4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
o useSingleCpuInput separates single-CPU input from single-CPU output |
o model/src: |
8 |
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
- move (from ini_forcing.F) initialisation of all arrays in header file |
9 |
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
10 |
|
(since Nov 2012) with option selectAddFluid=1. |
11 |
|
o pkg/shelfice: |
12 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
13 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
14 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
15 |
|
o pkg/seaice: two new runtime parameters: |
16 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
17 |
|
long overdue |
18 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
19 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
20 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
21 |
|
for LSR: move checking overlaps out of JFNK-if-block |
22 |
|
o pkg/atm_phys: |
23 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
24 |
|
new S/R ATM_PHYS_DYN2PHYS. |
25 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
26 |
|
fixed-in-time pressure levels). |
27 |
|
o pkg/mom_common (bottomdrag): |
28 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
29 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
30 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
31 |
|
o pkg/shelfice (u/v_drag): |
32 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
33 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
34 |
|
(now similar to shelfice_u_drag.F) |
35 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
36 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
37 |
|
o pkg/mom_common (bottomdrag): |
38 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
39 |
|
- add options for alternative discretisation of velocity norm in quadratic |
40 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
41 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
42 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
43 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
44 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
45 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
46 |
|
off by default since this also reduces model stability (explicit bottom |
47 |
|
friction). Changes produce different machine truncation with linear-drag |
48 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
49 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
50 |
|
o model/src & mom pkgs: |
51 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
52 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
53 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
54 |
|
just copy level Nr value to level Nr+1. |
55 |
|
o doc: |
56 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
57 |
|
o pkg/streamice: |
58 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
59 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
60 |
|
from array shelficemassinit, which is set in init_fixed and |
61 |
|
has option to be set from file; introduce array |
62 |
|
shelficeMassDynTend array, set thru file in init_fixed |
63 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
64 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
65 |
|
pkg/streamice |
66 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
67 |
|
SHELFICEMassStepping = .true. |
68 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
69 |
|
|
70 |
|
checkpoint65h (2014/12/17) |
71 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
72 |
|
- update to generic controls. |
73 |
|
o pkg/ctrl: |
74 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
75 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
76 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
77 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
78 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
79 |
|
add time variable weights and cyclic controls (time mean, |
80 |
|
seasonal cycle, etc) capabilities to gentim2d |
81 |
|
o pkg/ecco: |
82 |
|
- move reading of error, conversion to weights from |
83 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
84 |
|
o global_oce_llc90, cs32: |
85 |
|
- activte sbo. |
86 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
87 |
|
- activate the new genctrl capabilities. |
88 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
89 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
90 |
|
- add missing ctrl_init_rec.f |
91 |
|
o tools/OAD_support/keepOriginal: |
92 |
|
- add ctrl_init_rec.F |
93 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
94 |
|
- avoid recomputations of xx_gentim2d_dummy. |
95 |
|
o momentum diagnostics: |
96 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
97 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
98 |
|
o pkg/seaice/seaice_lsr.F: |
99 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
100 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
101 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
102 |
|
o verification/global_ocean.cs32x15/input.seaice |
103 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
104 |
|
methods for LSR |
105 |
|
- update results/output.seaice.txt |
106 |
|
o verification/tutorial_global_oce_biogeo: |
107 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
108 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
109 |
|
update output_adm,_oadm,_tlm.txt |
110 |
|
o pkg/dic: |
111 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
112 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
113 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
114 |
|
o verification/tutorial_global_oce_biogeo: |
115 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
116 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
117 |
|
update output_adm,_oadm,_tlm.txt |
118 |
|
o eesupp/src: |
119 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
120 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
121 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
122 |
|
LSR (following Hutchings et al. 2004) |
123 |
|
- introduce zetaZ as a global variable (requires adjustments in |
124 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
125 |
|
in seaice_calc_viscosities.F |
126 |
|
- new flag SEAICEuseStrImpCpl (default off) |
127 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
128 |
|
momentum equations |
129 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
130 |
|
(where it does not have any positive effect) |
131 |
|
o pkg/seaice |
132 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
133 |
