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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/shelfice: |
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- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
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with SHELFICEtopoFile in data.shelfice |
10 |
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- move code for reading ice shelf topography and modifying hFacC into separate |
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subroutines of the shelfice package |
12 |
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- separate initialisation of "fixed" and "variable" variables |
13 |
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- kTopC is not (yet) replaced by kSurfC, although this is possible |
14 |
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o fix a bug in diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
15 |
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o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
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and rename: |
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ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
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ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
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o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
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|
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checkpoint61c |
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o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
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to add mass source/sink of fluid in the interior (3-D generalisation |
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of oceanic real-fresh water flux). |
25 |
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o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
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o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
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o new pkg: down_slope |
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density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
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- presently, modify T & S inland (dwnslp_calc_rho.F). |
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can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
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- implementation for ocean in P-coords not tested. |
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- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
33 |
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o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
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(to facilitate conversion of oceanic pkg to p-coordinate). |
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o change FIND_RHO to FIND_RHO_2D : |
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pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
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o new pkg: cheapaml |
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|
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checkpoint61b |
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o exch2: |
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change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
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- no longer depend on the order sequence (N,S,E,W). |
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- 3rd exchange no longer needed (tested with 24 tiles). |
44 |
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- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
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- exch_UV_A-grid readily available (but not yet tested). |
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comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
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(both are no longer needed) in exch_uv: no effect in forward run; but |
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get truncation error differences with adjoint exch. |
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o exch2: |
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- change index-bounds storage (moved from target to local tile, |
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more intuitive this way) ; rename/remove some variables. |
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- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
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|
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checkpoint61a |
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o exch2/matlab-topology-generator: |
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fix bug in index bounds for N-S internal exchange (hard to tell if this |
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had any effect on the solution). |
58 |
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o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
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is exceeded |
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o testreport: modify syntax of awk, so that it works also with |
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awk, and not only with nawk and gawk |
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|
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checkpoint61 |
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o autodiff |
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Change default for TAF usage by removing argument '-nonew_arg' |
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This changes TAF subroutine argument list (ordering of active var.) |
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Omission of this flag leads to incompatibility w.r.t. TAMC |
68 |
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To restore TAMC-compatibility, need following modifs: |
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* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
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* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
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Tested TAF version is 1.9.22 |
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N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
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|
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checkpoint60 |
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--->>> This is the last checkpoint for which generating the adjoint |
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--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
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--->>> by default. |
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--->>> Future checkpoints will ommit this flag by default. |
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o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
80 |
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o pkg/grdchk: Add gradient check to etan0 perturbations. |
81 |
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o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
82 |
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o pkg/autodiff: more flexibility in zeroadj. |
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model/src: modifying do_oceanic_phys.F accordingly. |
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o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
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o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
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special setup of gmredi for which the adjoint is stable |
87 |
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enough for parameter optimization. |
88 |
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o bridging the gap between eddy stress and GM. |
89 |
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-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
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along with a change in CPP option (now ALLOW_EDDYPSI). |
91 |
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-> when using GM w/ GM_AdvForm: |
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The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
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is applied either in the tracer Eq. or in momentum Eq. |
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depending on data.gmredi (intro. GM_InMomAsStress). |
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-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
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The key modifications are in model/src/taueddy_external_forcing.F |
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pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
98 |
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|
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checkpoint59r |
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o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
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from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
102 |
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fix option to read coriolis(@ cell-corner) from files with CS-grid. |
103 |
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o pkg/mnc: add some attributes to standard 1D-coordinate variables |
104 |
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o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
105 |
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mass points, when using mnc for output |
106 |
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- add runtime parameter (missing_value, missing_value_int) to override |
107 |
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default (which is the value of getcon('UNDEF')) |
108 |
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o pkg/mnc: prepare mnc for the actual use of missing values with the |
109 |
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diagnostics package: small fix in mnc_cw_readwrite.template and more |
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initialisation of never used fields |
111 |
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- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
112 |
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versions |
113 |
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o pkg/thsice/thsice_ini_vars.F added default initial values so that |
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thermodynamics sea ice solver does not blow up when some initial fields |
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are missing. |
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o move from external_forcing_surf.F to ini_forcing.F |
117 |
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the p-coord. hack consisting in using pLoad to set phi0surf ; |
118 |
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update output of tutorial_global_oce_in_p (affected @ truncation level). |
119 |
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o Freshen up a bit hs94.1x64x5, notably: |
120 |
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remove rotationPeriod and tRef=5*0. (adjoint only), and add |
121 |
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exactConserv=.TRUE. |
122 |
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o pkg/generic_advdiff: |
123 |
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change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
124 |
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applies to files where Temperature & Salinity 2nd Order moments are used. |
125 |
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o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
126 |
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this uses a dynamically allocated internal state data structure |
127 |
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(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
128 |
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and requires a fortran 90 compiler |
129 |
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|
130 |
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checkpoint59q |
131 |
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o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
132 |
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(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
133 |
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o Refresh tutorial_global_oce_biogeo, notably: |
134 |
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- change bathymetry (put back seamounts in ACC, use hFacs) |
135 |
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- change EOS (POLY3 --> JMD95Z) |
136 |
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- use Bryan-Lewis vertical diffusivity |
137 |
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- use multidimensional advection |
138 |
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- remove old virtual virtual in dic pkg, now done through ptracer pkg |
139 |
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- change a couple of parameters in dic pkg |
140 |
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o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
141 |
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o pkg/obcs: change default to OBCSfixTopo = .true., |
142 |
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- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
143 |
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- replace "debugMode" with "debugLevel .GE. debLevB" |
144 |
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o implementation of TAF directives for gchem,cfc,dic |
145 |
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o remove "exp5" (replaced by tutorial_deep_convection). |
146 |
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o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
147 |
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this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
148 |
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the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
149 |
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--> changes results in exp4, seaice_obcs |
150 |
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o tutorial_deep_convection : |
151 |
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update the set-up and increase resolution and domain size ; start |
152 |
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from pseudo initial conditions = output at t=120mn in order to see |
153 |
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something happening when running testreport. |
154 |
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o pkg/seaice: add os7mp as an advection scheme |
155 |
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add check for advection schemes |
156 |
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add a flag for restoring T and S underneath sea ice |
157 |
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o pkg/my82: add netcdf-support and diagnostics |
158 |
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o thsice pkg: |
159 |
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- Now hsMax limits snow height by turning it into ice following |
160 |
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flooding scheme (and now conserving energy) |
161 |
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- Slight rewriting of the formula in thsice_calc_thick.F |
162 |
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- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
163 |
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--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
164 |
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|
165 |
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checkpoint59p |
166 |
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o gchem / dic / cfc : |
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- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
168 |
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- add new parameter files: "data.dic" & "data.cfc" ; |
169 |
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- various re-arrangement in initialisation & header file ; |
170 |
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- fix tutorial_global_oce_biogeo for multi-threaded test. |
171 |
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o pkg/dic: test for "pickup_dic" file when restarting ; |
172 |
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if no pickup-file, can restart with a re-initialised pH (same as it did |
173 |
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before) providing pickupStrictlyMatch is set to False. |
174 |
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o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
175 |
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+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
176 |
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o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
177 |
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and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
