3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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|
6 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
7 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
8 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
9 |
|
|
10 |
|
checkpoint54a_post |
11 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
12 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
13 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
14 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
15 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
16 |
|
checkpoint54a_pre |
17 |
|
|
18 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
19 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
20 |
|
|
21 |
|
checkpoint54 |
22 |
|
checkpoint53g_post |
23 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
24 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
25 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
26 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
27 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
28 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
29 |
|
o restore adjointability |
30 |
|
|
31 |
|
checkpoint53f_post |
32 |
|
o modifications that affect AIM experiment results (update output.txt): |
33 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
34 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
35 |
|
o AIM pkg: |
36 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
37 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
38 |
|
|
39 |
|
checkpoint53e_post |
40 |
|
o merged cylindrical coord configuration |
41 |
|
o added rotating_tank experiment |
42 |
|
checkpoint53e_pre |
43 |
|
|
44 |
|
checkpoint53d_post |
45 |
|
o faulks upgraded: re-generate output.txt that have changed: |
46 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
47 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
48 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
49 |
|
o added Sadourny discretization of Coriolis |
50 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
51 |
|
- re-enabled use of omega3 (useAbsVorticity) |
52 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
53 |
|
vector-invariant equations |
54 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
55 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
56 |
|
hopefully without new bugs |
57 |
|
- still to do: biharmonic friction for non-hydrostatic w |
58 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
59 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
60 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
61 |
|
of mom_common/ |
62 |
|
- simple re-arrangement of instructions within computing loop |
63 |
|
checkpoint53d_pre |
64 |
|
|
65 |
|
checkpoint53c_post |
66 |
|
o new version of coupler for AIM+thSIce and Ocean models |
67 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
68 |
|
- land: change Evaporation of snow |
69 |
|
- aim with thSIce: fix bug in snow-precip. |
70 |
|
o changes to calc_gw.F |
71 |
|
- bug fix for w^2 term near the bottom boundary |
72 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
73 |
|
partial/looped cells |
74 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
75 |
|
and plume on slope), change the lateral boundary condition from half slip |
76 |
|
to the value of no_slip_sides |
77 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
78 |
|
o Adjoint of EBM package + verification |
79 |
|
* TLM OK |
80 |
|
* ADM not sufficient accuracy yet (needs further testing) |
81 |
|
|
82 |
|
checkpoint53b_post |
83 |
|
o Commiting new energy balance model to repository |
84 |
|
* package is pkg/ebm |
85 |
|
* verif. is verification/global_ocean_ebm |
86 |
|
* references are in ebm_driver.F |
87 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
88 |
|
C Global thermohaline circulation. Part I: |
89 |
|
C Sensitivity to atmospheric moisture transport. |
90 |
|
C J. Climate 12(1), 71-82 |
91 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
92 |
|
C Global thermohaline circulation. Part II: |
93 |
|
C Sensitivity with interactive transport. |
94 |
|
C J. Climate 12(1), 83-91 |
95 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
96 |
|
C Destabilization of the thermohaline circulation |
97 |
|
C by atmospheric eddy transports. |
98 |
|
C J. Climate 7(12), 1870-1882 |
99 |
|
o Will need long integration testing. |
100 |
|
checkpoint53b_pre |
101 |
|
|
102 |
|
o created pkg/mom_common in preparation for variable viscosity code |
103 |
|
o renamed and split ini_mnc_io |
104 |
|
o pkg/land: only liquid water can diffuse or run-off |
105 |
|
o AIM using land: soil wetness availability account for snow |
106 |
|
o added printMapIncludesZeros to EEPARMS namelist |
107 |
|
|
108 |
|
checkpoint53a_post |
109 |
|
o restore TAMC compatiility for exf_constants.h |
110 |
|
(no usage of _d in .h) |
111 |
|
o Additional storing in KPP in an attempt to fix |
112 |
|
TAMC problem with adjoint of KPP code. |
113 |
|
(no success...) |
114 |
|
Identical code works fine with TAF. |
115 |
|
o Fixed verification/natl_box_adjoint experiments. |
116 |
|
Initial conditions for Experiments 4 and 5 are now |
