| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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>>>checkpoint51b_post |
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adjoint of ptracers |
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o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
| 9 |
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o extended state in checkpoint_lev?, etc. |
| 10 |
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o alternative ctrl/cost with tr1 or ptracer |
| 11 |
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o new comlev1_bibj_ptracers |
| 12 |
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o new ptracers.flow |
| 13 |
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o made ptracers_forcing same as external_forcing_s |
| 14 |
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o added verification for adjoint with ptracers |
| 15 |
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- adm. grdchk fail so far |
| 16 |
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- tlm. grdchk OK |
| 17 |
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- checked tapelev/comlev recomputations: OK |
| 18 |
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<<<checkpoint51b_pre |
| 19 |
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checkpoint51a_post |
| 21 |
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o added code for biogeochemistry package |
| 22 |
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- new pkgs: dic, gchem |
| 23 |
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- new subroutine in ptracers |
| 24 |
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o modify code for biogeo packages |
| 25 |
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- in model/src and pkg/ptracers |
| 26 |
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|
| 27 |
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checkpoint51 |
| 28 |
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o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
| 29 |
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- autodiff, ctrl, exf, grdchk, seaice |
| 30 |
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kept separate packages |
| 31 |
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- cost, ecco, obcs |
| 32 |
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o updating verification/internal_wave, verification/lab_sea |
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(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
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|
| 35 |
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checkpoint50i_post |
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o Preparing next differentiable checkpoint and sync |
| 37 |
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of MAIN vs. ecco-branch |
| 38 |
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- 1st step: this one is differentiable |
| 39 |
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- 2nd step: next(! not this) checkpoint will have updated packages |
| 40 |
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from ecco-branch) |
| 41 |
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|
| 42 |
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checkpoint50h_post |
| 43 |
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o new package "land": provide surface BC for AIM. |
| 44 |
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o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
| 45 |
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o AIM: use true log-P extrapolation for near surface temp (= as in |
| 46 |
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F.Molteni paper) ; update aim.5l_cs output. |
| 47 |
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o New variable in PARM03 for more flexible pickups |
| 48 |
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o somewhat cleaned package initialisation sequence for |
| 49 |
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ctrl/ cost/ ecco/ in packages_... routines |
| 50 |
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|
| 51 |
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checkpoint50g_post |
| 52 |
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o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
| 53 |
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- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
| 54 |
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- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
| 55 |
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made the default because of faster convergence than ADI |
| 56 |
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|
| 57 |
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checkpoint50f_post |
| 58 |
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o exf totally restructured |
| 59 |
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- replaced all exf_set_ routines by one generic exf_set_gen.F |
| 60 |
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and made sure it's still differentiable |
| 61 |
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- split exf_getffields.F into new exf_bulkformulae.F |
| 62 |
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- exf_inscal_/exf_outscal_ suffixes consistent with field names |
| 63 |
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- updated adjoint/makefile and relevant verif. accordingly |
| 64 |
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|
| 65 |
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checkpoint50f_pre |
| 66 |
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o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
| 67 |
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+ change Evap over land. (update aim.5l_cs output) |
| 68 |
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o added missing .cvsignores and made uniform across expts |
| 69 |
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o changed configuration of tidal_basin_2d expt |
| 70 |
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o added pkg/debug functions for tracing code in fatal crashes |
| 71 |
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o tidied pkg/monitor to use MONITOR_OPTIONS.h |
| 72 |
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o new fn in pkg/monitor to stop model if solution grows too big |
| 73 |
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o removed lots of single quotes from comments |
| 74 |
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|
| 75 |
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checkpoint50e_post |
| 76 |
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o make KPP work with PTRACERS |
| 77 |
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- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
| 78 |
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nearly a copy of kpp_transport_s |
| 79 |
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- there is no analogue to SurfaceTendencyS, so I have to use |
| 80 |
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gPtr(of the surface layer) instead |
| 81 |
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o add a new platform SunFire+mpi (SunFire 15000) to genmake |
| 82 |
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checkpoint50e_pre |
| 83 |
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|
| 84 |
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checkpoint50d_post |
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o change kpp output from multiple-record state files to single-record state |
