are |
128 |
|
prescribed at OB, not sure, needs testing. |
129 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
130 |
|
which simplifies the calls and passes the ifc check-bounds test |
131 |
|
|
132 |
|
checkpoint55b_post |
133 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
134 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
135 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
136 |
|
affects advect_cs results (for the wrong reason): update output.txt |
137 |
|
o use a more standard discretization for biharmonic viscosity ; |
138 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
139 |
|
affects results of dome set-up: update output.txt |
140 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
141 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
142 |
|
|
143 |
|
checkpoint55a_post |
144 |
|
o merged code to |
145 |
|
* prescribe/read time-dependent open boundaries |
146 |
|
(works in conjunction with exf, cal) |
147 |
|
* sponge layer code for open boundaries |
148 |
|
* each boundary N/S/E/W now has its own CPP option |
149 |
|
(healthy for the adjoint) |
150 |
|
|
151 |
|
checkpoint55 |
152 |
|
o up-to-date adjoint of previous breaks |
153 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
154 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
155 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
156 |
|
- carbon: * remove tr1-related adjoint verification |
157 |
|
* add ptracer as control variable |
158 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
159 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
160 |
|
|
161 |
|
checkpoint54f_post |
162 |
|
o in verification/carbin/ remove experiment related to |
163 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
164 |
|
code_ad/ input_ad/ results_ad |
165 |
|
|
166 |
|
o add two new packages |
167 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
168 |
|
+ subject to optimization (memory) |
169 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
170 |
|
+ subject to reordering (many GOTOs in the original code) |
171 |
|
+ so far opps is called for every (i,j) point, and then operates in |
172 |
|
the vertical; one may want to reorder the scheme in order operate in |
173 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
174 |
|
fields) |
175 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
176 |
|
- all verification tests compile and run with linux_ia32_g77 |
177 |
|
- defaults are compatible with current input files--nothing |
178 |
|
should change if you were not previously using MNC |
179 |
|
- MNC output has been added in numerous places (eg. timeave) |
180 |
|
but there are still a few writes not yet do-able with MNC |
181 |
|
(this is in progress) |
182 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
183 |
|
documentation will soon follow |
184 |
|
- numerous small formatting cleanups for ProTeX |
185 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
186 |
|
|
187 |
|
checkpoint54e_post |
188 |
|
o add two new packages |
189 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
190 |
|
stratification dependent mixing |
191 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
192 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
193 |
|
course), however there is only one diffusivity that is used for both |
194 |
|
temperature and salinity (and passive tracers)ç |
195 |
|
o add offline package |
196 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
197 |
|
provided by Stephanie Dutkiewicz |
198 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
199 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
200 |
|
|
201 |
|
checkpoint54d_post |
202 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
203 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
204 |
|
leading to additional shift by 5 days each year of integration |
205 |
|
(i.e. leading to considerable offset over the years) |
206 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
207 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
208 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
209 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
210 |
|
(external loading & cpl import/export stay in forward_step.F) |
211 |
|
o update coupling interface to work with new staggerTimeStep |
212 |
|
o change MDSIO ptracers_pickup. |
213 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
214 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
215 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
216 |
|
|
217 |
|
checkpoint54c_post |
218 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
219 |
|
this affects (truncation error) output.txt of test-exp: |
220 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
221 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
222 |
|
o change Qnet to always be the net heat flux, (+upward). |
223 |
|
affects (truncation error) output of natl_box exp.: updated |
224 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
225 |
|
o start to test mnc routinely in exp0 |
226 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
227 |
|
|
228 |
|
checkpoint54b_post |
229 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
230 |
|
impressive on Altix and Opteron systems) |
231 |
|
o diagnostics can now write NetCDF files through the mnc package |
232 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
233 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
234 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
235 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
236 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
237 |
|
|
238 |
|
checkpoint54a_post |
239 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
240 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
241 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
242 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
243 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
244 |
|
checkpoint54a_pre |
245 |
|
|
246 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
247 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
248 |
|
|
249 |
|
checkpoint54 |
250 |
|
checkpoint53g_post |
251 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
252 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
253 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