117 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
118 |
|
and hence gives results closer to that of Experiment 2. |
119 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
120 |
|
|
121 |
|
checkpoint53 |
122 |
|
o stable checkpoint with up to date adjoint |
123 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
124 |
|
this is a code problem or a problem with resetting code for g_ |
125 |
|
variables that is being autogenerated wrong. |
126 |
|
Otherwise: |
127 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
128 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
129 |
|
are both still in chaos following their security messes. |
130 |
|
|
131 |
|
checkpoint52n_post |
132 |
|
o various build (mostly genmake2) changes including: |
133 |
|
- ability to build/run more easily within Cygwin and MacOS X |
134 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
135 |
|
o pkg/seaice modifications |
136 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
137 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
138 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
139 |
|
- changed proxy for geostrophic velocity and updated |
140 |
|
verification/lab_sea/results/* accordingly |
141 |
|
- removed ADI dynamic solver from pkg/seaice |
142 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
143 |
|
they caused a segmentation fault under certain circumstances |
144 |
|
- removed unused field WATR |
145 |
|
o bug fix in exf-package: |
146 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
147 |
|
now reflect that. |
148 |
|
o small fixes in the cal-package: |
149 |
|
- set reference date to first of January for the 'model'-calendar |
150 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
151 |
|
warning |
152 |
|
o small modifications in exf-package to increase flexibility: |
153 |
|
- change climtempfreeze from a constant to a runtime parameter that |
154 |
|
is specified in data.exf_clim (default = -1.9) |
155 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
156 |
|
specified in data.exf |
157 |
|
o fix in pkg/thsice: |
158 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
159 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
160 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
161 |
|
|
162 |
|
checkpoint52m_post |
163 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
164 |
|
this does not change any of the results, because myIter=0 in swfrac always |
165 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
166 |
|
as a default |
167 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
168 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
169 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
170 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
171 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
172 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
173 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
174 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
175 |
|
o monitor package can write to NetCDF files and/or STDOUT |
176 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
177 |
|
o doc/api_reference added |
178 |
|
- a framework for building an API Reference Manual using all |
179 |
|
the "protex" comments embedded in the code |
180 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
181 |
|
o MNC: |
182 |
|
- make myThid the last argument for all subroutines |
183 |
|
- new default for the grid files: NO halos |
184 |
|
- add useMNC and other run-time flags |
185 |
|
- separate per-file-group handling of the unlimited dimension |
186 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
187 |
|
and lookup tables set in initialize_fixed |
188 |
|
- write all MNC output to a freshly-created directory |
189 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
190 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
191 |
|
o Added functionality to grdchk: |
192 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
193 |
|
|
194 |
|
checkpoint52l_post |
195 |
|
o new land formulation: |
196 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
197 |
|
energy conservation. |
198 |
|
b) account for water temperature and for latent heat of freezing |
199 |
|
in all processes (rain, run-off, ground storage) |
200 |
|
c) compute surface and ground temperature implicitly. |
201 |
|
o aim_v23 modification for new land model: |
202 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
203 |
|
to allow implicit computation of land & sea-ice surface temp. |
204 |
|
b) add snow precipitation. |
205 |
|
checkpoint52l_pre |
206 |
|
|
207 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
208 |
|
o fix bug in timeAve (u,vZetatave in common block) |
209 |
|
o no restoring terms under ice for pkg/seaice |
210 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
211 |
|
o bug fix for pkg/seaice pickups |
212 |
|
o change MNC call locations and add coordinate attributes |
213 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
214 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
215 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
216 |
|
o exf: Adding simple range check routine for exf fields after read |