178 |
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o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
179 |
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& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
180 |
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(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
181 |
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o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
182 |
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scheme to use for vorticty-term ; |
183 |
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- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
184 |
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(with default selectVortScheme, return to original discretisation) |
185 |
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- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
186 |
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o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
187 |
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o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
188 |
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bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
189 |
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also fix diagnostics VISCAHW & VISCA4W. |
190 |
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|
191 |
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checkpoint59o |
192 |
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o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
193 |
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o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
194 |
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move a few statemens out the main loop into separate loops |
195 |
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o pkg/shelfice: |
196 |
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- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
197 |
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(kg/m^2/s), does not break tests, because in verification/isomip, |
198 |
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rhoConstFresh=rhoConst (by accident) |
199 |
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- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
200 |
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- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
201 |
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new file model/src/seawater.F, so that they are available for all pkgs. |
202 |
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- convert potential temperature into in-situ temperature. This changes the |
203 |
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isomip tests => update tests |
204 |
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o add a flag writePickupAtEnd (default=true) to be able to suppress |
205 |
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writing a pickup at the last timestep |
206 |
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o tools/mpack-1.6 : |
207 |
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- disable automake (not working) and autoconf (not needed). |
208 |
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- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
209 |
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also cleaner with much less compilation warnings. |
210 |
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o pkg/profiles: |
211 |
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rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
212 |
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(for "less than 32 characters name" compiler requirement) |
213 |
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o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
214 |
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conditions that have a different sampling frequency than S/T/U/V obcs |
215 |
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o pkg/diagnostics (stats-diags): |
216 |
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- fix global Min/Max in case 1 processor get only empty tiles |
217 |
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o genmake2: replace (4 times) |
218 |
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make genmake_tc_1.o >> genmake_warnings 2>&1 |
219 |
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with |
220 |
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COMM="$CC $CFLAGS -c genmake_tc_1.c" |
221 |
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echo $COMM >> genmake_warnings |
222 |
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$COMM >> genmake_warnings 2>&1 |
223 |
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to make genmake2 always see the value of CC as specified in the optfile. |
224 |
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o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
225 |
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- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
226 |
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- modify verification advect_cs test to test SOM-advection on CS-grid. |
227 |
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o pkg/ctrl: |
228 |
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- Rewrite of ctrl_map_ini_ecco.F, |
229 |
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introducing a generic routine (ctrl_map_ini_gen.F). |
230 |
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- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
231 |
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|
232 |
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checkpoint59n |
233 |
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o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
234 |
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number in dedicate array "hdiag": |
235 |
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- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
236 |
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with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
237 |
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- many small changes (integer format) for large number of diagnostics |
238 |
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- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
239 |
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a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
240 |
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o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
241 |
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usingSphericalGrid, this allows to define the rotated grid coordinates |
242 |
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via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
243 |
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geographical coordinates according to the inverse of the rotation defined |
244 |
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by the Euler angles, so that Coriolis parameter and online-interpolation by |
245 |
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exf works with the geographical coordinates on XC/YC/XG/YG. |
246 |
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Naturally, this feature does not work with all packages, so some |
247 |
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combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
248 |
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profiles), because there the coordinates are assumed to be regular |
249 |
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spherical grid coordinates. |
250 |
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o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
251 |
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- introduce isopycnal diffusion coefficient control. |
252 |
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o tools/adjoint_options: |
253 |
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- additional control vector components. |
254 |
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o pkg/mnc: have mnc create marginally meaning full coordinate variables |
255 |
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(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
256 |
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o pkg/mypackage: |
257 |
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- add example of read/write pickup for state-var ; |
258 |
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- add entry points to the main code for state-vars diags & write-pickup. |
259 |
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o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
