4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
o fix a bug in diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
o pkg/ptracers: |
8 |
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apply zonal filter (if used) to all passive tracers |
9 |
|
|
10 |
|
checkpoint61w |
11 |
|
o adjoint: |
12 |
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* update and finish work on adjoint of dic package (G. Forget) |
13 |
|
* start adjoint of offline package |
14 |
|
* bug fix for cube-sphere TLM code (active_file_g.F) |
15 |
|
o tutorial_global_oce_optim: |
16 |
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now tested with 4 tiles (change data.grdchk and update output_adm.txt) |
17 |
|
and add SIZE.h_mpi for MPI testing |
18 |
|
o pkg autodiff |
19 |
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- fix bug in autodiff_restore |
20 |
|
- make genmake2 remove comments and empty lines from ad_input_code.f in |
21 |
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order to reduce file size (new script file remove_comments_sed) |
22 |
|
o allows to specify vertical profile of vertical viscosity (viscArNr) |
23 |
|
o pkg autodiff |
24 |
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autodiff_ini_model_io: comment out writing of grid information to netcdf |
25 |
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files, because at this time the grid fields are a bunch of zeros |
26 |
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(this is analogous to ini_mnc_vars.F) |
27 |
|
o pkg seaice/autodiff: |
28 |
|
left-over from removing the 3-time-level fields: |
29 |
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- small rearrangement of common blocks (SEAICE.h) |
30 |
|
- fix field declaration in order to get meaningful output in |
31 |
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adseaice.*.nc (adcommon.h) |
32 |
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o pkg obcs: |
33 |
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- go through NH code only if nonHydrostatic=T |
34 |
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- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
35 |
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- move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields |
36 |
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=> Update output of experiment seaice_obcs |
37 |
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- useOBCSbalance: code is wrong with multi-tile / proc: add a stop. |
38 |
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- fix NH+Orlanski restart (add wvel OBC value in pickup file) |
39 |
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- fix restart for useOBCSprescribe + useEXF |
40 |
|
o pkg ctrl |
41 |
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- make obcs as control parameter work also with useSingleCPUio |
42 |
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- replace a few sny and snx by Ny and Nx to be consistent with |
43 |
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ctrl_set_globfld_x/yz.F |
44 |
|
o pkg seaice |
45 |
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- re-introduce global field frWtrAtm for the case of |
46 |
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ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
47 |
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- catch the case of an empty filename in seaice_cost_init_fixed.F |
48 |
|
o pkg ecco: |
49 |
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- small bug fixes in the_main_loop |
50 |
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. fix order of monitor arguments |
51 |
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. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
52 |
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. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
53 |
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that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
54 |
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- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
55 |
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imbalance diagnostics for wmean_h/sflux = 0 |
56 |
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- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
57 |
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- catch the case of empty filenames in ecco_cost_init_fixed.F |
58 |
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and ecco_readparms.F |
59 |
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- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
60 |
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to make this statement meaningfull in ecco_cost_weights.F |
61 |
|
o pkg zonal_filt: |
62 |
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- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
63 |
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- when using rStar, filter uVel*hFacW instead of uVel |
64 |
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(tested without topography: fix a Pb of growing instability with NLFS) |
65 |
|
o pkg/aim/thsice: |
66 |
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-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
67 |
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(works as SST restoring) |
68 |
|
o pkg/thsice: |
69 |
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-add specific parameter for salt restoring in slab mixed-layer |
70 |
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(by default equal to the temperature restoring) |
71 |
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|
72 |
|
checkpoint61v |
73 |
|
o pkg/kpp: |
74 |
