| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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| 7 |
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checkpoint66b (2016/12/01) |
| 8 |
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o model & momentum pkgs: |
| 9 |
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- implement fully implicit bottom friction combined with implicit surf. |
| 10 |
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pressure, for now, only in hydrostic formulation: |
| 11 |
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+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
| 12 |
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and run with selectImplicitDrag=2 ; |
| 13 |
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+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
| 14 |
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- partial implicit time-stepping (bot. friction + vert. visc first, then |
| 15 |
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surf. press) corresponding to selectImplicitDrag=1 should be applicable |
| 16 |
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to NH formulation but not available until we solve for surf. pressure |
| 17 |
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increment (instead of full etaN). |
| 18 |
|
- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
| 19 |
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with implicit vertical viscosity. |
| 20 |
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o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
| 21 |
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- this is a first version that includes many regularisations that may |
| 22 |
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not all be necessary, to be sorted out, |
| 23 |
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- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
| 24 |
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- change one verification experiment in seaice_itd to use and test new code |
| 25 |
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- seaice_growth: catch a case where the argument of log can be zero |
| 26 |
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or smaller (important for code stability) |
| 27 |
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o model/src: |
| 28 |
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- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
| 29 |
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& solve_pentadiagonal.F to enable to re-used inverse matrix for solving |
| 30 |
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similar A.X'=Y' system (with same matrix A) in subsequent calls; |
| 31 |
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switch based on errCode (In/Out) argument value; in calling routines, |
| 32 |
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initialise errCode before first call. |
| 33 |
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|
| 34 |
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checkpoint66a (2016/10/18) |
| 35 |
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o pkg/bling: |
| 36 |
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- BLING package now loads in atmospheric pCO2 file using exf package routines |
| 37 |
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Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
| 38 |
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o model/src & pkg/ptracers: |
| 39 |
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- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
| 40 |
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GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
| 41 |
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implicitDiffusion (respectively) are used (even without momImplVertAdv |
| 42 |
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or temp,salt,PTRACERS_ImplVertAdv). |
| 43 |
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o model/src & generic_advdiff: |
| 44 |
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- add parenthesis in main diagonal calculation of implicit vertical |
| 45 |
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diffusion matrix (impldiff.F & gad_implicit_r.F). |
| 46 |
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This affects results at machine truncation level; update output of many |
| 47 |
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verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
| 48 |
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o pkg/mom_commom & generic_advdiff: |
| 49 |
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- add deep atmosphere and anelastic scaling factor in implicit vertical |
| 50 |
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advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
| 51 |
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o model/src: |
| 52 |
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- remove few unnecessary temp array copies in solve_tridiagonal.F |
| 53 |
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& solve_pentadiagonal.F |
| 54 |
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|
| 55 |
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checkpoint65z (2016/09/28) |
| 56 |
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o pkg/seaice: fix multithreading for seaice_fgmres.F |
| 57 |
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- remove unecessary variables from common blocks |
| 58 |
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- use extra dimension MAX_NO_THREADS for all variables of the Krylov space |
| 59 |
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basis, that are stored in commom blocks (including integer variable i1) |
| 60 |
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- clean up code a little by removing commented lines that refer to |
| 61 |
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original code |
| 62 |
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- turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. |
| 63 |
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o MITgcm manual: |
| 64 |
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- add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), |
| 65 |
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preliminary documentation for generic controls (8.3; ctrl.tex), |
| 66 |
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a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated |
| 67 |
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ecco_costfunction.tex |
| 68 |
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o pkg/ecco: |
| 69 |
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- update and cleanup list of CCP options |
| 70 |
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- re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' |
| 71 |
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is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM |
| 72 |
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- add checks that retired run-time options are not used, and in relation |