254 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
255 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
256 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
257 |
|
o restore adjointability |
258 |
|
|
259 |
|
checkpoint53f_post |
260 |
|
o modifications that affect AIM experiment results (update output.txt): |
261 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
262 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
263 |
|
o AIM pkg: |
264 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
265 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
266 |
|
|
267 |
|
checkpoint53e_post |
268 |
|
o merged cylindrical coord configuration |
269 |
|
o added rotating_tank experiment |
270 |
|
checkpoint53e_pre |
271 |
|
|
272 |
|
checkpoint53d_post |
273 |
|
o faulks upgraded: re-generate output.txt that have changed: |
274 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
275 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
276 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
277 |
|
o added Sadourny discretization of Coriolis |
278 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
279 |
|
- re-enabled use of omega3 (useAbsVorticity) |
280 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
281 |
|
vector-invariant equations |
282 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
283 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
284 |
|
hopefully without new bugs |
285 |
|
- still to do: biharmonic friction for non-hydrostatic w |
286 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
287 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
288 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
289 |
|
of mom_common/ |
290 |
|
- simple re-arrangement of instructions within computing loop |
291 |
|
checkpoint53d_pre |
292 |
|
|
293 |
|
checkpoint53c_post |
294 |
|
o new version of coupler for AIM+thSIce and Ocean models |
295 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
296 |
|
- land: change Evaporation of snow |
297 |
|
- aim with thSIce: fix bug in snow-precip. |
298 |
|
o changes to calc_gw.F |
299 |
|
- bug fix for w^2 term near the bottom boundary |
300 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
301 |
|
partial/looped cells |
302 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
303 |
|
and plume on slope), change the lateral boundary condition from half slip |
304 |
|
to the value of no_slip_sides |
305 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
306 |
|
o Adjoint of EBM package + verification |
307 |
|
* TLM OK |
308 |
|
* ADM not sufficient accuracy yet (needs further testing) |
309 |
|
|
310 |
|
checkpoint53b_post |
311 |
|
o Commiting new energy balance model to repository |
312 |
|
* package is pkg/ebm |
313 |
|
* verif. is verification/global_ocean_ebm |
314 |
|
* references are in ebm_driver.F |
315 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
316 |
|
C Global thermohaline circulation. Part I: |
317 |
|
C Sensitivity to atmospheric moisture transport. |
318 |
|
C J. Climate 12(1), 71-82 |
319 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
320 |
|
C Global thermohaline circulation. Part II: |
321 |
|
C Sensitivity with interactive transport. |
322 |
|
C J. Climate 12(1), 83-91 |
323 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
324 |
|
C Destabilization of the thermohaline circulation |
325 |
|
C by atmospheric eddy transports. |
326 |
|
C J. Climate 7(12), 1870-1882 |
327 |
|
o Will need long integration testing. |
328 |
|
checkpoint53b_pre |
329 |
|
|
330 |
|
o created pkg/mom_common in preparation for variable viscosity code |
331 |
|
o renamed and split ini_mnc_io |
332 |
|
o pkg/land: only liquid water can diffuse or run-off |
333 |
|
o AIM using land: soil wetness availability account for snow |
334 |
|
o added printMapIncludesZeros to EEPARMS namelist |
335 |
|
|
336 |
|
checkpoint53a_post |
337 |
|
o restore TAMC compatiility for exf_constants.h |
338 |
|
(no usage of _d in .h) |
339 |
|
o Additional storing in KPP in an attempt to fix |
340 |
|
TAMC problem with adjoint of KPP code. |
341 |
|
(no success...) |
342 |
|
Identical code works fine with TAF. |
343 |
|
o Fixed verification/natl_box_adjoint experiments. |
344 |
|
Initial conditions for Experiments 4 and 5 are now |
345 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
346 |
|
and hence gives results closer to that of Experiment 2. |
347 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
348 |
|
|
349 |
|
checkpoint53 |
350 |
|
o stable checkpoint with up to date adjoint |
351 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
352 |
|
this is a code problem or a problem with resetting code for g_ |
353 |
|
variables that is being autogenerated wrong. |
354 |
|
Otherwise: |
355 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
356 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
357 |
|
are both still in chaos following their security messes. |
358 |
|
|
359 |
|
checkpoint52n_post |
360 |
|
o various build (mostly genmake2) changes including: |
361 |
|
- ability to build/run more easily within Cygwin and MacOS X |
362 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
363 |
|
o pkg/seaice modifications |
364 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
365 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
366 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
367 |
|
- changed proxy for geostrophic velocity and updated |
368 |
|
verification/lab_sea/results/* accordingly |
369 |
|
- removed ADI dynamic solver from pkg/seaice |
370 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
371 |
|
they caused a segmentation fault under certain circumstances |
372 |
|
- removed unused field WATR |
373 |
|
o bug fix in exf-package: |
374 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
375 |
|
now reflect that. |
376 |
|
o small fixes in the cal-package: |
377 |
|
- set reference date to first of January for the 'model'-calendar |
378 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
379 |
|
warning |
380 |
|
o small modifications in exf-package to increase flexibility: |
381 |
|
- change climtempfreeze from a constant to a runtime parameter that |
382 |
|
is specified in data.exf_clim (default = -1.9) |
383 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
384 |
|
specified in data.exf |
385 |
|
o fix in pkg/thsice: |
386 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
387 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
388 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
389 |
|
|
390 |
|
checkpoint52m_post |
391 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
392 |
|
this does not change any of the results, because myIter=0 in swfrac always |
393 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
394 |
|
as a default |
395 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
396 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
397 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
398 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
399 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
400 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
401 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
402 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
403 |
|
o monitor package can write to NetCDF files and/or STDOUT |
404 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
405 |
|
o doc/api_reference added |
406 |
|
- a framework for building an API Reference Manual using all |
407 |
|
the "protex" comments embedded in the code |
408 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
409 |
|
o MNC: |
410 |
|
- make myThid the last argument for all subroutines |
411 |
|
- new default for the grid files: NO halos |
412 |
|
- add useMNC and other run-time flags |
413 |
|
- separate per-file-group handling of the unlimited dimension |
414 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
415 |
|
and lookup tables set in initialize_fixed |
416 |
|
- write all MNC output to a freshly-created directory |
417 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
418 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
419 |
|
o Added functionality to grdchk: |
420 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
421 |
|
|
422 |
|
checkpoint52l_post |
423 |
|
o new land formulation: |
424 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
425 |
|
energy conservation. |
426 |
|
b) account for water temperature and for latent heat of freezing |
427 |
|
in all processes (rain, run-off, ground storage) |
428 |
|
c) compute surface and ground temperature implicitly. |
429 |
|
o aim_v23 modification for new land model: |
430 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
431 |
|
to allow implicit computation of land & sea-ice surface temp. |
432 |
|
b) add snow precipitation. |
433 |
|
checkpoint52l_pre |
434 |
|
|
435 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
436 |
|
o fix bug in timeAve (u,vZetatave in common block) |
437 |
|
o no restoring terms under ice for pkg/seaice |
438 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
439 |
|
o bug fix for pkg/seaice pickups |
440 |
|
o change MNC call locations and add coordinate attributes |
441 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
442 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
443 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
444 |
|
o exf: Adding simple range check routine for exf fields after read |
445 |
|
|
446 |
|
checkpoint52k_post |
447 |
|
o removed top-level directory "diags" |
448 |
|
- we migrated these functions to pkg/timeave a long time ago |
449 |
|
o fixed bug introduced in pkg/monitor |
450 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
451 |
|
averaged fields (I/O via cost_averages) |
452 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
453 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
454 |
|
o added initial do_the_model_io to ecco |
455 |
|
o set all ...Freq to zero after cost_final |
456 |
|
taveFreq, dumpFreq, pChkptFreq |
457 |
|
o MAIN and ECCO differentiability restored |
458 |
|
|
459 |
|
checkpoint52j_post |
460 |
|
o fix nchklev in tamc.h for global_ocean... |
461 |
|
o Bringing flow and store directives up-to-date |
462 |
|
o Really weird thing! |
463 |
|
call do_the_model_io from the_main_loop with parameters |
464 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
465 |
|
TAF places a faulty re-call of initialise_varia |
466 |
|
after cost_final call which should not be there! |
467 |
|
checkpoint52j_pre |
468 |
|
|
469 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
470 |
|
error messages |
471 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
472 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
473 |
|
debug output |
474 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
475 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
476 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
477 |
|
o update AIM Equatorial Channel exp: |
478 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
479 |
|
o globalFile now works with exch2 |
480 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
481 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
482 |
|
o limit timeave output for hi-res integrations |
483 |
|
|
484 |
|
checkpoint52i_post |
485 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
486 |
|
o updated the tiling for global_ocean_pressure |
487 |
|
checkpoint52i_pre |
488 |
|
|
489 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
490 |
|
the old pkg/aim). |
491 |
|
|
492 |
|
checkpoint52h_pre |
493 |
|
o shortened offending lines in exch2_send_rx?.template |
494 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
495 |
|
o genmake2: add build & execute test for NetCDF code |
496 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
497 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
498 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
499 |
|
o added temporary hack for sea-ice dynamics on the cube: |
500 |
|
metric terms are ignored and it is assumed that |
501 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
502 |
|
|
503 |
|
checkpoint52f_post |
504 |
|
o added exch2 cube routines to pkg/exch2 |
505 |
|
o modified hs94.cs-32x32x5 to use it |
506 |
|
o added new grid files to hs94.cs-32x32x5 |
507 |
|
checkpoint52f_pre |
508 |
|
|
509 |
|
checkpoint52e_post |
510 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
511 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