217 |
|
|
218 |
|
checkpoint52k_post |
219 |
|
o removed top-level directory "diags" |
220 |
|
- we migrated these functions to pkg/timeave a long time ago |
221 |
|
o fixed bug introduced in pkg/monitor |
222 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
223 |
|
averaged fields (I/O via cost_averages) |
224 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
225 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
226 |
|
o added initial do_the_model_io to ecco |
227 |
|
o set all ...Freq to zero after cost_final |
228 |
|
taveFreq, dumpFreq, pChkptFreq |
229 |
|
o MAIN and ECCO differentiability restored |
230 |
|
|
231 |
|
checkpoint52j_post |
232 |
|
o fix nchklev in tamc.h for global_ocean... |
233 |
|
o Bringing flow and store directives up-to-date |
234 |
|
o Really weird thing! |
235 |
|
call do_the_model_io from the_main_loop with parameters |
236 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
237 |
|
TAF places a faulty re-call of initialise_varia |
238 |
|
after cost_final call which should not be there! |
239 |
|
checkpoint52j_pre |
240 |
|
|
241 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
242 |
|
error messages |
243 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
244 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
245 |
|
debug output |
246 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
247 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
248 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
249 |
|
o update AIM Equatorial Channel exp: |
250 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
251 |
|
o globalFile now works with exch2 |
252 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
253 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
254 |
|
o limit timeave output for hi-res integrations |
255 |
|
|
256 |
|
checkpoint52i_post |
257 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
258 |
|
o updated the tiling for global_ocean_pressure |
259 |
|
checkpoint52i_pre |
260 |
|
|
261 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
262 |
|
the old pkg/aim). |
263 |
|
|
264 |
|
checkpoint52h_pre |
265 |
|
o shortened offending lines in exch2_send_rx?.template |
266 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
267 |
|
o genmake2: add build & execute test for NetCDF code |
268 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
269 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
270 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
271 |
|
o added temporary hack for sea-ice dynamics on the cube: |
272 |
|
metric terms are ignored and it is assumed that |
273 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
274 |
|
|
275 |
|
checkpoint52f_post |
276 |
|
o added exch2 cube routines to pkg/exch2 |
277 |
|
o modified hs94.cs-32x32x5 to use it |
278 |
|
o added new grid files to hs94.cs-32x32x5 |
279 |
|
checkpoint52f_pre |
280 |
|
|
281 |
|
checkpoint52e_post |
282 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
283 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
284 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
285 |
|
to work with implicit vertical advection and AB ; |
286 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
287 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
288 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
289 |
|
checkpoint52e_pre |
290 |
|
|
291 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
292 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
293 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
294 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
295 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
296 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
297 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
298 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
299 |
|
|
300 |
|
checkpoint52d_post |
301 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
302 |
|
- updated output accordingly |
303 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
304 |
|
random number generator |
305 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
306 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
307 |
|
o changes to permit hi-res, cubed-sphere, configuration |
308 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
309 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
310 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
311 |
|
of surface winds for the cube |
312 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
313 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
314 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
315 |
|
complete with example surface forcing files and matlab scripts to look |
316 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
317 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
318 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
319 |
|
to conform to the common rule. |
320 |
|
o check-in the first version of the coupler + interfaces for multi-components |
321 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
322 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
