4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
|
o pkg/offline: |
8 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
9 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
10 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
11 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
12 |
|
These changes allow: |
13 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
14 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
15 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
16 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
17 |
|
b) no needs to switch on staggerTimeStep anymore; |
18 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
19 |
|
- update output of experiments tutorial_cfc_offline (11 to 13 digits left) |
20 |
|
and tutorial_dic_adjoffline (only 3 digits left). |
21 |
|
o pkg/offline: |
22 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
23 |
|
can easily recover previous offset-iter effect by setting offset-time |
24 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
25 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
26 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
27 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
28 |
|
o OpenAD |
29 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
30 |
|
Config. with ggl90 currently diverges after 64 time steps |
31 |
|
so will need more work to become more stable |
32 |
|
- Adding preliminary kpp test to OpenAD verification. |
33 |
|
required small tweakes in kpp_routines.F |
34 |
|
- Merge and update from Krishna Narayanan's contrib area: |
35 |
|
* Add one variable for preliminary OpenAD DIVA |
36 |
|
* Add replacement time-stepping for OpenAD DIVA |
37 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
38 |
|
* required modifs for OAD_support |
39 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
40 |
|
o pkg/seaice: |
41 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
42 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
43 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
44 |
|
(no effect on EVP) |
45 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
46 |
|
o pkg/seaice: |
47 |
|
add new parameter SEAICE_deltaMin that is used ***only*** |
48 |
|
for regularizing Delta (and nothing else, like the parameter |
49 |
|
which is also used for all sorts of things SEAICE_EPS). |
50 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
51 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
52 |
|
the wrong key by inialising it before use -> fixes a recomputation |
53 |
|
problem but does not fix the gradient |
54 |
|
o pkg/layers: |
55 |
|
- move resetting of flux arrays to outside the iLa loop |
56 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
57 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
58 |
|
o pkg/layers: |
59 |
|
- remove from common block 3D layers fields (used to diagnose transport |
60 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
61 |
|
o pkg/seaice: |
62 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
63 |
|
in lab_sea forward experiment (changes results -> updated) |
64 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
65 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
66 |
|
computations; for SEAICE_VECTORIZE_LSR |
67 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
68 |
|
sweep to the outside, |
69 |
|
- remove store directives and add "CADJ loop sequential" directives |
70 |
|
in analogy to model/src/solve_tridiagonal.F |
71 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
72 |
|
boundaries to yield more readable code. This has also the charming side |
73 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
74 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
75 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
76 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
77 |
|
an additional option) |
78 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
79 |
|
but the adjoint gradients (which are affected by this change) still explode. |
80 |
|
o coupler (atm & ocn _compon_interf): |
81 |
|
- avoid using Exch2 IO mapping if not suitable. |
82 |
|
|
83 |
|
checkpoint65m (2015/06/15) |
84 |
|
o pkg/layers: |
85 |
|
- clean-up old parameters setting (from Sep 2012): |
86 |
|
+ remove old parameters setting from common block (declared locally); |
87 |
|
+ stop if any old parameter is mixed with new parameters; |
88 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
89 |
|
- check that layers_bounds for Pot.Density are in the right range; |
90 |
|
this is supposed to catch un-updated setting after recently shifting |
91 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
92 |
|
o pkg/layers: |
93 |
|
- Added missing call to layers_fill for keeping track of tottend in |
94 |
|
pkg/diagnostics/diagnostics_fill_state.F |
95 |
|
o pkg/layers: |
96 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
97 |
|
of diapycnal fluxes |
98 |
|
o pkg/layers: |
99 |
|
- reverted changes to interpolation to previous treatment; there |
100 |
|
was never actually a problem |
101 |
|
o pkg/layers: |
102 |
|
- fix interpolation of layers tracers in the presence of partial cells |
103 |
|
- add lots of new functionality to compute water mass transformation |
104 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
105 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
106 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
107 |
|
for layers_thermodynamics calculations |
108 |
|
o pkg/ptracers: |
109 |
|
- add capability of stepping a passive tracer forward without advection |
110 |
|
by setting PTRACERS_advScheme to 0. |
111 |
|
o pkg/diagnostics: |
112 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
113 |
|
o pkg/layers: |
114 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
115 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
116 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
117 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
118 |
|
o pkg/layers: |
119 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
120 |
|
- fix calculation of layer non-weighted velocity and layer probability |
121 |
|
- add diagnostics for pot.density used for layer averaging |
122 |
|
o pkg/seaice: |
123 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