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-add double diffusive contributions as a hack, turned off by default |
75 |
|
for now, and the code can be excluded with a CPP-flag |
76 |
|
EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
77 |
|
-add a verification experiments to "vermix" to test this code |
78 |
|
o pkg/mom_common: |
79 |
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Move computation of length scales to mom_init_fixed.F (avoid recomputation |
80 |
|
at each time-steps*levels). |
81 |
|
o pkg/layers: |
82 |
|
Created a new package for computing volume fluxes in temperature or |
83 |
|
[not yet implemented] density layers, e.g. for calculating residual |
84 |
|
overturning circulations. |
85 |
|
o pkg/diagnostics: |
86 |
|
implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
87 |
|
o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
88 |
|
o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
89 |
|
To avoid mixing type (RS/RL) of input/output array argument, |
90 |
|
replace single mixed-type array with a pair from each type (RS/RL). |
91 |
|
o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
92 |
|
is now implemented for all pkgs (previously only done for the main pickup) |
93 |
|
|
94 |
|
checkpoint61u |
95 |
|
o pkg/obcs: |
96 |
|
- change OB?eta from _RS to _RL and put them into a separate commen block |
97 |
|
- add code to read OB?eta from a file via obcs_prescribe_read: the code |
98 |
|
compiles and does not destroy any other experiments, the data is read |
99 |
|
properly, but the code is not tested in actual applications |
100 |
|
o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
101 |
|
create a meaningful unit attribute for the time coordinate variable |
102 |
|
o pkg/ebm: add plenty of missing "_d 0" ; |
103 |
|
update results of experiment global_ocean_ebm (fwd + adjoint tests) |
104 |
|
Notes: several pieces of code only works for (very) specific set up |
105 |
|
(domain size, lat range, etc ...); should be documented & stop if one |
106 |
|
of those assumptions is not meet. |
107 |
|
o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
108 |
|
update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
109 |
|
and offline_exf_seaice (seaicetd + adjoint). |
110 |
|
o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
111 |
|
update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
112 |
|
seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
113 |
|
o few changes to pass when compiling with strick checking of arguments |
114 |
|
across S/R (allow to find few bugs in S/R calls). |
115 |
|
o pkg/seaice: |
116 |
|
- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
117 |
|
2d-fields, for slightly better performance |
118 |
|
|
119 |
|
checkpoint61t |
120 |
|
o pkg/seaice: |
121 |
|
- remove unused variables in seaice_evp |
122 |
|
- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
123 |
|
o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
124 |
|
named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
125 |
|
each processor opens a different file (a fix from Matt). |
126 |
|
o cg2d: |
127 |
|
use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
128 |
|
this reduces number of EXCH calls by 2 when using exch2. |
129 |
|
For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
130 |
|
directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
131 |
|
o pkg/thsice: |
132 |
|
add code for Near Infra-Red albedo (from Jeff) |
133 |
|
(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
134 |
|
o ini_model_io: |
135 |
|
move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
136 |
|
MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
137 |
|
to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
138 |
|
|
139 |
|
checkpoint61s |
140 |
|
o pkg/exch2 (exch2_rxN_cube*): |
141 |
|
remove last BARRIER (no need to synchronise after getting data from shared |
142 |
|
buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
143 |
|
o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
144 |
|
and generate new output (for the 2 tests) using default rotationPeriod. |
145 |
|
o pkg/exch2: |
146 |
|
- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
147 |
|
(was already the case with AUTODIFF_EXCH2 defined) |
148 |
|
- add bj in exch2 arrays and S/R. |
149 |
|
- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
150 |
|
MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
151 |
|
o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
152 |
|
- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
153 |
|
GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
154 |
|
- verification experiment natl_box.longstep |
155 |
|
o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
156 |
|
allow different versions of ifort (8 or 9) and different versions |
157 |
|
of mpi (mpich or mpich2) to be used with the same optfile. |
158 |
|
requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
159 |
|
optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
160 |
|
o pkg/seaice: |
161 |
|
fix previous modif (3-level field removed) for old-pickup reading |
162 |
|
|
163 |
|
checkpoint61r |
164 |
|
o pkg/seaice: |
165 |
|
- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
166 |
|
1. introduce fields for time step (N-1) |
167 |
|
2. do not use levels 2 and 3 anymore (but keep them) |
168 |
|
3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
169 |
|
includes changes to pkg/thsice/thsice_get_velocity.F, |
170 |
|
model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
171 |
|
pkg/obcs/obcs_apply_uvice.F. |
172 |
|
- completely remove code for leap-frog time stepping for second order |
173 |
|
advection |
174 |
|
- adjusted adjoint accordingly; |
175 |
|
gradient checks have improved by an order of magnitude! |