323 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
324 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
325 |
|
- exchanges between component and coupler is done in forward_step |
326 |
|
o new verification experiment, cpl_aim+ocn: |
327 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
328 |
|
|
329 |
|
checkpoint52d_pre |
330 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
331 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
332 |
|
|
333 |
|
checkpoint52c_post |
334 |
|
o Fixing OPTIONS files for use of exf: |
335 |
|
- ALLOW_ECCO not needed |
336 |
|
- ECCO_CPPOPTIONS.h should not be included from |
337 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
338 |
|
as has been the case in the past |
339 |
|
- All cal/exf related options are currently set in |
340 |
|
single header file. Should remain so until we |
341 |
|
agree on a consistent new policy. |
342 |
|
o Removed all CPP options for cal package. |
343 |
|
cal has no more CPP options. |
344 |
|
o modified STOREs in GAD_ADVECTION |
345 |
|
o corrected key comp. for passkey |
346 |
|
|
347 |
|
checkpoint52b_post |
348 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
349 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
350 |
|
- modify fluxes but do not change theta directly; |
351 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
352 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
353 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
354 |
|
o put back grid & coriolis monitor output. |
355 |
|
checkpoint52b_pre |
356 |
|
|
357 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
358 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
359 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
360 |
|
(need info on NUMBER_OF_PTRACERS) |
361 |
|
o missing PTRACERS headers in some routines |
362 |
|
o default tamc.h in pkg/autodiff supposed to crash |
363 |
|
to ensure proper customization |
364 |
|
|
365 |
|
checkpoint52a_post |
366 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
367 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
368 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
369 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
370 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
371 |
|
- keep the old version of FREEZE for backward compatibility; |
372 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
373 |
|
- corresponding modifs for TAF directives |
374 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
375 |
|
o time-averaged output for pkg/ptracers |
376 |
|
o fix problem with ECCO-related divided adjoint |
377 |
|
snapshot file was missing some ad-variables, |
378 |
|
but no warning issued by TAF |
379 |
|
|
380 |
|
checkpoint52a_pre |
381 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
382 |
|
|
383 |
|
checkpoint52 = ecco_c52_e35 |
384 |
|
o after testing adjoints of checkpoint51u_post |
385 |
|
|
386 |
|
checkpoint51u_post |
387 |
|
o this is the post-merge tag of the ecco-branch |
388 |
|
(needs another clean checkout and re-testing) |
389 |
|
o various natl_box_adjoint configs and results |
390 |
|
but no input fields |
391 |
|
o obcs adjoint not yet merged! |
392 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
393 |
|
o updated/extended some store directives for seaice |
394 |
|
o pkg/ecco now containes ecco-specific part of cost function |
395 |
|
o top level routines the_main_loop, forward_step |
396 |
|
supersede those in model/src/ |
397 |
|
previous input data.cost now in data.ecco |
398 |
|
(new namelist ecco_cost_nml) |
399 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
400 |
|
|
401 |
|
checkpoint51t_post |
402 |
|
o this is the pre-merge tag of the ecco-branch |
403 |
|
|
404 |
|
checkpoint51s_post |
405 |
|
o cleanup: removed various obsolete #define-s |
406 |
|
o pkg/grdchk |
407 |
|
- renamed 'ph-grd 3' to 'grad-res' |
408 |
|
- merged from ecco-branch |
409 |
|
(remaining bug fixes for obcs gradient checks) |
410 |
|
- additional high-precision output for testreport |
411 |
|
(grep for 'precision_grdchk_result') |
412 |
|
|
413 |
|
checkpoint51r_post |
414 |
|
o cleaned up or removed CPP_OPTIONS.h files |
415 |
|
o updated results for some of the tests to reflect the new |
416 |
|
optfiles (-ieee: -O0 instead of -O3) |
417 |
|
|
418 |
|
checkpoint51q_post |
419 |
|
o cd_code: |
420 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
421 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
422 |
|
- separated cd_code part from write_checkpoint |
423 |
|
- updated AD_SOURCE, generated .flow |
424 |
|
- added CD_CODE_VARS.h to the_main_loop |
425 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
426 |
|
o ctrl package totally restructured |
427 |
|
- pack/unpack now optional and decoupled from |
428 |
|
xx_/adxx_ I/O |
429 |
|
- ctrl_pack/unpack cleaned |
430 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
431 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
432 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
433 |
|
|
434 |
|
checkpoint51p_post |
435 |
|
o create initial cd_code package |
436 |
|
- WARNING: the initialization of fields within packages |
437 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
