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$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.281 2004/04/19 23:25:15 mlosch Exp $ |
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|
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Notes on tags used in MITgcmUV |
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============================== |
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|
6 |
o bug fix in exf-package: |
7 |
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
8 |
now reflect that. |
9 |
o small fixes in the cal-package: |
10 |
- set reference date to first of January for the 'model'-calendar |
11 |
- failing of cal_CheckDate in cal_FullDate now actually results in a |
12 |
warning |
13 |
o small modifications in exf-package to increase flexibility: |
14 |
- change climtempfreeze from a constant to a runtime parameter that |
15 |
is specified in data.exf_clim (default = -1.9) |
16 |
- introduce runtime parameter windstressmax (default = 2.0) that is |
17 |
specified in data.exf |
18 |
o fix in pkg/thsice: |
19 |
- update Evap (Tsf changes) to be consistent with Latent heat flux |
20 |
- maintain snow precipitation unchanged (even if Tsf >=0). |
21 |
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
22 |
|
23 |
checkpoint52m_post |
24 |
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
25 |
this does not change any of the results, because myIter=0 in swfrac always |
26 |
lead to jwtype=2 (the default anyway), but the call makes little sense |
27 |
as a default |
28 |
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
29 |
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
30 |
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
31 |
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
32 |
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
33 |
o extending useSingleCpuIO option to work with new exch2 I/O format |
34 |
- old-style, missing-tile I/O is still accessible by defining CPP |
35 |
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
36 |
o monitor package can write to NetCDF files and/or STDOUT |
37 |
o fix re-definition bug in MNC_GRID_INIT_ALL() |
38 |
o doc/api_reference added |
39 |
- a framework for building an API Reference Manual using all |
40 |
the "protex" comments embedded in the code |
41 |
- see pkg/generic_advdiff, pkg/mnc for examples |
42 |
o MNC: |
43 |
- make myThid the last argument for all subroutines |
44 |
- new default for the grid files: NO halos |
45 |
- add useMNC and other run-time flags |
46 |
- separate per-file-group handling of the unlimited dimension |
47 |
- early initialization of MNC w/ flags read at the eeboot stage |
48 |
and lookup tables set in initialize_fixed |
49 |
- write all MNC output to a freshly-created directory |
50 |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
51 |
o test exp. advect_cs: use the standard cs32 grid ; update output. |
52 |
o Added functionality to grdchk: |
53 |
pick global i,j,k position (or nearest wet) where to perform check. |
54 |
|
55 |
checkpoint52l_post |
56 |
o new land formulation: |
57 |
a) use ground enthalpy as prognostic variable to ensure exact |
58 |
energy conservation. |
59 |
b) account for water temperature and for latent heat of freezing |
60 |
in all processes (rain, run-off, ground storage) |
61 |
c) compute surface and ground temperature implicitly. |
62 |
o aim_v23 modification for new land model: |
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a) Treat separately land / ocean / sea-ice surface fluxes |
64 |
to allow implicit computation of land & sea-ice surface temp. |
65 |
b) add snow precipitation. |
66 |
checkpoint52l_pre |
67 |
|
68 |
o fix problem (when 1 tile is empty) in min/max monitor. |
69 |
o fix bug in timeAve (u,vZetatave in common block) |
70 |
o no restoring terms under ice for pkg/seaice |
71 |
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
72 |
o bug fix for pkg/seaice pickups |
73 |
o change MNC call locations and add coordinate attributes |
74 |
o mask vorticity at the corner ; affects global_ocean.cs output |
75 |
o fix ini_curvilinear_grid ; test CS experiments with mpi |
76 |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
77 |
o exf: Adding simple range check routine for exf fields after read |
78 |
|
79 |
checkpoint52k_post |
80 |
o removed top-level directory "diags" |
81 |
- we migrated these functions to pkg/timeave a long time ago |
82 |
o fixed bug introduced in pkg/monitor |
83 |
o accuracy ctrlprec = 32 insuffient for gradient checks using |
84 |
averaged fields (I/O via cost_averages) |
85 |
-> use ctrl.h in active_file*.F to control I/O precision. |
86 |
o paramter list of CALL ADTHE_MAIN_LOOP |
87 |
o added initial do_the_model_io to ecco |
88 |
o set all ...Freq to zero after cost_final |
89 |
taveFreq, dumpFreq, pChkptFreq |
90 |
o MAIN and ECCO differentiability restored |
91 |
|
92 |
checkpoint52j_post |
93 |
o fix nchklev in tamc.h for global_ocean... |
94 |
o Bringing flow and store directives up-to-date |
95 |
o Really weird thing! |
96 |
call do_the_model_io from the_main_loop with parameters |
97 |
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
98 |
TAF places a faulty re-call of initialise_varia |
99 |
after cost_final call which should not be there! |
100 |
checkpoint52j_pre |
101 |
|
102 |
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
103 |
error messages |
104 |
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
105 |
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
106 |
debug output |
107 |
o modfied mdsio_writefield.F to handle non-global files under exch2 |
108 |
o update AIM Cubed-Sphere exp (aim.5l_cs): |
109 |
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
110 |
o update AIM Equatorial Channel exp: |
111 |
use standard aim_v23 pkg and change the SST fields to be more realistic. |
112 |
o globalFile now works with exch2 |
113 |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
114 |
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
115 |
o limit timeave output for hi-res integrations |
116 |
|
117 |
checkpoint52i_post |
118 |
o removed CPP_EEOPTIONS.h from verification/*/code |
119 |
o updated the tiling for global_ocean_pressure |
120 |
checkpoint52i_pre |
121 |
|
122 |
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
123 |
the old pkg/aim). |
124 |
|
125 |
checkpoint52h_pre |
126 |
o shortened offending lines in exch2_send_rx?.template |
127 |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
128 |
o genmake2: add build & execute test for NetCDF code |
129 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
130 |
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
131 |
o added useSingleCPUIO flag to monitor.F and mon_out.F |
132 |
o added temporary hack for sea-ice dynamics on the cube: |
133 |
metric terms are ignored and it is assumed that |
134 |
there is no sea-ice on cube faces 1, 2, 4, and 5. |
135 |
|
136 |
checkpoint52f_post |
137 |
o added exch2 cube routines to pkg/exch2 |
138 |
o modified hs94.cs-32x32x5 to use it |
139 |
o added new grid files to hs94.cs-32x32x5 |
140 |
checkpoint52f_pre |
141 |
|
142 |
checkpoint52e_post |
143 |
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
144 |
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
145 |
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
146 |
to work with implicit vertical advection and AB ; |
147 |
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
148 |
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
149 |
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
150 |
checkpoint52e_pre |
151 |
|
152 |
o fix bug in impldiff when Nr=1 or Nr=2. |
153 |
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
154 |
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
155 |
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
156 |
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
157 |
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
158 |
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
159 |
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
160 |
|
161 |
checkpoint52d_post |
162 |
o re-tiled many expts to allow comparison in multi-processor mode |
163 |
- updated output accordingly |
164 |
- changed hs94.128x64x5 to use intial T from file rather than use the |
165 |
random number generator |
166 |
o add infrastructure in model routines for fizhi and gridalt packages |
167 |
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
168 |
o changes to permit hi-res, cubed-sphere, configuration |
169 |
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
170 |
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
171 |
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
172 |
of surface winds for the cube |
173 |
(A verification experiment, based on global_ocean.cs32x15, but with |
174 |
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
175 |
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
176 |
complete with example surface forcing files and matlab scripts to look |
177 |
at the output and compare it with that of global_ocean.cs32x15.) |
178 |
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
179 |
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
180 |
to conform to the common rule. |
181 |
o check-in the first version of the coupler + interfaces for multi-components |
182 |
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
183 |
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
184 |
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
185 |
- ocean and atmos. share the same horizontal grid (no interpolation). |
186 |
- exchanges between component and coupler is done in forward_step |
187 |
o new verification experiment, cpl_aim+ocn: |
188 |
coupled ocean - AIM atmosphere on cs32 grid. |
189 |
|
190 |
checkpoint52d_pre |
191 |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
