4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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|
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o pkg/thsice: |
8 |
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- account for ice velocity (ocean relative velocity) in turbulent heat flux |
9 |
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at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
10 |
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and offline_exf_seaice (main test). |
11 |
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|
12 |
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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. |
15 |
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o verification/isomip, pkg/shelfice and OpenAD: |
16 |
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- add OpenAD setup to this exp and make shelfice package work with OpenAD |
17 |
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o verification/tutorial_global_oce_biogeo: |
18 |
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- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
19 |
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o verification/offline_exf_seaice: |
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- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
21 |
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o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
22 |
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- add OpenAD setup to this exp and make ptracers package work with OpenAD |
23 |
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o pkg/seaice/seaice_evp.F: |
24 |
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mask the asymmetric contribution of the ice-ocean stress (when |
25 |
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the turningAngle is non-zero) over open water to avoid stripes |
26 |
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in the EVP-solutions after many EVP-substeps. This does not change |
27 |
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the verification experiment (because turningAngle=0 in that experiment), |
28 |
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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 |
34 |
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(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
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digits of matching. |
36 |
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o pkg/seaice: |
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modify lsr-algorithm so that it vectorizes AND converges by using a |
38 |
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"zebra" method: split vector loop into two with step size 2; this |
39 |
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solves a general convergence problem for the JFNK solver on a vector |
40 |
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computer. It has the potential to even improve convergence for |
41 |
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non-vector machines, but it does change the results so it is turned |
42 |
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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 |
44 |
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|
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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 |
48 |
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from ecco package, and revert to unified routine in model/src/ |
49 |
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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: |
53 |
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- implement compressible flow method for multi-dim advection (similar to |
54 |
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gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
55 |
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TAF generates many recomputations) to use it; no yet coded with implicit |
56 |
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vertical advection. |
57 |
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- change experiment advect_cs (new output) and advect_xy (same output) |
58 |
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to test compressible flow multi-dim advection. |
59 |
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o pkg/generic_advdiff: |
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- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
61 |
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cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
62 |
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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), |
65 |
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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 |
68 |
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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) |
70 |
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- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
71 |
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o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
72 |
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- new subroutines seaice_lsr_tridiagu/v |
73 |
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- introduce loop bounds i/jmin/max to be able to use a restricted |
74 |
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additive Schwarz method, but not used for now. |
75 |
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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; |
83 |
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- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
84 |
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ADAMS_BASHFORTH2. |
85 |
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o pkg/cheapaml: |
86 |
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- add new parameter (default=F, same as before) to disable full domain |
87 |
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(including land) periodicity in X & Y dir. |
88 |
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- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
89 |
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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. |
91 |
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|
92 |
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checkpoint64d (2013/02/17) |
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o pkg/monitor (angular momentum): |
94 |
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- do not add Eta contribution to the total AM if using rigid-lid; |
95 |
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- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
96 |
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- horizontal discretisation: compute Zonal wind contribution separately for |
97 |
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each component (instead of from cell centered averaged) and use the 4 |
98 |
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grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
99 |
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- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
100 |
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FreeSurf) if using vectorInvariant momentum. |
101 |
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o model/src (horizontal grid): |
102 |
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- move initialisation of all horizontal grid arrays to null value |
103 |
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from specific horizontal grid S/R to main S/R INI_GRID; |
104 |
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- add 2 new arrays to project model C-grid velocity on to zonal direction |
105 |
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(similar to AngleCosC & -AngleSinC but at U and V point location) and |
106 |
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compute them in S/R CALC_GRID_ANGLES. |
107 |
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o pkg/seaice: replace a hard coded parameter by a runtime parameter |
108 |
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SEAICE_JFNK_tolIter |
109 |
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o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
110 |
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preconditioner for JFNK (run LSR into the overlaps as far as possible, |
111 |
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i.e OLx/y-2, but overwrite the solution in the overlaps) |
112 |
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- extend loop range in seaice_calc_viscosity |
113 |
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- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
114 |
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- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
115 |
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- slightly modify loops in tridiagonal solver lsr-preconditioner |
116 |
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- by default remove the extra exchange in seaice_preconditioner with a |
117 |
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replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
118 |
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- modify offline_exf_seaice so that old results without RAS are reproduced |
119 |
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for output.dyn_jfnk.txt |
120 |
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in seaice_fgmres.F (unrelated to RAS) |
121 |
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- add a cpp-flag option for a re-ordered mapping (potentially more |
122 |
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efficient), but because this changes the results, turn it off by |
123 |
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default |
124 |
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- replace the save statement by local common blocks |
125 |
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o utils/matlab: |
126 |
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- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
127 |
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- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
128 |
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instead of local script "load_cs.m". |
129 |
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o pkg/seaice: |
130 |
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- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
131 |
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to the scalarProductMetric and the unrolling. By chance this does not |
132 |
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change the verification experiment, because of the particular domain |
133 |
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decomposition |
134 |
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o pkg/diagnostics: |
135 |
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- change default missing_value from UNSET_RL to -999. |
136 |
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o pkg/layers: improve vectorization of layers_fluxcalc.F |
137 |
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- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
138 |
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time spent in this routine by more than a factor of 3 on an NEC-SX8 |
139 |
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- step 2: replace search algorithm by a bisection algorithm found in |
140 |
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Press et al. Numerical Recipes in Fortran. This algorithm can be |
141 |
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vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
142 |
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For now, use this algorithm only for TARGET_NEC_SX defined. |
143 |
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- moved the search algorithm into a separate subroutine, that is kept |
144 |
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within the same file for automatic inlining. |
145 |
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- modified catching potential errors |
146 |
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o pkg/ecco: |
147 |
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- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
148 |
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o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
149 |
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- modifications for ALLOW_GENTIM2D_CONTROL |
150 |
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-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
151 |
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-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
152 |
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-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
153 |
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-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
154 |
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o model/src: |
155 |
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- account for moist thermodynamics in (dry) potential temperature equation; |
156 |
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update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
157 |
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and cpl_aim+ocn. |
158 |
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- also switch to standard compiler (gfortran, was using ifort previously) |
159 |
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for fizhi-cs experiments reference output. |
160 |
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o pkg/ctrl: |
161 |
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- 1st step toward generic time-varying control variable (2D) via CPP option |
162 |
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ALLOW_GENTIM2D_CONTROL |
163 |
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- note new namelist ctrl_nml_genarr in data.ctrl |
164 |
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o verification/global_ocean.cs32x15: |
165 |
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- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
166 |
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thsice calling sequence and update "output.icedyn.txt" output file. |
167 |
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o pkg/ptracers: |
168 |
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- from Ryan A.: code to allow to restart a tracer at regular time interval |
169 |
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specifying a reset frequency and a reset-phase (for each tracers). |
170 |
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o pkg/thsice: |
171 |
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- implement new sequence of calls for thsice+seaice: |
172 |
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previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
173 |
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new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
174 |
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- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
175 |
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in CPP_OPTIONS.h) to recover old sequence; |
176 |
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- update diagnostics for Intermediate State thsice diagnostics: now filled |
177 |
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just before advection (instead of just after advection in old sequence); |
178 |
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- update output of experiment offline_exf_seaice (standard test); |
179 |
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- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
180 |
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by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
181 |
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o pkg/aim_v23: |
182 |
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- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
183 |
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- use standard pkg/mdsio routines to read & write CO2 pickup file; |
184 |
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- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
185 |
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- Implement new sequence of calls for seaice advection (with thsice and |
186 |
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seaice diffusion): do ice advection after ice-Thermodynamic (previously |
187 |
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was done before); change aim_do_physics.F (split the bi,bj loops block); |
188 |
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- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
189 |
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o pkg/thsice: |
190 |
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- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
191 |
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where just seaice diffusion is used without seaice-dynamics. |
192 |
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|
193 |
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checkpoint64c (2013/01/18) |
194 |
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o pkg/seaice: |
195 |
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- add a parameter JFNKres_tFac that can replace JFNKres_t |
196 |
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(= JFNKres_tFac*JFNKresidual before JFNK solver) |
197 |
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- add a line search option to the JFNK solver |
198 |
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- move update of u/vIce and computation of initial residual into a separate |
199 |
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routine (same file); makes the code a little easier to read (?) |
200 |
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- the line search requires computation of the residual and for some reason |
201 |
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I cannot do the update of u/vIce at the beginning of the Newton loop |
202 |
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without changing the results, so we move computation of the new residual |
203 |
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also to the end of the Newton loop, even without the line search |
204 |
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o pkg/mdsio: |
205 |
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- write missing value (corresponding to undefined array value) to meta files; |
206 |
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skip this if missing value is one (UNSET_RL would be a better value for the |
207 |
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case of undefined missing value but it's current the default missing-value); |
208 |
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Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
209 |
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o pkg/exf & thsice: |
210 |
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- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
211 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
212 |
|
o verification/cfc_example: |
213 |
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- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
214 |
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illustrate how to use it). |
215 |
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o verification/offline_exf_seaice: |
216 |
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in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
217 |
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files to only one time-record. |
218 |
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in input.thermo: narrow the 2 bands of low initial ice-concentration near |
219 |
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N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
220 |
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snapshot output; same mcPheePiston value as in thsice with |
221 |
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surf-current=0.2m/s. |
222 |
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in input.thsice: similar set-up as in input.thermo (channel with same seaice |
223 |
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initial conditions). |
224 |
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o verification/cfc_example: |
225 |
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- update file "data" with more standard choice (default rotationPeriod, |
226 |
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exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
227 |
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set deltaTFreeSurf to deltaTtracer) and update the output. |
228 |
|
o pkg/layers: |
229 |
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- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
230 |
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- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
231 |
|
o verification/offline_exf_seaice: |
232 |
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- set all {field}period to zero for constant-in-time forcing (not tested |
233 |
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anywhere else). |
234 |
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o verification/offline_exf_seaice: |
235 |
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- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
236 |
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- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
237 |
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o model/src: |
238 |
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- implement Finite-Volume method for (hydrostatic) presure gradient |
239 |
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from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
240 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
241 |
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- In order to be compatible with the default EVP code, this requires changing |
242 |
|