438 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
439 |
|
This seems to be backwards since |
440 |
|
1) its important to initially zero the entire field including |
441 |
|
the "halo" region |
442 |
|
2) zeroing needs to be done *before* reading pickup info |
443 |
|
and the pickup call might or might not happen in any |
444 |
|
particular run |
445 |
|
- this needs an overhaul for R2 |
446 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
447 |
|
o cleanup testreport |
448 |
|
|
449 |
|
checkpoint51o_post |
450 |
|
o bringing AD-related verif's up to date with genmake2 |
451 |
|
- carbon/ |
452 |
|
- global_ocean.90x40x15/ |
453 |
|
- hs.94.1x64x5/ |
454 |
|
- (front_relax/ ) |
455 |
|
o (more) consistent directory structure for AD-related verif.'s |
456 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
457 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
458 |
|
o bug fix in find_alpha.F for MDJWF: |
459 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
460 |
|
change rho -> rho-rhoConst |
461 |
|
- replace call find_rho to find_rhonum |
462 |
|
o initialisation of rFlx extended to full array (required by TAF) |
463 |
|
and shifted to thermodynamics |
464 |
|
o removed PTRACERS.h in ptracers routine |
465 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
466 |
|
o Correcting initialisations for fVerU, fVerV. |
467 |
|
o helping TAF to recognize dependency on kUp for |
468 |
|
fVerU, fVerV |
469 |
|
o Replacing delZ by delR in pkg/ctrl/ |
470 |
|
checkpoint51o_pre |
471 |
|
|
472 |
|
o undid all of cp51 pending some cleanups and discussion |
473 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
474 |
|
it for adjoint/tl #defines |
475 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
476 |
|
o removed tools/genmake since it no longer works |
477 |
|
|
478 |
|
checkpoint51n_post |
479 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
480 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
481 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
482 |
|
- subroutine FREEZE now limits only surface temperature |
483 |
|
(this means new output.txt for global_ocean.90x40x15, |
484 |
|
global_ocean.cs32x15, and global_with_exf) |
485 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
486 |
|
|
487 |
|
checkpoint51n_pre |
488 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
489 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
490 |
|
defines: |
491 |
|
- ALLOW_ADJOINT_RUN |
492 |
|
- ALLOW_TANGENTLINEAR_RUN |
493 |
|
- ALLOW_ECCO_OPTIMIZATION |
494 |
|
|
495 |
|
checkpoint51m_post |
496 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
497 |
|
- added new TAMC/TAF targets to the Makefile |
498 |
|
- various cleanups related to package handling |
499 |
|
- these changes should have no impact on the forward model |
500 |
|
|
501 |
|
checkpoint51l_post |
502 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
503 |
|
- faster algorithm for cal_addtime.F |
504 |
|
- higher precision arithmetic, where needed |
505 |
|
- pkg/exf *startdate variables changed from calendar date to |
506 |
|
model integration time |
507 |
|
|
508 |
|
checkpoint51l_pre |
509 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
510 |
|
o enable to apply restoring on S & T only in a latitude band. |
511 |
|
o update output (external_forcing_surf modif. change truncation errors) |
512 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
513 |
|
|
514 |
|
checkpoint51k_post |
515 |
|
o change default to: useNHMTerms=.FALSE. |
516 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
517 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
518 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
519 |
|
exp1, ideal_2D_oce |
520 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
521 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
522 |
|
o set gravitySign automatically according to the vertical coordinate used |
523 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
524 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
525 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
526 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
527 |
|
|
528 |
|
checkpoint51j_post |
529 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
530 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
531 |
|
o added cubed-sphere case to test cost function |
532 |
|
o heckpoint_lev?_directives.h now include |
533 |
|
pkg-specific directives, whenever those are enabled. |
534 |
|
o Moving pkg-specific flow directives to corresponding pkg |
535 |
|
Moving pkg-specific differentiation list to corresponding pkg |
536 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
537 |
|
---> conventions are |
538 |
|
- pkg_ad.flow |
539 |
|
- pkg_ad_diff.list |
540 |
|
- pkg_ad_check_lev?_dir.h |
541 |
|
|
542 |
|
checkpoint51i_post |
543 |
|
o merge of the branch-genmake2 |
544 |
|
- knowingly breaks the older genmake |
545 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
546 |
|
- new testreport supersedes older testscript |
547 |
|
o large number of package inclusion and header cleanups |
548 |
|
checkpoint51i_pre |
549 |
|
|
550 |