192 |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
193 |
|
194 |
checkpoint52c_post |
195 |
o Fixing OPTIONS files for use of exf: |
196 |
- ALLOW_ECCO not needed |
197 |
- ECCO_CPPOPTIONS.h should not be included from |
198 |
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
199 |
as has been the case in the past |
200 |
- All cal/exf related options are currently set in |
201 |
single header file. Should remain so until we |
202 |
agree on a consistent new policy. |
203 |
o Removed all CPP options for cal package. |
204 |
cal has no more CPP options. |
205 |
o modified STOREs in GAD_ADVECTION |
206 |
o corrected key comp. for passkey |
207 |
|
208 |
checkpoint52b_post |
209 |
o new version: "thsice" of thermodynamic sea-ice pkg: |
210 |
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
211 |
- modify fluxes but do not change theta directly; |
212 |
- light cleaning of bulk_force pkg (still needed with thsice). |
213 |
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
214 |
+ output_thsice.txt to test thsice & bulk_force pkgs. |
215 |
o put back grid & coriolis monitor output. |
216 |
checkpoint52b_pre |
217 |
|
218 |
o call "do_the_model_io" at the beginning (=> dump initial state) |
219 |
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
220 |
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
221 |
(need info on NUMBER_OF_PTRACERS) |
222 |
o missing PTRACERS headers in some routines |
223 |
o default tamc.h in pkg/autodiff supposed to crash |
224 |
to ensure proper customization |
225 |
|
226 |
checkpoint52a_post |
227 |
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
228 |
- moved surfaceTendencyTice from pkg/seaice to main code |
229 |
- subroutine FREEZE_SURFACE now limits only surface temperature |
230 |
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
231 |
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
232 |
- keep the old version of FREEZE for backward compatibility; |
233 |
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
234 |
- corresponding modifs for TAF directives |
235 |
o added surface flux output variables to TIMEAVE_STATVARS |
236 |
o time-averaged output for pkg/ptracers |
237 |
o fix problem with ECCO-related divided adjoint |
238 |
snapshot file was missing some ad-variables, |
239 |
but no warning issued by TAF |
240 |
|
241 |
checkpoint52a_pre |
242 |
o some bug fixes for #undef REAL4_IS_SLOW |
243 |
|
244 |
checkpoint52 = ecco_c52_e35 |
245 |
o after testing adjoints of checkpoint51u_post |
246 |
|
247 |
checkpoint51u_post |
248 |
o this is the post-merge tag of the ecco-branch |
249 |
(needs another clean checkout and re-testing) |
250 |
o various natl_box_adjoint configs and results |
251 |
but no input fields |
252 |
o obcs adjoint not yet merged! |
253 |
o adding ECCO global 1x1 and 2x2 degree configs |
254 |
o updated/extended some store directives for seaice |
255 |
o pkg/ecco now containes ecco-specific part of cost function |
256 |
o top level routines the_main_loop, forward_step |
257 |
supersede those in model/src/ |
258 |
previous input data.cost now in data.ecco |
259 |
(new namelist ecco_cost_nml) |
260 |
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
261 |
|
262 |
checkpoint51t_post |
263 |
o this is the pre-merge tag of the ecco-branch |
264 |
|
265 |
checkpoint51s_post |
266 |
o cleanup: removed various obsolete #define-s |
267 |
o pkg/grdchk |
268 |
- renamed 'ph-grd 3' to 'grad-res' |
269 |
- merged from ecco-branch |
270 |
(remaining bug fixes for obcs gradient checks) |
271 |
- additional high-precision output for testreport |
272 |
(grep for 'precision_grdchk_result') |
273 |
|
274 |
checkpoint51r_post |
275 |
o cleaned up or removed CPP_OPTIONS.h files |
276 |
o updated results for some of the tests to reflect the new |
277 |
optfiles (-ieee: -O0 instead of -O3) |
278 |
|
279 |
checkpoint51q_post |
280 |
o cd_code: |
281 |
- moved cd_scheme.F -> cd_code_scheme.F |
282 |
- separate read_checkpoint from cd_code_ini_vars.F |
283 |
- separated cd_code part from write_checkpoint |
284 |
- updated AD_SOURCE, generated .flow |
285 |
- added CD_CODE_VARS.h to the_main_loop |
286 |
- Moving cd_code specific store dir.s to pkg/cd_code |
287 |
o ctrl package totally restructured |
288 |
- pack/unpack now optional and decoupled from |
289 |
xx_/adxx_ I/O |
290 |
- ctrl_pack/unpack cleaned |
291 |
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
292 |
- confined inclusion of AD_CONFIG.h to where necessary. |
293 |
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
294 |
|
295 |
checkpoint51p_post |
296 |
o create initial cd_code package |
297 |
- WARNING: the initialization of fields within packages |
298 |
is broken because INI_FIELDS (where READ_CHECKPOINT is |
299 |
called) is called *before* PACKAGES_INIT_VARIABLES. |
300 |
This seems to be backwards since |
301 |
1) its important to initially zero the entire field including |
302 |
the "halo" region |
303 |
2) zeroing needs to be done *before* reading pickup info |
304 |
and the pickup call might or might not happen in any |
305 |
particular run |
306 |
- this needs an overhaul for R2 |
307 |
o cleanup verification/*/code/GMREDI_OPTIONS.h |
308 |
o cleanup testreport |
309 |
|
310 |
checkpoint51o_post |
311 |
o bringing AD-related verif's up to date with genmake2 |
312 |
- carbon/ |
313 |
- global_ocean.90x40x15/ |
314 |
- hs.94.1x64x5/ |
315 |
- (front_relax/ ) |
316 |
o (more) consistent directory structure for AD-related verif.'s |
317 |
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
318 |
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
319 |
o bug fix in find_alpha.F for MDJWF: |
320 |
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
321 |
change rho -> rho-rhoConst |
322 |
- replace call find_rho to find_rhonum |
323 |
o initialisation of rFlx extended to full array (required by TAF) |
324 |
and shifted to thermodynamics |
325 |
o removed PTRACERS.h in ptracers routine |
326 |
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
327 |
o Correcting initialisations for fVerU, fVerV. |
328 |
o helping TAF to recognize dependency on kUp for |
329 |
fVerU, fVerV |
330 |
o Replacing delZ by delR in pkg/ctrl/ |
331 |
checkpoint51o_pre |
332 |
|
333 |
o undid all of cp51 pending some cleanups and discussion |
334 |
o added the [#include "AD_CONFIG.h"] statement to all files that need |
335 |
it for adjoint/tl #defines |
336 |
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
337 |
o removed tools/genmake since it no longer works |
338 |
|
339 |
checkpoint51n_post |
340 |
o modifications to make FREEZE flux visible to pkg/kpp |
341 |
- moved surfaceTendencyTice from pkg/seaice to main code |
342 |
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
343 |
- subroutine FREEZE now limits only surface temperature |
344 |
(this means new output.txt for global_ocean.90x40x15, |
345 |
global_ocean.cs32x15, and global_with_exf) |
346 |
o added surface flux output variables to TIMEAVE_STATVARS |
347 |
|
348 |
checkpoint51n_pre |
349 |
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
350 |
o added [#include "AD_CONFIG.h"] to all files that use the following |
351 |
defines: |
352 |
- ALLOW_ADJOINT_RUN |
353 |
- ALLOW_TANGENTLINEAR_RUN |
354 |
- ALLOW_ECCO_OPTIMIZATION |
355 |
|
356 |
checkpoint51m_post |
357 |
o incorporating changes to get TAMC/TAF working in genmake2 |
358 |
- added new TAMC/TAF targets to the Makefile |
359 |
- various cleanups related to package handling |
360 |
- these changes should have no impact on the forward model |
361 |
|
362 |
checkpoint51l_post |
363 |
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
364 |
- faster algorithm for cal_addtime.F |
365 |
- higher precision arithmetic, where needed |
366 |
- pkg/exf *startdate variables changed from calendar date to |
367 |
model integration time |
368 |
|
369 |
checkpoint51l_pre |
370 |
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
371 |
o enable to apply restoring on S & T only in a latitude band. |
372 |
o update output (external_forcing_surf modif. change truncation errors) |
373 |
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
374 |
|
375 |
checkpoint51k_post |
376 |
o change default to: useNHMTerms=.FALSE. |
377 |
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
378 |
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
379 |
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
380 |
exp1, ideal_2D_oce |
381 |
- change data file of oceanic exp (leave the results unchanged for now) |
382 |
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
383 |
o set gravitySign automatically according to the vertical coordinate used |
384 |
(and change sign: back to "logical" value: +1 when R increases downward) |
385 |
o added an include barrier to the default CPP_OPTIONS.h and |
386 |
removed the #include "PACKAGES_CONFIG.h" from it |
387 |
o fix a bug in mom_fluxform (from chk51j_post) |
388 |
|
389 |
checkpoint51j_post |
390 |
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
391 |
o adjusted some flow directives (dynamics, thermodynamics) |
392 |
o added cubed-sphere case to test cost function |
393 |
o heckpoint_lev?_directives.h now include |
394 |
pkg-specific directives, whenever those are enabled. |
395 |
o Moving pkg-specific flow directives to corresponding pkg |
396 |
Moving pkg-specific differentiation list to corresponding pkg |
397 |
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
398 |
---> conventions are |
399 |
- pkg_ad.flow |
400 |
- pkg_ad_diff.list |
401 |
- pkg_ad_check_lev?_dir.h |
402 |
|
403 |
checkpoint51i_post |
404 |
o merge of the branch-genmake2 |
405 |
- knowingly breaks the older genmake |
406 |
- automatic generation of all ALLOW_${PKG_NAME} defines |
407 |
- new testreport supersedes older testscript |
408 |
o large number of package inclusion and header cleanups |
409 |
checkpoint51i_pre |
