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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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|
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o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
8 |
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testreport accordingly |
9 |
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|
10 |
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checkpoint58e_post |
11 |
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o SEAICE_CGRID adjoint done |
12 |
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o R_STAR adjoint implemented. |
13 |
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* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
14 |
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* need to sort out init. of h0facc, etc. |
15 |
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o Make pkg/profile fully independent of ecco,cost, etc. stuff |
16 |
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to be able to use it in pure forward. |
17 |
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|
18 |
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checkpoint58d_post |
19 |
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o upgrade simple test-experiment to tutorial example: |
20 |
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step.1: duplicate the experiment and (step.2) will remove the old copy. |
21 |
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tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
22 |
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tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
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tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
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tutorial_global_oce_biogeo <- copy of dic_example |
25 |
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tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
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tutorial_plume_on_slope <- copy of plume_on_slope |
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tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
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tutorial_global_oce_optim <- empty for now (David ?) |
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tutorial_global_oce_in_p <- copy of global_ocean_pressure |
30 |
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some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
31 |
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o correct a sign problem in cost_scat.F |
32 |
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o obcs and ptracers: fix boundary conditions for advections schemes |
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with larger stencil |
34 |
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o thsice adjoint: start |
35 |
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o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
36 |
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completeness |
37 |
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o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
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and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
39 |
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o ptracers adjoint: |
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* avoid extensive recomputatations |
41 |
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* fix missing re-init. of gptr (missed by TAF) |
42 |
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o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
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me to turn off the excessive output to STDOUT that this package produces |
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o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
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and add those terms in Vector-Invariant formulation. |
46 |
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o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
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if the control period (xx_hfluxperiod etc) is 0 |
48 |
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o in profiles pkg, clean routines and fix details |
49 |
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o in ecco pkg, reading ssh data: |
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fix problem in case the model does not start at iter0=0 |
51 |
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o fix mnc-pickup/restart for ptracers |
52 |
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o new package prifiles: |
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code to compute profile-based cost by Gael Forget |
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(modifs in ecco, ctrl, autodiff) |
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o Benign bug fix in initialization (spotted by M. Mazloff) of |
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ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
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|
58 |
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checkpoint58c_post |
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o adjoint: finish NLFS adjoint and provide reference output in |
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verification/global_ocean.90x40x15/results_ad_nlfs |
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o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
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documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
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SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
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with SEAICE_CGRID defined. |
65 |
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o move calendarDumps from "data" to "data.cal" and clean-up the code |
66 |
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with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
67 |
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o add useEXF & useCAL flags (for now, set in hard-coded way) |
68 |
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o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
69 |
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(were missing in NH mode, and wrong in quasihydrostatic mode). |
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waiting for Chris updated version of calc_gw to add those CALLs. |
71 |
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o fix bug in quasihydrostatic S/R ; |
72 |
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add a test for this option: global_ocean.90x40x15.qshyd |
73 |
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o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
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(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
75 |
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o add on/off flag useOffLine for package OFFLINE |
76 |
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o seaice: |
77 |
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- modify advection so that it works also on the C-grid |
78 |
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- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
79 |
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problem in multi-tile runs with C-grid |
80 |
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- add flags for clipping ice velocities and/or masking solver forcing |
81 |
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- fix drag (ocean on ice) formulation and a bug that caused noise in the |
82 |
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C-grid solver |
83 |
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- added a few comments to seaice_diffusion.F |
84 |
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- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
85 |
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are now exclusive) |
86 |
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- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
87 |
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required re-ordering the code a little: |
88 |
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+ make DAIRN global variable (defined in SEAICE) |
89 |
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+ move computation of the viscosities eta and zeta into a new separate |
90 |
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routine (because I need to recompute them in seaice_ocean_stress.F) |
91 |
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|
92 |
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checkpoint58b_post |
93 |
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o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
94 |
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update output.txt of exp. aim.5l_cs.thSI |
95 |
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o various mnc cleanups and improvements: |
96 |
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+ shrink lookup tables by factor of ~4 |
97 |
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+ better error reporting when running out of lookup space |
98 |
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+ able to handle longer path/file names (up to 500 chars) |
99 |
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o adjoint: |
100 |
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- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
101 |
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- TBD: "hidden" mom_vecinv recomp. in dynamics |
102 |
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o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
103 |
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(allow to differentiate between forcing components using new integer flags: |
104 |
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momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
105 |
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and add new flag to put Dissipation tendency out of Adams-Bashforth. |
106 |
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o ecco |
107 |
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- enable trend removal from SSH anomaly obs. |
108 |
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o adjoint |
109 |
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- a fix for PmEpR when #undef EXACT_CONSERV |
110 |
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- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
111 |
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- try to fix "hidden" recomp. in forward_step for NLFS |
112 |
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(NLFS seems broken sometimes after I checked it in) |
113 |
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o seaice: |
114 |
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- add c-grid version of the dynamic solver: |
115 |
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+ three new routines that are the c-grid substitute lsr, dynsolver |
116 |
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and ostres |
117 |
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+ put a few fields that were local to dynsolver into global common |
118 |
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blocks, so that I can move the computation of stresses etc into |
119 |
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seaice_lsr (saves coding but may break the adjoint). |
120 |
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- replace more hardwired parameters by runtime parameters |
121 |
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- add ice masks that mask the rhs of the implicit solvers where there |
122 |
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is no ice (commented out in seaice_dynsolver, because i am not sure |
123 |
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if this works properly), eventually this should replace the clipping |
124 |
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of ice velocities in seaice_dynsolver to +/-40cm/s. |
125 |
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o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
126 |
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include it only where its needed |
127 |
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o move balancing of fluxes before the call of external_forcing_surf |
128 |
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o seaice: |
129 |
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- correct units of turning angles (now they are really in degrees) |
130 |
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- move computation of GWATX/Y out of main routine into dynsolver |
131 |
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- initialize GWATX/Y in seaice_init |
132 |
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o Apply mask on Fresh-Water flux (needed for SSH forcing). |
133 |
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update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
134 |
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o seaice: add runtime flags for turning angles (default to zero) |
135 |
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o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
136 |
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and trend from exf forcing and ctrl control adjustments |
137 |
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o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
138 |
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(since checkpoint57x_post) |
139 |
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o change the default rotation period to 86164.s = the Earth rotation |
140 |
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o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
141 |
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and based on a reference stratification. Tested within hs94.cs-32x32x5. |
142 |
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o seaice advection: add code for choosing between the default (2nd order |
143 |
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central differences) and multiDim advection schemes provided by |
144 |
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pkg/generic_advdiff |
145 |
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o seaice: |
146 |
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- removed all references to SEAICE_GRID.h fields from |
147 |
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dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
148 |
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(cubed-sphere configuration will change a little) |
149 |
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- grid computations in seaice_init are obsolete now. |
150 |
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- cleaned up code a little so that is easier to read (hopefully). |
151 |
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- added new (better?) discretizations of default advection and diffusion |
152 |
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(turn on with SEAICEuseFluxForm) |
153 |
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- replace 1 in 3d global fields by kSurface in growth.F |
154 |
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|
155 |
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checkpoint58a_post |
156 |
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o seaice: |
157 |
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- bug fix in advect.F |
158 |
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o shelfice: |
159 |
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- separate shelfice load anomaly from pload (breaks with time |
160 |
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dependent forcing), => introduce constant field shelficeLoadAnomaly. |
161 |
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Its default is 0., but it may be computed more cleverly from (unknown) |
162 |
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t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
163 |
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done offline. A good approximation of the pressure load anomaly is |
164 |
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necessary to avoid large initial adjustment processes underneath |
165 |
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deep-reaching shelfice. |
166 |
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- small fix in ISOMIP shelfice_thermodynamics |
167 |
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- add more sophisticated thermodynamics of Hellmer (1989), this is |
168 |
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now the default |
169 |
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- give a few constants more intuitive names |
170 |
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o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
171 |
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if bulk formulae are used in long integration (especially EmPmR). Turn |
172 |
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on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
173 |
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if balancePrintMean, the imbalance that is substracted is printed to |
174 |
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STDOUT. |
175 |
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o fix bug (typo) in obcs_apply_eta.F |
176 |
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o add a new package shelfice which enables us to model the circulation |
177 |
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underneath shelf-ice with draughts of hundreds of meters. |
178 |
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- works |
179 |
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- to do: + include improved thermodynamics |
180 |
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+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
181 |
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instead of new field kTopC |
182 |
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+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
183 |
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instead of new field R_shelfIce and new code in ini_depth.F |
184 |
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and ini_mask_etc.F? |
185 |
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+ adjust vertical mixing schemes? |
186 |
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o seaice pkg: |
187 |
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- add a cpp-flag to include a simple formula for a salinity dependent |
188 |
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freezing point of sea water at the surface |
189 |
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- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
190 |
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meridional stresses are now different (and hopefully correct) |
191 |
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o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
192 |
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update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
193 |
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and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
194 |
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o pkg/diagnostics: add options and parameters for regional-statistics |
195 |
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diagnostics ; define regions by reading a region-mask from a file |
196 |
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(might add other options later) |
197 |
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o pkg/bulk_force: |
198 |
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- add option and parameters to use AIM surface-flux formulae. |
199 |
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- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
200 |
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others forcing fields (defined in PARM05, parameter file "data") are loaded |
201 |
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from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
202 |
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- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
203 |
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- use the right EXCH call for uwind,vwind (to work on CS-grid). |
204 |
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- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
205 |
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and parameters (note: calcWindStress replaces .NOT.readwindstress). |
206 |
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- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
207 |
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|
208 |
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checkpoint58 |
209 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
210 |
|
tools can be compiled (as determined by genmake2) will turn on the |
211 |
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embed_files package which then embeds the entire MITgcm source code |
212 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
213 |
|
- requested by CNH but off by default |
214 |
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- adds a paltry <9MB to the mitgcmuv executable in most cases |
215 |
|
- only writes the output when useEMBEDSRC in eedata is true |
216 |
|
o clean up 3-dim. relaxation codes: |
217 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
218 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
219 |
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* Thanks to Tom Haine for testing! |
220 |
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|
221 |
|
checkpoint57z_post |
222 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
223 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
224 |
|
o fix the pickup behavior for obcs in combination with ptracers |
225 |
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o fix a bug in ptracers_external_fields_load |
226 |
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o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
227 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
228 |
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o transfered surface NH pressure to eta field (if exactConserv). |
229 |
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o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
230 |
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and update lab_sea output.txt file. |
231 |
|
o completing 3-dim. relaxation code: additional term |
232 |
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1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
233 |
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in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
234 |
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* At compile time, in "EXF_OPTIONS.h" set |
235 |
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#define ALLOW_CLIMTEMP_RELAXATION |
236 |
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#define ALLOW_CLIMSALT_RELAXATION |
237 |
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* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
238 |
|
tauThetaClimRelax3Dim = 15552000.0, |
239 |
|
tauSaltClimRelax3Dim = 15552000.0, |
240 |
|
* 3 cases: |
241 |
|
1) Use a constant-in-time 3-dim. field |
242 |
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2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
243 |
|
3) Real-time relax. to time-evolving prescribed field |
244 |
|
o Adding Laplacian-type smoothness constraint on |
245 |
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initial and boundary (forcing) controls (ic, bc) |
246 |
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* enable at compile-time via |
247 |
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ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
248 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
249 |
|
* Absolute scale somewhat unclear so far |
250 |
|
* no area weighting was included since no other cost term does so far |
251 |
|
|
252 |
|
checkpoint57y_post |
253 |
|
First step for a NLFS adjoint |
254 |
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o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
255 |
|
o new init. routines for calc_r_star, calc_surf_dr |
256 |
|
o still need to deal with ini_masks_etc |
257 |
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o testreport seemed happy |
258 |
|
checkpoint57y_pre |
259 |
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|
260 |
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o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
261 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
262 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
263 |
|
o cfc fixes for final year of integration |
264 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
265 |
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be in GCHEM_OPTIONS). |
266 |
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|
267 |
|
checkpoint57x_post |
268 |
|
o fix testreport Pb in multiple test experiment. |
269 |
|
o cleanup our namelist syntax in verification: |
270 |
|
- make it more F95 standards compliant (some work still needed) |
271 |
|
- allows the vast majority of our tests to work with gfortran |
272 |
|
o Non-Hydrostatic: |
273 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
274 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
275 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
276 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
277 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
278 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
279 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
280 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
281 |
|
o remove some unused variables (reduces number of compiler warnings) |
282 |
|
o adjoint |
283 |
|
* Disable useVariableViscosity for adjoint for time being |
284 |
|
(there are a number of extensive recomputations) |
285 |
|
* Initialize certain variables needed for adjoint |
286 |
|
|
287 |
|
checkpoint57w_post |
288 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
289 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
290 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
291 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
292 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
293 |
|
o tracer advection scheme: |
294 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
295 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
296 |
|
was not very convenient). |
297 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
298 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
299 |
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
300 |
and sRef for convenience, handy, when you want to initialize |
and sRef for convenience, handy, when you want to initialize |
301 |
ptracers in a large domain with a constant non-zero value. Also, |
ptracers in a large domain with a constant non-zero value. Also, |