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files analogous to write_state.F |
| 87 |
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o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
| 88 |
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analogous to the cg2d-related output. |
| 89 |
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o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
| 90 |
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so that writing to internal file fn (with length 512) fails. |
| 91 |
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checkpoint50d_pre |
| 92 |
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|
| 93 |
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checkpoint50c_post |
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o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
| 95 |
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o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
| 96 |
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o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
| 97 |
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o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
| 98 |
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o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
| 99 |
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|
| 100 |
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checkpoint50c_pre |
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Merging from release1_p13: |
| 102 |
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o bug fix for pkg/seaice dynamic solver |
| 103 |
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o Added SEAICE_initialHEFF to pkg/seaice |
| 104 |
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|
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checkpoint50b_post |
| 106 |
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o store u*,v* in gU,V instead of in guNm1,gvNm1 |
| 107 |
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o in order to put the momForcing out of the Adams-Bashforth: |
| 108 |
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move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
| 109 |
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to timestep.F |
| 110 |
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o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
| 111 |
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o re-generate output for highly sensitive test-exp: |
| 112 |
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global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
| 113 |
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|
| 114 |
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checkpoint50b_pre |
| 115 |
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o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
| 116 |
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o corrected CPP option mismatch in exf_Bulk... functions for case |
| 117 |
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#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
| 118 |
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|
| 119 |
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checkpoint50a_post |
| 120 |
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o Bug fix for merging between c50 and KPP. |
| 121 |
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ikey was passed from thermodynamics to kpp_calc via |
| 122 |
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common block rather than being recomputed in kpp_calc, |
| 123 |
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in contradiction with new key itdkey. |
| 124 |
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New key ikppkey created, and tamc.h headers updated. |
| 125 |
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|
| 126 |
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checkpoint50 |
| 127 |
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- 2nd step of merge with ecco-branch: |
| 128 |
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merge changes in ecco-branch back into main trunk |
| 129 |
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- bug fix in find_alpha |
| 130 |
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- more storing in gmredi_calc_tensor.F, kpp_routines.F |
| 131 |
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- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
| 132 |
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- merged some sliced AD support routines |
| 133 |
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|
| 134 |
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checkpoint49 |
| 135 |
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merged from ecco-branch: |
| 136 |
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o exf: |
| 137 |
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- Enable initialisation of forcing fields to constant |
| 138 |
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(runtime) values. |
| 139 |
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- in exf_getffields.F |
| 140 |
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Reduce i-/j-loop to interior domain, discarding overlaps. |
| 141 |
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That also fixes wrong TAF-key computations for key_1, key_2 |
| 142 |
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with bulf formulae. |
| 143 |
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- exf_init.F modify #ifdef for exf_init_evap |
| 144 |
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- exf_getffieldrec.F, ctrl_getrec.F |
| 145 |
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The following INT-usages are not safe: |
| 146 |
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fldsecs = int(fldsecs/fldperiod)*fldperiod |
| 147 |
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fldcount = int(fldsecs/fldperiod) + 1 |
| 148 |
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and were modified. |
| 149 |
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o autodiff: checkpoint_lev... |
| 150 |
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- updated storing for bulk formulae (some arrays were missing) |
| 151 |
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- added state for seaice package |
| 152 |
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- synchronized with main branch |
| 153 |
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o DIVA: |
| 154 |
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Modif.s in |
| 155 |
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- the_main_loop.F |
| 156 |
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- the_model_main.F |
| 157 |
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and added cost_final_restore.F cost_final_store.F |
| 158 |
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o With these changes, it is possible to fully separate |
| 159 |
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the first forward run to compute the cost function (mdthe_main_loop) |
| 160 |
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and adjoint runs over individual DIVA intervals (adthe_main_loop) |
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into separate model executions. |
| 162 |
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This enables better tuning of DIVA to given queue sizes. |
| 163 |
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o Loss of cost function value in consecutive DIVA runs is |