410 |
|
411 |
o new output for adjoin of global ocean vector invariant |
412 |
o fix for checkpoint of thermodynamic seaice and bulk_force |
413 |
o Steph gchem various cleanups |
414 |
|
415 |
checkpoint 51h_pre |
416 |
o fixed some single quotes |
417 |
o modify gchem pkg to be more versatile |
418 |
o modifications to clean up dic pkg |
419 |
o add pkg/cfc |
420 |
|
421 |
checkpoint51g_post |
422 |
o provide links for ARPACK and ADM*TLM |
423 |
o start removing verification/vero/ |
424 |
o update AD-related stuff |
425 |
(in particular some IF-statements in model/src/ routines) |
426 |
o adding to verification/global_ocean.90x40x15/ adjoint of |
427 |
vector invariant setup |
428 |
|
429 |
checkpoint51f_post |
430 |
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
431 |
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
432 |
of tracer Green's fucntions for ocean inversion project. |
433 |
|
434 |
checkpoint51f_pre |
435 |
o Added on-the-fly spatial interpolation capability |
436 |
"USE_EXF_INTERPOLATION" to pkg/exf. |
437 |
- This is a temporary Cartesian-grid hack until |
438 |
the super-duper ESMF coupler becomes available. |
439 |
- See verification/global_with_exf/README for usage example. |
440 |
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
441 |
flags and modified pkg/seaice accordingly. |
442 |
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
443 |
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
444 |
non-local transport term. |
445 |
|
446 |
checkpoint51e_post |
447 |
o pkg/mom_vecinv: |
448 |
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
449 |
- add time-ave diagnostic of vorticity advection. |
450 |
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
451 |
o atmospheric geopotential: - include water vapor effect; |
452 |
- use p^kappa in p* scaling. |
453 |
o land pkg: read initial state from files. |
454 |
o AIM : add stratospheric drag in the upper level |
455 |
|
456 |
checkpoint51d_post |
457 |
o change function ILNBLNK (=> last non-blank char.) to return zero |
458 |
(instead of the string length) when the string. char is empty |
459 |
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
460 |
o modif's to restore TAMC compatibility |
461 |
- avoid "_d" constructs in PARAMETER declarations |
462 |
- avoid interrupting lines by comment lines |
463 |
o Use cluster local disks for purely local I/O |
464 |
vs. globally visible disks needed for ctrl stuff |
465 |
(merged from ecco-branch) |
466 |
- new active_file_loc... and mdsio_..._loc routines |
467 |
- affected packages: autodiff, ctrl, grdchk, mdsio |
468 |
|
469 |
checkpoint51c_post |
470 |
o introducing integer flag debugLevel |
471 |
- debLevZero: suppress all output |
472 |
- debLevA: standard |
473 |
- debLevB: equivalent to current debugMode=.TRUE. |
474 |
o introducing pathname variable mdsioLocalDir for mdsio |
475 |
that can be specified at runtime |
476 |
(relevant for cluster I/O to local disk) |
477 |
` |
478 |
>>>checkpoint51b_post |
479 |
adjoint of ptracers |
480 |
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
481 |
o extended state in checkpoint_lev?, etc. |
482 |
o alternative ctrl/cost with tr1 or ptracer |
483 |
o new comlev1_bibj_ptracers |
484 |
o new ptracers.flow |
485 |
o made ptracers_forcing same as external_forcing_s |
486 |
o added verification for adjoint with ptracers |
487 |
- adm. grdchk fail so far |
488 |
- tlm. grdchk OK |
489 |
- checked tapelev/comlev recomputations: OK |
490 |
<<<checkpoint51b_pre |
491 |
|
492 |
checkpoint51a_post |
493 |
o added code for biogeochemistry package |
494 |
- new pkgs: dic, gchem |
495 |
- new subroutine in ptracers |
496 |
o modify code for biogeo packages |
497 |
- in model/src and pkg/ptracers |
498 |
|
499 |
checkpoint51 |
500 |
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
501 |
- autodiff, ctrl, exf, grdchk, seaice |
502 |
kept separate packages |
503 |
- cost, ecco, obcs |
504 |
o updating verification/internal_wave, verification/lab_sea |
505 |
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
506 |
|
507 |
checkpoint50i_post |
508 |
o Preparing next differentiable checkpoint and sync |
509 |
of MAIN vs. ecco-branch |
510 |
- 1st step: this one is differentiable |
511 |
- 2nd step: next(! not this) checkpoint will have updated packages |
512 |
from ecco-branch) |
513 |
|
514 |
checkpoint50h_post |
515 |
o new package "land": provide surface BC for AIM. |
516 |
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
517 |
o AIM: use true log-P extrapolation for near surface temp (= as in |
518 |
F.Molteni paper) ; update aim.5l_cs output. |
519 |
o New variable in PARM03 for more flexible pickups |
520 |
o somewhat cleaned package initialisation sequence for |
521 |
ctrl/ cost/ ecco/ in packages_... routines |
522 |
|
523 |
checkpoint50g_post |
524 |
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
525 |
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
526 |
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
527 |
made the default because of faster convergence than ADI |
528 |
|
529 |
checkpoint50f_post |
530 |
o exf totally restructured |
531 |
- replaced all exf_set_ routines by one generic exf_set_gen.F |
532 |
and made sure it's still differentiable |
533 |
- split exf_getffields.F into new exf_bulkformulae.F |
534 |
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
535 |
- updated adjoint/makefile and relevant verif. accordingly |
536 |
|
537 |
checkpoint50f_pre |
538 |
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
539 |
+ change Evap over land. (update aim.5l_cs output) |
540 |
o added missing .cvsignores and made uniform across expts |
541 |
o changed configuration of tidal_basin_2d expt |
542 |
o added pkg/debug functions for tracing code in fatal crashes |
543 |
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
544 |
o new fn in pkg/monitor to stop model if solution grows too big |
545 |
o removed lots of single quotes from comments |
546 |
|
547 |
checkpoint50e_post |
548 |
o make KPP work with PTRACERS |
549 |
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
550 |
nearly a copy of kpp_transport_s |
551 |
- there is no analogue to SurfaceTendencyS, so I have to use |
552 |
gPtr(of the surface layer) instead |
553 |
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
554 |
checkpoint50e_pre |
555 |
|
556 |
checkpoint50d_post |
557 |
o change kpp output from multiple-record state files to single-record state |
558 |
files analogous to write_state.F |
559 |
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
560 |
analogous to the cg2d-related output. |
561 |
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
562 |
so that writing to internal file fn (with length 512) fails. |
563 |
checkpoint50d_pre |
564 |
|
565 |
checkpoint50c_post |
566 |
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
567 |
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
568 |
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
569 |
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
570 |
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
571 |
|
572 |
checkpoint50c_pre |
573 |
Merging from release1_p13: |
574 |
o bug fix for pkg/seaice dynamic solver |
575 |
o Added SEAICE_initialHEFF to pkg/seaice |
576 |
|
577 |
checkpoint50b_post |
578 |
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
579 |
o in order to put the momForcing out of the Adams-Bashforth: |
580 |
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
581 |
to timestep.F |
582 |
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
583 |
o re-generate output for highly sensitive test-exp: |
584 |
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
585 |
|
586 |
checkpoint50b_pre |
587 |
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
588 |
o corrected CPP option mismatch in exf_Bulk... functions for case |
589 |
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
590 |
|
591 |
checkpoint50a_post |
592 |
o Bug fix for merging between c50 and KPP. |
593 |
ikey was passed from thermodynamics to kpp_calc via |
594 |
common block rather than being recomputed in kpp_calc, |
595 |
in contradiction with new key itdkey. |
596 |
New key ikppkey created, and tamc.h headers updated. |
597 |
|
598 |
checkpoint50 |
599 |
- 2nd step of merge with ecco-branch: |
600 |
merge changes in ecco-branch back into main trunk |
601 |
- bug fix in find_alpha |
602 |
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
603 |
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
604 |
- merged some sliced AD support routines |
605 |
|
606 |
checkpoint49 |
607 |
merged from ecco-branch: |
608 |
o exf: |
609 |
- Enable initialisation of forcing fields to constant |
610 |
(runtime) values. |
611 |
- in exf_getffields.F |
612 |
Reduce i-/j-loop to interior domain, discarding overlaps. |
613 |
That also fixes wrong TAF-key computations for key_1, key_2 |
614 |
with bulf formulae. |
615 |
- exf_init.F modify #ifdef for exf_init_evap |
616 |
- exf_getffieldrec.F, ctrl_getrec.F |
617 |
The following INT-usages are not safe: |
618 |
fldsecs = int(fldsecs/fldperiod)*fldperiod |
619 |
fldcount = int(fldsecs/fldperiod) + 1 |
620 |
and were modified. |
621 |
o autodiff: checkpoint_lev... |
622 |
- updated storing for bulk formulae (some arrays were missing) |
623 |
- added state for seaice package |
624 |
- synchronized with main branch |
625 |
o DIVA: |
626 |
Modif.s in |
627 |
- the_main_loop.F |
628 |
- the_model_main.F |
629 |
and added cost_final_restore.F cost_final_store.F |
630 |
o With these changes, it is possible to fully separate |
631 |
the first forward run to compute the cost function (mdthe_main_loop) |
632 |
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
633 |
into separate model executions. |
634 |
This enables better tuning of DIVA to given queue sizes. |
635 |
o Loss of cost function value in consecutive DIVA runs is |
636 |
fixed by storing to 'costfinal' file. |
637 |
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
638 |
beginning/end of adjoint integration is accounted for. |
639 |
The current changes apply to TAF-1.4.26. |
640 |
TAF has one remaining bug, requiring one manual change |
641 |
(see MITgcm manual). |
642 |
o cal: synchronized between MAIN and ecco-branch |
643 |
|
644 |
checkpoint48i_post |
645 |
o Changes to restore differentiability of code w.r.t. previous tag |
646 |
(mostly adding new routines to make list and replacing |
647 |
pressure by totPhiHyd). |
648 |
o Updated and merged grdchk package |
649 |
- has both ADM and TLM checks |
650 |
- works for single- and multi-proc. |
651 |
- output cleaned |
652 |
- worked successfully for parallel DIVA |
653 |
o genmake: |
654 |
- Adding -platform=SP4 |
655 |
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
656 |
o Modif. for DIVA: |
657 |
ctrl_unpack should not be called in intermediate DIVA interval. |
658 |
(similar thing would apply for active files such as |
659 |
tbar, sbar, psbar, which should not be reinitialised; |
660 |
only relevant for ecco-branch) |
661 |
|
662 |
checkpoint48h_post |
663 |
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
664 |
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
665 |
o Added SEAICE_initialHEFF to pkg/seaice |
666 |
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
667 |
|
668 |
checkpoint48g_post |
669 |
--- EOS: |
670 |
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
671 |
store total Potential in totPhyHyd for diagnostics & EOS. |
672 |
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
673 |
--- Pressure/geopotential gradient: |
674 |
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
675 |
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
676 |
( changes results of global_ocean_pressure ) |
677 |
o NLFS + z-coord.: add eta*Rho' contribution. |
678 |
o accurate phiHyd when using interface-W at the middle between 2 centers |
679 |
( changes results of ideal_2D_oce ) |
680 |
o includes r* 2nd term in potential gradient. |
681 |
|
682 |
checkpoint48f_post |
683 |
Merging from release1_p12: |
684 |
o Modifications for using pkg/exf with pkg/seaice |
685 |
- improved description of the various forcing configurations |
686 |
- added basic radiation bulk formulae to pkg/exf |
687 |
- units/sign fix for evap computation in exf_getffields.F |
688 |
- updated verification/global_with_exf/results/output.txt |
689 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
690 |
(SBO) core products, including oceanic mass, center-of-mass, |
691 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
692 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
693 |
to avoid negative values in shallow regions. |
694 |
- updated verification/natl_box/results/output.txt |
695 |
- updated verification/lab_sea/results/output.txt |
696 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
697 |
o Added useSingleCpuIO option (see PARAMS.h). |
698 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
699 |
work with multi-field files, e.g., for single-file pickup. |
700 |
o pkg/seaice: |
701 |
- bug fix in growth.F: QNET for no shortwave case |
702 |
- added HeffFile for specifying initial sea-ice thickness |
703 |
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
704 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
705 |
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
706 |
o pkg/seaice: |
707 |
- adjoint-friendly modifications |
708 |
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
709 |
|
710 |
checkpoint48e_post |
711 |
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
712 |
o dynamics: change definition of computational domain & adapt mom_fluxform |
713 |
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
714 |
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
715 |
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
716 |
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
717 |
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
718 |
inverted_barometer solid-body.cs-32x32x1 |
719 |
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
720 |
|
721 |
checkpoint48d_post |
722 |
o in preparation for r*: |
723 |
a) use pre-computed gradient of hydrostatic potential: |
724 |
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
725 |
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
726 |
=> affects results of glob_oce_pressure (different truncation error) |
727 |
update output.txt of ideal_2D_oce & global_ocean_pressure |
728 |
|
729 |
checkpoint48d_pre |
730 |
o in preparation for r*: |
731 |
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
732 |
pass the 2 comp. of the grad. as arguments to momentum S/R. |
733 |
but for the moment, only used if it does not change the results. |
734 |
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
735 |
|
736 |
checkpoint48c_post |
737 |
Modifications in treatment of initial flux forcing controls |
738 |
to avoid extra storing of flux fields. |
739 |
|
740 |
checkpoint48c_pre |
741 |
o Added tidal_basin_2d experiment (currently 1D!) |
742 |
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
743 |
|
744 |
checkpoint48b_post |
745 |
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
746 |
(modification to pressure gradient not yet implemented) |
747 |
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
748 |
(for U & V) that are used for vertical advection of momentum. |
749 |
|
750 |
checkpoint48a_post |
751 |
o In preparation for r*, use temp. array to compute vertical transport |
752 |
in flux-form momentum pkg. => change results of few test-exp. |
753 |
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
754 |
lab_sea, natl_box & plume_on_slope |
755 |
|
756 |
checkpoint48 |
757 |
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
758 |
|
759 |
checkpoint47j_post |
760 |
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
761 |
o moved adexch from forward_step to addummy_in_stepping |
762 |
o added exch in ctrl_map_... |
763 |
o aveFreq.=0. at end of cost_final to avoid overwrite in |
764 |
reverse checkpointing loop |
765 |
o Yet more changes in gmredi: |
766 |
* adgmredi_calc_tensor |
767 |
avoiding all recomputation of gmredi_slope_limit |
768 |
* adgmredi_x/y/rtransport |
769 |
added flag for excessive storing to avoid recomp. of |
770 |
u/v/rtans, dTdx/y/z |
771 |
-> this is not really necessary and very memory-consuming |
772 |
* adgmredi_slope_psi: |
773 |
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
774 |
* gmredi_slope_limit |
775 |
re-activated full calculation of taperfct for case 'ac02' |
776 |
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
777 |
|
778 |
checkpoint47i_post |
779 |
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
780 |
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
781 |
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
782 |
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
783 |
o gmredi: fix few bugs. |
784 |
|
785 |
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
786 |
This will be a good checkpoint to plug into the ecco-branch. |
787 |
o few modif.'s to get latest version adjointed |
788 |
(mainly kick out code in ini_linear_phisurf) |
789 |
o modif's to run adjoint with exactConserv |
790 |
o case GM_BOLUS_ADVEC should be cleaned |
791 |
S/R gmredi_slope_psi should be cleaned |
792 |
o verification/carbon now has exactConserv=.TRUE. |
793 |
|
794 |
checkpoint47g_post |
795 |
o time-average AIM output: becomes independent from statvars time-average |
796 |
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
797 |
o After TAF bug fix: |
798 |
Tested adjoint of gmredi package. |
799 |
Tests were done with checkpoint47 rather than with latest |
800 |
checkpoint47f_post since the latter is broken for the adjoint |
801 |
verification/carbon/ contains both ADM and TLM gradient checks. |
802 |
Here they are, before they get changed/lost/stolen. |
803 |
Mostly modif.'s to fix numerical sensitivities. |
804 |
Gradient checks OK for |
805 |
- GM_taper_scheme: |
806 |
* clipping |
807 |
* ac02 |
808 |
* linear |
809 |
* glw91 |
810 |
* dm95 |
811 |
* ldd97 |
812 |
- GMREDI_OPTIONS: |
813 |
* GM_VISBECK_VARIABLE_K |
814 |
* GM_NON_UNITY_DIAGONAL |
815 |
* GM_EXTRA_DIAGONAL |
816 |
* GM_BOLUS_ADVEC |
817 |
in conjunction with data.gmredi parameters to be checked in |
818 |
in a few minutes under verification/carbon/code/ |
819 |
|
820 |
checkpoint47f_post |
821 |
Merging from release1_p10: |
822 |
o modifications for using pkg/exf with pkg/seaice |
823 |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
824 |
and SEAICE_EXTERNAL_FLUXES |
825 |
- pkg/exf CPP options EXF_READ_EVAP and |
826 |
EXF_NO_BULK_COMPUTATIONS |
827 |
- usage examples are Experiments 8 and 9 in |
828 |
verification/lab_sea/README |
829 |
- verification/lab_sea default experiment now uses |
830 |
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
831 |
|
832 |
checkpoint47e_post |
833 |
o created a tag prior to creating a branch |
834 |
|
835 |
checkpoint47d_post |
836 |
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
837 |
at the bottom boundary had an erroneous half slip boundary condition |
838 |
o added bottom drag and no slip boundary condition capabilities to |
839 |
oceanic pressure coordinates code |
840 |
o added new verification experiment global_ocean_pressure, this experiment is |
841 |
also described in the tutorial section of the manual |
842 |
checkpoint47d_pre |
843 |
|
844 |
checkpoint47c_post |
845 |
o Added a verification experiment for a global cubed-sphere ocean run |
846 |
- verification/global_ocean.cubed32x32x30 |
847 |
- uses pkg/therm_seaice and pkg/bulk_forcing |
848 |
|
849 |
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
850 |
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
851 |
when using P-coordinate; only implemented for atmospheric config. |
852 |
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
853 |
NOTES: requires option NONLIN_FRSURF to be "#define". |
854 |
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
855 |
|
856 |
checkpoint47b_post |
857 |
Merging from release1_p9: |
858 |
o pkg/seaice |
859 |
- removed GOTO's and added taf directives |
860 |
- double precision constants to reduce the g77 (Linux) |
861 |
to F77 (SGI) differences reported in release1_p8 |
862 |
o tools/genmake |
863 |
- added SGI options |
864 |
o verification/testscript |
865 |
- updated to that of checkpoint47a_post |
866 |
o verification/global_ocean.90x40x15/input/eedata |
867 |
- modified for SGI f77 compatibility |
868 |
o verification/lab_sea |
869 |
- added description of sea-ice model |
870 |
- added missing matlab routines |
871 |
- added test of thermodynamics parallelization |
872 |
|
873 |
checkpoint47a_post |
874 |
o new pkg: aim_v23 |
875 |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
876 |
for now, keep the same surface forcing as before. |
877 |
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
878 |
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
879 |
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
880 |
o add diagnostic of surface correction term in monitor output |
881 |
|
882 |
o bulk_force and therm_seaice |
883 |
- Two packages: bulk_force (Bulk forcing) |
884 |
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
885 |
- Earlier integration from Stephaine Dutkiewicz |
886 |
and Patrick Heimbach. |
887 |
- Two ifdef statements for compile time, |
888 |
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
889 |
|
890 |
checkpoint47 |
891 |
differentiable version of checkpoint46n_post |
892 |
o bug fix in quasihydrostaticterms |
893 |
o * "clean" adjoint code (in terms of extensive recomputations) |
894 |
can now be obtained for all GMREDI options (i.e. for |
895 |
- GM_VISBECK_VARIABLE_K |
896 |
- GM_NON_UNITY_DIAGONAL |
897 |
- GM_EXTRA_DIAGONAL |
898 |
- GM_BOLUS_ADVEC ) |
899 |
* However, wrong gradient check problem remains unsolved. |
900 |
* New CPP options have been introduced for different |
901 |
tapering schemes |
902 |
o external_fields_load now part of differentiation list |
903 |
o pressure needs multiple storing; |
904 |
would be nice to have store_pressure at beginning or |
905 |
end of forward_step, e.g. by having phiHyd global (5-dim.) |
906 |
(NB: pressure is needed for certain cases in find_rho, |
907 |
which is also invoked through convective_adjustment). |
908 |
o recomputations in find_rho for cases |
909 |
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
910 |
o #define ATMOSPHERIC_LOADING should be differentiable |
911 |
o ini_forcing shifted to begining of initialise_varia |
912 |
o Incorporating QNVS line search routines into MITgcm |
913 |
(this is separate code, and therefore not under pkg) |
914 |
lsopt/, optim/ |
915 |
o Updated verification/carbon/ |
916 |
- #define GM_VISBECK_VARIABLE_K |
917 |
- GM_taper_scheme = 'ldd97' |
918 |
|
919 |
checkpoint46n_post |
920 |
Merging from release1_p8: |
921 |
o verification/natl_box: |
922 |
updating new external_fields_load routine |
923 |
o New package: pkg/seaice |
924 |
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
925 |
The sea-ice code is based on Hibler (1979-1980). |
926 |
Two sea-ice dynamic solvers, ADI and LSR, are included. |
927 |
In addition to computing prognostic sea-ice variables and diagnosing |
928 |
the forcing/external data fields that drive the ocean model, |
929 |
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
930 |
The implied surface heat flux is then stored in variable |
931 |
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
932 |
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
933 |
non-local transport term. Because this call precedes model |
934 |
thermodynamics, temperature under sea-ice may not be "exactly" at |
935 |
the freezing point by the time theta is dumped or time-averaged. |
936 |
N.B.: fairly large differences in accuracy occur across |
937 |
different platforms/compilers; comparison between |
938 |
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
939 |
generated output gives: |
940 |
T S U V |
941 |
C D M c m s m s m s m s |
942 |
n p a R g m m e . m m e . m m e . m m e . |
943 |
f n k u 2 i a a d i a a d i a a d i a a d |
944 |
g d e n d n x n . n x n . n x n . n x n . |
945 |
|
946 |
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
947 |
o GAD: |
948 |
- generated new common blocks to account for call of |
949 |
same gad routines with differing traceridentities |
950 |
(needed to modify tracerIdentity indices in GAD.h) |
951 |
- generated separate common blocks for case useCubedSphereExchange |
952 |
(Department of Futurology) |
953 |
- parameter lists to gmredi_?transport: added tracerIdentity |
954 |
- added new key indices to tamc.h |
955 |
o external_fields_load: |
956 |
- added this routine to TAF list |
957 |
- needed to make some common blocks global and additional storing |
958 |
along the same lines as exf package (checkpoint_lev?_directives.h) |
959 |
o exf: |
960 |
updated external forcing package |
961 |
- bug fixes carried over from ecco-branch |
962 |
(missing OBCS_OPTIONS.h in two routines) |
963 |
- enable easy to use "no forcing". |
964 |
- added exf I/O for atmospheric loading |
965 |
- added exf I/O for runoff data |
966 |
- transfered scaling between exf <-> MITgcm to exf namelist |
967 |
o Adding new verification experiment global_with_exf. |
968 |
This verification experiment is almost identical to the |
969 |
global_ocean.90x40x15 experiment, except that it uses |
970 |
the exf (and cal) package instead of the |
971 |
external_fields_load routine (cf README file). |
972 |
|
973 |
checkpoint46m_post |
974 |
o modified testscript to return -- when there are no lines of "%MON" output |
975 |
o added new flag "quasiHydrostatic" for QH mode |
976 |
and new routine quasihydrostaticterms() |
977 |
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
978 |
New routine: mom_u_coriolis_nh() |
979 |
o fixed sign of non-hydrostatic metric terms in u and v equations. |
980 |
Depend on correct sign of gravitySign. |
981 |
o added work.pc* to .cvsignore in aim directories using ifc |
982 |
o introduced flag for controllin non-hydrostatic metric terms |
983 |
o removed gravitySign from PARM04 |
984 |
o switched to g77/ifc from pgf77 in aim experiments |
985 |
|
986 |
checkpoint46l_post |
987 |
o made convective adjustment work with pressure coordinates: |
988 |
- changed the direction of k-loop in convective_adjustment.F for the |
989 |
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
990 |
- adjusted the reference pressure k-index in convective_adjustment.F |
991 |
- adjusted the convection condition in convect.F (in analogy to |
992 |
calc_ivdc.F) |
993 |
- convective_adjustment no longer computes anything on the halos |
994 |
- removed the warnings about negative salinity from find_rho.F and |
995 |
find_alpha.F; instead the new routine look_for_neg_salinity, called |
996 |
at the beginning of find_rho, find_alpha, and find_beta, does a |
997 |
check of the entire slice, if CPP-option |
998 |
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
999 |
checkpoint46l_pre |
1000 |
|
1001 |
checkpoint46k_post |
1002 |
o fixed the verification/global_ocean.90x40x15 experiment: |
1003 |
- new bathymetry (the world according to A., JMC, and M.) |
1004 |
- new initial fields and forcing fields (*.bin files) |
1005 |
- new POLY3.COEFFS (for the next release one should switch to a full |
1006 |
equation of state: JMD95P or MDJWF) |
1007 |
- fixed several errors and redundancies in the data file |
1008 |
- experiment uses looped cells |
1009 |
- added matlab directory with diagnostic scripts for plotting of output |
1010 |
|
1011 |
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
1012 |
- read AIM physics parameters from a file (data.aimphys) |
1013 |
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
1014 |
|
1015 |
checkpoint46j_post |
1016 |
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
1017 |
o move wVel computation at the end of the time step, in S/R integr_continuity |
1018 |
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
1019 |
o update timeave pkg for wVel diagnostic. |
1020 |
checkpoint46j_pre |
1021 |
|
1022 |
checkpoint46i_post |
1023 |
o Clean up AIM package (and keep the results unchanged): |
1024 |
include CPP_OPTION and use IMPLICT NONE in all routines ; |
1025 |
declare all the variables _RL ; use _d 0 for all numerical constants. |
1026 |
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
1027 |
|
1028 |
checkpoint46h_post |
1029 |
o cleaned up the use of rhoNil and rhoConst. |
1030 |
- rhoNil should only appear in the LINEAR equation of state, everywhere |
1031 |
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
1032 |
and the dynamical equations are all divided by rhoConst |
1033 |
o introduced new parameter rhoConstFresh, a reference density of fresh |
1034 |
water, to remove the fresh water flux's dependence on rhoNil. The default |
1035 |
value is 999.8 kg/m^3 |
1036 |
o cleanup up external_forcing.F and external_forcing_surf.F |
1037 |
- can now be used by both OCEANIC and OCEANICP |
1038 |
checkpoint46h_pre |
1039 |
|
1040 |
Added code to convert surface volume flux (fresh water) into |
1041 |
a mass flux when using P coordinates in the ocean (OCEANICP). |
1042 |
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
1043 |
|
1044 |
checkpoint46g_post |
1045 |
o Include a new diagnostic variable phiHydLow for the ocean model |
1046 |
- in z-coordinates, it is the bottom pressure anomaly |
1047 |
- in p-coordinates, it is the sea surface elevation |
1048 |
- in both cases, these variable have global drift, reflecting the mass |