512 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
513 |
|
to work with implicit vertical advection and AB ; |
514 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
515 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
516 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
517 |
|
checkpoint52e_pre |
518 |
|
|
519 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
520 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
521 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
522 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
523 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
524 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
525 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
526 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
527 |
|
|
528 |
|
checkpoint52d_post |
529 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
530 |
|
- updated output accordingly |
531 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
532 |
|
random number generator |
533 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
534 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
535 |
|
o changes to permit hi-res, cubed-sphere, configuration |
536 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
537 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
538 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
539 |
|
of surface winds for the cube |
540 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
541 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
542 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
543 |
|
complete with example surface forcing files and matlab scripts to look |
544 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
545 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
546 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
547 |
|
to conform to the common rule. |
548 |
|
o check-in the first version of the coupler + interfaces for multi-components |
549 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
550 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
551 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
552 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
553 |
|
- exchanges between component and coupler is done in forward_step |
554 |
|
o new verification experiment, cpl_aim+ocn: |
555 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
556 |
|
|
557 |
|
checkpoint52d_pre |
558 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
559 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
560 |
|
|
561 |
|
checkpoint52c_post |
562 |
|
o Fixing OPTIONS files for use of exf: |
563 |
|
- ALLOW_ECCO not needed |
564 |
|
- ECCO_CPPOPTIONS.h should not be included from |
565 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
566 |
|
as has been the case in the past |
567 |
|
- All cal/exf related options are currently set in |
568 |
|
single header file. Should remain so until we |
569 |
|
agree on a consistent new policy. |
570 |
|
o Removed all CPP options for cal package. |
571 |
|
cal has no more CPP options. |
572 |
|
o modified STOREs in GAD_ADVECTION |
573 |
|
o corrected key comp. for passkey |
574 |
|
|
575 |
|
checkpoint52b_post |
576 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
577 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
578 |
|
- modify fluxes but do not change theta directly; |
579 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
580 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
581 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
582 |
|
o put back grid & coriolis monitor output. |
583 |
|
checkpoint52b_pre |
584 |
|
|
585 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
586 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
587 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
588 |
|
(need info on NUMBER_OF_PTRACERS) |
589 |
|
o missing PTRACERS headers in some routines |
590 |
|
o default tamc.h in pkg/autodiff supposed to crash |
591 |
|
to ensure proper customization |
592 |
|
|
593 |
|
checkpoint52a_post |
594 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
595 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
596 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
597 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
598 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
599 |
|
- keep the old version of FREEZE for backward compatibility; |
600 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
601 |
|
- corresponding modifs for TAF directives |
602 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
603 |
|
o time-averaged output for pkg/ptracers |
604 |
|
o fix problem with ECCO-related divided adjoint |
605 |
|
snapshot file was missing some ad-variables, |
606 |
|
but no warning issued by TAF |
607 |
|
|
608 |
|
checkpoint52a_pre |
609 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
610 |
|
|
611 |
|
checkpoint52 = ecco_c52_e35 |
612 |
|
o after testing adjoints of checkpoint51u_post |
613 |
|
|
614 |
|
checkpoint51u_post |
615 |
|
o this is the post-merge tag of the ecco-branch |
616 |
|
(needs another clean checkout and re-testing) |
617 |
|
o various natl_box_adjoint configs and results |
618 |
|
but no input fields |
619 |
|
o obcs adjoint not yet merged! |
620 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
621 |
|
o updated/extended some store directives for seaice |
622 |
|
o pkg/ecco now containes ecco-specific part of cost function |
623 |
|
o top level routines the_main_loop, forward_step |
624 |
|
supersede those in model/src/ |
625 |
|
previous input data.cost now in data.ecco |
626 |
|
(new namelist ecco_cost_nml) |
627 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
628 |
|
|
629 |
|
checkpoint51t_post |
630 |
|
o this is the pre-merge tag of the ecco-branch |
631 |
|
|
632 |
|
checkpoint51s_post |
633 |
|
o cleanup: removed various obsolete #define-s |
634 |
|
o pkg/grdchk |
635 |
|
- renamed 'ph-grd 3' to 'grad-res' |
636 |
|
- merged from ecco-branch |
637 |
|
(remaining bug fixes for obcs gradient checks) |
638 |
|
- additional high-precision output for testreport |
639 |
|
(grep for 'precision_grdchk_result') |
640 |
|
|
641 |
|
checkpoint51r_post |
642 |
|
o cleaned up or removed CPP_OPTIONS.h files |
643 |
|
o updated results for some of the tests to reflect the new |
