| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
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| 7 |
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o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
| 8 |
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usingSphericalGrid, this allows to define the rotated grid coordinates |
| 9 |
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via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
| 10 |
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geographical coordinates according to the inverse of the rotation defined |
| 11 |
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by the Euler angles, so that Coriolis parameter and online-interpolation by |
| 12 |
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exf works with the geographical coordinates on XC/YC/XG/YG. |
| 13 |
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Naturally, this feature does not work with all packages, so some |
| 14 |
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combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
| 15 |
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profiles), because there the coordinates are assumed to be regular |
| 16 |
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spherical grid coordinates. |
| 17 |
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o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
| 18 |
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- introduce isopycnal diffusion coefficient control. |
| 19 |
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o tools/adjoint_options: |
| 20 |
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- additional control vector components. |
| 21 |
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o pkg/mnc: have mnc create marginally meaning full coordinate variables |
| 22 |
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(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
| 23 |
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o pkg/mypackage: |
| 24 |
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- add example of read/write pickup for state-var ; |
| 25 |
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- add entry points to the main code for state-vars diags & write-pickup. |
| 26 |
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o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
| 27 |
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transitions for useExfYearlyFields |
| 28 |
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- add new subroutine that determines the file to read from for |
| 29 |
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use*YearlyFields = .TRUE. and .FALSE. |
| 30 |
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- add a verification experiment to global_with_exf that tests |
| 31 |
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useExfYearlyFields with USE_EXF_INTERPOLATION defined |
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o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
| 33 |
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analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
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subroutines (which could be generated from a template, because they are |
| 35 |
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almost identical), for now they are included in obcs_prescribe_read.F for |
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simplicity |
| 37 |
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o pkg/exf: |
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- add a little more diagnostic to exf_interp_read (in analogy to |
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mds_read_field, can be turned off with debugLevel < debugLevA=1) |
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- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
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ugly but fast by unrolling short inner loops, inserting a unroll=8 |
| 42 |
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directive in routine lagran, and splitting a loop and making do while the |
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outermost loop (the latter requires the intoduction of index arrays) |
| 44 |
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o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
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o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
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http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
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o verification/seaice_obcs: updated for restart test and latest options |
| 48 |
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o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
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ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
| 50 |
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for now this is only available for the C-grid code and also within |
| 51 |
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#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
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|
| 53 |
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checkpoint59m |
| 54 |
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o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
| 55 |
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and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
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o gad_som : fix flux output (& diagnostics) to have same units as other |
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advection scheme fluxes (was previously multiplied by deltaT). |
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o added verification/seaice_obcs both to test seaice open boundaries |
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and to provide an example matlab scrpt for generating them |
| 60 |
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o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
| 61 |
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o pkg/salt_plume: clean up salt_plume_frac.F to |
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remove redundancy in PlumeMethod 1 and 4 |
| 63 |
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o pkg/kpp: added saltplume diagnostics |
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o pkg/obcs and pkg/seaice: |
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- do not set uice and vice to zero when OB*icefile are unspecified |
| 66 |
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- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
| 67 |
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- moved seaice tracer obcs after call to seaice_growth |
| 68 |
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o pkg/salt_plume: added various options for salt plume depth |
| 69 |
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criterion and for vertical distribution of the salt |
| 70 |
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|
| 71 |
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checkpoint59l |
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o pkg/ptracers: new version of ptracers pickup: |
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read meta file and write only fields which are needed to restart. |
| 74 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
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o pkg/seaice: |
| 76 |
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- add timescale for melting due to warm mixed layer as a means of |
| 77 |
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setting SEAICE_availHeatFrac more conveniently |
| 78 |
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- add a CPP-flag/runtime parameter check for flooding algorithm |
| 79 |
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- reformulated availHeat in seaice_growth.F to be independent of AREA |
| 80 |
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o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
| 81 |
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unit changes |
| 82 |
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o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
| 83 |
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o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
| 84 |
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SX vector computer. |
| 85 |
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o pkg/seaice: |
| 86 |
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- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
| 87 |
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seaice forcing fields can now be read only through pkg/exf |
| 88 |
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- removed some unused halos |
| 89 |
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o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
| 90 |
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o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
| 91 |
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or U/VICE from U/VWIND before computing U/VSTRESS |
| 92 |
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|
| 93 |
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checkpoint59k |
| 94 |
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o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
| 95 |
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dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
| 96 |
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o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
| 97 |
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all experiments pass when compile with un-initialised var. checking option. |
| 98 |
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o added pkg/salt_plume |
| 99 |
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o script to test restart (for now, in MITgcm_contrib/jmc_script) |
| 100 |
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o pkg/seaice: new read/write pickup version. |
| 101 |
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read meta file and write only fields which are needed to restart. |
| 102 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 103 |
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o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
| 104 |
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o lab_sea.hb87: modify the domain & update output.hb87.txt : |
| 105 |
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lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
| 106 |
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at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
| 107 |
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process. Fixed here by closing the domain at the Northern boundary. |
| 108 |
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o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
| 109 |
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o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
| 110 |
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a set of consecutive levels in/from a 3-D array. |
| 111 |
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o pkg/ptracers: |
| 112 |
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use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
| 113 |
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to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
| 114 |
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|
| 115 |
|
checkpoint59j |
| 116 |
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o in pkgs: dic, obcs, offline, rbcs: |
| 117 |
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standard way to compute coeff. for time interpolation between 2 time reccords |
| 118 |
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which retains full precision (& make results less dependent on compiler). |
| 119 |
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update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
| 120 |
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o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
| 121 |
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packages instead of reading ice cover and wind speed separately |
| 122 |
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o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
| 123 |
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(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
| 124 |
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to allow to compile customized code before the update) |
| 125 |
|
o cleaning-up: |
| 126 |
|
- fix CPP instruction syntax in pkg/obcs |
| 127 |
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- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
| 128 |
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add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
| 129 |
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- fix some threads issue in IO parts. |
| 130 |
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o pkg/dic: |
| 131 |
|
- add tons of "_d 0" (--> much better testreports !) |
| 132 |
|
and then update outputs of tutorial_global_oce_biogeo |
| 133 |
|
o pkg/mom_fluxform: |
| 134 |
|
add a special version of momentum advection intended to conserve momentum |
| 135 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
| 136 |
|
o new read/write pickup version: |
| 137 |
|
- for now, only implemented for main (mdsio) pickup file. |
| 138 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
| 139 |
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and main pickup together. |
| 140 |
|
- read meta file; read only what is needed to restart; stop if a field |
| 141 |
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is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
| 142 |
|
if it make sense (even if the restart is not perfect). |
| 143 |
|
- if no meta file, assume that pickup to read corresponds exactly to |
| 144 |
|
a pickup that would currently be written. |
| 145 |
|
- read pickup written in the old format (until checkpoint59i) if it |
| 146 |
|
recognizes an old meta file (no field-list). |
| 147 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
| 148 |
|
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
| 149 |
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e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
| 150 |
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b) a meta file describing the content of the associated pickup file |
| 151 |
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e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
| 152 |
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o pkg/mdsio & pkg/rw: |
| 153 |
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- new routine to read a meta file ; new set of routine to read |
| 154 |
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Multiple-fields file (with meta file). |
| 155 |
|
o added open boundary conditions capability for seaice |
| 156 |
|
HSNOW, HSALT, UICE, and VICE |
| 157 |
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|
| 158 |
|
checkpoint59i |
| 159 |
|
o adjoint: |
| 160 |
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* fix multiDimAdvection adjoint |
| 161 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
| 162 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
| 163 |
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* verification/global_ocean.90x45x15 adjoint now tests |
| 164 |
|
NLFS and multiDimAdvection using DST3 (=30) |
| 165 |
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* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
| 166 |
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o pkg/kpp: add "_d 0" to real constant (if missing); |
| 167 |
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update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
| 168 |
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and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
| 169 |
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o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
| 170 |
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for internal parameters related to restart process (formerly from PARAMS.h) |
| 171 |
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and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
| 172 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
| 173 |
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as argument. (only atm2d & obcs write_pickup have not yet been updated) |
| 174 |
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o pkg/monitor: |
| 175 |
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- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
| 176 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
| 177 |
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- account for deep Atmosphere factor and density factor (anelastic) |
| 178 |
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o added open boundary conditions capability for seaice HEFF and AREA |
| 179 |
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o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
| 180 |
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thermodynamics |
| 181 |
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- requires a little reorganization, which affects the testreport results |
| 182 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
| 183 |
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so that now the conservative form is tested |
| 184 |
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- add a few comments |
| 185 |
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o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
| 186 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
| 187 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
| 188 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
| 189 |
|
thermodynamic growth rates |
| 190 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
| 191 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
| 192 |
|
Affects results @ truncation level (cg2d match) and update output of |
| 193 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
| 194 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
| 195 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
| 196 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
| 197 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
| 198 |
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|
| 199 |
|
checkpoint59h |
| 200 |
|
o pkg/exf: |
| 201 |
|
- improve vectorization by moving if-statement out of loops in |
| 202 |
|
exf_mapfields, exf_radiation |
| 203 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
| 204 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
| 205 |
|
o testreport: |
| 206 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
| 207 |
|
monitor & update offline_exf_seaice exp. output. |
| 208 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
| 209 |
|
o pkg/seaice: |
| 210 |
|
- bug fix in the evp solver: boundary conditions were affected be |
| 211 |
|
masking of zMax/zMin (changes results) |
| 212 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
| 213 |
|
(changes results for no_slip) |
| 214 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
| 215 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
| 216 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
| 217 |
|
stress formulation and no-slip boundary conditions |
| 218 |
|
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
| 219 |
|
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
| 220 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
| 221 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
| 222 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
| 223 |
|
without requiring DO-IF statements |
| 224 |
|
o pkg/thsice: |
| 225 |
|
use continuous power-law function for partition of energy between lateral |
| 226 |
|
melting/freezing and thinning/thickening ; old code using step function |
| 227 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
| 228 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
| 229 |
|
o testreport: change AD testing : check against results/output_adm.txt |
| 230 |
|
using same scripts as for forward test. |
| 231 |
|
|
| 232 |
|
checkpoint59g |
| 233 |
|
o adjoint testing: in preparation for changing testreport: |
| 234 |
|
- output format: cost and grad written on separated lines |
| 235 |
|
- ad output results in directory "results" (instead of "results_ad") |
| 236 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 237 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
| 238 |
|
o pkg/ecco: allow user defined cost function contributions |
| 239 |
|
o testreport: |
| 240 |
|
Allow to choose (per experiment) the list of tested output variables |
| 241 |
|
and the main variable (used to issue a pass/FAIL ) ; |
| 242 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 243 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 244 |
|
Also modify printing of summary: |
| 245 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
| 246 |
|
b) echo the list of tested variables in the individual summary.txt of |
| 247 |
|
each experiment. |
| 248 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 249 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 250 |
|
(but still depend on the tile decompostion of the domain). |
| 251 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
| 252 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
| 253 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
| 254 |
|
the solution to the stress coupling issues with the B-grid. |
| 255 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
| 256 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
| 257 |
|
o pkg/thsice: |
| 258 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 259 |
|
- fix reshaping of sea-ice just after advection: |
| 260 |
|
melt all the ice only if ice-volume is too small. |
| 261 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 262 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 263 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 264 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 265 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 266 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 267 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 268 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 269 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 270 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
| 271 |
|
-> update output.txt |
| 272 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 273 |
|
this affects truncation error: -> update output.txt of exp: |
| 274 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 275 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 276 |
|
|
| 277 |
|
checkpoint59f |
| 278 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 279 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 280 |
|
a bounded range (in forward mode) |
| 281 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
| 282 |
|
internal parameter controls, completements of implementations |
| 283 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 284 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 285 |
|
(not seem any difference in testing results). |
| 286 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 287 |
|
at face corners. |
| 288 |
|
o pkg/generic_advdiff: |
| 289 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 290 |
|
loop range indices for computing vertical advection tendency |
| 291 |
|
and do the calculation in the interior only (no overlap) ; |
| 292 |
|
for now, only implemented for SOM advection (to save CPU time). |
| 293 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 294 |
o exch2 adjoint |
o exch2 adjoint |
| 295 |
First set of changes: |
First set of changes: |
| 296 |
- add exch2 hand-written adjoint templates |
- add exch2 hand-written adjoint templates |
| 300 |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 301 |
that used to hide exch2 or cubed-sphere specific code |
that used to hide exch2 or cubed-sphere specific code |
| 302 |
(commented via 'cph-exch2') |
(commented via 'cph-exch2') |
| 303 |
|
o pkg/seaice |
| 304 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 305 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 306 |
|
output of global_ocean.cs32x15.thsice . |
| 307 |
|
|
| 308 |
checkpoint59e |
checkpoint59e |
| 309 |
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 503 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
| 504 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
| 505 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
| 506 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
| 507 |
|
are no longer updating the vertical diffusivity array |
| 508 |
|
(passed as argument) but are (re-) setting those arrays. |
| 509 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
| 510 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
| 511 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |
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