1049 |
drift in z-coordinates and the volume drift in p-coordinates |
1050 |
- included time averaging for phiHydLow, be aware of the drift! |
1051 |
o depth-dependent computation of Bo_surf for pressure coordinates |
1052 |
in the ocean (buoyancyRelation='OCEANICP') |
1053 |
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
1054 |
Theta, Salinity, and Pressure in the parameter list. This routine is |
1055 |
presently contained in find_rho.F. This routine does not give the |
1056 |
correct density for 'POLY3', which would be a z-dependent reference |
1057 |
density. |
1058 |
o cleaned up find_rho |
1059 |
- removed obsolete 'eqn' from the parameter list. |
1060 |
o added two new verification experiments: gop and goz |
1061 |
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
1062 |
checkpoint46g_pre |
1063 |
|
1064 |
checkpoint46f_post |
1065 |
o Enable tangent linear (forward mode) gradient checks: |
1066 |
- extended active file handling to g_... files |
1067 |
- added TANGENT_SIMULATION to theSimulationMode |
1068 |
- extended grdchk package accordingly |
1069 |
o added tangent linear setup in verification/carbon/code_ftl |
1070 |
o added adjoint setup in verification/front_relax/code_ad |
1071 |
|
1072 |
checkpoint46e_post |
1073 |
o Added new equation of state -> MDJWF |
1074 |
- EOS of McDougall et al., 2002, JAOT, submitted |
1075 |
- caveat: the equation of state is only valid for a smaller (more |
1076 |
realistic?) range of values than JMD95P/Z and UNESCO |
1077 |
- added masks to the calculation of pressure in store_pressure |
1078 |
- added more check values for density in check_eos (ini_eos.F), some of |
1079 |
the old check values are out of the range of the MDJWF-eos, so don't |
1080 |
expect perfect matches for those |
1081 |
checkpoint46e_pre |
1082 |
|
1083 |
checkpoint46d_post |
1084 |
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
1085 |
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
1086 |
case of pressure coordinates. eosType='JMD95Z' in |
1087 |
combination with buoyancyRelation='OCEANICP' now causes an error. |
1088 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1089 |
in find_alpha/beta. |
1090 |
checkpoint46d_pre |
1091 |
|
1092 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
1093 |
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
1094 |
|
1095 |
checkpoint46c_post |
1096 |
o Changes necessary for ocean in p-coordinates |
1097 |
- Added new buoyancy relation = 'OCEANICP' |
1098 |
- Added new parameters = gravitySign (this used to be contained inside |
1099 |
the factor dRdZ which I added when we first switched to R coordinates). |
1100 |
X GM/Redi is not compatible (yet) |
1101 |
X bottom drag and no-slip need to be debugged. |
1102 |
checkpoint46c_pre |
1103 |
|
1104 |
checkpoint46b_post |
1105 |
o Added new equation of state -> JMD95Z and JMD95P |
1106 |
- EOS of Jackett and McDougall, 1995, JAOT |
1107 |
- moved all EOS parameters into EOS.h |
1108 |
- new routines ini_eos.F, store_pressure.F |
1109 |
o Added UNESCO EOS, but not recommended because it requires |
1110 |
in-situ temperature (see JMD95) |
1111 |
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
1112 |
unesco.f to be used with POLY3 |
1113 |
checkpoint46b_pre |
1114 |
|
1115 |
checkpoint46a_post |
1116 |
o Added (atmospheric) pressure loading |
1117 |
- new field in FFIELDS.h, etc... |
1118 |
- new cpp flag ATMOSPHERIC_LOADING |
1119 |
o Changed hFacC to _hFacC in calc_phi_hyd.F |
1120 |
o Added SHORTWAVE_HEATING to some files for consistency |
1121 |
checkpoint46a_pre |
1122 |
|
1123 |
checkpoint46 |
1124 |
further merges from release1_p5 |
1125 |
o new ctrl package |
1126 |
- adopted from ECCO environment to enable optimization |
1127 |
- added Eliassen Palm fluxes to controls |
1128 |
o added Eliassen Palm flux controls to gradient check package |
1129 |
o cost package |
1130 |
- Compatible with new ctrl package |
1131 |
- added Eliassen Palm cost hooks |
1132 |
- modif's of existing cost functions |
1133 |
o Adjoint-related bug fixes in kpp: |
1134 |
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
1135 |
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
1136 |
o autodiff package |
1137 |
- flow directives: |
1138 |
+ new for S/R do_the_model_io |
1139 |
+ enhanced for S/R checkpoint |
1140 |
+ new gmredi.flow |
1141 |
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
1142 |
disable adcommon.h/g_common.h by default. |
1143 |
- fixed problem for adjoint of global_max |
1144 |
o modified verification/carbon/ |
1145 |
o New setup for adjoint of global_ocean |
1146 |
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
1147 |
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
1148 |
o incorporated hooks for sponge layer code (external_forcing.F) |
1149 |
|
1150 |
checkpoint45d_post |
1151 |
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
1152 |
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
1153 |
(affects plume_on_slope "cg2d" output) |
1154 |
o add new parameter deltaTfreesurf for free-surface time stepping |
1155 |
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
1156 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
1157 |
o change phiMin in exp1 (to agree with documentation) |
1158 |
o add new flags: |
1159 |
- T,S forcing inside/outside Adams-Bashforth |
1160 |
- turn off temp,salt advection and/or forcing |
1161 |
- for each tracer, define internal flag for multiDimAdvection & A-B |
1162 |
o monitor: change definition of KE to check conservation of Energy |
1163 |
|
1164 |
checkpoint45c_post |
1165 |
o Removed f90 comments ("!") |
1166 |
o Modified initialisations to enable exf package for MITgcm |
1167 |
(without invoking ECCO_PACKAGE). |
1168 |
o modifications to gradient check package (Martin Losch) |
1169 |
- enable centered differences |
1170 |
- modified format of standard output |
1171 |
|
1172 |
checkpoint45b_post |
1173 |
o cleaned exchange calls in cg2d |
1174 |
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
1175 |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
1176 |
to configure barotropic setup (Martin Losch) |
1177 |
o moved some initialisations within bi,bj loop in dynamics |
1178 |
(TAF flow dependency) |
1179 |
o in initialise_varia, moved call packages_init_variables |
1180 |
before convective_adjustment_init |
1181 |
(corresponding adjustment of TAF tape initialisation). |
1182 |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
1183 |
|
1184 |
checkpoint45a_post |
1185 |
o compute Rho over the whole domain (extend iMin,jMin indices) |
1186 |
o specific exchange for X-slice domain (case Ny=1) |
1187 |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
1188 |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
1189 |
|
1190 |
checkpoint44h_post = checkpoint45 |
1191 |
o Fix to restore differentiability: |
1192 |
place at which packages_init_variables is called in |
1193 |
initialise_varia is crucial for reverse control flow. |
1194 |
o modifications in GMRedi to enable stable adjoint |
1195 |
(corresponding modif's in thermodynamics, dynamics) |
1196 |
o added missing hook for sponge layer code in external_forcing |
1197 |
o modified test cost functions |
1198 |
o storing in gad_advection (plus removal of write(0,*)! |
1199 |
o missing headers TR1.h added in convective_adjustment routines |
1200 |
o errorMessageUnit set non-equal zero in eeboot |
1201 |
(conflict on some platforms, e.g. IBM SP3) |
1202 |
o modified carbon verif. |
1203 |
|
1204 |
checkpoint44h_pre |
1205 |
o vertical grid option: allow to put the Interface at the middle between |
1206 |
2 cell-centers ; replace delZ in pkg/kpp by drF. |
1207 |
o GM Advective form: Tracers are advected using the residual transport (= |
1208 |
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
1209 |
|
1210 |
checkpoint44g_post |
1211 |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
1212 |
results) ; ifdef missing in thermodynamics.F |
1213 |
|
1214 |
checkpoint44f_pre,checkpoint44f_post |
1215 |
o added PTRACERS package |
1216 |
This allows an arbitrary number of passive tracers to be integrated |
1217 |
forward simultaneously with the dynamicaly model. |
1218 |
+ Implemented so far: |
1219 |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
1220 |
- I/O and checkpointing |
1221 |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
1222 |
+ Not implemented so far: |
1223 |
- KPP |
1224 |
- OBCS |
1225 |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
1226 |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
1227 |
line in data.pkg. |
1228 |
+ This package is disabled by default since it increases storage. |
1229 |
|
1230 |
|
1231 |
o testscript: added -cleanup option |
1232 |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
1233 |
b) enable to filter 2D fields. |
1234 |
|
1235 |
checkpoint44e_pre,post |
1236 |
o re-wrote convective adjustment to use pre-calculated weights |
1237 |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
1238 |
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
1239 |
Original calls to convect() still in place. |
1240 |
|
1241 |
chkpt44d_pre,post |
1242 |
o added missing EXCLUDE_MONITOR flags |
1243 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
1244 |
(incompatible typ in MIN/MAX expressions caused problems |
1245 |
on IBM SP3) |
1246 |
o in genmake added variable MAKEDEPEND |
1247 |
plus resetting for case SunOS |
1248 |
o added timer_stats.c routine for IBM SP3 |
1249 |
o removed variables in dynamics |
1250 |
!!! I forgot to create tag chkpt44d_pre !!! |
1251 |
!!! But chkpt44d_pre = chkpt44c_post !!! |
1252 |
|
1253 |
o real fresh water flux implemented with non-linear free-surface. |
1254 |
|
1255 |
chkpt44c_pre,post |
1256 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
1257 |
USE_NATURAL_BCS in solve_for_P); |
1258 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