644 |
|
optfiles (-ieee: -O0 instead of -O3) |
645 |
|
|
646 |
|
checkpoint51q_post |
647 |
|
o cd_code: |
648 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
649 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
650 |
|
- separated cd_code part from write_checkpoint |
651 |
|
- updated AD_SOURCE, generated .flow |
652 |
|
- added CD_CODE_VARS.h to the_main_loop |
653 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
654 |
|
o ctrl package totally restructured |
655 |
|
- pack/unpack now optional and decoupled from |
656 |
|
xx_/adxx_ I/O |
657 |
|
- ctrl_pack/unpack cleaned |
658 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
659 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
660 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
661 |
|
|
662 |
|
checkpoint51p_post |
663 |
|
o create initial cd_code package |
664 |
|
- WARNING: the initialization of fields within packages |
665 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
666 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
667 |
|
This seems to be backwards since |
668 |
|
1) its important to initially zero the entire field including |
669 |
|
the "halo" region |
670 |
|
2) zeroing needs to be done *before* reading pickup info |
671 |
|
and the pickup call might or might not happen in any |
672 |
|
particular run |
673 |
|
- this needs an overhaul for R2 |
674 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
675 |
|
o cleanup testreport |
676 |
|
|
677 |
|
checkpoint51o_post |
678 |
|
o bringing AD-related verif's up to date with genmake2 |
679 |
|
- carbon/ |
680 |
|
- global_ocean.90x40x15/ |
681 |
|
- hs.94.1x64x5/ |
682 |
|
- (front_relax/ ) |
683 |
|
o (more) consistent directory structure for AD-related verif.'s |
684 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
685 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
686 |
|
o bug fix in find_alpha.F for MDJWF: |
687 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
688 |
|
change rho -> rho-rhoConst |
689 |
|
- replace call find_rho to find_rhonum |
690 |
|
o initialisation of rFlx extended to full array (required by TAF) |
691 |
|
and shifted to thermodynamics |
692 |
|
o removed PTRACERS.h in ptracers routine |
693 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
694 |
|
o Correcting initialisations for fVerU, fVerV. |
695 |
|
o helping TAF to recognize dependency on kUp for |
696 |
|
fVerU, fVerV |
697 |
|
o Replacing delZ by delR in pkg/ctrl/ |
698 |
|
checkpoint51o_pre |
699 |
|
|
700 |
|
o undid all of cp51 pending some cleanups and discussion |
701 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
702 |
|
it for adjoint/tl #defines |
703 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
704 |
|
o removed tools/genmake since it no longer works |
705 |
|
|
706 |
|
checkpoint51n_post |
707 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
708 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
709 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
710 |
|
- subroutine FREEZE now limits only surface temperature |
711 |
|
(this means new output.txt for global_ocean.90x40x15, |
712 |
|
global_ocean.cs32x15, and global_with_exf) |
713 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
714 |
|
|
715 |
|
checkpoint51n_pre |
716 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
717 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
718 |
|
defines: |
719 |
|
- ALLOW_ADJOINT_RUN |
720 |
|
- ALLOW_TANGENTLINEAR_RUN |
721 |
|
- ALLOW_ECCO_OPTIMIZATION |
722 |
|
|
723 |
|
checkpoint51m_post |
724 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
725 |
|
- added new TAMC/TAF targets to the Makefile |
726 |
|
- various cleanups related to package handling |
727 |
|
- these changes should have no impact on the forward model |
728 |
|
|
729 |
|
checkpoint51l_post |
730 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
731 |
|
- faster algorithm for cal_addtime.F |
732 |
|
- higher precision arithmetic, where needed |
733 |
|
- pkg/exf *startdate variables changed from calendar date to |
734 |
|
model integration time |
735 |
|
|
736 |
|
checkpoint51l_pre |
737 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
738 |
|
o enable to apply restoring on S & T only in a latitude band. |
739 |
|
o update output (external_forcing_surf modif. change truncation errors) |
740 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
741 |
|
|
742 |
|
checkpoint51k_post |
743 |
|
o change default to: useNHMTerms=.FALSE. |
744 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
745 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
746 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
747 |
|
exp1, ideal_2D_oce |
748 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
749 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
750 |
|
o set gravitySign automatically according to the vertical coordinate used |
751 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
752 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
753 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
754 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
755 |
|
|
756 |
|
checkpoint51j_post |
757 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
758 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
759 |
|
o added cubed-sphere case to test cost function |
760 |
|
o heckpoint_lev?_directives.h now include |
761 |
|
pkg-specific directives, whenever those are enabled. |
762 |
|
o Moving pkg-specific flow directives to corresponding pkg |
763 |
|
Moving pkg-specific differentiation list to corresponding pkg |
764 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
765 |
|
---> conventions are |
766 |
|
- pkg_ad.flow |
767 |
|
- pkg_ad_diff.list |
768 |
|
- pkg_ad_check_lev?_dir.h |
769 |
|
|
770 |
|
checkpoint51i_post |
771 |
|
o merge of the branch-genmake2 |
772 |
|
- knowingly breaks the older genmake |
773 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
774 |
|
- new testreport supersedes older testscript |
775 |
|
o large number of package inclusion and header cleanups |
776 |
|
checkpoint51i_pre |
777 |
|
|
778 |
|
o new output for adjoin of global ocean vector invariant |
779 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
780 |
|