124 |
|
positiveness, modify a few comments and improve variable names, |
125 |
|
- the changed computation of deltaC affects most seaice-related |
126 |
|
experiments at the truncation level. |
127 |
|
seaice_itd.thermo is affected by far the most, with |
128 |
|
only 7 digits of agreement remaining; update experiments. |
129 |
|
|
130 |
|
checkpoint65l (2015/05/04) |
131 |
|
o pkg/shelfice: |
132 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
133 |
|
factor drKp1 to zero where it is negative (ie. do not use |
134 |
|
SHELFICEBoundaryLayer if hFacC>1) |
135 |
|
- the same for factor drLoc in shelfice_forcing.F |
136 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
137 |
|
with modules in ptracers, when using testreport option "-small_f" |
138 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
139 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
140 |
|
o verification/testreport |
141 |
|
- add new option -small_f |
142 |
|
with this option testreport first makes the target small_f (*.f files) |
143 |
|
before running make (all). This is useful for explicit inlining when |
144 |
|
all sources need to be full available. |
145 |
|
o pkg/exf/exf_interp.F: |
146 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
147 |
|
|
148 |
|
checkpoint65k (2015/04/01) |
149 |
|
o pkg/ecco: |
150 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
151 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
152 |
|
instead of active read/write |
153 |
|
o pkg/ctrl: |
154 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
155 |
|
instead of active read/write. |
156 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
157 |
|
return if .NOT.useAUTODIFF |
158 |
|
o pkg/seaice: add CPP brackets (cost function related). |
159 |
|
o model/src: |
160 |
|
add useAUTODIFF run time switch. |
161 |
|
o pkg/exf/exf_interp.F: |
162 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
163 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
164 |
|
this feature. |
165 |
|
o verification/testreport: |
166 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
167 |
|
implementations of grep that cannot do contextual searches |
168 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
169 |
|
of "cat" have the option "-n" |
170 |
|
o model/src: |
171 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
172 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
173 |
|
convert from conservative to potential temperature. For now they are not |
174 |
|
called anywhere. |
175 |
|
o pkg/ggl90: make "useIDEMIX" useful |
176 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
177 |
|
are different for idemix into separate loops (changes verification |
178 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
179 |
|
- requires 2 new 2D fields KappaM, verticalShear |
180 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
181 |
|
s/r ggl90_idemix |
182 |
|
- fix and improve some comments |
183 |
|
|
184 |
|
checkpoint65j (2015/02/25) |
185 |
|
o pkg/openad |
186 |
|
- synchronize seawater.F with version in model/src: replace routine |
187 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
188 |
|
o pkg/mnc: |
189 |
|
- change default value of pickup_read/write_mnc params to FALSE |
190 |
|
(since few features are missing in reading MNC pickup files). |
191 |
|
o model/src: |
192 |
|
- change default (background) vertical diffusivity for salt to be the |
193 |
|
temperature (background) vertical diffusivity. |
194 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
195 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
196 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
197 |
|
consistent with vertical mixing schemes. |
198 |
|
o verification/testreport: |
199 |
|
- fix typo in "-pcls" option ; |
200 |
|
- put temp files in /tmp (instead of in local dir) |
201 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
202 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
203 |
|
o pkg/ggl90 (idemix code): |
204 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
205 |
|
global_ocean.90x40x15.idemix |
206 |
|
o OpenAD |
207 |
|
- enable active file I/O and begin removal of work-around code |
208 |
|
for OpenAD for handling control variables (memory vs. active files) |
209 |
|
- new CPP options file OPENAD_OPTIONS.h |
210 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
211 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
212 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
213 |
|
o tools/genmake2: |
214 |
|
- add option for an alternative Makefile (from Martin) where multiple |
215 |
|
source files are sent to TAF (instead of all in one file). |
216 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
217 |
|
- code provided by Carsten Eden as an extension of ggl90 |
218 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
219 |
|
compile time; a runtime flag implementation is not yet complete |
220 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
221 |
|
o verification: |
222 |
|
- reduce length of the AD test run by half for experiments |
223 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
224 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
225 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
226 |
|
o verification/testreport: |
227 |
|
- fix two non-POSIX sed statements so that there are no error messages |
228 |
|
on Mac OS X |
229 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
230 |
|
o model/src/seawater.F: |
231 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
232 |
|
(following the matlab code), which would have avoided the bug caught |
233 |
|
by Matt (see below) in the first place |
234 |
|
o pkg/shelfice: |
235 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
236 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
237 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
238 |
|
ice-shelf case (i.e., within surface level). |
239 |
|
- add config summary in shelfice_check.F |
240 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
241 |
|
variable recip_latentHeat |
242 |
|
- introduce diagnostics for friction velocity uStar (in case of |
243 |
|
SHELFICEuseGammaFrict) |
244 |
|
- change verification experiment isomip.htd: |
245 |
|
