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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o model/src: |
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- store in common bloc array "rhoInSitu" the virtual potential temperature |
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anomaly that is used to compute geopotential: this make the atmos code |
10 |
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more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
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o pkg/seaice/seaice_lsr.F |
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- rename integer variable ilcall to ipass (that's what it is called |
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in the residual diagnostics |
14 |
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- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
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default) for improved non-linear convergence of the first few steps |
16 |
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- adjust a few comments and add new ones to explain some of the store |
17 |
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directives |
18 |
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o pkg/generic_advdiff (& ptracers): |
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- re-work the code to check for valid advection scheme and for minimum |
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size of overlap (now stored in local common bloc in gad_advscheme.F) |
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o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
22 |
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- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
23 |
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- add an auxilliary variable "bet" and fix store directives and keys in |
24 |
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seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
25 |
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less exact gradients in my tests); but there are still |
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recomputation warning (although gradients are sort of OK), when |
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SEAICE_LSR_VECTORIZE is not defined, so this flag and |
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SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
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- update verification experiments lab_sea. |
30 |
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- change some comments in S/R seaice_calc_viscosities |
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o model/src: |
32 |
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- if staggerTimeStep=T, always apply exchange to velocity field in |
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do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
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(independent of using multi-dim advection or not); no effect on FWD run |
35 |
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but affects AD results (at machine truncation level): update output of |
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experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
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and isomip (oad: 12.d). |
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o pkg/generic_advdiff: |
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- stop if doAB_onGtGs is set to FALSE but ignored |
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- refine warning related to stability of tracer time-stepping |
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regarding internal wave dynamics. |
42 |
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- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
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on staggerTimeStep & implicitIntGravWave (will now get a warning |
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if potentially unstable). |
45 |
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o pkg/kl10: |
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- add new pkg "kl10" for mixing due to internal wave breaking, from |
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http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
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(contribution from Jody Klymak), tested in verification experiment |
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verification/internal_wave/input.kl10/ |
50 |
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o isomip experiment: |
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- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
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(input.htd) and update the output. |
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o cd_code experiments: |
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- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
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#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
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global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
57 |
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update the corresponding output. |
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o pkg/seaice: |
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- reduce the number of include files and store directives in |
60 |
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S/R seaice_lsr_tridiagu/v |
61 |
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- change the order of loops in one case in S/R seaice_lsr_tridiagv |
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(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
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get rid off one store directive (a TAF bug?) |
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- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
65 |
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S/R seaice_lsr_tridiagv to change the loop range for consistency |
66 |
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- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
67 |
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- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
68 |
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S/R seaice_lsr_tridiagu/v (requires update of |
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offline_exf_seaice/input.dyn_jfnk) |
70 |
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|
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checkpoint65a (2014/07/27) |
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o model/src: |
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- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
74 |
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surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
75 |
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(topo in p-coords, ice-shelf in z-coords); update output of experiments |
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tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
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o model/src: |
78 |
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- collect momentum forcing tendency into local 2-D array (passed as argument |
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to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
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parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
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affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
82 |
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- collect T & S forcing tendency into local 2-D array (passed as argument to |
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apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
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affects results at machine truncation level (e.g., ocean: if using |
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SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0) |
86 |