1259 |
|
1260 |
checkpoint44b_pre/_post |
1261 |
o merge of relevant stuff from the ecco-branch: |
1262 |
- genmake: removed $S64 overwrite for case SunOS |
1263 |
- pkg/exf: update and corrections for field swapping and obcs |
1264 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
1265 |
harmonized between ECCO and MITgcm |
1266 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
1267 |
updated checkpointing_lev... lists for obcs |
1268 |
- model/src: minor changes in forward_step, plot_field |
1269 |
added directive for divided adjoint in the_main_loop |
1270 |
- pkg/mdsio: added mdsio_gl_slice |
1271 |
|
1272 |
o check parameters & config (chkpt44a_pre,post) |
1273 |
o OBC and NonLin_FrSurf. |
1274 |
|
1275 |
checkpoint44 |
1276 |
o fix bug in mom_vi_del2uv |
1277 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
1278 |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
1279 |
o update AIM experiments (NCEP input files) |
1280 |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
1281 |
o added some stuff for AD |
1282 |
|
1283 |
checkpoint43 |
1284 |
o added two new advection tests |
1285 |
o added global 4x4 degree ocean test |
1286 |
o added test of H&S94 with free surface on cube |
1287 |
o some final mods for gradient check, adjoint,... |
1288 |
|
1289 |
checkpoint42 |
1290 |
Fixed AD-related problems: |
1291 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
1292 |
(mainly thermodynamics.F) |
1293 |
o New store directives for multi-dim. advection schemes |
1294 |
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
1295 |
* new common block and key passkey |
1296 |
(mainly gad_advection.F) |
1297 |
o Modified store directives for split of dynamics/thermodynamics |
1298 |
for the case ALLOW_KPP |
1299 |
o Cleaned argument list for timestep_tracer.F |
1300 |
|
1301 |
checkpoint41 |
1302 |
o re-formatted/added comments in prologues of key subroutines |
1303 |
to work with protex |
1304 |
|
1305 |
checkpoint40 |
1306 |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
1307 |
o added FLT (floats) package from Arne along with demo. experiment |
1308 |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
1309 |
implementation of forward-in-time forcing terms |
1310 |
o more mods for non-linear free-surface including new variable |
1311 |
o modified multi-dim method to work on cube |
1312 |
o bug fix in KPP (from DM) |
1313 |
|
1314 |
checkpoint40pre9 |
1315 |
o added DST advection schemes |
1316 |
o fix MPI bug on SGI's |
1317 |
o modifications for non-linear free-surface |
1318 |
o fixed conditionals for fixed flow/passive tracer only mode |
1319 |
o added tension/strain form of stress tensor |
1320 |
o changes to commenting of arguments for TAF/TAMC |
1321 |
o added/updated many matlab scripts |
1322 |
o added multi-dimensional advection method for tracers |
1323 |
|
1324 |
checkpoint40pre8 |
1325 |
o new package rw/ |
1326 |
Added method for dumping intermediate local arrays: |
1327 |
mdsio_writetile - same as mdsio_writefield except works from inside |
1328 |
bi,bj loop |
1329 |
mdsio_writelocal - same as mdsio_writetile except works for local |
1330 |
arrays |
1331 |
write_local_r? - higher-level wrapper for mdsio_writelocal |
1332 |
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
1333 |
Example given at end of mom_vecinv.F that dumps some local arrays. |
1334 |
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
1335 |
control flux-form versus vector invariant code. |
1336 |
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
1337 |
or genmake -DISABLE ... |
1338 |
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
1339 |
(additional storing is now needed for case vecinv; |
1340 |
currently nothing implemented to switch this storing off |
1341 |
in case fluxform is used since no CPP flag available). |
1342 |
|
1343 |
checkpoint40pre7 |
1344 |
o bug fix in dynamics.F |
1345 |
calc_viscosity called before k=1,Nr loop. |
1346 |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
1347 |
o cleaned initialisations in ctrl_map_ini |
1348 |
related to TAF |
1349 |
|
1350 |
checkpoint40pre6 |
1351 |
o split dynamics into thermodynamics & dynamics |
1352 |
o corresponding split of calc_diffusivity into |
1353 |
calc_diffusivity, calc_viscosity |
1354 |
(kpp_calc_diff, kpp_calc_visc). |
1355 |
o Added diffkr, kapgm to control variables |
1356 |
o bug fix in gmredi_slope_limit for ldd97 |
1357 |
|
1358 |
checkpoint40pre5 |
1359 |
o proper initialization of Adams-Bashforth time stepping |
1360 |
+ uses forward step for very first step of model (iter=0) |
1361 |
o re-generated *all* output since almost all output is modified by this |
1362 |
change (sorry but we've been putting this one off for about 2 years) |
1363 |
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
1364 |
*not* regenerated since they are already out of date and I don't |
1365 |
want to create the impression that they are suddenly working. |
1366 |
o removed KAP stuff for DEC's |
1367 |
o modified/added many .cvsignore files in */code and */input |
1368 |
o added new expt "solid-body.cs-32x32x1" |
1369 |
+ this uses an alternative form of ini_curvilinear_grid.F which |
1370 |
is not necessarily any better than the current one... |
1371 |
|
1372 |
checkpoint40pre4 |
1373 |
o added re-initialisations of utrans,vtrans,rtrans in |
1374 |
calc_common_factors which are crucial for TAF. |
1375 |
o extended iMin,jMin range for calc_common_factors, |
1376 |
calc_diffusivity |
1377 |
o added option ALLOW_PASSIVE_TRACER |
1378 |
o a few minor updates and fixes |
1379 |
|
1380 |
checkpoint40pre3 |
1381 |
o created calc_gtr1.F for gad package |
1382 |
o split the_main_loop and re-introduced forward_step |
1383 |
o some recomputations of nIter0 for TAMC |
1384 |
|
1385 |
checkpoint40pre2 |
1386 |
o Updated to latest branch of AJA, JMC |
1387 |
o Added gradient check package |
1388 |
o Added routines for passive tracer handling |
1389 |
o Added carbon sequestration sensitivity experiment |
1390 |
|
1391 |
checkpoint39 |
1392 |
o Modifications and fixes to support TAMC |
1393 |
(mainly missing or wrong directives) |
1394 |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
1395 |
in addummy_in_stepping |
1396 |
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
1397 |
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
1398 |
o Included following packages: |
1399 |
cal: calendar |
1400 |
exf: external forcing |
1401 |
ecco: essential routines to control use of cal, exf |
1402 |
(NB: this is not the full ECCO environment) |
1403 |
o disabled some packages by default in genmake |
1404 |
|
1405 |
checkpoint38 |
1406 |
o see notes_c37_adj.txt |
1407 |
o corrected wrong layer index in external_forcing_t |
1408 |
o replaced the_main_loop/forward_step by the_main_loop |
1409 |
o removed forceoutput from write_state |
1410 |
(replaced criteria for initial/final state) |
1411 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
1412 |
|
1413 |
checkpoint37 |
1414 |
o mdsio.F routine split and packaged in pkg/mdsio |
1415 |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
1416 |
used unless genmake -disable=mdsio) |
1417 |
o allow a more precise surface-geopotential gradient for the atmosphere |
1418 |
taking into account the change in space of Alpha (=1/rho) at the surface. |
1419 |
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
1420 |
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
1421 |
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
1422 |
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
1423 |
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
1424 |
o Time-Average diagnostics defined as a pseudo package "timeave". |
1425 |
o pickup files : old pickup (before c35) did not work with new code (c35 |
1426 |
and after) unless activating 2 commented lines in initialise-varia. |
1427 |
o Non-Hydrostatic pickup file Pb fixed. |
1428 |
o bug with Rigid-lid version (since c35) fixed. |
1429 |
|
1430 |
checkpoint36 |
1431 |
o implement Crank-Nickelson barotropic time-stepping |
1432 |
o recover Time-Average diagnostics |
1433 |
o fix Pb in checkpoint (PR#19) |
1434 |
o AIM become a standard package ; clean unused CPP_kees |
1435 |
|
1436 |
checkpoint35 |
1437 |
o subtantial rewrite of dynamics.f |
1438 |
o allows staggered time-stepping |
1439 |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
1440 |
o added bottom drag (linear + quadratic) |
1441 |
|
1442 |
checkpoint34 |
1443 |
o Modified exchange routines for correct reverse simulation. |
1444 |
o Added verification output to comply with bug fix in impldiff.F |
1445 |
as of c33 (exp2, natl_box). |
1446 |
o Corrected store directives in dynamics.F |
1447 |
o Corrected array boundaries in impldiff.F |
1448 |
o Corrected array dimensions in gmredi. |
1449 |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
1450 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
1451 |
o Added mdsio_gl.F for ECCO purposes. |
1452 |
|
1453 |
checkpoint33 |
1454 |
o Fixed bug in lower BC in impldiff.F |
1455 |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
1456 |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
1457 |
- Removed verification/natl_box/code/external_fields_scale.F |
1458 |
(did not differ from that in model/src) |
1459 |
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
1460 |
(see FFIELDS.h for description) |
1461 |
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
1462 |
kpp_calc.F and kpp_transport_t.F |
1463 |
- Removed model/src/external_fields_scale.F and calls to it |
1464 |
- verification/natl_box uses flux data with "atmospheric" sign so |
1465 |
a special version of external_fields_load.F is used to |
1466 |
change the data as it's read in. This way, the arrays |
1467 |
have the right units and signs at all times tha a user could |
1468 |
possibly use them. |
1469 |
o Corrected genmake to delete a temporary file during configuration |
1470 |
|
1471 |
checkpoint32 |
1472 |
o Scaling of forcing fields moved from external_forcing.F to |
1473 |
external_fields_scale.F, called directly after loading fields. |
1474 |
o Surface relaxation terms added to surface tendency fields in |
1475 |
extra subroutine. |
1476 |
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
1477 |
fields. |
1478 |
o Changes in GMRedi to comply with packaging structure. |
1479 |
o Modifications and bug fixes in KPP package. |
1480 |
o Verification experiment for KPP added (verification/nat_box/) |
1481 |
|
1482 |
checkpoint31 |
1483 |
o Packages interface brought in line with defined standard |
1484 |
-> new routines packages_...F |
1485 |
-> changes in initialise_fixed.F, initialise_varia.F |
1486 |
-> enables initialisation interface for ECCO package |
1487 |
o Rescaling of external forcing fields immediately after read |
1488 |
(removed from external_forcing.F) |
1489 |
-> new: surface_fields_scale.F |
1490 |
-> affects ini_foorcing.F, external_fields_load.F |
1491 |
o Computation of surface tendencies before tendency updates. |
1492 |
-> new: external_forcing_surf.F |
1493 |
o Change of variable names useGMRedi, useKPP, useECCO |
1494 |
o Further changes in dynamics.F, impldiff.F for TAMC |
1495 |
o Tested for experiments 0, 2, 4. |
1496 |
- not yet tested for GMRedi. |
1497 |
- not yet tested for KPP. |
1498 |
|
1499 |
checkpoint30 |
1500 |
o Updates for OBCs |
1501 |
o New experiment for test OBCs (internal_wave) |
1502 |
o New output.txt in verification/exp4/results/ |
1503 |
o Updates for KPP: calculation of viscosity corrected, new variables |
1504 |
kpp_dumpFreq and kpp_taveFreq |
1505 |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
1506 |
and entry for T90 in genmake |
1507 |
|
1508 |
checkpoint29 |
1509 |
o packaged KPP and GM/Redi |
1510 |
|
1511 |
checkpoint28 |
1512 |
o Corrected initialization of hFacMin for difference vertical coordinates |
1513 |
o Modified calculation of partial cell thickness to more robust algorithm |
1514 |
o config_summary.F: replaced write_1D_... by write_0D_... |
1515 |
read_write.F: added subroutines write_0D_... |
1516 |
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
1517 |
included some initialisations required for TAMC. |
1518 |
o routine calc_isoslopes: modified sqrt computation to make it |
1519 |
differentiable for zero argument. |
1520 |
o routines dynamics, impldiff: |
1521 |
included store directives and tape key computations required for TAMC. |
1522 |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
1523 |
|
1524 |
checkpoint27 |
1525 |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
1526 |
formulation works properly with variable resolution. |
1527 |
o restructured the calling tree between the_model_main() and dynamics() |
1528 |
o split initialise() into initialise_fixed() and initialise_varia() |
1529 |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
1530 |
in new routine ini_psurf() |
1531 |
|
1532 |
checkpoint26 |
1533 |
o moved some #ifdef in optional routines to encompass everything |
1534 |
except the argument declarations. This was using up some memory. |
1535 |
o fixed macros like _ADT to work with both versions of Linux cpp |
1536 |
o cleaned up some unused and uninitialized variables |
1537 |
(helps when debugging with strict compile options) |
1538 |
o split up CPP_EEOPTIONS.h into options and macros |
1539 |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
1540 |
o patch for 2 processor JAM mode |
1541 |
|
1542 |
checkpoint25 |
1543 |
o updates for OBCs and NH |
1544 |
o dramatically reduced memory usage |
1545 |
o added "JAM" routines for use on Artic network |
1546 |
o parameterization of convection by implicit vertical diffusion |
1547 |
o added a diagnostic of convective index |
1548 |
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
1549 |
(this is was partly for OBCs and NH but also in anticipation of |
1550 |
an explicit free-surface option) |
1551 |
o initial state input files for U and V |
1552 |
|
1553 |
checkpoint24 |
1554 |
o Removed some spurious "REAL"s |
1555 |
o Updated KPP to latest version from JPL |
1556 |
o Added a COS(latitude) in horizontal viscosity |
1557 |
|
1558 |
checkpoint23 |
1559 |
o Added del^4 diffusion for salt and temperature |
1560 |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
1561 |
|
1562 |
checkpoint22 |
1563 |
o Made many small changes: implicit none, format(i5), etc... |
1564 |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
1565 |
|
1566 |
checkpoint21 |
1567 |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
1568 |
o Split-up mid-level I/O routines |
1569 |
o Updated input data for experiments 0,1,2,4 and 5 |
1570 |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
1571 |
|
1572 |
checkpoint20 |
1573 |
o Tidied up open-boundaries some more |
1574 |
o Added non-hydrostatic code |
1575 |
o Fixed some input data |
1576 |
o Modified MPI start-up to work in "coupled" context. |
1577 |
|
1578 |
checkpoint19 |
1579 |
o Tidied up directory structure for verification experiments. |
1580 |
o Added new code for open boundaries. |
1581 |
o Corrected advective terms near boundaries. |
1582 |
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
1583 |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
1584 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
1585 |
|
1586 |
checkpoint18 |
1587 |
o Further changes for optional code generation with |
1588 |
CPP - ugh! |
1589 |
|
1590 |
checkpoint17 |
1591 |
o Beginning to incorporating modularity |
1592 |
for supporting atmos. and ocean configs. |
1593 |
o Small changes for TAMC complinace |
1594 |
o New ultra simple test case. Barotropic box |
1595 |
configuration "exp0". |
1596 |
|
1597 |
checkpoint16 |
1598 |
o Minor changes to exchange routines to support |
1599 |
accumulation in reverse mode. Adjoint of an |
1600 |
assignment is an addition. |
1601 |
o Changes to support compilation by TAMC (LR(1) |
1602 |
syntax) and by g77 under Linux ( 72 character |
1603 |
limit ). |
1604 |
|
1605 |
checkpoint15 |
1606 |
Rewrote exchange routines to allow |
1607 |
o General tile <-> tile connectivity. |
1608 |
o TAMC reverse mode flag ( is this really needed? ) |
1609 |
o Variable width overlap and exchange region widths. |
1610 |
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
1611 |
shmput/shmget, VIA, SYSV shmem and every other cool |
1612 |
communication method. |
1613 |
|
1614 |
checkpoint14 |
1615 |
Consistent isomorphism chages made. These allow dynamical core |
1616 |
to support both pressure and meters as a vertical coordinate. |
1617 |
|
1618 |
checkpoint13 |
1619 |
Release which corrects global_max problem and a couple |
1620 |
of KGM time-averaging diagnostic errors. Also contains |
1621 |
a double-gyre experiment setup as well as the baseline |
1622 |
4 degree global template. The double gyre template is |
1623 |
organised to allow it to be applied automatically to |
1624 |
the baseline configuration. |
1625 |
|
1626 |
branch-point-rdot |
1627 |
A few tidy-ups have been made bt the real point of this |
1628 |
check-point (excuse the pun) is to allow a branch to be |
1629 |
made for the purposes of adding the rDot alterations. |
1630 |
I don't want to commit the rDot to the main-trunk until |
1631 |
we've actually tested it... |
1632 |
|
1633 |
checkpoint12 |
1634 |
Tidy up and added generic genmake script (formerly |
1635 |
configure script). |
1636 |
Released to testers. |
1637 |
|
1638 |
checkpoint11 |
1639 |
Re-arranged initialise() and introduced ini_vertical_grid() |
1640 |
and ini_masks_etc(). |
1641 |
|
1642 |
checkpoint10 |
1643 |
Introduced the configure script. |
1644 |
Separated out the diags package. |
1645 |
Added template for writing time-averages of tile/intermediate quantities. |
1646 |
Updated SIZE.h in exp2 and made the data big-endian. |
1647 |
|
1648 |
checkpoint9 |
1649 |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
1650 |
General tidy-up. |
1651 |
SST.bin SSS.bin added to verification/exp2 |
1652 |
|
1653 |
checkpoint8 |
1654 |
Inludes time-dependant forcing and time-averaging. |
1655 |
Works at 4x4 and 2.8125x2.8125 global |
1656 |
|
1657 |
checkpoint7-4degree-ref |
1658 |
Branch from checkpoint7. Released for application to |
1659 |
global modeling and general modeling - process studies, regional |
1660 |
model etc.. |
1661 |
Configured for verification/exp2 - 4 degree global, two process. |
1662 |
|
1663 |
checkpoint7 |
1664 |
Created by cnh |
1665 |
Simple 4 degree global simulation |
1666 |
configuration. |
1667 |
Includes climatological wind, |
1668 |
hydrography, bathymetry etc |
1669 |
Does not include Heat Flux and E-P |
1670 |
|
1671 |
checkpoint6 |
1672 |
Created by cnh |
1673 |
merged checkpoint5 with CD and |
1674 |
spherical polar code. |
1675 |
Still some problems with GM Redi |
1676 |
abd full topography. |
1677 |
|
1678 |
checkpoint5 |
1679 |
Created by AJA |
1680 |
contains updates to GM Redi |
1681 |
and reordered timestepping loop |
1682 |
for Implicit Diffusion. |
1683 |
|
1684 |
checkpoint4 |
1685 |
Created by cnh |
1686 |
Contains memory saving macros ( _rdxc etc..) for when |
1687 |
grid variations are limited. |
1688 |
Contains polynomial coeffs for EOS and knudsen program |
1689 |
for generation. |
1690 |
|
1691 |
checkpoint3 |
1692 |
Created by cnh |
1693 |
Added extra flags for runtime options |
1694 |
Added this file |
1695 |
Added implicit free-surface |
1696 |
Added pre-conditioner |
1697 |
Put compare01 into repository ( compare01/... ) |
1698 |
Put data and eedata into repository ( verification/exp1 ) |
1699 |
|
1700 |
checkpoint2 |
1701 |
Created by AJA |
1702 |
Added GM/Redi |
1703 |
|
1704 |
checkpoint1 |
1705 |
Created by AJA |
1706 |
Restructured kloop in dynamics.F |
1707 |
Added non-linear EOS |
1708 |
|
1709 |
baseline |
1710 |
Original checked in code |