+ start from pickup (as input_ad at nIter0=8640) |
246 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
247 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
248 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
249 |
|
o model/src: |
250 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
251 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
252 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
253 |
|
o pkg/shelfice: |
254 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
255 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
256 |
|
ice-shelf is. |
257 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
258 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
259 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
260 |
|
for thermodynamic calculations |
261 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
262 |
|
affects results of some verification experiments by up to 4 digits: |
263 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
264 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
265 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
266 |
|
-> updated |
267 |
|
|
268 |
|
checkpoint65i (2015/01/23) |
269 |
|
o model/src: |
270 |
|
- change units of frictionHeating field from W to W/m^2 |
271 |
|
- fix bug in frictional heating from stratospheric drag in |
272 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
273 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
274 |
|
field from load_fields_driver.F to thermodynamics.F ; |
275 |
|
- add diagnostics for frictional heating. |
276 |
|
o model/src & gmredi K3D: |
277 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
278 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
279 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
280 |
|
and name in pickup file). |
281 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
282 |
|
o model/src: |
283 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
284 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
285 |
|
(since Nov 2012) with option selectAddFluid=1. |
286 |
|
o pkg/shelfice: |
287 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
288 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
289 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
290 |
|
o pkg/seaice: two new runtime parameters: |
291 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
292 |
|
long overdue |
293 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
294 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
295 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
296 |
|
for LSR: move checking overlaps out of JFNK-if-block |
297 |
|
o pkg/atm_phys: |
298 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
299 |
|
new S/R ATM_PHYS_DYN2PHYS. |
300 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
301 |
|
fixed-in-time pressure levels). |
302 |
|
o pkg/mom_common (bottomdrag): |
303 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
304 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
305 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
306 |
|
o pkg/shelfice (u/v_drag): |
307 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
308 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
309 |
|
(now similar to shelfice_u_drag.F) |
310 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
311 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
312 |
|
o pkg/mom_common (bottomdrag): |
313 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
314 |
|
- add options for alternative discretisation of velocity norm in quadratic |
315 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
316 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
317 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
318 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
319 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
320 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
321 |
|
off by default since this also reduces model stability (explicit bottom |
322 |
|
friction). Changes produce different machine truncation with linear-drag |
323 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
324 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
325 |
|
o model/src & mom pkgs: |
326 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
327 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
328 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
329 |
|
just copy level Nr value to level Nr+1. |
330 |
|
o doc: |
331 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
332 |
|
o pkg/streamice: |
333 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
334 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
335 |
|
from array shelficemassinit, which is set in init_fixed and |
336 |
|
has option to be set from file; introduce array |
337 |
|
shelficeMassDynTend array, set thru file in init_fixed |
338 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
339 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
340 |
|
pkg/streamice |
341 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
342 |
|
SHELFICEMassStepping = .true. |
343 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
344 |
|
|
345 |
|
checkpoint65h (2014/12/17) |
346 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
347 |
|
- update to generic controls. |
348 |
|
o pkg/ctrl: |
349 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
350 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
351 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
352 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
353 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
354 |
|
add time variable weights and cyclic controls (time mean, |
355 |
|
seasonal cycle, etc) capabilities to gentim2d |
356 |
|
o pkg/ecco: |
357 |
|
- move reading of error, conversion to weights from |
358 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
359 |
|
o global_oce_llc90, cs32: |
360 |
|
- activte sbo. |
361 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
362 |
|
- activate the new genctrl capabilities. |
363 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
364 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
365 |
|
- add missing ctrl_init_rec.f |
366 |
|
o tools/OAD_support/keepOriginal: |
