4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o pkg/icefront & pkg/exf: |
8 |
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- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
9 |
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from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
10 |
|
o pkg/exf: |
11 |
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- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
12 |
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"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
13 |
|
(add suffix "_out" instead of a prefix); keep same record number as in |
14 |
|
input file but always write record 1 first (to avoid a STOP in I/O S/R). |
15 |
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Change output file content by writing interpolated field before applying |
16 |
|
land-sea mask (helpful for debug). |
17 |
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- 2 compon. vector interpolation with rotation: apply scaling factor on |
18 |
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each compon. (Eastward and Northward) just before rotation. |
19 |
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o pkg/bling: |
20 |
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- Cleaned package. Removed not needed code and comments. |
21 |
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- adjoint example now works |
22 |
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(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
23 |
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o pkg/ptracers: |
24 |
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- add Bruno Deremble's code to complete the linear surface correction |
25 |
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for tracer conservation; |
26 |
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- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
27 |
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|
28 |
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checkpoint65y (2016/07/29) |
29 |
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o pkg/debug (stats): |
30 |
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- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
31 |
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proc/thread mapping); |
32 |
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- fix Min & Max for case where 1 thread has only empty tiles; |
33 |
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- use RL variable to count number of wet grid points (with big domain, |
34 |
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can be too large to fit into integer*4). |
35 |
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o pkg/monitor: |
36 |
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- use RL variable to count number of wet grid points (but used only for del2) |
37 |
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- add new routine to compute Advective CFL within tracer time-stepping with |
38 |
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writing delayed until next monitor output. |
39 |
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o pkg/obcs: |
40 |
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- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
41 |
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o pkg/cal: |
42 |
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- calandar-dump: treat case myTime < timePhase in the same way as in |
43 |
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eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
44 |
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o pkg/dic & seaice: |
45 |
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- fix compilation of ocean component for coupled atm+ocn model with |
46 |
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seaice dynamics & dic. |
47 |
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|
48 |
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checkpoint65x (2016/06/11) |
49 |
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o add a license text file in main MITgcm tree. |
50 |
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o added pkg/bling: |
51 |
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- intermediate complexity biogeochemical model |
52 |
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- see bling_description.txt for details |
53 |
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- verification experiment is global_oce_biogeo_bling (for now, in |
54 |
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Contrib/verification_other/); tested daily on baudelaire with gfortran. |
55 |
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- add entry point in pkg/gchem for new pkg "bling". |
56 |
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o pkg/seaice: fix tensile stength computation |
57 |
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- replace global field tensileStrength by tensileStrFac |
58 |
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- tensileStrFac can be computed once in S/R seaice_init_varia |
59 |
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- fortunately that does not affect any verification results |
60 |
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|
61 |
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checkpoint65w (2016/05/12) |
62 |
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o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
63 |
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with ECCO_CTRL_DEPRECATED defined |
64 |
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o verification/global_ocean.cs32x15: |
65 |
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- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
66 |
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with "selectNHfreeSurf=1". |
67 |
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o model/src (non-hydrostatic free-surface): |
68 |
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- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
69 |
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was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
70 |
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- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
71 |
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for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
72 |
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and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
73 |
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This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
74 |
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- Update output (changes at machine truncation level) of verification exp: |
75 |
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exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
76 |
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short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
77 |
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o pkg/seaice: ITD code |
78 |
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- fix picking up from a single category model by initialising |
79 |
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heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
80 |
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- split a long warning message in seaice_check_pickup.F into two lines, |
81 |
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because NEC SX-ACE cannot deal with the long line. |
82 |
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o model/src: |
83 |
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- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
84 |
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o pkg/seaice: |
85 |
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- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
86 |
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o pkg/seaice: |
87 |
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- add basal stress as parameterisation for grounding ice |
88 |
|
following Lemieux et al. (2015) |
89 |
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- turn on by setting new parameter SEAICEbasalDragK2 to a value |
90 |
|
larger than 0. Lemieux et al. (2015) recommend 15. |
91 |
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- The adjoint complains with extra recomputations so there is also a |
92 |
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new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
93 |
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order to postpone the problem |
94 |
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- compile the new code in lab_sea |
95 |
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o verification/halfpipe_streamice: |
96 |
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- update both TAF and OpenAD adm output (machine truncation differences) |
97 |
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|
98 |
|
checkpoint65v (2016/04/08) |
99 |
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o verification/advect_xz: |
100 |
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- increase overlap size from 3 to 4 and add new secondary test for PQM |
101 |
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advection scheme (with mono & wino limiter). |
102 |
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- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
103 |
|
o model/src: |
104 |
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- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
105 |
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added phi0Ref) to set vertical axis origin and phiRef origin; |
106 |
|
keep Ro_SeaLevel for backward compatibility (with a warning). |
107 |
|
According to coordinate and fluid type: |
108 |
|
OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
109 |
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ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
110 |
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OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
111 |
|
ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
112 |
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- remove Ro_SeaLevel from ATM experiment parameter files; |
113 |
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- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
114 |
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complement; update output.txt (changes at machine truncation level). |
115 |
|
o pkg/seaice/seaice_evp.F |
116 |
|
- simplify computation of deltaZ and zetaZ to simple averaging following |
117 |
|
Bouillon et al. (2013). This removes a lot of code, but also changes |
118 |
|
verification experiment lab_sea.hb87 -> updated |
119 |
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|
120 |
|
checkpoint65u (2016/03/14) |
121 |
|
o pkg/generic_advdiff: |
122 |
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- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
123 |
|
with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
124 |
|
Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
125 |
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testing and not for actual use. |
126 |
|
o model/src: |
127 |
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- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
128 |
|
origin r = rF(1); |
129 |
|
- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
130 |
|
in EOS for height coordinate: enable to include NH Pressure or to use |
131 |
|
more accurate pressure vertical profile; options not linked to EOS type |
132 |
|
(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
133 |
|
- start to implement variable gravity (along vertical): for now, only with |
134 |
|
z-coords (not even z*). |
135 |
|
- add Ideal Gas equation of state for height coordinate. |
136 |
|
- update OpenAD output (affected at machine truncation level) of exp: |
137 |
|
global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
138 |
|
o pkg/exf: |
139 |
|
- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
140 |
|
of exf interpolation (before any rescaling, rotation or interpolation |
141 |
|
to velocity point) for each field that gets loaded from file. This option |
142 |
|
identically mimics the input file organization (e.g. record numbers in year |
143 |
|
by year input files) besides the change in horizontal grid. |
144 |
|
- add rotateStressOnAgrid run-time switch so that wind stress fields |
145 |
|
can be provided on the A-grid in zonal/meridional direction and |
146 |
|
rotated on the fly. This only applies to the case when the exf |
147 |
|
interpolation is off and rotateStressOnAgrid is false by default. |
148 |
|
o model/src: |
149 |
|
- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
150 |
|
it's also used with pkg/atm_phys) and add few more parameters (but still |
151 |
|
inactive, src code yet to come) |
152 |
|
|
153 |
|
checkpoint65t (2016/02/10) |
154 |
|
o pkg/atm_phys: |
155 |
|
- from Ruth Geen: add optical depth dependence on CO2 concentration. |
156 |
|
o model/src: |
157 |
|
- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
158 |
|
for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
159 |
|
Update output of exp. deep_anelastic (changes at truncation level). |
160 |
|
o tools: |
161 |
|
- add a hack in "remove_comments_sed" (used only with TAF) for recent |
162 |
|
version of OpenMPI (shipped with FC.23): comment out the new header |
163 |
|
file "mpif-sizeof.h" which causes problems to TAF. |
164 |
|
o pkg/seaice: |
165 |
|
- change the termination criterion so that maxits (SEAICElinearIterMax) |
166 |
|
has an effect |
167 |
|
- unify iteration parameters for implicit solvers (JFNK and Picard) |
168 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
169 |
|
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
170 |
|
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
171 |
|
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
172 |
|
SEAICEnonLinTol replaces JFNKgamma_nonlin |
173 |
|
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
174 |
|
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
175 |
|
use with SEAICEuseKrylov |
176 |
|
o pkg/seaice/seaice_lsr.F |
177 |
|
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
178 |
|
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
179 |
|
an effect. |
180 |
|
o pkg/seaice: add two new parameters |
181 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
182 |
|
parameter is not in any namelist) |
183 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
184 |
|
a preconditioner for the non-linear Newton iteration of the JFNK |
185 |
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solver |
186 |
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o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
187 |
|
affects some experiments at truncation level: |
188 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
189 |
|
- global_ocean.cs32x15.seaice (11 digits), |
190 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
191 |
|
- also update global_ocean.cs32x15 adjoint and tangent-linear results |
192 |
|
o pkg/salt_plume & pkg/thsice: |
193 |
|
- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
194 |
|
connect salt_plume flux to ATM-OCN coupling pkgs interface: |
195 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
196 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
197 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
198 |
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(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
199 |
|
o pkg/dic: |
200 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
201 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
202 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
203 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
204 |
|
(previously done in ocn_apply_import.F). |
205 |
|
o tools/adjoint_options: |
206 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
207 |
|
has been changed on Jan 14, 2016. |
208 |
|
o pkg/ggl90: |
209 |
|
- add alternative discretisation of vertical shear (off by default), to |
210 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
211 |
|
vertical shear of mean flow (@ grid-cell center). |
212 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
213 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
214 |
|
o pkg/atm_compon_interf: |
215 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
216 |
|
pass last value, stored directly before export to CPL ; |
217 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
218 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
219 |
|
|
220 |
|
checkpoint65s (2016/01/13) |
221 |
|
o eesupp & genmake2: |
222 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
223 |
|
ETIME and consistent output; use the appropriate version in timers.F |
224 |
|
o model/src: |
225 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
226 |
|
integr_continuity; turned off by default. |
227 |
|
o pkg/dic: |
228 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
229 |
|
o tools/tst_2+2: |
230 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
231 |
|
to fail for no good reason. |
232 |
|
o eesupp & genmake2: |
233 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
234 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
235 |
|
o coupler pkgs: |
236 |
|
Finish implementation of optionally-exchanged variable switches (started on |
237 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
238 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
239 |
|
advection in OCN component; this requires sequential coupling. |
240 |
|
coupler (pkg/atm_ocn_coupler): |
241 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
242 |
|
routines (useful for debug). |
243 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
244 |
|
flux, DIC fields) if corresponding switch is ON. |
245 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
246 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
247 |
|
components (pkg/atm_ & ocn_compon_interf): |
248 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
249 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
250 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
251 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
252 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
253 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
254 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
255 |
|
- hold in common block coupler optionally-exchanged variable switch |
256 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
257 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
258 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
259 |
|
to contain new additional exchanged fields). |
260 |
|
o pkg/dic: |
261 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
262 |
|
o pkg/thsice: |
263 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
264 |
|
and writing of thsice pickup files. |
265 |
|
o pkg/atm_compon_interf: |
266 |
|
- move all field individual export-call out of cpl_export_import_data.F |
267 |
|
into new S/R ATM_EXPORT_FIELDS |
268 |
|
o pkg/atm_compon_interf: |
269 |
|
- store state variables (for now, only thSIce fields) just before beeing |
270 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
271 |
|
atm_store_my_data.F like all exported fluxes. |
272 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
273 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
274 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
275 |
|
o pkg/dic: |
276 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
277 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
278 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
279 |
|
value can be from domain [0,1] to average between the two methods |
280 |
|
o pkg/atm_phys: |
281 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
282 |
|
hold fixed in time). |
283 |
|
|
284 |
|
checkpoint65r (2015/12/21) |
285 |
|
o pkg/seaice: |
286 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
287 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
288 |
|
o pkg/seaice: |
289 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
290 |
|
when SEAICEscaleSurfStress=.TRUE., |
291 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
292 |
|
o pkg/atm_phys: |
293 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
294 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
295 |
|
for individual contribution (convection, LSC cond, radiation) |
296 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
297 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
298 |
|
o pkg/ggl90: |
299 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
300 |
|
avoid instability problems in the explicit horizontal diffusion term for |
301 |
|
long time steps or high resolution |
302 |
|
o pkg/diagnostics: |
303 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
304 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
305 |
|
o testreport: |
306 |
|
- remove "-v" (verbose option) in default mpirun command. |
307 |
|
o pkg/seaice/seaice_growth: |
308 |
|
- catch potential division by zero in ITD code, does not change |
309 |
|
verification results |
310 |
|
o pkg/ecco: |
311 |
|
- retire old codes to the Attic. The calls to retired functions are |
312 |
|
left in a commented form in case they ever need to be re-activated. |
313 |
|
- ecco_check.F: issue warning if any old CPP option is |
314 |
|
defined that corresponds to retired codes -- then stop. |
315 |
|
o pkg/atm_compon_interf: |
316 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
317 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
318 |
|
time-step, similar to what is done for seaIceMass. |
319 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
320 |
|
o eesupp & genmake2: |
321 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
322 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
323 |
|
o pkg/seaice/seaice_evp: |
324 |
|
- refine residual computation |
325 |
|
|
326 |
|
checkpoint65q (2015/11/18) |
327 |
|
o pkg/seaice/seaice_evp: |
328 |
|
- fix residual computations so that they no longer affect the actual |
329 |
|
simulation code |
330 |
|
- fix seaice_readparams to be able to actually set new parameters |
331 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
332 |
|
o model/src: |
333 |
|
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
334 |
|
like: deltaT*FLOAT(myIter) when myIter is large: |
335 |
|
a) replaced by DFLOAT (if not seen by TAF); |
336 |
|
b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
337 |
|
o pkg/aim_v23: |
338 |
|
- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
339 |
|
when pickupSuff is set ; do write rolling pickups + at the end of the run. |
340 |
|
o pkg/atm_ocn_coupler + ocn_compon_interf: |
341 |
|
- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
342 |
|
coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
343 |
|
add corresponding call in DO_OCEANIC_PHYS. |
344 |
|
o coupler pkgs: |
345 |
|
Start a new way to set-up optionally-exchanged variables (previously, only |
346 |
|
there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
347 |
|
data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
348 |
|
send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
349 |
|
compononent param default can be set accordingly). |
350 |
|
Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
351 |
|
but rather applies to a group a fields (going both ways like for DIC) |
352 |
|
and corresponds to an option of coupling config. |
353 |
|
coupler (pkg/atm_ocn_coupler): |
354 |
|
- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
355 |
|
and read namelist directly (without eessup S/R calls) instead of |
356 |
|
in the very un-flexible old way, 1 param per line, in fixed order; |
357 |
|
- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
358 |
|
cleanly in CPL_CHECK_CPLCONFIG |
359 |
|
- add new coupling-exchange selectors (some not yet active) including |
360 |
|
cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
361 |
|
and ocnCpl_exchange_DIC=T in OCNIDS.h); |
362 |
|
- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
363 |
|
component ; called directly from coupler.F, after comp. registrations; |
364 |
|
- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
365 |
|
atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
366 |
|
-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
367 |
|
components (pkg/atm_ & ocn_compon_interf): |
368 |
|
- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
369 |
|
CPP header file in all pkg source files. |
370 |
|
- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
371 |
|
ATM/OCN_CHECK_CPLCONFIG; |
372 |
|
- add error-counter to track errors (e.g., in "data.cpl") and to stop |
373 |
|
cleanly in ATM/OCN_CHECK_CPLCONFIG; |
374 |
|
- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
375 |
|
from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
376 |
|
before PACKAGES_READPARMS; |
377 |
|
verification/cpl_aim+ocn/: |
378 |
|
- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
379 |
|
"data.cpl" for coupler (in input_cpl). |
380 |
|
o eesupp/inc: |
381 |
|
- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
382 |
|
#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
383 |
|
to always cumulate tile local-sum in the same order (still uses |
384 |
|
MPI_Allreduce like standard code). |
385 |
|
- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
386 |
|
that are now identical to standard version (in eesupp/inc). |
387 |
|
o pkg/shelfice: |
388 |
|
- add SHELFICETransCoeffTFile for initializing spatially varying |
389 |
|
heat and salt transfer coefficients |
390 |
|
o pkg/atm_compon_interf & ocn_compon_interf: |
391 |
|
- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
392 |
|
S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
393 |
|
- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
394 |
|
o pkg/atm_ocn_coupler: |
395 |
|
- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
396 |
|
o pkg/rbcs: |
397 |
|
- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
398 |
|
to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
399 |
|
- add a short report (to STDOUT) about RBCS-mask settings. |
400 |
|
|
401 |
|
checkpoint65p (2015/10/23) |
402 |
|
o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
403 |
|
there is no adjoint test for EVP, we don't know what it does to the adjoint |
404 |
|
solution, but at least there are no more recomputation warnings left |
405 |
|
o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
406 |
|
a chance of giving the same results as a fully converged VP (JFNK) solver |
407 |
|
o tools/adjoint_options/adjoint_diva: |
408 |
|
- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
409 |
|
o pkg/streamice: |
410 |
|
- spotted bug in streamice_driving_stress using dyG where should have been dxG |
411 |
|
o pkg/exf: |
412 |
|
- remove STOP statement that prevented to use wind or (wind-)stress |
413 |
|
interpolation for constant-in-time forcing fields (wind/stress period = 0). |
414 |
|
o pkg/seaice: |
415 |
|
- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
416 |
|
5 additionals 2D fields and 6 new store directives |
417 |
|
- change logic in seaice_readparms.F: EVP code can now be turned on in |
418 |
|
various ways, setting SEAICE_deltaTev is no longer required, |
419 |
|
alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
420 |
|
or SEAICEaEVPcoeff |
421 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
422 |
|
- redefining uLoc/vLoc to u/v, instead of 2u/v |
423 |
|
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
424 |
|
- this is an intermediate state of a truely converging EVP that has |
425 |
|
the potential of outperforming implicit VP methods, I do not recommend |
426 |
|
using it yet. |
427 |
|
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
428 |
|
and all parameters are hardwired |
429 |
|
- for convergence it still requires very smooth regularisations, that means, |
430 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
431 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
432 |
|
specific averaging appears to be required, still subject to tuning |
433 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
434 |
|
- add code to compute and print residuals of iteration, compile with |
435 |
|
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
436 |
|
o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
437 |
|
that entered with r1.54 on Sep04, 2015, -> update results |
438 |
|
|
439 |
|
checkpoint65o (2015/09/14) |
440 |
|
o pkg/mom_vecinv & mom_common: |
441 |
|
- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
442 |
|
called from there. |
443 |
|
- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
444 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
445 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
446 |
|
and Koenig-Beatty+Holland (2012) |
447 |
|
- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
448 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
449 |
|
- requires an extra input argument for S/R seaice_calc_viscosities |
450 |
|
- tensileStrength's depth dependence is different from Itkin et al. (2015) |
451 |
|
(to be changed and played with, for now exponential) |
452 |
|
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
453 |
|
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
454 |
|
by AREA according to Connelly et al. (2004), JPO. |
455 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
456 |
|
the only non-zero term in the denominator when there is no ice (which |
457 |
|
prevented running the model with zero ice-ocean drag). If |
458 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
459 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
460 |
|
consequence is that for open water, the momentum equation reduce |
461 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
462 |
|
they happen to be zero, often leading to a non-zero solution over |
463 |
|
open water. |
464 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
465 |
|
efficient EVP method. |
466 |
|
- introduce area-weighted averages for e12 (analogously to |
467 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
468 |
|
remain, but also changing the order of terms in the previous average |
469 |
|
changed the results as much) -> update experiment |
470 |
|
- add SEAICE_DELTA_SMOOTHREG code |
471 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
472 |
|
TEM-code |
473 |
|
- adjust loop bounds so that only required fields are computed |
474 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
475 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
476 |
|
results again), but will replace old code eventually |
477 |
|
o eesupp/src: |
478 |
|
- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
479 |
|
to always cumulate tile local-sum in the same order |
480 |
|
(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
481 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
482 |
|
and should be faster than GLOBAL_SUM_SEND_RECV code. |
483 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
484 |
|
(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
485 |
|
- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
486 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
487 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
488 |
|
natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
489 |
|
tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
490 |
|
|
491 |
|
checkpoint65n (2015/07/29) |
492 |
|
o pkg/thsice: |
493 |
|
- add a warning when used with pkg/aim but without updating SST |
494 |
|
(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
495 |
|
o pkg/offline: |
496 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
497 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
498 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
499 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
500 |
|
These changes allow: |
501 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
502 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
503 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
504 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
505 |
|
b) no needs to switch on staggerTimeStep anymore; |
506 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
507 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
508 |
|
o pkg/offline: |
509 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
510 |
|
can easily recover previous offset-iter effect by setting offset-time |
511 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
512 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
513 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
514 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
515 |
|
o OpenAD |
516 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
517 |
|
Config. with ggl90 currently diverges after 64 time steps |
518 |
|
so will need more work to become more stable |
519 |
|
- Adding preliminary kpp test to OpenAD verification. |
520 |
|
required small tweakes in kpp_routines.F |
521 |
|
- Merge and update from Krishna Narayanan's contrib area: |
522 |
|
* Add one variable for preliminary OpenAD DIVA |
523 |
|
* Add replacement time-stepping for OpenAD DIVA |
524 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
525 |
|
* required modifs for OAD_support |
526 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
527 |
|
o pkg/seaice: |
528 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
529 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
530 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
531 |
|
(no effect on EVP) |
532 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
533 |
|
o pkg/seaice: |
534 |
|
add new parameter SEAICE_deltaMin that is used ***only*** |
535 |
|
for regularizing Delta (and nothing else, like the parameter |
536 |
|
which is also used for all sorts of things SEAICE_EPS). |
537 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
538 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
539 |
|
the wrong key by inialising it before use -> fixes a recomputation |
540 |
|
problem but does not fix the gradient |
541 |
|
o pkg/layers: |
542 |
|
- move resetting of flux arrays to outside the iLa loop |
543 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
544 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
545 |
|
o pkg/layers: |
546 |
|
- remove from common block 3D layers fields (used to diagnose transport |
547 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
548 |
|
o pkg/seaice: |
549 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
550 |
|
in lab_sea forward experiment (changes results -> updated) |
551 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
552 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
553 |
|
computations; for SEAICE_VECTORIZE_LSR |
554 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
555 |
|
sweep to the outside, |
556 |
|
- remove store directives and add "CADJ loop sequential" directives |
557 |
|
in analogy to model/src/solve_tridiagonal.F |
558 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
559 |
|
boundaries to yield more readable code. This has also the charming side |
560 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
561 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
562 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
563 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
564 |
|
an additional option) |
565 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
566 |
|
but the adjoint gradients (which are affected by this change) still explode. |
567 |
|
o coupler (atm & ocn _compon_interf): |
568 |
|
- avoid using Exch2 IO mapping if not suitable. |
569 |
|
|
570 |
|
checkpoint65m (2015/06/15) |
571 |
|
o pkg/layers: |
572 |
|
- clean-up old parameters setting (from Sep 2012): |
573 |
|
+ remove old parameters setting from common block (declared locally); |
574 |
|
+ stop if any old parameter is mixed with new parameters; |
575 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
576 |
|
- check that layers_bounds for Pot.Density are in the right range; |
577 |
|
this is supposed to catch un-updated setting after recently shifting |
578 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
579 |
|
o pkg/layers: |
580 |
|
- Added missing call to layers_fill for keeping track of tottend in |
581 |
|
pkg/diagnostics/diagnostics_fill_state.F |
582 |
|
o pkg/layers: |
583 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
584 |
|
of diapycnal fluxes |
585 |
|
o pkg/layers: |
586 |
|
- reverted changes to interpolation to previous treatment; there |
587 |
|
was never actually a problem |
588 |
|
o pkg/layers: |
589 |
|
- fix interpolation of layers tracers in the presence of partial cells |
590 |
|
- add lots of new functionality to compute water mass transformation |
591 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
592 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
593 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
594 |
|
for layers_thermodynamics calculations |
595 |
|
o pkg/ptracers: |
596 |
|
- add capability of stepping a passive tracer forward without advection |
597 |
|
by setting PTRACERS_advScheme to 0. |
598 |
|
o pkg/diagnostics: |
599 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
600 |
|
o pkg/layers: |
601 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
602 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
603 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
604 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
605 |
|
o pkg/layers: |
606 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
607 |
|
- fix calculation of layer non-weighted velocity and layer probability |
608 |
|
- add diagnostics for pot.density used for layer averaging |
609 |
|
o pkg/seaice: |
610 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
611 |
|
positiveness, modify a few comments and improve variable names, |
612 |
|
- the changed computation of deltaC affects most seaice-related |
613 |
|
experiments at the truncation level. |
614 |
|
seaice_itd.thermo is affected by far the most, with |
615 |
|
only 7 digits of agreement remaining; update experiments. |
616 |
|
|
617 |
|
checkpoint65l (2015/05/04) |
618 |
|
o pkg/shelfice: |
619 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
620 |
|
factor drKp1 to zero where it is negative (ie. do not use |
621 |
|
SHELFICEBoundaryLayer if hFacC>1) |
622 |
|
- the same for factor drLoc in shelfice_forcing.F |
623 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
624 |
|
with modules in ptracers, when using testreport option "-small_f" |
625 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
626 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
627 |
|
o verification/testreport |
628 |
|
- add new option -small_f |
629 |
|
with this option testreport first makes the target small_f (*.f files) |
630 |
|
before running make (all). This is useful for explicit inlining when |
631 |
|
all sources need to be full available. |
632 |
|
o pkg/exf/exf_interp.F: |
633 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
634 |
|
|
635 |
|
checkpoint65k (2015/04/01) |
636 |
|
o pkg/ecco: |
637 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
638 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
639 |
|
instead of active read/write |
640 |
|
o pkg/ctrl: |
641 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
642 |
|
instead of active read/write. |
643 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
644 |
|
return if .NOT.useAUTODIFF |
645 |
|
o pkg/seaice: add CPP brackets (cost function related). |
646 |
|
o model/src: |
647 |
|
add useAUTODIFF run time switch. |
648 |
|
o pkg/exf/exf_interp.F: |
649 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
650 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
651 |
|
this feature. |
652 |
|
o verification/testreport: |
653 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
654 |
|
implementations of grep that cannot do contextual searches |
655 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
656 |
|
of "cat" have the option "-n" |
657 |
|
o model/src: |
658 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
659 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
660 |
|
convert from conservative to potential temperature. For now they are not |
661 |
|
called anywhere. |
662 |
|
o pkg/ggl90: make "useIDEMIX" useful |
663 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
664 |
|
are different for idemix into separate loops (changes verification |
665 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
666 |
|
- requires 2 new 2D fields KappaM, verticalShear |
667 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
668 |
|
s/r ggl90_idemix |
669 |
|
- fix and improve some comments |
670 |
|
|
671 |
|
checkpoint65j (2015/02/25) |
672 |
|
o pkg/openad |
673 |
|
- synchronize seawater.F with version in model/src: replace routine |
674 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
675 |
|
o pkg/mnc: |
676 |
|
- change default value of pickup_read/write_mnc params to FALSE |
677 |
|
(since few features are missing in reading MNC pickup files). |
678 |
|
o model/src: |
679 |
|
- change default (background) vertical diffusivity for salt to be the |
680 |
|
temperature (background) vertical diffusivity. |
681 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
682 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
683 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
684 |
|
consistent with vertical mixing schemes. |
685 |
|
o verification/testreport: |
686 |
|
- fix typo in "-pcls" option ; |
687 |
|
- put temp files in /tmp (instead of in local dir) |
688 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
689 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
690 |
|
o pkg/ggl90 (idemix code): |
691 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
692 |
|
global_ocean.90x40x15.idemix |
693 |
|
o OpenAD |
694 |
|
- enable active file I/O and begin removal of work-around code |
695 |
|
for OpenAD for handling control variables (memory vs. active files) |
696 |
|
- new CPP options file OPENAD_OPTIONS.h |
697 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
698 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
699 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
700 |
|
o tools/genmake2: |
701 |
|
- add option for an alternative Makefile (from Martin) where multiple |
702 |
|
source files are sent to TAF (instead of all in one file). |
703 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
704 |
|
- code provided by Carsten Eden as an extension of ggl90 |
705 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
706 |
|
compile time; a runtime flag implementation is not yet complete |
707 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
708 |
|
o verification: |
709 |
|
- reduce length of the AD test run by half for experiments |
710 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
711 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
712 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
713 |
|
o verification/testreport: |
714 |
|
- fix two non-POSIX sed statements so that there are no error messages |
715 |
|
on Mac OS X |
716 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
717 |
|
o model/src/seawater.F: |
718 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
719 |
|
(following the matlab code), which would have avoided the bug caught |
720 |
|
by Matt (see below) in the first place |
721 |
|
o pkg/shelfice: |
722 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
723 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
724 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
725 |
|
ice-shelf case (i.e., within surface level). |
726 |
|
- add config summary in shelfice_check.F |
727 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
728 |
|
variable recip_latentHeat |
729 |
|
- introduce diagnostics for friction velocity uStar (in case of |
730 |
|
SHELFICEuseGammaFrict) |
731 |
|
- change verification experiment isomip.htd: |
732 |
|
+ start from pickup (as input_ad at nIter0=8640) |
733 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
734 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
735 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
736 |
|
o model/src: |
737 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
738 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
739 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
740 |
|
o pkg/shelfice: |
741 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
742 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
743 |
|
ice-shelf is. |
744 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
745 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
746 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
747 |
|
for thermodynamic calculations |
748 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
749 |
|
affects results of some verification experiments by up to 4 digits: |
750 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
751 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
752 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
753 |
|
-> updated |
754 |
|
|
755 |
|
checkpoint65i (2015/01/23) |
756 |
|
o model/src: |
757 |
|
- change units of frictionHeating field from W to W/m^2 |
758 |
|
- fix bug in frictional heating from stratospheric drag in |
759 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
760 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
761 |
|
field from load_fields_driver.F to thermodynamics.F ; |
762 |
|
- add diagnostics for frictional heating. |
763 |
|
o model/src & gmredi K3D: |
764 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
765 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
766 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
767 |
|
and name in pickup file). |
768 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
769 |
|
o model/src: |
770 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
771 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
772 |
|
(since Nov 2012) with option selectAddFluid=1. |
773 |
|
o pkg/shelfice: |
774 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
775 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
776 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
777 |
|
o pkg/seaice: two new runtime parameters: |
778 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
779 |
|
long overdue |
780 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
781 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
782 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
783 |
|
for LSR: move checking overlaps out of JFNK-if-block |
784 |
|
o pkg/atm_phys: |
785 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
786 |
|
new S/R ATM_PHYS_DYN2PHYS. |
787 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
788 |
|
fixed-in-time pressure levels). |
789 |
|
o pkg/mom_common (bottomdrag): |
790 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
791 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
792 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
793 |
|
o pkg/shelfice (u/v_drag): |
794 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
795 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
796 |
|
(now similar to shelfice_u_drag.F) |
797 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
798 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
799 |
|
o pkg/mom_common (bottomdrag): |
800 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
801 |
|
- add options for alternative discretisation of velocity norm in quadratic |
802 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
803 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
804 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
805 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
806 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
807 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
808 |
|
off by default since this also reduces model stability (explicit bottom |
809 |
|
friction). Changes produce different machine truncation with linear-drag |
810 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
811 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
812 |
|
o model/src & mom pkgs: |
813 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
814 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
815 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
816 |
|
just copy level Nr value to level Nr+1. |
817 |
|
o doc: |
818 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
819 |
|
o pkg/shelfice: |
820 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
821 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
822 |
|
from array shelficemassinit, which is set in init_fixed and |
823 |
|
has option to be set from file; introduce array |
824 |
|
shelficeMassDynTend array, set thru file in init_fixed |
825 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
826 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
827 |
|
pkg/streamice |
828 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
829 |
|
SHELFICEMassStepping = .true. |
830 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
831 |
|
|
832 |
|
checkpoint65h (2014/12/17) |
833 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
834 |
|
- update to generic controls. |
835 |
|
o pkg/ctrl: |
836 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
837 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
838 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
839 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
840 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
841 |
|
add time variable weights and cyclic controls (time mean, |
842 |
|
seasonal cycle, etc) capabilities to gentim2d |
843 |
|
o pkg/ecco: |
844 |
|
- move reading of error, conversion to weights from |
845 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
846 |
|
o global_oce_llc90, cs32: |
847 |
|
- activte sbo. |
848 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
849 |
|
- activate the new genctrl capabilities. |
850 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
851 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
852 |
|
- add missing ctrl_init_rec.f |
853 |
|
o tools/OAD_support/keepOriginal: |
854 |
|
- add ctrl_init_rec.F |
855 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
856 |
|
- avoid recomputations of xx_gentim2d_dummy. |
857 |
|
o momentum diagnostics: |
858 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
859 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
860 |
|
o pkg/seaice/seaice_lsr.F: |
861 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
862 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
863 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
864 |
|
o verification/global_ocean.cs32x15/input.seaice |
865 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
866 |
|
methods for LSR |
867 |
|
- update results/output.seaice.txt |
868 |
|
o verification/tutorial_global_oce_biogeo: |
869 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
870 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
871 |
|
update output_adm,_oadm,_tlm.txt |
872 |
|
o pkg/dic: |
873 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
874 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
875 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
876 |
|
o verification/tutorial_global_oce_biogeo: |
877 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
878 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
879 |
|
update output_adm,_oadm,_tlm.txt |
880 |
|
o eesupp/src: |
881 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
882 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
883 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
884 |
|
LSR (following Hutchings et al. 2004) |
885 |
|
- introduce zetaZ as a global variable (requires adjustments in |
886 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
887 |
|
in seaice_calc_viscosities.F |
888 |
|
- new flag SEAICEuseStrImpCpl (default off) |
889 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
890 |
|
momentum equations |
891 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
892 |
|
(where it does not have any positive effect) |
893 |
|
o pkg/seaice |
894 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
895 |
|
turn it off by default (because it only seems to work for non-cubed |
896 |
|
sphere/llc topologies) |
897 |
|
o pkg/autodiff |
898 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
899 |
|
o pkg/seaice: |
900 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
901 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
902 |
|
o pkg/obcs: |
903 |
|
- add option to specify domain-connected piece Id along OB though files |
904 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
905 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
906 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
907 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
908 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
909 |
|
o pkg/diagnostics: |
910 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
911 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
912 |
|
outside OB (i.e, where tracer OBCS are applied). |
913 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
914 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
915 |
|
|
916 |
|
checkpoint65g (2014/11/19) |
917 |
|
o pkg/diagnostcis: |
918 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
919 |
|
o pkg/my82,pp81,kl10: |
920 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
921 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
922 |
|
o pkg/seaice: |
923 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
924 |
|
Bouillon et al 2013) |
925 |
|
- add SEAICE_evpAlpha/Beta to namelist |
926 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
927 |
|
involve trivial re-ordering of divisions/multiplications that should not |
928 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
929 |
|
that only 2 digits of agreement remain, in line with the general |
930 |
|
instability/fragility of the evp-code. For now, I do not care and just |
931 |
|
update the verification experiment |
932 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
933 |
|
- remove xx_genarr2d_numsmooth etc |
934 |
|
- use xx_genarr2d_preproc etc instead |
935 |
|
- carry out smooth_correl2D at initialization stage rather than during |
936 |
|
time stepping. |
937 |
|
- get smoothOpNb from xx_gentim2d_preproc |
938 |
|
o global_oce_cs32 : |
939 |
|
- add test of generic ecco capabilities. |
940 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
941 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
942 |
|
o pkg/ctrl,ecco : |
943 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
944 |
|
is defined. |
945 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
946 |
|
o model/src: |
947 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
948 |
|
diffusivity (background) is specified but ignored. |
949 |
|
o verification: |
950 |
|
- in testreport, convert hostname to lower case for default output dir name |
951 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
952 |
|
o pkg/dic: add modifications from Hajoon: |
953 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
954 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
955 |
|
(read from file). |
956 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
957 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
958 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
959 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
960 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
961 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
962 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
963 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
964 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
965 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
966 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
967 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
968 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
969 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
970 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
971 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
972 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
973 |
|
o pkg/ctrl,ecco,exf : |
974 |
|
- remove variables associated with NON-generic costs, |
975 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
976 |
|
- remove NON-generic NON-obcs controls, |
977 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
978 |
|
o pkg/ctrl : added ctrl_local_params.h |
979 |
|
o pkg/ecco : added ecco_local_params.h |
980 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
981 |
|
experiments, which will progressively be removed once the |
982 |
|
experiments are revised to use only generic controls/costs. |
983 |
|
|
984 |
|
checkpoint65f (2014/10/13) |
985 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
986 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
987 |
|
cost function and control capabilities added since checkpoint65c. |
988 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
989 |
|
o pkg/ecco: increase modularity and improve logic |
990 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
991 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
992 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
993 |
|
- cost_gencal.F (new) : determine filnames and records. |
994 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
995 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
996 |
|
and exploit the above functions leading to more compact code. |
997 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
998 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
999 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
1000 |
|
o pkg/ecco: extend generic cost capabilities |
1001 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
1002 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
1003 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
1004 |
|
gencost_outputlevel arguments to cost_generic |
1005 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
1006 |
|
and active_read, making room for gencost_preproc to take effect. |
1007 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
1008 |
|
- pkg/ecco/cost_generic.F : |
1009 |
|
compute and store misfit maks*(model-data) in localdif that is |
1010 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
1011 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
1012 |
|
rather gencost_barfile for deciding whether to write barfile |
1013 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
1014 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
1015 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
1016 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
1017 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
1018 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
1019 |
|
o pkg/ecco: internal re-organization |
1020 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
1021 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
1022 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
1023 |
|
make sure gencost routines only include ecco.h) |
1024 |
|
- throughout : add missing CCP switches, rm unused variables, |
1025 |
|
and rm un-necessary CPP switches |
1026 |
|
- throughout gencost routines : replace modelstartdate with |
1027 |
|
gencost_startdate when needed |
1028 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
1029 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
1030 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
1031 |
|
- ecco_phys.F : compute etanFull |
1032 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
1033 |
|
bpv4-grace to gencost list, initialize added parameters |
1034 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
1035 |
|
|
1036 |
|
checkpoint65e (2014/09/28) |
1037 |
|
o pkg/obcs: |
1038 |
|
- replaced the just-added CPP options with run-time variables |
1039 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
1040 |
|
o pkg/obcs: |
1041 |
|
- add additional CPP options for sponge boundary layers |
1042 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
1043 |
|
o pkg/atm_phys: |
1044 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
1045 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
1046 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
1047 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
1048 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
1049 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
1050 |
|
- implement gentim2d for xx_tauu, xx_tauv |
1051 |
|
o pkg/ctrl, pkg/ecco : |
1052 |
|
- fix and complement the generic controls implementation |
1053 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
1054 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
1055 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
1056 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
1057 |
|
- add weight in CTRL_GET_GEN calls |
1058 |
|
o pkg/ctrl : |
1059 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
1060 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
1061 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
1062 |
|
o pkg/ctrl : |
1063 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
1064 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
1065 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
1066 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
1067 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
1068 |
|
o pkg/ecco, pkg/ctrl : |
1069 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
1070 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
1071 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
1072 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
1073 |
|
|
1074 |
|
checkpoint65d (2014/09/15) |
1075 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
1076 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
1077 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
1078 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
1079 |
|
- remove compilation failure |
1080 |
|
- replace hard coded example |
1081 |
|
- use ctrl_map_ini_gen2D, 3D |
1082 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
1083 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
1084 |
|
o src/packages_init_variables.F : |
1085 |
|
- regroup pkg/estimation calls |
1086 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
1087 |
|
(moved to ctrl_init_variables) |
1088 |
|
o cost/cost_init_varia.F : |
1089 |
|
- remove ecco_cost_init_varia |
1090 |
|
(moved to ecco_init_varia) |
1091 |
|
o ctrl/ctrl_init_variables.F : |
1092 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
1093 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
1094 |
|
o ctrl/ctrl_map_ini.F : |
1095 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
1096 |
|
(moved to ctrl_init_variables) |
1097 |
|
o ctrl/ctrl_map_ini_ecco.F : |
1098 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
1099 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
1100 |
|
o ecco/ecco_ad_diff.list : |
1101 |
|
- add ecco_init_varia.f |
1102 |
|
o ecco/ecco_init_varia.F |
1103 |
|
- new routine |
1104 |
|
o pkg/streamice: |
1105 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
1106 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
1107 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
1108 |
|
o pkg/generic_advdiff: |
1109 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
1110 |
|
o pkg/exf: |
1111 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
1112 |
|
xxg_precip capability |
1113 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
1114 |
|
o pkg/ctrl: |
1115 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
1116 |
|
o model/src/load_fields_driver.F : |
1117 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
1118 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
1119 |
|
o OpenAD verification experiments: |
1120 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
1121 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
1122 |
|
for now, only in pkgs used in OpenAD verification experiments. |
1123 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
1124 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
1125 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
1126 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
1127 |
|
o OpenAD verification tests: |
1128 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
1129 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
1130 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
1131 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
1132 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
1133 |
|
o model/src & generic_advdiff: |
1134 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
1135 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
1136 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
1137 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
1138 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
1139 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
1140 |
|
setting in temp/salt/ptracer_integrate.F |
1141 |
|
o pkg/dic: |
1142 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
1143 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
1144 |
|
in gchem_forcing_sep.F |
1145 |
|
o pkg/autodiff & obcs: |
1146 |
|
- add storage of current OB values for U & V (was already done for T & S). |
1147 |
|
|
1148 |
|
checkpoint65c (2014/08/30) |
1149 |
|
o pkg/dic: |
1150 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
1151 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
1152 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
1153 |
|
o verification: |
1154 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
1155 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
1156 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
1157 |
|
conditions from t=1.yr while keeping the same forcing. |
1158 |
|
o model/src: |
1159 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
1160 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
1161 |
|
o pkg/diagnostics (Stats-Diags): |
1162 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
1163 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
1164 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
1165 |
|
c) extend regional stats over the region edges (for U or V pt location). |
1166 |
|
o pkg/gchem: |
1167 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
1168 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
1169 |
|
o verification (hs94): |
1170 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
1171 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
1172 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
1173 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
1174 |
|
o pkg/ptracers: |
1175 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
1176 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
1177 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
1178 |
|
with AB-2 code (so that it get tested). |
1179 |
|
o model/src: |
1180 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
1181 |
|
with AB-2 code (previously only available with AB-3 code). |
1182 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
1183 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
1184 |
|
there, by calling CYCLE_AB_TRACER). |
1185 |
|
o pkg/generic_advdiff: |
1186 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
1187 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
1188 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
1189 |
|
S/R temp/salt/ptracers_integrate.F |
1190 |
|
o model/src & pkg/ptracers: |
1191 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
1192 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
1193 |
|
- remove common block variable gPtr. |
1194 |
|
o model/src & pkgs: |
1195 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
1196 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
1197 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
1198 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
1199 |
|
+ change accordingly all calling S/R. |
1200 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
1201 |
|
in S/R temp/salt/ptracers_integrate.F |
1202 |
|
o pkg/seaice: |
1203 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
1204 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
1205 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
1206 |
|
in seaice_lsr |
1207 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
1208 |
|
in s/r seaice_lsr_calc_coeffs |
1209 |
|
o pkg/mdsio: |
1210 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
1211 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
1212 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
1213 |
|
|
1214 |
|
checkpoint65b (2014/08/12) |
1215 |
|
o pkg/matrix: |
1216 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
1217 |
|
o model/src: |
1218 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
1219 |
|
natl_box verification experiment. |
1220 |
|
o model/src & pkg/down_slope: |
1221 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
1222 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
1223 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
1224 |
|
results at machine truncation level: update output of experiments |
1225 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
1226 |
|
o pkg/diagnostics (Stats-Diags): |
1227 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
1228 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
1229 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
1230 |
|
times (but Min,Max and StD are still wrong). |
1231 |
|
o model/src: |
1232 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
1233 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
1234 |
|
o model/src: |
1235 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
1236 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
1237 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
1238 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
1239 |
|
o model/src: |
1240 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
1241 |
|
anomaly that is used to compute geopotential: this make the atmos code |
1242 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
1243 |
|
o pkg/seaice/seaice_lsr.F |
1244 |
|
- rename integer variable ilcall to ipass (that's what it is called |
1245 |
|
in the residual diagnostics |
1246 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
1247 |
|
default) for improved non-linear convergence of the first few steps |
1248 |
|
- adjust a few comments and add new ones to explain some of the store |
1249 |
|
directives |
1250 |
|
o pkg/generic_advdiff (& ptracers): |
1251 |
|
- re-work the code to check for valid advection scheme and for minimum |
1252 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
1253 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
1254 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
1255 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
1256 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
1257 |
|
less exact gradients in my tests); but there are still |
1258 |
|
recomputation warning (although gradients are sort of OK), when |
1259 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
1260 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
1261 |
|
- update verification experiments lab_sea. |
1262 |
|
- change some comments in S/R seaice_calc_viscosities |
1263 |
|
o model/src: |
1264 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
1265 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
1266 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
1267 |
|
but affects AD results (at machine truncation level): update output of |
1268 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
1269 |
|
and isomip (oad: 12.d). |
1270 |
|
o pkg/generic_advdiff: |
1271 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
1272 |
|
- refine warning related to stability of tracer time-stepping |
1273 |
|
regarding internal wave dynamics. |
1274 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
1275 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
1276 |
|
if potentially unstable). |
1277 |
|
o pkg/kl10: |
1278 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
1279 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
1280 |
|
(contribution from Jody Klymak), tested in verification experiment |
1281 |
|
verification/internal_wave/input.kl10/ |
1282 |
|
o isomip experiment: |
1283 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
1284 |
|
(input.htd) and update the output. |
1285 |
|
o cd_code experiments: |
1286 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
1287 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
1288 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
1289 |
|
update the corresponding output. |
1290 |
|
o pkg/seaice: |
1291 |
|
- reduce the number of include files and store directives in |
1292 |
|
S/R seaice_lsr_tridiagu/v |
1293 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
1294 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
1295 |
|
get rid off one store directive (a TAF bug?) |
1296 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
1297 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
1298 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
1299 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
1300 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
1301 |
|
offline_exf_seaice/input.dyn_jfnk) |
1302 |
|
|
1303 |
|
checkpoint65a (2014/07/27) |
1304 |
|
o model/src: |
1305 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
1306 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
1307 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
1308 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
1309 |
|
o model/src: |
1310 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
1311 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
1312 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
1313 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
1314 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
1315 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
1316 |
|
affects results at machine truncation level (e.g., ocean: if using |
1317 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
1318 |
|
correction due to vertical advection). |
1319 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
1320 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
1321 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
1322 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
1323 |
|
o pkg/ptracers & diagnostics: |
1324 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
1325 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
1326 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
1327 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
1328 |
|
|
1329 |
|
checkpoint65 (2014/07/18) |
1330 |
|
o pkg/fizhi: |
1331 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
1332 |
|
affects results at machine truncation level. Update output of experiments |
1333 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
1334 |
|
o pkg/seaice: more clean up |
1335 |
|
- rename TAF common block tapes to be more consistent and remove |
1336 |
|
unnecessary duplicates |
1337 |
|
- add store directives to remove more recomputations, but use smaller |
1338 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
1339 |
|
The idea behind this flag is to reduce the memory footprint when the |
1340 |
|
adjoint of the LSR is not required. As of now, defining the flag |
1341 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
1342 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
1343 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
1344 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
1345 |
|
this experiment): |
1346 |
|
> size mitgcmuv_ad |
1347 |
|
text data bss dec hex |
1348 |
|
5100659 1216 220458952 225560827 d71c8fb |
1349 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
1350 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
1351 |
|
text data bss dec hex |
1352 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
1353 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
1354 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
1355 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
1356 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
1357 |
|
- in general, the AD gradients still are wrong |
1358 |
|
o OpenAD |
1359 |
|
- clean up code_oad/ directories somewhat by moving files |
1360 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
1361 |
|
o model/src: |
1362 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
1363 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
1364 |
|
tendencies (previously done after). |
1365 |
|
o pkg/diagnostics: |
1366 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
1367 |
|
o pkg/down_slope: |
1368 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
1369 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
1370 |
|
o model/src: |
1371 |
|
- new file "apply_forcing.F" containing all the code previously in |
1372 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
1373 |
|
the current level tendency array to update (instead of a direct update |
1374 |
|
of the common bloc array). Change the corresponding calls. |
1375 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
1376 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
1377 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
1378 |
|
- rearrange some code blocks, so that now all calculations for |
1379 |
|
setting up the right-hand-sides done within one single block |
1380 |
|
(I find that easier to read and understand) |
1381 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
1382 |
|
- adjust some indentations and comments |
1383 |
|
|
1384 |
|
checkpoint64z (2014/07/10) |
1385 |
|
o model/src and several pkgs: |
1386 |
|
- change argument list of all S/R called from external_forcing.F and |
1387 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
1388 |
|
to pass, as argument, the current level tendency array to update |
1389 |
|
(instead of a direct update of the common bloc array). |
1390 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
1391 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
1392 |
|
o pkg/seaice/seaice_lsr.F |
1393 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
1394 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
1395 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
1396 |
|
keep it in bi/bj loop; this seems to be essential |
1397 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
1398 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
1399 |
|
o pkg/seaice |
1400 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
1401 |
|
generates unnecessary code in seaice_lsr_ad |
1402 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
1403 |
|
in seaice_lsr_ad |
1404 |
|
- exclude some residual computations in seaice_lsr when |
1405 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
1406 |
|
in seaice_lsr_ad |
1407 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
1408 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
1409 |
|
and klockey should be checked by a specialist) |
1410 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
1411 |
|
and update lab_sea after previous changes in pkg/seaice below |
1412 |
|
o pkg/autodiff: |
1413 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
1414 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
1415 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
1416 |
|
o pkg/ecco: |
1417 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
1418 |
|
temperature (for use in adjoint sensitivity studies). |
1419 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
1420 |
|
o pkg/mom_common/mom_calc_visc.F: |
1421 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
1422 |
|
o pkg/seaice/seaice_summary.F: |
1423 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
1424 |
|
o pkg/seaice: |
1425 |
|
- remove some store directives and add new ones in an effort to get |
1426 |
|
finally rid off the recomputation warnings. This is successful |
1427 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
1428 |
|
defined (i.e. no extensive recomputation warnings left), but there |
1429 |
|
are still too many recomputations on the solver iteration level |
1430 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
1431 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
1432 |
|
SEAICE_SIZE.h |
1433 |
|
- add a store directive in S/R seaice_calc_viscosities |
1434 |
|
o pkg/seaice (ITD code): |
1435 |
|
- fix definition of Hlimit for multi-threaded case |
1436 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
1437 |
|
update output of experiment seaice_itd. |
1438 |
|
o replace content of verification/seaice_itd |
1439 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
1440 |
|
to test the ice thickness distribution code with ridging |
1441 |
|
- this is a first shot at this experiment |
1442 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
1443 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
1444 |
|
and lot of new comments. |
1445 |
|
|
1446 |
|
checkpoint64y (2014/06/20) |
1447 |
|
o pkg/seaice/seaice_reg_ridge.F: |
1448 |
|
- modify the regularization of very small volumes of ice; only check |
1449 |
|
total volume HEFF, and do not apply correction to individual ice |
1450 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
1451 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
1452 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
1453 |
|
o pkg/exf: |
1454 |
|
- add code to process the case field period = -12. with UV interpolation. |
1455 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
1456 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
1457 |
|
o verification/global_with_exf: |
1458 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
1459 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
1460 |
|
o pkg/cal: |
1461 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
1462 |
|
o pkg/exf: |
1463 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
1464 |
|
to replace logical switch "exf_verbose" |
1465 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
1466 |
|
o pkg/sbo: |
1467 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
1468 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
1469 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
1470 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
1471 |
|
- fix some multi-threading issues (in output part). |
1472 |
|
o model/src & most packages: |
1473 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
1474 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
1475 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
1476 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
1477 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
1478 |
|
+ call LAND_READPARMS from packages_readparms.F |
1479 |
|
o pkg/seaice: |
1480 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
1481 |
|
replace it by a warning in S/R seaice_check |
1482 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
1483 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
1484 |
|
SEAICE_ITD is defined) |
1485 |
|
|
1486 |
|
checkpoint64x (2014/05/24) |
1487 |
|
o verification/lab_sea: |
1488 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
1489 |
|
- un-do the update after putting back local recip_Cp in few places. |
1490 |
|
o pkg/salt_plume: modifications by An Nguyen: |
1491 |
|
- add capability to do brine rejection (salt-plume) as function of |
1492 |
|
volume+tracers (instead of only salinity tracer). |
1493 |
|
- conserve volume by exchanging volume from each kLev to above to |
1494 |
|
accommodate in-coming brine volume |
1495 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
1496 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
1497 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
1498 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
1499 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
1500 |
|
in East/West Arctic. |
1501 |
|
o pkg/sbo: |
1502 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
1503 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
1504 |
|
output for future testreport verification (unfinished). |
1505 |
|
o pkg/atm_phys: |
1506 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
1507 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
1508 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
1509 |
|
o pkg/seaice |
1510 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
1511 |
|
(affects truncation) |
1512 |
|
seaice_do_ridging.F: clean up the insectarium |
1513 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
1514 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
1515 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
1516 |
|
- add some debugging information and error messages (warnings) |
1517 |
|
o model/src: modifications relatd to atmosphere p*: |
1518 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
1519 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
1520 |
|
of vertical profile tRef in geopotential background and anomaly. |
1521 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
1522 |
|
and pkg/atm_phys. |
1523 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
1524 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
1525 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
1526 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
1527 |
|
not used right now, but can be used in BGC packages to fix conservation. |
1528 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
1529 |
|
other packages too. |
1530 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
1531 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
1532 |
|
o model/src: |
1533 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
1534 |
|
as local variable (no longer in common block) to avoid any confusion. |
1535 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
1536 |
|
o pkg/exf: |
1537 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
1538 |
|
air density as function of air Temp, Humidity and atm pressure. |
1539 |
|
|
1540 |
|
checkpoint64w (2014/05/02) |
1541 |
|
o verification: |
1542 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
1543 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
1544 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
1545 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
1546 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
1547 |
|
o model/src: for atmosphere in p* coords: |
1548 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
1549 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
1550 |
|
but not yet activated. |
1551 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
1552 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
1553 |
|
- this changes the results (but not for any verification experiment, because |
1554 |
|
none tests this), but avoids having an extra field in the restart files |
1555 |
|
o pkg/seaice: remove global variable TICE (not needed) |