260 |
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transitions for useExfYearlyFields |
261 |
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- add new subroutine that determines the file to read from for |
262 |
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use*YearlyFields = .TRUE. and .FALSE. |
263 |
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- add a verification experiment to global_with_exf that tests |
264 |
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useExfYearlyFields with USE_EXF_INTERPOLATION defined |
265 |
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o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
266 |
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analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
267 |
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subroutines (which could be generated from a template, because they are |
268 |
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almost identical), for now they are included in obcs_prescribe_read.F for |
269 |
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simplicity |
270 |
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o pkg/exf: |
271 |
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- add a little more diagnostic to exf_interp_read (in analogy to |
272 |
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mds_read_field, can be turned off with debugLevel < debugLevA=1) |
273 |
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- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
274 |
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ugly but fast by unrolling short inner loops, inserting a unroll=8 |
275 |
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directive in routine lagran, and splitting a loop and making do while the |
276 |
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outermost loop (the latter requires the intoduction of index arrays) |
277 |
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o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
278 |
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o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
279 |
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http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
280 |
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o verification/seaice_obcs: updated for restart test and latest options |
281 |
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o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
282 |
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ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
283 |
|
for now this is only available for the C-grid code and also within |
284 |
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#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
285 |
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|
286 |
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checkpoint59m |
287 |
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o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
288 |
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and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
289 |
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o gad_som : fix flux output (& diagnostics) to have same units as other |
290 |
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advection scheme fluxes (was previously multiplied by deltaT). |
291 |
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o added verification/seaice_obcs both to test seaice open boundaries |
292 |
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and to provide an example matlab scrpt for generating them |
293 |
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o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
294 |
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o pkg/salt_plume: clean up salt_plume_frac.F to |
295 |
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remove redundancy in PlumeMethod 1 and 4 |
296 |
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o pkg/kpp: added saltplume diagnostics |
297 |
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o pkg/obcs and pkg/seaice: |
298 |
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- do not set uice and vice to zero when OB*icefile are unspecified |
299 |
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- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
300 |
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- moved seaice tracer obcs after call to seaice_growth |
301 |
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o pkg/salt_plume: added various options for salt plume depth |
302 |
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criterion and for vertical distribution of the salt |
303 |
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|
304 |
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checkpoint59l |
305 |
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o pkg/ptracers: new version of ptracers pickup: |
306 |
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read meta file and write only fields which are needed to restart. |
307 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
308 |
|
o pkg/seaice: |
309 |
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- add timescale for melting due to warm mixed layer as a means of |
310 |
|
setting SEAICE_availHeatFrac more conveniently |
311 |
|
- add a CPP-flag/runtime parameter check for flooding algorithm |
312 |
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- reformulated availHeat in seaice_growth.F to be independent of AREA |
313 |
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o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
314 |
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unit changes |
315 |
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o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
316 |
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o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
317 |
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SX vector computer. |
318 |
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o pkg/seaice: |
319 |
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- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
320 |
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seaice forcing fields can now be read only through pkg/exf |
321 |
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- removed some unused halos |
322 |
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o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
323 |
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o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
324 |
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or U/VICE from U/VWIND before computing U/VSTRESS |
325 |
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|
326 |
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checkpoint59k |
327 |
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o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
328 |
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dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
329 |
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o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
330 |
|
all experiments pass when compile with un-initialised var. checking option. |
331 |
|
o added pkg/salt_plume |
332 |
|
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
333 |
|
o pkg/seaice: new read/write pickup version. |
334 |
|
read meta file and write only fields which are needed to restart. |
335 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
336 |
|
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
337 |
|
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
338 |
|
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
339 |
|
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
340 |
|
process. Fixed here by closing the domain at the Northern boundary. |
341 |
|
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
342 |
|
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
343 |
|
a set of consecutive levels in/from a 3-D array. |
344 |
|
o pkg/ptracers: |
345 |
|
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
346 |
|
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
347 |
|
|
348 |
|
checkpoint59j |
349 |
|
o in pkgs: dic, obcs, offline, rbcs: |
350 |
|
standard way to compute coeff. for time interpolation between 2 time reccords |
351 |
|
which retains full precision (& make results less dependent on compiler). |
352 |
|
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
353 |
|
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
354 |
|
packages instead of reading ice cover and wind speed separately |