367 |
|
- add ctrl_init_rec.F |
368 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
369 |
|
- avoid recomputations of xx_gentim2d_dummy. |
370 |
|
o momentum diagnostics: |
371 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
372 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
373 |
|
o pkg/seaice/seaice_lsr.F: |
374 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
375 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
376 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
377 |
|
o verification/global_ocean.cs32x15/input.seaice |
378 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
379 |
|
methods for LSR |
380 |
|
- update results/output.seaice.txt |
381 |
|
o verification/tutorial_global_oce_biogeo: |
382 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
383 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
384 |
|
update output_adm,_oadm,_tlm.txt |
385 |
|
o pkg/dic: |
386 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
387 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
388 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
389 |
|
o verification/tutorial_global_oce_biogeo: |
390 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
391 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
392 |
|
update output_adm,_oadm,_tlm.txt |
393 |
|
o eesupp/src: |
394 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
395 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
396 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
397 |
|
LSR (following Hutchings et al. 2004) |
398 |
|
- introduce zetaZ as a global variable (requires adjustments in |
399 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
400 |
|
in seaice_calc_viscosities.F |
401 |
|
- new flag SEAICEuseStrImpCpl (default off) |
402 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
403 |
|
momentum equations |
404 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
405 |
|
(where it does not have any positive effect) |
406 |
|
o pkg/seaice |
407 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
408 |
|
turn it off by default (because it only seems to work for non-cubed |
409 |
|
sphere/llc topologies) |
410 |
|
o pkg/autodiff |
411 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
412 |
|
o pkg/seaice: |
413 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
414 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
415 |
|
o pkg/obcs: |
416 |
|
- add option to specify domain-connected piece Id along OB though files |
417 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
418 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
419 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
420 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
421 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
422 |
|
o pkg/diagnostics: |
423 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
424 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
425 |
|
outside OB (i.e, where tracer OBCS are applied). |
426 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
427 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
428 |
|
|
429 |
|
checkpoint65g (2014/11/19) |
430 |
|
o pkg/diagnostcis: |
431 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
432 |
|
o pkg/my82,pp81,kl10: |
433 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
434 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
435 |
|
o pkg/seaice: |
436 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
437 |
|
Bouillon et al 2013) |
438 |
|
- add SEAICE_evpAlpha/Beta to namelist |
439 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
440 |
|
involve trivial re-ordering of divisions/multiplications that should not |
441 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
442 |
|
that only 2 digits of agreement remain, in line with the general |
443 |
|
instability/fragility of the evp-code. For now, I do not care and just |
444 |
|
update the verification experiment |
445 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
446 |
|
- remove xx_genarr2d_numsmooth etc |
447 |
|
- use xx_genarr2d_preproc etc instead |
448 |
|
- carry out smooth_correl2D at initialization stage rather than during |
449 |
|
time stepping. |
450 |
|
- get smoothOpNb from xx_gentim2d_preproc |
451 |
|
o global_oce_cs32 : |
452 |
|
- add test of generic ecco capabilities. |
453 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
454 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
455 |
|
o pkg/ctrl,ecco : |
456 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
457 |
|
is defined. |
458 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
459 |
|
o model/src: |
460 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
461 |
|
diffusivity (background) is specified but ignored. |
462 |
|
o verification: |
463 |
|
- in testreport, convert hostname to lower case for default output dir name |
464 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
465 |
|
o pkg/dic: add modifications from Hajoon: |
466 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
467 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
468 |
|
(read from file). |
469 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
470 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
471 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
472 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
473 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
474 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
475 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
476 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
477 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
478 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
479 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
480 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
481 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
482 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
483 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
484 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
485 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
486 |
|
o pkg/ctrl,ecco,exf : |
487 |
|
- remove variables associated with NON-generic costs, |
488 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
