4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013, Eden and Olbers, 2014) |
8 |
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
- code provided by Carsten Eden as an extension of ggl90 |
9 |
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
- so far the code is turned on within ggl90 by setting a CPP-flag at |
10 |
approach where CPP_OPTIONS.h includes an omnipotent |
compile time; a runtime flag implementation is not yet complete |
11 |
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
- tested in new verification experiment global_ocean.90x40x15.idemix |
12 |
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
o verification: |
13 |
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
- reduce length of the AD test run by half for experiments |
14 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
15 |
|
o verification/testreport: |
16 |
|
- fix two non-POSIX sed statements so that there are no error messages |
17 |
|
on Mac OS X |
18 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
19 |
|
o model/src/seawater.F: |
20 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
21 |
|
(following the matlab code), which would have avoided the bug caught |
22 |
|
by Matt (see below) in the first place |
23 |
|
o pkg/shelfice: |
24 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
25 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
26 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
27 |
|
ice-shelf case (i.e., within surface level). |
28 |
|
- add config summary in shelfice_check.F |
29 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
30 |
|
variable recip_latentHeat |
31 |
|
- introduce diagnostics for friction velocity uStar (in case of |
32 |
|
SHELFICEuseGammaFrict) |
33 |
|
- change verification experiment isomip.htd: |
34 |
|
+ start from pickup (as input_ad at nIter0=8640) |
35 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
36 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
37 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
38 |
|
o model/src: |
39 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
40 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
41 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
42 |
|
o pkg/shelfice: |
43 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
44 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
45 |
|
ice-shelf is. |
46 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
47 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
48 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
49 |
|
for thermodynamic calculations |
50 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
51 |
|
affects results of some verification experiments by up to 4 digits: |
52 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
53 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
54 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
55 |
|
-> updated |
56 |
|
|
57 |
|
checkpoint65i (2015/01/23) |
58 |
|
o model/src: |
59 |
|
- change units of frictionHeating field from W to W/m^2 |
60 |
|
- fix bug in frictional heating from stratospheric drag in |
61 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
62 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
63 |
|
field from load_fields_driver.F to thermodynamics.F ; |
64 |
|
- add diagnostics for frictional heating. |
65 |
|
o model/src & gmredi K3D: |
66 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
67 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
68 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
69 |
|
and name in pickup file). |
70 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
71 |
|
o model/src: |
72 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
73 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
74 |
|
(since Nov 2012) with option selectAddFluid=1. |
75 |
|
o pkg/shelfice: |
76 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
77 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
78 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
79 |
|
o pkg/seaice: two new runtime parameters: |
80 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
81 |
|
long overdue |
82 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
83 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
84 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
85 |
|
for LSR: move checking overlaps out of JFNK-if-block |
86 |
|
o pkg/atm_phys: |
87 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
88 |
|
new S/R ATM_PHYS_DYN2PHYS. |
89 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
90 |
|
fixed-in-time pressure levels). |
91 |
|
o pkg/mom_common (bottomdrag): |
92 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
93 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
94 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
95 |
|
o pkg/shelfice (u/v_drag): |
96 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
97 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
98 |
|
(now similar to shelfice_u_drag.F) |
99 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
100 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
101 |
|
o pkg/mom_common (bottomdrag): |
102 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
103 |
|
- add options for alternative discretisation of velocity norm in quadratic |
104 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
105 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
106 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
107 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
108 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
109 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
110 |
|
off by default since this also reduces model stability (explicit bottom |
111 |
|
friction). Changes produce different machine truncation with linear-drag |
112 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
113 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
114 |
|
o model/src & mom pkgs: |
115 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
116 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
117 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
118 |
|
just copy level Nr value to level Nr+1. |
119 |
|
o doc: |
120 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
121 |
|
o pkg/streamice: |
122 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
123 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
124 |
|
from array shelficemassinit, which is set in init_fixed and |
125 |
|
has option to be set from file; introduce array |
126 |
|
shelficeMassDynTend array, set thru file in init_fixed |
127 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
128 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
129 |
|
pkg/streamice |
130 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
131 |
|
SHELFICEMassStepping = .true. |
132 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
133 |
|
|
134 |
|
checkpoint65h (2014/12/17) |
135 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
136 |
|
- update to generic controls. |
137 |
|
o pkg/ctrl: |
138 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
139 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
140 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
141 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
142 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
143 |
|
add time variable weights and cyclic controls (time mean, |
144 |
|
seasonal cycle, etc) capabilities to gentim2d |
145 |
|
o pkg/ecco: |
146 |
|
- move reading of error, conversion to weights from |
147 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
148 |
|
o global_oce_llc90, cs32: |
149 |
|
- activte sbo. |
150 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
151 |
|
- activate the new genctrl capabilities. |
152 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
153 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
154 |
|
- add missing ctrl_init_rec.f |
155 |
|
o tools/OAD_support/keepOriginal: |
156 |
|
- add ctrl_init_rec.F |
157 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
158 |
|
- avoid recomputations of xx_gentim2d_dummy. |
159 |
|
o momentum diagnostics: |
160 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
161 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
162 |
|
o pkg/seaice/seaice_lsr.F: |
163 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
164 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
165 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
166 |
|
o verification/global_ocean.cs32x15/input.seaice |
167 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
168 |
|
methods for LSR |
169 |
|
- update results/output.seaice.txt |
170 |
|
o verification/tutorial_global_oce_biogeo: |
171 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
172 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
173 |
|
update output_adm,_oadm,_tlm.txt |
174 |
|
o pkg/dic: |
175 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
176 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
177 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
178 |
|
o verification/tutorial_global_oce_biogeo: |
179 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
180 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
181 |
|
update output_adm,_oadm,_tlm.txt |
182 |
|
o eesupp/src: |
183 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
184 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
185 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
186 |
|
LSR (following Hutchings et al. 2004) |
187 |
|
- introduce zetaZ as a global variable (requires adjustments in |
188 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
189 |
|
in seaice_calc_viscosities.F |
190 |
|
- new flag SEAICEuseStrImpCpl (default off) |
191 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
192 |
|
momentum equations |
193 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
194 |
|
(where it does not have any positive effect) |
195 |
|
o pkg/seaice |
196 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
197 |
|
turn it off by default (because it only seems to work for non-cubed |
198 |
|
sphere/llc topologies) |
199 |
|
o pkg/autodiff |
200 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
201 |
|
o pkg/seaice: |
202 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
203 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
204 |
|
o pkg/obcs: |
205 |
|
- add option to specify domain-connected piece Id along OB though files |
206 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
207 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
208 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
209 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
210 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
211 |
|
o pkg/diagnostics: |
212 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
213 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
214 |
|
outside OB (i.e, where tracer OBCS are applied). |
215 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
216 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
217 |
|
|
218 |
|
checkpoint65g (2014/11/19) |
219 |
|
o pkg/diagnostcis: |
220 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
221 |
|
o pkg/my82,pp81,kl10: |
222 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
223 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
224 |
|
o pkg/seaice: |
225 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
226 |
|
Bouillon et al 2013) |
227 |
|
- add SEAICE_evpAlpha/Beta to namelist |
228 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
229 |
|
involve trivial re-ordering of divisions/multiplications that should not |
230 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
231 |
|
that only 2 digits of agreement remain, in line with the general |
232 |
|
instability/fragility of the evp-code. For now, I do not care and just |
233 |
|
update the verification experiment |
234 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
235 |
|
- remove xx_genarr2d_numsmooth etc |
236 |
|
- use xx_genarr2d_preproc etc instead |
237 |
|
- carry out smooth_correl2D at initialization stage rather than during |
238 |
|
time stepping. |
239 |
|
- get smoothOpNb from xx_gentim2d_preproc |
240 |
|
o global_oce_cs32 : |
241 |
|
- add test of generic ecco capabilities. |
242 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
243 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
244 |
|
o pkg/ctrl,ecco : |
245 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
246 |
|
is defined. |
247 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
248 |
|
o model/src: |
249 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
250 |
|
diffusivity (background) is specified but ignored. |
251 |
|
o verification: |
252 |
|
- in testreport, convert hostname to lower case for default output dir name |
253 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
254 |
|
o pkg/dic: add modifications from Hajoon: |
255 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
256 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
257 |
|
(read from file). |
258 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
259 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
260 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
261 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
262 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
263 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
264 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
265 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
266 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
267 |
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
268 |
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
269 |
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
270 |
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
271 |
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
272 |
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
273 |
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
274 |
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
275 |
o pkg/ctrl,ecco,exf : |
o pkg/ctrl,ecco,exf : |
276 |
- remove variables associated with NON-generic costs, |
- remove variables associated with NON-generic costs, |
277 |
unless ECCO_CTRL_DEPRECATED is defined. |
unless ECCO_CTRL_DEPRECATED is defined. |
278 |
- remove NON-generic NON-obcs controls, |
- remove NON-generic NON-obcs controls, |
279 |
unless ECCO_CTRL_DEPRECATED is defined. |
unless ECCO_CTRL_DEPRECATED is defined. |
280 |
o pkg/ctrl : added ctrl_local_params.h |
o pkg/ctrl : added ctrl_local_params.h |
281 |
o pkg/ecco : added ecco_local_params.h |
o pkg/ecco : added ecco_local_params.h |
282 |
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
283 |
experiments, which will progressively be removed once the |
experiments, which will progressively be removed once the |
284 |
experiments are revised to use only generic controls/costs. |
experiments are revised to use only generic controls/costs. |
285 |
|
|
286 |
checkpoint65f (2014/10/13) |
checkpoint65f (2014/10/13) |
287 |
o pkg/ctrl, ecco, seaice : minor changes in headers |
o pkg/ctrl, ecco, seaice : minor changes in headers |
288 |
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
289 |
cost function and control capabilities added since checkpoint65c. |
cost function and control capabilities added since checkpoint65c. |
290 |
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
291 |
o pkg/ecco: increase modularity and improve logic |
o pkg/ecco: increase modularity and improve logic |
292 |
- ecco_toolbox.F (new) : basic operations that are often used, |
- ecco_toolbox.F (new) : basic operations that are often used, |
646 |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
647 |
this experiment): |
this experiment): |
648 |
> size mitgcmuv_ad |
> size mitgcmuv_ad |
649 |
text data bss dec hex |
text data bss dec hex |
650 |
5100659 1216 220458952 225560827 d71c8fb |
5100659 1216 220458952 225560827 d71c8fb |
651 |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
652 |
but only a moderate increase of 36% for global_ocean.cs32x15: |
but only a moderate increase of 36% for global_ocean.cs32x15: |
653 |
text data bss dec hex |
text data bss dec hex |