o Steph gchem various cleanups |
781 |
|
|
782 |
|
checkpoint 51h_pre |
783 |
|
o fixed some single quotes |
784 |
|
o modify gchem pkg to be more versatile |
785 |
|
o modifications to clean up dic pkg |
786 |
|
o add pkg/cfc |
787 |
|
|
788 |
|
checkpoint51g_post |
789 |
|
o provide links for ARPACK and ADM*TLM |
790 |
|
o start removing verification/vero/ |
791 |
|
o update AD-related stuff |
792 |
|
(in particular some IF-statements in model/src/ routines) |
793 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
794 |
|
vector invariant setup |
795 |
|
|
796 |
|
checkpoint51f_post |
797 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
798 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
799 |
|
of tracer Green's fucntions for ocean inversion project. |
800 |
|
|
801 |
|
checkpoint51f_pre |
802 |
|
o Added on-the-fly spatial interpolation capability |
803 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
804 |
|
- This is a temporary Cartesian-grid hack until |
805 |
|
the super-duper ESMF coupler becomes available. |
806 |
|
- See verification/global_with_exf/README for usage example. |
807 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
808 |
|
flags and modified pkg/seaice accordingly. |
809 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
810 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
811 |
|
non-local transport term. |
812 |
|
|
813 |
|
checkpoint51e_post |
814 |
|
o pkg/mom_vecinv: |
815 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
816 |
|
- add time-ave diagnostic of vorticity advection. |
817 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
818 |
|
o atmospheric geopotential: - include water vapor effect; |
819 |
|
- use p^kappa in p* scaling. |
820 |
|
o land pkg: read initial state from files. |
821 |
|
o AIM : add stratospheric drag in the upper level |
822 |
|
|
823 |
|
checkpoint51d_post |
824 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
825 |
|
(instead of the string length) when the string. char is empty |
826 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
827 |
|
o modif's to restore TAMC compatibility |
828 |
|
- avoid "_d" constructs in PARAMETER declarations |
829 |
|
- avoid interrupting lines by comment lines |
830 |
|
o Use cluster local disks for purely local I/O |
831 |
|
vs. globally visible disks needed for ctrl stuff |
832 |
|
(merged from ecco-branch) |
833 |
|
- new active_file_loc... and mdsio_..._loc routines |
834 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
835 |
|
|
836 |
|
checkpoint51c_post |
837 |
|
o introducing integer flag debugLevel |
838 |
|
- debLevZero: suppress all output |
839 |
|
- debLevA: standard |
840 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
841 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
842 |
|
that can be specified at runtime |
843 |
|
(relevant for cluster I/O to local disk) |
844 |
|
` |
845 |
|
>>>checkpoint51b_post |
846 |
|
adjoint of ptracers |
847 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
848 |
|
o extended state in checkpoint_lev?, etc. |
849 |
|
o alternative ctrl/cost with tr1 or ptracer |
850 |
|
o new comlev1_bibj_ptracers |
851 |
|
o new ptracers.flow |
852 |
|
o made ptracers_forcing same as external_forcing_s |
853 |
|
o added verification for adjoint with ptracers |
854 |
|
- adm. grdchk fail so far |
855 |
|
- tlm. grdchk OK |
856 |
|
- checked tapelev/comlev recomputations: OK |
857 |
|
<<<checkpoint51b_pre |
858 |
|
|
859 |
|
checkpoint51a_post |
860 |
|
o added code for biogeochemistry package |
861 |
|
- new pkgs: dic, gchem |
862 |
|
- new subroutine in ptracers |
863 |
|
o modify code for biogeo packages |
864 |
|
- in model/src and pkg/ptracers |
865 |
|
|
866 |
|
checkpoint51 |
867 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
868 |
|
- autodiff, ctrl, exf, grdchk, seaice |
869 |
|
kept separate packages |
870 |
|
- cost, ecco, obcs |
871 |
|
o updating verification/internal_wave, verification/lab_sea |
872 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
873 |
|
|
874 |
|
checkpoint50i_post |
875 |
|
o Preparing next differentiable checkpoint and sync |
876 |
|
of MAIN vs. ecco-branch |
877 |
|
- 1st step: this one is differentiable |
878 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
879 |
|
from ecco-branch) |
880 |
|
|
881 |
|
checkpoint50h_post |
882 |
|
o new package "land": provide surface BC for AIM. |
883 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
884 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
885 |
|
F.Molteni paper) ; update aim.5l_cs output. |
886 |
|
o New variable in PARM03 for more flexible pickups |
887 |
|
o somewhat cleaned package initialisation sequence for |
888 |
|
ctrl/ cost/ ecco/ in packages_... routines |
889 |
|
|
890 |
|
checkpoint50g_post |
891 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
892 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
893 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
894 |
|
made the default because of faster convergence than ADI |
895 |
|
|
896 |
|
checkpoint50f_post |
897 |
|
o exf totally restructured |
898 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
899 |
|
and made sure it's still differentiable |
900 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
901 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
902 |
|
- updated adjoint/makefile and relevant verif. accordingly |
903 |
|
|
904 |
|
checkpoint50f_pre |
905 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
906 |
|
+ change Evap over land. (update aim.5l_cs output) |
907 |
|
o added missing .cvsignores and made uniform across expts |
908 |
|
o changed configuration of tidal_basin_2d expt |
909 |
|
o added pkg/debug functions for tracing code in fatal crashes |
910 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
911 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
912 |
|
o removed lots of single quotes from comments |
913 |
|
|
914 |
|
checkpoint50e_post |
915 |
|
o make KPP work with PTRACERS |
916 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
917 |
|
nearly a copy of kpp_transport_s |
918 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
919 |
|
gPtr(of the surface layer) instead |
920 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
921 |
|