| 73 |
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to gencost_mask and gencost_errfile |
| 74 |
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- finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and |
| 75 |
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gencost_nrecperiod |
| 76 |
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- fix m_eta computation for virtual salt flux case |
| 77 |
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- add m_horflux_vol case (selected via gencost_barfile) that computes |
| 78 |
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transports via cost_gencost_boxmean (gencost_flag=-3) |
| 79 |
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- use gencost_flag more systematically (i.e., avoid using gencost_name) |
| 80 |
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for code switches (aside from physical variable selection) |
| 81 |
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o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first |
| 82 |
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attempt appears to be a bit of a hack and my need some repair down the road |
| 83 |
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o pkg/exf: |
| 84 |
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- interpolation near South Pole: fix criteria on input field latitude. |
| 85 |
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o pkg/icefront & pkg/exf: |
| 86 |
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- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
| 87 |
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from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
| 88 |
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o pkg/exf: |
| 89 |
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- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
| 90 |
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"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
| 91 |
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(add suffix "_out" instead of a prefix); keep same record number as in |
| 92 |
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input file but always write record 1 first (to avoid a STOP in I/O S/R). |
| 93 |
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Change output file content by writing interpolated field before applying |
| 94 |
|
land-sea mask (helpful for debug). |
| 95 |
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- 2 compon. vector interpolation with rotation: apply scaling factor on |
| 96 |
|
each compon. (Eastward and Northward) just before rotation. |
| 97 |
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o pkg/bling: |
| 98 |
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- Cleaned package. Removed not needed code and comments. |
| 99 |
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- adjoint example now works |
| 100 |
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(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
| 101 |
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o pkg/ptracers: |
| 102 |
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- add Bruno Deremble's code to complete the linear surface correction |
| 103 |
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for tracer conservation; |
| 104 |
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- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
| 105 |
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|
| 106 |
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checkpoint65y (2016/07/29) |
| 107 |
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o pkg/debug (stats): |
| 108 |
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- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
| 109 |
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proc/thread mapping); |
| 110 |
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- fix Min & Max for case where 1 thread has only empty tiles; |
| 111 |
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- use RL variable to count number of wet grid points (with big domain, |
| 112 |
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can be too large to fit into integer*4). |
| 113 |
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o pkg/monitor: |
| 114 |
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- use RL variable to count number of wet grid points (but used only for del2) |
| 115 |
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- add new routine to compute Advective CFL within tracer time-stepping with |
| 116 |
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writing delayed until next monitor output. |
| 117 |
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o pkg/obcs: |
| 118 |
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- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
| 119 |
|
o pkg/cal: |
| 120 |
|
- calandar-dump: treat case myTime < timePhase in the same way as in |
| 121 |
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eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
| 122 |
|
o pkg/dic & seaice: |
| 123 |
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- fix compilation of ocean component for coupled atm+ocn model with |
| 124 |
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seaice dynamics & dic. |
| 125 |
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|
| 126 |
|
checkpoint65x (2016/06/11) |
| 127 |
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o add a license text file in main MITgcm tree. |
| 128 |
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o added pkg/bling: |
| 129 |
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- intermediate complexity biogeochemical model |
| 130 |
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- see bling_description.txt for details |
| 131 |
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- verification experiment is global_oce_biogeo_bling (for now, in |
| 132 |
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Contrib/verification_other/); tested daily on baudelaire with gfortran. |
| 133 |
|
- add entry point in pkg/gchem for new pkg "bling". |
| 134 |
|
o pkg/seaice: fix tensile stength computation |
| 135 |
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- replace global field tensileStrength by tensileStrFac |
| 136 |
|
- tensileStrFac can be computed once in S/R seaice_init_varia |
| 137 |
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- fortunately that does not affect any verification results |
| 138 |
|
|
| 139 |
|
checkpoint65w (2016/05/12) |
| 140 |
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o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
| 141 |
|
with ECCO_CTRL_DEPRECATED defined |
| 142 |
|
o verification/global_ocean.cs32x15: |
| 143 |
|
- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
| 144 |
|
with "selectNHfreeSurf=1". |
| 145 |
|
o model/src (non-hydrostatic free-surface): |
| 146 |
|
- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
| 147 |
|
was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
| 148 |
|
- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
| 149 |
|