489 |
|
- remove NON-generic NON-obcs controls, |
490 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
491 |
|
o pkg/ctrl : added ctrl_local_params.h |
492 |
|
o pkg/ecco : added ecco_local_params.h |
493 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
494 |
|
experiments, which will progressively be removed once the |
495 |
|
experiments are revised to use only generic controls/costs. |
496 |
|
|
497 |
|
checkpoint65f (2014/10/13) |
498 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
499 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
500 |
|
cost function and control capabilities added since checkpoint65c. |
501 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
502 |
|
o pkg/ecco: increase modularity and improve logic |
503 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
504 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
505 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
506 |
|
- cost_gencal.F (new) : determine filnames and records. |
507 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
508 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
509 |
|
and exploit the above functions leading to more compact code. |
510 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
511 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
512 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
513 |
|
o pkg/ecco: extend generic cost capabilities |
514 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
515 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
516 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
517 |
|
gencost_outputlevel arguments to cost_generic |
518 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
519 |
|
and active_read, making room for gencost_preproc to take effect. |
520 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
521 |
|
- pkg/ecco/cost_generic.F : |
522 |
|
compute and store misfit maks*(model-data) in localdif that is |
523 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
524 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
525 |
|
rather gencost_barfile for deciding whether to write barfile |
526 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
527 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
528 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
529 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
530 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
531 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
532 |
|
o pkg/ecco: internal re-organization |
533 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
534 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
535 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
536 |
|
make sure gencost routines only include ecco.h) |
537 |
|
- throughout : add missing CCP switches, rm unused variables, |
538 |
|
and rm un-necessary CPP switches |
539 |
|
- throughout gencost routines : replace modelstartdate with |
540 |
|
gencost_startdate when needed |
541 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
542 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
543 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
544 |
|
- ecco_phys.F : compute etanFull |
545 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
546 |
|
bpv4-grace to gencost list, initialize added parameters |
547 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
548 |
|
|
549 |
|
checkpoint65e (2014/09/28) |
550 |
|
o pkg/obcs: |
551 |
|
- replaced the just-added CPP options with run-time variables |
552 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
553 |
|
o pkg/obcs: |
554 |
|
- add additional CPP options for sponge boundary layers |
555 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
556 |
|
o pkg/atm_phys: |
557 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
558 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
559 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
560 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
561 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
562 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
563 |
|
- implement gentim2d for xx_tauu, xx_tauv |
564 |
|
o pkg/ctrl, pkg/ecco : |
565 |
|
- fix and complement the generic controls implementation |
566 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
567 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
568 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
569 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
570 |
|
- add weight in CTRL_GET_GEN calls |
571 |
|
o pkg/ctrl : |
572 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
573 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
574 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
575 |
|
o pkg/ctrl : |
576 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
577 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
578 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
579 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
580 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
581 |
|
o pkg/ecco, pkg/ctrl : |
582 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
583 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
584 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
585 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
586 |
|
|
587 |
|
checkpoint65d (2014/09/15) |
588 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
589 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
590 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
591 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
592 |
|
- remove compilation failure |
593 |
|
- replace hard coded example |
594 |
|
- use ctrl_map_ini_gen2D, 3D |
595 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
596 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
597 |
|
o src/packages_init_variables.F : |
598 |
|
- regroup pkg/estimation calls |
599 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
600 |
|
(moved to ctrl_init_variables) |
601 |
|
o cost/cost_init_varia.F : |
602 |
|
- remove ecco_cost_init_varia |
603 |
|
(moved to ecco_init_varia) |
604 |
|
o ctrl/ctrl_init_variables.F : |
605 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