176 |
|
|
177 |
|
checkpoint61q |
178 |
|
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
179 |
|
- the boundary conditions along open boundaries are unclear, because the |
180 |
|
associated masks are set to zero and are thus treated as closed when |
181 |
|
applying the slip-boundary conditions. |
182 |
|
- move initialisation of grid variables from seaice_init_varia to _fixed |
183 |
|
o adding doc/diags_changes.txt |
184 |
|
o model/src: |
185 |
|
do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
186 |
|
to avoid "_diags" naming if no relation to pkg/diagnostics. |
187 |
|
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
188 |
|
file and only call PLOT_FIELD_XYZ if debugMode=T. |
189 |
|
remove few PLOT_FIELD_XY calls outside initialisation. |
190 |
|
remove few unnecessary BARRIER. |
191 |
|
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
192 |
|
of salt_plume package in Southern Ocean |
193 |
|
o pkg/thsice: |
194 |
|
- fix hOceMxL in overlap (needed for sea-ice advection); |
195 |
|
update output of experiment global_ocean.cs32x15.icedyn. |
196 |
|
o pkg/seaice: |
197 |
|
- make the (placeholder-)tracer IceAge a little more meaningful |
198 |
|
by avoiding ridging of age due to convergent ice flow |
199 |
|
- add diagnostics for surface temperature, atmospheric and oceanic |
200 |
|
heat flux, and atmospheric and oceanic ice growth |
201 |
|
|
202 |
|
checkpoint61p |
203 |
|
o eesupp (global_max & global_sum): |
204 |
|
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
205 |
|
- remove starting & endding barrier (no longer needed) |
206 |
|
o pkg/mdsio, writelocal: |
207 |
|
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
208 |
|
(remove the STOP): uses shared buffer IO to store data from all threads |
209 |
|
and then let master-thread write nThreads tiles. |
210 |
|
o pkg/mdsio (read/write field): |
211 |
|
- tiled IO done in 1 piece (all levels at a time); |
212 |
|
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
213 |
|
- multi-threaded: allow to read/write local (non-shared) array |
214 |
|
(was already working with singleCpuIO ; now works also without); |
215 |
|
=> no longer needs barrier call after reading a file (added inside |
216 |
|
mds_read/write field). |
217 |
|
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
218 |
|
o pkg/obcs/exf |
219 |
|
- exf_getffieldrec.F: add a few ". _d 0" and |
220 |
|
add code to catch the case fldperiod = 0. |
221 |
|
- obcs_precribe_read.F: change if statements so that they match |
222 |
|
the variable type (_RL) |
223 |
|
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
224 |
|
exf_iprec) as part of namelist EXF_NML_01 |
225 |
|
o pkg/mdsio: |
226 |
|
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
227 |
|
(instead of segment of length sNx); expected to speed up tiled IO. |
228 |
|
o pkg/exch2: |
229 |
|
- take buffer copy from/to array out of S/R exch2_send/recv into new |
230 |
|
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
231 |
|
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
232 |
|
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
233 |
|
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
234 |
|
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
235 |
|
including Topology header file (and common blocks). |
236 |
|
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
237 |
|
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
238 |
|
- document S/R arg. list (+ update some comments) |
239 |
|
o pkg/seaice: |
240 |
|
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
241 |
|
temperature and humidity over sea ice based on climatological values. |
242 |
|
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
243 |
|
of LSR (this change is expected to change the results slightly because now |
244 |
|
it uses slightly difference moduli from the second last LSR solution, but |
245 |
|
that is more consistent with the stress computations; this part of the code |
246 |
|
is not tested in the verification experiments) |
247 |
|
- fix diagnostics for flux of ice in case of B-grid |
248 |
|
- turn strain rates eij and press into global fields within global |
249 |
|
common block in SEAICE.h for more straighforward diagnostics |
250 |
|
- fix diagnostics for principal stress components, press, zeta, eta |
251 |
|
to give something meaning full |
252 |
|
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
253 |
|
new output (all 4 tests) using default rotationPeriod. |
254 |
|
o pkg KPP: |
255 |
|
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
256 |
|
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
257 |
|
and normal grid from 1 to Nr) |
258 |
|
o Fix computations of L4rdt in mom_calc_visc.F |
259 |
|
o eesupp: |
260 |
|
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
261 |
|
should be called before a "stop" if we know that all process are going |
262 |
|
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
263 |
|
|
264 |
|
checkpoint61o |
265 |
|
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
266 |
|
o model/src/ini_curvilinear_grid.F: |
267 |
|
compute angleSin/CosC when they are not read from a file |
268 |
|
o pkg/seaice: |
269 |
|
add pseudo time stepping for LSOR |
270 |
|
o pkg/exch2: |
271 |
|
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
272 |
|
o pkg/seaice: |
273 |
|
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
274 |
|
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
275 |
|
o SingleCpuIO: |
276 |
|
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
277 |
|
o pkg/seaice: |
278 |
|
put exchanged variable in (local) common block for MPI+Multi-Threads |
279 |
|
to work (necessary with exch1, and for now with exch2 too). |
280 |
|