|
turn it off by default (because it only seems to work for non-cubed |
134 |
|
sphere/llc topologies) |
135 |
|
o pkg/autodiff |
136 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
137 |
|
o pkg/seaice: |
138 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
139 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
140 |
|
o pkg/obcs: |
141 |
|
- add option to specify domain-connected piece Id along OB though files |
142 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
143 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
144 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
145 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
146 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
147 |
|
o pkg/diagnostics: |
148 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
149 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
150 |
|
outside OB (i.e, where tracer OBCS are applied). |
151 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
152 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
153 |
|
|
154 |
|
checkpoint65g (2014/11/19) |
155 |
|
o pkg/diagnostcis: |
156 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
157 |
|
o pkg/my82,pp81,kl10: |
158 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
159 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
160 |
|
o pkg/seaice: |
161 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
162 |
|
Bouillon et al 2013) |
163 |
|
- add SEAICE_evpAlpha/Beta to namelist |
164 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
165 |
|
involve trivial re-ordering of divisions/multiplications that should not |
166 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
167 |
|
that only 2 digits of agreement remain, in line with the general |
168 |
|
instability/fragility of the evp-code. For now, I do not care and just |
169 |
|
update the verification experiment |
170 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
171 |
|
- remove xx_genarr2d_numsmooth etc |
172 |
|
- use xx_genarr2d_preproc etc instead |
173 |
|
- carry out smooth_correl2D at initialization stage rather than during |
174 |
|
time stepping. |
175 |
|
- get smoothOpNb from xx_gentim2d_preproc |
176 |
|
o global_oce_cs32 : |
177 |
|
- add test of generic ecco capabilities. |
178 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
179 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
180 |
|
o pkg/ctrl,ecco : |
181 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
182 |
|
is defined. |
183 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
184 |
|
o model/src: |
185 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
186 |
|
diffusivity (background) is specified but ignored. |
187 |
|
o verification: |
188 |
|
- in testreport, convert hostname to lower case for default output dir name |
189 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
190 |
|
o pkg/dic: add modifications from Hajoon: |
191 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
192 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
193 |
|
(read from file). |
194 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
195 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
196 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
197 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
198 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
199 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
200 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
201 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
202 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
203 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
204 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
205 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
206 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
207 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
208 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
209 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
210 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
211 |
|
o pkg/ctrl,ecco,exf : |
212 |
|
- remove variables associated with NON-generic costs, |
213 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
214 |
|
- remove NON-generic NON-obcs controls, |
215 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
216 |
|
o pkg/ctrl : added ctrl_local_params.h |
217 |
|
o pkg/ecco : added ecco_local_params.h |
218 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
219 |
|
experiments, which will progressively be removed once the |
220 |
|
experiments are revised to use only generic controls/costs. |
221 |
|
|
222 |
|
checkpoint65f (2014/10/13) |
223 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
224 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
225 |
|
cost function and control capabilities added since checkpoint65c. |
226 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
227 |
|
o pkg/ecco: increase modularity and improve logic |
228 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
229 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
230 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
231 |
|
- cost_gencal.F (new) : determine filnames and records. |
232 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
233 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
234 |
|
and exploit the above functions leading to more compact code. |
235 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
236 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
237 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
238 |
|
o pkg/ecco: extend generic cost capabilities |
239 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
240 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
241 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
242 |
|
gencost_outputlevel arguments to cost_generic |
243 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
244 |
|
and active_read, making room for gencost_preproc to take effect. |
245 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
246 |
|
- pkg/ecco/cost_generic.F : |
247 |
|
compute and store misfit maks*(model-data) in localdif that is |
248 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
249 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
250 |
|
rather gencost_barfile for deciding whether to write barfile |
251 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
252 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
253 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
254 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
