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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 model/src: |
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- move (from ini_forcing.F) initialisation of all arrays in header file |
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FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
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(since Nov 2012) with option selectAddFluid=1. |
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o pkg/shelfice: |
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- change units (+ document) of newly added field "shelfIceMassDynTendency" |
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- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
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o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
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o pkg/seaice: two new runtime parameters: |
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- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
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long overdue |
18 |
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- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
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parameterization of tensil stress for fast ice (does not do anything yet) |
20 |
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o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
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for LSR: move checking overlaps out of JFNK-if-block |
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o pkg/atm_phys: |
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- move copy of grid and dynamical fields out of atm_phys_driver.F into |
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new S/R ATM_PHYS_DYN2PHYS. |
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- fix level height for Linear Free-Surf case (to be consistent with |
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fixed-in-time pressure levels). |
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o pkg/mom_common (bottomdrag): |
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- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
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to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
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update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
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o pkg/shelfice (u/v_drag): |
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- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
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- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
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(now similar to shelfice_u_drag.F) |
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- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
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from mom_vecinv.F (similar to mom_fluxform calls). |
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o pkg/mom_common (bottomdrag): |
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- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
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- add options for alternative discretisation of velocity norm in quadratic |
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bottom drag: averaging of grid-cell-center KE to U.point and V.point |
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(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
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improves when averaging only the other component (e.g. vVel for U bottom |
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drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
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- add options (bottomVisc_pCell) to account for partial-cell in bottom |
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friction (no-slip BC) thus getting the true distance from the bottom; |
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off by default since this also reduces model stability (explicit bottom |
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friction). Changes produce different machine truncation with linear-drag |
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+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
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front_relax (bvp & mxl, 10 & 11 digits). |
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o model/src & mom pkgs: |
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- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
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since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
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- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
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just copy level Nr value to level Nr+1. |
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o doc: |
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- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
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o pkg/streamice: |
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- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
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SHELFICE.h: move array shelficemass to init_varia, initialise |
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from array shelficemassinit, which is set in init_fixed and |
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has option to be set from file; introduce array |
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shelficeMassDynTend array, set thru file in init_fixed |
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- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
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shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
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pkg/streamice |
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- shelfice_thermodynamics.F: call shelfice_step_icemass if |
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SHELFICEMassStepping = .true. |
68 |
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- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
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|
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checkpoint65h (2014/12/17) |
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o verification/global_ocean.90x40x15, global_ocean_ebm: |
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- update to generic controls. |
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o pkg/ctrl: |
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- ctrl_map_ini_genarr.F: test for igen>0 |
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- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
76 |
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- move gentim2d part of ctrl_map_ini_genarr.F to |
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new separate routine : ctrl_map_ini_gentim2d.F |
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- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
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add time variable weights and cyclic controls (time mean, |
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seasonal cycle, etc) capabilities to gentim2d |
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o pkg/ecco: |
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- move reading of error, conversion to weights from |
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ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
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o global_oce_llc90, cs32: |
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- activte sbo. |
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- CTRL_SIZE.h : add maxCtrlProc. |
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- activate the new genctrl capabilities. |
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- update following reorganization of global_oce_input_fields.tar.gz |
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o pkg/ctrl/ctrl_ad_diff.list: |
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- add missing ctrl_init_rec.f |
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o tools/OAD_support/keepOriginal: |
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- add ctrl_init_rec.F |
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o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
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- avoid recomputations of xx_gentim2d_dummy. |
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o momentum diagnostics: |
96 |
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- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
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mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
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o pkg/seaice/seaice_lsr.F: |
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- fix computation of BU/BV, make sure they are non-zero, only necessary |
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for cubed sphere exchanges and SEAICE_OLx/y>0. |
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This makes calling s/r fill_cs_corner_rl obsolete (removed). |
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o verification/global_ocean.cs32x15/input.seaice |
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- add test for strong implicit coupling and restricted addtive Schwarz |
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methods for LSR |
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- update results/output.seaice.txt |
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o verification/tutorial_global_oce_biogeo: |
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- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
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and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
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update output_adm,_oadm,_tlm.txt |
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o pkg/dic: |
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- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
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- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
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for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
114 |
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o verification/tutorial_global_oce_biogeo: |
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- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
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dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
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update output_adm,_oadm,_tlm.txt |
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o eesupp/src: |
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- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
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and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
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o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
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LSR (following Hutchings et al. 2004) |
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- introduce zetaZ as a global variable (requires adjustments in |
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seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
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in seaice_calc_viscosities.F |
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- new flag SEAICEuseStrImpCpl (default off) |
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- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
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momentum equations |
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- JFNK-solver (preconditioner) adjusted to allow using this method |
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(where it does not have any positive effect) |
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o pkg/seaice |
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- add overlap for restrictive additive Schwartz method also to LSR, but |
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turn it off by default (because it only seems to work for non-cubed |
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sphere/llc topologies) |
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o pkg/autodiff |
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- add extra exchanges in addummy_in_steppging also for mnc output |
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o pkg/seaice: |
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- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
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to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
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o pkg/obcs: |
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- add option to specify domain-connected piece Id along OB though files |
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(for now, only used to diagnose PhiVel; default =1 -> global correction) |
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- modify obcs_diag_balance.F to process each connected-part separately; |
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exclude OB where Id = 0 but keep the full divergence there (-> constant |
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Psi along this portion of OB and all inflow derived from grad(Phi)) |
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- add example of OB-conect files in verification/so_box_biogeo/input. |
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o pkg/diagnostics: |
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- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
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a) use non zero matrix element across OB and solve for Phi 1 grid point |
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outside OB (i.e, where tracer OBCS are applied). |
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b) global imbalance of inFlow/outFlow across OB: instead of modifying |
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velocity across OB, spread it uniformly along the OB in the RHS. |
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checkpoint65g (2014/11/19) |
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o pkg/diagnostcis: |
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- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
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o pkg/my82,pp81,kl10: |
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- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
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field diffKr as background diffusivity to set minimum diffusivity value. |
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o pkg/seaice: |
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- add new parameter SEAICEuseEVPrev (for revisited EVP by |
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Bouillon et al 2013) |
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- add SEAICE_evpAlpha/Beta to namelist |
164 |
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- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
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involve trivial re-ordering of divisions/multiplications that should not |
166 |
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have any effects, but ... they do change the results of lab_sea.hb87 so |
167 |
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that only 2 digits of agreement remain, in line with the general |
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instability/fragility of the evp-code. For now, I do not care and just |
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update the verification experiment |
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o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
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- remove xx_genarr2d_numsmooth etc |
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- use xx_genarr2d_preproc etc instead |
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- carry out smooth_correl2D at initialization stage rather than during |
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time stepping. |
175 |
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- get smoothOpNb from xx_gentim2d_preproc |
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o global_oce_cs32 : |
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- add test of generic ecco capabilities. |
178 |
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o pkg/exf/exf_getsurfacefluxes.F : |
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- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
180 |
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o pkg/ctrl,ecco : |
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- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
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is defined. |
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o pkg/seaice: add diagnostics for Delta (deformation parameter) |
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o model/src: |
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- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
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diffusivity (background) is specified but ignored. |
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o verification: |
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- in testreport, convert hostname to lower case for default output dir name |
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o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
190 |
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o pkg/dic: add modifications from Hajoon: |
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- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
192 |
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- light attenuation: add self-shading effect by climatological Chlorophyll |
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(read from file). |
194 |
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o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
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compiles when SEAICE_ALLOW_DYNAMICS is undefined |
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o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
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AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
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ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
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approach where CPP_OPTIONS.h includes an omnipotent |
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ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
201 |
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o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
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ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
203 |
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o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
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to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
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(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
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o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
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add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
208 |
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- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
209 |
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- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
210 |
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- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
211 |
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o pkg/ctrl,ecco,exf : |
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- remove variables associated with NON-generic costs, |
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unless ECCO_CTRL_DEPRECATED is defined. |
214 |
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- remove NON-generic NON-obcs controls, |
215 |
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unless ECCO_CTRL_DEPRECATED is defined. |
216 |
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o pkg/ctrl : added ctrl_local_params.h |
217 |
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o pkg/ecco : added ecco_local_params.h |
218 |
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o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
219 |
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experiments, which will progressively be removed once the |
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experiments are revised to use only generic controls/costs. |
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|
222 |
checkpoint65f (2014/10/13) |
checkpoint65f (2014/10/13) |
223 |
o pkg/ctrl, ecco, seaice : minor changes in headers |
o pkg/ctrl, ecco, seaice : minor changes in headers |
224 |
o global_oce_llc90 : |
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
225 |
- ecco_v4 verification experiments now test generic cost |
cost function and control capabilities added since checkpoint65c. |
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function and control capabilities added since checkpoint65c. |
|
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o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
227 |
o pkg/ecco: increase modularity and improve logic |
o pkg/ecco: increase modularity and improve logic |
228 |
- ecco_toolbox.F (new) : basic operations that are often used, |
- ecco_toolbox.F (new) : basic operations that are often used, |
582 |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
583 |
this experiment): |
this experiment): |
584 |
> size mitgcmuv_ad |
> size mitgcmuv_ad |
585 |
text data bss dec hex |
text data bss dec hex |
586 |
5100659 1216 220458952 225560827 d71c8fb |
5100659 1216 220458952 225560827 d71c8fb |
587 |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
588 |
but only a moderate increase of 36% for global_ocean.cs32x15: |
but only a moderate increase of 36% for global_ocean.cs32x15: |
589 |
text data bss dec hex |
text data bss dec hex |