the EVP code around a little; and because any small change immediately |
243 |
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breaks the lab_sea.hb87 verification experiment, the reference output is |
244 |
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updated two times (each time the remaining aggrement was only 2 digits): |
245 |
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- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
246 |
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- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
247 |
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The adjoint test lab_sea.evp also needed to be updated. |
248 |
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- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
249 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
250 |
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a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
251 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
252 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
253 |
|
kept obscure, because I need to test it a little more. |
254 |
|
o pkg/cheapaml: |
255 |
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- fix few incorrect type (_RL/_RS) in subroutine calls. |
256 |
|
o pkg/seaice: |
257 |
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- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
258 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
259 |
|
o model/src: |
260 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
261 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
262 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
263 |
|
o pkg/cheapaml: |
264 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
265 |
|
update output of experiment cheapAML_box. |
266 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
267 |
|
and set them only in one place (cheapaml_readparms.F). |
268 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
269 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
270 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
271 |
|
o model/src/the_main_loop.F: |
272 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
273 |
|
o pkg/seaice: |
274 |
|
- remove legacy branch code. |
275 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
276 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
277 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
278 |
|
SEAICE_CAP_HEFF). |
279 |
|
o pkg/cheapaml: |
280 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
281 |
|
to load new forcing fields. |
282 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
283 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
284 |
|
cheapAML_box, keep same output (small trucation error differences). |
285 |
|
o verification/offline_exf_seaice: |
286 |
|
- add thermodynamics only test. |
287 |
|
o verification/cheapAML_box: |
288 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
289 |
|
keep same output (same 14 digits for cg2d). |
290 |
|
- switch on "-r8" compiler option (some numerical values are missing |
291 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
292 |
|
|
293 |
|
checkpoint64b (2012/12/24) |
294 |
|
o pkg/cheapaml: |
295 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
296 |
|
- store tendency of advected variables into cheapaml pickup file |
297 |
|
and fix the AB-2 restart. |
298 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
299 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
300 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
301 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
302 |
|
- update results after change of experiment seaice. |
303 |
|
o pkg/seaice: |
304 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
305 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
306 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
307 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
308 |
|
o model/src: |
309 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
310 |
|
(in case of a poor convergence). |
311 |
|
o pkg/seaice/seaice_lsr.F |
312 |
|
- move calculation of matrix coefficients into new |
313 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
314 |
|
file; the main purpose of this change is to be able to reuse the code |
315 |
|
in S/R SEAICE_PRECONDITIONER |
316 |
|
- modify the computation of the residual so that the mass of sea-ice |
317 |
|
is not used twice; this simplifies the calculations, but since |
318 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
319 |
|
not tested in testreport---this does not affect the testreport results. |
320 |
|
o verification/seaice_obcs: |
321 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
322 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
323 |
|
o model/src: |
324 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
325 |
|
o pkg/seaice: |
326 |
|
- improve description of parameters in seaice_fgmres.F and start |
327 |
|
cleaning up the code |
328 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
329 |
|
second argument |
330 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
331 |
|
results of offline_exf_seaice.dyn_jfnk |
332 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
333 |
|
o pkg/aim_v23: |
334 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
335 |
|
o model/src + pkg/seaice: |
336 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
337 |
|
along X and Y lines, respectively for U and V component. |
338 |
|
Note: 1) MPI and cube-exchange not yet coded. |
339 |
|
2) probably not accurate for poorly conditioned / large size problem. |
340 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
341 |
|
default: not compiled and not used. |
342 |
|
o pkg/seaice: |
343 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
344 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
345 |
|
mpi_allreduce in seaice_fgmres.F |
346 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
347 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
348 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
349 |
|
o verification: |
350 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
351 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
352 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
353 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
354 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
355 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
356 |
|
o pkg/exf: |
357 |
|
- disable "sstExtrapol" when Nr=1 |
358 |
|
o verification: |
359 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
360 |
|
to test pkg/cheapaml. |
361 |
|
o pkg/aim_v23 & pkg/shap_filt: |
362 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
363 |
|
o pkg/seaice: |
364 |
|
- remove unused field pressPre from jfnk solver |
365 |
|
- rename two subroutines in seaice_preconditioner.F |
366 |
|
o eesupp/src: |
367 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
368 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
369 |
|
- remove wrong parts of the rhs and the lhs (were in there |
370 |
|
because I did not understand the concept of this preconditioner) |
371 |
|
- add an exchange between u- and v-sweep. This increases communication |
372 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
373 |
|
one would like the u- and v-sweep to be independent. So far within |
374 |
|
undocumented ifdefs |
375 |
|
- reorganize the extra computations for printing the residuals |
376 |
|
o tools/genmake2: |
377 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
378 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
379 |
|
|
380 |
|
checkpoint64a (2012/11/16) |
381 |
|
o pkg/autodiff: |
382 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
383 |
|
autodiff_readparms.F no longer depends on calling order (within |
384 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
385 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
386 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
387 |
|
o pkg/obcs: |
388 |
|
- adding tidal velocity forcing capability to obcs |
389 |
|
for usage example, see verification/seaice_obcs/input.tides |
390 |
|
o pkg/seaice: |
391 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
392 |
|
SEAICE_LSRrelaxU/V |
393 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
394 |
|
o pkg/aim_v23: |
395 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
396 |
|
o pkg/shap_filt: |
397 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
398 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
399 |
|
o model/src: |
400 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
401 |
|
time-constant addMass field from file (addMassFile); |
402 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
403 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
404 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
405 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
406 |
|
o pkg/seaice: |
407 |
|
- complete merge of ITD code into seaice_growth.F |
408 |
|
from MITgcm_contrib/torge/itd/code/ |
409 |
|
no verification so far, but Torge Martin tested |
410 |
|
"1-D test case and Beaufort set up; |
411 |
|
deliver okay results after 1 model year." |
412 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
413 |
|
- move computation of eta at Z-points into calc_viscosities |
414 |
|
+ introduce global field etaZ |
415 |
|
+ add different methods for computing etaZ, for now the old |
416 |
|
method (simple averages of eta to Z-points) is hardwired |
417 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
418 |
|
seaice_preconditioner |
419 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
420 |
|
- seaice_preconditioner: |
421 |
|
+ replace one remaining press by pressLoc (mistake) |
422 |
|
+ adjust printing of residuals |
423 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
424 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
425 |
|
seaice_init_fixed.F) |
426 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
427 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
428 |
|
interval to STDOUT |
429 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
430 |
|
some operations |
431 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
432 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
433 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
434 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
435 |
|
a serious convergence problem when open boundaries are involved |
436 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
437 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
438 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
439 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
440 |
|
o pkg/autodiff |
441 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
442 |
|
SEAICEuseDYNAMICSinAdMode |
443 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
444 |
|
o pkg/seaice |
445 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
446 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
447 |
|
The code implements concept laid out in Thorndike et al. (1975); |
448 |
|
code is enabled via CPP flag SEAICE_ITD |
449 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
450 |
|
code is not complete yet!! |
451 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
452 |
|
o verification (using seaice): |
453 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
454 |
|
global_ocean.cs32x15.seaice ; update results. |
455 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
456 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
457 |
|
offline_exf_seaice (previously compiling B-grid). |
458 |
|
o pkg/exf: |
459 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
460 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
461 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
462 |
|
o pkg/layers (adjust changes from Sept 19): |
463 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
464 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
465 |
|
o pkg/layers (adjust changes from Sept 19): |
466 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
467 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
468 |
|
- remove layers variables when corresponding CPP option is undef. |
469 |
|
o pkg/layers: |
470 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
471 |
|
velocity in layer) |
472 |
|
o pkg/seaice: |
473 |
|
- simplify (?) ocean-drag coefficent computations by using |
474 |
|
the same routine in all three solvers (saves some code lines) |
475 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
476 |
|
declare them locally in lsr.F (the only place where they are |
477 |
|
still used) |
478 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
479 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
480 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
481 |
|
and SEAICEuseJFNK=.true. A few things to note: |
482 |
|
- involves a FGMRES, that is parallel but very inefficient, |
483 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
484 |
|
orthogonalization method. Needs to be replaced. Original code |
485 |
|
from J.-F. Lemieux |
486 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
487 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
488 |
|
preconditioner. For the preconditioner, the default is set to 10. |
489 |
|
- Jacobian times vector is computed with finite differences |
490 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
491 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
492 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
493 |
|
does not need this regularization in the first place). Define |
494 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
495 |
|
o eesupp/src: |
496 |
|
- check in genmake2 that intrinsic S/R flush is available. |
497 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
498 |
|
- flush standard & error msg unit before MPI termination |
499 |
|
- if debugMode, flush IO unit after printing msg |
500 |
|
o pkg/ctrl: |
501 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
502 |
|
to ctrl_set_unpack_xyz. |
503 |
|
|
504 |
|
checkpoint64 (2012/10/09) |
505 |
|
o pkg/shelfice |
506 |
|
- in mom_fluxform.F, mom_vecinv.F: |
507 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
508 |
|
Bug fix KappaRU -> KappaRV |
509 |
|
does not change verification/isomip but may change other setups |
510 |
|
(presumably constant KappaRU=KappaRV) |
511 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
512 |
|
o pkg/obcs: |
513 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
514 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
515 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
516 |
|
o pkg/seaice: |
517 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
518 |
|
default is off for now. |
519 |
|
o pkg/obcs: |
520 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
521 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
522 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
523 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
524 |
|
o pkg/layers : |
525 |
|
- add diagnostics to pkg/layers |
526 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
527 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
528 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
