| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
o model/src: |
| 8 |
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
- change units of frictionHeating field from W to W/m^2 |
| 9 |
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
- fix bug in frictional heating from stratospheric drag in |
| 10 |
approach where CPP_OPTIONS.h includes an omnipotent |
S/R ATM_PHYS_TENDENCY_APPLY_V |
| 11 |
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 12 |
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
field from load_fields_driver.F to thermodynamics.F ; |
| 13 |
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
- add diagnostics for frictional heating. |
| 14 |
|
o model/src & gmredi K3D: |
| 15 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 16 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 17 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
| 18 |
|
and name in pickup file). |
| 19 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 20 |
|
o model/src: |
| 21 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
| 22 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 23 |
|
(since Nov 2012) with option selectAddFluid=1. |
| 24 |
|
o pkg/shelfice: |
| 25 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 26 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 27 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 28 |
|
o pkg/seaice: two new runtime parameters: |
| 29 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 30 |
|
long overdue |
| 31 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 32 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
| 33 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 34 |
|
for LSR: move checking overlaps out of JFNK-if-block |
| 35 |
|
o pkg/atm_phys: |
| 36 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 37 |
|
new S/R ATM_PHYS_DYN2PHYS. |
| 38 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
| 39 |
|
fixed-in-time pressure levels). |
| 40 |
|
o pkg/mom_common (bottomdrag): |
| 41 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 42 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 43 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 44 |
|
o pkg/shelfice (u/v_drag): |
| 45 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 46 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 47 |
|
(now similar to shelfice_u_drag.F) |
| 48 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 49 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
| 50 |
|
o pkg/mom_common (bottomdrag): |
| 51 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 52 |
|
- add options for alternative discretisation of velocity norm in quadratic |
| 53 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 54 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 55 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
| 56 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 57 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 58 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
| 59 |
|
off by default since this also reduces model stability (explicit bottom |
| 60 |
|
friction). Changes produce different machine truncation with linear-drag |
| 61 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 62 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
| 63 |
|
o model/src & mom pkgs: |
| 64 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 65 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 66 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 67 |
|
just copy level Nr value to level Nr+1. |
| 68 |
|
o doc: |
| 69 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 70 |
|
o pkg/streamice: |
| 71 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 72 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 73 |
|
from array shelficemassinit, which is set in init_fixed and |
| 74 |
|
has option to be set from file; introduce array |
| 75 |
|
shelficeMassDynTend array, set thru file in init_fixed |
| 76 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 77 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 78 |
|
pkg/streamice |
| 79 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 80 |
|
SHELFICEMassStepping = .true. |
| 81 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 82 |
|
|
| 83 |
|
checkpoint65h (2014/12/17) |
| 84 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 85 |
|
- update to generic controls. |
| 86 |
|
o pkg/ctrl: |
| 87 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
| 88 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 89 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 90 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
| 91 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 92 |
|
add time variable weights and cyclic controls (time mean, |
| 93 |
|
seasonal cycle, etc) capabilities to gentim2d |
| 94 |
|
o pkg/ecco: |
| 95 |
|
- move reading of error, conversion to weights from |
| 96 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
| 97 |
|
o global_oce_llc90, cs32: |
| 98 |
|
- activte sbo. |
| 99 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
| 100 |
|
- activate the new genctrl capabilities. |
| 101 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
| 102 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
| 103 |
|
- add missing ctrl_init_rec.f |
| 104 |
|
o tools/OAD_support/keepOriginal: |
| 105 |
|
- add ctrl_init_rec.F |
| 106 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
| 107 |
|
- avoid recomputations of xx_gentim2d_dummy. |
| 108 |
|
o momentum diagnostics: |
| 109 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
| 110 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
| 111 |
|
o pkg/seaice/seaice_lsr.F: |
| 112 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
| 113 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
| 114 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
| 115 |
|
o verification/global_ocean.cs32x15/input.seaice |
| 116 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
| 117 |
|
methods for LSR |
| 118 |
|
- update results/output.seaice.txt |
| 119 |
|
o verification/tutorial_global_oce_biogeo: |
| 120 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
| 121 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
| 122 |
|
update output_adm,_oadm,_tlm.txt |
| 123 |
|
o pkg/dic: |
| 124 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
| 125 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
| 126 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
| 127 |
|
o verification/tutorial_global_oce_biogeo: |
| 128 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
| 129 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
| 130 |
|
update output_adm,_oadm,_tlm.txt |
| 131 |
|
o eesupp/src: |
| 132 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
| 133 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
| 134 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
| 135 |
|
LSR (following Hutchings et al. 2004) |
| 136 |
|
- introduce zetaZ as a global variable (requires adjustments in |
| 137 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
| 138 |
|
in seaice_calc_viscosities.F |
| 139 |
|
- new flag SEAICEuseStrImpCpl (default off) |
| 140 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
| 141 |
|
momentum equations |
| 142 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
| 143 |
|
(where it does not have any positive effect) |
| 144 |
|
o pkg/seaice |
| 145 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
| 146 |
|
turn it off by default (because it only seems to work for non-cubed |
| 147 |
|
sphere/llc topologies) |
| 148 |
|
o pkg/autodiff |
| 149 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
| 150 |
|
o pkg/seaice: |
| 151 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
| 152 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
| 153 |
|
o pkg/obcs: |
| 154 |
|
- add option to specify domain-connected piece Id along OB though files |
| 155 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
| 156 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
| 157 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
| 158 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
| 159 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
| 160 |
|
o pkg/diagnostics: |
| 161 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
| 162 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
| 163 |
|
outside OB (i.e, where tracer OBCS are applied). |
| 164 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
| 165 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
| 166 |
|
|
| 167 |
|
checkpoint65g (2014/11/19) |
| 168 |
|
o pkg/diagnostcis: |
| 169 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
| 170 |
|
o pkg/my82,pp81,kl10: |
| 171 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
| 172 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
| 173 |
|
o pkg/seaice: |
| 174 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
| 175 |
|
Bouillon et al 2013) |
| 176 |
|
- add SEAICE_evpAlpha/Beta to namelist |
| 177 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
| 178 |
|
involve trivial re-ordering of divisions/multiplications that should not |
| 179 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
| 180 |
|
that only 2 digits of agreement remain, in line with the general |
| 181 |
|
instability/fragility of the evp-code. For now, I do not care and just |
| 182 |
|
update the verification experiment |
| 183 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
| 184 |
|
- remove xx_genarr2d_numsmooth etc |
| 185 |
|
- use xx_genarr2d_preproc etc instead |
| 186 |
|
- carry out smooth_correl2D at initialization stage rather than during |
| 187 |
|
time stepping. |
| 188 |
|
- get smoothOpNb from xx_gentim2d_preproc |
| 189 |
|
o global_oce_cs32 : |
| 190 |
|
- add test of generic ecco capabilities. |
| 191 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
| 192 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
| 193 |
|
o pkg/ctrl,ecco : |
| 194 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
| 195 |
|
is defined. |
| 196 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
| 197 |
|
o model/src: |
| 198 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
| 199 |
|
diffusivity (background) is specified but ignored. |
| 200 |
|
o verification: |
| 201 |
|
- in testreport, convert hostname to lower case for default output dir name |
| 202 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
| 203 |
|
o pkg/dic: add modifications from Hajoon: |
| 204 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
| 205 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
| 206 |
|
(read from file). |
| 207 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
| 208 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
| 209 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
| 210 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
| 211 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
| 212 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
| 213 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
| 214 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
| 215 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
| 216 |
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
| 217 |
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
| 218 |
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
| 219 |
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
| 220 |
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
| 221 |
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
| 222 |
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
| 223 |
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
| 224 |
o pkg/ctrl,ecco,exf : |
o pkg/ctrl,ecco,exf : |
| 225 |
- remove variables associated with NON-generic costs, |
- remove variables associated with NON-generic costs, |
| 226 |
unless ECCO_CTRL_DEPRECATED is defined. |
unless ECCO_CTRL_DEPRECATED is defined. |
| 227 |
- remove NON-generic NON-obcs controls, |
- remove NON-generic NON-obcs controls, |
| 228 |
unless ECCO_CTRL_DEPRECATED is defined. |
unless ECCO_CTRL_DEPRECATED is defined. |
| 229 |
o pkg/ctrl : added ctrl_local_params.h |
o pkg/ctrl : added ctrl_local_params.h |
| 230 |
o pkg/ecco : added ecco_local_params.h |
o pkg/ecco : added ecco_local_params.h |
| 231 |
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
| 232 |
experiments, which will progressively be removed once the |
experiments, which will progressively be removed once the |
| 233 |
experiments are revised to use only generic controls/costs. |
experiments are revised to use only generic controls/costs. |
| 234 |
|
|
| 235 |
checkpoint65f (2014/10/13) |
checkpoint65f (2014/10/13) |
| 236 |
o pkg/ctrl, ecco, seaice : minor changes in headers |
o pkg/ctrl, ecco, seaice : minor changes in headers |
| 237 |
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
| 238 |
cost function and control capabilities added since checkpoint65c. |
cost function and control capabilities added since checkpoint65c. |
| 239 |
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
| 240 |
o pkg/ecco: increase modularity and improve logic |
o pkg/ecco: increase modularity and improve logic |
| 241 |
- ecco_toolbox.F (new) : basic operations that are often used, |
- ecco_toolbox.F (new) : basic operations that are often used, |
| 595 |
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 |
| 596 |
this experiment): |
this experiment): |
| 597 |
> size mitgcmuv_ad |
> size mitgcmuv_ad |
| 598 |
text data bss dec hex |
text data bss dec hex |
| 599 |
5100659 1216 220458952 225560827 d71c8fb |
5100659 1216 220458952 225560827 d71c8fb |
| 600 |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 601 |
but only a moderate increase of 36% for global_ocean.cs32x15: |
but only a moderate increase of 36% for global_ocean.cs32x15: |
| 602 |
text data bss dec hex |
text data bss dec hex |
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