255 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
256 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
257 |
|
o pkg/ecco: internal re-organization |
258 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
259 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
260 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
261 |
|
make sure gencost routines only include ecco.h) |
262 |
|
- throughout : add missing CCP switches, rm unused variables, |
263 |
|
and rm un-necessary CPP switches |
264 |
|
- throughout gencost routines : replace modelstartdate with |
265 |
|
gencost_startdate when needed |
266 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
267 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
268 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
269 |
|
- ecco_phys.F : compute etanFull |
270 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
271 |
|
bpv4-grace to gencost list, initialize added parameters |
272 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
273 |
|
|
274 |
|
checkpoint65e (2014/09/28) |
275 |
|
o pkg/obcs: |
276 |
|
- replaced the just-added CPP options with run-time variables |
277 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
278 |
|
o pkg/obcs: |
279 |
|
- add additional CPP options for sponge boundary layers |
280 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
281 |
|
o pkg/atm_phys: |
282 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
283 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
284 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
285 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
286 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
287 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
288 |
|
- implement gentim2d for xx_tauu, xx_tauv |
289 |
|
o pkg/ctrl, pkg/ecco : |
290 |
|
- fix and complement the generic controls implementation |
291 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
292 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
293 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
294 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
295 |
|
- add weight in CTRL_GET_GEN calls |
296 |
|
o pkg/ctrl : |
297 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
298 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
299 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
300 |
|
o pkg/ctrl : |
301 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
302 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
303 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
304 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
305 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
306 |
|
o pkg/ecco, pkg/ctrl : |
307 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
308 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
309 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
310 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
311 |
|
|
312 |
|
checkpoint65d (2014/09/15) |
313 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
314 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
315 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
316 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
317 |
|
- remove compilation failure |
318 |
|
- replace hard coded example |
319 |
|
- use ctrl_map_ini_gen2D, 3D |
320 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
321 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
322 |
|
o src/packages_init_variables.F : |
323 |
|
- regroup pkg/estimation calls |
324 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
325 |
|
(moved to ctrl_init_variables) |
326 |
|
o cost/cost_init_varia.F : |
327 |
|
- remove ecco_cost_init_varia |
328 |
|
(moved to ecco_init_varia) |
329 |
|
o ctrl/ctrl_init_variables.F : |
330 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
331 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
332 |
|
o ctrl/ctrl_map_ini.F : |
333 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
334 |
|
(moved to ctrl_init_variables) |
335 |
|
o ctrl/ctrl_map_ini_ecco.F : |
336 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
337 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
338 |
|
o ecco/ecco_ad_diff.list : |
339 |
|
- add ecco_init_varia.f |
340 |
|
o ecco/ecco_init_varia.F |
341 |
|
- new routine |
342 |
|
o pkg/streamice: |
343 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
344 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
345 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
346 |
|
o pkg/generic_advdiff: |
347 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
348 |
|
o pkg/exf: |
349 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
350 |
|
xxg_precip capability |
351 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
352 |
|
o pkg/ctrl: |
353 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
354 |
|
o model/src/load_fields_driver.F : |
355 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
356 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
357 |
|
o OpenAD verification experiments: |
358 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
359 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
360 |
|
for now, only in pkgs used in OpenAD verification experiments. |
361 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
362 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
363 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
364 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
365 |
|
o OpenAD verification tests: |
366 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
367 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
368 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
369 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
370 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
371 |
|
o model/src & generic_advdiff: |
372 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
373 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
374 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
375 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
376 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
377 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
378 |
|
setting in temp/salt/ptracer_integrate.F |
379 |
|
o pkg/dic: |
380 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
381 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
382 |
|
in gchem_forcing_sep.F |
383 |
|
o pkg/autodiff & obcs: |
384 |
|
- add storage of current OB values for U & V (was already done for T & S). |
