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| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
| 5 |
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| 6 |
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o fix MNC coordinate variables so that they now contain per-face index |
| 7 |
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values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
| 8 |
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general, EXCH2 grids are only aligned to a "local" coordinate system |
| 9 |
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o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
| 10 |
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o Implement instantaneous output within pkg diagnostics: |
| 11 |
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setting a negative frequency in data.diagnostics produces |
| 12 |
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"snap-shot" output (as opposed to time-average if freq > 0) |
| 13 |
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o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
| 14 |
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NOTE: change ptracer diagnostics name: use 2 characters to work with |
| 15 |
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more than 9 tracers. Add also diagnostics of advect & diffus flux. |
| 16 |
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o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
| 17 |
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becomes the coordinate variable for the 'T' dimension |
| 18 |
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o add CF-style coordinate variables to MNC |
| 19 |
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- just a first cut: numbers are meaningless on the cubesphere and |
| 20 |
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missing along the T axis but otherwise it works! |
| 21 |
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o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
| 22 |
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o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
| 23 |
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o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
| 24 |
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this is based directly on what the model compute, so that the content of |
| 25 |
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each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
| 26 |
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o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
| 27 |
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o clean up build options files for SunOS, in particular |
| 28 |
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- remove -traditional from xmakedepend |
| 29 |
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- change -xarch=v9 to -xarch=native for f77 |
| 30 |
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- restore use of make (not gmake) |
| 31 |
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- add CC=gcc if using g77 |
| 32 |
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o changes per discussion of AM, JMC, & EH3 today: |
| 33 |
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- move redundant "grid" variables out of "state" -- in preparation of |
| 34 |
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creating proper CF-style coordinate variables and in recognition |
| 35 |
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that any/all grid variables can be easily copied (eg. w/NCO) from |
| 36 |
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the grid files into any of the other NetCDF files |
| 37 |
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- *always* output grid variables with MDSIO (this will eventually be |
| 38 |
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changed) |
| 39 |
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- output MNC grid file if useMNC is true |
| 40 |
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o every instance of _END_MASTER() has been found and replaced with |
| 41 |
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_END_MASTER( myThid ) in order to satisfy certain picky Sun |
| 42 |
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preprocessors |
| 43 |
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o re-arrange diagnostics pkg initialisation: |
| 44 |
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- allow each package to extend the available diagnostics list |
| 45 |
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- add some checking and fix small problems (multi-threaded, ...) |
| 46 |
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- new S/R diagnostics_fill (replace fill_diagnostics): |
| 47 |
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look through the short list of active diag. (instead of the long list) |
| 48 |
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create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
| 49 |
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| 50 |
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checkpoint57a_post |
| 51 |
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o this set of changes restores TAMC compatibility |
| 52 |
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tested for global_ocean.90x40x15 adjoint on trough |
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(what a pain) |
| 54 |
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| 55 |
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checkpoint57a_pre |
| 56 |
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o some modifs in tools/build_options for sunos |
| 57 |
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o call ctrl_pack for ctrl at end for optimcycle=0 |
| 58 |
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|
| 59 |
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checkpoint57 |
| 60 |
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o add horizontal bi-harmonic viscosity for vertical velocity |
| 61 |
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- new parameter viscA4W (defaults to viscA4) |
| 62 |
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- affects only non-hydrostatic code |
| 63 |
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- to be done: no-slip lateral boundary conditions |
| 64 |
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o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 65 |
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o implement Implicit Vertical advection for pTracers |
| 66 |
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o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 67 |
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(implemented also for implicit vertical diffusion & advection) |
| 68 |
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o OBCS: extend application of tracer open boundary conditions |
| 69 |
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to a strip beyond the boundary of width Olx/Oly |
| 70 |
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o add call monitor to TAF set of required calls (flow directives) |
| 71 |
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and include in natl_box_adjoint |
| 72 |
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o untangle a few ifdefs related to cost, ctrl, autodiff |
| 73 |
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untangel a few ALLOW_ECCO_OPTIMIZATION |
| 74 |
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o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
| 75 |
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(theta2, salt2 in ecco_cost_weights) |
| 76 |
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| 77 |
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checkpoint56c_post |
| 78 |
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o OBCS as control variables |
| 79 |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 80 |
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- remove balance of obcs controls from default |
| 81 |
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- fix index bug nobcs in ctrl_init |
| 82 |
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- fix dummy fields filen in ctrl_pack |
| 83 |
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- add dummy weights for obcs |
| 84 |
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o lsopt: comment out fort.94 output |
| 85 |
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o optim: |
| 86 |
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- remove unnecessary header files |
| 87 |
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- adjusted namelists |
| 88 |
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- add xerbla.F to Makefile |
| 89 |
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o exf: |
| 90 |
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- multiple modifications of exf_check_range |
| 91 |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
| 92 |
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o mdsio: |
| 93 |
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- i/o-vector change debugLevel from debLevA to debLevB |
| 94 |
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|
| 95 |
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checkpoint56b_post |
| 96 |
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o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 97 |
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is called from DO_THE_MODEL_IO |
| 98 |
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- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 99 |
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 100 |
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- clean up PTRACERS_WRITE_TIMEAVE a little |
| 101 |
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o add another verification experiment that tests both the cfc-pkg and |
| 102 |
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the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 103 |
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reactive tendencies treated inline with regular timestepping |
| 104 |
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o testreport previously did a lousy job of comparing small numbers, so |
| 105 |
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we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 106 |
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implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 107 |
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testreport. |
| 108 |
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o ptracers_monitor: bug fix for MPI |
| 109 |
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|
| 110 |
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checkpoint56a_post |
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o GCHEM: finish reorganizating the package |
| 112 |
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- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 113 |
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(introduces another 3D-array for each passive tracer, but only if |
| 114 |
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GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 115 |
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gchemTendency is not needed because the timestep is done separately) |
| 116 |
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- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 117 |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 118 |
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- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 119 |
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so clear to me how that should be done in a general way. |
| 120 |
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o CFC: improve formatting of output in CFC_ATMOS |
| 121 |
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o PTRACERS: |
| 122 |
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- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 123 |
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that ALL experiments with ptracers enable can be checked. This makes |
| 124 |
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GCHEM_MONITOR obsolete. |
| 125 |
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- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 126 |
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monitorFreq |
| 127 |
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- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 128 |
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o add PTRACERS (PTR0[1-5]) to testreport output |
| 129 |
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o exf_check_range: |
| 130 |
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* default changed to .TRUE. |
| 131 |
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* will check values for niter0 if debLevA, every timestep if debLevB |
| 132 |
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* STOP in exf_check_range if 'out of range' |
| 133 |
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* range chosen generous to allow for potential extema |
| 134 |
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TBD: a version with stricter range |
| 135 |
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permitted range would be runtime parameters |
| 136 |
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o GMredi: |
| 137 |
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- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 138 |
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- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 139 |
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- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 140 |
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o GCHEM: |
| 141 |
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- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 142 |
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the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 143 |
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- introduced a useGCHEM runtime flag and applied it everywhere. |
| 144 |
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- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 145 |
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this flag is now only visible within GCHEM-pkg routines. |
| 146 |
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- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 147 |
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be replaced by a 3D array that is computed before thermodynamics; for |
| 148 |
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this, the tracer ID iTracer had to be included into the parameter list |
| 149 |
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of ptracers_forcing |
| 150 |
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- set up forward_step to call gchem_forcing, that will replace |
| 151 |
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gchem_forcing_int in ptracers_forcing |
| 152 |
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- cleaning up |
| 153 |
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o small cleaning of exch2: remove files that are also in eesupp/src |
| 154 |
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|
| 155 |
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checkpoint56 |
| 156 |
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o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 157 |
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o mnc: cleanup "full" files--fixes out-of-memory problem |
| 158 |
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o ECCO-GODAE |
| 159 |
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* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 160 |
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* fully merged and updated from SIO code |
| 161 |
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windstress sign change affects |
| 162 |
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- exf_inscal_[u/v]stress |
| 163 |
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- sign of xx_tau[u/v] adjustments |
| 164 |
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- signs in cost_scat |
| 165 |
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* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 166 |
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* natl_box_adjoint updated and compressed |
| 167 |
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* 2-level checkpoint switch added |
| 168 |
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(tested in EXP. 1 of natl_box_adjoint) |
| 169 |
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* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 170 |
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o SVD |
| 171 |
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* first complete, non-hacked version for SVD calculations |
| 172 |
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* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 173 |
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performed via direct access files admtlm_vector.it???? |
| 174 |
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(via ctrl_[un]pack) |
| 175 |
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* optimcycle is used for ARPACK iteration counter |
| 176 |
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(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 177 |
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* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 178 |
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and add linear transforms where necessary |
| 179 |
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* controls are initial/final SST, SSS (can be extended; need to check |
| 180 |
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ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 181 |
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o mdsio: filename info to both stderr, stdout |
| 182 |
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o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 183 |
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from sign change |
| 184 |
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|
| 185 |
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checkpoint55j_post |
| 186 |
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o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 187 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 188 |
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o add consistent build directories and .cvsignore files to verification |
| 189 |
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o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 190 |
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o make all subroutines 30 or less characters in length for certain older |
| 191 |
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compilers to work (a thorough search only turns up two routines in |
| 192 |
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pkg/ptracers) |
| 193 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 194 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 195 |
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|
| 196 |
|
checkpoint55i_post |
| 197 |
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o change arrays for total vertical diffusivity (2.D if explicit, |
| 198 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 199 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 200 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 201 |
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ITRDA and other clusters without the mpirun "-wd" option |
| 202 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 203 |
|
configuration |
| 204 |
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o give MNC the ability to create additional files rather than |
| 205 |
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exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 206 |
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- the default is just less than 2GB which is a practical limit |
| 207 |
|
on many systems |
| 208 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 209 |
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or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 210 |
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|
| 211 |
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checkpoint55h_post |
| 212 |
|
o add verification test "vermix" |
| 213 |
|
o remove all the *_ioinc flags and replace with the single global |
| 214 |
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outputTypesInclusive flag |
| 215 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 216 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 217 |
|
o useMNC moved from data.mnc to data.pkg |
| 218 |
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|
| 219 |
|
checkpoint55g_post |
| 220 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 221 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 222 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 223 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 224 |
|
Works well for global_ocean.90x40x15, |
| 225 |
|
but recomp. issue remains for carbon |
| 226 |
|
o Updating adjoint output for natl_box_adjoint after |
| 227 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 228 |
|
|
| 229 |
|
checkpoint55f_post |
| 230 |
|
o rename to timeave_init_fixed |
| 231 |
|
|
| 232 |
|
checkpoint55e_post |
| 233 |
|
o some delicate re-shuffle of store directives to avoid one |
| 234 |
|
extra call of do_oceanic_physics |
| 235 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 236 |
|
checkpoint_lev1_directives.h |
| 237 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 238 |
|
but it is clear how to fix it. Will do later, need this now. |
| 239 |
|
|
| 240 |
|
checkpoint55d_post |
| 241 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 242 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 243 |
|
o modifs to allow observations to be read in as |
| 244 |
|
single file or yearly files |
| 245 |
|
o enable to read exf forcing fields as either |
| 246 |
|
single file or yearly files (flag useExfYearlyFields) |
| 247 |
|
checkpoint55d_pre |
| 248 |
|
|
| 249 |
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o switch between 2-level and 3-level checkpointing |
| 250 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 251 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 252 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 253 |
|
array indicies |
| 254 |
|
- used in mom_vecinv() to write the diagFreq output |
| 255 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 256 |
|
o further mnc-ification |
| 257 |
|
- add verification/lab_sea to the list with mnc setups |
| 258 |
|
- fix undefined mnc v-names in cd_code |
| 259 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 260 |
|
o non-hydrostatic code |
| 261 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 262 |
|
in calc_gw.F |
| 263 |
|
- defaults to viscAh |
| 264 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 265 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 266 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 267 |
|
o pkg/cost |
| 268 |
|
extend simple cost functions to treat time mean quantities |
| 269 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 270 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 271 |
|
be 2 times larger than the minimum size the advection scheme requires. |
| 272 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 273 |
|
o GGL90 (Gaspar's TKE mixed layer) |
| 274 |
|
- add horizontal diffusion of TKE, requires exchanges in |
| 275 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
| 276 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
| 277 |
|
mixing coefficients are computed from a horizontal average of TKE of |
| 278 |
|
6 points or so. I think that diffusion has a little more physical |
| 279 |
|
justification. |
| 280 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
| 281 |
|
was in vain) |
| 282 |
|
- mask tke-variable in ggl90_init |
| 283 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
| 284 |
|
o fix biharmonic diffusion on CS-grid. |
| 285 |
|
o more obcs stuff |
| 286 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
| 287 |
|
for reading boundary values. This routine is called from |
| 288 |
|
obcs_prescribe_read |
| 289 |
|
- updated obcs_check |
| 290 |
|
- changed sponge layer relaxation parameter units for days to seconds |
| 291 |
|
- turned off sponge layer by default |
| 292 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 293 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 294 |
|
|
| 295 |
|
checkpoint55c_post |
| 296 |
|
o obcs stuff |
| 297 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
| 298 |
|
- re-arranged obcs_calc |
| 299 |
|
- moved exf_getobcs to obcs_prescibe_read |
| 300 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
| 301 |
|
and independent of it (executable can contain all). |
| 302 |
|
- updated obcs_check |
| 303 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
| 304 |
|
These may be necessary only if tangential velocities are |
| 305 |
|
prescribed at OB, not sure, needs testing. |
| 306 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
| 307 |
|
which simplifies the calls and passes the ifc check-bounds test |
| 308 |
|
|
| 309 |
|
checkpoint55b_post |
| 310 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
| 311 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
| 312 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
| 313 |
|
affects advect_cs results (for the wrong reason): update output.txt |
| 314 |
o use a more standard discretization for biharmonic viscosity ; |
o use a more standard discretization for biharmonic viscosity ; |
| 315 |
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
| 316 |
affects results of dome set-up: update output.txt |
affects results of dome set-up: update output.txt |
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