| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
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|
| 7 |
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o pkg ggl90: |
| 8 |
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- in ggl90_cal.F: compute only one set of visc/diff, used to |
| 9 |
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step forward TKE/T/S/momentum |
| 10 |
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- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
| 11 |
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have Prandlt =1) |
| 12 |
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o gmredi(fm07): |
| 13 |
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- add lower limit on Transition layer thickness + lower limit on 1/lambda |
| 14 |
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- allow to set few more params from data.gmredi |
| 15 |
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o pkg ggl90: |
| 16 |
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- add missing sqrt(2) factor in computation of mixing length |
| 17 |
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scale in ggl90_calc.F |
| 18 |
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(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
| 19 |
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|
| 20 |
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checkpoint61d |
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o adjoint modifs |
| 22 |
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- adapt to new field rhoInSitu |
| 23 |
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- allow to revert from StoreDynVars2D, StoreDynVars3D |
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to individual fields |
| 25 |
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(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
| 26 |
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o store 3-D (in-situ) density in commom block (DYNVARS.h) |
| 27 |
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- save 1 rho computation. |
| 28 |
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- no longer modify T & S inland when using down_slope pkg. |
| 29 |
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o gad_som : allow to switch to SOM advection for T & S without corresponding |
| 30 |
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pickup files (using new S/R: MDS_CHECK4FILE). |
| 31 |
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o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
| 32 |
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(for useSingleCpuIO to work in multi-threaded) |
| 33 |
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o pkg/shelfice: |
| 34 |
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- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
| 35 |
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with SHELFICEtopoFile in data.shelfice |
| 36 |
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- move code for reading ice shelf topography and modifying hFacC into separate |
| 37 |
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subroutines of the shelfice package |
| 38 |
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- separate initialisation of "fixed" and "variable" variables |
| 39 |
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- kTopC is not (yet) replaced by kSurfC, although this is possible |
| 40 |
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o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
| 41 |
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o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
| 42 |
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and rename: |
| 43 |
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ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
| 44 |
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ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
| 45 |
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o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
| 46 |
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|
| 47 |
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checkpoint61c |
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o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
| 49 |
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to add mass source/sink of fluid in the interior (3-D generalisation |
| 50 |
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of oceanic real-fresh water flux). |
| 51 |
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o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
| 52 |
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o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
| 53 |
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o new pkg: down_slope |
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density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
| 55 |
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- presently, modify T & S inland (dwnslp_calc_rho.F). |
| 56 |
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can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
| 57 |
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- implementation for ocean in P-coords not tested. |
| 58 |
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- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
| 59 |
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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). |
| 61 |
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o change FIND_RHO to FIND_RHO_2D : |
| 62 |
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pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
| 63 |
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o new pkg: cheapaml |
| 64 |
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|
| 65 |
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checkpoint61b |
| 66 |
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o exch2: |
| 67 |
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change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
| 68 |
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- no longer depend on the order sequence (N,S,E,W). |
| 69 |
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- 3rd exchange no longer needed (tested with 24 tiles). |
| 70 |
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- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
| 71 |
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- exch_UV_A-grid readily available (but not yet tested). |
| 72 |
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comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
| 73 |
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(both are no longer needed) in exch_uv: no effect in forward run; but |
| 74 |
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get truncation error differences with adjoint exch. |
| 75 |
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o exch2: |
| 76 |
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- change index-bounds storage (moved from target to local tile, |
| 77 |
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more intuitive this way) ; rename/remove some variables. |
| 78 |
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- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
| 79 |
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|
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checkpoint61a |
| 81 |
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o exch2/matlab-topology-generator: |
| 82 |
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fix bug in index bounds for N-S internal exchange (hard to tell if this |
| 83 |
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had any effect on the solution). |
| 84 |
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o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
| 85 |
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is exceeded |
| 86 |
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o testreport: modify syntax of awk, so that it works also with |
| 87 |
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awk, and not only with nawk and gawk |
| 88 |
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|
| 89 |
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checkpoint61 |
| 90 |
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o autodiff |
| 91 |
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Change default for TAF usage by removing argument '-nonew_arg' |
| 92 |
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This changes TAF subroutine argument list (ordering of active var.) |
| 93 |
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Omission of this flag leads to incompatibility w.r.t. TAMC |
| 94 |
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To restore TAMC-compatibility, need following modifs: |
| 95 |
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* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
| 96 |
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* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
| 97 |
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Tested TAF version is 1.9.22 |
| 98 |
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N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
| 99 |
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|
| 100 |
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checkpoint60 |
| 101 |
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--->>> This is the last checkpoint for which generating the adjoint |
| 102 |
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--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
| 103 |
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--->>> by default. |
| 104 |
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--->>> Future checkpoints will ommit this flag by default. |
| 105 |
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o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
| 106 |
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o pkg/grdchk: Add gradient check to etan0 perturbations. |
| 107 |
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o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
| 108 |
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o pkg/autodiff: more flexibility in zeroadj. |
| 109 |
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model/src: modifying do_oceanic_phys.F accordingly. |
| 110 |
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o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
| 111 |
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o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
| 112 |
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special setup of gmredi for which the adjoint is stable |
| 113 |
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enough for parameter optimization. |
| 114 |
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o bridging the gap between eddy stress and GM. |
| 115 |
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-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
| 116 |
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along with a change in CPP option (now ALLOW_EDDYPSI). |
| 117 |
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-> when using GM w/ GM_AdvForm: |
| 118 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
| 119 |
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is applied either in the tracer Eq. or in momentum Eq. |
| 120 |
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depending on data.gmredi (intro. GM_InMomAsStress). |
| 121 |
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-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
| 122 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
| 123 |
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pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
| 124 |
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|
| 125 |
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checkpoint59r |
| 126 |
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o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
| 127 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
| 128 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
| 129 |
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o pkg/mnc: add some attributes to standard 1D-coordinate variables |
| 130 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
| 131 |
|
mass points, when using mnc for output |
| 132 |
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- add runtime parameter (missing_value, missing_value_int) to override |
| 133 |
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default (which is the value of getcon('UNDEF')) |
| 134 |
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o pkg/mnc: prepare mnc for the actual use of missing values with the |
| 135 |
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diagnostics package: small fix in mnc_cw_readwrite.template and more |
| 136 |
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initialisation of never used fields |
| 137 |
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- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
| 138 |
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versions |
| 139 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
| 140 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
| 141 |
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are missing. |
| 142 |
|
o move from external_forcing_surf.F to ini_forcing.F |
| 143 |
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the p-coord. hack consisting in using pLoad to set phi0surf ; |
| 144 |
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update output of tutorial_global_oce_in_p (affected @ truncation level). |
| 145 |
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o Freshen up a bit hs94.1x64x5, notably: |
| 146 |
|
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
| 147 |
|
exactConserv=.TRUE. |
| 148 |
|
o pkg/generic_advdiff: |
| 149 |
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change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
| 150 |
|
applies to files where Temperature & Salinity 2nd Order moments are used. |
| 151 |
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o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
| 152 |
|
this uses a dynamically allocated internal state data structure |
| 153 |
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(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
| 154 |
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and requires a fortran 90 compiler |
| 155 |
|
|
| 156 |
|
checkpoint59q |
| 157 |
|
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
| 158 |
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(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
| 159 |
|
o Refresh tutorial_global_oce_biogeo, notably: |
| 160 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
| 161 |
|
- change EOS (POLY3 --> JMD95Z) |
| 162 |
|
- use Bryan-Lewis vertical diffusivity |
| 163 |
|
- use multidimensional advection |
| 164 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
| 165 |
|
- change a couple of parameters in dic pkg |
| 166 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
| 167 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
| 168 |
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- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
| 169 |
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- replace "debugMode" with "debugLevel .GE. debLevB" |
| 170 |
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o implementation of TAF directives for gchem,cfc,dic |
| 171 |
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o remove "exp5" (replaced by tutorial_deep_convection). |
| 172 |
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o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
| 173 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
| 174 |
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the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
| 175 |
|
--> changes results in exp4, seaice_obcs |
| 176 |
|
o tutorial_deep_convection : |
| 177 |
|
update the set-up and increase resolution and domain size ; start |
| 178 |
|
from pseudo initial conditions = output at t=120mn in order to see |
| 179 |
|
something happening when running testreport. |
| 180 |
|
o pkg/seaice: add os7mp as an advection scheme |
| 181 |
|
add check for advection schemes |
| 182 |
|
add a flag for restoring T and S underneath sea ice |
| 183 |
|
o pkg/my82: add netcdf-support and diagnostics |
| 184 |
|
o thsice pkg: |
| 185 |
|
- Now hsMax limits snow height by turning it into ice following |
| 186 |
|
flooding scheme (and now conserving energy) |
| 187 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
| 188 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
| 189 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
| 190 |
|
|
| 191 |
|
checkpoint59p |
| 192 |
|
o gchem / dic / cfc : |
| 193 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
| 194 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
| 195 |
|
- various re-arrangement in initialisation & header file ; |
| 196 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
| 197 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
| 198 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
| 199 |
|
before) providing pickupStrictlyMatch is set to False. |
| 200 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
| 201 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
| 202 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
| 203 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
| 204 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
| 205 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
| 206 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
| 207 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
| 208 |
|
scheme to use for vorticty-term ; |
| 209 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
| 210 |
|
(with default selectVortScheme, return to original discretisation) |
| 211 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
| 212 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
| 213 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
| 214 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
| 215 |
|
also fix diagnostics VISCAHW & VISCA4W. |
| 216 |
|
|
| 217 |
|
checkpoint59o |
| 218 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
| 219 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
| 220 |
|
move a few statemens out the main loop into separate loops |
| 221 |
|
o pkg/shelfice: |
| 222 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
| 223 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
| 224 |
|
rhoConstFresh=rhoConst (by accident) |
| 225 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
| 226 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
| 227 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
| 228 |
|
- convert potential temperature into in-situ temperature. This changes the |
| 229 |
|
isomip tests => update tests |
| 230 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
| 231 |
|
writing a pickup at the last timestep |
| 232 |
|
o tools/mpack-1.6 : |
| 233 |
|
- disable automake (not working) and autoconf (not needed). |
| 234 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
| 235 |
|
also cleaner with much less compilation warnings. |
| 236 |
|
o pkg/profiles: |
| 237 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
| 238 |
|
(for "less than 32 characters name" compiler requirement) |
| 239 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
| 240 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
| 241 |
|
o pkg/diagnostics (stats-diags): |
| 242 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
| 243 |
|
o genmake2: replace (4 times) |
| 244 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
| 245 |
|
with |
| 246 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
| 247 |
|
echo $COMM >> genmake_warnings |
| 248 |
|
$COMM >> genmake_warnings 2>&1 |
| 249 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
| 250 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
| 251 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
| 252 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
| 253 |
|
o pkg/ctrl: |
| 254 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
| 255 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
| 256 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
| 257 |
|
|
| 258 |
|
checkpoint59n |
| 259 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
| 260 |
|
number in dedicate array "hdiag": |
| 261 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
| 262 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
| 263 |
|
- many small changes (integer format) for large number of diagnostics |
| 264 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
| 265 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
| 266 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
| 267 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
| 268 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
| 269 |
|
geographical coordinates according to the inverse of the rotation defined |
| 270 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
| 271 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
| 272 |
|
Naturally, this feature does not work with all packages, so some |
| 273 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
| 274 |
|
profiles), because there the coordinates are assumed to be regular |
| 275 |
|
spherical grid coordinates. |
| 276 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
| 277 |
|
- introduce isopycnal diffusion coefficient control. |
| 278 |
|
o tools/adjoint_options: |
| 279 |
|
- additional control vector components. |
| 280 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
| 281 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
| 282 |
|
o pkg/mypackage: |
| 283 |
|
- add example of read/write pickup for state-var ; |
| 284 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
| 285 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
| 286 |
|
transitions for useExfYearlyFields |
| 287 |
|
- add new subroutine that determines the file to read from for |
| 288 |
|
use*YearlyFields = .TRUE. and .FALSE. |
| 289 |
|
- add a verification experiment to global_with_exf that tests |
| 290 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
| 291 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
| 292 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
| 293 |
|
subroutines (which could be generated from a template, because they are |
| 294 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
| 295 |
|
simplicity |
| 296 |
|
o pkg/exf: |
| 297 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
| 298 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
| 299 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
| 300 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
| 301 |
|
directive in routine lagran, and splitting a loop and making do while the |
| 302 |
|
outermost loop (the latter requires the intoduction of index arrays) |
| 303 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
| 304 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
| 305 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
| 306 |
|
o verification/seaice_obcs: updated for restart test and latest options |
| 307 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
| 308 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
| 309 |
|
for now this is only available for the C-grid code and also within |
| 310 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
| 311 |
|
|
| 312 |
|
checkpoint59m |
| 313 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
| 314 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
| 315 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
| 316 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
| 317 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
| 318 |
|
and to provide an example matlab scrpt for generating them |
| 319 |
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o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
| 320 |
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o pkg/salt_plume: clean up salt_plume_frac.F to |
| 321 |
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remove redundancy in PlumeMethod 1 and 4 |
| 322 |
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o pkg/kpp: added saltplume diagnostics |
| 323 |
o pkg/obcs and pkg/seaice: |
o pkg/obcs and pkg/seaice: |
| 324 |
- do not set uice and vice to zero when OB*icefile are unspecified |
- do not set uice and vice to zero when OB*icefile are unspecified |
| 325 |
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
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