| 164 |
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fixed by storing to 'costfinal' file. |
| 165 |
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o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
| 166 |
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beginning/end of adjoint integration is accounted for. |
| 167 |
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The current changes apply to TAF-1.4.26. |
| 168 |
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TAF has one remaining bug, requiring one manual change |
| 169 |
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(see MITgcm manual). |
| 170 |
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o cal: synchronized between MAIN and ecco-branch |
| 171 |
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|
| 172 |
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checkpoint48i_post |
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o Changes to restore differentiability of code w.r.t. previous tag |
| 174 |
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(mostly adding new routines to make list and replacing |
| 175 |
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pressure by totPhiHyd). |
| 176 |
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o Updated and merged grdchk package |
| 177 |
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- has both ADM and TLM checks |
| 178 |
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- works for single- and multi-proc. |
| 179 |
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- output cleaned |
| 180 |
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- worked successfully for parallel DIVA |
| 181 |
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o genmake: |
| 182 |
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- Adding -platform=SP4 |
| 183 |
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- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
| 184 |
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o Modif. for DIVA: |
| 185 |
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ctrl_unpack should not be called in intermediate DIVA interval. |
| 186 |
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(similar thing would apply for active files such as |
| 187 |
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tbar, sbar, psbar, which should not be reinitialised; |
| 188 |
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only relevant for ecco-branch) |
| 189 |
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|
| 190 |
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checkpoint48h_post |
| 191 |
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o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
| 192 |
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o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
| 193 |
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o Added SEAICE_initialHEFF to pkg/seaice |
| 194 |
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o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
| 195 |
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|
| 196 |
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checkpoint48g_post |
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--- EOS: |
| 198 |
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o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
| 199 |
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store total Potential in totPhyHyd for diagnostics & EOS. |
| 200 |
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o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
| 201 |
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--- Pressure/geopotential gradient: |
| 202 |
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o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
| 203 |
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o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
| 204 |
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( changes results of global_ocean_pressure ) |
| 205 |
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o NLFS + z-coord.: add eta*Rho' contribution. |
| 206 |
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o accurate phiHyd when using interface-W at the middle between 2 centers |
| 207 |
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( changes results of ideal_2D_oce ) |
| 208 |
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o includes r* 2nd term in potential gradient. |
| 209 |
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|
| 210 |
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checkpoint48f_post |
| 211 |
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Merging from release1_p12: |
| 212 |
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o Modifications for using pkg/exf with pkg/seaice |
| 213 |
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- improved description of the various forcing configurations |
| 214 |
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- added basic radiation bulk formulae to pkg/exf |
| 215 |
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- units/sign fix for evap computation in exf_getffields.F |
| 216 |
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- updated verification/global_with_exf/results/output.txt |
| 217 |
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o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
| 218 |
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(SBO) core products, including oceanic mass, center-of-mass, |
| 219 |
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angular, and bottom pressure (see pkg/sbo/README.sbo). |
| 220 |
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o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
| 221 |
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to avoid negative values in shallow regions. |
| 222 |
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- updated verification/natl_box/results/output.txt |
| 223 |
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- updated verification/lab_sea/results/output.txt |
| 224 |
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o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
| 225 |
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o Added useSingleCpuIO option (see PARAMS.h). |
| 226 |
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o Updated useSingleCpuIO option in mdsio_writefield.F to |
| 227 |
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work with multi-field files, e.g., for single-file pickup. |
| 228 |
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o pkg/seaice: |
| 229 |
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- bug fix in growth.F: QNET for no shortwave case |
| 230 |
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- added HeffFile for specifying initial sea-ice thickness |
| 231 |
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- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
| 232 |
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o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
| 233 |
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kpp_transport_t.F, forward_step.F, and the_main_loop.F |
| 234 |
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o pkg/seaice: |
| 235 |
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- adjoint-friendly modifications |
| 236 |
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- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
| 237 |
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|
| 238 |
