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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 pkg/seaice: add a line search option to the JFNK solver |
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
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(compile when SEAICE_ALLOW_JFNK is defined) |
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o pkg/thsice: |
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- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
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implementation): move THSICE_AVE call after the advection (called directly |
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from thsice_do_advect.F). |
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o verification/global_ocean.90x40x15 and OpenAD: |
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New experiment for OpenAD is identical to the one in input_ad except that |
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multiDimAdvection=.FALSE., |
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There is still an issue with this. |
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o pkg/thsice: |
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- account for ice velocity (ocean relative velocity) in turbulent heat flux |
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at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
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and offline_exf_seaice (main test). |
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|
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checkpoint64f (2013/03/31) |
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o verification/OpenAD: |
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- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
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o verification/isomip, pkg/shelfice and OpenAD: |
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- add OpenAD setup to this exp and make shelfice package work with OpenAD |
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o verification/tutorial_global_oce_biogeo: |
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- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
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o verification/offline_exf_seaice: |
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- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
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o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
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- add OpenAD setup to this exp and make ptracers package work with OpenAD |
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o pkg/seaice/seaice_evp.F: |
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mask the asymmetric contribution of the ice-ocean stress (when |
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the turningAngle is non-zero) over open water to avoid stripes |
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in the EVP-solutions after many EVP-substeps. This does not change |
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the verification experiment (because turningAngle=0 in that experiment), |
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but will affect other EVP solutions with turningAngle.ne.0 |
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o verification, AD & TLM output: |
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- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
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additions and multiplications which affect results at machine truncation |
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level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
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lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
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(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
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digits of matching. |
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o pkg/seaice: |
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modify lsr-algorithm so that it vectorizes AND converges by using a |
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"zebra" method: split vector loop into two with step size 2; this |
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solves a general convergence problem for the JFNK solver on a vector |
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computer. It has the potential to even improve convergence for |
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non-vector machines, but it does change the results so it is turned |
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off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
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SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
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checkpoint64e (2013/03/05) |
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o pkg/ecco and several verification experiments: |
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Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
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from ecco package, and revert to unified routine in model/src/ |
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Adjust verification experiments accordingly, especially gloal_oce_llc90 |
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Should conclude long-standing work by Gael to reconsile the_main_loop with |
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ECCO and will enable OpenAD's revolve loop in ECCO setup. |
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o pkg/generic_advdiff: |
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- implement compressible flow method for multi-dim advection (similar to |
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gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
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TAF generates many recomputations) to use it; no yet coded with implicit |
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vertical advection. |
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- change experiment advect_cs (new output) and advect_xy (same output) |
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to test compressible flow multi-dim advection. |
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o pkg/generic_advdiff: |
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- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
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cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
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o pkg/seaice: |
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- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
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bug affects two verification experiments (lab_sea and lab_sea.hb87), |
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recover old (wrong) results by setting noSlipFac = 2. in |
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seaice_calc_strainrates.F; |
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- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
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- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
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gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
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- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
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o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
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- new subroutines seaice_lsr_tridiagu/v |
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- introduce loop bounds i/jmin/max to be able to use a restricted |
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additive Schwarz method, but not used for now. |
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- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
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- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
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o OpenAD support |
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Reorganize S/R call for overall time-stepping loop to facilitate |
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OpenAD revolve loop replacement |
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(new S/R main_do_loop.F) |
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o model/src: |
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- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
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- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
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ADAMS_BASHFORTH2. |
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o pkg/cheapaml: |
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- add new parameter (default=F, same as before) to disable full domain |
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(including land) periodicity in X & Y dir. |
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- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
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prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
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into single S/R CHEAPAML_TIMESTEP. |
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checkpoint64d (2013/02/17) |
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o pkg/monitor (angular momentum): |
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- do not add Eta contribution to the total AM if using rigid-lid; |
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- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
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- horizontal discretisation: compute Zonal wind contribution separately for |
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each component (instead of from cell centered averaged) and use the 4 |
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grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
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- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
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FreeSurf) if using vectorInvariant momentum. |
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o model/src (horizontal grid): |
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- move initialisation of all horizontal grid arrays to null value |
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from specific horizontal grid S/R to main S/R INI_GRID; |
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- add 2 new arrays to project model C-grid velocity on to zonal direction |
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(similar to AngleCosC & -AngleSinC but at U and V point location) and |
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compute them in S/R CALC_GRID_ANGLES. |
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o pkg/seaice: replace a hard coded parameter by a runtime parameter |
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SEAICE_JFNK_tolIter |
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o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
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preconditioner for JFNK (run LSR into the overlaps as far as possible, |
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i.e OLx/y-2, but overwrite the solution in the overlaps) |
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- extend loop range in seaice_calc_viscosity |
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- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
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- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
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- slightly modify loops in tridiagonal solver lsr-preconditioner |
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- by default remove the extra exchange in seaice_preconditioner with a |
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replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
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- modify offline_exf_seaice so that old results without RAS are reproduced |
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for output.dyn_jfnk.txt |
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in seaice_fgmres.F (unrelated to RAS) |
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- add a cpp-flag option for a re-ordered mapping (potentially more |
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efficient), but because this changes the results, turn it off by |
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default |
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- replace the save statement by local common blocks |
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o utils/matlab: |
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- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
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- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
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instead of local script "load_cs.m". |
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o pkg/seaice: |
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- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
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to the scalarProductMetric and the unrolling. By chance this does not |
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change the verification experiment, because of the particular domain |
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decomposition |
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o pkg/diagnostics: |
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- change default missing_value from UNSET_RL to -999. |
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o pkg/layers: improve vectorization of layers_fluxcalc.F |
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- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
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time spent in this routine by more than a factor of 3 on an NEC-SX8 |
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- step 2: replace search algorithm by a bisection algorithm found in |
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Press et al. Numerical Recipes in Fortran. This algorithm can be |
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vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
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For now, use this algorithm only for TARGET_NEC_SX defined. |
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- moved the search algorithm into a separate subroutine, that is kept |
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within the same file for automatic inlining. |
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- modified catching potential errors |
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o pkg/ecco: |
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- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
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o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
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- modifications for ALLOW_GENTIM2D_CONTROL |
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-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
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-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
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-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
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-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
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o model/src: |
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- account for moist thermodynamics in (dry) potential temperature equation; |
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update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
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and cpl_aim+ocn. |
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- also switch to standard compiler (gfortran, was using ifort previously) |
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for fizhi-cs experiments reference output. |
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o pkg/ctrl: |
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- 1st step toward generic time-varying control variable (2D) via CPP option |
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ALLOW_GENTIM2D_CONTROL |
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- note new namelist ctrl_nml_genarr in data.ctrl |
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o verification/global_ocean.cs32x15: |
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- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
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thsice calling sequence and update "output.icedyn.txt" output file. |
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o pkg/ptracers: |
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- from Ryan A.: code to allow to restart a tracer at regular time interval |
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specifying a reset frequency and a reset-phase (for each tracers). |
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o pkg/thsice: |
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- implement new sequence of calls for thsice+seaice: |
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previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
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new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
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- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
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in CPP_OPTIONS.h) to recover old sequence; |
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- update diagnostics for Intermediate State thsice diagnostics: now filled |
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just before advection (instead of just after advection in old sequence); |
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- update output of experiment offline_exf_seaice (standard test); |
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- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
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by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
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o pkg/aim_v23: |
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- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
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- use standard pkg/mdsio routines to read & write CO2 pickup file; |
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- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
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- Implement new sequence of calls for seaice advection (with thsice and |
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seaice diffusion): do ice advection after ice-Thermodynamic (previously |
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was done before); change aim_do_physics.F (split the bi,bj loops block); |
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- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
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o pkg/thsice: |
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- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
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where just seaice diffusion is used without seaice-dynamics. |
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|
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checkpoint64c (2013/01/18) |
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o pkg/seaice: |
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- add a parameter JFNKres_tFac that can replace JFNKres_t |
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(= JFNKres_tFac*JFNKresidual before JFNK solver) |
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- add a line search option to the JFNK solver |
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- move update of u/vIce and computation of initial residual into a separate |
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routine (same file); makes the code a little easier to read (?) |
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- the line search requires computation of the residual and for some reason |
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I cannot do the update of u/vIce at the beginning of the Newton loop |
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without changing the results, so we move computation of the new residual |
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also to the end of the Newton loop, even without the line search |
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o pkg/mdsio: |
o pkg/mdsio: |
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- write missing value (corresponding to undefined array value) to meta files; |
- write missing value (corresponding to undefined array value) to meta files; |
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skip this if missing value is one (UNSET_RL would be a better value for the |
skip this if missing value is one (UNSET_RL would be a better value for the |
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case of undefined missing value but it's current the default missing-value); |
case of undefined missing value but it's current the default missing-value); |
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Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
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o pkg/exf & thsice: |
o pkg/exf & thsice: |
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- for diagnostics purpose, fill-up and update Qsw array (+ fill the diagnostics) |
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
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even when SHORTWAVE_HEATING is #undef; |
diagnostics) even when SHORTWAVE_HEATING is #undef; |
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o verification/cfc_example: |
o verification/cfc_example: |
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- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to illustrate |
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
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how to use it). |
illustrate how to use it). |
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o verification/offline_exf_seaice: |
o verification/offline_exf_seaice: |
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in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
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files to only one time-record. |
files to only one time-record. |
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in input.thermo: narrow the 2 bands of low initial ice-concentration near |
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
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N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
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snapshot output; same mcPheePiston value as in thsice with surf-current=0.2m/s. |
snapshot output; same mcPheePiston value as in thsice with |
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surf-current=0.2m/s. |
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in input.thsice: similar set-up as in input.thermo (channel with same seaice |
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
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initial conditions). |
initial conditions). |
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o verification/cfc_example: |
o verification/cfc_example: |
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