4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
|
o pkg/gchem: |
8 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
9 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
10 |
|
o verification (hs94): |
11 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
12 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
13 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
14 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
15 |
|
o pkg/ptracers: |
16 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
17 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
18 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
19 |
|
with AB-2 code (so that it get tested). |
20 |
|
o model/src: |
21 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
22 |
|
with AB-2 code (previously only available with AB-3 code). |
23 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
24 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
25 |
|
there, by calling CYCLE_AB_TRACER). |
26 |
|
o pkg/generic_advdiff: |
27 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
28 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
29 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
30 |
|
S/R temp/salt/ptracers_integrate.F |
31 |
|
o model/src & pkg/ptracers: |
32 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
33 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
34 |
|
- remove common block variable gPtr. |
35 |
|
o model/src & pkgs: |
36 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
37 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
38 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
39 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
40 |
|
+ change accordingly all calling S/R. |
41 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
42 |
|
in S/R temp/salt/ptracers_integrate.F |
43 |
|
o pkg/seaice: |
44 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
45 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
46 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
47 |
|
in seaice_lsr |
48 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
49 |
|
in s/r seaice_lsr_calc_coeffs |
50 |
|
o pkg/mdsio: |
51 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
52 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
53 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
54 |
|
|
55 |
|
checkpoint65b (2014/08/12) |
56 |
|
o pkg/matrix: |
57 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
58 |
|
o model/src: |
59 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
60 |
|
natl_box verification experiment. |
61 |
|
o model/src & pkg/down_slope: |
62 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
63 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
64 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
65 |
|
results at machine truncation level: update output of experiments |
66 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
67 |
|
o pkg/diagnostics (Stats-Diags): |
68 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
69 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
70 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
71 |
|
times (but Min,Max and StD are still wrong). |
72 |
|
o model/src: |
73 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
74 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
75 |
|
o model/src: |
76 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
77 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
78 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
79 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
80 |
|
o model/src: |
81 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
82 |
|
anomaly that is used to compute geopotential: this make the atmos code |
83 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
84 |
|
o pkg/seaice/seaice_lsr.F |
85 |
|
- rename integer variable ilcall to ipass (that's what it is called |
86 |
|
in the residual diagnostics |
87 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
88 |
|
default) for improved non-linear convergence of the first few steps |
89 |
|
- adjust a few comments and add new ones to explain some of the store |
90 |
|
directives |
91 |
|
o pkg/generic_advdiff (& ptracers): |
92 |
|
- re-work the code to check for valid advection scheme and for minimum |
93 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
94 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
95 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
96 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
97 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
98 |
|
less exact gradients in my tests); but there are still |
99 |
|
recomputation warning (although gradients are sort of OK), when |
100 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
101 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
102 |
|
- update verification experiments lab_sea. |
103 |
|
- change some comments in S/R seaice_calc_viscosities |
104 |
|
o model/src: |
105 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
106 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
107 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
108 |
|
but affects AD results (at machine truncation level): update output of |
109 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
110 |
|
and isomip (oad: 12.d). |
111 |
|
o pkg/generic_advdiff: |
112 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
113 |
|
- refine warning related to stability of tracer time-stepping |
114 |
|
regarding internal wave dynamics. |
115 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
116 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
117 |
|
if potentially unstable). |
118 |
|
o pkg/kl10: |
119 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
120 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
121 |
|
(contribution from Jody Klymak), tested in verification experiment |
122 |
|
verification/internal_wave/input.kl10/ |
123 |
|
o isomip experiment: |
124 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
125 |
|
(input.htd) and update the output. |
126 |
|
o cd_code experiments: |
127 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
128 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
129 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
130 |
|
update the corresponding output. |
131 |
|
o pkg/seaice: |
132 |
|
- reduce the number of include files and store directives in |
133 |
|
S/R seaice_lsr_tridiagu/v |
134 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
135 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
136 |
|
get rid off one store directive (a TAF bug?) |
137 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
138 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
139 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
140 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
141 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
142 |
|
offline_exf_seaice/input.dyn_jfnk) |
143 |
|
|
144 |
|
checkpoint65a (2014/07/27) |
145 |
|
o model/src: |
146 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
147 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
148 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
149 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
150 |
|
o model/src: |
151 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
152 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
153 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
154 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
155 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
156 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
157 |
|
affects results at machine truncation level (e.g., ocean: if using |
158 |
|
SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0) |
159 |
|
moist correction due to vertical advection). |
160 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
161 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
162 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
163 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
164 |
|
o pkg/ptracers & diagnostics: |
165 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
166 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
167 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
168 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
169 |
|
|
170 |
|
checkpoint65 (2014/07/18) |
171 |
|
o pkg/fizhi: |
172 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
173 |
|
