| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 8 |
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- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 9 |
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- add an auxilliary variable "bet" and fix store directives and keys in |
| 10 |
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seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 11 |
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less exact gradients in my tests); but there are still |
| 12 |
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recomputation warning (although gradients are sort of OK), when |
| 13 |
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SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 14 |
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SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 15 |
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- update verification experiments lab_sea. |
| 16 |
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- change some comments in S/R seaice_calc_viscosities |
| 17 |
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o model/src: |
| 18 |
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- if staggerTimeStep=T, always apply exchange to velocity field in |
| 19 |
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do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 20 |
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(independent of using multi-dim advection or not); no effect on FWD run |
| 21 |
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but affects AD results (at machine truncation level): update output of |
| 22 |
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experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 23 |
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and isomip (oad: 12.d). |
| 24 |
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o pkg/generic_advdiff: |
| 25 |
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- stop if doAB_onGtGs is set to FALSE but ignored |
| 26 |
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- refine warning related to stability of tracer time-stepping |
| 27 |
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regarding internal wave dynamics. |
| 28 |
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- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 29 |
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on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 30 |
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if potentially unstable). |
| 31 |
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o pkg/kl10: |
| 32 |
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- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 33 |
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http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 34 |
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(contribution from Jody Klymak), tested in verification experiment |
| 35 |
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verification/internal_wave/input.kl10/ |
| 36 |
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o isomip experiment: |
| 37 |
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- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 38 |
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(input.htd) and update the output. |
| 39 |
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o cd_code experiments: |
| 40 |
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- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 41 |
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#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 42 |
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global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 43 |
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update the corresponding output. |
| 44 |
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o pkg/seaice: |
| 45 |
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- reduce the number of include files and store directives in |
| 46 |
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S/R seaice_lsr_tridiagu/v |
| 47 |
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- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 48 |
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(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 49 |
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get rid off one store directive (a TAF bug?) |
| 50 |
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- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 51 |
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S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 52 |
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- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 53 |
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- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 54 |
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S/R seaice_lsr_tridiagu/v (requires update of |
| 55 |
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offline_exf_seaice/input.dyn_jfnk) |
| 56 |
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|
| 57 |
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checkpoint65a (2014/07/27) |
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o model/src: |
| 59 |
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- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 60 |
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surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 61 |
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(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 62 |
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tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 63 |
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o model/src: |
| 64 |
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- collect momentum forcing tendency into local 2-D array (passed as argument |
| 65 |
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to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 66 |
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parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 67 |
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affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 68 |
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- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 69 |
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apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 70 |
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affects results at machine truncation level (e.g., ocean: if using |
| 71 |
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SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0) |
| 72 |
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moist correction due to vertical advection). |
| 73 |
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- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 74 |
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global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 75 |
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seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 76 |
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obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 77 |
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o pkg/ptracers & diagnostics: |
| 78 |
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- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 79 |
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title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 80 |
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- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 81 |
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to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 82 |
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|
| 83 |
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checkpoint65 (2014/07/18) |
| 84 |
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o pkg/fizhi: |
| 85 |
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- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
| 86 |
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affects results at machine truncation level. Update output of experiments |
| 87 |
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fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
| 88 |
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o pkg/seaice: more clean up |
| 89 |
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- rename TAF common block tapes to be more consistent and remove |
| 90 |
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unnecessary duplicates |
| 91 |
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- add store directives to remove more recomputations, but use smaller |
| 92 |
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tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
| 93 |
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The idea behind this flag is to reduce the memory footprint when the |
| 94 |
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adjoint of the LSR is not required. As of now, defining the flag |
| 95 |
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SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
| 96 |
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a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
| 97 |
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For experiment offline_exf_seaice, this means on a linux box with gfortran |
| 98 |
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nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 99 |
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this experiment): |
| 100 |
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> size mitgcmuv_ad |
| 101 |
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text data bss dec hex |
| 102 |
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5100659 1216 220458952 225560827 d71c8fb |
| 103 |
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5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 104 |
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but only a moderate increase of 36% for global_ocean.cs32x15: |
| 105 |
|
text data bss dec hex |
| 106 |
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6695027 1648 1014578664 1021275339 3cdf6ccb |
| 107 |
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6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
| 108 |
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- note: there are still recomputations in global_ocean.cs32x15 and |
| 109 |
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offline_exf_seaice and the gradient agreement changes (gets a |
| 110 |
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little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
| 111 |
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- in general, the AD gradients still are wrong |
| 112 |
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o OpenAD |
| 113 |
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- clean up code_oad/ directories somewhat by moving files |
| 114 |
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dontCompile, dontTransform, keepOriginal to OAD_support/ |
| 115 |
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o model/src: |
| 116 |
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- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
| 117 |
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(not currently tested): add dissipation terms before NLFS rescaling of |
| 118 |
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tendencies (previously done after). |
| 119 |
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o pkg/diagnostics: |
| 120 |
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- write stats-diags in ascii file with more digits (same as in monitor). |
| 121 |
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o pkg/down_slope: |
| 122 |
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- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
| 123 |
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NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
| 124 |
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o model/src: |
| 125 |
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- new file "apply_forcing.F" containing all the code previously in |
| 126 |
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external_forcing.F, but with new argument list: pass, as new argument, |
| 127 |
|
the current level tendency array to update (instead of a direct update |
| 128 |
|
of the common bloc array). Change the corresponding calls. |
| 129 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
| 130 |
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EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
| 131 |
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o pkg/seaice/seaice_lsr, a little bit of clean up |
| 132 |
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- rearrange some code blocks, so that now all calculations for |
| 133 |
|
setting up the right-hand-sides done within one single block |
| 134 |
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(I find that easier to read and understand) |
| 135 |
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- rearrange freedrift-code to reduce the number of ifdefs |
| 136 |
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- adjust some indentations and comments |
| 137 |
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|
| 138 |
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checkpoint64z (2014/07/10) |
| 139 |
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o model/src and several pkgs: |
| 140 |
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- change argument list of all S/R called from external_forcing.F and |
| 141 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
| 142 |
|
to pass, as argument, the current level tendency array to update |
| 143 |
|
(instead of a direct update of the common bloc array). |
| 144 |
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- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
