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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 script to test restart (for now, in MITgcm_contrib/jmc_script) |
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o pkg/seaice: new read/write pickup version. |
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read meta file and write only fields which are needed to restart. |
| 10 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 11 |
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o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
| 12 |
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o lab_sea.hb87: modify the domain & update output.hb87.txt : |
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lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
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at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
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process. Fixed here by closing the domain at the Northern boundary. |
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o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
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o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
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a set of consecutive levels in/from a 3-D array. |
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o pkg/ptracers: |
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use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
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to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
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|
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checkpoint59j |
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o in pkgs: dic, obcs, offline, rbcs: |
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standard way to compute coeff. for time interpolation between 2 time reccords |
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which retains full precision (& make results less dependent on compiler). |
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update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
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o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
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packages instead of reading ice cover and wind speed separately |
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o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
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(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
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to allow to compile customized code before the update) |
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o cleaning-up: |
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- fix CPP instruction syntax in pkg/obcs |
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- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
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add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
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- fix some threads issue in IO parts. |
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o pkg/dic: |
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- add tons of "_d 0" (--> much better testreports !) |
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and then update outputs of tutorial_global_oce_biogeo |
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o pkg/mom_fluxform: |
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add a special version of momentum advection intended to conserve momentum |
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next to a bathymetry step or a coastline edge. (default = off = #undef) |
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o new read/write pickup version: |
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- for now, only implemented for main (mdsio) pickup file. |
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- write out only what is needed to restart; merge pickup_nh , pickup_ph |
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and main pickup together. |
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- read meta file; read only what is needed to restart; stop if a field |
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is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
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if it make sense (even if the restart is not perfect). |
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- if no meta file, assume that pickup to read corresponds exactly to |
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a pickup that would currently be written. |
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- read pickup written in the old format (until checkpoint59i) if it |
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recognizes an old meta file (no field-list). |
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- add a meta file in exp. which starts from a pickup: 2 cases: |
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a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
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e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
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b) a meta file describing the content of the associated pickup file |
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e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
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o pkg/mdsio & pkg/rw: |
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- new routine to read a meta file ; new set of routine to read |
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Multiple-fields file (with meta file). |
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o added open boundary conditions capability for seaice |
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HSNOW, HSALT, UICE, and VICE |
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checkpoint59i |
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o adjoint: |
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* fix multiDimAdvection adjoint |
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(partial recomputation problem by TAF for fVerT(:,:,kDown) |
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and comlev1 size definition (maxpass vs. max. number of tracers) |
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* verification/global_ocean.90x45x15 adjoint now tests |
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NLFS and multiDimAdvection using DST3 (=30) |
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* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
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o pkg/kpp: add "_d 0" to real constant (if missing); |
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update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
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and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
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o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
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for internal parameters related to restart process (formerly from PARAMS.h) |
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and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
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o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
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as argument. (only atm2d & obcs write_pickup have not yet been updated) |
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o pkg/monitor: |
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- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
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- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
| 85 |
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- account for deep Atmosphere factor and density factor (anelastic) |
| 86 |
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o added open boundary conditions capability for seaice HEFF and AREA |
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o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
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thermodynamics |
| 89 |
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- requires a little reorganization, which affects the testreport results |
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of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
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so that now the conservative form is tested |
| 92 |
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- add a few comments |
| 93 |
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o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
| 94 |
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o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
| 95 |
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o add new diagnostics to seaice: advective, diffusive fluxes (only for |
| 96 |
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multidim-advection, for scheme 2 they are not filled) and transports, |
| 97 |
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thermodynamic growth rates |
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o change units of EmPmR (inside the code, + within coupling interface) |
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from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
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Affects results @ truncation level (cg2d match) and update output of |
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experiments: lab_sea(6), global_ocean.90x40x15(10), |
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global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
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+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
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Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
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Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
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checkpoint59h |
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o pkg/exf: |
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- improve vectorization by moving if-statement out of loops in |
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exf_mapfields, exf_radiation |
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- exf_bulkformulae.F: introduce 2D fields and vectorize code |
| 112 |
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o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
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o testreport: |
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- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
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monitor & update offline_exf_seaice exp. output. |
| 116 |
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- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
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o pkg/seaice: |
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- bug fix in the evp solver: boundary conditions were affected be |
| 119 |
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masking of zMax/zMin (changes results) |
| 120 |
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- minor bug fix in boundary conditions in seaice_calc_strainrates |
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(changes results for no_slip) |
| 122 |
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- seaice_lsr.F: make interpolation of eta dependent on boundaries |
| 123 |
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- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
| 124 |
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- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
| 125 |
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stress formulation and no-slip boundary conditions |
| 126 |
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o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
| 127 |
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in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
| 128 |
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o pkg/seaice: a first HSALT time stepping equation has been checked in |
| 129 |
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o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
| 130 |
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in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
| 131 |
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without requiring DO-IF statements |
| 132 |
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o pkg/thsice: |
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use continuous power-law function for partition of energy between lateral |
| 134 |
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melting/freezing and thinning/thickening ; old code using step function |
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still available with #undef THSICE_FRACEN_POWERLAW |
| 136 |
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update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
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o testreport: change AD testing : check against results/output_adm.txt |
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using same scripts as for forward test. |
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|
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checkpoint59g |
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o adjoint testing: in preparation for changing testreport: |
| 142 |
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- output format: cost and grad written on separated lines |
| 143 |
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- ad output results in directory "results" (instead of "results_ad") |
| 144 |
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o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 145 |
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o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
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o pkg/ecco: allow user defined cost function contributions |
| 147 |
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o testreport: |
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Allow to choose (per experiment) the list of tested output variables |
| 149 |
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and the main variable (used to issue a pass/FAIL ) ; |
| 150 |
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- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 151 |
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- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 152 |
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Also modify printing of summary: |
| 153 |
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a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
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b) echo the list of tested variables in the individual summary.txt of |
| 155 |
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each experiment. |
| 156 |
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o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 157 |
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threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 158 |
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(but still depend on the tile decompostion of the domain). |
| 159 |
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o pkg/seaice: change a discretization detail to make the B-grid code |
| 160 |
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"more symmetric". This change is likely to remove all "ridges/leads" that |
| 161 |
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where quasi-aligned with the grid in B-grid solutions. It may also be |
| 162 |
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the solution to the stress coupling issues with the B-grid. |
| 163 |
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o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
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remove .cvsignore from input dir. (since testreport no longer run here). |
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o pkg/thsice: |
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- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 167 |
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- fix reshaping of sea-ice just after advection: |
| 168 |
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melt all the ice only if ice-volume is too small. |
| 169 |
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- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 170 |
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prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 171 |
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and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 172 |
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o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 173 |
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tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 174 |
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o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 175 |
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forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 176 |
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(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 177 |
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and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 178 |
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of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
| 179 |
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-> update output.txt |
| 180 |
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o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 181 |
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this affects truncation error: -> update output.txt of exp: |
| 182 |
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global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 183 |
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ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 184 |
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|
| 185 |
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checkpoint59f |
| 186 |
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o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 187 |
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o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 188 |
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a bounded range (in forward mode) |
| 189 |
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o pkg/ecco, ctrl, autodiff and mom_common: |
| 190 |
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internal parameter controls, completements of implementations |
| 191 |
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o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 192 |
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o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 193 |
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(not seem any difference in testing results). |
| 194 |
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o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 195 |
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at face corners. |
| 196 |
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o pkg/generic_advdiff: |
| 197 |
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- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 198 |
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loop range indices for computing vertical advection tendency |
| 199 |
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and do the calculation in the interior only (no overlap) ; |
| 200 |
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for now, only implemented for SOM advection (to save CPU time). |
| 201 |
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- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 202 |
o exch2 adjoint |
o exch2 adjoint |
| 203 |
First set of changes: |
First set of changes: |
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- add exch2 hand-written adjoint templates |
- add exch2 hand-written adjoint templates |
| 208 |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 209 |
that used to hide exch2 or cubed-sphere specific code |
that used to hide exch2 or cubed-sphere specific code |
| 210 |
(commented via 'cph-exch2') |
(commented via 'cph-exch2') |
| 211 |
|
o pkg/seaice |
| 212 |
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- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 213 |
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o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 214 |
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output of global_ocean.cs32x15.thsice . |
| 215 |
|
|
| 216 |
checkpoint59e |
checkpoint59e |
| 217 |
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: |
| 411 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
| 412 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
| 413 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
| 414 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
| 415 |
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are no longer updating the vertical diffusivity array |
| 416 |
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(passed as argument) but are (re-) setting those arrays. |
| 417 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
| 418 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
| 419 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |
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