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
281 |
|
change tiling of: |
282 |
|
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
283 |
|
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
284 |
|
update output of exp: |
285 |
|
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
286 |
|
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
287 |
|
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
288 |
|
(note: output.txt generated on faulks using only 1 tile) |
289 |
|
o eesupp & mdsio (SingleCpuIO): |
290 |
|
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
291 |
|
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
292 |
|
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
293 |
|
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
294 |
|
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
295 |
|
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
296 |
|
o pkg/exch2: |
297 |
|
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
298 |
|
read parameter file "data.exch2" if it exists; otherwise try default regular |
299 |
|
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
300 |
|
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
301 |
|
with new code (not to be used, just as a backup solution). |
302 |
|
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
303 |
|
in utils/exch2/input. |
304 |
|
|
305 |
|
checkpoint61n |
306 |
|
o eesupp & mdsio (SingleCpuIO): |
307 |
|
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
308 |
|
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
309 |
|
receive real*4 array (instead of real*8) to read/write 32.bit files. |
310 |
|
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
311 |
|
and remove new mapping S/R) |
312 |
|
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
313 |
|
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
314 |
|
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
315 |
|
when using exch2. Add S/R to map global io-buffer to global model array. |
316 |
|
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
317 |
|
|
318 |
|
checkpoint61m |
319 |
|
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
320 |
|
and add 3 other S/R for other types (R4,R8,RS). |
321 |
|
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
322 |
|
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
323 |
|
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
324 |
|
- reduce number of macro definitions (keep only those which are used); |
325 |
|
can always call directly the corrresponding S/R if needed. |
326 |
|
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
327 |
|
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
328 |
|
Fixed wrong type of arg in: |
329 |
|
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
330 |
|
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
331 |
|
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
332 |
|
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
333 |
|
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
334 |
|
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
335 |
|
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
336 |
|
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
337 |
|
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
338 |
|
edges are closed (zero depth); might happen with "blank tiles"; |
339 |
|
for now, disabled if using OBCS. |
340 |
|
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
341 |
|
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
342 |
|
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
343 |
|
to reduce length of 1.D array print in STDOUT. |
344 |
|
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
345 |
|
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
346 |
|
o start to test MPI + multi-threaded (change testreport to skip tests |
347 |
|
where number of tiles do not match). |
348 |
|
o genmake2: add option "-omp" to turn on Open-MP ; |
349 |
|
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
350 |
|
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
351 |
|
and keep the original tile numbering. Note: compatible with old |
352 |
|
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
353 |
|
|
354 |
|
checkpoint61l |
355 |
|
o Overlaps had been forgotten in calculating ijk keys : fixed |
356 |
|
o fix cyrus makedepend for gcc 4.4 |
357 |
|
o experiment fizhi-cs-aqualev20: |
358 |
|
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
359 |
|
and generate new output. Note: new output is much closer to the old |
360 |
|
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
361 |
|
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
362 |
|
o pkg/fizhi: |
363 |
|
- change to avoid indices going deliberately over array-bounds |
364 |
|
- remove unnecessary MPI stuff |
365 |
|
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
366 |
|
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
367 |
|
does not go over array-bounds and therefore returns reliable output. |
368 |
|
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
369 |
|
this S/R has 4 output arguments, which are used inside "get_alarm"; |
370 |
|
when it is called with the same variable "ndum" in place of several |
371 |
|
output arguments, this produces weird side effect inside "get_alarm" |
372 |
|
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
373 |
|
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
374 |
|
address) and produces error. |
375 |
|
o tools/gemake2: (March 27-29 2009) |
376 |
|
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
377 |
|
testreport does). |
378 |
|
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
379 |
|
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
380 |
|
update lab_sea.lsr & lab_sea.salt_plume results |