affects results at machine truncation level. Update output of experiments |
174 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
175 |
|
o pkg/seaice: more clean up |
176 |
|
- rename TAF common block tapes to be more consistent and remove |
177 |
|
unnecessary duplicates |
178 |
|
- add store directives to remove more recomputations, but use smaller |
179 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
180 |
|
The idea behind this flag is to reduce the memory footprint when the |
181 |
|
adjoint of the LSR is not required. As of now, defining the flag |
182 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
183 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
184 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
185 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
186 |
|
this experiment): |
187 |
|
> size mitgcmuv_ad |
188 |
|
text data bss dec hex |
189 |
|
5100659 1216 220458952 225560827 d71c8fb |
190 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
191 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
192 |
|
text data bss dec hex |
193 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
194 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
195 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
196 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
197 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
198 |
|
- in general, the AD gradients still are wrong |
199 |
|
o OpenAD |
200 |
|
- clean up code_oad/ directories somewhat by moving files |
201 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
202 |
|
o model/src: |
203 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
204 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
205 |
|
tendencies (previously done after). |
206 |
|
o pkg/diagnostics: |
207 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
208 |
|
o pkg/down_slope: |
209 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
210 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
211 |
|
o model/src: |
212 |
|
- new file "apply_forcing.F" containing all the code previously in |
213 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
214 |
|
the current level tendency array to update (instead of a direct update |
215 |
|
of the common bloc array). Change the corresponding calls. |
216 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
217 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
218 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
219 |
|
- rearrange some code blocks, so that now all calculations for |
220 |
|
setting up the right-hand-sides done within one single block |
221 |
|
(I find that easier to read and understand) |
222 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
223 |
|
- adjust some indentations and comments |
224 |
|
|
225 |
|
checkpoint64z (2014/07/10) |
226 |
|
o model/src and several pkgs: |
227 |
|
- change argument list of all S/R called from external_forcing.F and |
228 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
229 |
|
to pass, as argument, the current level tendency array to update |
230 |
|
(instead of a direct update of the common bloc array). |
231 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
232 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
233 |
|
o pkg/seaice/seaice_lsr.F |
234 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
235 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
236 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
237 |
|
keep it in bi/bj loop; this seems to be essential |
238 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
239 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
240 |
|
o pkg/seaice |
241 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
242 |
|
generates unnecessary code in seaice_lsr_ad |
243 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
244 |
|
in seaice_lsr_ad |
245 |
|
- exclude some residual computations in seaice_lsr when |
246 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
247 |
|
in seaice_lsr_ad |
248 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
249 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
250 |
|
and klockey should be checked by a specialist) |
251 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
252 |
|
and update lab_sea after previous changes in pkg/seaice below |
253 |
|
o pkg/autodiff: |
254 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
255 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
256 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
257 |
|
o pkg/ecco: |
258 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
259 |
|
temperature (for use in adjoint sensitivity studies). |
260 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
261 |
|
o pkg/mom_common/mom_calc_visc.F: |
262 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
263 |
|
o pkg/seaice/seaice_summary.F: |
264 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
265 |
|
o pkg/seaice: |
266 |
|
- remove some store directives and add new ones in an effort to get |
267 |
|
finally rid off the recomputation warnings. This is successful |
268 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
269 |
|
defined (i.e. no extensive recomputation warnings left), but there |
270 |
|
are still too many recomputations on the solver iteration level |
271 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
272 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
273 |
|
SEAICE_SIZE.h |
274 |
|
- add a store directive in S/R seaice_calc_viscosities |
275 |
|
o pkg/seaice (ITD code): |
276 |
|
- fix definition of Hlimit for multi-threaded case |
277 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
278 |
|
update output of experiment seaice_itd. |
279 |
|
o replace content of verification/seaice_itd |
280 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
281 |
|
to test the ice thickness distribution code with ridging |
282 |
|
- this is a first shot at this experiment |
283 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
284 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
285 |
|
and lot of new comments. |
286 |
|
|
287 |
|
checkpoint64y (2014/06/20) |
288 |
|
o pkg/seaice/seaice_reg_ridge.F: |
289 |
|
- modify the regularization of very small volumes of ice; only check |
290 |
|
total volume HEFF, and do not apply correction to individual ice |
291 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
292 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
293 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
294 |
|
o pkg/exf: |
295 |
|
- add code to process the case field period = -12. with UV interpolation. |
296 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
297 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
298 |
o verification/global_with_exf: |
o verification/global_with_exf: |
299 |
- swith all fields period to -12. (was previously untested) in input/data.exf |
- switch all fields period to -12. (was previously untested) in input/data.exf |
300 |
(but keep secondary test ".yearly" unchanged); update the reference output. |
(but keep secondary test ".yearly" unchanged); update the reference output. |
301 |
o pkg/cal: |
o pkg/cal: |
302 |
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
303 |
o pkg/exf: |
o pkg/exf: |
304 |
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
305 |
to replace logical switch "exf_verbose" |
to replace logical switch "exf_verbose" |
306 |
- report in STDOUT when loading a new reccord (if exf_debugLev >= 3) |
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
307 |
o pkg/sbo: |
o pkg/sbo: |
308 |
- update from Katherine Quinn: evaluate mass directly from density and SSH |
- update from Katherine Quinn: evaluate mass directly from density and SSH |
309 |
(budget using Finite Volume method) instead of from bottom pressure. |
(budget using Finite Volume method) instead of from bottom pressure. |
319 |
+ call LAND_READPARMS from packages_readparms.F |
+ call LAND_READPARMS from packages_readparms.F |
320 |
o pkg/seaice: |
o pkg/seaice: |
321 |
- remove code that resets useThSice in S/R seaice_readparms and |
- remove code that resets useThSice in S/R seaice_readparms and |
322 |
replace by a warning in S/R seaice_check |
replace it by a warning in S/R seaice_check |
323 |
- remove parameter MULTDIM, replace with nITD and runtime |
- remove parameter MULTDIM, replace with nITD and runtime |
324 |
parameter SEAICE_multDim (still hard-wired to nITD if |
parameter SEAICE_multDim (still hard-wired to nITD if |
325 |
SEAICE_ITD is defined) |
SEAICE_ITD is defined) |