| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
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Revision history for branch c24_e25_ice |
| 7 |
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(branch for adding sea-ice code to ecco-branch) |
| 8 |
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| 9 |
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02/11/03 cvs tag ecco_ice1 |
| 10 |
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Updated verification/natl_box_forward and natl_box_adjoint |
| 11 |
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for SGI platform |
| 12 |
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| 13 |
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12/06/02 |
| 14 |
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Branched off tag ecco_c44_e25 |
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================================================================= |
| 17 |
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| 18 |
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ecco_c44_e25 |
| 19 |
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o Merging some GM changes from main trunk (c47) to ecco-branch. |
| 20 |
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o Updating verif. natl_box_adjoint with GMRedi. |
| 21 |
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o Adding setup with explicit differentiaton of pressure solver. |
| 22 |
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o Bug fix: missing OBCS_OPTIONS.h for sponge layer code. |
| 23 |
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o (Re-?) Commiting old bug fixes in kpp to ecco-branch |
| 24 |
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(kpp_calc.F, kpp_routines.F) |
| 25 |
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o exf: |
| 26 |
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updated external forcing package |
| 27 |
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- cleaned old exfa stuff |
| 28 |
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- bug fixes |
| 29 |
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(missing OBCS_OPTIONS.h in two routines) |
| 30 |
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- enable easy to use "no forcing". |
| 31 |
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- added exf I/O for atmospheric loading |
| 32 |
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- added exf I/O for runoff data |
| 33 |
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- transfered scaling between exf <-> MITgcm to exf namelist |
| 34 |
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|
| 35 |
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ecco_c44_e24 |
| 36 |
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o modifications to gradient check package (Martin Losch) |
| 37 |
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- enable centered differences |
| 38 |
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- modified format of standard output |
| 39 |
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o bug fix for nwettile contents |
| 40 |
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so far assumed global sum in first entry (1,1,k), |
| 41 |
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needed for global control vector |
| 42 |
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-> introduced new variable nwet[c/w/s]global(nr) |
| 43 |
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o shifts of calls to cal/exf package to be accessible |
| 44 |
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in MITgcm stand-alone |
| 45 |
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o shifted packages_init_variables before convective_adjustment_ini |
| 46 |
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(corresponding update of TAF tape initialisation). |
| 47 |
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o removed auxiliary field in impldiff |
| 48 |
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(caused numerical differences for GMRedi cases) |
| 49 |
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o updated obcs control part (G. Gebbie) |
| 50 |
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o removed some f90 comments ("!") |
| 51 |
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o Bug fixes and updates in cost package |
| 52 |
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* cost_final: correct multiplier mult_tauv, mult_sflux |
| 53 |
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* cost_hyd: added call cost_ssh |
| 54 |
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* cost_init_barfiles.F: replaced arrays by tmpfld's |
| 55 |
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* cost_readtopexmean.F: ersmask -> tpmeanmask |
| 56 |
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* cost_weights.F: corrected wtheta[2], wsalt[2] |
| 57 |
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o cleaned exchanges in cg2d.F |
| 58 |
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|
| 59 |
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ecco_c44_e23 |
| 60 |
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merged patches between release1_p1 and release1_p2: |
| 61 |
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o fixed array boundary problem for adjoint |
| 62 |
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(related to partial recomputation within subroutine |
| 63 |
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related to dynamics -> calc_viscosity -> mom_... |
| 64 |
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o fixed recomputation in thermodynamics |
| 65 |
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o prepare (but not complete) recomputation problem in impldiff |
| 66 |
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o fixed problem for adjoint of global_max |
| 67 |
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o switched off sponge layer code in external_forcing |
| 68 |
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Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie) |
| 69 |
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| 70 |
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ecco_c44_e22 |
| 71 |
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o Finally, the merges with the Scripps cost function terms: |
| 72 |
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Various additions, modifications, quality checks. |
| 73 |
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o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle |
| 74 |
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monitoring of adjoint state. |
| 75 |
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o Plus: removed comm_stats, ini_communication_patterns from diff. list |
| 76 |
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(no more need to "keep" MPI headers for adjoint generation) |
| 77 |
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o Plus: exf changes: |
| 78 |
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o added run-off routine |
| 79 |
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o additional storing needed for ustress,vstess |
| 80 |
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because of state-dependent quality check |
| 81 |
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o added missing initialisations |
| 82 |
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o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch |
| 83 |
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NB: - verification/natl_box_adjoint/ 240 steps run |
| 84 |
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* looks ok under Linux (twain.lcs.mit.edu) |
| 85 |
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* looks ok on MIT SUN's (fjord.mit.edu) |
| 86 |
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* NaN in reverse mode on Scripps SUN's at iter=214 |
| 87 |
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* NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204 |
| 88 |
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- 1 year forward int. global 2x2 deg. produces similar cost functions |
| 89 |
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* all cost terms of new code are slightly smaller (0.5 to 3%). |
| 90 |
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|
| 91 |
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ecco_c44_e21 |
| 92 |
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o reversed order of ctrl/cost initialisation |
| 93 |
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o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions |
| 94 |
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o modified to enable ctrl field swapping |
| 95 |
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o bug fix for global sum of ncvarlength in ctrl_init |
| 96 |
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o no more call to ctrl_unpack from ctrl_init |
| 97 |
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o no more write of ctrl vector in ctrl_pack |
| 98 |
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however, init. of control vector from ctrl_unpack |
| 99 |
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o various bug fixes & consistent nobcs handling in |
| 100 |
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ctrl_pack/unpack routines (by G. Gebbie) |
| 101 |
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o optim package: Added obcs control part for lsopt I/O |
| 102 |
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(by G. Gebbie) |
| 103 |
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o missing call to obcs_diags |
| 104 |
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o moved calls in packages_init_fixed to packages_readparms |
| 105 |
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because some quantities are needed earlier. |
| 106 |
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|
| 107 |
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ecco_c44_e20 |
| 108 |
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o before major merges from the Scripps setup |
| 109 |
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here are two small updates: |
| 110 |
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- field swapping for surface flux controls enabled |
| 111 |
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(remains t.b.d. for atmos. state plus obcs) |
| 112 |
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- bug fix in active_file.F for xz-/yz- routines |
| 113 |
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- added missing xz-/yz- routines to active_file_ad.F |
| 114 |
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|
| 115 |
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ecco_c44_e19 |
| 116 |
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o merged necessary patches: |
| 117 |
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- AD-related changes for GMRedi |
| 118 |
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- fixes i KPP (delZ -> drF) |
| 119 |
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- hook to OBCS songe layer code in external_forcing |
| 120 |
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- errorMessageUnit non-zero in eeboot.F |
| 121 |
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- included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. |
| 122 |
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|
| 123 |
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ecco_c44_e18 |
| 124 |
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o sponge layer code for obcs was missing |
| 125 |
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- added hook in external_forcing.F |
| 126 |
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- added storing for TAF |
| 127 |
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o new routine cost_init_barfiles to initialise |
| 128 |
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adjoint fields adtbar, adsbar, adpsbar |
| 129 |
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(needed in conjunction with corrected ladinit for active I/O) |
| 130 |
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o cleaned up and corrected order in packages_readparms, ecco_readparms |
| 131 |
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o corrected and simplified weights for obcs controls |
| 132 |
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- weight fields simplified |
| 133 |
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- bug fix in ctrl_pack |
| 134 |
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- no more write of control vector in ctrl_pack |
| 135 |
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o i/j index bug fixes in cost_ssh_mean |
| 136 |
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|
| 137 |
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ecco_c44_e17 |
| 138 |
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o bug fixes in cost package |
| 139 |
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* wrong identifier for active I/O of monthly mean psbar |
| 140 |
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(cost_averagesfields, cost_ssh) xx_psbar_dummy |
| 141 |
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* cleaned all identifier for active I/O of monthly fields |
| 142 |
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* wrong ladinit in various cost routines |
| 143 |
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o merge with interval (chkpt44c_post - chkpt44d_post) |
| 144 |
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* added missing EXCLUDE_MONITOR flags |
| 145 |
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* changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 146 |
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(incompatible typ in MIN/MAX expressions caused problems |
| 147 |
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on IBM SP3) |
| 148 |
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* in genmake added variable MAKEDEPEND |
| 149 |
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plus resetting for case SunOS |
| 150 |
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added timer_stats.c routine for IBM SP3 |
| 151 |
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* removed variables in dynamics |
| 152 |
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|
| 153 |
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ecco_c44_e16 |
| 154 |
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o new ECCO checkpoint, the first since ecco_c43_e15 |
| 155 |
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which is branched from MITgcm. |
| 156 |
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All changes were merged in between (see ecco-branch-mod? tags). |
| 157 |
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o last changes: |
| 158 |
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* assuming path for TAF and TAMC are known (e.g. in $path) |
| 159 |
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* genmake: |
| 160 |
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- added tools/xmakedepend to circumvene shortcoming of |
| 161 |
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SUN's makedepend (size too small) |
| 162 |
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- invoking ../tools/xmakedepend instead of makedepend |
| 163 |
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- changed compiler flags for case SunOS |
| 164 |
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|
| 165 |
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ecco-branch-mod5 |
| 166 |
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o mod's to reproduce open boundary run |
| 167 |
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o enable field swapping for OB's and climatology |
| 168 |
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o update store directives for OB control |
| 169 |
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o added option ALLOW_OBCS_PRESCRIBE |
| 170 |
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o call of getobcs now out of obcs_calc (param. list modified) |
| 171 |
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|
| 172 |
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ecco-branch-mod4 |
| 173 |
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o this is the second part of changes necessary to reconcile |
| 174 |
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the natl_box_adjoint verification (with and without grdchk). |
| 175 |
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>>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<< |
| 176 |
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>>>!!! AND ecco-branch-mod4 !!!<<< |
| 177 |
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>>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK !!!<<< |
| 178 |
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- genmake: removed $S64 overwrite for case SunOS |
| 179 |
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- pkg/exf: update and corrections for field swapping and obcs |
| 180 |
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- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 181 |
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harmonized between ECCO and MITgcm |
| 182 |
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- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 183 |
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updated checkpointing_lev... lists for obcs |
| 184 |
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- model/src: minor changes in forward_step, plot_field |
| 185 |
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- pkg/mdsio: added mdsio_gl_slice |
| 186 |
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|
| 187 |
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ecco-branch-mod3 |
| 188 |
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o this is the first part of changes necessary to reconcile |
| 189 |
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natl_box_adjoint verification (with and without grdchk). |
| 190 |
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This set of changes is relevant for ECCO only. |
| 191 |
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The next set/tag of changes (ecco-branch-mod4) |
| 192 |
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should be merged into the main trunk. |
| 193 |
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- update some options |
| 194 |
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- parameter lists of ecco_the_model_main and ecco_the_main_loop |
| 195 |
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differed from those of the MITgcm counterparts. |
| 196 |
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|
| 197 |
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ecco-branch-mod2 |
| 198 |
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o update ecco-branch-mod1 to checkpoint44 |
| 199 |
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o exclude from updates: |
| 200 |
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- verification/ |
| 201 |
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- adjoint/ |
| 202 |
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- pkg/cost |
| 203 |
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- pkg/ctrl |
| 204 |
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- pkg/ecco |
| 205 |
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- pkg/obcs |
| 206 |
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- model/src/the_model_main.F |
| 207 |
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- model/src/the_main_loop.F |
| 208 |
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|
| 209 |
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checkpoint44 |
| 210 |
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o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping) |
| 211 |
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o fix bug in mom_vi_del2uv |
| 212 |
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o added some stuff for AD |
| 213 |
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|
| 214 |
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ecco-branch-mod1 |
| 215 |
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o based on c43 |
| 216 |
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o replaced packages cost, ctrl, ecco, obcs |
| 217 |
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o removed MITgcm verif.'s, added ECCO verif.'s |
| 218 |
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o added lsopt, optim for line search optimization. |
| 219 |
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|
| 220 |
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checkpoint43 |
| 221 |
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o added two new advection tests |
| 222 |
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o added global 4x4 degree ocean test |
| 223 |
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o added test of H&S94 with free surface on cube |
| 224 |
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o some final mods for gradient check, adjoint,... |
| 225 |
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|
| 226 |
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checkpoint42 |
| 227 |
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Fixed AD-related problems: |
| 228 |
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o Store directives up-to-date with re-arranged Adams-Bashforth |
| 229 |
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(mainly thermodynamics.F) |
| 230 |
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o New store directives for multi-dim. advection schemes |
| 231 |
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* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
| 232 |
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* new common block and key passkey |
| 233 |
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(mainly gad_advection.F) |
| 234 |
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o Modified store directives for split of dynamics/thermodynamics |
| 235 |
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for the case ALLOW_KPP |
| 236 |
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o Cleaned argument list for timestep_tracer.F |
| 237 |
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|
| 238 |
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checkpoint41 |
| 239 |
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o re-formatted/added comments in prologues of key subroutines |
| 240 |
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to work with protex |
| 241 |
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|
| 242 |
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checkpoint40 |
| 243 |
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o moved calc_gs, calc_gt and calc_tr1 back to model/src |
| 244 |
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o added FLT (floats) package from Arne along with demo. experiment |
| 245 |
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o re-arranged Adams-Bashforth scheme for tracers to allow easier |
| 246 |
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implementation of forward-in-time forcing terms |
| 247 |
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o more mods for non-linear free-surface including new variable |
| 248 |
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o modified multi-dim method to work on cube |
| 249 |
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o bug fix in KPP (from DM) |
| 250 |
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|
| 251 |
|
checkpoint40pre9 |
| 252 |
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o added DST advection schemes |
| 253 |
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o fix MPI bug on SGI's |
| 254 |
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o modifications for non-linear free-surface |
| 255 |
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o fixed conditionals for fixed flow/passive tracer only mode |
| 256 |
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o added tension/strain form of stress tensor |
| 257 |
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o changes to commenting of arguments for TAF/TAMC |
| 258 |
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o added/updated many matlab scripts |
| 259 |
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o added multi-dimensional advection method for tracers |
| 260 |
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|
| 261 |
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checkpoint40pre8 |
| 262 |
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o new package rw/ |
| 263 |
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Added method for dumping intermediate local arrays: |
| 264 |
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mdsio_writetile - same as mdsio_writefield except works from inside |
| 265 |
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bi,bj loop |
| 266 |
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mdsio_writelocal - same as mdsio_writetile except works for local |
| 267 |
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arrays |
| 268 |
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write_local_r? - higher-level wrapper for mdsio_writelocal |
| 269 |
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Controlled by diagFreq. Defaults to zero (ie. no dumps) |
| 270 |
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Example given at end of mom_vecinv.F that dumps some local arrays. |
| 271 |
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o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
| 272 |
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control flux-form versus vector invariant code. |
| 273 |
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Switch is runtime flag vectorInvariantMomentum (defaults to false) |
| 274 |
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or genmake -DISABLE ... |
| 275 |
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o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
| 276 |
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(additional storing is now needed for case vecinv; |
| 277 |
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currently nothing implemented to switch this storing off |
| 278 |
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in case fluxform is used since no CPP flag available). |
| 279 |
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|
| 280 |
|
checkpoint40pre7 |
| 281 |
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o bug fix in dynamics.F |
| 282 |
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calc_viscosity called before k=1,Nr loop. |
| 283 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
| 284 |
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o cleaned initialisations in ctrl_map_ini |
| 285 |
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related to TAF |
| 286 |
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|
| 287 |
|
checkpoint40pre6 |
| 288 |
|
o split dynamics into thermodynamics & dynamics |
| 289 |
|
o corresponding split of calc_diffusivity into |
| 290 |
|
calc_diffusivity, calc_viscosity |
| 291 |
|
(kpp_calc_diff, kpp_calc_visc). |
| 292 |
|
o Added diffkr, kapgm to control variables |
| 293 |
|
o bug fix in gmredi_slope_limit for ldd97 |
| 294 |
|
|
| 295 |
|
checkpoint40pre5 |
| 296 |
|
o proper initialization of Adams-Bashforth time stepping |
| 297 |
|
+ uses forward step for very first step of model (iter=0) |
| 298 |
|
o re-generated *all* output since almost all output is modified by this |
| 299 |
|
change (sorry but we've been putting this one off for about 2 years) |
| 300 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
| 301 |
|
*not* regenerated since they are already out of date and I don't |
| 302 |
|
want to create the impression that they are suddenly working. |
| 303 |
|
o removed KAP stuff for DEC's |
| 304 |
|
o modified/added many .cvsignore files in */code and */input |
| 305 |
|
o added new expt "solid-body.cs-32x32x1" |
| 306 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
| 307 |
|
is not necessarily any better than the current one... |
| 308 |
|
|
| 309 |
|
checkpoint40pre4 |
| 310 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
| 311 |
|
calc_common_factors which are crucial for TAF. |
| 312 |
|
o extended iMin,jMin range for calc_common_factors, |
| 313 |
|
calc_diffusivity |
| 314 |
|
o added option ALLOW_PASSIVE_TRACER |
| 315 |
|
o a few minor updates and fixes |
| 316 |
|
|
| 317 |
|
checkpoint40pre3 |
| 318 |
|
o created calc_gtr1.F for gad package |
| 319 |
|
o split the_main_loop and re-introduced forward_step |
| 320 |
|
o some recomputations of nIter0 for TAMC |
| 321 |
|
|
| 322 |
|
checkpoint40pre2 |
| 323 |
|
o Updated to latest branch of AJA, JMC |
| 324 |
|
o Added gradient check package |
| 325 |
|
o Added routines for passive tracer handling |
| 326 |
|
o Added carbon sequestration sensitivity experiment |
| 327 |
|
|
| 328 |
|
checkpoint39 |
| 329 |
|
o Modifications and fixes to support TAMC |
| 330 |
|
(mainly missing or wrong directives) |
| 331 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
| 332 |
|
in addummy_in_stepping |
| 333 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
| 334 |
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
| 335 |
|
o Included following packages: |
| 336 |
|
cal: calendar |
| 337 |
|
exf: external forcing |
| 338 |
|
ecco: essential routines to control use of cal, exf |
| 339 |
|
(NB: this is not the full ECCO environment) |
| 340 |
|
o disabled some packages by default in genmake |
| 341 |
|
|
| 342 |
|
checkpoint38 |
| 343 |
|
o see notes_c37_adj.txt |
| 344 |
|
o corrected wrong layer index in external_forcing_t |
| 345 |
|
o replaced the_main_loop/forward_step by the_main_loop |
| 346 |
|
o removed forceoutput from write_state |
| 347 |
|
(replaced criteria for initial/final state) |
| 348 |
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
| 349 |
|
|
| 350 |
|
checkpoint37 |
| 351 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
| 352 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
| 353 |
|
used unless genmake -disable=mdsio) |
| 354 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
| 355 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
| 356 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
| 357 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
| 358 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
| 359 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
| 360 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
| 361 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
| 362 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
| 363 |
|
and after) unless activating 2 commented lines in initialise-varia. |
| 364 |
|
o Non-Hydrostatic pickup file Pb fixed. |
| 365 |
|
o bug with Rigid-lid version (since c35) fixed. |
| 366 |
|
|
| 367 |
|
checkpoint36 |
| 368 |
|
o implement Crank-Nickelson barotropic time-stepping |
| 369 |
|
o recover Time-Average diagnostics |
| 370 |
|
o fix Pb in checkpoint (PR#19) |
| 371 |
|
o AIM become a standard package ; clean unused CPP_kees |
| 372 |
|
|
| 373 |
|
checkpoint35 |
| 374 |
|
o subtantial rewrite of dynamics.f |
| 375 |
|
o allows staggered time-stepping |
| 376 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
| 377 |
|
o added bottom drag (linear + quadratic) |
| 378 |
|
|
| 379 |
|
checkpoint34 |
| 380 |
|
o Modified exchange routines for correct reverse simulation. |
| 381 |
|
o Added verification output to comply with bug fix in impldiff.F |
| 382 |
|
as of c33 (exp2, natl_box). |
| 383 |
|
o Corrected store directives in dynamics.F |
| 384 |
|
o Corrected array boundaries in impldiff.F |
| 385 |
|
o Corrected array dimensions in gmredi. |
| 386 |
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
| 387 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
| 388 |
|
o Added mdsio_gl.F for ECCO purposes. |
| 389 |
|
|
| 390 |
|
checkpoint33 |
| 391 |
|
o Fixed bug in lower BC in impldiff.F |
| 392 |
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
| 393 |
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
| 394 |
|
- Removed verification/natl_box/code/external_fields_scale.F |
| 395 |
|
(did not differ from that in model/src) |
| 396 |
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
| 397 |
|
(see FFIELDS.h for description) |
| 398 |
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
| 399 |
|
kpp_calc.F and kpp_transport_t.F |
| 400 |
|
- Removed model/src/external_fields_scale.F and calls to it |
| 401 |
|
- verification/natl_box uses flux data with "atmospheric" sign so |
| 402 |
|
a special version of external_fields_load.F is used to |
| 403 |
|
change the data as it's read in. This way, the arrays |
| 404 |
|
have the right units and signs at all times tha a user could |
| 405 |
|
possibly use them. |
| 406 |
|
o Corrected genmake to delete a temporary file during configuration |
| 407 |
|
|
| 408 |
checkpoint32 |
checkpoint32 |
| 409 |
o Scaling of forcing fields moved from external_forcing.F to |
o Scaling of forcing fields moved from external_forcing.F to |
| 410 |
external_fields_scale.F, called directly after loading fields. |
external_fields_scale.F, called directly after loading fields. |
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