606 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
607 |
|
o ctrl/ctrl_map_ini.F : |
608 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
609 |
|
(moved to ctrl_init_variables) |
610 |
|
o ctrl/ctrl_map_ini_ecco.F : |
611 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
612 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
613 |
|
o ecco/ecco_ad_diff.list : |
614 |
|
- add ecco_init_varia.f |
615 |
|
o ecco/ecco_init_varia.F |
616 |
|
- new routine |
617 |
|
o pkg/streamice: |
618 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
619 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
620 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
621 |
|
o pkg/generic_advdiff: |
622 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
623 |
|
o pkg/exf: |
624 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
625 |
|
xxg_precip capability |
626 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
627 |
|
o pkg/ctrl: |
628 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
629 |
|
o model/src/load_fields_driver.F : |
630 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
631 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
632 |
|
o OpenAD verification experiments: |
633 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
634 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
635 |
|
for now, only in pkgs used in OpenAD verification experiments. |
636 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
637 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
638 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
639 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
640 |
|
o OpenAD verification tests: |
641 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
642 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
643 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
644 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
645 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
646 |
|
o model/src & generic_advdiff: |
647 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
648 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
649 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
650 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
651 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
652 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
653 |
|
setting in temp/salt/ptracer_integrate.F |
654 |
|
o pkg/dic: |
655 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
656 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
657 |
|
in gchem_forcing_sep.F |
658 |
|
o pkg/autodiff & obcs: |
659 |
|
- add storage of current OB values for U & V (was already done for T & S). |
660 |
|
|
661 |
|
checkpoint65c (2014/08/30) |
662 |
|
o pkg/dic: |
663 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
664 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
665 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
666 |
|
o verification: |
667 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
668 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
669 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
670 |
|
conditions from t=1.yr while keeping the same forcing. |
671 |
|
o model/src: |
672 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
673 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
674 |
|
o pkg/diagnostics (Stats-Diags): |
675 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
676 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
677 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
678 |
|
c) extend regional stats over the region edges (for U or V pt location). |
679 |
|
o pkg/gchem: |
680 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
681 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
682 |
|
o verification (hs94): |
683 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
684 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
685 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
686 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
687 |
|
o pkg/ptracers: |
688 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
689 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
690 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
691 |
|
with AB-2 code (so that it get tested). |
692 |
|
o model/src: |
693 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
694 |
|
with AB-2 code (previously only available with AB-3 code). |
695 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
696 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
697 |
|
there, by calling CYCLE_AB_TRACER). |
698 |
|
o pkg/generic_advdiff: |
699 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
700 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
701 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
702 |
|
S/R temp/salt/ptracers_integrate.F |
703 |
|
o model/src & pkg/ptracers: |
704 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
705 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
706 |
|
- remove common block variable gPtr. |
707 |
|
o model/src & pkgs: |
708 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
709 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
710 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
711 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
712 |
|
+ change accordingly all calling S/R. |
713 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
714 |
|
in S/R temp/salt/ptracers_integrate.F |
715 |
|
o pkg/seaice: |
716 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
717 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
718 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
719 |
|
in seaice_lsr |
720 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
721 |
|
in s/r seaice_lsr_calc_coeffs |
722 |
|
o pkg/mdsio: |
723 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
724 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
725 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
726 |
|
|
727 |
|
checkpoint65b (2014/08/12) |
728 |
|
o pkg/matrix: |
729 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
730 |
|
o model/src: |
731 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
732 |
|
natl_box verification experiment. |
733 |
|