for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
| 150 |
|
and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
| 151 |
|
This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
| 152 |
|
- Update output (changes at machine truncation level) of verification exp: |
| 153 |
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exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
| 154 |
|
short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
| 155 |
|
o pkg/seaice: ITD code |
| 156 |
|
- fix picking up from a single category model by initialising |
| 157 |
|
heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
| 158 |
|
- split a long warning message in seaice_check_pickup.F into two lines, |
| 159 |
|
because NEC SX-ACE cannot deal with the long line. |
| 160 |
|
o model/src: |
| 161 |
|
- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
| 162 |
|
o pkg/seaice: |
| 163 |
|
- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
| 164 |
|
o pkg/seaice: |
| 165 |
|
- add basal stress as parameterisation for grounding ice |
| 166 |
|
following Lemieux et al. (2015) |
| 167 |
|
- turn on by setting new parameter SEAICEbasalDragK2 to a value |
| 168 |
|
larger than 0. Lemieux et al. (2015) recommend 15. |
| 169 |
|
- The adjoint complains with extra recomputations so there is also a |
| 170 |
|
new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
| 171 |
|
order to postpone the problem |
| 172 |
|
- compile the new code in lab_sea |
| 173 |
|
o verification/halfpipe_streamice: |
| 174 |
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- update both TAF and OpenAD adm output (machine truncation differences) |
| 175 |
|
|
| 176 |
|
checkpoint65v (2016/04/08) |
| 177 |
|
o verification/advect_xz: |
| 178 |
|
- increase overlap size from 3 to 4 and add new secondary test for PQM |
| 179 |
|
advection scheme (with mono & wino limiter). |
| 180 |
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- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
| 181 |
|
o model/src: |
| 182 |
|
- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
| 183 |
|
added phi0Ref) to set vertical axis origin and phiRef origin; |
| 184 |
|
keep Ro_SeaLevel for backward compatibility (with a warning). |
| 185 |
|
According to coordinate and fluid type: |
| 186 |
|
OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
| 187 |
|
ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
| 188 |
|
OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
| 189 |
|
ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
| 190 |
|
- remove Ro_SeaLevel from ATM experiment parameter files; |
| 191 |
|
- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
| 192 |
|
complement; update output.txt (changes at machine truncation level). |
| 193 |
|
o pkg/seaice/seaice_evp.F |
| 194 |
|
- simplify computation of deltaZ and zetaZ to simple averaging following |
| 195 |
|
Bouillon et al. (2013). This removes a lot of code, but also changes |
| 196 |
|
verification experiment lab_sea.hb87 -> updated |
| 197 |
|
|
| 198 |
|
checkpoint65u (2016/03/14) |
| 199 |
|
o pkg/generic_advdiff: |
| 200 |
|
- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
| 201 |
|
with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
| 202 |
|
Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
| 203 |
|
testing and not for actual use. |
| 204 |
|
o model/src: |
| 205 |
|
- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
| 206 |
|
origin r = rF(1); |
| 207 |
|
- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
| 208 |
|
in EOS for height coordinate: enable to include NH Pressure or to use |
| 209 |
|
more accurate pressure vertical profile; options not linked to EOS type |
| 210 |
|
(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
| 211 |
|
- start to implement variable gravity (along vertical): for now, only with |
| 212 |
|
z-coords (not even z*). |
| 213 |
|
- add Ideal Gas equation of state for height coordinate. |
| 214 |
|
- update OpenAD output (affected at machine truncation level) of exp: |
| 215 |
|
global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
| 216 |
|
o pkg/exf: |
| 217 |
|
- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
| 218 |
|
of exf interpolation (before any rescaling, rotation or interpolation |
| 219 |
|
to velocity point) for each field that gets loaded from file. This option |
| 220 |
|
identically mimics the input file organization (e.g. record numbers in year |
| 221 |
|
by year input files) besides the change in horizontal grid. |
| 222 |
|
- add rotateStressOnAgrid run-time switch so that wind stress fields |
| 223 |
|
can be provided on the A-grid in zonal/meridional direction and |
| 224 |
|
rotated on the fly. This only applies to the case when the exf |
| 225 |
|
interpolation is off and rotateStressOnAgrid is false by default. |
| 226 |
|
o model/src: |
| 227 |
|
- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
| 228 |
|
it's also used with pkg/atm_phys) and add few more parameters (but still |
| 229 |
|
inactive, src code yet to come) |
| 230 |
|
|
| 231 |
|
checkpoint65t (2016/02/10) |
| 232 |
|
o pkg/atm_phys: |
| 233 |
|
- from Ruth Geen: add optical depth dependence on CO2 concentration. |
| 234 |
|
o model/src: |
| 235 |
|
- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
| 236 |
|
for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
| 237 |
|
Update output of exp. deep_anelastic (changes at truncation level). |
| 238 |
|
o tools: |
| 239 |
|
- add a hack in "remove_comments_sed" (used only with TAF) for recent |
| 240 |
|
version of OpenMPI (shipped with FC.23): comment out the new header |
| 241 |
|
file "mpif-sizeof.h" which causes problems to TAF. |
| 242 |
|
o pkg/seaice: |
| 243 |
|
- change the termination criterion so that maxits (SEAICElinearIterMax) |
| 244 |
|
has an effect |
| 245 |
|
- unify iteration parameters for implicit solvers (JFNK and Picard) |
| 246 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
| 247 |
|
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
| 248 |
|
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
| 249 |
|
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
| 250 |
|
SEAICEnonLinTol replaces JFNKgamma_nonlin |
| 251 |
|
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
| 252 |
|
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
| 253 |
|
use with SEAICEuseKrylov |
| 254 |
|
o pkg/seaice/seaice_lsr.F |
| 255 |
|
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
| 256 |
|
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
| 257 |
|
an effect. |
| 258 |
|
o pkg/seaice: add two new parameters |
| 259 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
| 260 |
|
parameter is not in any namelist) |
| 261 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
| 262 |
|
a preconditioner for the non-linear Newton iteration of the JFNK |
| 263 |
|
solver |
| 264 |
|
o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
| 265 |
|
affects some experiments at truncation level: |
| 266 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
| 267 |
|
- global_ocean.cs32x15.seaice (11 digits), |
| 268 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
| 269 |
|
- also update global_ocean.cs32x15 adjoint and tangent-linear results |
| 270 |
|
o pkg/salt_plume & pkg/thsice: |
| 271 |
|
- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
| 272 |
|
connect salt_plume flux to ATM-OCN coupling pkgs interface: |
| 273 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
| 274 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
| 275 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
| 276 |
|
(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
| 277 |
|
o pkg/dic: |
| 278 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
| 279 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
| 280 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
| 281 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
| 282 |
|
(previously done in ocn_apply_import.F). |
| 283 |
|
o tools/adjoint_options: |
| 284 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
| 285 |
|
has been changed on Jan 14, 2016. |
| 286 |
|
o pkg/ggl90: |
| 287 |
|
- add alternative discretisation of vertical shear (off by default), to |
| 288 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
| 289 |
|
vertical shear of mean flow (@ grid-cell center). |
| 290 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
| 291 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
| 292 |
|
o pkg/atm_compon_interf: |
| 293 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
| 294 |
|
pass last value, stored directly before export to CPL ; |
| 295 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
| 296 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
| 297 |
|
|
| 298 |
|
checkpoint65s (2016/01/13) |
| 299 |
|
o eesupp & genmake2: |
| 300 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
| 301 |
|
ETIME and consistent output; use the appropriate version in timers.F |
| 302 |
|
o model/src: |
| 303 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
| 304 |
|
integr_continuity; turned off by default. |
| 305 |
|
o pkg/dic: |
| 306 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
| 307 |
|
o tools/tst_2+2: |
| 308 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
| 309 |
|
to fail for no good reason. |
| 310 |
|
o eesupp & genmake2: |
| 311 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
| 312 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
| 313 |
|
o coupler pkgs: |
| 314 |
|
Finish implementation of optionally-exchanged variable switches (started on |
| 315 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
| 316 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
| 317 |
|
advection in OCN component; this requires sequential coupling. |
| 318 |
|
coupler (pkg/atm_ocn_coupler): |
| 319 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
| 320 |
|
routines (useful for debug). |
| 321 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
| 322 |
|
flux, DIC fields) if corresponding switch is ON. |
| 323 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
| 324 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
| 325 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 326 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
| 327 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
| 328 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
| 329 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
| 330 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
| 331 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
| 332 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
| 333 |
|
- hold in common block coupler optionally-exchanged variable switch |
| 334 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
| 335 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
| 336 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
| 337 |
|
to contain new additional exchanged fields). |
| 338 |
|
o pkg/dic: |
| 339 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
| 340 |
|
o pkg/thsice: |
| 341 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
| 342 |
|
and writing of thsice pickup files. |
| 343 |
|
o pkg/atm_compon_interf: |
| 344 |
|
- move all field individual export-call out of cpl_export_import_data.F |
| 345 |
|
into new S/R ATM_EXPORT_FIELDS |
| 346 |
|
o pkg/atm_compon_interf: |
| 347 |
|
- store state variables (for now, only thSIce fields) just before beeing |
| 348 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
| 349 |
|
atm_store_my_data.F like all exported fluxes. |
| 350 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
| 351 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
| 352 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
| 353 |
|
o pkg/dic: |
| 354 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
| 355 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
| 356 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
| 357 |
|
value can be from domain [0,1] to average between the two methods |
| 358 |
|
o pkg/atm_phys: |
| 359 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
| 360 |
|
hold fixed in time). |
| 361 |
|
|
| 362 |
|
checkpoint65r (2015/12/21) |
| 363 |
|
o pkg/seaice: |
| 364 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
| 365 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
| 366 |
|
o pkg/seaice: |
| 367 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
| 368 |
|
when SEAICEscaleSurfStress=.TRUE., |
| 369 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
| 370 |
|
o pkg/atm_phys: |
| 371 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
| 372 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
| 373 |
|
for individual contribution (convection, LSC cond, radiation) |
| 374 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
| 375 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
| 376 |
|
o pkg/ggl90: |
| 377 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
| 378 |
|
avoid instability problems in the explicit horizontal diffusion term for |
| 379 |
|
long time steps or high resolution |
| 380 |
|
o pkg/diagnostics: |
| 381 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
| 382 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
| 383 |
|
o testreport: |
| 384 |
|
- remove "-v" (verbose option) in default mpirun command. |
| 385 |
|
o pkg/seaice/seaice_growth: |
| 386 |
|
- catch potential division by zero in ITD code, does not change |
| 387 |
|
verification results |
| 388 |
|
o pkg/ecco: |
| 389 |
|
- retire old codes to the Attic. The calls to retired functions are |
| 390 |
|
left in a commented form in case they ever need to be re-activated. |
| 391 |
|
- ecco_check.F: issue warning if any old CPP option is |
| 392 |
|
defined that corresponds to retired codes -- then stop. |
| 393 |
|
o pkg/atm_compon_interf: |
| 394 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
| 395 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
| 396 |
|
time-step, similar to what is done for seaIceMass. |
| 397 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
| 398 |
|
o eesupp & genmake2: |
| 399 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
| 400 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
| 401 |
|
o pkg/seaice/seaice_evp: |
| 402 |
|
- refine residual computation |
| 403 |
|
|
| 404 |
|
checkpoint65q (2015/11/18) |
| 405 |
|
o pkg/seaice/seaice_evp: |
| 406 |
|
- fix residual computations so that they no longer affect the actual |
| 407 |
|
simulation code |
| 408 |
|
- fix seaice_readparams to be able to actually set new parameters |
| 409 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
| 410 |
|
o model/src: |
| 411 |
|
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
| 412 |
|
like: deltaT*FLOAT(myIter) when myIter is large: |
| 413 |
|
a) replaced by DFLOAT (if not seen by TAF); |
| 414 |
|
b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
| 415 |
|
o pkg/aim_v23: |
| 416 |
|
- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
| 417 |
|
when pickupSuff is set ; do write rolling pickups + at the end of the run. |
| 418 |
|
o pkg/atm_ocn_coupler + ocn_compon_interf: |
| 419 |
|
- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
| 420 |
|
coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
| 421 |
|
add corresponding call in DO_OCEANIC_PHYS. |
| 422 |
|
o coupler pkgs: |
| 423 |
|
Start a new way to set-up optionally-exchanged variables (previously, only |
| 424 |
|
there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
| 425 |
|
data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
| 426 |
|
send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
| 427 |
|
compononent param default can be set accordingly). |
| 428 |
|
Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
| 429 |
|
but rather applies to a group a fields (going both ways like for DIC) |
| 430 |
|
and corresponds to an option of coupling config. |
| 431 |
|
coupler (pkg/atm_ocn_coupler): |
| 432 |
|
- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
| 433 |
|
and read namelist directly (without eessup S/R calls) instead of |
| 434 |
|
in the very un-flexible old way, 1 param per line, in fixed order; |
| 435 |
|
- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
| 436 |
|
cleanly in CPL_CHECK_CPLCONFIG |
| 437 |
|
- add new coupling-exchange selectors (some not yet active) including |
| 438 |
|
cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
| 439 |
|
and ocnCpl_exchange_DIC=T in OCNIDS.h); |
| 440 |
|
- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
| 441 |
|
component ; called directly from coupler.F, after comp. registrations; |
| 442 |
|
- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
| 443 |
|
atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
| 444 |
|
-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
| 445 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 446 |
|
- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
| 447 |
|
CPP header file in all pkg source files. |
| 448 |
|
- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
| 449 |
|
ATM/OCN_CHECK_CPLCONFIG; |
| 450 |
|
- add error-counter to track errors (e.g., in "data.cpl") and to stop |
| 451 |
|
cleanly in ATM/OCN_CHECK_CPLCONFIG; |
| 452 |
|
- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
| 453 |
|
from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
| 454 |
|
before PACKAGES_READPARMS; |
| 455 |
|
verification/cpl_aim+ocn/: |
| 456 |
|
- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
| 457 |
|
"data.cpl" for coupler (in input_cpl). |
| 458 |
|
o eesupp/inc: |
| 459 |
|
- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
| 460 |
|
#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
| 461 |
|
to always cumulate tile local-sum in the same order (still uses |
| 462 |
|
MPI_Allreduce like standard code). |
| 463 |
|
- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
| 464 |
|
that are now identical to standard version (in eesupp/inc). |
| 465 |
|
o pkg/shelfice: |
| 466 |
|
- add SHELFICETransCoeffTFile for initializing spatially varying |
| 467 |
|
heat and salt transfer coefficients |
| 468 |
|
o pkg/atm_compon_interf & ocn_compon_interf: |
| 469 |
|
- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
| 470 |
|
S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
| 471 |
|
- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
| 472 |
|
o pkg/atm_ocn_coupler: |
| 473 |
|
- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
| 474 |
|
o pkg/rbcs: |
| 475 |
|
- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
| 476 |
|
to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
| 477 |
|
- add a short report (to STDOUT) about RBCS-mask settings. |
| 478 |
|
|
| 479 |
|
checkpoint65p (2015/10/23) |
| 480 |
|
o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
| 481 |
|
there is no adjoint test for EVP, we don't know what it does to the adjoint |
| 482 |
|
solution, but at least there are no more recomputation warnings left |
| 483 |
|
o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
| 484 |
|
a chance of giving the same results as a fully converged VP (JFNK) solver |
| 485 |
|
o tools/adjoint_options/adjoint_diva: |
| 486 |
|
- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
| 487 |
|
o pkg/streamice: |
| 488 |
|
- spotted bug in streamice_driving_stress using dyG where should have been dxG |
| 489 |
|
o pkg/exf: |
| 490 |
|
- remove STOP statement that prevented to use wind or (wind-)stress |
| 491 |
|
interpolation for constant-in-time forcing fields (wind/stress period = 0). |
| 492 |
|
o pkg/seaice: |
| 493 |
|
- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
| 494 |
|
5 additionals 2D fields and 6 new store directives |
| 495 |
|
- change logic in seaice_readparms.F: EVP code can now be turned on in |
| 496 |
|
various ways, setting SEAICE_deltaTev is no longer required, |
| 497 |
|
alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
| 498 |
|
or SEAICEaEVPcoeff |
| 499 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
| 500 |
|
- redefining uLoc/vLoc to u/v, instead of 2u/v |
| 501 |
|
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
| 502 |
|
- this is an intermediate state of a truely converging EVP that has |
| 503 |
|
the potential of outperforming implicit VP methods, I do not recommend |
| 504 |
|
using it yet. |
| 505 |
|
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
| 506 |
|
and all parameters are hardwired |
| 507 |
|
- for convergence it still requires very smooth regularisations, that means, |
| 508 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
| 509 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
| 510 |
|
specific averaging appears to be required, still subject to tuning |
| 511 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
| 512 |
|
- add code to compute and print residuals of iteration, compile with |
| 513 |
|
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
| 514 |
|
o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
| 515 |
|
that entered with r1.54 on Sep04, 2015, -> update results |
| 516 |
|
|
| 517 |
|
checkpoint65o (2015/09/14) |
| 518 |
|
o pkg/mom_vecinv & mom_common: |
| 519 |
|
- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
| 520 |
|
called from there. |
| 521 |
|
- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
| 522 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
| 523 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
| 524 |
|
and Koenig-Beatty+Holland (2012) |
| 525 |
|
- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
| 526 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
| 527 |
|
- requires an extra input argument for S/R seaice_calc_viscosities |
| 528 |
|
- tensileStrength's depth dependence is different from Itkin et al. (2015) |
| 529 |
|
(to be changed and played with, for now exponential) |
| 530 |
|
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
| 531 |
|
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
| 532 |
|
by AREA according to Connelly et al. (2004), JPO. |
| 533 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
| 534 |
|
the only non-zero term in the denominator when there is no ice (which |
| 535 |
|
prevented running the model with zero ice-ocean drag). If |
| 536 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
| 537 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
| 538 |
|
consequence is that for open water, the momentum equation reduce |
| 539 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
| 540 |
|
they happen to be zero, often leading to a non-zero solution over |
| 541 |
|
open water. |
| 542 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
| 543 |
|
efficient EVP method. |
| 544 |
|
- introduce area-weighted averages for e12 (analogously to |
| 545 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
| 546 |
|
remain, but also changing the order of terms in the previous average |
| 547 |
|
changed the results as much) -> update experiment |
| 548 |
|
- add SEAICE_DELTA_SMOOTHREG code |
| 549 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
| 550 |
|
TEM-code |
| 551 |
|
- adjust loop bounds so that only required fields are computed |
| 552 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
| 553 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
| 554 |
|
results again), but will replace old code eventually |
| 555 |
|
o eesupp/src: |
| 556 |
|
- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
| 557 |
|
to always cumulate tile local-sum in the same order |
| 558 |
|
(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
| 559 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
| 560 |
|
and should be faster than GLOBAL_SUM_SEND_RECV code. |
| 561 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
| 562 |
|
(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
| 563 |
|
- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
| 564 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
| 565 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
| 566 |
|
natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
| 567 |
|
tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
| 568 |
|
|
| 569 |
|
checkpoint65n (2015/07/29) |
| 570 |
|
o pkg/thsice: |
| 571 |
|
- add a warning when used with pkg/aim but without updating SST |
| 572 |
|
(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
| 573 |
|
o pkg/offline: |
| 574 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
| 575 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
| 576 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
| 577 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
| 578 |
|
These changes allow: |
| 579 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
| 580 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
| 581 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
| 582 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
| 583 |
|
b) no needs to switch on staggerTimeStep anymore; |
| 584 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
| 585 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
| 586 |
|
o pkg/offline: |
| 587 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
| 588 |
|
can easily recover previous offset-iter effect by setting offset-time |
| 589 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
| 590 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
| 591 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
| 592 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
| 593 |
|
o OpenAD |
| 594 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
| 595 |
|
Config. with ggl90 currently diverges after 64 time steps |
| 596 |
|
so will need more work to become more stable |
| 597 |
|
- Adding preliminary kpp test to OpenAD verification. |
| 598 |
|
required small tweakes in kpp_routines.F |
| 599 |
|
- Merge and update from Krishna Narayanan's contrib area: |
| 600 |
|
* Add one variable for preliminary OpenAD DIVA |
| 601 |
|
* Add replacement time-stepping for OpenAD DIVA |
| 602 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
| 603 |
|
* required modifs for OAD_support |
| 604 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
| 605 |
|
o pkg/seaice: |
| 606 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
| 607 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
| 608 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
| 609 |
|
(no effect on EVP) |
| 610 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
| 611 |
|
o pkg/seaice: |
| 612 |
|
add new parameter SEAICE_deltaMin that is used ***only*** |
| 613 |
|
for regularizing Delta (and nothing else, like the parameter |
| 614 |
|
which is also used for all sorts of things SEAICE_EPS). |
| 615 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
| 616 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
| 617 |
|
the wrong key by inialising it before use -> fixes a recomputation |
| 618 |
|
problem but does not fix the gradient |
| 619 |
|
o pkg/layers: |
| 620 |
|
- move resetting of flux arrays to outside the iLa loop |
| 621 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
| 622 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
| 623 |
|
o pkg/layers: |
| 624 |
|
- remove from common block 3D layers fields (used to diagnose transport |
| 625 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
| 626 |
|
o pkg/seaice: |
| 627 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
| 628 |
|
in lab_sea forward experiment (changes results -> updated) |
| 629 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
| 630 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
| 631 |
|
computations; for SEAICE_VECTORIZE_LSR |
| 632 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
| 633 |
|
sweep to the outside, |
| 634 |
|
- remove store directives and add "CADJ loop sequential" directives |
| 635 |
|
in analogy to model/src/solve_tridiagonal.F |
| 636 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
| 637 |
|
boundaries to yield more readable code. This has also the charming side |
| 638 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
| 639 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
| 640 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
| 641 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
| 642 |
|
an additional option) |
| 643 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
| 644 |
|
but the adjoint gradients (which are affected by this change) still explode. |
| 645 |
|
o coupler (atm & ocn _compon_interf): |
| 646 |
|
- avoid using Exch2 IO mapping if not suitable. |
| 647 |
|
|
| 648 |
|
checkpoint65m (2015/06/15) |
| 649 |
|
o pkg/layers: |
| 650 |
|
- clean-up old parameters setting (from Sep 2012): |
| 651 |
|
+ remove old parameters setting from common block (declared locally); |
| 652 |
|
+ stop if any old parameter is mixed with new parameters; |
| 653 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
| 654 |
|
- check that layers_bounds for Pot.Density are in the right range; |
| 655 |
|
this is supposed to catch un-updated setting after recently shifting |
| 656 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
| 657 |
|
o pkg/layers: |
| 658 |
|
- Added missing call to layers_fill for keeping track of tottend in |
| 659 |
|
pkg/diagnostics/diagnostics_fill_state.F |
| 660 |
|
o pkg/layers: |
| 661 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
| 662 |
|
of diapycnal fluxes |
| 663 |
|
o pkg/layers: |
| 664 |
|
- reverted changes to interpolation to previous treatment; there |
| 665 |
|
was never actually a problem |
| 666 |
|
o pkg/layers: |
| 667 |
|
- fix interpolation of layers tracers in the presence of partial cells |
| 668 |
|
- add lots of new functionality to compute water mass transformation |
| 669 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
| 670 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
| 671 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
| 672 |
|
for layers_thermodynamics calculations |
| 673 |
|
o pkg/ptracers: |
| 674 |
|
- add capability of stepping a passive tracer forward without advection |
| 675 |
|
by setting PTRACERS_advScheme to 0. |
| 676 |
|
o pkg/diagnostics: |
| 677 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
| 678 |
|
o pkg/layers: |
| 679 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
| 680 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
| 681 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
| 682 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
| 683 |
|
o pkg/layers: |
| 684 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
| 685 |
|
- fix calculation of layer non-weighted velocity and layer probability |
| 686 |
|
- add diagnostics for pot.density used for layer averaging |
| 687 |
|
o pkg/seaice: |
| 688 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
| 689 |
|
positiveness, modify a few comments and improve variable names, |
| 690 |
|
- the changed computation of deltaC affects most seaice-related |
| 691 |
|
experiments at the truncation level. |
| 692 |
|
seaice_itd.thermo is affected by far the most, with |
| 693 |
|
only 7 digits of agreement remaining; update experiments. |
| 694 |
|
|
| 695 |
|
checkpoint65l (2015/05/04) |
| 696 |
|
o pkg/shelfice: |
| 697 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
| 698 |
|
factor drKp1 to zero where it is negative (ie. do not use |
| 699 |
|
SHELFICEBoundaryLayer if hFacC>1) |
| 700 |
|
- the same for factor drLoc in shelfice_forcing.F |
| 701 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
| 702 |
|
with modules in ptracers, when using testreport option "-small_f" |
| 703 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
| 704 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
| 705 |
|
o verification/testreport |
| 706 |
|
- add new option -small_f |
| 707 |
|
with this option testreport first makes the target small_f (*.f files) |
| 708 |
|
before running make (all). This is useful for explicit inlining when |
| 709 |
|
all sources need to be full available. |
| 710 |
|
o pkg/exf/exf_interp.F: |
| 711 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
| 712 |
|
|
| 713 |
|
checkpoint65k (2015/04/01) |
| 714 |
|
o pkg/ecco: |
| 715 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
| 716 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 717 |
|
instead of active read/write |
| 718 |
|
o pkg/ctrl: |
| 719 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 720 |
|
instead of active read/write. |
| 721 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
| 722 |
|
return if .NOT.useAUTODIFF |
| 723 |
|
o pkg/seaice: add CPP brackets (cost function related). |
| 724 |
|
o model/src: |
| 725 |
|
add useAUTODIFF run time switch. |
| 726 |
|
o pkg/exf/exf_interp.F: |
| 727 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
| 728 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
| 729 |
|
this feature. |
| 730 |
|
o verification/testreport: |
| 731 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
| 732 |
|
implementations of grep that cannot do contextual searches |
| 733 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
| 734 |
|
of "cat" have the option "-n" |
| 735 |
|
o model/src: |
| 736 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
| 737 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
| 738 |
|
convert from conservative to potential temperature. For now they are not |
| 739 |
|
called anywhere. |
| 740 |
|
o pkg/ggl90: make "useIDEMIX" useful |
| 741 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
| 742 |
|
are different for idemix into separate loops (changes verification |
| 743 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
| 744 |
|
- requires 2 new 2D fields KappaM, verticalShear |
| 745 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
| 746 |
|
s/r ggl90_idemix |
| 747 |
|
- fix and improve some comments |
| 748 |
|
|
| 749 |
|
checkpoint65j (2015/02/25) |
| 750 |
|
o pkg/openad |
| 751 |
|
- synchronize seawater.F with version in model/src: replace routine |
| 752 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
| 753 |
|
o pkg/mnc: |
| 754 |
|
- change default value of pickup_read/write_mnc params to FALSE |
| 755 |
|
(since few features are missing in reading MNC pickup files). |
| 756 |
|
o model/src: |
| 757 |
|
- change default (background) vertical diffusivity for salt to be the |
| 758 |
|
temperature (background) vertical diffusivity. |
| 759 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
| 760 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
| 761 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
| 762 |
|
consistent with vertical mixing schemes. |
| 763 |
|
o verification/testreport: |
| 764 |
|
- fix typo in "-pcls" option ; |
| 765 |
|
- put temp files in /tmp (instead of in local dir) |
| 766 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
| 767 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
| 768 |
|
o pkg/ggl90 (idemix code): |
| 769 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
| 770 |
|
global_ocean.90x40x15.idemix |
| 771 |
|
o OpenAD |
| 772 |
|
- enable active file I/O and begin removal of work-around code |
| 773 |
|
for OpenAD for handling control variables (memory vs. active files) |
| 774 |
|
- new CPP options file OPENAD_OPTIONS.h |
| 775 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
| 776 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
| 777 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
| 778 |
|
o tools/genmake2: |
| 779 |
|
- add option for an alternative Makefile (from Martin) where multiple |
| 780 |
|
source files are sent to TAF (instead of all in one file). |
| 781 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
| 782 |
|
- code provided by Carsten Eden as an extension of ggl90 |
| 783 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
| 784 |
|
compile time; a runtime flag implementation is not yet complete |
| 785 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
| 786 |
|
o verification: |
| 787 |
|
- reduce length of the AD test run by half for experiments |
| 788 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
| 789 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
| 790 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
| 791 |
|
o verification/testreport: |
| 792 |
|
- fix two non-POSIX sed statements so that there are no error messages |
| 793 |
|
on Mac OS X |
| 794 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
| 795 |
|
o model/src/seawater.F: |
| 796 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
| 797 |
|
(following the matlab code), which would have avoided the bug caught |
| 798 |
|
by Matt (see below) in the first place |
| 799 |
|
o pkg/shelfice: |
| 800 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
| 801 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
| 802 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
| 803 |
|
ice-shelf case (i.e., within surface level). |
| 804 |
|
- add config summary in shelfice_check.F |
| 805 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
| 806 |
|
variable recip_latentHeat |
| 807 |
|
- introduce diagnostics for friction velocity uStar (in case of |
| 808 |
|
SHELFICEuseGammaFrict) |
| 809 |
|
- change verification experiment isomip.htd: |
| 810 |
|
+ start from pickup (as input_ad at nIter0=8640) |
| 811 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
| 812 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
| 813 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
| 814 |
|
o model/src: |
| 815 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
| 816 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
| 817 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
| 818 |
|
o pkg/shelfice: |
| 819 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
| 820 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
| 821 |
|
ice-shelf is. |
| 822 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
| 823 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
| 824 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
| 825 |
|
for thermodynamic calculations |
| 826 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
| 827 |
|
affects results of some verification experiments by up to 4 digits: |
| 828 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
| 829 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
| 830 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
| 831 |
|
-> updated |
| 832 |
|
|
| 833 |
|
checkpoint65i (2015/01/23) |
| 834 |
|
o model/src: |
| 835 |
|
- change units of frictionHeating field from W to W/m^2 |
| 836 |
|
- fix bug in frictional heating from stratospheric drag in |
| 837 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
| 838 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 839 |
|
field from load_fields_driver.F to thermodynamics.F ; |
| 840 |
|
- add diagnostics for frictional heating. |
| 841 |
|
o model/src & gmredi K3D: |
| 842 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 843 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 844 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
| 845 |
|
and name in pickup file). |
| 846 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 847 |
|
o model/src: |
| 848 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
| 849 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 850 |
|
(since Nov 2012) with option selectAddFluid=1. |
| 851 |
|
o pkg/shelfice: |
| 852 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 853 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 854 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 855 |
|
o pkg/seaice: two new runtime parameters: |
| 856 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 857 |
|
long overdue |
| 858 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 859 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
| 860 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 861 |
|
for LSR: move checking overlaps out of JFNK-if-block |
| 862 |
|
o pkg/atm_phys: |
| 863 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 864 |
|
new S/R ATM_PHYS_DYN2PHYS. |
| 865 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
| 866 |
|
fixed-in-time pressure levels). |
| 867 |
|
o pkg/mom_common (bottomdrag): |
| 868 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 869 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 870 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 871 |
|
o pkg/shelfice (u/v_drag): |
| 872 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 873 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 874 |
|
(now similar to shelfice_u_drag.F) |
| 875 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 876 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
| 877 |
|
o pkg/mom_common (bottomdrag): |
| 878 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 879 |
|
- add options for alternative discretisation of velocity norm in quadratic |
| 880 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 881 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 882 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
| 883 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 884 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 885 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
| 886 |
|
off by default since this also reduces model stability (explicit bottom |
| 887 |
|
friction). Changes produce different machine truncation with linear-drag |
| 888 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 889 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
| 890 |
|
o model/src & mom pkgs: |
| 891 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 892 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 893 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 894 |
|
just copy level Nr value to level Nr+1. |
| 895 |
|
o doc: |
| 896 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 897 |
|
o pkg/shelfice: |
| 898 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 899 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 900 |
|
from array shelficemassinit, which is set in init_fixed and |
| 901 |
|
has option to be set from file; introduce array |
| 902 |
|
shelficeMassDynTend array, set thru file in init_fixed |
| 903 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 904 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 905 |
|
pkg/streamice |
| 906 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 907 |
|
SHELFICEMassStepping = .true. |
| 908 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 909 |
|
|
| 910 |
|
checkpoint65h (2014/12/17) |
| 911 |
o verification/global_ocean.90x40x15, global_ocean_ebm: |
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 912 |
- update to generic controls. |
- update to generic controls. |
| 913 |
o pkg/ctrl: |
o pkg/ctrl: |
| 914 |
- ctrl_map_ini_genarr.F: test for igen>0 |
- ctrl_map_ini_genarr.F: test for igen>0 |
| 915 |
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 916 |
- move gentim2d part of ctrl_map_ini_genarr.F to |
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 917 |
new separate routine : ctrl_map_ini_gentim2d.F |
new separate routine : ctrl_map_ini_gentim2d.F |
| 918 |
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 919 |
add time variable weights and cyclic controls (time mean, |
add time variable weights and cyclic controls (time mean, |
| 920 |
seasonal cycle, etc) capabilities to gentim2d |
seasonal cycle, etc) capabilities to gentim2d |
| 921 |
o pkg/ecco: |
o pkg/ecco: |
| 922 |
- move reading of error, conversion to weights from |
- move reading of error, conversion to weights from |
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