| 145 |
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- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
| 146 |
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o pkg/seaice/seaice_lsr.F |
| 147 |
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- always initialize local arrays in seaice_lsr_tridiagu/v |
| 148 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
| 149 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
| 150 |
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keep it in bi/bj loop; this seems to be essential |
| 151 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
| 152 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
| 153 |
|
o pkg/seaice |
| 154 |
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- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
| 155 |
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generates unnecessary code in seaice_lsr_ad |
| 156 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
| 157 |
|
in seaice_lsr_ad |
| 158 |
|
- exclude some residual computations in seaice_lsr when |
| 159 |
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ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
| 160 |
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in seaice_lsr_ad |
| 161 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
| 162 |
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another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
| 163 |
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and klockey should be checked by a specialist) |
| 164 |
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- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
| 165 |
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and update lab_sea after previous changes in pkg/seaice below |
| 166 |
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o pkg/autodiff: |
| 167 |
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- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
| 168 |
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viscFacInAd : run time parameters allowing for adjoint switches |
| 169 |
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note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
| 170 |
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o pkg/ecco: |
| 171 |
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- introduce cost_gencost_boxmean.F that computes a box mean |
| 172 |
|
temperature (for use in adjoint sensitivity studies). |
| 173 |
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o model/src/set_defaults.F : initialize viscFacAdj to 1. |
| 174 |
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o pkg/mom_common/mom_calc_visc.F: |
| 175 |
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- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
| 176 |
|
o pkg/seaice/seaice_summary.F: |
| 177 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
| 178 |
|
o pkg/seaice: |
| 179 |
|
- remove some store directives and add new ones in an effort to get |
| 180 |
|
finally rid off the recomputation warnings. This is successful |
| 181 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
| 182 |
|
defined (i.e. no extensive recomputation warnings left), but there |
| 183 |
|
are still too many recomputations on the solver iteration level |
| 184 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
| 185 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
| 186 |
|
SEAICE_SIZE.h |
| 187 |
|
- add a store directive in S/R seaice_calc_viscosities |
| 188 |
|
o pkg/seaice (ITD code): |
| 189 |
|
- fix definition of Hlimit for multi-threaded case |
| 190 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
| 191 |
|
update output of experiment seaice_itd. |
| 192 |
|
o replace content of verification/seaice_itd |
| 193 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
| 194 |
|
to test the ice thickness distribution code with ridging |
| 195 |
|
- this is a first shot at this experiment |
| 196 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
| 197 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
| 198 |
|
and lot of new comments. |
| 199 |
|
|
| 200 |
|
checkpoint64y (2014/06/20) |
| 201 |
|
o pkg/seaice/seaice_reg_ridge.F: |
| 202 |
|
- modify the regularization of very small volumes of ice; only check |
| 203 |
|
total volume HEFF, and do not apply correction to individual ice |
| 204 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
| 205 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
| 206 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
| 207 |
|
o pkg/exf: |
| 208 |
|
- add code to process the case field period = -12. with UV interpolation. |
| 209 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
| 210 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
| 211 |
|
o verification/global_with_exf: |
| 212 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
| 213 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
| 214 |
|
o pkg/cal: |
| 215 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
| 216 |
|
o pkg/exf: |
| 217 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
| 218 |
|
to replace logical switch "exf_verbose" |
| 219 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
| 220 |
|
o pkg/sbo: |
| 221 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
| 222 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
| 223 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
| 224 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
| 225 |
|
- fix some multi-threading issues (in output part). |
| 226 |
|
o model/src & most packages: |
| 227 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
| 228 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
| 229 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
| 230 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
| 231 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
| 232 |
|
+ call LAND_READPARMS from packages_readparms.F |
| 233 |
|
o pkg/seaice: |
| 234 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
| 235 |
|
replace it by a warning in S/R seaice_check |
| 236 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
| 237 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
| 238 |
|
SEAICE_ITD is defined) |
| 239 |
|
|
| 240 |
|
checkpoint64x (2014/05/24) |
| 241 |
|
o verification/lab_sea: |
| 242 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
| 243 |
|
- un-do the update after putting back local recip_Cp in few places. |
| 244 |
|
o pkg/salt_plume: modifications by An Nguyen: |
| 245 |
|
- add capability to do brine rejection (salt-plume) as function of |
| 246 |
|
volume+tracers (instead of only salinity tracer). |
| 247 |
|
- conserve volume by exchanging volume from each kLev to above to |
| 248 |
|
accommodate in-coming brine volume |
| 249 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
| 250 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
| 251 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
| 252 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
| 253 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
| 254 |
|
in East/West Arctic. |
| 255 |
|
o pkg/sbo: |
| 256 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