o model/src & pkg/down_slope: |
734 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
735 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
736 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
737 |
|
results at machine truncation level: update output of experiments |
738 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
739 |
|
o pkg/diagnostics (Stats-Diags): |
740 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
741 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
742 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
743 |
|
times (but Min,Max and StD are still wrong). |
744 |
|
o model/src: |
745 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
746 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
747 |
|
o model/src: |
748 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
749 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
750 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
751 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
752 |
|
o model/src: |
753 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
754 |
|
anomaly that is used to compute geopotential: this make the atmos code |
755 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
756 |
|
o pkg/seaice/seaice_lsr.F |
757 |
|
- rename integer variable ilcall to ipass (that's what it is called |
758 |
|
in the residual diagnostics |
759 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
760 |
|
default) for improved non-linear convergence of the first few steps |
761 |
|
- adjust a few comments and add new ones to explain some of the store |
762 |
|
directives |
763 |
|
o pkg/generic_advdiff (& ptracers): |
764 |
|
- re-work the code to check for valid advection scheme and for minimum |
765 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
766 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
767 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
768 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
769 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
770 |
|
less exact gradients in my tests); but there are still |
771 |
|
recomputation warning (although gradients are sort of OK), when |
772 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
773 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
774 |
|
- update verification experiments lab_sea. |
775 |
|
- change some comments in S/R seaice_calc_viscosities |
776 |
|
o model/src: |
777 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
778 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
779 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
780 |
|
but affects AD results (at machine truncation level): update output of |
781 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
782 |
|
and isomip (oad: 12.d). |
783 |
|
o pkg/generic_advdiff: |
784 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
785 |
|
- refine warning related to stability of tracer time-stepping |
786 |
|
regarding internal wave dynamics. |
787 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
788 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
789 |
|
if potentially unstable). |
790 |
|
o pkg/kl10: |
791 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
792 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
793 |
|
(contribution from Jody Klymak), tested in verification experiment |
794 |
|
verification/internal_wave/input.kl10/ |
795 |
|
o isomip experiment: |
796 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
797 |
|
(input.htd) and update the output. |
798 |
|
o cd_code experiments: |
799 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
800 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
801 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
802 |
|
update the corresponding output. |
803 |
|
o pkg/seaice: |
804 |
|
- reduce the number of include files and store directives in |
805 |
|
S/R seaice_lsr_tridiagu/v |
806 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
807 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
808 |
|
get rid off one store directive (a TAF bug?) |
809 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
810 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
811 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
812 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
813 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
814 |
|
offline_exf_seaice/input.dyn_jfnk) |
815 |
|
|
816 |
|
checkpoint65a (2014/07/27) |
817 |
|
o model/src: |
818 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
819 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
820 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
821 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
822 |
|
o model/src: |
823 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
824 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
825 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
826 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
827 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
828 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
829 |
|
affects results at machine truncation level (e.g., ocean: if using |
830 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
831 |
|
correction due to vertical advection). |
832 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
833 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
834 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
835 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
836 |
|
o pkg/ptracers & diagnostics: |
837 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
838 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
839 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
840 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
841 |
|
|
842 |
|
checkpoint65 (2014/07/18) |
843 |
|
o pkg/fizhi: |
844 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
845 |
|
affects results at machine truncation level. Update output of experiments |
846 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
847 |
|
o pkg/seaice: more clean up |
848 |
|
- rename TAF common block tapes to be more consistent and remove |
849 |
|
unnecessary duplicates |
850 |
|
- add store directives to remove more recomputations, but use smaller |