381 |
|
o pkg/seaice: |
382 |
|
Major overhaul of the LSOR solver: change discretization from original |
383 |
|
finite differences to finite volume. The old routine is still in the |
384 |
|
file seaice_lsr.F and can be turned on with the CPP-flag |
385 |
|
SEAICE_OLD_AND_BAD_DISCRETIZATION |
386 |
|
Along with this change, the discretization of the strain rates is changed. |
387 |
|
The same flag turns on the old discretization in seaice_calc_strainrates.F |
388 |
|
All verification experiments with seaice are affected (except for |
389 |
|
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
390 |
|
results by setting the above flag. |
391 |
|
Further changes involve changes in defaults: |
392 |
|
- ALLOW_FLOODING is defined and turned on by default |
393 |
|
- SEAICEadvSnow = .true. is now the default |
394 |
|
- SEAICEadvSalt = .true. is now the default |
395 |
|
- SEAICEadvAge = .true. is now the default |
396 |
|
- SEAICE_clipVelocities = .false. is now the default |
397 |
|
(as per J. Zhang's recommendation) |
398 |
|
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
399 |
|
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
400 |
|
- seaice_growth: replace computation of UG by a simple copy from wspeed |
401 |
|
|
402 |
|
checkpoint61k |
403 |
|
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
404 |
|
seaice_lsr: fixed a few metric terms, |
405 |
|
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
406 |
|
add more debugging diagnostics |
407 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
408 |
|
of stress divergence |
409 |
|
affects lab_sea, lab_sea.hb87 |
410 |
|
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
411 |
|
of stress divergence for non-evp solver |
412 |
|
(this part is not tested anywhere) |
413 |
|
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
414 |
|
they were effectively only half slip |
415 |
|
affects lab_sea.hb87 |
416 |
|
updated all relevant verification experiments (except lab_sea//output_adm.txt |
417 |
|
which was left over, but fails at level 7 & 6) |
418 |
|
|
419 |
|
checkpoint61j |
420 |
|
o pkg/seaice: turn a few hard wired parameters into run time parameters |
421 |
|
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
422 |
|
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
423 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
424 |
|
that are not cubed-sphere grids |
425 |
|
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
426 |
|
o pkg/ctrl: |
427 |
|
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
428 |
|
o non-hydrostatic (calc_gw.F): |
429 |
|
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
430 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
431 |
|
o remove backward compatibility for thetaMin,phiMin |
432 |
|
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
433 |
|
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
434 |
|
interpolated wind field not only for curvilineargrid=.true., but also |
435 |
|
for a rotated grid (rotateGrid=.true.) |
436 |
|
o pkg/exf: add capability to bypass interpolation for runoff |
437 |
|
by setting yet another CPP-flag |
438 |
|
o eesupp/src, B-grid exchange: |
439 |
|
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
440 |
|
o autodiff |
441 |
|
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
442 |
|
allows to switch to single-prec common blocks; |
443 |
|
corresponding switch occurs in tamc.h, integer isbyte |
444 |
|
TAF store directivs "byte" and "kind" seem equivalent; |
445 |
|
Most tamc.h have been updated correspondingly. |
446 |
|
|
447 |
|
checkpoint61i |
448 |
|
o autodiff: |
449 |
|
fix autodiff_sore/_restore indices for obcs |
450 |
|
(spotted by I. Hoteit, M. Mazloff) |
451 |
|
o pkg/autodiff, pkg/ctrl: |
452 |
|
Add flag to reduce all tapelev I/O to single-prec. |
453 |
|
In data.ctrl set |
454 |
|
doSinglePrecTapelev = .TRUE. |
455 |
|
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
456 |
|
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
457 |
|
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
458 |
|
real fresh water flux (not yet) |
459 |
|
o pkg/mdsio & rw: |
460 |
|
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
461 |
|
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
462 |
|
o pkg/flt: |
463 |
|
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
464 |
|
init_fixed & ini_varia. |
465 |
|
- clean-up & simplify linear interpolation S/R: |
466 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
467 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
468 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
469 |
|
- add vert. coordinate & horiz. indices to output files. |
470 |
|
- change vertical position in initial condition, from index to depth [m]. |
471 |
|
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
472 |
|
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
473 |
|
o pkg/ggl90: a few modifications: |
474 |
|
- fix bottom boundary condition, and interpolation of KappaE |
475 |
|
near top and bottom |
476 |
|
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
477 |
|
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
478 |
|
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
479 |
|
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
480 |
|
(maintain temporary backward compatibility, until next checkpoint) |
481 |
|
|
482 |
|
checkpoint61h |
483 |
|
o pkg/diagnostics with "periodic averaging diagnostics": |
484 |
|
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
485 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
486 |
|
o pkg/obcs: fix loop ranges for balancing code |
487 |
|
o pkg/flt: |
488 |
|
- improve criteria for finding which tile owns a float. |
489 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
