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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint57a_pre |
| 7 |
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o some modifs in tools/build_options for sunos |
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o call ctrl_pack for ctrl at end for optimcycle=0 |
| 9 |
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| 10 |
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checkpoint57 |
| 11 |
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o add horizontal bi-harmonic viscosity for vertical velocity |
| 12 |
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- new parameter viscA4W (defaults to viscA4) |
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- affects only non-hydrostatic code |
| 14 |
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- to be done: no-slip lateral boundary conditions |
| 15 |
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o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 16 |
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o implement Implicit Vertical advection for pTracers |
| 17 |
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o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 18 |
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(implemented also for implicit vertical diffusion & advection) |
| 19 |
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o OBCS: extend application of tracer open boundary conditions |
| 20 |
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to a strip beyond the boundary of width Olx/Oly |
| 21 |
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o add call monitor to TAF set of required calls (flow directives) |
| 22 |
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and include in natl_box_adjoint |
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o untangle a few ifdefs related to cost, ctrl, autodiff |
| 24 |
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untangel a few ALLOW_ECCO_OPTIMIZATION |
| 25 |
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o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
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(theta2, salt2 in ecco_cost_weights) |
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checkpoint56c_post |
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o OBCS as control variables |
| 30 |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 31 |
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- remove balance of obcs controls from default |
| 32 |
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- fix index bug nobcs in ctrl_init |
| 33 |
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- fix dummy fields filen in ctrl_pack |
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- add dummy weights for obcs |
| 35 |
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o lsopt: comment out fort.94 output |
| 36 |
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o optim: |
| 37 |
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- remove unnecessary header files |
| 38 |
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- adjusted namelists |
| 39 |
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- add xerbla.F to Makefile |
| 40 |
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o exf: |
| 41 |
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- multiple modifications of exf_check_range |
| 42 |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
| 43 |
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o mdsio: |
| 44 |
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- i/o-vector change debugLevel from debLevA to debLevB |
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checkpoint56b_post |
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o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
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is called from DO_THE_MODEL_IO |
| 49 |
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- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 50 |
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 51 |
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- clean up PTRACERS_WRITE_TIMEAVE a little |
| 52 |
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o add another verification experiment that tests both the cfc-pkg and |
| 53 |
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the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 54 |
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reactive tendencies treated inline with regular timestepping |
| 55 |
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o testreport previously did a lousy job of comparing small numbers, so |
| 56 |
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we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 57 |
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implemented in the little c-progam tmp_cmpnum.c which is embedded in |
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testreport. |
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o ptracers_monitor: bug fix for MPI |
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| 61 |
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checkpoint56a_post |
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o GCHEM: finish reorganizating the package |
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- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
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(introduces another 3D-array for each passive tracer, but only if |
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GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
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gchemTendency is not needed because the timestep is done separately) |
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- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 69 |
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- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 70 |
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so clear to me how that should be done in a general way. |
| 71 |
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o CFC: improve formatting of output in CFC_ATMOS |
| 72 |
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o PTRACERS: |
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- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 74 |
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that ALL experiments with ptracers enable can be checked. This makes |
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GCHEM_MONITOR obsolete. |
| 76 |
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- include a runtime parameter PTRACERS_monitorFreq that defaults to |
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monitorFreq |
| 78 |
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- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 79 |
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o add PTRACERS (PTR0[1-5]) to testreport output |
| 80 |
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o exf_check_range: |
| 81 |
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* default changed to .TRUE. |
| 82 |
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* will check values for niter0 if debLevA, every timestep if debLevB |
| 83 |
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* STOP in exf_check_range if 'out of range' |
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* range chosen generous to allow for potential extema |
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TBD: a version with stricter range |
| 86 |
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permitted range would be runtime parameters |
| 87 |
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o GMredi: |
| 88 |
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- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 89 |
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- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 90 |
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- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
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o GCHEM: |
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- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 93 |
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the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 94 |
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- introduced a useGCHEM runtime flag and applied it everywhere. |
| 95 |
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- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 96 |
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this flag is now only visible within GCHEM-pkg routines. |
| 97 |
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- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 98 |
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be replaced by a 3D array that is computed before thermodynamics; for |
| 99 |
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this, the tracer ID iTracer had to be included into the parameter list |
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of ptracers_forcing |
| 101 |
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- set up forward_step to call gchem_forcing, that will replace |
| 102 |
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gchem_forcing_int in ptracers_forcing |
| 103 |
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- cleaning up |
| 104 |
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o small cleaning of exch2: remove files that are also in eesupp/src |
| 105 |
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checkpoint56 |
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o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 108 |
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o mnc: cleanup "full" files--fixes out-of-memory problem |
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o ECCO-GODAE |
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* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
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* fully merged and updated from SIO code |
| 112 |
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windstress sign change affects |
| 113 |
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- exf_inscal_[u/v]stress |
| 114 |
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- sign of xx_tau[u/v] adjustments |
| 115 |
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- signs in cost_scat |
| 116 |
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* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 117 |
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* natl_box_adjoint updated and compressed |
| 118 |
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* 2-level checkpoint switch added |
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(tested in EXP. 1 of natl_box_adjoint) |
| 120 |
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* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 121 |
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o SVD |
| 122 |
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* first complete, non-hacked version for SVD calculations |
| 123 |
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* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
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performed via direct access files admtlm_vector.it???? |
| 125 |
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(via ctrl_[un]pack) |
| 126 |
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* optimcycle is used for ARPACK iteration counter |
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(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 128 |
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* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 129 |
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and add linear transforms where necessary |
| 130 |
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* controls are initial/final SST, SSS (can be extended; need to check |
| 131 |
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ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 132 |
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o mdsio: filename info to both stderr, stdout |
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o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
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from sign change |
| 135 |
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| 136 |
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checkpoint55j_post |
| 137 |
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o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 138 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 139 |
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o add consistent build directories and .cvsignore files to verification |
| 140 |
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o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 141 |
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o make all subroutines 30 or less characters in length for certain older |
| 142 |
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compilers to work (a thorough search only turns up two routines in |
| 143 |
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pkg/ptracers) |
| 144 |
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o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 145 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 146 |
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| 147 |
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checkpoint55i_post |
| 148 |
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o change arrays for total vertical diffusivity (2.D if explicit, |
| 149 |
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3.D if implicit) ; each ptracer uses its own background value. |
| 150 |
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o added mnc/NetCDF output capability to ocn_compon_interf |
| 151 |
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- added bits to verification/cpl_aim+ocn so that it can run on |
| 152 |
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ITRDA and other clusters without the mpirun "-wd" option |
| 153 |
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o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 154 |
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configuration |
| 155 |
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o give MNC the ability to create additional files rather than |
| 156 |
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exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 157 |
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- the default is just less than 2GB which is a practical limit |
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on many systems |
| 159 |
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o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 160 |
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or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
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checkpoint55h_post |
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o add verification test "vermix" |
| 164 |
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o remove all the *_ioinc flags and replace with the single global |
| 165 |
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outputTypesInclusive flag |
| 166 |
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o allow to set a vertical profile of vertical diffusivity for T & S |
| 167 |
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o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 168 |
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o useMNC moved from data.mnc to data.pkg |
| 169 |
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|
| 170 |
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checkpoint55g_post |
| 171 |
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o Renaming carbon AD experiments to comply with testreport conventions |
| 172 |
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o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 173 |
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o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 174 |
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have been fixed to avoid recomp. of do_oceanic_phys |
| 175 |
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Works well for global_ocean.90x40x15, |
| 176 |
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but recomp. issue remains for carbon |
| 177 |
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o Updating adjoint output for natl_box_adjoint after |
| 178 |
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pkg/ecco has been modified (see taga c55d_post) |
| 179 |
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|
| 180 |
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checkpoint55f_post |
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o rename to timeave_init_fixed |
| 182 |
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| 183 |
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checkpoint55e_post |
| 184 |
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o some delicate re-shuffle of store directives to avoid one |
| 185 |
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extra call of do_oceanic_physics |
| 186 |
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affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 187 |
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checkpoint_lev1_directives.h |
| 188 |
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o NB: this may break global_ocean adjoint temporarily, |
| 189 |
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but it is clear how to fix it. Will do later, need this now. |
| 190 |
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|
| 191 |
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checkpoint55d_post |
| 192 |
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o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 193 |
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o ecco_cost_weights is modified to 1x1 runs |
| 194 |
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o modifs to allow observations to be read in as |
| 195 |
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single file or yearly files |
| 196 |
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o enable to read exf forcing fields as either |
| 197 |
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single file or yearly files (flag useExfYearlyFields) |
| 198 |
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checkpoint55d_pre |
| 199 |
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|
| 200 |
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o switch between 2-level and 3-level checkpointing |
| 201 |
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o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 202 |
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the full 3D field is never actually stored) arrays to NetCDF files |
| 203 |
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with the correct (that is, the complete multi-dimensional) set of |
| 204 |
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array indicies |
| 205 |
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- used in mom_vecinv() to write the diagFreq output |
| 206 |
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- tested (demonstrated) in verification/aim.5l_cs |
| 207 |
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o further mnc-ification |
| 208 |
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- add verification/lab_sea to the list with mnc setups |
| 209 |
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- fix undefined mnc v-names in cd_code |
| 210 |
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- add kpp to mnc output (both snapshot and timeave) |
| 211 |
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o non-hydrostatic code |
| 212 |
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- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 213 |
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in calc_gw.F |
| 214 |
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- defaults to viscAh |
| 215 |
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- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 216 |
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friction or Leith) in non-hydrostatic mode, as long as there is |
| 217 |
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no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 218 |
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o pkg/cost |
| 219 |
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extend simple cost functions to treat time mean quantities |
| 220 |
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(T,U,V) via cost_accumulate_state from cost_tile |
| 221 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 222 |
be 2 times larger than the minimum size the advection scheme requires. |
be 2 times larger than the minimum size the advection scheme requires. |
| 223 |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 240 |
- updated obcs_check |
- updated obcs_check |
| 241 |
- changed sponge layer relaxation parameter units for days to seconds |
- changed sponge layer relaxation parameter units for days to seconds |
| 242 |
- turned off sponge layer by default |
- turned off sponge layer by default |
| 243 |
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- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 244 |
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- fixed about 35 bugs in obcs_external_fields_load |
| 245 |
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|
| 246 |
checkpoint55c_post |
checkpoint55c_post |
| 247 |
o obcs stuff |
o obcs stuff |
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