| 257 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
| 258 |
|
output for future testreport verification (unfinished). |
| 259 |
|
o pkg/atm_phys: |
| 260 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
| 261 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
| 262 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
| 263 |
|
o pkg/seaice |
| 264 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
| 265 |
|
(affects truncation) |
| 266 |
|
seaice_do_ridging.F: clean up the insectarium |
| 267 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
| 268 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
| 269 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
| 270 |
|
- add some debugging information and error messages (warnings) |
| 271 |
|
o model/src: modifications relatd to atmosphere p*: |
| 272 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
| 273 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
| 274 |
|
of vertical profile tRef in geopotential background and anomaly. |
| 275 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
| 276 |
|
and pkg/atm_phys. |
| 277 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
| 278 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
| 279 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
| 280 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
| 281 |
|
not used right now, but can be used in BGC packages to fix conservation. |
| 282 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
| 283 |
|
other packages too. |
| 284 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
| 285 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
| 286 |
|
o model/src: |
| 287 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
| 288 |
|
as local variable (no longer in common block) to avoid any confusion. |
| 289 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
| 290 |
|
o pkg/exf: |
| 291 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
| 292 |
|
air density as function of air Temp, Humidity and atm pressure. |
| 293 |
|
|
| 294 |
|
checkpoint64w (2014/05/02) |
| 295 |
|
o verification: |
| 296 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
| 297 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
| 298 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
| 299 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
| 300 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
| 301 |
|
o model/src: for atmosphere in p* coords: |
| 302 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
| 303 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
| 304 |
|
but not yet activated. |
| 305 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
| 306 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
| 307 |
|
- this changes the results (but not for any verification experiment, because |
| 308 |
|
none tests this), but avoids having an extra field in the restart files |
| 309 |
|
o pkg/seaice: remove global variable TICE (not needed) |
| 310 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
| 311 |
|
seaice_diagnostics_state) |
| 312 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
| 313 |
|
- use specific read/write routines for reading and writing individual leves |
| 314 |
|
of a multilevel field |
| 315 |
|
o pkg/ctrl & model/inc: |
| 316 |
|
- move additional anomaly fields of control vars (related to options: |
| 317 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
| 318 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
| 319 |
|
o pkg/seaice: some small modifications to the ridging code |
| 320 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
| 321 |
|
seaice_growth |
| 322 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
| 323 |
|
computed only in one place and compute it in the same way as in |
| 324 |
|
seaice_growth |
| 325 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
| 326 |
|
point exceptions over land |
| 327 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
| 328 |
|
- move most of "PART 1" of S/R seaice_growth into a new and separate |
| 329 |
|
S/R seaice_reg_ridge that will both regularize the state variable after |
| 330 |
|
advection call the actual ridging routine; |
| 331 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
| 332 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
| 333 |
|
- remove ridging code from seaice_advdiff |
| 334 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
| 335 |
|
more readable (this is probably subjective) |
| 336 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
| 337 |
|
conditions in the correct category |
| 338 |
|
- finally: add new ridging routine for ITD code |
| 339 |
|
|
| 340 |
|
checkpoint64v (2014/04/11) |
| 341 |
|
o pkg/ecco: |
| 342 |
|
- add runtime parameters mdt[start,end]date[1,2] |
| 343 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
| 344 |
|
o pkg/seaice: |
| 345 |
|
- make deltaC a global variable, so that it can be used in ridging code |
| 346 |
|
- first step towards ridging: introduce new routines that compute |
| 347 |
|
ice strength based on ridging parameters |
| 348 |
|
- add diagnostic for HSNOWITD |
| 349 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
| 350 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
| 351 |
|
- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
| 352 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
| 353 |
|
o verification/hs94.1x64x5: |
| 354 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
| 355 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
| 356 |
|
o autodiff: |
| 357 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
| 358 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
| 359 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
| 360 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
| 361 |
|
which are specific to TAF/TAMC). |
| 362 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
| 363 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
| 364 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
| 365 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
| 366 |
|
building mitgcmuv_ad (make adAll). |
| 367 |
|
o pkg/ecco: |
| 368 |
|
- cost_gencost_seaicev4.F: |
| 369 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
| 370 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
| 371 |
|
- add stop statement if old names siv4-[sst,vol] are used |
| 372 |
|
- add snapshots + cost reports for atmospheric longwave |
| 373 |
|
- remove factor 0.1 in front of wtau[u,v] |
| 374 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
| 375 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
| 376 |
|
o pkg/atm_phys: |
| 377 |
|
- add some diagnostics for Short-wave and for convection S/R. |
| 378 |
|
o pkg/seaice/seaice_growth: |
| 379 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
| 380 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
| 381 |
|
- rearrange loop order for better vector code in the same code block |
| 382 |
|
- rewrite the floeDiameter formula to have fewer divisions |
| 383 |
|
- (miraculously) none of this changes the results of seaice_itd |
| 384 |
|
o pkg/smooth: |
| 385 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
| 386 |
|
o pkg/salt_plume: |