490 |
|
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
491 |
|
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
492 |
|
with ocean biogeo) |
493 |
|
o pkg/flt: |
494 |
|
- do some cleaning and fix the restart ; |
495 |
|
- add output.txt in flt_example/results to get this pkg tested. |
496 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
497 |
|
for now, cannot be turned on on command line (only through genmake_local) |
498 |
|
o pkg/mdsio: read/write vector: |
499 |
|
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
500 |
|
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
501 |
|
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
502 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
503 |
|
(drop to 4 digits matching for grad). But this test does not look very |
504 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
505 |
|
|
506 |
|
checkpoint61g |
507 |
|
o pkg/flt: |
508 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
509 |
|
+ make OPTIONS file more standard. |
510 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
511 |
|
- fix _BYTESWAPIO CPP-Flag |
512 |
|
- standard reading of file-parameter "data.flt" |
513 |
|
- fix argument list of S/R FLT_RESTART |
514 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
515 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
516 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
517 |
|
a still unfixed compiler/optimization bug |
518 |
|
|
519 |
|
checkpoint61f |
520 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
521 |
|
update results of global_ocean.cs32x15.icedyn test. |
522 |
|
o move getcon.F from model/src to pkg/fizhi. |
523 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
524 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
525 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
526 |
|
(e.g., when using NonLin Free-Surface). |
527 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
528 |
|
o gmredi (Visbeck-variable-K): |
529 |
|
- add more parameters to Visbeck-variable-K. |
530 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
531 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
532 |
|
- update output of ideal_2D_oce experiment. |
533 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
534 |
|
(#undef REAL4_IS_SLOW) |
535 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
536 |
|
coordinate variable |
537 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
538 |
|
(surface forcing fields), removes some of the functionality |
539 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
540 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
541 |
|
probably not all: copy _RS surface flux fields to RL field before |
542 |
|
calling DIAGNOSTICS_FILL |
543 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
544 |
|
real*4 (CALL EXCH_*_RS) versions. |
545 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
546 |
|
(generate new output). |
547 |
|
|
548 |
|
checkpoint61e |
549 |
|
o gmredi (Visbeck-variable-K): |
550 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
551 |
|
- change computation of Visbeck-K where Slope > Smax : |
552 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
553 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
554 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
555 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
556 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
557 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
558 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
559 |
|
solver); update ideal_2D_oce output. |
560 |
|
o pkg ggl90: |
561 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
562 |
|
step forward TKE/T/S/momentum |
563 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
564 |
|
have Prandlt =1) |
565 |
|
o gmredi (fm07): |
566 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
567 |
|
- allow to set few more params from data.gmredi |
568 |
|
o pkg ggl90: |
569 |
|
- add missing sqrt(2) factor in computation of mixing length |
570 |
|
scale in ggl90_calc.F |
571 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
572 |
|
|
573 |
|
checkpoint61d |
574 |
|
o adjoint modifs |
575 |
|
- adapt to new field rhoInSitu |
576 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
577 |
|
to individual fields |
578 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
579 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
580 |
|
- save 1 rho computation. |
581 |
|
- no longer modify T & S inland when using down_slope pkg. |
582 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
583 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
584 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
585 |
|
(for useSingleCpuIO to work in multi-threaded) |
586 |
|
o pkg/shelfice: |
587 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
588 |
|
with SHELFICEtopoFile in data.shelfice |
589 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
590 |
|
subroutines of the shelfice package |
591 |
|
- separate initialisation of "fixed" and "variable" variables |
592 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
593 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
594 |
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
595 |
and rename: |
and rename: |
596 |
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
2799 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
2800 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
2801 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
2802 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
2803 |
o add offline package |
o add offline package |
2804 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
2805 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |