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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
8 |
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affects some experiments at truncation level: |
9 |
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- global_ocean.cs32x15.icedyn (11 digits), |
10 |
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- global_ocean.cs32x15.seaice (11 digits), |
11 |
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- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
12 |
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- also update global_ocean.cs32x15 adjoint and tangent-linear results |
13 |
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o pkg/salt_plume & pkg/thsice: |
14 |
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- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
15 |
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connect salt_plume flux to ATM-OCN coupling pkgs interface: |
16 |
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a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
17 |
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export to coupler interface) even without compiling pkg/salt_plume ; |
18 |
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b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
19 |
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(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
20 |
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o pkg/dic: |
21 |
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- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
22 |
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instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
23 |
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called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
24 |
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- move also update with values from ATM-OCN Coupler in the same new S/R |
25 |
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(previously done in ocn_apply_import.F). |
26 |
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o tools/adjoint_options: |
27 |
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- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
28 |
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has been changed on Jan 14, 2016. |
29 |
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o pkg/ggl90: |
30 |
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- add alternative discretisation of vertical shear (off by default), to |
31 |
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compute the mean (@ grid-cell center) of vertical shear compon instead of |
32 |
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vertical shear of mean flow (@ grid-cell center). |
33 |
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- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
34 |
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results on adjacent faces of cubed-sphere grids; this fix the restart. |
35 |
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o pkg/atm_compon_interf: |
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- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
37 |
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pass last value, stored directly before export to CPL ; |
38 |
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Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
39 |
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- remove atmSLPr from pickup files (no longer needed for restart) |
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|
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checkpoint65s (2016/01/13) |
42 |
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o eesupp & genmake2: |
43 |
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- first check for Function ETIME and, if it fails, then check for subroutine |
44 |
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ETIME and consistent output; use the appropriate version in timers.F |
45 |
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o model/src: |
46 |
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- to check restart test, add option to apply EXCH to U,V earlier, just before |
47 |
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integr_continuity; turned off by default. |
48 |
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o pkg/dic: |
49 |
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- remove CPP option USE_ATMOSCO2 (not needed) |
50 |
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o tools/tst_2+2: |
51 |
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- try to ignore difference between +0 and -0 in binary file, causing test |
52 |
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to fail for no good reason. |
53 |
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o eesupp & genmake2: |
54 |
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- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
55 |
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but also check (in genmake2) that test runs and returns meaningful results. |
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o coupler pkgs: |
57 |
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Finish implementation of optionally-exchanged variable switches (started on |
58 |
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Nov 12) with addition of few more exchanged fields, including 2-way exchange |
59 |
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of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
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advection in OCN component; this requires sequential coupling. |
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coupler (pkg/atm_ocn_coupler): |
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- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
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routines (useful for debug). |
64 |
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- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
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flux, DIC fields) if corresponding switch is ON. |
66 |
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- add option to export RunOff to OCN (to use for DIC river input) |
67 |
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- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
68 |
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components (pkg/atm_ & ocn_compon_interf): |
69 |
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- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
70 |
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optionally exchanged fields; add a check & stop in cpl_readparms.F. |
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ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
72 |
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OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
73 |
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- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
74 |
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+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
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- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
76 |
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- hold in common block coupler optionally-exchanged variable switch |
77 |
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and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
78 |
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- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
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this is intended to replace the OCN cplFldtave.* output files (not updated |
80 |
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to contain new additional exchanged fields). |
81 |
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o pkg/dic: |
82 |
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- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
83 |
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o pkg/thsice: |
84 |
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- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
85 |
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and writing of thsice pickup files. |
86 |
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o pkg/atm_compon_interf: |
87 |
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- move all field individual export-call out of cpl_export_import_data.F |
88 |
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into new S/R ATM_EXPORT_FIELDS |
89 |
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o pkg/atm_compon_interf: |
90 |
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- store state variables (for now, only thSIce fields) just before beeing |
91 |
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exported (in cpl_export_import_data.F, like on ocean side) instead of from |
92 |
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atm_store_my_data.F like all exported fluxes. |
93 |
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- new version of pickup_cpl: write field names into meta file and read meta |
94 |
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file to find field postion in pickup. Also only write/read fields meeded for |
95 |
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restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
96 |
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o pkg/dic: |
97 |
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- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
98 |
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o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
99 |
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pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
100 |
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value can be from domain [0,1] to average between the two methods |
101 |
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o pkg/atm_phys: |
102 |
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- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
103 |
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hold fixed in time). |
104 |
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|
105 |
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checkpoint65r (2015/12/21) |
106 |
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o pkg/seaice: |
107 |
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fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
108 |
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solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
109 |
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o pkg/seaice: |
110 |
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- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
111 |
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when SEAICEscaleSurfStress=.TRUE., |
112 |
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- apply areaW and areaS in S/R seaice_calc_lhs |
113 |
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o pkg/atm_phys: |
114 |
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- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
115 |
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(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
116 |
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for individual contribution (convection, LSC cond, radiation) |
117 |
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- add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp. |
118 |
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information); activated with: solar_exponent=0. and wv_exponent=-1. |
119 |
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o pkg/ggl90: |
120 |
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- within IDEMIX add upper limit for horizontal group velocity to |
121 |
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avoid instability problems in the explicit horizontal diffusion term for |
122 |
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long time steps or high resolution |
123 |
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o pkg/diagnostics: |
124 |
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- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
125 |
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(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
126 |
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o testreport: |
127 |
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- remove "-v" (verbose option) in default mpirun command. |
128 |
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o pkg/seaice/seaice_growth: |
129 |
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- catch potential division by zero in ITD code, does not change |
130 |
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verification results |
131 |
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o pkg/ecco: |
132 |
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- retire old codes to the Attic. The calls to retired functions are |
133 |
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left in a commented form in case they ever need to be re-activated. |
134 |
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- ecco_check.F: issue warning if any old CPP option is |
135 |
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defined that corresponds to retired codes -- then stop. |
136 |
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o pkg/atm_compon_interf: |
137 |
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- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
138 |
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coupler: use last time-step value instead of average over cplSendFrq_iter |
139 |
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time-step, similar to what is done for seaIceMass. |
140 |
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This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
141 |
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o eesupp & genmake2: |
142 |
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- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
143 |
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<= remove until a fix is found for some ifort version on ia32 machine. |
144 |
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o pkg/seaice/seaice_evp: |
145 |
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- refine residual computation |
146 |
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|
147 |
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checkpoint65q (2015/11/18) |
148 |
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o pkg/seaice/seaice_evp: |
149 |
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- fix residual computations so that they no longer affect the actual |
150 |
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simulation code |
151 |
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- fix seaice_readparams to be able to actually set new parameters |
152 |
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SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
153 |
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o model/src: |
154 |
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- fix wrong truncation (single prec) from "FLOAT" function in expressions |
155 |
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like: deltaT*FLOAT(myIter) when myIter is large: |
156 |
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a) replaced by DFLOAT (if not seen by TAF); |
157 |
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b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
158 |
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o pkg/aim_v23: |
159 |
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- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
160 |
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when pickupSuff is set ; do write rolling pickups + at the end of the run. |
161 |
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o pkg/atm_ocn_coupler + ocn_compon_interf: |
162 |
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- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
163 |
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coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
164 |
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add corresponding call in DO_OCEANIC_PHYS. |
165 |
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o coupler pkgs: |
166 |
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Start a new way to set-up optionally-exchanged variables (previously, only |
167 |
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there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
168 |
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data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
169 |
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send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
170 |
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compononent param default can be set accordingly). |
171 |
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Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
172 |
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but rather applies to a group a fields (going both ways like for DIC) |
173 |
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and corresponds to an option of coupling config. |
174 |
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coupler (pkg/atm_ocn_coupler): |
175 |
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- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
176 |
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and read namelist directly (without eessup S/R calls) instead of |
177 |
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in the very un-flexible old way, 1 param per line, in fixed order; |
178 |
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- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
179 |
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cleanly in CPL_CHECK_CPLCONFIG |
180 |
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- add new coupling-exchange selectors (some not yet active) including |
181 |
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cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
182 |
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and ocnCpl_exchange_DIC=T in OCNIDS.h); |
183 |
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- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
184 |
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component ; called directly from coupler.F, after comp. registrations; |
185 |
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- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
186 |
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atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
187 |
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-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
188 |
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components (pkg/atm_ & ocn_compon_interf): |
189 |
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- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
190 |
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CPP header file in all pkg source files. |
191 |
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- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
192 |
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ATM/OCN_CHECK_CPLCONFIG; |
193 |
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- add error-counter to track errors (e.g., in "data.cpl") and to stop |
194 |
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cleanly in ATM/OCN_CHECK_CPLCONFIG; |
195 |
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- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
196 |
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from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
197 |
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before PACKAGES_READPARMS; |
198 |
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verification/cpl_aim+ocn/: |
199 |
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- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
200 |
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"data.cpl" for coupler (in input_cpl). |
201 |
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o eesupp/inc: |
202 |
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- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
203 |
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#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
204 |
|
to always cumulate tile local-sum in the same order (still uses |
205 |
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MPI_Allreduce like standard code). |
206 |
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- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
207 |
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that are now identical to standard version (in eesupp/inc). |
208 |
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o pkg/shelfice: |
209 |
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- add SHELFICETransCoeffTFile for initializing spatially varying |
210 |
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heat and salt transfer coefficients |
211 |
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o pkg/atm_compon_interf & ocn_compon_interf: |
212 |
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- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
213 |
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S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
214 |
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- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
215 |
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o pkg/atm_ocn_coupler: |
216 |
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- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
217 |
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o pkg/rbcs: |
218 |
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- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
219 |
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to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
220 |
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- add a short report (to STDOUT) about RBCS-mask settings. |
221 |
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|
222 |
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checkpoint65p (2015/10/23) |
223 |
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o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
224 |
|
there is no adjoint test for EVP, we don't know what it does to the adjoint |
225 |
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solution, but at least there are no more recomputation warnings left |
226 |
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o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
227 |
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a chance of giving the same results as a fully converged VP (JFNK) solver |
228 |
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o tools/adjoint_options/adjoint_diva: |
229 |
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- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
230 |
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o pkg/streamice: |
231 |
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- spotted bug in streamice_driving_stress using dyG where should have been dxG |
232 |
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o pkg/exf: |
233 |
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- remove STOP statement that prevented to use wind or (wind-)stress |
234 |
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interpolation for constant-in-time forcing fields (wind/stress period = 0). |
235 |
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o pkg/seaice: |
236 |
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- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
237 |
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5 additionals 2D fields and 6 new store directives |
238 |
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- change logic in seaice_readparms.F: EVP code can now be turned on in |
239 |
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various ways, setting SEAICE_deltaTev is no longer required, |
240 |
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alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
241 |
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or SEAICEaEVPcoeff |
242 |
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o pkg/shelfice/shelfice_thermodynamics.F |
243 |
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- redefining uLoc/vLoc to u/v, instead of 2u/v |
244 |
|
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
245 |
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- this is an intermediate state of a truely converging EVP that has |
246 |
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the potential of outperforming implicit VP methods, I do not recommend |
247 |
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using it yet. |
248 |
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- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
249 |
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and all parameters are hardwired |
250 |
|
- for convergence it still requires very smooth regularisations, that means, |
251 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
252 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
253 |
|
specific averaging appears to be required, still subject to tuning |
254 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
255 |
|
- add code to compute and print residuals of iteration, compile with |
256 |
|
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
257 |
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o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
258 |
|
that entered with r1.54 on Sep04, 2015, -> update results |
259 |
|
|
260 |
|
checkpoint65o (2015/09/14) |
261 |
|
o pkg/mom_vecinv & mom_common: |
262 |
|
- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
263 |
|
called from there. |
264 |
|
- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
265 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
266 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
267 |
|
and Koenig-Beatty+Holland (2012) |
268 |
|
- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
269 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
270 |
|
- requires an extra input argument for S/R seaice_calc_viscosities |
271 |
|
- tensileStrength's depth dependence is different from Itkin et al. (2015) |
272 |
|
(to be changed and played with, for now exponential) |
273 |
|
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
274 |
|
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
275 |
|
by AREA according to Connelly et al. (2004), JPO. |
276 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
277 |
|
the only non-zero term in the denominator when there is no ice (which |
278 |
|
prevented running the model with zero ice-ocean drag). If |
279 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
280 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
281 |
|
consequence is that for open water, the momentum equation reduce |
282 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
283 |
|
they happen to be zero, often leading to a non-zero solution over |
284 |
|
open water. |
285 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
286 |
|
efficient EVP method. |
287 |
|
- introduce area-weighted averages for e12 (analogously to |
288 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
289 |
|
remain, but also changing the order of terms in the previous average |
290 |
|
changed the results as much) -> update experiment |
291 |
|
- add SEAICE_DELTA_SMOOTHREG code |
292 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
293 |
|
TEM-code |
294 |
|
- adjust loop bounds so that only required fields are computed |
295 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
296 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
297 |
|
results again), but will replace old code eventually |
298 |
|
o eesupp/src: |
299 |
|
- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
300 |
|
to always cumulate tile local-sum in the same order |
301 |
|
(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
302 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
303 |
|
and should be faster than GLOBAL_SUM_SEND_RECV code. |
304 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
305 |
|
(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
306 |
|
- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
307 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
308 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
309 |
|
natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
310 |
|
tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
311 |
|
|
312 |
|
checkpoint65n (2015/07/29) |
313 |
|
o pkg/thsice: |
314 |
|
- add a warning when used with pkg/aim but without updating SST |
315 |
|
(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
316 |
|
o pkg/offline: |
317 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
318 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
319 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
320 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
321 |
|
These changes allow: |
322 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
323 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
324 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
325 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
326 |
|
b) no needs to switch on staggerTimeStep anymore; |
327 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
328 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
329 |
|
o pkg/offline: |
330 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
331 |
|
can easily recover previous offset-iter effect by setting offset-time |
332 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
333 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
334 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
335 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
336 |
|
o OpenAD |
337 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
338 |
|
Config. with ggl90 currently diverges after 64 time steps |
339 |
|
so will need more work to become more stable |
340 |
|
- Adding preliminary kpp test to OpenAD verification. |
341 |
|
required small tweakes in kpp_routines.F |
342 |
|
- Merge and update from Krishna Narayanan's contrib area: |
343 |
|
* Add one variable for preliminary OpenAD DIVA |
344 |
|
* Add replacement time-stepping for OpenAD DIVA |
345 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
346 |
|
* required modifs for OAD_support |
347 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
348 |
|
o pkg/seaice: |
349 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
350 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
351 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
352 |
|
(no effect on EVP) |
353 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
354 |
|
o pkg/seaice: |
355 |
|
add new parameter SEAICE_deltaMin that is used ***only*** |
356 |
|
for regularizing Delta (and nothing else, like the parameter |
357 |
|
which is also used for all sorts of things SEAICE_EPS). |
358 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
359 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
360 |
|
the wrong key by inialising it before use -> fixes a recomputation |
361 |
|
problem but does not fix the gradient |
362 |
|
o pkg/layers: |
363 |
|
- move resetting of flux arrays to outside the iLa loop |
364 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
365 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
366 |
|
o pkg/layers: |
367 |
|
- remove from common block 3D layers fields (used to diagnose transport |
368 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
369 |
|
o pkg/seaice: |
370 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
371 |
|
in lab_sea forward experiment (changes results -> updated) |
372 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
373 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
374 |
|
computations; for SEAICE_VECTORIZE_LSR |
375 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
376 |
|
sweep to the outside, |
377 |
|
- remove store directives and add "CADJ loop sequential" directives |
378 |
|
in analogy to model/src/solve_tridiagonal.F |
379 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
380 |
|
boundaries to yield more readable code. This has also the charming side |
381 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
382 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
383 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
384 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
385 |
|
an additional option) |
386 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
387 |
|
but the adjoint gradients (which are affected by this change) still explode. |
388 |
|
o coupler (atm & ocn _compon_interf): |
389 |
|
- avoid using Exch2 IO mapping if not suitable. |
390 |
|
|
391 |
|
checkpoint65m (2015/06/15) |
392 |
|
o pkg/layers: |
393 |
|
- clean-up old parameters setting (from Sep 2012): |
394 |
|
+ remove old parameters setting from common block (declared locally); |
395 |
|
+ stop if any old parameter is mixed with new parameters; |
396 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
397 |
|
- check that layers_bounds for Pot.Density are in the right range; |
398 |
|
this is supposed to catch un-updated setting after recently shifting |
399 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
400 |
|
o pkg/layers: |
401 |
|
- Added missing call to layers_fill for keeping track of tottend in |
402 |
|
pkg/diagnostics/diagnostics_fill_state.F |
403 |
|
o pkg/layers: |
404 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
405 |
|
of diapycnal fluxes |
406 |
|
o pkg/layers: |
407 |
|
- reverted changes to interpolation to previous treatment; there |
408 |
|
was never actually a problem |
409 |
|
o pkg/layers: |
410 |
|
- fix interpolation of layers tracers in the presence of partial cells |
411 |
|
- add lots of new functionality to compute water mass transformation |
412 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
413 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
414 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
415 |
|
for layers_thermodynamics calculations |
416 |
|
o pkg/ptracers: |
417 |
|
- add capability of stepping a passive tracer forward without advection |
418 |
|
by setting PTRACERS_advScheme to 0. |
419 |
|
o pkg/diagnostics: |
420 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
421 |
|
o pkg/layers: |
422 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
423 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
424 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
425 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
426 |
|
o pkg/layers: |
427 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
428 |
|
- fix calculation of layer non-weighted velocity and layer probability |
429 |
|
- add diagnostics for pot.density used for layer averaging |
430 |
|
o pkg/seaice: |
431 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
432 |
|
positiveness, modify a few comments and improve variable names, |
433 |
|
- the changed computation of deltaC affects most seaice-related |
434 |
|
experiments at the truncation level. |
435 |
|
seaice_itd.thermo is affected by far the most, with |
436 |
|
only 7 digits of agreement remaining; update experiments. |
437 |
|
|
438 |
|
checkpoint65l (2015/05/04) |
439 |
|
o pkg/shelfice: |
440 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
441 |
|
factor drKp1 to zero where it is negative (ie. do not use |
442 |
|
SHELFICEBoundaryLayer if hFacC>1) |
443 |
|
- the same for factor drLoc in shelfice_forcing.F |
444 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
445 |
|
with modules in ptracers, when using testreport option "-small_f" |
446 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
447 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
448 |
|
o verification/testreport |
449 |
|
- add new option -small_f |
450 |
|
with this option testreport first makes the target small_f (*.f files) |
451 |
|
before running make (all). This is useful for explicit inlining when |
452 |
|
all sources need to be full available. |
453 |
|
o pkg/exf/exf_interp.F: |
454 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
455 |
|
|
456 |
|
checkpoint65k (2015/04/01) |
457 |
|
o pkg/ecco: |
458 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
459 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
460 |
|
instead of active read/write |
461 |
|
o pkg/ctrl: |
462 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
463 |
|
instead of active read/write. |
464 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
465 |
|
return if .NOT.useAUTODIFF |
466 |
|
o pkg/seaice: add CPP brackets (cost function related). |
467 |
|
o model/src: |
468 |
|
add useAUTODIFF run time switch. |
469 |
|
o pkg/exf/exf_interp.F: |
470 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
471 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
472 |
|
this feature. |
473 |
|
o verification/testreport: |
474 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
475 |
|
implementations of grep that cannot do contextual searches |
476 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
477 |
|
of "cat" have the option "-n" |
478 |
|
o model/src: |
479 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
480 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
481 |
|
convert from conservative to potential temperature. For now they are not |
482 |
|
called anywhere. |
483 |
|
o pkg/ggl90: make "useIDEMIX" useful |
484 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
485 |
|
are different for idemix into separate loops (changes verification |
486 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
487 |
|
- requires 2 new 2D fields KappaM, verticalShear |
488 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
489 |
|
s/r ggl90_idemix |
490 |
|
- fix and improve some comments |
491 |
|
|
492 |
|
checkpoint65j (2015/02/25) |
493 |
|
o pkg/openad |
494 |
|
- synchronize seawater.F with version in model/src: replace routine |
495 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
496 |
|
o pkg/mnc: |
497 |
|
- change default value of pickup_read/write_mnc params to FALSE |
498 |
|
(since few features are missing in reading MNC pickup files). |
499 |
|
o model/src: |
500 |
|
- change default (background) vertical diffusivity for salt to be the |
501 |
|
temperature (background) vertical diffusivity. |
502 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
503 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
504 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
505 |
|
consistent with vertical mixing schemes. |
506 |
|