385 |
|
|
386 |
|
checkpoint65c (2014/08/30) |
387 |
|
o pkg/dic: |
388 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
389 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
390 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
391 |
|
o verification: |
392 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
393 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
394 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
395 |
|
conditions from t=1.yr while keeping the same forcing. |
396 |
|
o model/src: |
397 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
398 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
399 |
|
o pkg/diagnostics (Stats-Diags): |
400 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
401 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
402 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
403 |
|
c) extend regional stats over the region edges (for U or V pt location). |
404 |
|
o pkg/gchem: |
405 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
406 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
407 |
|
o verification (hs94): |
408 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
409 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
410 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
411 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
412 |
|
o pkg/ptracers: |
413 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
414 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
415 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
416 |
|
with AB-2 code (so that it get tested). |
417 |
|
o model/src: |
418 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
419 |
|
with AB-2 code (previously only available with AB-3 code). |
420 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
421 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
422 |
|
there, by calling CYCLE_AB_TRACER). |
423 |
|
o pkg/generic_advdiff: |
424 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
425 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
426 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
427 |
|
S/R temp/salt/ptracers_integrate.F |
428 |
|
o model/src & pkg/ptracers: |
429 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
430 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
431 |
|
- remove common block variable gPtr. |
432 |
|
o model/src & pkgs: |
433 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
434 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
435 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
436 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
437 |
|
+ change accordingly all calling S/R. |
438 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
439 |
|
in S/R temp/salt/ptracers_integrate.F |
440 |
|
o pkg/seaice: |
441 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
442 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
443 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
444 |
|
in seaice_lsr |
445 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
446 |
|
in s/r seaice_lsr_calc_coeffs |
447 |
|
o pkg/mdsio: |
448 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
449 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
450 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
451 |
|
|
452 |
|
checkpoint65b (2014/08/12) |
453 |
|
o pkg/matrix: |
454 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
455 |
|
o model/src: |
456 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
457 |
|
natl_box verification experiment. |
458 |
|
o model/src & pkg/down_slope: |
459 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
460 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
461 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
462 |
|
results at machine truncation level: update output of experiments |
463 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
464 |
|
o pkg/diagnostics (Stats-Diags): |
465 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
466 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
467 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
468 |
|
times (but Min,Max and StD are still wrong). |
469 |
|
o model/src: |
470 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
471 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
472 |
|
o model/src: |
473 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
474 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
475 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
476 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
477 |
|
o model/src: |
478 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
479 |
|
anomaly that is used to compute geopotential: this make the atmos code |
480 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
481 |
|
o pkg/seaice/seaice_lsr.F |
482 |
|
- rename integer variable ilcall to ipass (that's what it is called |
483 |
|
in the residual diagnostics |
484 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
485 |
|
default) for improved non-linear convergence of the first few steps |
486 |
|
- adjust a few comments and add new ones to explain some of the store |
487 |
|
directives |
488 |
|
o pkg/generic_advdiff (& ptracers): |
489 |
|
- re-work the code to check for valid advection scheme and for minimum |
490 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
491 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
492 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
493 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
494 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
495 |
|
less exact gradients in my tests); but there are still |
496 |
|
recomputation warning (although gradients are sort of OK), when |
497 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
498 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
499 |
|
- update verification experiments lab_sea. |
500 |
|
- change some comments in S/R seaice_calc_viscosities |
501 |
|
o model/src: |
502 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
503 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
504 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
505 |
|
but affects AD results (at machine truncation level): update output of |
506 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
507 |
|
and isomip (oad: 12.d). |
508 |
|
o pkg/generic_advdiff: |
509 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
510 |
|
- refine warning related to stability of tracer time-stepping |
511 |
|
regarding internal wave dynamics. |