1556 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
1557 |
|
seaice_diagnostics_state) |
1558 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
1559 |
|
- use specific read/write routines for reading and writing individual leves |
1560 |
|
of a multilevel field |
1561 |
|
o pkg/ctrl & model/inc: |
1562 |
|
- move additional anomaly fields of control vars (related to options: |
1563 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
1564 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
1565 |
|
o pkg/seaice: some small modifications to the ridging code |
1566 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
1567 |
|
seaice_growth |
1568 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
1569 |
|
computed only in one place and compute it in the same way as in |
1570 |
|
seaice_growth |
1571 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
1572 |
|
point exceptions over land |
1573 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
1574 |
|
- move most of "PART 1" of S/R seaice_growth into a new and separate |
1575 |
|
S/R seaice_reg_ridge that will both regularize the state variable after |
1576 |
|
advection call the actual ridging routine; |
1577 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
1578 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
1579 |
|
- remove ridging code from seaice_advdiff |
1580 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
1581 |
|
more readable (this is probably subjective) |
1582 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
1583 |
|
conditions in the correct category |
1584 |
|
- finally: add new ridging routine for ITD code |
1585 |
|
|
1586 |
|
checkpoint64v (2014/04/11) |
1587 |
|
o pkg/ecco: |
1588 |
|
- add runtime parameters mdt[start,end]date[1,2] |
1589 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
1590 |
|
o pkg/seaice: |
1591 |
|
- make deltaC a global variable, so that it can be used in ridging code |
1592 |
|
- first step towards ridging: introduce new routines that compute |
1593 |
|
ice strength based on ridging parameters |
1594 |
|
- add diagnostic for HSNOWITD |
1595 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
1596 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
1597 |
|
- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
1598 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
1599 |
|
o verification/hs94.1x64x5: |
1600 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
1601 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
1602 |
|
o autodiff: |
1603 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
1604 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
1605 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
1606 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
1607 |
|
which are specific to TAF/TAMC). |
1608 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
1609 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
1610 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
1611 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
1612 |
|
building mitgcmuv_ad (make adAll). |
1613 |
|
o pkg/ecco: |
1614 |
|
- cost_gencost_seaicev4.F: |
1615 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
1616 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
1617 |
|
- add stop statement if old names siv4-[sst,vol] are used |
1618 |
|
- add snapshots + cost reports for atmospheric longwave |
1619 |
|
- remove factor 0.1 in front of wtau[u,v] |
1620 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
1621 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
1622 |
|
o pkg/atm_phys: |
1623 |
|
- add some diagnostics for Short-wave and for convection S/R. |
1624 |
|
o pkg/seaice/seaice_growth: |
1625 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
1626 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
1627 |
|
- rearrange loop order for better vector code in the same code block |
1628 |
|
- rewrite the floeDiameter formula to have fewer divisions |
1629 |
|
- (miraculously) none of this changes the results of seaice_itd |
1630 |
|
o pkg/smooth: |
1631 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
1632 |
|
o pkg/salt_plume: |
1633 |
|
- salt_plume_frac.F: |
1634 |
|
clean up local param names |
1635 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
1636 |
|
o pkg/rw: |
1637 |
|
- add RS version of S/R READ_MFLDS_LEV. |
1638 |
|
o pkg/streamice: |
1639 |
|
- fix the restart test by writing/reading pickup_streamice files. |
1640 |
|
o pkg/seaice: |
1641 |
|
- refine checks for jfnk-related parameters |
1642 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
1643 |
|
is no IMEX code to avoid confusion and surprises |
1644 |
|
|
1645 |
|
checkpoint64u (2014/03/07) |
1646 |
|
o verification/MLAdjust: |
1647 |
|
- rename secondary test suffix: |
1648 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
1649 |
|
0.leithD -> AhFlxF + switch to flux-form |
1650 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
1651 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
1652 |
|
o pkg/mom_vecinv: |
1653 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
1654 |
|
to be before mom_calc_visc.F) |
1655 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
1656 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
1657 |
|
this is simpler for the adjoint and for diagnostics. |
1658 |
|
o model/src + pkg/momentum: |
1659 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
1660 |
|
(e.g., to add "thin-wall" where it is =1). |
1661 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
1662 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
1663 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
1664 |
|
coords; not working with CD-scheme neither. |
1665 |
|
o pkg/seaice: |
1666 |
|
- rename recently introduced parameters from (wrong name) AB to |
1667 |
|
BDF (backward difference time discretisation) |
1668 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
1669 |
|
o tools/adjoint_options: |
1670 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
1671 |
|
|
1672 |
|
checkpoint64t (2014/02/01) |
1673 |
|
o pkg/ecco |
1674 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
1675 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
1676 |
|
- replace hard-coded record number and period which only work for monthly |
1677 |
|
with read-in runtime param that works for other periods (month,day,year) |
1678 |
|
o pkg/thsice |
1679 |
|
- corrected store directive fixes thsice adjoint gradient checks |
1680 |
|
o genmake2 & testreport: |
1681 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
1682 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
1683 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
1684 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
1685 |
|
o pkg/shelfice: |
1686 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
1687 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
1688 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
1689 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
1690 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
1691 |
|
o model/src/temp_integrate.F and salt_integrate.F |
1692 |
|
- re-include store directives that were removed on Dec 27th. |
1693 |
|
o model/src/external_forcing_surf.F |
1694 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
1695 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
1696 |
|
turned off in the adjoint. The resolved issue dated back to July when |
1697 |
|
EXTERNAL_FORCING_SURF call was moved. |
1698 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
1699 |
|
o pkg/exf/exf_check.F |
1700 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
1701 |
|
- streamline error output |
1702 |
|
o pkg/streamice and aim_v23: |
1703 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
1704 |
|
Apple's /usr/bin/cpp knows what to do: |
1705 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
1706 |
|
Target: x86_64-apple-darwin13.0.0 |
1707 |
|
|
1708 |
|
checkpoint64s (2014/01/05) |
1709 |
|
o tools/adjoint_options: |
1710 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
1711 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
1712 |
|
o model/src: |
1713 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
1714 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
1715 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
1716 |
|
o model/src & pkg/ptracers: |
1717 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
1718 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
1719 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
1720 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
1721 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
1722 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
1723 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
1724 |
|
for now only implemented for in exf_interp_read.F |
1725 |
|
o verification/advect_xy: |
1726 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
1727 |
|
o momentum diagnostics: |
1728 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
1729 |
|
- fix typo in diagnostics for momentum tendency from AB. |
1730 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
1731 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
1732 |
|
|
1733 |
|
checkpoint64r (2013/12/08) |
1734 |
|
o verification/*/results: |
1735 |
|
- Update reference output of experiments that were passing with just 13 digits |
1736 |
|
(make it easier to detect future changes in results) |
1737 |
|
o model/src & pkg/ptracers: |
1738 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
1739 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
1740 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
1741 |
|
o coupling interface pkgs: |
1742 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
1743 |
|
- change the config check to test the agreement of Ocean Depth |
1744 |
|
with ATM land/sea mask (instead of ATM orography); |
1745 |
|
- send to coupler the number of coupler time-steps to do for this run: |
1746 |
|
this allows to check for consistency and don't need anymore to be |
1747 |
|
specified in parameter file "data"; |
1748 |
|
in coupler: |
1749 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
1750 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
1751 |
|
o pkg/compon_communic: |
1752 |
|
- add coupling send/receive for non-tiled integer vector; |
1753 |
|
- add S/R to check and stop if any proc has an error (similar to |
1754 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
1755 |
|
o pkg/exch2: |
1756 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
1757 |
|
through list of all tiles my proc owns. |
1758 |
|
o model/src: |
1759 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
1760 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
1761 |
|
calling S/R); this affects AD results at machine truncation level: |
1762 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
1763 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
1764 |
|
o tools/build_options: |
1765 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
1766 |
|
o coupling interface pkgs: |
1767 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
1768 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
1769 |
|
to each S/R that needs it; remove un-used variables. |
1770 |
|
- change component tile registration (cpl_register.F in both compon_interf |
1771 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
1772 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
1773 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
1774 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
1775 |
|
a) can now use different tiling between atm & ocn comp. |
1776 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
1777 |
|
even if using the same tiling between atm & ocn). |
1778 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
1779 |
|
full land tiles); not yet tested. |
1780 |
|
- check for valid mapping from comp. tile to coupler global array |
1781 |
|
- improve report of tile registration results to log file. |
1782 |
|
o pkg/exch2: |
1783 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
1784 |
|
tile-registration (CPL_REGISTER); |
1785 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
1786 |
|
store the local bi,bj indices of each tile; |
1787 |
|
- also print bi,bj in local report to log file; |
1788 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
1789 |
|
Jun 2009 modif of pkg/exch2). |
1790 |
|
o testing on baudelaire: |
1791 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
1792 |
|
get the full set of test done earlier |
1793 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
1794 |
|
o model/src/thermodynamics.F and routines called from it: |
1795 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
1796 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
1797 |
|
velocity (outp) by adding bolus velocity. |
1798 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
1799 |
|
mass transport from velocity + lateral grid cell area |
1800 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
1801 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
1802 |
|
in thermodynamics.F |
1803 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
1804 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
1805 |
|
loop). |
1806 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
1807 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
1808 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
1809 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
1810 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
1811 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
1812 |
|
tutorial_tracer_adjsens (+ TLM output). |
1813 |
|
o tools/OAD_support and (verification/*/) code_oad: |
1814 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
1815 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
1816 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
1817 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
1818 |
|
o model/src: |
1819 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
1820 |
|
retired list of parameters (routine FREEZE has been replace by surface |
1821 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
1822 |
|
o pkg/gmredi: |
1823 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
1824 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
1825 |
|
- update output of FWD experiments: front_relax.bvp, |
1826 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
1827 |
|
|
1828 |
|
checkpoint64q (2013/11/17) |
1829 |
|
o verification: |
1830 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
1831 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
1832 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
1833 |
|
updating the input pickup_seaice files (previously wrong). |
1834 |
|
o pkg/cost: |
1835 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
1836 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
1837 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
1838 |
|
cannot be applied to var in common block). |
1839 |
|
o allows to get results independent of tile-per-proc setting (if using |
1840 |
|
slower GLOBAL_SUM_SEND_RECV option). |
1841 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
1842 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
1843 |
|
forward gradients: update output). |
1844 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
1845 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
1846 |
|
o pkg/mom_common: |
1847 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
1848 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
1849 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
1850 |
|
ensure that all field value that are used are set. |
1851 |
|
o tutorial_deep_convection (smag3d): |
1852 |
|
- add missing scaling in mom_calc_smag_3d.F; |
1853 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
1854 |
|
o pkg/dic: |
1855 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
1856 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
1857 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
1858 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
1859 |
|
o eesupp/src & pkg/mdsio: |
1860 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
1861 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
1862 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
1863 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
1864 |
|
o verification/isomip: |
1865 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
1866 |
|
o tools/build_options: |
1867 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
1868 |
|
to get a working restart for all experiments, add "-fp-model source" |
1869 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
1870 |
|
|
1871 |
|
checkpoint64p (2013/10/20) |
1872 |
|
o pkg/autodiff: |
1873 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
1874 |
|
criteria, return to simple (default) tape IO format. |
1875 |
|
o pkg/mdsio (+ eesupp/src): |
1876 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
1877 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
1878 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
1879 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
1880 |
|
template) corresponding to simpler global mapping. |
1881 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
1882 |
|
to globalFile when parameter globalFiles is set to True. |
1883 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
1884 |
|
o pkg/autodiff: |
1885 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
1886 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
1887 |
|
missing, just add a STOP if array type do not match. |
1888 |
|
o pkg/exf: |
1889 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
1890 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
1891 |
|
and rename array obsSIce to exf_iceFraction. |
1892 |
|
o tutorial_deep_convection: |
1893 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
1894 |
|
for now all in this exp. code dir. |
1895 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
1896 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
1897 |
|
o eesupp/src: |
1898 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
1899 |
|
very large number of processors did not work with existing set-up |
1900 |
|
|
1901 |
|
checkpoint64o (2013/09/25) |
1902 |
|
o pkg/atm_phys & atm_compon_interf: |
1903 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
1904 |
|
o tools/build_options: |
1905 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
1906 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
1907 |
|
remove CPP setting (was identical to genmake2 default). |
1908 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
1909 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
1910 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
1911 |
|
external forcing via taueddy_external_forcing.F |
1912 |
|
- at the moment, it is very experimental and only works with the variable eddy |
1913 |
|
diffusivity calculated in gmredi_k3d.F |
1914 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
1915 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
1916 |
|
o testreport (& tools/do_tst_2+2): |
1917 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
1918 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
1919 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
1920 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
1921 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
1922 |
|
o pkg/atm_compon_interf: |
1923 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
1924 |
|
(which accumalate in time each coupling field) |
1925 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
1926 |
|
update accordingly + simplify aim_do_physics.F |
1927 |
|
|
1928 |
|
checkpoint64n (2013/08/26) |
1929 |
|
o pkg/bbl: |
1930 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
1931 |
|
- replaced horizontal and vertical transport parameters with velocities |
1932 |
|
- changes results for verification/global_with_exf.yearly |
1933 |
|
o verification/halfpipe_streamice: |
1934 |
|
- change to matrix construction; update both Fwd & AD output. |
1935 |
|
o verification/tutorial_tracer_adjsens: |
1936 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
1937 |
|
rStar causes problems with OpenAD; update output. |
1938 |
|
o tools: |
1939 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
1940 |
|
to local /tmp disk (but would be easy to move them back); |
1941 |
|
- xmakedepend: apply the same switch for temp-files. |
1942 |
|
o pkg/offline: |
1943 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
1944 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
1945 |
|
output files) and apply r* scaling at each time-step (function of the time |
1946 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
1947 |
|
o adjoint with OpenAD: |
1948 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
1949 |
|
package openad. This package has to be compiled for all runs with OpenAD |
1950 |
|
instead of specifying code_oad_all as a modification directory. |
1951 |
|
- link the fortran templates from tools/OAD_support to the build directory |
1952 |
|
for preprocessing to avoid conflicts between different setups compiled |
1953 |
|
simultaneously and simplify cleanup. |
1954 |
|
o pkg/exf: |
1955 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
1956 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
1957 |
|
o model/src: |
1958 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
1959 |
|
(similar to do_fields_blocking_exchanges.F). |
1960 |
|
o tools/genmake2: |
1961 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
1962 |
|
built, will stop if things go wrong with staf). |
1963 |
|
- fix target "adobj" (left from TAF version-2 transition) |
1964 |
|
o pkg/diagnostics: |
1965 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
1966 |
|
this replace/extend the use of logical param "settingDiags" (to check |
1967 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
1968 |
|
New S/R to print error message and stop when pkgStatus is not right. |
1969 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
1970 |
|
|
1971 |
|
checkpoint64m (2013/08/13) |
1972 |
|
o model/inc: |
1973 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
1974 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
1975 |
|
o pkg/kpp & aim_v23: |
1976 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
1977 |
|
o pkg/seaice: |
1978 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
1979 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
1980 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
1981 |
|
o eesupp/src: |
1982 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
1983 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
1984 |
|
o switch to TAF version-2: |
1985 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
1986 |
|
are used in I/O routines of adjoint state and associated common blocks |
1987 |
|
that are used in adcommon.h (backward compatible with version-1) |
1988 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
1989 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
1990 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
1991 |
|
out except for diva). |
1992 |
|
- the major change with TAF version-2 is that both the differentiated |
1993 |
|
routines and the forward routines (new) are returned as part of the TAF |
1994 |
|
output source code. Update genmake2 accordingly. |
1995 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
1996 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
1997 |
|
output show minor changes (machine truncation level); update the few AD & |
1998 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
1999 |
|
|
2000 |
|
checkpoint64l (2013/08/05) |
2001 |
|
o model/src: |
2002 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
2003 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
2004 |
|
when using TAF but only if using OpenAD. |
2005 |
|
o pkg/mom_common+fluxform+vecinv: |
2006 |
|
- always set horiz. viscosity arrays to background value before calling |
2007 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
2008 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
2009 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
2010 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
2011 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
2012 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
2013 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
2014 |
|
useBiharmonicVisc & useVariableVisc. |
2015 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
2016 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
2017 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
2018 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
2019 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
2020 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
2021 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
2022 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
2023 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
2024 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
2025 |
|
default viscAh,viscA4 is zero). |
2026 |
|
o model/src: |
2027 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
2028 |
|
o Divided Adjoint (DIVA) with MPI: |
2029 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
2030 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
2031 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
2032 |
|
|
2033 |
|
checkpoint64k (2013/07/23) |
2034 |
|
o tools/OAD_support: |
2035 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
2036 |
|
and remove it from genmake2. |
2037 |
|
o tools/build_options: |
2038 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
2039 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
2040 |
|
o verification/halfpipe_streamice: |
2041 |
|
- change to driving stress formulation; update both Fwd & AD output. |
2042 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
2043 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
2044 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
2045 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
2046 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
2047 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
2048 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
2049 |
|
o testreport: |
2050 |
|
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
2051 |
|
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
2052 |
|
from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
2053 |
|
o verification/lab_sea (AD test): |
2054 |
|
- change to test Divided Adjoint Run in this set-up (both standard AD test |
2055 |
|
and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
2056 |
|
o pkg atm_ & ocn_compon_interf: |
2057 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
2058 |
|
staggerTimeStep implementation) and disable (retired) corresponding |
2059 |
|
parameter. |
2060 |
|
o pkg/offline: |
2061 |
|
- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
2062 |
|
- add S/R OFFLINE_CHECK to print offline parameter summary |
2063 |
|
and stop if loading a file that is not used; |
2064 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
2065 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
2066 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
2067 |
|
for monitoring CFL numbers and checking offline fields. |
2068 |
|
o OpenAD: |
2069 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
2070 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
2071 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
2072 |
|
o model/src: |
2073 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
2074 |
|
(where external_forcing_adjust was called) and change list of arguments; |
2075 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
2076 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
2077 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
2078 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
2079 |
|
arrays in FFIELDS.h. |
2080 |
|
- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
2081 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
2082 |
|
ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
2083 |
|
- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
2084 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
2085 |
|
error in AD code). |
2086 |
|
|
2087 |
|
checkpoint64j (2013/07/04) |
2088 |
|
o pkg/offline: |
2089 |
|
- to enable the use of other features with pkg offline (e.g., obcs), |
2090 |
|
also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
2091 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
2092 |
|
o pkg/exf ALLOW_RUNOFTEMP |
2093 |
|
- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
2094 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
2095 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
2096 |
|
o pkg/atm_phys: |
2097 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
2098 |
o verification, ad-tests: |
o verification, ad-tests: |
2099 |
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
2100 |
global_ocean_ebm and offline_exf_seaice.thsice. |
global_ocean_ebm and offline_exf_seaice.thsice. |