| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o vertical grid option: allow to put the Interface at the middle between |
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2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 8 |
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o GM Advective form: Tracers are advected using the residual transport (= |
| 9 |
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Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 10 |
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| 11 |
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checkpoint44g_post |
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o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 13 |
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results) ; ifdef missing in thermodynamics.F |
| 14 |
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| 15 |
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checkpoint44f_pre,checkpoint44f_post |
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o added PTRACERS package |
| 17 |
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This allows an arbitrary number of passive tracers to be integrated |
| 18 |
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forward simultaneously with the dynamicaly model. |
| 19 |
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+ Implemented so far: |
| 20 |
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- basic forward algorithm (time-stepping, advection, diffusion, convection) |
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- I/O and checkpointing |
| 22 |
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- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 23 |
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+ Not implemented so far: |
| 24 |
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- KPP |
| 25 |
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- OBCS |
| 26 |
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+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
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necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
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line in data.pkg. |
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+ This package is disabled by default since it increases storage. |
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| 31 |
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o testscript: added -cleanup option |
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o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
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b) enable to filter 2D fields. |
| 35 |
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checkpoint44e_pre,post |
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o re-wrote convective adjustment to use pre-calculated weights |
| 38 |
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Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
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Adds: model/src/convective_weights.F, convectively_mixtracer.F |
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Original calls to convect() still in place. |
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chkpt44d_pre,post |
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o added missing EXCLUDE_MONITOR flags |
| 44 |
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o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
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(incompatible typ in MIN/MAX expressions caused problems |
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on IBM SP3) |
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o in genmake added variable MAKEDEPEND |
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plus resetting for case SunOS |
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o added timer_stats.c routine for IBM SP3 |
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o removed variables in dynamics |
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!!! I forgot to create tag chkpt44d_pre !!! |
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!!! But chkpt44d_pre = chkpt44c_post !!! |
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o real fresh water flux implemented with non-linear free-surface. |
| 55 |
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chkpt44c_pre,post |
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o few fix (mask in shap_s2, EmPmR in external_field_load, |
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USE_NATURAL_BCS in solve_for_P); |
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o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 60 |
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| 61 |
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checkpoint44b_pre/_post |
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o merge of relevant stuff from the ecco-branch: |
| 63 |
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- genmake: removed $S64 overwrite for case SunOS |
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- pkg/exf: update and corrections for field swapping and obcs |
| 65 |
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- pkg/ecco: parameter lists for the_model_main, the_main_loop |
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harmonized between ECCO and MITgcm |
| 67 |
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- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 68 |
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updated checkpointing_lev... lists for obcs |
| 69 |
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- model/src: minor changes in forward_step, plot_field |
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added directive for divided adjoint in the_main_loop |
| 71 |
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- pkg/mdsio: added mdsio_gl_slice |
| 72 |
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| 73 |
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o check parameters & config (chkpt44a_pre,post) |
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o OBC and NonLin_FrSurf. |
| 75 |
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| 76 |
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checkpoint44 |
| 77 |
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o fix bug in mom_vi_del2uv |
| 78 |
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o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 79 |
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o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 80 |
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o update AIM experiments (NCEP input files) |
| 81 |
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o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 82 |
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o added some stuff for AD |
| 83 |
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| 84 |
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checkpoint43 |
| 85 |
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o added two new advection tests |
| 86 |
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o added global 4x4 degree ocean test |
| 87 |
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o added test of H&S94 with free surface on cube |
| 88 |
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o some final mods for gradient check, adjoint,... |
| 89 |
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|
| 90 |
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checkpoint42 |
| 91 |
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Fixed AD-related problems: |
| 92 |
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o Store directives up-to-date with re-arranged Adams-Bashforth |
| 93 |
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(mainly thermodynamics.F) |
| 94 |
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o New store directives for multi-dim. advection schemes |
| 95 |
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* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
| 96 |
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* new common block and key passkey |
| 97 |
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(mainly gad_advection.F) |
| 98 |
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o Modified store directives for split of dynamics/thermodynamics |
| 99 |
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for the case ALLOW_KPP |
| 100 |
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o Cleaned argument list for timestep_tracer.F |
| 101 |
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|
| 102 |
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checkpoint41 |
| 103 |
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o re-formatted/added comments in prologues of key subroutines |
| 104 |
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to work with protex |
| 105 |
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| 106 |
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checkpoint40 |
| 107 |
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o moved calc_gs, calc_gt and calc_tr1 back to model/src |
| 108 |
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o added FLT (floats) package from Arne along with demo. experiment |
| 109 |
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o re-arranged Adams-Bashforth scheme for tracers to allow easier |
| 110 |
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implementation of forward-in-time forcing terms |
| 111 |
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o more mods for non-linear free-surface including new variable |
| 112 |
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o modified multi-dim method to work on cube |
| 113 |
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o bug fix in KPP (from DM) |
| 114 |
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|
| 115 |
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checkpoint40pre9 |
| 116 |
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o added DST advection schemes |
| 117 |
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o fix MPI bug on SGI's |
| 118 |
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o modifications for non-linear free-surface |
| 119 |
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o fixed conditionals for fixed flow/passive tracer only mode |
| 120 |
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o added tension/strain form of stress tensor |
| 121 |
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o changes to commenting of arguments for TAF/TAMC |
| 122 |
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o added/updated many matlab scripts |
| 123 |
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o added multi-dimensional advection method for tracers |
| 124 |
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| 125 |
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checkpoint40pre8 |
| 126 |
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o new package rw/ |
| 127 |
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Added method for dumping intermediate local arrays: |
| 128 |
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mdsio_writetile - same as mdsio_writefield except works from inside |
| 129 |
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bi,bj loop |
| 130 |
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mdsio_writelocal - same as mdsio_writetile except works for local |
| 131 |
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arrays |
| 132 |
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write_local_r? - higher-level wrapper for mdsio_writelocal |
| 133 |
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Controlled by diagFreq. Defaults to zero (ie. no dumps) |
| 134 |
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Example given at end of mom_vecinv.F that dumps some local arrays. |
| 135 |
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o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
| 136 |
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control flux-form versus vector invariant code. |
| 137 |
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Switch is runtime flag vectorInvariantMomentum (defaults to false) |
| 138 |
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or genmake -DISABLE ... |
| 139 |
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o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
| 140 |
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(additional storing is now needed for case vecinv; |
| 141 |
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currently nothing implemented to switch this storing off |
| 142 |
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in case fluxform is used since no CPP flag available). |
| 143 |
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|
| 144 |
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checkpoint40pre7 |
| 145 |
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o bug fix in dynamics.F |
| 146 |
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calc_viscosity called before k=1,Nr loop. |
| 147 |
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o added some #ifdef's ALLOW_PASSIVE_TRACER |
| 148 |
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o cleaned initialisations in ctrl_map_ini |
| 149 |
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related to TAF |
| 150 |
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|
| 151 |
|
checkpoint40pre6 |
| 152 |
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o split dynamics into thermodynamics & dynamics |
| 153 |
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o corresponding split of calc_diffusivity into |
| 154 |
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calc_diffusivity, calc_viscosity |
| 155 |
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(kpp_calc_diff, kpp_calc_visc). |
| 156 |
|
o Added diffkr, kapgm to control variables |
| 157 |
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o bug fix in gmredi_slope_limit for ldd97 |
| 158 |
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|
| 159 |
|
checkpoint40pre5 |
| 160 |
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o proper initialization of Adams-Bashforth time stepping |
| 161 |
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+ uses forward step for very first step of model (iter=0) |
| 162 |
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o re-generated *all* output since almost all output is modified by this |
| 163 |
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change (sorry but we've been putting this one off for about 2 years) |
| 164 |
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+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
| 165 |
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*not* regenerated since they are already out of date and I don't |
| 166 |
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want to create the impression that they are suddenly working. |
| 167 |
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o removed KAP stuff for DEC's |
| 168 |
|
o modified/added many .cvsignore files in */code and */input |
| 169 |
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o added new expt "solid-body.cs-32x32x1" |
| 170 |
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+ this uses an alternative form of ini_curvilinear_grid.F which |
| 171 |
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is not necessarily any better than the current one... |
| 172 |
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|
| 173 |
|
checkpoint40pre4 |
| 174 |
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o added re-initialisations of utrans,vtrans,rtrans in |
| 175 |
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calc_common_factors which are crucial for TAF. |
| 176 |
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o extended iMin,jMin range for calc_common_factors, |
| 177 |
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calc_diffusivity |
| 178 |
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o added option ALLOW_PASSIVE_TRACER |
| 179 |
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o a few minor updates and fixes |
| 180 |
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|
| 181 |
|
checkpoint40pre3 |
| 182 |
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o created calc_gtr1.F for gad package |
| 183 |
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o split the_main_loop and re-introduced forward_step |
| 184 |
|
o some recomputations of nIter0 for TAMC |
| 185 |
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|
| 186 |
|
checkpoint40pre2 |
| 187 |
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o Updated to latest branch of AJA, JMC |
| 188 |
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o Added gradient check package |
| 189 |
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o Added routines for passive tracer handling |
| 190 |
|
o Added carbon sequestration sensitivity experiment |
| 191 |
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|
| 192 |
|
checkpoint39 |
| 193 |
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o Modifications and fixes to support TAMC |
| 194 |
|
(mainly missing or wrong directives) |
| 195 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
| 196 |
|
in addummy_in_stepping |
| 197 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
| 198 |
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o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
| 199 |
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o Included following packages: |
| 200 |
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cal: calendar |
| 201 |
|
exf: external forcing |
| 202 |
|
ecco: essential routines to control use of cal, exf |
| 203 |
|
(NB: this is not the full ECCO environment) |
| 204 |
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o disabled some packages by default in genmake |
| 205 |
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|
| 206 |
|
checkpoint38 |
| 207 |
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o see notes_c37_adj.txt |
| 208 |
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o corrected wrong layer index in external_forcing_t |
| 209 |
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o replaced the_main_loop/forward_step by the_main_loop |
| 210 |
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o removed forceoutput from write_state |
| 211 |
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(replaced criteria for initial/final state) |
| 212 |
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o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
| 213 |
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|
| 214 |
|
checkpoint37 |
| 215 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
| 216 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
| 217 |
|
used unless genmake -disable=mdsio) |
| 218 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
| 219 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
| 220 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
| 221 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
| 222 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
| 223 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
| 224 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
| 225 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
| 226 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
| 227 |
|
and after) unless activating 2 commented lines in initialise-varia. |
| 228 |
|
o Non-Hydrostatic pickup file Pb fixed. |
| 229 |
|
o bug with Rigid-lid version (since c35) fixed. |
| 230 |
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|
| 231 |
|
checkpoint36 |
| 232 |
|
o implement Crank-Nickelson barotropic time-stepping |
| 233 |
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o recover Time-Average diagnostics |
| 234 |
|
o fix Pb in checkpoint (PR#19) |
| 235 |
|
o AIM become a standard package ; clean unused CPP_kees |
| 236 |
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|
| 237 |
|
checkpoint35 |
| 238 |
|
o subtantial rewrite of dynamics.f |
| 239 |
|
o allows staggered time-stepping |
| 240 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
| 241 |
|
o added bottom drag (linear + quadratic) |
| 242 |
|
|
| 243 |
|
checkpoint34 |
| 244 |
|
o Modified exchange routines for correct reverse simulation. |
| 245 |
|
o Added verification output to comply with bug fix in impldiff.F |
| 246 |
|
as of c33 (exp2, natl_box). |
| 247 |
|
o Corrected store directives in dynamics.F |
| 248 |
|
o Corrected array boundaries in impldiff.F |
| 249 |
|
o Corrected array dimensions in gmredi. |
| 250 |
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
| 251 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
| 252 |
|
o Added mdsio_gl.F for ECCO purposes. |
| 253 |
|
|
| 254 |
|
checkpoint33 |
| 255 |
|
o Fixed bug in lower BC in impldiff.F |
| 256 |
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
| 257 |
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
| 258 |
|
- Removed verification/natl_box/code/external_fields_scale.F |
| 259 |
|
(did not differ from that in model/src) |
| 260 |
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
| 261 |
|
(see FFIELDS.h for description) |
| 262 |
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
| 263 |
|
kpp_calc.F and kpp_transport_t.F |
| 264 |
|
- Removed model/src/external_fields_scale.F and calls to it |
| 265 |
|
- verification/natl_box uses flux data with "atmospheric" sign so |
| 266 |
|
a special version of external_fields_load.F is used to |
| 267 |
|
change the data as it's read in. This way, the arrays |
| 268 |
|
have the right units and signs at all times tha a user could |
| 269 |
|
possibly use them. |
| 270 |
|
o Corrected genmake to delete a temporary file during configuration |
| 271 |
|
|
| 272 |
|
checkpoint32 |
| 273 |
|
o Scaling of forcing fields moved from external_forcing.F to |
| 274 |
|
external_fields_scale.F, called directly after loading fields. |
| 275 |
|
o Surface relaxation terms added to surface tendency fields in |
| 276 |
|
extra subroutine. |
| 277 |
|
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
| 278 |
|
fields. |
| 279 |
|
o Changes in GMRedi to comply with packaging structure. |
| 280 |
|
o Modifications and bug fixes in KPP package. |
| 281 |
|
o Verification experiment for KPP added (verification/nat_box/) |
| 282 |
|
|
| 283 |
|
checkpoint31 |
| 284 |
|
o Packages interface brought in line with defined standard |
| 285 |
|
-> new routines packages_...F |
| 286 |
|
-> changes in initialise_fixed.F, initialise_varia.F |
| 287 |
|
-> enables initialisation interface for ECCO package |
| 288 |
|
o Rescaling of external forcing fields immediately after read |
| 289 |
|
(removed from external_forcing.F) |
| 290 |
|
-> new: surface_fields_scale.F |
| 291 |
|
-> affects ini_foorcing.F, external_fields_load.F |
| 292 |
|
o Computation of surface tendencies before tendency updates. |
| 293 |
|
-> new: external_forcing_surf.F |
| 294 |
|
o Change of variable names useGMRedi, useKPP, useECCO |
| 295 |
|
o Further changes in dynamics.F, impldiff.F for TAMC |
| 296 |
|
o Tested for experiments 0, 2, 4. |
| 297 |
|
- not yet tested for GMRedi. |
| 298 |
|
- not yet tested for KPP. |
| 299 |
|
|
| 300 |
|
checkpoint30 |
| 301 |
|
o Updates for OBCs |
| 302 |
|
o New experiment for test OBCs (internal_wave) |
| 303 |
|
o New output.txt in verification/exp4/results/ |
| 304 |
|
o Updates for KPP: calculation of viscosity corrected, new variables |
| 305 |
|
kpp_dumpFreq and kpp_taveFreq |
| 306 |
|
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
| 307 |
|
and entry for T90 in genmake |
| 308 |
|
|
| 309 |
|
checkpoint29 |
| 310 |
|
o packaged KPP and GM/Redi |
| 311 |
|
|
| 312 |
|
checkpoint28 |
| 313 |
|
o Corrected initialization of hFacMin for difference vertical coordinates |
| 314 |
|
o Modified calculation of partial cell thickness to more robust algorithm |
| 315 |
|
o config_summary.F: replaced write_1D_... by write_0D_... |
| 316 |
|
read_write.F: added subroutines write_0D_... |
| 317 |
|
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
| 318 |
|
included some initialisations required for TAMC. |
| 319 |
|
o routine calc_isoslopes: modified sqrt computation to make it |
| 320 |
|
differentiable for zero argument. |
| 321 |
|
o routines dynamics, impldiff: |
| 322 |
|
included store directives and tape key computations required for TAMC. |
| 323 |
|
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
| 324 |
|
|
| 325 |
|
checkpoint27 |
| 326 |
|
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
| 327 |
|
formulation works properly with variable resolution. |
| 328 |
|
o restructured the calling tree between the_model_main() and dynamics() |
| 329 |
|
o split initialise() into initialise_fixed() and initialise_varia() |
| 330 |
|
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
| 331 |
|
in new routine ini_psurf() |
| 332 |
|
|
| 333 |
|
checkpoint26 |
| 334 |
|
o moved some #ifdef in optional routines to encompass everything |
| 335 |
|
except the argument declarations. This was using up some memory. |
| 336 |
|
o fixed macros like _ADT to work with both versions of Linux cpp |
| 337 |
|
o cleaned up some unused and uninitialized variables |
| 338 |
|
(helps when debugging with strict compile options) |
| 339 |
|
o split up CPP_EEOPTIONS.h into options and macros |
| 340 |
|
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
| 341 |
|
o patch for 2 processor JAM mode |
| 342 |
|
|
| 343 |
|
checkpoint25 |
| 344 |
|
o updates for OBCs and NH |
| 345 |
|
o dramatically reduced memory usage |
| 346 |
|
o added "JAM" routines for use on Artic network |
| 347 |
|
o parameterization of convection by implicit vertical diffusion |
| 348 |
|
o added a diagnostic of convective index |
| 349 |
|
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
| 350 |
|
(this is was partly for OBCs and NH but also in anticipation of |
| 351 |
|
an explicit free-surface option) |
| 352 |
|
o initial state input files for U and V |
| 353 |
|
|
| 354 |
|
checkpoint24 |
| 355 |
|
o Removed some spurious "REAL"s |
| 356 |
|
o Updated KPP to latest version from JPL |
| 357 |
|
o Added a COS(latitude) in horizontal viscosity |
| 358 |
|
|
| 359 |
|
checkpoint23 |
| 360 |
|
o Added del^4 diffusion for salt and temperature |
| 361 |
|
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
| 362 |
|
|
| 363 |
|
checkpoint22 |
| 364 |
|
o Made many small changes: implicit none, format(i5), etc... |
| 365 |
|
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
| 366 |
|
|
| 367 |
|
checkpoint21 |
| 368 |
|
o Introduced new I/O package that supports direct-access records (mdsio.F) |
| 369 |
|
o Split-up mid-level I/O routines |
| 370 |
|
o Updated input data for experiments 0,1,2,4 and 5 |
| 371 |
|
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
| 372 |
|
|
| 373 |
|
checkpoint20 |
| 374 |
|
o Tidied up open-boundaries some more |
| 375 |
|
o Added non-hydrostatic code |
| 376 |
|
o Fixed some input data |
| 377 |
|
o Modified MPI start-up to work in "coupled" context. |
| 378 |
|
|
| 379 |
|
checkpoint19 |
| 380 |
|
o Tidied up directory structure for verification experiments. |
| 381 |
|
o Added new code for open boundaries. |
| 382 |
|
o Corrected advective terms near boundaries. |
| 383 |
|
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
| 384 |
|
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
| 385 |
|
o Split default parameters out of ini_parms.F into set_defaults.F. |
| 386 |
|
|
| 387 |
|
checkpoint18 |
| 388 |
|
o Further changes for optional code generation with |
| 389 |
|
CPP - ugh! |
| 390 |
|
|
| 391 |
|
checkpoint17 |
| 392 |
|
o Beginning to incorporating modularity |
| 393 |
|
for supporting atmos. and ocean configs. |
| 394 |
|
o Small changes for TAMC complinace |
| 395 |
|
o New ultra simple test case. Barotropic box |
| 396 |
|
configuration "exp0". |
| 397 |
|
|
| 398 |
checkpoint16 |
checkpoint16 |
| 399 |
o Minor changes to exchange routines to support |
o Minor changes to exchange routines to support |
| 400 |
accumulation in reverse mode. Adjoint of an |
accumulation in reverse mode. Adjoint of an |
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