512 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
513 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
514 |
|
if potentially unstable). |
515 |
|
o pkg/kl10: |
516 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
517 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
518 |
|
(contribution from Jody Klymak), tested in verification experiment |
519 |
|
verification/internal_wave/input.kl10/ |
520 |
|
o isomip experiment: |
521 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
522 |
|
(input.htd) and update the output. |
523 |
|
o cd_code experiments: |
524 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
525 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
526 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
527 |
|
update the corresponding output. |
528 |
|
o pkg/seaice: |
529 |
|
- reduce the number of include files and store directives in |
530 |
|
S/R seaice_lsr_tridiagu/v |
531 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
532 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
533 |
|
get rid off one store directive (a TAF bug?) |
534 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
535 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
536 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
537 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
538 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
539 |
|
offline_exf_seaice/input.dyn_jfnk) |
540 |
|
|
541 |
|
checkpoint65a (2014/07/27) |
542 |
|
o model/src: |
543 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
544 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
545 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
546 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
547 |
|
o model/src: |
548 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
549 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
550 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
551 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
552 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
553 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
554 |
|
affects results at machine truncation level (e.g., ocean: if using |
555 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
556 |
|
correction due to vertical advection). |
557 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
558 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
559 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
560 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
561 |
|
o pkg/ptracers & diagnostics: |
562 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
563 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
564 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
565 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
566 |
|
|
567 |
|
checkpoint65 (2014/07/18) |
568 |
|
o pkg/fizhi: |
569 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
570 |
|
affects results at machine truncation level. Update output of experiments |
571 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
572 |
|
o pkg/seaice: more clean up |
573 |
|
- rename TAF common block tapes to be more consistent and remove |
574 |
|
unnecessary duplicates |
575 |
|
- add store directives to remove more recomputations, but use smaller |
576 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
577 |
|
The idea behind this flag is to reduce the memory footprint when the |
578 |
|
adjoint of the LSR is not required. As of now, defining the flag |
579 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
580 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
581 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
582 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
583 |
|
this experiment): |
584 |
|
> size mitgcmuv_ad |
585 |
|
text data bss dec hex |
586 |
|
5100659 1216 220458952 225560827 d71c8fb |
587 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
588 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
589 |
|
text data bss dec hex |
590 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
591 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
592 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
593 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
594 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
595 |
|
- in general, the AD gradients still are wrong |
596 |
|
o OpenAD |
597 |
|
- clean up code_oad/ directories somewhat by moving files |
598 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
599 |
|
o model/src: |
600 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
601 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
602 |
|
tendencies (previously done after). |
603 |
|
o pkg/diagnostics: |
604 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
605 |
|
o pkg/down_slope: |
606 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
607 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
608 |
|
o model/src: |
609 |
|
- new file "apply_forcing.F" containing all the code previously in |
610 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
611 |
|
the current level tendency array to update (instead of a direct update |
612 |
|
of the common bloc array). Change the corresponding calls. |
613 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
614 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
615 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
616 |
|
- rearrange some code blocks, so that now all calculations for |
617 |
|
setting up the right-hand-sides done within one single block |
618 |
|
(I find that easier to read and understand) |
619 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
620 |
|
- adjust some indentations and comments |
621 |
|
|
622 |
|
checkpoint64z (2014/07/10) |
623 |
|
o model/src and several pkgs: |
624 |
|
- change argument list of all S/R called from external_forcing.F and |
625 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
626 |
|
to pass, as argument, the current level tendency array to update |
627 |
|
(instead of a direct update of the common bloc array). |
628 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
629 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
630 |
|
o pkg/seaice/seaice_lsr.F |
631 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
632 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
633 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
634 |
|
keep it in bi/bj loop; this seems to be essential |
635 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
636 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
