4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
|
o model/src: move balancing of relaxation terms to new S/R balance_relax.F. |
8 |
|
o pkg/autodiff: |
9 |
|
re-write active I/O high-level (control) S/R: |
10 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
11 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
12 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
13 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
14 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
15 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
16 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
17 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
18 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
19 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
20 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
21 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
22 |
|
right type. |
23 |
|
o autodiff and RS=real*4: |
24 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
25 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
26 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
27 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
28 |
|
o pkg/thsice: |
29 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
30 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
31 |
|
fresh-water flux: uniform correction or proportional to local precip. |
32 |
|
o pkg/ctrl: |
33 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
34 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
35 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
36 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
37 |
|
|
38 |
|
checkpoint63q (2012/07/30) |
39 |
|
o pkg/autodiff: |
40 |
|
note about monitor and snap-shot of ad-variables: |
41 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
42 |
|
overlap contributions (was done for adjDump but missing for monitor). |
43 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
44 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
45 |
|
the time-stepping (although mathematically identical). |
46 |
|
modifs: |
47 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
48 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
49 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
50 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
51 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
52 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
53 |
|
ad-vars (initially not used by default -> output unchanged). |
54 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
55 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
56 |
|
and both tutorial_tracer_adjsens tests). |
57 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
58 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
59 |
|
o pkg/ctrl: |
60 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
61 |
|
generic control variables via |
62 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
63 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
64 |
|
(routine in repository contains example) |
65 |
|
o pkg/exf: |
66 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
67 |
|
o verification (adjoint exp): |
68 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
69 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
70 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
71 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
72 |
|
of KE that can occur with aggressive optimization |
73 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
74 |
|
using bottomDragQuadratic) |
75 |
|
o model/src: CG2D_NSA |
76 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
77 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
78 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
79 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
80 |
|
RHS ; this fix global_max Pb with TAF); update output. |
81 |
|
o verification/tutorial_tracer_adjsens: |
82 |
|
improve parameter consistency (and get rid of warnings): |
83 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
84 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
85 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
86 |
|
o pkg/exch2: |
87 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
88 |
|
reset to 0 = 1 long line in X) |
89 |
|
o pkg/mdsio: |
90 |
|
- fix reading of dimensions from meta file for large-size domain |
91 |
|
o model/src: |
92 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
93 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
94 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
95 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
96 |
|
globalArea and to set hasWetCSCorners. |
97 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
98 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
99 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
100 |
|
useCDscheme and useCubedSphereExchange). |
101 |
|
o pkg/seaice/seaice_growth.F : |
102 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
103 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
104 |
|
when the previous code was not correct. |
105 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
106 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
107 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
108 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
109 |
|
o verification/global_ocean.cs32x15/input.seaice : |
110 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
111 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
112 |
|
- update results (output.seaice.txt) accordingly. |
113 |
|
o verification/lab_sea/input/data.seaice : |
114 |
|
- remove SEAICEheatConsFix, which is now be tested |
115 |
|
in global_ocean.cs32x15. The presently coded fix |
116 |
|
is only consistent with real fresh water + nlfs. |
117 |
|
- update results (output.txt) accordingly. |
118 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
119 |
|
o AD_CONFIG.h file: |
120 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
121 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
122 |
|
add it explicitly in each fortran src file where it is needed. |
123 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
124 |
|
thus introducing potentially wrong dependency; therefore, better to include |
125 |
|
it only where it's really needed, and after any other included OPTIONS file |
126 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
127 |
|
or ALLOW_TANGENTLINEAR_RUN). |
128 |
|
|
129 |
|
checkpoint63p (2012/07/06) |
130 |
|
o pkg/autodiff: |
131 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
132 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
133 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
134 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
135 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
136 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
137 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
138 |
|
o verification/tutorial_tracer_adjsens/ |
139 |
|
- add extra sub-verification which uses "SOM" advection scheme |
140 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
141 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
142 |
|
and in data: |
143 |
|
multiDimAdvection=.TRUE., |
144 |
|
tempAdvScheme=81, |
145 |
|
saltAdvScheme=81, |
146 |
|
o model/src: |
147 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
148 |
|
of the global mean of relaxation terms by setting |
149 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
150 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
151 |
|
This case is now treated appropriately in seaice_growth.F |
152 |
|
o pkg/seaice: |
153 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
154 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
155 |
|
and EMPMR. Works best in real fresh water. |
156 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
157 |
|
out of the diagnotics bloc, and stored in global arrays. |
158 |
|
|
159 |
|
checkpoint63o (2012/06/29) |
160 |
|
o vertical mixing schemes: |
161 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
162 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
163 |
|
to S/R FIND_RHO_SCALAR |
164 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
165 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
166 |
|
affects output (vermix.ggl90) at truncation level. |
167 |
|
o testreport: |
168 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
169 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
170 |
|
o model/src: |
171 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
172 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
173 |
|
o verification/tutorial_tracer_adjsens/ |
174 |
|
- compile with ALLOW_CG2D_NSA |
175 |
|
- run with nonlinFreeSurf=3 |
176 |
|
- update reference output_adm.txt |
177 |
|
o tools/genmake2: |
178 |
|
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
179 |
|
refine usePROFILES switching off (only when NetCDF is not available). |
180 |
|
o verification (atmospheric set-up): |
181 |
|
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
182 |
|
o pkg/profiles : refine profiles and files handling. |
183 |
|
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
184 |
|
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
185 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
186 |
|
in ecco type adjoint runs. |
187 |
|
o model/src: |
188 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
189 |
|
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
190 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
191 |
|
o model/src: |
192 |
|
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
193 |
|
update output of test experiment bottom_ctrl_5x5. |
194 |
|
o pkg/generic_advdiff: |
195 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
196 |
|
only explicitly). |
197 |
|
o verification/bottom_ctrl_5x5/ |
198 |
|
update reference output (results changed quite some time ago, |
199 |
|
not sure when; but new reference results look ok in terms of grdchk) |
200 |
|
o verification/1D_ocean_ice_column/ |
201 |
|
For verification purposes, the exact adjoint rather than an approx. |
202 |
|
should be used (e.g., to comare against F.D. or TLM). |
203 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
204 |
|
Update results/ accordingly. |
205 |
|
o pkg/cal: |
206 |
|
- change cal_getdate.F so that output date is function of input time only |
207 |
|
(less ambiguous, not mixed up with input iteration number). |
208 |
|
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
209 |
|
o pkg/diagnostics: |
210 |
|
- implement calendarDumps also for stats-diags |
211 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
212 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
213 |
|
|
214 |
checkpoint63n (2012/06/04) |
checkpoint63n (2012/06/04) |
215 |
o model/src: |
o model/src: |
216 |
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |