| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
| 5 |
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| 6 |
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o corrected CPP option mismatch in exf_Bulk... functions for case |
| 7 |
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#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
| 8 |
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|
| 9 |
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checkpoint50a_post |
| 10 |
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o Bug fix for merging between c50 and KPP. |
| 11 |
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ikey was passed from thermodynamics to kpp_calc via |
| 12 |
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common block rather than being recomputed in kpp_calc, |
| 13 |
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in contradiction with new key itdkey. |
| 14 |
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New key ikppkey created, and tamc.h headers updated. |
| 15 |
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|
| 16 |
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checkpoint50 |
| 17 |
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- 2nd step of merge with ecco-branch: |
| 18 |
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merge changes in ecco-branch back into main trunk |
| 19 |
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- bug fix in find_alpha |
| 20 |
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- more storing in gmredi_calc_tensor.F, kpp_routines.F |
| 21 |
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- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
| 22 |
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- merged some sliced AD support routines |
| 23 |
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|
| 24 |
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checkpoint49 |
| 25 |
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merged from ecco-branch: |
| 26 |
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o exf: |
| 27 |
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- Enable initialisation of forcing fields to constant |
| 28 |
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(runtime) values. |
| 29 |
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- in exf_getffields.F |
| 30 |
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Reduce i-/j-loop to interior domain, discarding overlaps. |
| 31 |
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That also fixes wrong TAF-key computations for key_1, key_2 |
| 32 |
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with bulf formulae. |
| 33 |
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- exf_init.F modify #ifdef for exf_init_evap |
| 34 |
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- exf_getffieldrec.F, ctrl_getrec.F |
| 35 |
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The following INT-usages are not safe: |
| 36 |
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fldsecs = int(fldsecs/fldperiod)*fldperiod |
| 37 |
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fldcount = int(fldsecs/fldperiod) + 1 |
| 38 |
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and were modified. |
| 39 |
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o autodiff: checkpoint_lev... |
| 40 |
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- updated storing for bulk formulae (some arrays were missing) |
| 41 |
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- added state for seaice package |
| 42 |
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- synchronized with main branch |
| 43 |
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o DIVA: |
| 44 |
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Modif.s in |
| 45 |
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- the_main_loop.F |
| 46 |
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- the_model_main.F |
| 47 |
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and added cost_final_restore.F cost_final_store.F |
| 48 |
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o With these changes, it is possible to fully separate |
| 49 |
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the first forward run to compute the cost function (mdthe_main_loop) |
| 50 |
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and adjoint runs over individual DIVA intervals (adthe_main_loop) |
| 51 |
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into separate model executions. |
| 52 |
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This enables better tuning of DIVA to given queue sizes. |
| 53 |
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o Loss of cost function value in consecutive DIVA runs is |
| 54 |
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fixed by storing to 'costfinal' file. |
| 55 |
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o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
| 56 |
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beginning/end of adjoint integration is accounted for. |
| 57 |
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The current changes apply to TAF-1.4.26. |
| 58 |
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TAF has one remaining bug, requiring one manual change |
| 59 |
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(see MITgcm manual). |
| 60 |
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o cal: synchronized between MAIN and ecco-branch |
| 61 |
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|
| 62 |
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checkpoint48i_post |
| 63 |
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o Changes to restore differentiability of code w.r.t. previous tag |
| 64 |
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(mostly adding new routines to make list and replacing |
| 65 |
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pressure by totPhiHyd). |
| 66 |
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o Updated and merged grdchk package |
| 67 |
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- has both ADM and TLM checks |
| 68 |
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- works for single- and multi-proc. |
| 69 |
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- output cleaned |
| 70 |
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- worked successfully for parallel DIVA |
| 71 |
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o genmake: |
| 72 |
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- Adding -platform=SP4 |
| 73 |
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- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
| 74 |
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o Modif. for DIVA: |
| 75 |
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ctrl_unpack should not be called in intermediate DIVA interval. |
| 76 |
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(similar thing would apply for active files such as |
| 77 |
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tbar, sbar, psbar, which should not be reinitialised; |
| 78 |
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only relevant for ecco-branch) |
| 79 |
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|
| 80 |
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checkpoint48h_post |
| 81 |
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o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
| 82 |
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o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
| 83 |
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o Added SEAICE_initialHEFF to pkg/seaice |
| 84 |
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o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
| 85 |
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|
| 86 |
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checkpoint48g_post |
| 87 |
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--- EOS: |
| 88 |
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o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
| 89 |
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store total Potential in totPhyHyd for diagnostics & EOS. |
| 90 |
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o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
| 91 |
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--- Pressure/geopotential gradient: |
| 92 |
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o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
| 93 |
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o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
| 94 |
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( changes results of global_ocean_pressure ) |
| 95 |
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o NLFS + z-coord.: add eta*Rho' contribution. |
| 96 |
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o accurate phiHyd when using interface-W at the middle between 2 centers |
| 97 |
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( changes results of ideal_2D_oce ) |
| 98 |
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o includes r* 2nd term in potential gradient. |
| 99 |
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|
| 100 |
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checkpoint48f_post |
| 101 |
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Merging from release1_p12: |
| 102 |
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o Modifications for using pkg/exf with pkg/seaice |
| 103 |
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- improved description of the various forcing configurations |
| 104 |
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- added basic radiation bulk formulae to pkg/exf |
| 105 |
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- units/sign fix for evap computation in exf_getffields.F |
| 106 |
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- updated verification/global_with_exf/results/output.txt |
| 107 |
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o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
| 108 |
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(SBO) core products, including oceanic mass, center-of-mass, |
| 109 |
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angular, and bottom pressure (see pkg/sbo/README.sbo). |
| 110 |
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o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
| 111 |
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to avoid negative values in shallow regions. |
| 112 |
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- updated verification/natl_box/results/output.txt |
| 113 |
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- updated verification/lab_sea/results/output.txt |
| 114 |
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o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
| 115 |
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o Added useSingleCpuIO option (see PARAMS.h). |
| 116 |
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o Updated useSingleCpuIO option in mdsio_writefield.F to |
| 117 |
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work with multi-field files, e.g., for single-file pickup. |
| 118 |
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o pkg/seaice: |
| 119 |
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- bug fix in growth.F: QNET for no shortwave case |
| 120 |
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- added HeffFile for specifying initial sea-ice thickness |
| 121 |
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- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
| 122 |
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o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
| 123 |
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kpp_transport_t.F, forward_step.F, and the_main_loop.F |
| 124 |
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o pkg/seaice: |
| 125 |
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- adjoint-friendly modifications |
| 126 |
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- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
| 127 |
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|
| 128 |
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checkpoint48e_post |
| 129 |
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o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
| 130 |
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o dynamics: change definition of computational domain & adapt mom_fluxform |
| 131 |
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accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
| 132 |
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o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
| 133 |
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adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
| 134 |
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exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
| 135 |
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global_ocean.90x40x15 global_with_exf global_ocean_pressure |
| 136 |
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inverted_barometer solid-body.cs-32x32x1 |
| 137 |
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(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
| 138 |
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|
| 139 |
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checkpoint48d_post |
| 140 |
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o in preparation for r*: |
| 141 |
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a) use pre-computed gradient of hydrostatic potential: |
| 142 |
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changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
| 143 |
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b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
| 144 |
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=> affects results of glob_oce_pressure (different truncation error) |
| 145 |
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update output.txt of ideal_2D_oce & global_ocean_pressure |
| 146 |
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|
| 147 |
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checkpoint48d_pre |
| 148 |
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o in preparation for r*: |
| 149 |
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new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
| 150 |
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pass the 2 comp. of the grad. as arguments to momentum S/R. |
| 151 |
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but for the moment, only used if it does not change the results. |
| 152 |
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o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
| 153 |
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|
| 154 |
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checkpoint48c_post |
| 155 |
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Modifications in treatment of initial flux forcing controls |
| 156 |
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to avoid extra storing of flux fields. |
| 157 |
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|
| 158 |
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checkpoint48c_pre |
| 159 |
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o Added tidal_basin_2d experiment (currently 1D!) |
| 160 |
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o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
| 161 |
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| 162 |
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checkpoint48b_post |
| 163 |
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o r* coordinate added in #ifdef NONLIN_FRSURF block. |
| 164 |
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(modification to pressure gradient not yet implemented) |
| 165 |
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o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
| 166 |
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(for U & V) that are used for vertical advection of momentum. |
| 167 |
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| 168 |
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checkpoint48a_post |
| 169 |
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o In preparation for r*, use temp. array to compute vertical transport |
| 170 |
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in flux-form momentum pkg. => change results of few test-exp. |
| 171 |
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Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
| 172 |
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lab_sea, natl_box & plume_on_slope |
| 173 |
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| 174 |
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checkpoint48 |
| 175 |
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o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
| 176 |
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| 177 |
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checkpoint47j_post |
| 178 |
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o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
| 179 |
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o moved adexch from forward_step to addummy_in_stepping |
| 180 |
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o added exch in ctrl_map_... |
| 181 |
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o aveFreq.=0. at end of cost_final to avoid overwrite in |
| 182 |
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reverse checkpointing loop |
| 183 |
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o Yet more changes in gmredi: |
| 184 |
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* adgmredi_calc_tensor |
| 185 |
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avoiding all recomputation of gmredi_slope_limit |
| 186 |
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* adgmredi_x/y/rtransport |
| 187 |
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added flag for excessive storing to avoid recomp. of |
| 188 |
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u/v/rtans, dTdx/y/z |
| 189 |
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-> this is not really necessary and very memory-consuming |
| 190 |
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* adgmredi_slope_psi: |
| 191 |
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consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
| 192 |
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* gmredi_slope_limit |
| 193 |
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re-activated full calculation of taperfct for case 'ac02' |
| 194 |
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o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
| 195 |
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|
| 196 |
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checkpoint47i_post |
| 197 |
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o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
| 198 |
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o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
| 199 |
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default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
| 200 |
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o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
| 201 |
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o gmredi: fix few bugs. |
| 202 |
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|
| 203 |
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checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
| 204 |
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This will be a good checkpoint to plug into the ecco-branch. |
| 205 |
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o few modif.'s to get latest version adjointed |
| 206 |
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(mainly kick out code in ini_linear_phisurf) |
| 207 |
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o modif's to run adjoint with exactConserv |
| 208 |
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o case GM_BOLUS_ADVEC should be cleaned |
| 209 |
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S/R gmredi_slope_psi should be cleaned |
| 210 |
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o verification/carbon now has exactConserv=.TRUE. |
| 211 |
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|
| 212 |
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checkpoint47g_post |
| 213 |
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o time-average AIM output: becomes independent from statvars time-average |
| 214 |
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(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
| 215 |
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o After TAF bug fix: |
| 216 |
|
Tested adjoint of gmredi package. |
| 217 |
|
Tests were done with checkpoint47 rather than with latest |
| 218 |
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checkpoint47f_post since the latter is broken for the adjoint |
| 219 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
| 220 |
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Here they are, before they get changed/lost/stolen. |
| 221 |
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Mostly modif.'s to fix numerical sensitivities. |
| 222 |
|
Gradient checks OK for |
| 223 |
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- GM_taper_scheme: |
| 224 |
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* clipping |
| 225 |
|
* ac02 |
| 226 |
|
* linear |
| 227 |
|
* glw91 |
| 228 |
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* dm95 |
| 229 |
|
* ldd97 |
| 230 |
|
- GMREDI_OPTIONS: |
| 231 |
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* GM_VISBECK_VARIABLE_K |
| 232 |
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* GM_NON_UNITY_DIAGONAL |
| 233 |
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* GM_EXTRA_DIAGONAL |
| 234 |
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* GM_BOLUS_ADVEC |
| 235 |
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in conjunction with data.gmredi parameters to be checked in |
| 236 |
|
in a few minutes under verification/carbon/code/ |
| 237 |
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|
| 238 |
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checkpoint47f_post |
| 239 |
|
Merging from release1_p10: |
| 240 |
|
o modifications for using pkg/exf with pkg/seaice |
| 241 |
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
| 242 |
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and SEAICE_EXTERNAL_FLUXES |
| 243 |
|
- pkg/exf CPP options EXF_READ_EVAP and |
| 244 |
|
EXF_NO_BULK_COMPUTATIONS |
| 245 |
|
- usage examples are Experiments 8 and 9 in |
| 246 |
|
verification/lab_sea/README |
| 247 |
|
- verification/lab_sea default experiment now uses |
| 248 |
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
| 249 |
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|
| 250 |
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checkpoint47e_post |
| 251 |
|
o created a tag prior to creating a branch |
| 252 |
|
|
| 253 |
|
checkpoint47d_post |
| 254 |
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o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
| 255 |
|
at the bottom boundary had an erroneous half slip boundary condition |
| 256 |
|
o added bottom drag and no slip boundary condition capabilities to |
| 257 |
|
oceanic pressure coordinates code |
| 258 |
|
o added new verification experiment global_ocean_pressure, this experiment is |
| 259 |
|
also described in the tutorial section of the manual |
| 260 |
|
checkpoint47d_pre |
| 261 |
|
|
| 262 |
|
checkpoint47c_post |
| 263 |
|
o Added a verification experiment for a global cubed-sphere ocean run |
| 264 |
|
- verification/global_ocean.cubed32x32x30 |
| 265 |
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- uses pkg/therm_seaice and pkg/bulk_forcing |
| 266 |
|
|
| 267 |
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o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
| 268 |
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o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
| 269 |
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when using P-coordinate; only implemented for atmospheric config. |
| 270 |
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o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
| 271 |
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NOTES: requires option NONLIN_FRSURF to be "#define". |
| 272 |
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
| 273 |
|
|
| 274 |
|
checkpoint47b_post |
| 275 |
|
Merging from release1_p9: |
| 276 |
|
o pkg/seaice |
| 277 |
|
- removed GOTO's and added taf directives |
| 278 |
|
- double precision constants to reduce the g77 (Linux) |
| 279 |
|
to F77 (SGI) differences reported in release1_p8 |
| 280 |
|
o tools/genmake |
| 281 |
|
- added SGI options |
| 282 |
|
o verification/testscript |
| 283 |
|
- updated to that of checkpoint47a_post |
| 284 |
|
o verification/global_ocean.90x40x15/input/eedata |
| 285 |
|
- modified for SGI f77 compatibility |
| 286 |
|
o verification/lab_sea |
| 287 |
|
- added description of sea-ice model |
| 288 |
|
- added missing matlab routines |
| 289 |
|
- added test of thermodynamics parallelization |
| 290 |
|
|
| 291 |
checkpoint47a_post |
checkpoint47a_post |
| 292 |
o new pkg: aim_v23 |
o new pkg: aim_v23 |
| 293 |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
| 298 |
o add diagnostic of surface correction term in monitor output |
o add diagnostic of surface correction term in monitor output |
| 299 |
|
|
| 300 |
o bulk_force and therm_seaice |
o bulk_force and therm_seaice |
| 301 |
|
- Two packages: bulk_force (Bulk forcing) |
| 302 |
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
| 303 |
|
- Earlier integration from Stephaine Dutkiewicz |
| 304 |
|
and Patrick Heimbach. |
| 305 |
|
- Two ifdef statements for compile time, |
| 306 |
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
| 307 |
|
|
| 308 |
checkpoint47 |
checkpoint47 |
| 309 |
differentiable version of checkpoint46n_post |
differentiable version of checkpoint46n_post |
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