637 |
|
o pkg/seaice |
638 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
639 |
|
generates unnecessary code in seaice_lsr_ad |
640 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
641 |
|
in seaice_lsr_ad |
642 |
|
- exclude some residual computations in seaice_lsr when |
643 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
644 |
|
in seaice_lsr_ad |
645 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
646 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
647 |
|
and klockey should be checked by a specialist) |
648 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
649 |
|
and update lab_sea after previous changes in pkg/seaice below |
650 |
|
o pkg/autodiff: |
651 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
652 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
653 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
654 |
|
o pkg/ecco: |
655 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
656 |
|
temperature (for use in adjoint sensitivity studies). |
657 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
658 |
|
o pkg/mom_common/mom_calc_visc.F: |
659 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
660 |
|
o pkg/seaice/seaice_summary.F: |
661 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
662 |
|
o pkg/seaice: |
663 |
|
- remove some store directives and add new ones in an effort to get |
664 |
|
finally rid off the recomputation warnings. This is successful |
665 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
666 |
|
defined (i.e. no extensive recomputation warnings left), but there |
667 |
|
are still too many recomputations on the solver iteration level |
668 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
669 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
670 |
|
SEAICE_SIZE.h |
671 |
|
- add a store directive in S/R seaice_calc_viscosities |
672 |
|
o pkg/seaice (ITD code): |
673 |
|
- fix definition of Hlimit for multi-threaded case |
674 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
675 |
|
update output of experiment seaice_itd. |
676 |
|
o replace content of verification/seaice_itd |
677 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
678 |
|
to test the ice thickness distribution code with ridging |
679 |
|
- this is a first shot at this experiment |
680 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
681 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
682 |
|
and lot of new comments. |
683 |
|
|
684 |
|
checkpoint64y (2014/06/20) |
685 |
|
o pkg/seaice/seaice_reg_ridge.F: |
686 |
|
- modify the regularization of very small volumes of ice; only check |
687 |
|
total volume HEFF, and do not apply correction to individual ice |
688 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
689 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
690 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
691 |
|
o pkg/exf: |
692 |
|
- add code to process the case field period = -12. with UV interpolation. |
693 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
694 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
695 |
|
o verification/global_with_exf: |
696 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
697 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
698 |
|
o pkg/cal: |
699 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
700 |
|
o pkg/exf: |
701 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
702 |
|
to replace logical switch "exf_verbose" |
703 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
704 |
|
o pkg/sbo: |
705 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
706 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
707 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
708 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
709 |
|
- fix some multi-threading issues (in output part). |
710 |
|
o model/src & most packages: |
711 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
712 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
713 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
714 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
715 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
716 |
|
+ call LAND_READPARMS from packages_readparms.F |
717 |
|
o pkg/seaice: |
718 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
719 |
|
replace it by a warning in S/R seaice_check |
720 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
721 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
722 |
|
SEAICE_ITD is defined) |
723 |
|
|
724 |
|
checkpoint64x (2014/05/24) |
725 |
|
o verification/lab_sea: |
726 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
727 |
|
- un-do the update after putting back local recip_Cp in few places. |
728 |
|
o pkg/salt_plume: modifications by An Nguyen: |
729 |
|
- add capability to do brine rejection (salt-plume) as function of |
730 |
|
volume+tracers (instead of only salinity tracer). |
731 |
|
- conserve volume by exchanging volume from each kLev to above to |
732 |
|
accommodate in-coming brine volume |
733 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
734 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
735 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
736 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
737 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
738 |
|
in East/West Arctic. |
739 |
|
o pkg/sbo: |
740 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
741 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
742 |
|
output for future testreport verification (unfinished). |
743 |
|
o pkg/atm_phys: |
744 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
745 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
746 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
747 |
|
o pkg/seaice |
748 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
749 |
|
(affects truncation) |
750 |
|
seaice_do_ridging.F: clean up the insectarium |
751 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
752 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
753 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
754 |
|
- add some debugging information and error messages (warnings) |
755 |
|
o model/src: modifications relatd to atmosphere p*: |
756 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
757 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
758 |
|
of vertical profile tRef in geopotential background and anomaly. |
759 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
760 |
|
and pkg/atm_phys. |
