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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/layers: |
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- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
| 9 |
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- fix calculation of layer non-weighted velocity and layer probability |
| 10 |
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- add diagnostics for pot.density used for layer averaging |
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o pkg/seaice: |
| 12 |
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- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
| 13 |
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positiveness, modify a few comments and improve variable names, |
| 14 |
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- the changed computation of deltaC affects most seaice-related |
| 15 |
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experiments at the truncation level. |
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seaice_itd.thermo is affected by far the most, with |
| 17 |
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only 7 digits of agreement remaining; update experiments. |
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|
| 19 |
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checkpoint65l (2015/05/04) |
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o pkg/shelfice: |
| 21 |
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- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
| 22 |
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factor drKp1 to zero where it is negative (ie. do not use |
| 23 |
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SHELFICEBoundaryLayer if hFacC>1) |
| 24 |
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- the same for factor drLoc in shelfice_forcing.F |
| 25 |
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o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
| 26 |
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with modules in ptracers, when using testreport option "-small_f" |
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o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
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- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
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o verification/testreport |
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- add new option -small_f |
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with this option testreport first makes the target small_f (*.f files) |
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before running make (all). This is useful for explicit inlining when |
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all sources need to be full available. |
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o pkg/exf/exf_interp.F: |
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remove previous changes related to reverse (decreasing) input grids latitude |
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|
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checkpoint65k (2015/04/01) |
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o pkg/ecco: |
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fix missing cosphi initialization; use eccoiter in place of optimcycle; |
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if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
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instead of active read/write |
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o pkg/ctrl: |
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if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
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instead of active read/write. |
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o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
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return if .NOT.useAUTODIFF |
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o pkg/seaice: add CPP brackets (cost function related). |
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o model/src: |
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add useAUTODIFF run time switch. |
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o pkg/exf/exf_interp.F: |
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add code to allow input grids with latitude starting in the north (i.e. when |
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j=1 corresponds to northern edge of field); modify global_with_exf to test |
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this feature. |
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o verification/testreport: |
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- replace "grep -A3" with POSIX conformal sed command, because there are |
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implementations of grep that cannot do contextual searches |
| 57 |
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- replace "cat -n" by "nl" (two occurrences), because not all implementations |
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of "cat" have the option "-n" |
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o model/src: |
| 60 |
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add new file gsw_teos10.F that contains 3 functions, more or less a copy |
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of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
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convert from conservative to potential temperature. For now they are not |
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called anywhere. |
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o pkg/ggl90: make "useIDEMIX" useful |
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- re-organize code in s/r ggl90_calc a little to move computations that |
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are different for idemix into separate loops (changes verification |
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experiment idemix at truncation level, 12 digits remain -> updated) |
| 68 |
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- requires 2 new 2D fields KappaM, verticalShear |
| 69 |
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- make hFacI and recip_hFacI local 3D variables that are passed to |
| 70 |
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s/r ggl90_idemix |
| 71 |
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- fix and improve some comments |
| 72 |
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checkpoint65j (2015/02/25) |
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o pkg/openad |
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- synchronize seawater.F with version in model/src: replace routine |
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body of sw_temp by calling sw_ptmp and fix/add a few comments. |
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o pkg/mnc: |
| 78 |
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- change default value of pickup_read/write_mnc params to FALSE |
| 79 |
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(since few features are missing in reading MNC pickup files). |
| 80 |
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o model/src: |
| 81 |
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- change default (background) vertical diffusivity for salt to be the |
| 82 |
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temperature (background) vertical diffusivity. |
| 83 |
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- change background vertical diffusivity in vertical mixing pkgs ggl90, |
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kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
| 85 |
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This makes ptracers default diffusivity (that uses salt diffKr) more |
| 86 |
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consistent with vertical mixing schemes. |
| 87 |
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o verification/testreport: |
| 88 |
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- fix typo in "-pcls" option ; |
| 89 |
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- put temp files in /tmp (instead of in local dir) |
| 90 |
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- add option "-ncad" to use genmake2 new option "-nocat4ad" |
| 91 |
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- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
| 92 |
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o pkg/ggl90 (idemix code): |
| 93 |
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- apply few fixes ; add some missing "_d 0" ; update output of exp. |
| 94 |
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global_ocean.90x40x15.idemix |
| 95 |
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o OpenAD |
| 96 |
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- enable active file I/O and begin removal of work-around code |
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for OpenAD for handling control variables (memory vs. active files) |
| 98 |
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- new CPP options file OPENAD_OPTIONS.h |
| 99 |
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- revert to genarr2d gradient check for hs94.1x64x5 |
| 100 |
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- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
| 101 |
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- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
| 102 |
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o tools/genmake2: |
| 103 |
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- add option for an alternative Makefile (from Martin) where multiple |
| 104 |
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source files are sent to TAF (instead of all in one file). |
| 105 |
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o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
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- code provided by Carsten Eden as an extension of ggl90 |
| 107 |
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- so far the code is turned on within ggl90 by setting a CPP-flag at |
| 108 |
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compile time; a runtime flag implementation is not yet complete |
| 109 |
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- tested in new verification experiment global_ocean.90x40x15.idemix |
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o verification: |
| 111 |
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- reduce length of the AD test run by half for experiments |
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global_ocean.cs32x15 (std + thsice) and isomip |
| 113 |
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- enable active file I/O for OpenAD, adjust verifications accordingly |
| 114 |
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- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
| 115 |
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o verification/testreport: |
| 116 |
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- fix two non-POSIX sed statements so that there are no error messages |
| 117 |
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on Mac OS X |
| 118 |
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- replace hostname -s with hostname | sed 's/\..*$//' |
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o model/src/seawater.F: |
| 120 |
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- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
| 121 |
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(following the matlab code), which would have avoided the bug caught |
| 122 |
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by Matt (see below) in the first place |
| 123 |
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o pkg/shelfice: |
| 124 |
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- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
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and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
| 126 |
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- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
| 127 |
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ice-shelf case (i.e., within surface level). |
| 128 |
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- add config summary in shelfice_check.F |
| 129 |
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- remove global variable recip_SHELFICElatentHeat and replace by a local |
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variable recip_latentHeat |
| 131 |
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- introduce diagnostics for friction velocity uStar (in case of |
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SHELFICEuseGammaFrict) |
| 133 |
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- change verification experiment isomip.htd: |
| 134 |
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+ start from pickup (as input_ad at nIter0=8640) |
| 135 |
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+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
| 136 |
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+ test SHELFICEuseGammaFrict = .TRUE. |
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+ test SHELFICEadvDiffHeatFlux = .TRUE. |
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o model/src: |
| 139 |
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- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
| 140 |
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in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
| 141 |
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update output of experiments global_with_exf.yearly and isomip (all 6). |
| 142 |
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o pkg/shelfice: |
| 143 |
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- change setting of kTopC to also be zero where there is no ice-shelf. |
| 144 |
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- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
| 145 |
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ice-shelf is. |
| 146 |
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- first attempt to get RealFreshWaterFlux effects: for now, only without |
| 147 |
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SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
| 148 |
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o pkg/seaice: add the option to prescribe a fixed thickness PDF |
| 149 |
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for thermodynamic calculations |
| 150 |
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- because of divisions of the type 7/7 not exactly equal to 1, this change |
| 151 |
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affects results of some verification experiments by up to 4 digits: |
| 152 |
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global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
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seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
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adjoint: lab_sea, lab_sea.noseaicedyn |
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-> updated |
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|
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checkpoint65i (2015/01/23) |
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o model/src: |
| 159 |
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- change units of frictionHeating field from W to W/m^2 |
| 160 |
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- fix bug in frictional heating from stratospheric drag in |
| 161 |
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S/R ATM_PHYS_TENDENCY_APPLY_V |
| 162 |
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- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 163 |
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field from load_fields_driver.F to thermodynamics.F ; |
| 164 |
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- add diagnostics for frictional heating. |
| 165 |
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o model/src & gmredi K3D: |
| 166 |
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- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 167 |
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- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 168 |
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- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
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and name in pickup file). |
| 170 |
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- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 171 |
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o model/src: |
| 172 |
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- move (from ini_forcing.F) initialisation of all arrays in header file |
| 173 |
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FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 174 |
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(since Nov 2012) with option selectAddFluid=1. |
| 175 |
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o pkg/shelfice: |
| 176 |
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- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 177 |
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- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 178 |
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o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 179 |
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o pkg/seaice: two new runtime parameters: |
| 180 |
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- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 181 |
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long overdue |
| 182 |
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- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 183 |
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parameterization of tensil stress for fast ice (does not do anything yet) |
| 184 |
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o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 185 |
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for LSR: move checking overlaps out of JFNK-if-block |
| 186 |
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o pkg/atm_phys: |
| 187 |
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- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 188 |
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new S/R ATM_PHYS_DYN2PHYS. |
| 189 |
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- fix level height for Linear Free-Surf case (to be consistent with |
| 190 |
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fixed-in-time pressure levels). |
| 191 |
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o pkg/mom_common (bottomdrag): |
| 192 |
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- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 193 |
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to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 194 |
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update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 195 |
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o pkg/shelfice (u/v_drag): |
| 196 |
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- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 197 |
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- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 198 |
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(now similar to shelfice_u_drag.F) |
| 199 |
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- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 200 |
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from mom_vecinv.F (similar to mom_fluxform calls). |
| 201 |
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o pkg/mom_common (bottomdrag): |
| 202 |
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- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 203 |
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- add options for alternative discretisation of velocity norm in quadratic |
| 204 |
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bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 205 |
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(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 206 |
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improves when averaging only the other component (e.g. vVel for U bottom |
| 207 |
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drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 208 |
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- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 209 |
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friction (no-slip BC) thus getting the true distance from the bottom; |
| 210 |
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off by default since this also reduces model stability (explicit bottom |
| 211 |
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friction). Changes produce different machine truncation with linear-drag |
| 212 |
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+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 213 |
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front_relax (bvp & mxl, 10 & 11 digits). |
| 214 |
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o model/src & mom pkgs: |
| 215 |
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- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 216 |
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since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 217 |
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- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 218 |
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just copy level Nr value to level Nr+1. |
| 219 |
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o doc: |
| 220 |
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- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 221 |
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o pkg/streamice: |
| 222 |
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- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 223 |
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SHELFICE.h: move array shelficemass to init_varia, initialise |
| 224 |
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from array shelficemassinit, which is set in init_fixed and |
| 225 |
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has option to be set from file; introduce array |
| 226 |
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shelficeMassDynTend array, set thru file in init_fixed |
| 227 |
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- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 228 |
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shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 229 |
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pkg/streamice |
| 230 |
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- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 231 |
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SHELFICEMassStepping = .true. |
| 232 |
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- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 233 |
|
|
| 234 |
|
checkpoint65h (2014/12/17) |
| 235 |
o verification/global_ocean.90x40x15, global_ocean_ebm: |
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 236 |
- update to generic controls. |
- update to generic controls. |
| 237 |
o pkg/ctrl: |
o pkg/ctrl: |
| 238 |
- ctrl_map_ini_genarr.F: test for igen>0 |
- ctrl_map_ini_genarr.F: test for igen>0 |
| 239 |
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 240 |
- move gentim2d part of ctrl_map_ini_genarr.F to |
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 241 |
new separate routine : ctrl_map_ini_gentim2d.F |
new separate routine : ctrl_map_ini_gentim2d.F |
| 242 |
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 243 |
add time variable weights and cyclic controls (time mean, |
add time variable weights and cyclic controls (time mean, |
| 244 |
seasonal cycle, etc) capabilities to gentim2d |
seasonal cycle, etc) capabilities to gentim2d |
| 245 |
o pkg/ecco: |
o pkg/ecco: |
| 246 |
- move reading of error, conversion to weights from |
- move reading of error, conversion to weights from |
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