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checkpoint48e_post |
| 239 |
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o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
| 240 |
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o dynamics: change definition of computational domain & adapt mom_fluxform |
| 241 |
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accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
| 242 |
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o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
| 243 |
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adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
| 244 |
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exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
| 245 |
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global_ocean.90x40x15 global_with_exf global_ocean_pressure |
| 246 |
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inverted_barometer solid-body.cs-32x32x1 |
| 247 |
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(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
| 248 |
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|
| 249 |
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checkpoint48d_post |
| 250 |
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o in preparation for r*: |
| 251 |
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a) use pre-computed gradient of hydrostatic potential: |
| 252 |
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changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
| 253 |
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b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
| 254 |
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=> affects results of glob_oce_pressure (different truncation error) |
| 255 |
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update output.txt of ideal_2D_oce & global_ocean_pressure |
| 256 |
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|
| 257 |
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checkpoint48d_pre |
| 258 |
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o in preparation for r*: |
| 259 |
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new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
| 260 |
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pass the 2 comp. of the grad. as arguments to momentum S/R. |
| 261 |
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but for the moment, only used if it does not change the results. |
| 262 |
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o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
| 263 |
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|
| 264 |
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checkpoint48c_post |
| 265 |
|
Modifications in treatment of initial flux forcing controls |
| 266 |
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to avoid extra storing of flux fields. |
| 267 |
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|
| 268 |
|
checkpoint48c_pre |
| 269 |
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o Added tidal_basin_2d experiment (currently 1D!) |
| 270 |
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o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
| 271 |
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|
| 272 |
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checkpoint48b_post |
| 273 |
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o r* coordinate added in #ifdef NONLIN_FRSURF block. |
| 274 |
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(modification to pressure gradient not yet implemented) |
| 275 |
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o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
| 276 |
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(for U & V) that are used for vertical advection of momentum. |
| 277 |
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|
| 278 |
|
checkpoint48a_post |
| 279 |
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o In preparation for r*, use temp. array to compute vertical transport |
| 280 |
|
in flux-form momentum pkg. => change results of few test-exp. |
| 281 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
| 282 |
|
lab_sea, natl_box & plume_on_slope |
| 283 |
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|
| 284 |
|
checkpoint48 |
| 285 |
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o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
| 286 |
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|
| 287 |
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checkpoint47j_post |
| 288 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
| 289 |
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o moved adexch from forward_step to addummy_in_stepping |
| 290 |
|
o added exch in ctrl_map_... |
| 291 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
| 292 |
|
reverse checkpointing loop |
| 293 |
|
o Yet more changes in gmredi: |
| 294 |
|
* adgmredi_calc_tensor |
| 295 |
|
avoiding all recomputation of gmredi_slope_limit |
| 296 |
|
* adgmredi_x/y/rtransport |
| 297 |
|
added flag for excessive storing to avoid recomp. of |
| 298 |
|
u/v/rtans, dTdx/y/z |
| 299 |
|
-> this is not really necessary and very memory-consuming |
| 300 |
|
* adgmredi_slope_psi: |
| 301 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
| 302 |
|
* gmredi_slope_limit |
| 303 |
|
re-activated full calculation of taperfct for case 'ac02' |
| 304 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
| 305 |
|
|
| 306 |
|
checkpoint47i_post |
| 307 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
| 308 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
| 309 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
| 310 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
| 311 |
|
o gmredi: fix few bugs. |
| 312 |
|
|
| 313 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
| 314 |
|
This will be a good checkpoint to plug into the ecco-branch. |
| 315 |
|
o few modif.'s to get latest version adjointed |
| 316 |
|
(mainly kick out code in ini_linear_phisurf) |
| 317 |
|
o modif's to run adjoint with exactConserv |
| 318 |
|
o case GM_BOLUS_ADVEC should be cleaned |
| 319 |
|
S/R gmredi_slope_psi should be cleaned |
| 320 |
|
o verification/carbon now has exactConserv=.TRUE. |
| 321 |
|
|
| 322 |
|
checkpoint47g_post |
| 323 |
o time-average AIM output: becomes independent from statvars time-average |
o time-average AIM output: becomes independent from statvars time-average |
| 324 |
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
| 325 |
|
o After TAF bug fix: |
| 326 |
|
Tested adjoint of gmredi package. |
| 327 |
|
Tests were done with checkpoint47 rather than with latest |
| 328 |
|
checkpoint47f_post since the latter is broken for the adjoint |
| 329 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
| 330 |
|
Here they are, before they get changed/lost/stolen. |
| 331 |
|
Mostly modif.'s to fix numerical sensitivities. |
| 332 |
|
Gradient checks OK for |
| 333 |
|
- GM_taper_scheme: |
| 334 |
|
* clipping |
| 335 |
|
* ac02 |
| 336 |
|
* linear |
| 337 |
|
* glw91 |
| 338 |
|
* dm95 |
| 339 |
|
* ldd97 |
| 340 |
|
- GMREDI_OPTIONS: |
| 341 |
|
* GM_VISBECK_VARIABLE_K |
| 342 |
|
* GM_NON_UNITY_DIAGONAL |
| 343 |
|
* GM_EXTRA_DIAGONAL |
| 344 |
|
* GM_BOLUS_ADVEC |
| 345 |
|
in conjunction with data.gmredi parameters to be checked in |
| 346 |
|
in a few minutes under verification/carbon/code/ |
| 347 |
|
|
| 348 |
checkpoint47f_post |
checkpoint47f_post |
| 349 |
Merging from release1_p10: |
Merging from release1_p10: |
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