355 |
|
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
356 |
|
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
357 |
|
to allow to compile customized code before the update) |
358 |
|
o cleaning-up: |
359 |
|
- fix CPP instruction syntax in pkg/obcs |
360 |
|
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
361 |
|
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
362 |
|
- fix some threads issue in IO parts. |
363 |
|
o pkg/dic: |
364 |
|
- add tons of "_d 0" (--> much better testreports !) |
365 |
|
and then update outputs of tutorial_global_oce_biogeo |
366 |
|
o pkg/mom_fluxform: |
367 |
|
add a special version of momentum advection intended to conserve momentum |
368 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
369 |
|
o new read/write pickup version: |
370 |
|
- for now, only implemented for main (mdsio) pickup file. |
371 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
372 |
|
and main pickup together. |
373 |
|
- read meta file; read only what is needed to restart; stop if a field |
374 |
|
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
375 |
|
if it make sense (even if the restart is not perfect). |
376 |
|
- if no meta file, assume that pickup to read corresponds exactly to |
377 |
|
a pickup that would currently be written. |
378 |
|
- read pickup written in the old format (until checkpoint59i) if it |
379 |
|
recognizes an old meta file (no field-list). |
380 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
381 |
|
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
382 |
|
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
383 |
|
b) a meta file describing the content of the associated pickup file |
384 |
|
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
385 |
|
o pkg/mdsio & pkg/rw: |
386 |
|
- new routine to read a meta file ; new set of routine to read |
387 |
|
Multiple-fields file (with meta file). |
388 |
|
o added open boundary conditions capability for seaice |
389 |
|
HSNOW, HSALT, UICE, and VICE |
390 |
|
|
391 |
|
checkpoint59i |
392 |
|
o adjoint: |
393 |
|
* fix multiDimAdvection adjoint |
394 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
395 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
396 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
397 |
|
NLFS and multiDimAdvection using DST3 (=30) |
398 |
|
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
399 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
400 |
|
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
401 |
|
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
402 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
403 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
404 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
405 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
406 |
|
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
407 |
|
o pkg/monitor: |
408 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
409 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
410 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
411 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
412 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
413 |
|
thermodynamics |
414 |
|
- requires a little reorganization, which affects the testreport results |
415 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
416 |
|
so that now the conservative form is tested |
417 |
|
- add a few comments |
418 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
419 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
420 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
421 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
422 |
|
thermodynamic growth rates |
423 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
424 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
425 |
|
Affects results @ truncation level (cg2d match) and update output of |
426 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
427 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
428 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
429 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
430 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
431 |
|
|
432 |
|
checkpoint59h |
433 |
|
o pkg/exf: |
434 |
|
- improve vectorization by moving if-statement out of loops in |
435 |
|
exf_mapfields, exf_radiation |
436 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
437 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
438 |
|
o testreport: |
439 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
440 |
|
monitor & update offline_exf_seaice exp. output. |
441 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
442 |
|
o pkg/seaice: |
443 |
|
- bug fix in the evp solver: boundary conditions were affected be |
444 |
|
masking of zMax/zMin (changes results) |
445 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
446 |
|
(changes results for no_slip) |
447 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
448 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
449 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
450 |
|
stress formulation and no-slip boundary conditions |
451 |
|
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
452 |
|
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
453 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
454 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
455 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
456 |
|
without requiring DO-IF statements |
457 |
|
o pkg/thsice: |
458 |
|
use continuous power-law function for partition of energy between lateral |
459 |
|
melting/freezing and thinning/thickening ; old code using step function |
460 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
461 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
462 |
|
o testreport: change AD testing : check against results/output_adm.txt |
463 |
|
using same scripts as for forward test. |
464 |
|
|
465 |
|
checkpoint59g |
466 |
|
o adjoint testing: in preparation for changing testreport: |
467 |
|
- output format: cost and grad written on separated lines |
468 |
|
- ad output results in directory "results" (instead of "results_ad") |
469 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
470 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
471 |
|
o pkg/ecco: allow user defined cost function contributions |
472 |
|
o testreport: |
473 |
|
Allow to choose (per experiment) the list of tested output variables |
474 |
|
and the main variable (used to issue a pass/FAIL ) ; |
475 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
476 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
477 |
|
Also modify printing of summary: |
478 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
479 |
|
b) echo the list of tested variables in the individual summary.txt of |
480 |
|
each experiment. |
481 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
482 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
483 |
|
(but still depend on the tile decompostion of the domain). |
484 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
485 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
486 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
487 |
|
the solution to the stress coupling issues with the B-grid. |
488 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
489 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
490 |
|
o pkg/thsice: |
491 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
492 |
|
- fix reshaping of sea-ice just after advection: |
493 |
|
melt all the ice only if ice-volume is too small. |
494 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
495 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
496 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
497 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
498 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
499 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
500 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
501 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
502 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
503 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
504 |
|
-> update output.txt |
505 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
506 |
|
this affects truncation error: -> update output.txt of exp: |
507 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
508 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
509 |
|
|
510 |
|
checkpoint59f |
511 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
512 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
513 |
|
a bounded range (in forward mode) |
514 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
515 |
|
internal parameter controls, completements of implementations |
516 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
517 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
518 |
|