| 387 |
|
- salt_plume_frac.F: |
| 388 |
|
clean up local param names |
| 389 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
| 390 |
|
o pkg/rw: |
| 391 |
|
- add RS version of S/R READ_MFLDS_LEV. |
| 392 |
|
o pkg/streamice: |
| 393 |
|
- fix the restart test by writing/reading pickup_streamice files. |
| 394 |
|
o pkg/seaice: |
| 395 |
|
- refine checks for jfnk-related parameters |
| 396 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
| 397 |
|
is no IMEX code to avoid confusion and surprises |
| 398 |
|
|
| 399 |
|
checkpoint64u (2014/03/07) |
| 400 |
|
o verification/MLAdjust: |
| 401 |
|
- rename secondary test suffix: |
| 402 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
| 403 |
|
0.leithD -> AhFlxF + switch to flux-form |
| 404 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
| 405 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
| 406 |
|
o pkg/mom_vecinv: |
| 407 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
| 408 |
|
to be before mom_calc_visc.F) |
| 409 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
| 410 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
| 411 |
|
this is simpler for the adjoint and for diagnostics. |
| 412 |
|
o model/src + pkg/momentum: |
| 413 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
| 414 |
|
(e.g., to add "thin-wall" where it is =1). |
| 415 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
| 416 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
| 417 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
| 418 |
|
coords; not working with CD-scheme neither. |
| 419 |
|
o pkg/seaice: |
| 420 |
|
- rename recently introduced parameters from (wrong name) AB to |
| 421 |
|
BDF (backward difference time discretisation) |
| 422 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
| 423 |
|
o tools/adjoint_options: |
| 424 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
| 425 |
|
|
| 426 |
|
checkpoint64t (2014/02/01) |
| 427 |
|
o pkg/ecco |
| 428 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
| 429 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
| 430 |
|
- replace hard-coded record number and period which only work for monthly |
| 431 |
|
with read-in runtime param that works for other periods (month,day,year) |
| 432 |
|
o pkg/thsice |
| 433 |
|
- corrected store directive fixes thsice adjoint gradient checks |
| 434 |
|
o genmake2 & testreport: |
| 435 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
| 436 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
| 437 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
| 438 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
| 439 |
|
o pkg/shelfice: |
| 440 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
| 441 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
| 442 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
| 443 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
| 444 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
| 445 |
|
o model/src/temp_integrate.F and salt_integrate.F |
| 446 |
|
- re-include store directives that were removed on Dec 27th. |
| 447 |
|
o model/src/external_forcing_surf.F |
| 448 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
| 449 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
| 450 |
|
turned off in the adjoint. The resolved issue dated back to July when |
| 451 |
|
EXTERNAL_FORCING_SURF call was moved. |
| 452 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
| 453 |
|
o pkg/exf/exf_check.F |
| 454 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
| 455 |
|
- streamline error output |
| 456 |
|
o pkg/streamice and aim_v23: |
| 457 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
| 458 |
|
Apple's /usr/bin/cpp knows what to do: |
| 459 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
| 460 |
|
Target: x86_64-apple-darwin13.0.0 |
| 461 |
|
|
| 462 |
|
checkpoint64s (2014/01/05) |
| 463 |
|
o tools/adjoint_options: |
| 464 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
| 465 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
| 466 |
|
o model/src: |
| 467 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
| 468 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
| 469 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
| 470 |
|
o model/src & pkg/ptracers: |
| 471 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
| 472 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
| 473 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
| 474 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
| 475 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
| 476 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
| 477 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
| 478 |
|
for now only implemented for in exf_interp_read.F |
| 479 |
|
o verification/advect_xy: |
| 480 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
| 481 |
|
o momentum diagnostics: |
| 482 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
| 483 |
|
- fix typo in diagnostics for momentum tendency from AB. |
| 484 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
| 485 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
| 486 |
|
|
| 487 |
|
checkpoint64r (2013/12/08) |
| 488 |
|
o verification/*/results: |
| 489 |
|
- Update reference output of experiments that were passing with just 13 digits |
| 490 |
|
(make it easier to detect future changes in results) |
| 491 |
|
o model/src & pkg/ptracers: |
| 492 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
| 493 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
| 494 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
| 495 |
|
o coupling interface pkgs: |
| 496 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
| 497 |
|
- change the config check to test the agreement of Ocean Depth |
| 498 |
|
with ATM land/sea mask (instead of ATM orography); |
| 499 |
|
- send to coupler the number of coupler time-steps to do for this run: |
| 500 |
|
this allows to check for consistency and don't need anymore to be |
| 501 |
|
specified in parameter file "data"; |
| 502 |
|
in coupler: |
| 503 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
| 504 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
| 505 |
|
o pkg/compon_communic: |
| 506 |
|
- add coupling send/receive for non-tiled integer vector; |
| 507 |
|
- add S/R to check and stop if any proc has an error (similar to |
| 508 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
| 509 |
|
o pkg/exch2: |
| 510 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
| 511 |
|
through list of all tiles my proc owns. |
| 512 |
|
o model/src: |
| 513 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
| 514 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
| 515 |
|
calling S/R); this affects AD results at machine truncation level: |
| 516 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
| 517 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
| 518 |
|
o tools/build_options: |
| 519 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
| 520 |
|
o coupling interface pkgs: |
| 521 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
| 522 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
| 523 |
|
to each S/R that needs it; remove un-used variables. |
| 524 |
|
- change component tile registration (cpl_register.F in both compon_interf |
| 525 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
| 526 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
| 527 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
| 528 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
| 529 |
|
a) can now use different tiling between atm & ocn comp. |
| 530 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
| 531 |
|
even if using the same tiling between atm & ocn). |
| 532 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
| 533 |
|
full land tiles); not yet tested. |
| 534 |
|
- check for valid mapping from comp. tile to coupler global array |
| 535 |
|
- improve report of tile registration results to log file. |
| 536 |
|
o pkg/exch2: |
| 537 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
| 538 |
|
tile-registration (CPL_REGISTER); |
| 539 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
| 540 |
|
store the local bi,bj indices of each tile; |
| 541 |
|
- also print bi,bj in local report to log file; |
| 542 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
| 543 |
|
Jun 2009 modif of pkg/exch2). |
| 544 |
|
o testing on baudelaire: |
| 545 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
| 546 |
|
get the full set of test done earlier |
| 547 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
| 548 |
|
o model/src/thermodynamics.F and routines called from it: |
| 549 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
| 550 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
| 551 |
|
velocity (outp) by adding bolus velocity. |
| 552 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
| 553 |
|
mass transport from velocity + lateral grid cell area |
| 554 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
| 555 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
| 556 |
|
in thermodynamics.F |
| 557 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
| 558 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
| 559 |
|
loop). |
| 560 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
| 561 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
| 562 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
| 563 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
| 564 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
| 565 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
| 566 |
|
tutorial_tracer_adjsens (+ TLM output). |
| 567 |
|
o tools/OAD_support and (verification/*/) code_oad: |
| 568 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
| 569 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
| 570 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
| 571 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
| 572 |
|
o model/src: |
| 573 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
| 574 |
|
retired list of parameters (routine FREEZE has been replace by surface |
| 575 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
| 576 |
|
o pkg/gmredi: |
| 577 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
| 578 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
| 579 |
|
- update output of FWD experiments: front_relax.bvp, |
| 580 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
| 581 |
|
|
| 582 |
|
checkpoint64q (2013/11/17) |
| 583 |
|
o verification: |
| 584 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
| 585 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
| 586 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
| 587 |
|
updating the input pickup_seaice files (previously wrong). |
| 588 |
|
o pkg/cost: |
| 589 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
| 590 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
| 591 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
| 592 |
|
cannot be applied to var in common block). |
| 593 |
|
o allows to get results independent of tile-per-proc setting (if using |
| 594 |
|
slower GLOBAL_SUM_SEND_RECV option). |
| 595 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
| 596 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
| 597 |
|
forward gradients: update output). |
| 598 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
| 599 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
| 600 |
|
o pkg/mom_common: |
| 601 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
| 602 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
| 603 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
| 604 |
|
ensure that all field value that are used are set. |
| 605 |
|
o tutorial_deep_convection (smag3d): |
| 606 |
|
- add missing scaling in mom_calc_smag_3d.F; |
| 607 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
| 608 |
|
o pkg/dic: |
| 609 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
| 610 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
| 611 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
| 612 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
| 613 |
|
o eesupp/src & pkg/mdsio: |
| 614 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
| 615 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
| 616 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
| 617 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
| 618 |
|
o verification/isomip: |
| 619 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
| 620 |
|
o tools/build_options: |
| 621 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
| 622 |
|
to get a working restart for all experiments, add "-fp-model source" |
| 623 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
| 624 |
|
|
| 625 |
|
checkpoint64p (2013/10/20) |
| 626 |
|
o pkg/autodiff: |
| 627 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
| 628 |
|
criteria, return to simple (default) tape IO format. |
| 629 |
|
o pkg/mdsio (+ eesupp/src): |
| 630 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
| 631 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
| 632 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
| 633 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
| 634 |
|
template) corresponding to simpler global mapping. |
| 635 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
| 636 |
|
to globalFile when parameter globalFiles is set to True. |
| 637 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
| 638 |
|
o pkg/autodiff: |
| 639 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
| 640 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
| 641 |
|
missing, just add a STOP if array type do not match. |
| 642 |
|
o pkg/exf: |
| 643 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
| 644 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
| 645 |
|
and rename array obsSIce to exf_iceFraction. |
| 646 |
|
o tutorial_deep_convection: |
| 647 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
| 648 |
|
for now all in this exp. code dir. |
| 649 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
| 650 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
| 651 |
|
o eesupp/src: |
| 652 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
| 653 |
|
very large number of processors did not work with existing set-up |
| 654 |
|
|
| 655 |
|
checkpoint64o (2013/09/25) |
| 656 |
|
o pkg/atm_phys & atm_compon_interf: |
| 657 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
| 658 |
|
o tools/build_options: |
| 659 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
| 660 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
| 661 |
|
remove CPP setting (was identical to genmake2 default). |
| 662 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
| 663 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
| 664 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
| 665 |
|
external forcing via taueddy_external_forcing.F |
| 666 |
|
- at the moment, it is very experimental and only works with the variable eddy |
| 667 |
|
diffusivity calculated in gmredi_k3d.F |
| 668 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
| 669 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
| 670 |
|
o testreport (& tools/do_tst_2+2): |
| 671 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
| 672 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
| 673 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
| 674 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
| 675 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
| 676 |
|
o pkg/atm_compon_interf: |
| 677 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
| 678 |
|
(which accumalate in time each coupling field) |
| 679 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
| 680 |
|
update accordingly + simplify aim_do_physics.F |
| 681 |
|
|
| 682 |
|
checkpoint64n (2013/08/26) |
| 683 |
|
o pkg/bbl: |
| 684 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
| 685 |
|
- replaced horizontal and vertical transport parameters with velocities |
| 686 |
|
- changes results for verification/global_with_exf.yearly |
| 687 |
|
o verification/halfpipe_streamice: |
| 688 |
|
- change to matrix construction; update both Fwd & AD output. |
| 689 |
|
o verification/tutorial_tracer_adjsens: |
| 690 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
| 691 |
|
rStar causes problems with OpenAD; update output. |
| 692 |
|
o tools: |
| 693 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
| 694 |
|
to local /tmp disk (but would be easy to move them back); |
| 695 |
|
- xmakedepend: apply the same switch for temp-files. |
| 696 |
|
o pkg/offline: |
| 697 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
| 698 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
| 699 |
|
output files) and apply r* scaling at each time-step (function of the time |
| 700 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
| 701 |
|
o adjoint with OpenAD: |
| 702 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
| 703 |
|
package openad. This package has to be compiled for all runs with OpenAD |
| 704 |
|
instead of specifying code_oad_all as a modification directory. |
| 705 |
|
- link the fortran templates from tools/OAD_support to the build directory |
| 706 |
|
for preprocessing to avoid conflicts between different setups compiled |
| 707 |
|
simultaneously and simplify cleanup. |
| 708 |
|
o pkg/exf: |
| 709 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
| 710 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
| 711 |
|
o model/src: |
| 712 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
| 713 |
|
(similar to do_fields_blocking_exchanges.F). |
| 714 |
|
o tools/genmake2: |
| 715 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
| 716 |
|
built, will stop if things go wrong with staf). |
| 717 |
|
- fix target "adobj" (left from TAF version-2 transition) |
| 718 |
|
o pkg/diagnostics: |
| 719 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
| 720 |
|
this replace/extend the use of logical param "settingDiags" (to check |
| 721 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
| 722 |
|
New S/R to print error message and stop when pkgStatus is not right. |
| 723 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
| 724 |
|
|
| 725 |
|
checkpoint64m (2013/08/13) |
| 726 |
|
o model/inc: |
| 727 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 728 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 729 |
|
o pkg/kpp & aim_v23: |
| 730 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 731 |
|
o pkg/seaice: |
| 732 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 733 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 734 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 735 |
|
o eesupp/src: |
| 736 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 737 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 738 |
|
o switch to TAF version-2: |
| 739 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
| 740 |
|
are used in I/O routines of adjoint state and associated common blocks |
| 741 |
|
that are used in adcommon.h (backward compatible with version-1) |
| 742 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 743 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
| 744 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
| 745 |
|
out except for diva). |
| 746 |
|
- the major change with TAF version-2 is that both the differentiated |
| 747 |
|
routines and the forward routines (new) are returned as part of the TAF |
| 748 |
|
output source code. Update genmake2 accordingly. |
| 749 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
| 750 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
| 751 |
|
output show minor changes (machine truncation level); update the few AD & |
| 752 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
| 753 |
|
|
| 754 |
|
checkpoint64l (2013/08/05) |
| 755 |
|
o model/src: |
| 756 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
| 757 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
| 758 |
|
when using TAF but only if using OpenAD. |
| 759 |
|
o pkg/mom_common+fluxform+vecinv: |
| 760 |
|
- always set horiz. viscosity arrays to background value before calling |
| 761 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
| 762 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
| 763 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
| 764 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
| 765 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
| 766 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
| 767 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
| 768 |
|
useBiharmonicVisc & useVariableVisc. |
| 769 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 770 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
| 771 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 772 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 773 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
| 774 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 775 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
| 776 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 777 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 778 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
| 779 |
|
default viscAh,viscA4 is zero). |
| 780 |
|
o model/src: |
| 781 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
| 782 |
o Divided Adjoint (DIVA) with MPI: |
o Divided Adjoint (DIVA) with MPI: |
| 783 |
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
| 784 |
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
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