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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o add "--embed-source" option to genmake2 which, when the supporting |
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tools can be compiled (as determined by genmake2) will turn on the |
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embed_files package which then embeds the entire MITgcm source code |
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(*.[fFhc] + Makefile) used for the build within the executable |
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- requested by CNH but off by default |
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- adds a paltry <9MB to the mitgcmuv executable in most cases |
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- only writes the output when useEMBEDSRC in eedata is true |
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o clean up 3-dim. relaxation codes: |
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* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
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* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
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* Thanks to Tom Haine for testing! |
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checkpoint57z_post |
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o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
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affects output (@ truncation level) of exp. plume_on_slope ; updated. |
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o fix the pickup behavior for obcs in combination with ptracers |
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o fix a bug in ptracers_external_fields_load |
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o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
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affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
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o transfered surface NH pressure to eta field (if exactConserv). |
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o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
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and update lab_sea output.txt file. |
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o completing 3-dim. relaxation code: additional term |
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1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
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in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
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* At compile time, in "EXF_OPTIONS.h" set |
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#define ALLOW_CLIMTEMP_RELAXATION |
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#define ALLOW_CLIMSALT_RELAXATION |
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* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
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tauThetaClimRelax3Dim = 15552000.0, |
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tauSaltClimRelax3Dim = 15552000.0, |
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* 3 cases: |
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1) Use a constant-in-time 3-dim. field |
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2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
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3) Real-time relax. to time-evolving prescribed field |
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o Adding Laplacian-type smoothness constraint on |
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initial and boundary (forcing) controls (ic, bc) |
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* enable at compile-time via |
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ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
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* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
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* Absolute scale somewhat unclear so far |
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* no area weighting was included since no other cost term does so far |
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checkpoint57y_post |
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First step for a NLFS adjoint |
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o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
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o new init. routines for calc_r_star, calc_surf_dr |
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o still need to deal with ini_masks_etc |
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o testreport seemed happy |
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checkpoint57y_pre |
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o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
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o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
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o add new offset feature to offline pkg (plus minor cleanup) |
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o cfc fixes for final year of integration |
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o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
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be in GCHEM_OPTIONS). |
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checkpoint57x_post |
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o fix testreport Pb in multiple test experiment. |
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o cleanup our namelist syntax in verification: |
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- make it more F95 standards compliant (some work still needed) |
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- allows the vast majority of our tests to work with gfortran |
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o Non-Hydrostatic: |
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- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
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- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
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o Allow to apply AB on T,S rather than on AB(gT,gS): |
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- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
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- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
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time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
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- need a "clever" read_pickup to restart from the other AB formulation |
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o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
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o remove some unused variables (reduces number of compiler warnings) |
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o adjoint |
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* Disable useVariableViscosity for adjoint for time being |
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(there are a number of extensive recomputations) |
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* Initialize certain variables needed for adjoint |
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checkpoint57w_post |
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o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
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fix the singleCpuIO RS version of MDSWRITEFIELD |
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and add a WARNING if using globalFiles=T with multi-processors. |
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o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
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using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
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o tracer advection scheme: |
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add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
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those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
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was not very convenient). |
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add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
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(further tests needed for the implicit DST & Flux-Limiter schemes). |
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o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
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and sRef for convenience, handy, when you want to initialize |
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ptracers in a large domain with a constant non-zero value. Also, |
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untangle ptracers_init.F a little. |
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checkpoint57v_post |
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o change dome exp. to use variable viscosity in side-drag terms. |
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o remove all the files from the cfc_offline test since they are now |
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incorporated into tutorial_cfc_offline which has been producing |
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identical results for a few days of testing |
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o add new parameter: sideDragFactor to enable half-slip-side BC |
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and change side-drag S/R to use viscosity from mom_calc_visc |
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(can switch back by setting sideDragFactor=0.); affects results at |
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truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
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global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
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o vorticity & strain are now computed without masking, to account for |
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no-slip-side BC in variable viscosity calculation ; mask is applied |
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anyway later on, before computing advection/coriolis terms. |
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o modify exp4 to test new obcs support for reading from external files |
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and for passive tracers |
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o fix behavior of ptracers_monitor when monitor output is written to a |
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netcdf-file; still not independent of monitor.F (writes in the same |
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file). |
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o change default value of tRef (put a uniform, meaningful value for ocean |
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& atmos) and initialize sRef (was missing, as Martin mentioned). |
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o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
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to be proportional to enstrophy dissipation length. Thus, |
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viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
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This is now consistent with Smagorinsky and with the manual. |
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checkpoint57u_post |
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o OBCS and PTRACERS: add open boundary support for passive tracers |
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- either use homogenous (pseudo) v.Neumann conditions or prescribe |
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OB-values from file; this is not different from the way theta and salinity |
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are treated |
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- however, Orlanski-radiation conditions are not supported, and the model |
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will stop if you use pTracers and Orlanski at the same time. |
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- beefed up the rountine obcs_external_fields_load: now only those open |
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boundary values are overwritten with values from files for which there |
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are really files, otherwise the OB-fields remain untouched. This makes |
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it possible to use different OBs at different ends of the domain (as |
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with EXF) |
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o reduce number of exch calls in shap_filt (s2). |
| 140 |
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o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
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truncation level) 4/5 MLAdjust test results (11&12 digits match). |
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checkpoint57t_post |
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o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
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o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
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same truncation, independent of the face number: affects affects several |
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test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
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o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
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note that biharmonic viscosity + no-slip was not tested in any experiment. |
| 150 |
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o fix bug in non-linear free-surf side-drag ; generate new output for |
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global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
| 152 |
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o make mnc honor the writeBinaryPrec flag for most kinds of output |
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o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
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o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
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error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
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o add brackets in multi-terms sum to get same truncation, independent of |
| 157 |
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the face number (manage to get exactly same value of gU,gV at the cs-edge) |
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affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
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o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
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and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 161 |
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a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 162 |
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in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
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Suggested values of viscosity parameters found in mom_calc_visc. |
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Many new viscosity diagnostics available. |
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checkpoint57s_post |
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o Add clearing-house for viscosity calculations, mom_calc_visc and |
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correct numerous bugs in LeithD and Smagorinsky discretizations. |
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mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
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used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 171 |
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Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
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and with Strain-Tension viscous term calculation (mom_hdissip.F). |
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The Strain-Tension form is now called with useStrainTensonVisc=.true. |
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ViscAhStrain and viscAhTension are now retired. |
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o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
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o In response to JMC's bug report, genmake2 now ignores any soft-links |
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that it finds in the *current* directory when searching for files. |
| 178 |
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Soft-links found in any other source directories will still work as |
| 179 |
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they did before. |
| 180 |
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o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 181 |
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a C routine to unlimit the stack size |
| 182 |
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o mnc-ify pkg/aim snapshot vars |
| 183 |
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o mnc-ify pkg/land as requested by Daniel |
| 184 |
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o various changes to mnc including: |
| 185 |
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- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 186 |
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- output can now be grouped so that all files within a group |
| 187 |
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change the ITER portion of their names in lock-step together |
| 188 |
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- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 189 |
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and works with both EXCH1 and EXCH2 (but needs more testing) |
| 190 |
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- writing works for all verification test cases w/ g77 on Linux |
| 191 |
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|
| 192 |
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checkpoint57r_post |
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o make MNC variable initialization happen earlier |
| 194 |
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o add diagnostics for (almost) each term of the momentum Eq. |
| 195 |
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o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 196 |
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o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 197 |
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o remove MINIMAL_TAVE_OUTPUT option ; |
| 198 |
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add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 199 |
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o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 200 |
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allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 201 |
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o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 202 |
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o add time-dependent SST, SSS control |
| 203 |
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o cost terms in ecco/ modularized (new cost_generic.F) |
| 204 |
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o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 205 |
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o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 206 |
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* driver from the_main_loop.F is seaice_cost_driver.F |
| 207 |
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* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 208 |
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* gradient check in Exp. 6a of natl_box_adjoint/ |
| 209 |
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o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 210 |
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(see README file) |
| 211 |
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|
| 212 |
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checkpoint57q_post |
| 213 |
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o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 214 |
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o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 215 |
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- bug was reported by Jean-Michel and Ian Fenty |
| 216 |
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o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 217 |
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update exp. cpl_aim+ocn output. |
| 218 |
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o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 219 |
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Needed for high-res. runs with large global files |
| 220 |
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to be able to limit tapelev size |
| 221 |
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o Changed some tests for adjoint: |
| 222 |
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* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 223 |
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* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 224 |
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* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 225 |
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o Modifications to enable scripted COMMON to MODULE conversion |
| 226 |
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* verification/OpenAD/code/ has necessary scripts and description; |
| 227 |
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* converts, compiles and runs successfully; |
| 228 |
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|
| 229 |
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checkpoint57p_post |
| 230 |
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o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 231 |
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o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 232 |
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(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 233 |
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o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 234 |
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o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 235 |
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(was already the case for dissipation with mom_vecinv, |
| 236 |
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and also the case for grad.PhiHyd when staggered-timeStep) |
| 237 |
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This will allow to put dissipation out-off the AB time-stepping. |
| 238 |
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Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 239 |
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(cg2d matching number) and leave the others for later: front_relax(10), |
| 240 |
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global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 241 |
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matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 242 |
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|
| 243 |
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checkpoint57o_post |
| 244 |
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 245 |
(2) its ready to be documented during the 20050801 DocFest |
(2) its ready to be documented during the 20050801 DocFest |
| 246 |
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 247 |
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 248 |
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o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 249 |
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in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 250 |
|
(worth another tag) |
| 251 |
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|
| 252 |
checkpoint57n_post |
checkpoint57n_post |
| 253 |
o adding precip control xx_precip 32 |
o adding precip control xx_precip 32 |
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