(not seem any difference in testing results). |
519 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
520 |
|
at face corners. |
521 |
|
o pkg/generic_advdiff: |
522 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
523 |
|
loop range indices for computing vertical advection tendency |
524 |
|
and do the calculation in the interior only (no overlap) ; |
525 |
|
for now, only implemented for SOM advection (to save CPU time). |
526 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
527 |
|
o exch2 adjoint |
528 |
|
First set of changes: |
529 |
|
- add exch2 hand-written adjoint templates |
530 |
|
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
531 |
|
This will require cleanup in pkg/autodiff/*.F |
532 |
|
(changed routines currently kept separate in verif. code/) |
533 |
|
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
534 |
|
that used to hide exch2 or cubed-sphere specific code |
535 |
|
(commented via 'cph-exch2') |
536 |
|
o pkg/seaice |
537 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
538 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
539 |
|
output of global_ocean.cs32x15.thsice . |
540 |
|
|
541 |
|
checkpoint59e |
542 |
|
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
543 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
544 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
545 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
546 |
|
(#ifdef ALLOW_SALT_PLUME) |
547 |
|
o gather_2d/scatter_2d: removed halo regions |
548 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
549 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
550 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
551 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
552 |
|
so maybe GM/Redi adjoint is now broken. |
553 |
|
o seaice adjoint |
554 |
|
* add AREA, HEFF, HSNOW as control variable |
555 |
|
(should not change lab_sea results) |
556 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
557 |
|
o pkg/seaice: |
558 |
|
* added computation of saltFlux in seaice_growth; |
559 |
|
For time being, sea ice salinity is assumed constant |
560 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
561 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
562 |
|
defaults to 0.0 in order to maintain backward compatibility. |
563 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
564 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
565 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
566 |
|
heat content used to melt or grow ice |
567 |
|
* commented out cap of HICE: it helps keep ice thinner |
568 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
569 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
570 |
|
|
571 |
|
checkpoint59d |
572 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
573 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
574 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
575 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
576 |
|
and change default value of parameter "GM_Small_Number"; |
577 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
578 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
579 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
580 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
581 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
582 |
|
o pkg/seaice: |
583 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
584 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
585 |
|
changes verification/lab_sea |
586 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
587 |
|
read, understand, and debug. This causes changes at the truncation level. |
588 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
589 |
|
part) of the LSR solver. Changes all LSR results. |
590 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
591 |
|
is initilized with small values - does not change lab_sea results. |
592 |
|
- added HsnowFile initialization capability |
593 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
594 |
|
initialization of pkg/smooth and application to control vector |
595 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
596 |
|
o dependencies: pkg/profiles requires pkg/cal |
597 |
|
o pkg/profiles: |
598 |
|
- added option ALLOW_PROFILES_GENERICGRID |
599 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
600 |
|
that interpolation information (grid points and coefficients) is provided |
601 |
|
within the netcdf input files. |
602 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
603 |
|
that allow you to prepare netcdf input files. |
604 |
|
- also modified: cleaner include statements, cleaner error print statements, |
605 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
606 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
607 |
|
o pkg/seaice: |
608 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
609 |
|
requires a new routine: seaice_diagnostics_fill.F |
610 |
|
- make sure that seaice does not move if not forced (pressure replacement |
611 |
|
method, Hibler and Ip, 1995), changes results |
612 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
613 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
614 |
|
It is turned off by default (=-1.), because it changes the results. |
615 |
|
- make it possible to read AREA from a file, too. |
616 |
|
|
617 |
|
checkpoint59c |
618 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
619 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
620 |
|
o pkg/thsice: |
621 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
622 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
623 |
|
o pkg/obcs: |
624 |
|
- bug fix for balance code |
625 |
o pkg/seaice: |
o pkg/seaice: |
626 |
- allow values of SEAICE_elaticParm > 1 |
- allow values of SEAICE_elasticParm > 1 |
627 |
- make lsr boundary conditions free slip (by default, changes results of |
- add new parameter SEAICE_evpTauRelax as an alternative |
628 |
lsr solver) |
to SEAICE_elasticParm |
629 |
- no slip boundary conditions for lsr will follow |
- make lsr boundary conditions free slip (by default), changes result |
630 |
|
- add code for no slip boundary conditions for lsr |
631 |
- set minimum of zeta to zero (and not 4e8) (changes results) |
- set minimum of zeta to zero (and not 4e8) (changes results) |
632 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
633 |
o change calculation of Visbeck K: |
o change calculation of Visbeck K: |
634 |
- no longer depend on tapering scheme; instead, compute slope (limited |
- no longer depend on tapering scheme; instead, compute slope (limited |
635 |
by GM_maxSlope). this is equivalent to what was comuted before with |
by GM_maxSlope). this is equivalent to what was comuted before with |
636 |
clipping or linear tappering. |
clipping or linear tappering. |
637 |
- fix vertical averaging (wrong by 1 level) |
- fix vertical averaging (wrong by 1/2 level) |
638 |
- leave the old version (but will not be maintained) within |
- leave the old version (but will not be maintained) within |
639 |
#ifdef OLD_VISBECK_CALC / #endif |
#ifdef OLD_VISBECK_CALC / #endif |
640 |
|
- update output of exp. ideal_2D_oce |
641 |
o change error catch in calc_r_star to improve vectorization |
o change error catch in calc_r_star to improve vectorization |
642 |
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
643 |
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
644 |
|
o adjoint: |
645 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
646 |
|
(but with modifs/completions/cleanups) |
647 |
|
Storing is now bundled into large arrays to optimized I/O |
648 |
|
(and second step in cleanup of the_main_loop) |
649 |
|
|
650 |
checkpoint59b |
checkpoint59b |
651 |
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
699 |
o pkg/thsice: |
o pkg/thsice: |
700 |
fix few little problems, in thsice_calc_thickn.F: |
fix few little problems, in thsice_calc_thickn.F: |
701 |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
702 |
- melt laterally only if hIce < hThinIce (as the comments say) |
- melt only laterally if hIce < hThinIce (as the comments say) |
703 |
and in thsice_extend.F: |
and in thsice_extend.F: |
704 |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
705 |
- start to form ice as soon as the minimum ice-volume is reachable. |
- start to form ice as soon as the minimum ice-volume is reachable. |
736 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
737 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
738 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
739 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
740 |
|
are no longer updating the vertical diffusivity array |
741 |
|
(passed as argument) but are (re-) setting those arrays. |
742 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
743 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
744 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |