| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
|
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
| 8 |
|
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
| 9 |
|
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
| 10 |
|
backward compatiblity |
| 11 |
|
o model/src: use sigmaR in calc_ivdc |
| 12 |
|
|
| 13 |
|
checkpoint63g (2011/12/16) |
| 14 |
|
o pkg/seaice/seaice_growth.F: |
| 15 |
|
fix heat conservation of the coupled ocean-seaice system. |
| 16 |
|
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
| 17 |
|
solid vs liquid water treatment is resolved via QNET. |
| 18 |
|
o pkg/seaice/seaice_growth.F: |
| 19 |
|
add missing term for sublimation in saltFlux, which was breaking conservation. |
| 20 |
|
o pkg/seaice/seaice_model.F: |
| 21 |
|
Remove this patholigical case treatment in evolution branch, |
| 22 |
|
where it is un-necessary and breaks conservation. |
| 23 |
|
Update global_ocean.cs32x15/results accordingly for |
| 24 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
| 25 |
|
o model/src: |
| 26 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
| 27 |
|
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
| 28 |
|
o pkg/obcs: |
| 29 |
|
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
| 30 |
|
tendency for temperature and salinity that is then applied to update |
| 31 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
| 32 |
|
horizontal advection and diffusion contributions on the boundary (in |
| 33 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
| 34 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
| 35 |
|
that the updated tracer values include contributions from the surface |
| 36 |
|
forcing and vertical diffusion. |
| 37 |
|
This modification changes exp4.stevens because of vertical diffusion. |
| 38 |
|
o model/src: |
| 39 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
| 40 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
| 41 |
|
face dimensions. |
| 42 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
| 43 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
| 44 |
|
and INI_SPHERICAL_POLAR_GRID. |
| 45 |
|
change test-experiment global_ocean.90x40x15: |
| 46 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
| 47 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
| 48 |
|
- update results of both test (std & dwnslp). |
| 49 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
| 50 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
| 51 |
|
o model/src: |
| 52 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
| 53 |
|
and fix initialisation when using sigma-coords. |
| 54 |
|
o model/src: |
| 55 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
| 56 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
| 57 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
| 58 |
|
- set doResetHFactors=T in the following test exp: |
| 59 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
| 60 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
| 61 |
|
and tutorial_global_oce_in_p (nonLinFS in p) |
| 62 |
|
o pkg/ecco |
| 63 |
|
- added IES cost term |
| 64 |
|
o verification/advect_xz |
| 65 |
|
- scale down the depth by 1/100 (from 200 km to just 2.km) |
| 66 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
| 67 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
| 68 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
| 69 |
|
o pkg/rbcs: |
| 70 |
|
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
| 71 |
|
o pkg/obcs (Stevens BCs): |
| 72 |
|
- fix various problems in the phase speed computations of the Stevens |
| 73 |
|
boundary conditions: |
| 74 |
|
- sign error for western and southern boundaries, |
| 75 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
| 76 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
| 77 |
|
from difference between previous (n) time level and the one before (n-1); |
| 78 |
|
this requires storing a field per tracer per boundary, also in the pickup |
| 79 |
|
files. |
| 80 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
| 81 |
|
- set default phase velocity to cflMer/Zon |
| 82 |
|
- update verification experiment exp4.stevens |
| 83 |
|
o pkg/generic_advdiff (implicit_r): |
| 84 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
| 85 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
| 86 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
| 87 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
| 88 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
| 89 |
|
solver S/R ; |
| 90 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
| 91 |
|
when using implicit vert. advection; |
| 92 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
| 93 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
| 94 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
| 95 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
| 96 |
|
o pkg/diagnostics: |
| 97 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
| 98 |
|
|
| 99 |
|
checkpoint63f (2011/11/30) |
| 100 |
|
o pkg/obcs/obcs_calc_stevens.F: |
| 101 |
|
- join some loops to reduce number of if-statements |
| 102 |
|
- fix a bug in code for northern and southern boundaries. |
| 103 |
|
o pkg/seaice/seaice_init_varia.F |
| 104 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
| 105 |
|
caused zero ice-velocities for the B-grid code |
| 106 |
|
o pkg/seaice/seaice_init_fixed.F |
| 107 |
|
- fix a bug in the initialisation of the second metric terms |
| 108 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
| 109 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
| 110 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
| 111 |
|
= .true. (default) |
| 112 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
| 113 |
|
icedyn, seaice, and seaice_dynmix (AD) |
| 114 |
|
o pkg/thsice/thsice_diagnostics_state.F |
| 115 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
| 116 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
| 117 |
|
o model/src: |
| 118 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
| 119 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
| 120 |
|
(previously called from momentum_correction_step.F) |
| 121 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
| 122 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
| 123 |
|
o model/src/do_oceanic_phys.F: |
| 124 |
|
- reset addMass to zero only if useICEFRONT ; |
| 125 |
|
- separated k-loop for rhoInSitu calculation ; |
| 126 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
| 127 |
|
and at constant T,S (= WdRHOdP); |
| 128 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
| 129 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
| 130 |
|
transport of locally-referenced potential density); |
| 131 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
| 132 |
|
o gluemnc: |
| 133 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
| 134 |
|
- change the way variables without record dimensions are handled so that |
| 135 |
|
files that have variables with and without record variables can be glued: |
| 136 |
|
add a record dimension with a new unique name to be able to differentiate |
| 137 |
|
between variable with and without a-prior record dimensions. Remove |
| 138 |
|
this record dimension before adding the variable to the *.glob.nc file. |
| 139 |
|
This procedure automatically works also for grid.*.nc files that do not |
| 140 |
|
have any record dimension. |
| 141 |
|
o verification/cpl_aim+ocn: |
| 142 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
| 143 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
| 144 |
|
o pkg/obcs/obcs_calc_stevens.F: |
| 145 |
|
- add code for northern and southern boundaries. |
| 146 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
| 147 |
|
o model/src: |
| 148 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
| 149 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
| 150 |
|
- update test-exp. AD output: |
| 151 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
| 152 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
| 153 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
| 154 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
| 155 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
| 156 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
| 157 |
|
tutorial_plume_on_slope. |
| 158 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
| 159 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
| 160 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
| 161 |
|
does not even come with an F77 compiler anymore, this should not be |
| 162 |
|
a limitation |
| 163 |
|
|
| 164 |
|
checkpoint63e (2011/11/06) |
| 165 |
|
o pkg/seaice adjoint of LSR: |
| 166 |
|
- substantially rework STORE dirs. |
| 167 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
| 168 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
| 169 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
| 170 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
| 171 |
|
always goes to same record, meaning that the last forward field will be |
| 172 |
|
the one used in the adjoint - an approximation. |
| 173 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
| 174 |
|
An's zonal (x-z) test case (to be checked in) |
| 175 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
| 176 |
|
(but these are screwed up by the thermodynamics in the first place); |
| 177 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
| 178 |
|
output_adm.txt also reflects changes to seaice_lsr |
| 179 |
|
- global_ocean.cs32x15: |
| 180 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
| 181 |
|
(output_adm.seaice.txt was updated) |
| 182 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
| 183 |
|
(output_adm.seaice_dynmix.txt) |
| 184 |
|
o test-exp. exp4+stevens: |
| 185 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
| 186 |
|
o pkg/seaice (lsr solver): |
| 187 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
| 188 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
| 189 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
| 190 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
| 191 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
| 192 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
| 193 |
|
and final residual of linearised system. |
| 194 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
| 195 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
| 196 |
|
o pkg/obcs: Stevens BCs (still only for east and west) |
| 197 |
|
- fix Stevens BCs by using intermediate velocities of previous |
| 198 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
| 199 |
|
inside the boundaries; more consistent but makes the entire treatment |
| 200 |
|
more complicated, requires new pickup files and two new S/Rs: |
| 201 |
|
obcs_copy_uv_n and obcs_save_uv_n |
| 202 |
|
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
| 203 |
|
(undefined by default) |
| 204 |
|
- silently move computation of some grid factors into separate loops to |
| 205 |
|
save some recomputations |
| 206 |
|
- add a hack for non-linear free surface |
| 207 |
|
- add a verification experiment to exp4 that tests this code |
| 208 |
|
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
| 209 |
|
|
| 210 |
|
checkpoint63d (2011/10/25) |
| 211 |
|
o pkg/obcs + seaice-dynamics: |
| 212 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
| 213 |
|
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
| 214 |
|
values (consistent with an implicit method). |
| 215 |
|
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
| 216 |
|
return to older implementation (same results as before); note that none of |
| 217 |
|
the "experimental" OBCS_SEAICE options are implemented in the new version. |
| 218 |
|
- switch test exp. seaice_obcs to use new version (update output). |
| 219 |
|
o pkg/seaice: |
| 220 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
| 221 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
| 222 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
| 223 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
| 224 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
| 225 |
|
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
| 226 |
|
o pkg/layers: |
| 227 |
|
- Include potential density as new coordinate (Thanks to David Munday) |
| 228 |
|
o pkg/dic: |
| 229 |
|
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
| 230 |
|
carbonate computation/output to CALC_PCO2_APPROX |
| 231 |
|
o pkg/generic_advdiff |
| 232 |
|
- make TAF generate code that vectorizes: |
| 233 |
|
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
| 234 |
|
o model/src: |
| 235 |
|
- improve vectorization also for adjoint code of |
| 236 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
| 237 |
|
5 new 3D-fields, this code is only turned on for the combination of |
| 238 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
| 239 |
|
for singular matrix check (only for TARGET_NEC_SX). |
| 240 |
|
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
| 241 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
| 242 |
|
solve_tri/pentadiagonal.F |
| 243 |
|
o pkg/exf: |
| 244 |
|
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
| 245 |
|
optional namelist EXF_NML_OBCS). |
| 246 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
| 247 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
| 248 |
|
- rearrange loops so that vectorization is improved and in particular |
| 249 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
| 250 |
|
think easier to read. |
| 251 |
|
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
| 252 |
|
o pkg/seaice: |
| 253 |
|
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
| 254 |
|
o pkg/exch2: |
| 255 |
|
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
| 256 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
| 257 |
|
o tools/build_options: |
| 258 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
| 259 |
|
the modified default optfile support both built (using genmake2 -mpi |
| 260 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
| 261 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
| 262 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
| 263 |
|
|
| 264 |
|
checkpoint63c (2011/09/28) |
| 265 |
|
o pkg/ebm: |
| 266 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
| 267 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
| 268 |
|
o pkg/seaice (SItracer pickup) |
| 269 |
|
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
| 270 |
|
To be done: |
| 271 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
| 272 |
|
- thorough matching between generic tracers and specific fields used |
| 273 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
| 274 |
|
o pkg/grdchk: |
| 275 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
| 276 |
|
- change description output used by testreport; |
| 277 |
|
- AD testing: also compare and report Finite-difference gradient; |
| 278 |
|
=> update all output_adm*.txt |
| 279 |
|
o test exp. global_ocean_ebm: |
| 280 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
| 281 |
|
and turn on exactConserve; update (fwd) output. |
| 282 |
|
o pkg/seaice (LSR): |
| 283 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
| 284 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
| 285 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
| 286 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
| 287 |
|
(differences due to convergence criteria, since nb of iterations changed) |
| 288 |
|
* expect some differences on lat-lon-cap grid. |
| 289 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
| 290 |
o pkg/exch2: |
o pkg/exch2: |
| 291 |
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
| 292 |
many tiles); until alternative coding is added, just add a stop. |
many tiles); until alternative coding is added, just add a stop. |
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