761 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
762 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
763 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
764 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
765 |
|
not used right now, but can be used in BGC packages to fix conservation. |
766 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
767 |
|
other packages too. |
768 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
769 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
770 |
|
o model/src: |
771 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
772 |
|
as local variable (no longer in common block) to avoid any confusion. |
773 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
774 |
|
o pkg/exf: |
775 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
776 |
|
air density as function of air Temp, Humidity and atm pressure. |
777 |
|
|
778 |
|
checkpoint64w (2014/05/02) |
779 |
|
o verification: |
780 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
781 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
782 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
783 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
784 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
785 |
|
o model/src: for atmosphere in p* coords: |
786 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
787 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
788 |
|
but not yet activated. |
789 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
790 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
791 |
|
- this changes the results (but not for any verification experiment, because |
792 |
|
none tests this), but avoids having an extra field in the restart files |
793 |
|
o pkg/seaice: remove global variable TICE (not needed) |
794 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
795 |
|
seaice_diagnostics_state) |
796 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
797 |
|
- use specific read/write routines for reading and writing individual leves |
798 |
|
of a multilevel field |
799 |
|
o pkg/ctrl & model/inc: |
800 |
|
- move additional anomaly fields of control vars (related to options: |
801 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
802 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
803 |
|
o pkg/seaice: some small modifications to the ridging code |
804 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
805 |
|
seaice_growth |
806 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
807 |
|
computed only in one place and compute it in the same way as in |
808 |
|
seaice_growth |
809 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
810 |
|
point exceptions over land |
811 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
812 |
|
- move most of "PART 1" of S/R seaice_growth into a new and separate |
813 |
|
S/R seaice_reg_ridge that will both regularize the state variable after |
814 |
|
advection call the actual ridging routine; |
815 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
816 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
817 |
|
- remove ridging code from seaice_advdiff |
818 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
819 |
|
more readable (this is probably subjective) |
820 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
821 |
|
conditions in the correct category |
822 |
|
- finally: add new ridging routine for ITD code |
823 |
|
|
824 |
|
checkpoint64v (2014/04/11) |
825 |
|
o pkg/ecco: |
826 |
|
- add runtime parameters mdt[start,end]date[1,2] |
827 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
828 |
|
o pkg/seaice: |
829 |
|
- make deltaC a global variable, so that it can be used in ridging code |
830 |
|
- first step towards ridging: introduce new routines that compute |
831 |
|
ice strength based on ridging parameters |
832 |
|
- add diagnostic for HSNOWITD |
833 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
834 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
835 |
|
- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
836 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
837 |
|
o verification/hs94.1x64x5: |
838 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
839 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
840 |
|
o autodiff: |
841 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
842 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
843 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
844 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
845 |
|
which are specific to TAF/TAMC). |
846 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
847 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
848 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
849 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
850 |
|
building mitgcmuv_ad (make adAll). |
851 |
|
o pkg/ecco: |
852 |
|
- cost_gencost_seaicev4.F: |
853 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
854 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
855 |
|
- add stop statement if old names siv4-[sst,vol] are used |
856 |
|
- add snapshots + cost reports for atmospheric longwave |
857 |
|
- remove factor 0.1 in front of wtau[u,v] |
858 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
859 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
860 |
|
o pkg/atm_phys: |
861 |
|
- add some diagnostics for Short-wave and for convection S/R. |
862 |
|
o pkg/seaice/seaice_growth: |
863 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
864 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
865 |
|
- rearrange loop order for better vector code in the same code block |
866 |
|
- rewrite the floeDiameter formula to have fewer divisions |
867 |
|
- (miraculously) none of this changes the results of seaice_itd |
868 |
|
o pkg/smooth: |
869 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
870 |
|
o pkg/salt_plume: |
871 |
|
- salt_plume_frac.F: |
872 |
|
clean up local param names |
873 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
874 |
|
o pkg/rw: |
875 |
|
- add RS version of S/R READ_MFLDS_LEV. |
876 |
|
o pkg/streamice: |
877 |
|
- fix the restart test by writing/reading pickup_streamice files. |
878 |
|
o pkg/seaice: |
879 |
|
- refine checks for jfnk-related parameters |
880 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
881 |
|
is no IMEX code to avoid confusion and surprises |
882 |
|
|
883 |
|
checkpoint64u (2014/03/07) |
884 |
|
o verification/MLAdjust: |
885 |
|
- rename secondary test suffix: |
886 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
887 |
|
0.leithD -> AhFlxF + switch to flux-form |
888 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
889 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
890 |
|
o pkg/mom_vecinv: |
891 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
892 |
|
to be before mom_calc_visc.F) |
893 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
894 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
895 |
|
this is simpler for the adjoint and for diagnostics. |
896 |
|
o model/src + pkg/momentum: |
897 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
898 |
|
(e.g., to add "thin-wall" where it is =1). |
899 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
900 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
901 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
902 |
|
coords; not working with CD-scheme neither. |
903 |
|
o pkg/seaice: |
904 |
|
- rename recently introduced parameters from (wrong name) AB to |
905 |
|
BDF (backward difference time discretisation) |
906 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
907 |
|
o tools/adjoint_options: |
908 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
909 |
|
|
910 |
|
checkpoint64t (2014/02/01) |
911 |
|
o pkg/ecco |
912 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
913 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
914 |
|
- replace hard-coded record number and period which only work for monthly |
915 |
|
with read-in runtime param that works for other periods (month,day,year) |
916 |
|
o pkg/thsice |
917 |
|
- corrected store directive fixes thsice adjoint gradient checks |
918 |
|
o genmake2 & testreport: |
919 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
920 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
921 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
922 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
923 |
|
o pkg/shelfice: |
924 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
925 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
926 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
927 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
928 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
929 |
|
o model/src/temp_integrate.F and salt_integrate.F |
930 |
|
- re-include store directives that were removed on Dec 27th. |
931 |
|
o model/src/external_forcing_surf.F |
932 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
933 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
934 |
|
turned off in the adjoint. The resolved issue dated back to July when |
935 |
|
EXTERNAL_FORCING_SURF call was moved. |
936 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
937 |
|
o pkg/exf/exf_check.F |
938 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
939 |
|
- streamline error output |
940 |
|
o pkg/streamice and aim_v23: |
941 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
942 |
|
Apple's /usr/bin/cpp knows what to do: |
943 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
944 |
|
Target: x86_64-apple-darwin13.0.0 |
945 |
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|
946 |
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checkpoint64s (2014/01/05) |
947 |
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o tools/adjoint_options: |
948 |
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- switch to fastopt.net TAF server (instead of default fastopt.de) for |
949 |
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AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
950 |
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o model/src: |
951 |
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- remove some unnecessary TAF storage directives in forward_step.F and |
952 |
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in dynamics.F (note: not always removed by TAF, e.g., double storage |
953 |
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of kappaRU,kappaRV in former version of dynamics.F). |
954 |
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o model/src & pkg/ptracers: |
955 |
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- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
956 |
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salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
957 |
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and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
958 |
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- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
959 |
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- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
960 |
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- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
961 |
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o useSingleCpuInput separates single-CPU input from single-CPU output; |
962 |
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for now only implemented for in exf_interp_read.F |
963 |
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o verification/advect_xy: |
964 |
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- fix missing EXCH call in local version of ini_salt.F and update output. |
965 |
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o momentum diagnostics: |
966 |
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- fix which deltaT is used in Total-Tendency diagnostics. |
967 |
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- fix typo in diagnostics for momentum tendency from AB. |
968 |
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o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
969 |
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SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
970 |
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|
971 |
checkpoint64r (2013/12/08) |
checkpoint64r (2013/12/08) |
972 |
o verification/*/results: |
o verification/*/results: |
1072 |
o pkg/cost: |
o pkg/cost: |
1073 |
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
1074 |
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
1075 |
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL |
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
1076 |
cannot be applied to var in common block). |
cannot be applied to var in common block). |
1077 |
o allows to get results independent of tile-per-proc setting (if using |
o allows to get results independent of tile-per-proc setting (if using |
1078 |
slower GLOBAL_SUM_SEND_RECV option). |
slower GLOBAL_SUM_SEND_RECV option). |