o verification/testreport: |
507 |
|
- fix typo in "-pcls" option ; |
508 |
|
- put temp files in /tmp (instead of in local dir) |
509 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
510 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
511 |
|
o pkg/ggl90 (idemix code): |
512 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
513 |
|
global_ocean.90x40x15.idemix |
514 |
|
o OpenAD |
515 |
|
- enable active file I/O and begin removal of work-around code |
516 |
|
for OpenAD for handling control variables (memory vs. active files) |
517 |
|
- new CPP options file OPENAD_OPTIONS.h |
518 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
519 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
520 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
521 |
|
o tools/genmake2: |
522 |
|
- add option for an alternative Makefile (from Martin) where multiple |
523 |
|
source files are sent to TAF (instead of all in one file). |
524 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
525 |
|
- code provided by Carsten Eden as an extension of ggl90 |
526 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
527 |
|
compile time; a runtime flag implementation is not yet complete |
528 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
529 |
|
o verification: |
530 |
|
- reduce length of the AD test run by half for experiments |
531 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
532 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
533 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
534 |
|
o verification/testreport: |
535 |
|
- fix two non-POSIX sed statements so that there are no error messages |
536 |
|
on Mac OS X |
537 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
538 |
|
o model/src/seawater.F: |
539 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
540 |
|
(following the matlab code), which would have avoided the bug caught |
541 |
|
by Matt (see below) in the first place |
542 |
|
o pkg/shelfice: |
543 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
544 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
545 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
546 |
|
ice-shelf case (i.e., within surface level). |
547 |
|
- add config summary in shelfice_check.F |
548 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
549 |
|
variable recip_latentHeat |
550 |
|
- introduce diagnostics for friction velocity uStar (in case of |
551 |
|
SHELFICEuseGammaFrict) |
552 |
|
- change verification experiment isomip.htd: |
553 |
|
+ start from pickup (as input_ad at nIter0=8640) |
554 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
555 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
556 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
557 |
|
o model/src: |
558 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
559 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
560 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
561 |
|
o pkg/shelfice: |
562 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
563 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
564 |
|
ice-shelf is. |
565 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
566 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
567 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
568 |
|
for thermodynamic calculations |
569 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
570 |
|
affects results of some verification experiments by up to 4 digits: |
571 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
572 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
573 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
574 |
|
-> updated |
575 |
|
|
576 |
|
checkpoint65i (2015/01/23) |
577 |
|
o model/src: |
578 |
|
- change units of frictionHeating field from W to W/m^2 |
579 |
|
- fix bug in frictional heating from stratospheric drag in |
580 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
581 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
582 |
|
field from load_fields_driver.F to thermodynamics.F ; |
583 |
|
- add diagnostics for frictional heating. |
584 |
|
o model/src & gmredi K3D: |
585 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
586 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
587 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
588 |
|
and name in pickup file). |
589 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
590 |
|
o model/src: |
591 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
592 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
593 |
|
(since Nov 2012) with option selectAddFluid=1. |
594 |
|
o pkg/shelfice: |
595 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
596 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
597 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
598 |
|
o pkg/seaice: two new runtime parameters: |
599 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
600 |
|
long overdue |
601 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
602 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
603 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
604 |
|
for LSR: move checking overlaps out of JFNK-if-block |
605 |
|
o pkg/atm_phys: |
606 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
607 |
|
new S/R ATM_PHYS_DYN2PHYS. |
608 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
609 |
|
fixed-in-time pressure levels). |
610 |
|
o pkg/mom_common (bottomdrag): |
611 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
612 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
613 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
614 |
|
o pkg/shelfice (u/v_drag): |
615 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
616 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
617 |
|
(now similar to shelfice_u_drag.F) |
618 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
619 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
620 |
|
o pkg/mom_common (bottomdrag): |
621 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
622 |
|
- add options for alternative discretisation of velocity norm in quadratic |
623 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
624 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
625 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
626 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
627 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
628 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
629 |
|
off by default since this also reduces model stability (explicit bottom |
630 |
|
friction). Changes produce different machine truncation with linear-drag |
631 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
632 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
633 |
|
o model/src & mom pkgs: |
634 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
635 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
636 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
637 |
|
just copy level Nr value to level Nr+1. |
638 |
|
o doc: |
639 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
640 |
|
o pkg/streamice: |
641 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
642 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
643 |
|
from array shelficemassinit, which is set in init_fixed and |
644 |
|
has option to be set from file; introduce array |
645 |
|
shelficeMassDynTend array, set thru file in init_fixed |
646 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
647 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
648 |
|
pkg/streamice |
649 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
650 |
|
SHELFICEMassStepping = .true. |
651 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
652 |
|
|
653 |
checkpoint65h (2014/12/17) |
checkpoint65h (2014/12/17) |
654 |
o verification/global_ocean.90x40x15, global_ocean_ebm: |
o verification/global_ocean.90x40x15, global_ocean_ebm: |
655 |
- update to generic controls. |
- update to generic controls. |