checkpoint50e_pre |
922 |
|
|
923 |
|
checkpoint50d_post |
924 |
|
o change kpp output from multiple-record state files to single-record state |
925 |
|
files analogous to write_state.F |
926 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
927 |
|
analogous to the cg2d-related output. |
928 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
929 |
|
so that writing to internal file fn (with length 512) fails. |
930 |
|
checkpoint50d_pre |
931 |
|
|
932 |
|
checkpoint50c_post |
933 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
934 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
935 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
936 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
937 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
938 |
|
|
939 |
|
checkpoint50c_pre |
940 |
|
Merging from release1_p13: |
941 |
|
o bug fix for pkg/seaice dynamic solver |
942 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
943 |
|
|
944 |
|
checkpoint50b_post |
945 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
946 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
947 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
948 |
|
to timestep.F |
949 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
950 |
|
o re-generate output for highly sensitive test-exp: |
951 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
952 |
|
|
953 |
|
checkpoint50b_pre |
954 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
955 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
956 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
957 |
|
|
958 |
|
checkpoint50a_post |
959 |
|
o Bug fix for merging between c50 and KPP. |
960 |
|
ikey was passed from thermodynamics to kpp_calc via |
961 |
|
common block rather than being recomputed in kpp_calc, |
962 |
|
in contradiction with new key itdkey. |
963 |
|
New key ikppkey created, and tamc.h headers updated. |
964 |
|
|
965 |
|
checkpoint50 |
966 |
|
- 2nd step of merge with ecco-branch: |
967 |
|
merge changes in ecco-branch back into main trunk |
968 |
|
- bug fix in find_alpha |
969 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
970 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
971 |
|
- merged some sliced AD support routines |
972 |
|
|
973 |
|
checkpoint49 |
974 |
|
merged from ecco-branch: |
975 |
|
o exf: |
976 |
|
- Enable initialisation of forcing fields to constant |
977 |
|
(runtime) values. |
978 |
|
- in exf_getffields.F |
979 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
980 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
981 |
|
with bulf formulae. |
982 |
|
- exf_init.F modify #ifdef for exf_init_evap |
983 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
984 |
|
The following INT-usages are not safe: |
985 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
986 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
987 |
|
and were modified. |
988 |
|
o autodiff: checkpoint_lev... |
989 |
|
- updated storing for bulk formulae (some arrays were missing) |
990 |
|
- added state for seaice package |
991 |
|
- synchronized with main branch |
992 |
|
o DIVA: |
993 |
|
Modif.s in |
994 |
|
- the_main_loop.F |
995 |
|
- the_model_main.F |
996 |
|
and added cost_final_restore.F cost_final_store.F |
997 |
|
o With these changes, it is possible to fully separate |
998 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
999 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
1000 |
|
into separate model executions. |
1001 |
|
This enables better tuning of DIVA to given queue sizes. |
1002 |
|
o Loss of cost function value in consecutive DIVA runs is |
1003 |
|
fixed by storing to 'costfinal' file. |
1004 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
1005 |
|
beginning/end of adjoint integration is accounted for. |
1006 |
|
The current changes apply to TAF-1.4.26. |
1007 |
|
TAF has one remaining bug, requiring one manual change |
1008 |
|
(see MITgcm manual). |
1009 |
|
o cal: synchronized between MAIN and ecco-branch |
1010 |
|
|
1011 |
|
checkpoint48i_post |
1012 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
1013 |
|
(mostly adding new routines to make list and replacing |
1014 |
|
pressure by totPhiHyd). |
1015 |
|
o Updated and merged grdchk package |
1016 |
|
- has both ADM and TLM checks |
1017 |
|
- works for single- and multi-proc. |
1018 |
|
- output cleaned |
1019 |
|
- worked successfully for parallel DIVA |
1020 |
|
o genmake: |
1021 |
|
- Adding -platform=SP4 |
1022 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
1023 |
|
o Modif. for DIVA: |
1024 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
1025 |
|
(similar thing would apply for active files such as |
1026 |
|
tbar, sbar, psbar, which should not be reinitialised; |
1027 |
|
only relevant for ecco-branch) |
1028 |
|
|
1029 |
|
checkpoint48h_post |
1030 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
1031 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
1032 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
1033 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
1034 |
|
|
1035 |
|
checkpoint48g_post |
1036 |
|
--- EOS: |
1037 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
1038 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
1039 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
1040 |
|
--- Pressure/geopotential gradient: |
1041 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
1042 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
1043 |
|
( changes results of global_ocean_pressure ) |
1044 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
1045 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
1046 |
|
( changes results of ideal_2D_oce ) |
1047 |
|
o includes r* 2nd term in potential gradient. |
1048 |
|
|
1049 |
|
checkpoint48f_post |
1050 |
|
Merging from release1_p12: |
1051 |
|
o Modifications for using pkg/exf with pkg/seaice |
1052 |
|
- improved description of the various forcing configurations |
1053 |
|
- added basic radiation bulk formulae to pkg/exf |
1054 |
|
- units/sign fix for evap computation in exf_getffields.F |
1055 |
|
- updated verification/global_with_exf/results/output.txt |
1056 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
1057 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
1058 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
1059 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
1060 |
|
to avoid negative values in shallow regions. |
1061 |
|
- updated verification/natl_box/results/output.txt |
1062 |
|
- updated verification/lab_sea/results/output.txt |
1063 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
1064 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
1065 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
1066 |
|
work with multi-field files, e.g., for single-file pickup. |
1067 |
|
o pkg/seaice: |
1068 |
|
- bug fix in growth.F: QNET for no shortwave case |
1069 |
|
- added HeffFile for specifying initial sea-ice thickness |
1070 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
1071 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
1072 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
1073 |
|
o pkg/seaice: |
1074 |
|
- adjoint-friendly modifications |
1075 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
1076 |
|
|
1077 |
|
checkpoint48e_post |
1078 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
1079 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
1080 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
1081 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
1082 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
1083 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
1084 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
1085 |
|
inverted_barometer solid-body.cs-32x32x1 |
1086 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
1087 |
|
|
1088 |
|
checkpoint48d_post |
1089 |
|
o in preparation for r*: |
1090 |
|
a) use pre-computed gradient of hydrostatic potential: |
1091 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
1092 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
1093 |
|
=> affects results of glob_oce_pressure (different truncation error) |
1094 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
1095 |
|
|
1096 |
|
checkpoint48d_pre |
1097 |
|
o in preparation for r*: |
1098 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
1099 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
1100 |
|
but for the moment, only used if it does not change the results. |
1101 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
1102 |
|
|
1103 |
|
checkpoint48c_post |
1104 |
|
Modifications in treatment of initial flux forcing controls |
1105 |
|
to avoid extra storing of flux fields. |
1106 |
|
|
1107 |
|
checkpoint48c_pre |
1108 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
1109 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
1110 |
|
|
1111 |
|
checkpoint48b_post |
1112 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
1113 |
|
(modification to pressure gradient not yet implemented) |
1114 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
1115 |
|
(for U & V) that are used for vertical advection of momentum. |
1116 |
|
|
1117 |
|
checkpoint48a_post |
1118 |
|
o In preparation for r*, use temp. array to compute vertical transport |
1119 |
|
in flux-form momentum pkg. => change results of few test-exp. |
1120 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
1121 |
|
lab_sea, natl_box & plume_on_slope |
1122 |
|
|
1123 |
|
checkpoint48 |
1124 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
1125 |
|
|
1126 |
|
checkpoint47j_post |
1127 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
1128 |
|
o moved adexch from forward_step to addummy_in_stepping |
1129 |
|
o added exch in ctrl_map_... |
1130 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
1131 |
|
reverse checkpointing loop |
1132 |
|
o Yet more changes in gmredi: |
1133 |
|
* adgmredi_calc_tensor |
1134 |
|
avoiding all recomputation of gmredi_slope_limit |
1135 |
|
* adgmredi_x/y/rtransport |
1136 |
|
added flag for excessive storing to avoid recomp. of |
1137 |
|
u/v/rtans, dTdx/y/z |
1138 |
|
-> this is not really necessary and very memory-consuming |
1139 |
|
* adgmredi_slope_psi: |
1140 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
1141 |
|
* gmredi_slope_limit |
1142 |
|
re-activated full calculation of taperfct for case 'ac02' |
1143 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
1144 |
|
|
1145 |
|
checkpoint47i_post |
1146 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
1147 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
1148 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
1149 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
1150 |
|
o gmredi: fix few bugs. |
1151 |
|
|
1152 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
1153 |
|
This will be a good checkpoint to plug into the ecco-branch. |
1154 |
|
o few modif.'s to get latest version adjointed |
1155 |
|
(mainly kick out code in ini_linear_phisurf) |
1156 |
|
o modif's to run adjoint with exactConserv |
1157 |
|
o case GM_BOLUS_ADVEC should be cleaned |
1158 |
|
S/R gmredi_slope_psi should be cleaned |
1159 |
|
o verification/carbon now has exactConserv=.TRUE. |
1160 |
|
|
1161 |
|
checkpoint47g_post |
1162 |
|
o time-average AIM output: becomes independent from statvars time-average |
1163 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
1164 |
|
o After TAF bug fix: |
1165 |
|
Tested adjoint of gmredi package. |
1166 |
|
Tests were done with checkpoint47 rather than with latest |
1167 |
|
checkpoint47f_post since the latter is broken for the adjoint |
1168 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
1169 |
|
Here they are, before they get changed/lost/stolen. |
1170 |
|
Mostly modif.'s to fix numerical sensitivities. |
1171 |
|
Gradient checks OK for |
1172 |
|
- GM_taper_scheme: |
1173 |
|
* clipping |
1174 |
|
* ac02 |
1175 |
|
* linear |
1176 |
|
* glw91 |
1177 |
|
* dm95 |
1178 |
|
* ldd97 |
1179 |
|
- GMREDI_OPTIONS: |
1180 |
|
* GM_VISBECK_VARIABLE_K |
1181 |
|
* GM_NON_UNITY_DIAGONAL |
1182 |
|
* GM_EXTRA_DIAGONAL |
1183 |
|
* GM_BOLUS_ADVEC |
1184 |
|
in conjunction with data.gmredi parameters to be checked in |
1185 |
|
in a few minutes under verification/carbon/code/ |
1186 |
|
|
1187 |
checkpoint47f_post |
checkpoint47f_post |
1188 |
Merging from release1_p10: |
Merging from release1_p10: |
1189 |
o modifications for using pkg/exf with pkg/seaice |
o modifications for using pkg/exf with pkg/seaice |