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moist correction due to vertical advection). |
87 |
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- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
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global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
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seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
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obcs_ctrl (ad & fwd grd @ 12 & 7). |
91 |
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o pkg/ptracers & diagnostics: |
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- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
93 |
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title (to avoid some unexpected truncation); sort out ptracers diags units. |
94 |
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- collect ptracer forcing tendency into local 2-D array (passed as argument |
95 |
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to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
96 |
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|
97 |
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checkpoint65 (2014/07/18) |
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o pkg/fizhi: |
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- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
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affects results at machine truncation level. Update output of experiments |
101 |
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fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
102 |
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o pkg/seaice: more clean up |
103 |
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- rename TAF common block tapes to be more consistent and remove |
104 |
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unnecessary duplicates |
105 |
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- add store directives to remove more recomputations, but use smaller |
106 |
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tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
107 |
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The idea behind this flag is to reduce the memory footprint when the |
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adjoint of the LSR is not required. As of now, defining the flag |
109 |
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SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
110 |
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a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
111 |
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For experiment offline_exf_seaice, this means on a linux box with gfortran |
112 |
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nearly a factor of 10 (but keep in mind there is mostly seaice code in |
113 |
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this experiment): |
114 |
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> size mitgcmuv_ad |
115 |
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text data bss dec hex |
116 |
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5100659 1216 220458952 225560827 d71c8fb |
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5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
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but only a moderate increase of 36% for global_ocean.cs32x15: |
119 |
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text data bss dec hex |
120 |
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6695027 1648 1014578664 1021275339 3cdf6ccb |
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6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
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- note: there are still recomputations in global_ocean.cs32x15 and |
123 |
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offline_exf_seaice and the gradient agreement changes (gets a |
124 |
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little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
125 |
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- in general, the AD gradients still are wrong |
126 |
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o OpenAD |
127 |
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- clean up code_oad/ directories somewhat by moving files |
128 |
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dontCompile, dontTransform, keepOriginal to OAD_support/ |
129 |
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o model/src: |
130 |
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- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
131 |
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(not currently tested): add dissipation terms before NLFS rescaling of |
132 |
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tendencies (previously done after). |
133 |
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o pkg/diagnostics: |
134 |
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- write stats-diags in ascii file with more digits (same as in monitor). |
135 |
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o pkg/down_slope: |
136 |
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- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
137 |
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NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
138 |
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o model/src: |
139 |
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- new file "apply_forcing.F" containing all the code previously in |
140 |
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external_forcing.F, but with new argument list: pass, as new argument, |
141 |
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the current level tendency array to update (instead of a direct update |
142 |
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of the common bloc array). Change the corresponding calls. |
143 |
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- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
144 |
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EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
145 |
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o pkg/seaice/seaice_lsr, a little bit of clean up |
146 |
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- rearrange some code blocks, so that now all calculations for |
147 |
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setting up the right-hand-sides done within one single block |
148 |
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(I find that easier to read and understand) |
149 |
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- rearrange freedrift-code to reduce the number of ifdefs |
150 |
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- adjust some indentations and comments |
151 |
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|
152 |
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checkpoint64z (2014/07/10) |
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o model/src and several pkgs: |
154 |
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- change argument list of all S/R called from external_forcing.F and |
155 |
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called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
156 |
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to pass, as argument, the current level tendency array to update |
157 |
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(instead of a direct update of the common bloc array). |
158 |
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- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
159 |
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- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
160 |
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o pkg/seaice/seaice_lsr.F |
161 |
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- always initialize local arrays in seaice_lsr_tridiagu/v |
162 |
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- add more local tapes to seaice_lsr_tridiagu/v |
163 |
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- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
164 |
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keep it in bi/bj loop; this seems to be essential |
165 |
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- gradients are still wrong but only by 4-7 orders of magnitude |
166 |
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instead of 15 orders of magnitude, lab_sea improves a little |
167 |
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o pkg/seaice |
168 |
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- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
169 |
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generates unnecessary code in seaice_lsr_ad |
170 |
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- add more store directives in seaice_lsr to avoid unnecessary code |
171 |
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in seaice_lsr_ad |
172 |
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- exclude some residual computations in seaice_lsr when |
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ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
174 |
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in seaice_lsr_ad |
175 |
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- add more storing, a new tape (model/src/the_main_loop.F) and |
176 |
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another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
177 |
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and klockey should be checked by a specialist) |
178 |
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- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
179 |
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and update lab_sea after previous changes in pkg/seaice below |
180 |
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o pkg/autodiff: |
181 |
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- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
182 |
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viscFacInAd : run time parameters allowing for adjoint switches |
183 |
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note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
184 |
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o pkg/ecco: |
185 |
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- introduce cost_gencost_boxmean.F that computes a box mean |
186 |
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temperature (for use in adjoint sensitivity studies). |
187 |
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o model/src/set_defaults.F : initialize viscFacAdj to 1. |
188 |
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o pkg/mom_common/mom_calc_visc.F: |
189 |
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- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
190 |
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o pkg/seaice/seaice_summary.F: |
191 |
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- statement for SEAICEadjMODE now in autodiff_readparms.F |
192 |
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o pkg/seaice: |
193 |
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- remove some store directives and add new ones in an effort to get |
194 |
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finally rid off the recomputation warnings. This is successful |
195 |
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when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
196 |
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defined (i.e. no extensive recomputation warnings left), but there |
197 |
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are still too many recomputations on the solver iteration level |
198 |
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- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
199 |
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- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
200 |
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SEAICE_SIZE.h |
201 |
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- add a store directive in S/R seaice_calc_viscosities |
202 |
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o pkg/seaice (ITD code): |
203 |
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- fix definition of Hlimit for multi-threaded case |
204 |
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- use double precision arithmetic to compute Hlimit: this affects results; |
205 |
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update output of experiment seaice_itd. |
206 |
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o replace content of verification/seaice_itd |
207 |
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- instead of a 1D column use the configuration of offline_exf_seaice |
208 |
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to test the ice thickness distribution code with ridging |
209 |
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- this is a first shot at this experiment |
210 |
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- change of some defaults of ridging parameters SEAICEhStar (from |
211 |
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100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
212 |
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and lot of new comments. |
213 |
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|
214 |
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checkpoint64y (2014/06/20) |
215 |
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o pkg/seaice/seaice_reg_ridge.F: |
216 |
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- modify the regularization of very small volumes of ice; only check |
217 |
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total volume HEFF, and do not apply correction to individual ice |
218 |
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classes because that leads to funny patterns in the heat and fw-fluxes |
219 |
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into the ocean. Adjust seaice_itd/results/output.txt |
220 |
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- replace nITD by SEAICE_multDim in loop-ranges |
221 |
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o pkg/exf: |
222 |
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- add code to process the case field period = -12. with UV interpolation. |
223 |
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- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
224 |
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into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
225 |
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o verification/global_with_exf: |
226 |
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- switch all fields period to -12. (was previously untested) in input/data.exf |
227 |
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(but keep secondary test ".yearly" unchanged); update the reference output. |
228 |
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o pkg/cal: |
229 |
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- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
230 |
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o pkg/exf: |
231 |
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- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
232 |
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to replace logical switch "exf_verbose" |
233 |
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- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
234 |
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o pkg/sbo: |
235 |
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- update from Katherine Quinn: evaluate mass directly from density and SSH |
236 |
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(budget using Finite Volume method) instead of from bottom pressure. |
237 |
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- allow testreport to collect few selected SBO output ; tested in exp. |
238 |
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global_ocean.90x40x15 (after updating the results, to include SBO output). |
239 |
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- fix some multi-threading issues (in output part). |
240 |
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o model/src & most packages: |
241 |
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- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
242 |
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- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
243 |
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PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
244 |
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"data.{pkg}" exist ; and leave the S/R (return) just after. |
245 |
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- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
246 |
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+ call LAND_READPARMS from packages_readparms.F |
247 |
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o pkg/seaice: |
248 |
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- remove code that resets useThSice in S/R seaice_readparms and |
249 |
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replace it by a warning in S/R seaice_check |
250 |
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- remove parameter MULTDIM, replace with nITD and runtime |
251 |
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parameter SEAICE_multDim (still hard-wired to nITD if |
252 |
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SEAICE_ITD is defined) |
253 |
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|
254 |
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checkpoint64x (2014/05/24) |
255 |
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o verification/lab_sea: |
256 |
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- update adjoint and TLM output following changes to pkg/salt_plume |
257 |
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- un-do the update after putting back local recip_Cp in few places. |
258 |
|
o pkg/salt_plume: modifications by An Nguyen: |
259 |
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- add capability to do brine rejection (salt-plume) as function of |
260 |
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volume+tracers (instead of only salinity tracer). |
261 |
|
- conserve volume by exchanging volume from each kLev to above to |
262 |
|
accommodate in-coming brine volume |
263 |
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- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
264 |
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- switch KPP surf buoyancy due to brine forcing to 3-d |
265 |
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(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
266 |
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- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
267 |
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- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
268 |
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in East/West Arctic. |
269 |
|
o pkg/sbo: |
270 |
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- incorporate modifications from Katherine Quinn to enable the use of sbo |
271 |
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pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
272 |
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output for future testreport verification (unfinished). |
273 |
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o pkg/atm_phys: |
274 |
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- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
275 |
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skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
276 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
277 |
|
o pkg/seaice |
278 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
279 |
|
(affects truncation) |
280 |
|
seaice_do_ridging.F: clean up the insectarium |
281 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
282 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
283 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
284 |
|
- add some debugging information and error messages (warnings) |
285 |
|
o model/src: modifications relatd to atmosphere p*: |
286 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
287 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
288 |
|
of vertical profile tRef in geopotential background and anomaly. |
289 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
290 |
|
and pkg/atm_phys. |
291 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
292 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
293 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
294 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
295 |
|
not used right now, but can be used in BGC packages to fix conservation. |
296 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
297 |
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other packages too. |
298 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
299 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
300 |
|
o model/src: |
301 |
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- since we have several heat capacity (even in model/src), define "recip_Cp" |
302 |
|
as local variable (no longer in common block) to avoid any confusion. |
303 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
304 |
|
o pkg/exf: |
305 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
306 |
|
air density as function of air Temp, Humidity and atm pressure. |
307 |
|
|
308 |
|
checkpoint64w (2014/05/02) |
309 |
|
o verification: |
310 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
311 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
312 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
313 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
314 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
315 |
|
o model/src: for atmosphere in p* coords: |
316 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
317 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
318 |
|
but not yet activated. |
319 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
320 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
321 |
|
- this changes the results (but not for any verification experiment, because |
322 |
|
none tests this), but avoids having an extra field in the restart files |
323 |
|
o pkg/seaice: remove global variable TICE (not needed) |
324 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
325 |
|
seaice_diagnostics_state) |
326 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
327 |
|
- use specific read/write routines for reading and writing individual leves |
328 |
|
of a multilevel field |
329 |
|
o pkg/ctrl & model/inc: |
330 |
|
- move additional anomaly fields of control vars (related to options: |
331 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
332 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
333 |
|
o pkg/seaice: some small modifications to the ridging code |
334 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
335 |
|
seaice_growth |
336 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
337 |
|
computed only in one place and compute it in the same way as in |
338 |
|
seaice_growth |
339 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
340 |
|
point exceptions over land |
341 |
o pkg/seaice: preparations for ridging code and first real ridging code |
o pkg/seaice: preparations for ridging code and first real ridging code |
342 |
- move most of "PART 1" of S/R seaice_growth into a new and separate |
- move most of "PART 1" of S/R seaice_growth into a new and separate |
343 |
S/R seaice_reg_ridge that will both regularize the state variable after |
S/R seaice_reg_ridge that will both regularize the state variable after |
344 |
advection call the actual ridging routine; |
advection call the actual ridging routine; |
345 |
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
346 |
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
347 |
- remove ridging code from seaice_advdiff |
- remove ridging code from seaice_advdiff |
348 |
- clean up remaining part 1 of seaice_growth in an attempt to make it |
- clean up remaining part 1 of seaice_growth in an attempt to make it |
349 |
more readable (this is probably subjective) |
more readable (this is probably subjective) |
350 |
- call seaice_itd_redist once in the initialisation phase to have the initial |
- call seaice_itd_redist once in the initialisation phase to have the initial |
351 |
conditions in the correct category |
conditions in the correct category |