851 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
852 |
|
The idea behind this flag is to reduce the memory footprint when the |
853 |
|
adjoint of the LSR is not required. As of now, defining the flag |
854 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
855 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
856 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
857 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
858 |
|
this experiment): |
859 |
|
> size mitgcmuv_ad |
860 |
|
text data bss dec hex |
861 |
|
5100659 1216 220458952 225560827 d71c8fb |
862 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
863 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
864 |
|
text data bss dec hex |
865 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
866 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
867 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
868 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
869 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
870 |
|
- in general, the AD gradients still are wrong |
871 |
|
o OpenAD |
872 |
|
- clean up code_oad/ directories somewhat by moving files |
873 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
874 |
|
o model/src: |
875 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
876 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
877 |
|
tendencies (previously done after). |
878 |
|
o pkg/diagnostics: |
879 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
880 |
|
o pkg/down_slope: |
881 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
882 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
883 |
|
o model/src: |
884 |
|
- new file "apply_forcing.F" containing all the code previously in |
885 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
886 |
|
the current level tendency array to update (instead of a direct update |
887 |
|
of the common bloc array). Change the corresponding calls. |
888 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
889 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
890 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
891 |
|
- rearrange some code blocks, so that now all calculations for |
892 |
|
setting up the right-hand-sides done within one single block |
893 |
|
(I find that easier to read and understand) |
894 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
895 |
|
- adjust some indentations and comments |
896 |
|
|
897 |
|
checkpoint64z (2014/07/10) |
898 |
|
o model/src and several pkgs: |
899 |
|
- change argument list of all S/R called from external_forcing.F and |
900 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
901 |
|
to pass, as argument, the current level tendency array to update |
902 |
|
(instead of a direct update of the common bloc array). |
903 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
904 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
905 |
|
o pkg/seaice/seaice_lsr.F |
906 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
907 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
908 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
909 |
|
keep it in bi/bj loop; this seems to be essential |
910 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
911 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
912 |
|
o pkg/seaice |
913 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
914 |
|
generates unnecessary code in seaice_lsr_ad |
915 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
916 |
|
in seaice_lsr_ad |
917 |
|
- exclude some residual computations in seaice_lsr when |
918 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
919 |
|
in seaice_lsr_ad |
920 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
921 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
922 |
|
and klockey should be checked by a specialist) |
923 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
924 |
|
and update lab_sea after previous changes in pkg/seaice below |
925 |
|
o pkg/autodiff: |
926 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
927 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
928 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
929 |
|
o pkg/ecco: |
930 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
931 |
|
temperature (for use in adjoint sensitivity studies). |
932 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
933 |
|
o pkg/mom_common/mom_calc_visc.F: |
934 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
935 |
|
o pkg/seaice/seaice_summary.F: |
936 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
937 |
|
o pkg/seaice: |
938 |
|
- remove some store directives and add new ones in an effort to get |
939 |
|
finally rid off the recomputation warnings. This is successful |
940 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
941 |
|
defined (i.e. no extensive recomputation warnings left), but there |
942 |
|
are still too many recomputations on the solver iteration level |
943 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
944 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
945 |
|
SEAICE_SIZE.h |
946 |
|
- add a store directive in S/R seaice_calc_viscosities |
947 |
|
o pkg/seaice (ITD code): |
948 |
|
- fix definition of Hlimit for multi-threaded case |
949 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
950 |
|
update output of experiment seaice_itd. |
951 |
o replace content of verification/seaice_itd |
o replace content of verification/seaice_itd |
952 |
- instead of a 1D column use the configuration of offline_exf_seaice |
- instead of a 1D column use the configuration of offline_exf_seaice |
953 |
to test the ice thickness distribution code with ridging |
to test the ice thickness distribution code with ridging |
954 |
- this is a first shot at this experiment |
- this is a first shot at this experiment |
955 |
- change of some defaults of ridging parameters SEAICEhStar (from |
- change of some defaults of ridging parameters SEAICEhStar (from |
956 |
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
957 |
and lost of new comments |
and lot of new comments. |
958 |
|
|
959 |
checkpoint64y (2014/06/20) |
checkpoint64y (2014/06/20) |
960 |
o pkg/seaice/seaice_reg_ridge.F: |
o pkg/seaice/seaice_reg_ridge.F: |