529 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
530 |
|
o pkg/seaice/seaice_growth.F: |
531 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
532 |
|
o pkg/obcs: |
533 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
534 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
535 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
536 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
537 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
538 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
539 |
|
o pkg/obcs: |
540 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
541 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
542 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
543 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
544 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
545 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
546 |
|
to replace hard-coded null index value of zero. |
547 |
|
o pkg/exch2: |
548 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
549 |
|
always check buffer-size (but outside the loop); move checking for valid |
550 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
551 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
552 |
|
o pkg/ctrl (pack & unpack): |
553 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
554 |
|
(locally defined) for different variables (+ remove the variable-specific |
555 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
556 |
|
(to be extended to other local file names in ctrl.h). |
557 |
|
o pkg/flt: |
558 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
559 |
|
o pkg/mdsio: |
560 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
561 |
|
o tools/genmake2: |
562 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
563 |
|
(added by Alistair in version 1.51 for building without make depend); |
564 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
565 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
566 |
|
place in version 1.23): this save going through staf when unrelated header |
567 |
|
file has been modified. |
568 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
569 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
570 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
571 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
572 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
573 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
574 |
|
upper/lower case ; account for space between "#" and undef/define) |
575 |
|
o pkg/flt (with exch2): |
576 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
577 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
578 |
|
|
579 |
|
checkpoint63s (2012/09/05) |
580 |
|
o pkg/ecco: |
581 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
582 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
583 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
584 |
|
o pkg/ctrl: |
585 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
586 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
587 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
588 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
589 |
|
ctrlSmoothCorrel3D (new). |
590 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
591 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
592 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
593 |
|
controls when useAtmWind, and vice versa. |
594 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
595 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
596 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
597 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
598 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
599 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
600 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
601 |
|
o pkg/smooth: |
602 |
|
- remove un-necessary includes. |
603 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
604 |
|
Those CPP options were never defined, and not necessary. |
605 |
|
o model/src: |
606 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
607 |
|
- standard treatment of useSMOOTH. |
608 |
|
o pkg/autodiff: |
609 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
610 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
611 |
|
o pkg/exch2: |
612 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
613 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
614 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
615 |
|
and tiles to process mapping. |
616 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
617 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
618 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
619 |
|
from w2_eeboot.F to w2_readparms.F. |
620 |
|
o eesupp/src: |
621 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
622 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
623 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
624 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
625 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
626 |
|
has been called. |
627 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
628 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
629 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
630 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
631 |
|
useCubedSphereExchange with EXCH-1 (safer). |
632 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
633 |
|
o pkg/ggl90: |
634 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
635 |
|
used in ALLOW_GGL90_SMOOTH code. |
636 |
|
o pkg/flt: |
637 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
638 |
|
floats at the Southern end of the domain). |
639 |
|
o eesupp/inc: |
640 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
641 |
|
but not used (and not to be used) anywhere, just for documentation. |
642 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
643 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
644 |
|
a) can damage previously written records in any other multi-record files. |
645 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
646 |
|
o tools/genmake2: |
647 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
648 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
649 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
650 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
651 |
|
- always print usual warning comment 'this file is automatically generated' |
652 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
653 |
|
o pkg/cheapaml: |
654 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
655 |
|
o pkg/exf: |
656 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
657 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
658 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
659 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
660 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
661 |
|
o pkg/ctrl, ecco: |
662 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
663 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
664 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
665 |
|
o tools/genmake2: |
666 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
667 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
668 |
|
- source local config file "genmake_local" just after processing the genmake2 |
669 |
|
command arguments (previously done before processing arg). |
670 |
o pkg/grdchk: |
o pkg/grdchk: |
671 |
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
672 |
to this routine from cost_final has been dropped in g_cost_final) |
to this routine from cost_final has been dropped in g_cost_final) |