|
o new output for adjoin of global ocean vector invariant |
551 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
552 |
|
o Steph gchem various cleanups |
553 |
|
|
554 |
|
checkpoint 51h_pre |
555 |
|
o fixed some single quotes |
556 |
|
o modify gchem pkg to be more versatile |
557 |
|
o modifications to clean up dic pkg |
558 |
|
o add pkg/cfc |
559 |
|
|
560 |
|
checkpoint51g_post |
561 |
|
o provide links for ARPACK and ADM*TLM |
562 |
|
o start removing verification/vero/ |
563 |
|
o update AD-related stuff |
564 |
|
(in particular some IF-statements in model/src/ routines) |
565 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
566 |
|
vector invariant setup |
567 |
|
|
568 |
|
checkpoint51f_post |
569 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
570 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
571 |
|
of tracer Green's fucntions for ocean inversion project. |
572 |
|
|
573 |
|
checkpoint51f_pre |
574 |
|
o Added on-the-fly spatial interpolation capability |
575 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
576 |
|
- This is a temporary Cartesian-grid hack until |
577 |
|
the super-duper ESMF coupler becomes available. |
578 |
|
- See verification/global_with_exf/README for usage example. |
579 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
580 |
|
flags and modified pkg/seaice accordingly. |
581 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
582 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
583 |
|
non-local transport term. |
584 |
|
|
585 |
|
checkpoint51e_post |
586 |
|
o pkg/mom_vecinv: |
587 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
588 |
|
- add time-ave diagnostic of vorticity advection. |
589 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
590 |
|
o atmospheric geopotential: - include water vapor effect; |
591 |
|
- use p^kappa in p* scaling. |
592 |
|
o land pkg: read initial state from files. |
593 |
|
o AIM : add stratospheric drag in the upper level |
594 |
|
|
595 |
|
checkpoint51d_post |
596 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
597 |
|
(instead of the string length) when the string. char is empty |
598 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
599 |
|
o modif's to restore TAMC compatibility |
600 |
|
- avoid "_d" constructs in PARAMETER declarations |
601 |
|
- avoid interrupting lines by comment lines |
602 |
|
o Use cluster local disks for purely local I/O |
603 |
|
vs. globally visible disks needed for ctrl stuff |
604 |
|
(merged from ecco-branch) |
605 |
|
- new active_file_loc... and mdsio_..._loc routines |
606 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
607 |
|
|
608 |
|
checkpoint51c_post |
609 |
|
o introducing integer flag debugLevel |
610 |
|
- debLevZero: suppress all output |
611 |
|
- debLevA: standard |
612 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
613 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
614 |
|
that can be specified at runtime |
615 |
|
(relevant for cluster I/O to local disk) |
616 |
|
` |
617 |
|
>>>checkpoint51b_post |
618 |
|
adjoint of ptracers |
619 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
620 |
|
o extended state in checkpoint_lev?, etc. |
621 |
|
o alternative ctrl/cost with tr1 or ptracer |
622 |
|
o new comlev1_bibj_ptracers |
623 |
|
o new ptracers.flow |
624 |
|
o made ptracers_forcing same as external_forcing_s |
625 |
|
o added verification for adjoint with ptracers |
626 |
|
- adm. grdchk fail so far |
627 |
|
- tlm. grdchk OK |
628 |
|
- checked tapelev/comlev recomputations: OK |
629 |
|
<<<checkpoint51b_pre |
630 |
|
|
631 |
|
checkpoint51a_post |
632 |
|
o added code for biogeochemistry package |
633 |
|
- new pkgs: dic, gchem |
634 |
|
- new subroutine in ptracers |
635 |
|
o modify code for biogeo packages |
636 |
|
- in model/src and pkg/ptracers |
637 |
|
|
638 |
|
checkpoint51 |
639 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
640 |
|
- autodiff, ctrl, exf, grdchk, seaice |
641 |
|
kept separate packages |
642 |
|
- cost, ecco, obcs |
643 |
|
o updating verification/internal_wave, verification/lab_sea |
644 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
645 |
|
|
646 |
|
checkpoint50i_post |
647 |
|
o Preparing next differentiable checkpoint and sync |
648 |
|
of MAIN vs. ecco-branch |
649 |
|
- 1st step: this one is differentiable |
650 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
651 |
|
from ecco-branch) |
652 |
|
|
653 |
|
checkpoint50h_post |
654 |
|
o new package "land": provide surface BC for AIM. |
655 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
656 |
o AIM: use true log-P extrapolation for near surface temp (= as in |
o AIM: use true log-P extrapolation for near surface temp (= as in |
657 |
F.Molteni paper) ; update aim.5l_cs output. |
F.Molteni paper) ; update aim.5l_cs output. |
658 |
o New variable in PARM03 for more flexible pickups |
o New variable in PARM03 for more flexible pickups |
659 |
|
o somewhat cleaned package initialisation sequence for |
660 |
|
ctrl/ cost/ ecco/ in packages_... routines |
661 |
|
|
662 |
checkpoint50g_post |
checkpoint50g_post |
663 |
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |