4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/ptracers & diagnostics: |
8 |
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- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
9 |
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title (to avoid some unexpected truncation); sort out ptracers diags units. |
10 |
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|
11 |
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checkpoint65 (2014/07/18) |
12 |
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o pkg/fizhi: |
13 |
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- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
14 |
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affects results at machine truncation level. Update output of experiments |
15 |
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fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
16 |
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o pkg/seaice: more clean up |
17 |
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- rename TAF common block tapes to be more consistent and remove |
18 |
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unnecessary duplicates |
19 |
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- add store directives to remove more recomputations, but use smaller |
20 |
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tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
21 |
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The idea behind this flag is to reduce the memory footprint when the |
22 |
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adjoint of the LSR is not required. As of now, defining the flag |
23 |
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SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
24 |
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a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
25 |
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For experiment offline_exf_seaice, this means on a linux box with gfortran |
26 |
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nearly a factor of 10 (but keep in mind there is mostly seaice code in |
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this experiment): |
28 |
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> size mitgcmuv_ad |
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text data bss dec hex |
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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: |
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text data bss dec hex |
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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 |
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offline_exf_seaice and the gradient agreement changes (gets a |
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little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
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- in general, the AD gradients still are wrong |
40 |
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o OpenAD |
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- clean up code_oad/ directories somewhat by moving files |
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dontCompile, dontTransform, keepOriginal to OAD_support/ |
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o model/src: |
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- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
45 |
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(not currently tested): add dissipation terms before NLFS rescaling of |
46 |
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tendencies (previously done after). |
47 |
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o pkg/diagnostics: |
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- write stats-diags in ascii file with more digits (same as in monitor). |
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o pkg/down_slope: |
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- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
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NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
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o model/src: |
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- new file "apply_forcing.F" containing all the code previously in |
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external_forcing.F, but with new argument list: pass, as new argument, |
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the current level tendency array to update (instead of a direct update |
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of the common bloc array). Change the corresponding calls. |
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- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
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EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
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o pkg/seaice/seaice_lsr, a little bit of clean up |
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- rearrange some code blocks, so that now all calculations for |
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setting up the right-hand-sides done within one single block |
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(I find that easier to read and understand) |
63 |
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- rearrange freedrift-code to reduce the number of ifdefs |
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- adjust some indentations and comments |
65 |
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|
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checkpoint64z (2014/07/10) |
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o model/src and several pkgs: |
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- change argument list of all S/R called from external_forcing.F and |
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called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
70 |
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to pass, as argument, the current level tendency array to update |
71 |
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(instead of a direct update of the common bloc array). |
72 |
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- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
73 |
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- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
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o pkg/seaice/seaice_lsr.F |
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- always initialize local arrays in seaice_lsr_tridiagu/v |
76 |
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- add more local tapes to seaice_lsr_tridiagu/v |
77 |
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- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
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keep it in bi/bj loop; this seems to be essential |
79 |
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- gradients are still wrong but only by 4-7 orders of magnitude |
80 |
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instead of 15 orders of magnitude, lab_sea improves a little |
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o pkg/seaice |
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- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
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generates unnecessary code in seaice_lsr_ad |
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- add more store directives in seaice_lsr to avoid unnecessary code |
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in seaice_lsr_ad |
86 |
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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 |
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in seaice_lsr_ad |
89 |
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- add more storing, a new tape (model/src/the_main_loop.F) and |
90 |
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another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
91 |
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and klockey should be checked by a specialist) |
92 |
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- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
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and update lab_sea after previous changes in pkg/seaice below |
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o pkg/autodiff: |
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- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
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viscFacInAd : run time parameters allowing for adjoint switches |
97 |
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note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
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o pkg/ecco: |
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- introduce cost_gencost_boxmean.F that computes a box mean |
100 |
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temperature (for use in adjoint sensitivity studies). |
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o model/src/set_defaults.F : initialize viscFacAdj to 1. |
102 |
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o pkg/mom_common/mom_calc_visc.F: |
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- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
104 |
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o pkg/seaice/seaice_summary.F: |
105 |
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- statement for SEAICEadjMODE now in autodiff_readparms.F |
106 |
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o pkg/seaice: |
107 |
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- remove some store directives and add new ones in an effort to get |
108 |
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finally rid off the recomputation warnings. This is successful |
109 |
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when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
110 |
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defined (i.e. no extensive recomputation warnings left), but there |
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are still too many recomputations on the solver iteration level |
112 |
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- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
113 |
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- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
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SEAICE_SIZE.h |
115 |
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- add a store directive in S/R seaice_calc_viscosities |
116 |
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o pkg/seaice (ITD code): |
117 |
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- fix definition of Hlimit for multi-threaded case |
118 |
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- use double precision arithmetic to compute Hlimit: this affects results; |
119 |
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update output of experiment seaice_itd. |
120 |
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o replace content of verification/seaice_itd |
121 |
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- instead of a 1D column use the configuration of offline_exf_seaice |
122 |
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to test the ice thickness distribution code with ridging |
123 |
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- this is a first shot at this experiment |
124 |
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- change of some defaults of ridging parameters SEAICEhStar (from |
125 |
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100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
126 |
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and lot of new comments. |
127 |
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|
128 |
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checkpoint64y (2014/06/20) |
129 |
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o pkg/seaice/seaice_reg_ridge.F: |
130 |
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- modify the regularization of very small volumes of ice; only check |
131 |
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total volume HEFF, and do not apply correction to individual ice |
132 |
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classes because that leads to funny patterns in the heat and fw-fluxes |
133 |
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into the ocean. Adjust seaice_itd/results/output.txt |
134 |
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- replace nITD by SEAICE_multDim in loop-ranges |
135 |
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o pkg/exf: |
136 |
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- add code to process the case field period = -12. with UV interpolation. |
137 |
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- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
138 |
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into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
139 |
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o verification/global_with_exf: |
140 |
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- switch all fields period to -12. (was previously untested) in input/data.exf |
141 |
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(but keep secondary test ".yearly" unchanged); update the reference output. |
142 |
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o pkg/cal: |
143 |
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- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
144 |
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o pkg/exf: |
145 |
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- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
146 |
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to replace logical switch "exf_verbose" |
147 |
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- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
148 |
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o pkg/sbo: |
149 |
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- update from Katherine Quinn: evaluate mass directly from density and SSH |
150 |
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(budget using Finite Volume method) instead of from bottom pressure. |
151 |
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- allow testreport to collect few selected SBO output ; tested in exp. |
152 |
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global_ocean.90x40x15 (after updating the results, to include SBO output). |
153 |
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- fix some multi-threading issues (in output part). |
154 |
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o model/src & most packages: |
155 |
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- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
156 |
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- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
157 |
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PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
158 |
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"data.{pkg}" exist ; and leave the S/R (return) just after. |
159 |
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- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
160 |
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+ call LAND_READPARMS from packages_readparms.F |
161 |
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o pkg/seaice: |
162 |
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- remove code that resets useThSice in S/R seaice_readparms and |
163 |
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replace it by a warning in S/R seaice_check |
164 |
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- remove parameter MULTDIM, replace with nITD and runtime |
165 |
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parameter SEAICE_multDim (still hard-wired to nITD if |
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SEAICE_ITD is defined) |
167 |
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|
168 |
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checkpoint64x (2014/05/24) |
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o verification/lab_sea: |
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- update adjoint and TLM output following changes to pkg/salt_plume |
171 |
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- un-do the update after putting back local recip_Cp in few places. |
172 |
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o pkg/salt_plume: modifications by An Nguyen: |
173 |
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- add capability to do brine rejection (salt-plume) as function of |
174 |
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volume+tracers (instead of only salinity tracer). |
175 |
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- conserve volume by exchanging volume from each kLev to above to |
176 |
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accommodate in-coming brine volume |
177 |
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- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
178 |
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- switch KPP surf buoyancy due to brine forcing to 3-d |
179 |
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(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
180 |
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- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
181 |
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- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
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in East/West Arctic. |
183 |
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o pkg/sbo: |
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- incorporate modifications from Katherine Quinn to enable the use of sbo |
185 |
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pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
186 |
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output for future testreport verification (unfinished). |
187 |
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o pkg/atm_phys: |
188 |
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- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
189 |
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skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
190 |
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output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
191 |
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o pkg/seaice |
192 |
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seaice_calc_ice_strength.F: modify expression to avoid divisions |
193 |
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(affects truncation) |
194 |
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seaice_do_ridging.F: clean up the insectarium |
195 |
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- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
196 |
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- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
197 |
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- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
198 |
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- add some debugging information and error messages (warnings) |
199 |
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o model/src: modifications relatd to atmosphere p*: |
200 |
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- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
201 |
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- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
202 |
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of vertical profile tRef in geopotential background and anomaly. |
203 |
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- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
204 |
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and pkg/atm_phys. |
205 |
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- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
206 |
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fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
207 |
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o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
208 |
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o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
209 |
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not used right now, but can be used in BGC packages to fix conservation. |
210 |
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o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
211 |
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other packages too. |
212 |
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o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
213 |
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SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
214 |
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o model/src: |
215 |
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- since we have several heat capacity (even in model/src), define "recip_Cp" |
216 |
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as local variable (no longer in common block) to avoid any confusion. |
217 |
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- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
218 |
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o pkg/exf: |
219 |
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- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
220 |
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air density as function of air Temp, Humidity and atm pressure. |
221 |
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|
222 |
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checkpoint64w (2014/05/02) |
223 |
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o verification: |
224 |
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- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
225 |
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seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
226 |
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code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
227 |
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seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
228 |
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(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
229 |
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o model/src: for atmosphere in p* coords: |
230 |
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- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
231 |
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- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
232 |
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but not yet activated. |
233 |
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o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
234 |
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- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
235 |
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- this changes the results (but not for any verification experiment, because |
236 |
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none tests this), but avoids having an extra field in the restart files |
237 |
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o pkg/seaice: remove global variable TICE (not needed) |
238 |
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- replace by TICES or local variable where necessary (cost_seaice_test, |
239 |
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seaice_diagnostics_state) |
240 |
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- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
241 |
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- use specific read/write routines for reading and writing individual leves |
242 |
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of a multilevel field |
243 |
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o pkg/ctrl & model/inc: |
244 |
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- move additional anomaly fields of control vars (related to options: |
245 |
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ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
246 |
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from DYNVARS.h into new header file: CTRL_FIELDS.h |
247 |
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o pkg/seaice: some small modifications to the ridging code |
248 |
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- make fw2ObyRidge a global variable and add the freshwater flux to |
249 |
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seaice_growth |
250 |
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- pass actual thickness from seaice_prepare_ridging, so that it is |
251 |
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computed only in one place and compute it in the same way as in |
252 |
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seaice_growth |
253 |
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- initialise more fields in seaice_do_ridging that where cause floating |
254 |
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point exceptions over land |
255 |
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o pkg/seaice: preparations for ridging code and first real ridging code |
256 |
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- move most of "PART 1" of S/R seaice_growth into a new and separate |
257 |
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S/R seaice_reg_ridge that will both regularize the state variable after |
258 |
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advection call the actual ridging routine; |
259 |
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- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
260 |
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d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
261 |
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- remove ridging code from seaice_advdiff |
262 |
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- clean up remaining part 1 of seaice_growth in an attempt to make it |
263 |
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more readable (this is probably subjective) |
264 |
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- call seaice_itd_redist once in the initialisation phase to have the initial |
265 |
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conditions in the correct category |
266 |
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- finally: add new ridging routine for ITD code |
267 |
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|
268 |
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checkpoint64v (2014/04/11) |
269 |
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o pkg/ecco: |
270 |
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- add runtime parameters mdt[start,end]date[1,2] |
271 |
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- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
272 |
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o pkg/seaice: |
273 |
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- make deltaC a global variable, so that it can be used in ridging code |
274 |
|
- first step towards ridging: introduce new routines that compute |
275 |
|
ice strength based on ridging parameters |
276 |
|
- add diagnostic for HSNOWITD |
277 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
278 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
279 |
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- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
280 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
281 |
|
o verification/hs94.1x64x5: |
282 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
283 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
284 |
|
o autodiff: |
285 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
286 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
287 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
288 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
289 |
|
which are specific to TAF/TAMC). |
290 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
291 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
292 |
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is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
293 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
294 |
|
building mitgcmuv_ad (make adAll). |
295 |
|
o pkg/ecco: |
296 |
|
- cost_gencost_seaicev4.F: |
297 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
298 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
299 |
|
- add stop statement if old names siv4-[sst,vol] are used |
300 |
|
- add snapshots + cost reports for atmospheric longwave |
301 |
|
- remove factor 0.1 in front of wtau[u,v] |
302 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
303 |
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ALLOW_TMI_SST_COST_CONTRIBUTION |
304 |
|
o pkg/atm_phys: |
305 |
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- add some diagnostics for Short-wave and for convection S/R. |
306 |
|
o pkg/seaice/seaice_growth: |
307 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
308 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
309 |
|
- rearrange loop order for better vector code in the same code block |
310 |
|
- rewrite the floeDiameter formula to have fewer divisions |
311 |
|
- (miraculously) none of this changes the results of seaice_itd |
312 |
|
o pkg/smooth: |
313 |
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- move param smooth2Ddiffnbt to pkg/ecco |
314 |
|
o pkg/salt_plume: |
315 |
|
- salt_plume_frac.F: |
316 |
|
clean up local param names |
317 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
318 |
|
o pkg/rw: |
319 |
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- add RS version of S/R READ_MFLDS_LEV. |
320 |
|
o pkg/streamice: |
321 |
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- fix the restart test by writing/reading pickup_streamice files. |
322 |
|
o pkg/seaice: |
323 |
|
- refine checks for jfnk-related parameters |
324 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
325 |
|
is no IMEX code to avoid confusion and surprises |
326 |
|
|
327 |
|
checkpoint64u (2014/03/07) |
328 |
|
o verification/MLAdjust: |
329 |
|
- rename secondary test suffix: |
330 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
331 |
|
0.leithD -> AhFlxF + switch to flux-form |
332 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
333 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
334 |
|
o pkg/mom_vecinv: |
335 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
336 |
|
to be before mom_calc_visc.F) |
337 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
338 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
339 |
|
this is simpler for the adjoint and for diagnostics. |
340 |
|
o model/src + pkg/momentum: |
341 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
342 |
|
(e.g., to add "thin-wall" where it is =1). |
343 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
344 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
345 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
346 |
|
coords; not working with CD-scheme neither. |
347 |
|
o pkg/seaice: |
348 |
|
- rename recently introduced parameters from (wrong name) AB to |
349 |
|
BDF (backward difference time discretisation) |
350 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
351 |
|
o tools/adjoint_options: |
352 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
353 |
|
|
354 |
|
checkpoint64t (2014/02/01) |
355 |
|
o pkg/ecco |
356 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
357 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
358 |
|
- replace hard-coded record number and period which only work for monthly |
359 |
|
with read-in runtime param that works for other periods (month,day,year) |
360 |
|
o pkg/thsice |
361 |
|
- corrected store directive fixes thsice adjoint gradient checks |
362 |
|
o genmake2 & testreport: |
363 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
364 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
365 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
366 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
367 |
|
o pkg/shelfice: |
368 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
369 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
370 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
371 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
372 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
373 |
|
o model/src/temp_integrate.F and salt_integrate.F |
374 |
|
- re-include store directives that were removed on Dec 27th. |
375 |
|
o model/src/external_forcing_surf.F |
376 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
377 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
378 |
|
turned off in the adjoint. The resolved issue dated back to July when |
379 |
|
EXTERNAL_FORCING_SURF call was moved. |
380 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
381 |
|
o pkg/exf/exf_check.F |
382 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
383 |
|
- streamline error output |
384 |
|
o pkg/streamice and aim_v23: |
385 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
386 |
|
Apple's /usr/bin/cpp knows what to do: |
387 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
388 |
|
Target: x86_64-apple-darwin13.0.0 |
389 |
|
|
390 |
|
checkpoint64s (2014/01/05) |
391 |
|
o tools/adjoint_options: |
392 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
393 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
394 |
|
o model/src: |
395 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
396 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
397 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
398 |
|
o model/src & pkg/ptracers: |
399 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
400 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
401 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
402 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
403 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
404 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
405 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
406 |
|
for now only implemented for in exf_interp_read.F |
407 |
|
o verification/advect_xy: |
408 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
409 |
|
o momentum diagnostics: |
410 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
411 |
|
- fix typo in diagnostics for momentum tendency from AB. |
412 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
413 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
414 |
|
|
415 |
|
checkpoint64r (2013/12/08) |
416 |
|
o verification/*/results: |
417 |
|
- Update reference output of experiments that were passing with just 13 digits |
418 |
|
(make it easier to detect future changes in results) |
419 |
|
o model/src & pkg/ptracers: |
420 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
421 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
422 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
423 |
|
o coupling interface pkgs: |
424 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
425 |
|
- change the config check to test the agreement of Ocean Depth |
426 |
|
with ATM land/sea mask (instead of ATM orography); |
427 |
|
- send to coupler the number of coupler time-steps to do for this run: |
428 |
|
this allows to check for consistency and don't need anymore to be |
429 |
|
specified in parameter file "data"; |
430 |
|
in coupler: |
431 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
432 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
433 |
|
o pkg/compon_communic: |
434 |
|
- add coupling send/receive for non-tiled integer vector; |
435 |
|
- add S/R to check and stop if any proc has an error (similar to |
436 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
437 |
|
o pkg/exch2: |
438 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
439 |
|
through list of all tiles my proc owns. |
440 |
|
o model/src: |
441 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
442 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
443 |
|
calling S/R); this affects AD results at machine truncation level: |
444 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
445 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
446 |
|
o tools/build_options: |
447 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
448 |
|
o coupling interface pkgs: |
449 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
450 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
451 |
|
to each S/R that needs it; remove un-used variables. |
452 |
|
- change component tile registration (cpl_register.F in both compon_interf |
453 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
454 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
455 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
456 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
457 |
|
a) can now use different tiling between atm & ocn comp. |
458 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
459 |
|
even if using the same tiling between atm & ocn). |
460 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
461 |
|
full land tiles); not yet tested. |
462 |
|
- check for valid mapping from comp. tile to coupler global array |
463 |
|
- improve report of tile registration results to log file. |
464 |
|
o pkg/exch2: |
465 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
466 |
|
tile-registration (CPL_REGISTER); |
467 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
468 |
|
store the local bi,bj indices of each tile; |
469 |
|
- also print bi,bj in local report to log file; |
470 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
471 |
|
Jun 2009 modif of pkg/exch2). |
472 |
|
o testing on baudelaire: |
473 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
474 |
|
get the full set of test done earlier |
475 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
476 |
|
o model/src/thermodynamics.F and routines called from it: |
477 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
478 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
479 |
|
velocity (outp) by adding bolus velocity. |
480 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
481 |
|
mass transport from velocity + lateral grid cell area |
482 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
483 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
484 |
|
in thermodynamics.F |
485 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
486 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
487 |
|
loop). |
488 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
489 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
490 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
491 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
492 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
493 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
494 |
|
tutorial_tracer_adjsens (+ TLM output). |
495 |
|
o tools/OAD_support and (verification/*/) code_oad: |
496 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
497 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
498 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
499 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
500 |
|
o model/src: |
501 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
502 |
|
retired list of parameters (routine FREEZE has been replace by surface |
503 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
504 |
|
o pkg/gmredi: |
505 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
506 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
507 |
|
- update output of FWD experiments: front_relax.bvp, |
508 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
509 |
|
|
510 |
|
checkpoint64q (2013/11/17) |
511 |
|
o verification: |
512 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
513 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
514 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
515 |
|
updating the input pickup_seaice files (previously wrong). |
516 |
|
o pkg/cost: |
517 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
518 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
519 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
520 |
|
cannot be applied to var in common block). |
521 |
|
o allows to get results independent of tile-per-proc setting (if using |
522 |
|
slower GLOBAL_SUM_SEND_RECV option). |
523 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
524 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
525 |
|
forward gradients: update output). |
526 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
527 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
528 |
|
o pkg/mom_common: |
529 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
530 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
531 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
532 |
|
ensure that all field value that are used are set. |
533 |
|
o tutorial_deep_convection (smag3d): |
534 |
|
- add missing scaling in mom_calc_smag_3d.F; |
535 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
536 |
|
o pkg/dic: |
537 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
538 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
539 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
540 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
541 |
|
o eesupp/src & pkg/mdsio: |
542 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
543 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
544 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
545 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
546 |
|
o verification/isomip: |
547 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
548 |
|
o tools/build_options: |
549 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
550 |
|
to get a working restart for all experiments, add "-fp-model source" |
551 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
552 |
|
|
553 |
|
checkpoint64p (2013/10/20) |
554 |
|
o pkg/autodiff: |
555 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
556 |
|
criteria, return to simple (default) tape IO format. |
557 |
|
o pkg/mdsio (+ eesupp/src): |
558 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
559 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
560 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
561 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
562 |
|
template) corresponding to simpler global mapping. |
563 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
564 |
|
to globalFile when parameter globalFiles is set to True. |
565 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
566 |
|
o pkg/autodiff: |
567 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
568 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
569 |
|
missing, just add a STOP if array type do not match. |
570 |
|
o pkg/exf: |
571 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
572 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
573 |
|
and rename array obsSIce to exf_iceFraction. |
574 |
|
o tutorial_deep_convection: |
575 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
576 |
|
for now all in this exp. code dir. |
577 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
578 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
579 |
|
o eesupp/src: |
580 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
581 |
|
very large number of processors did not work with existing set-up |
582 |
|
|
583 |
|
checkpoint64o (2013/09/25) |
584 |
|
o pkg/atm_phys & atm_compon_interf: |
585 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
586 |
|
o tools/build_options: |
587 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
588 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
589 |
|
remove CPP setting (was identical to genmake2 default). |
590 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
591 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
592 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
593 |
|
external forcing via taueddy_external_forcing.F |
594 |
|
- at the moment, it is very experimental and only works with the variable eddy |
595 |
|
diffusivity calculated in gmredi_k3d.F |
596 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
597 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
598 |
|
o testreport (& tools/do_tst_2+2): |
599 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
600 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
601 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
602 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
603 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
604 |
|
o pkg/atm_compon_interf: |
605 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
606 |
|
(which accumalate in time each coupling field) |
607 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
608 |
|
update accordingly + simplify aim_do_physics.F |
609 |
|
|
610 |
|
checkpoint64n (2013/08/26) |
611 |
|
o pkg/bbl: |
612 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
613 |
|
- replaced horizontal and vertical transport parameters with velocities |
614 |
|
- changes results for verification/global_with_exf.yearly |
615 |
|
o verification/halfpipe_streamice: |
616 |
|
- change to matrix construction; update both Fwd & AD output. |
617 |
|
o verification/tutorial_tracer_adjsens: |
618 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
619 |
|
rStar causes problems with OpenAD; update output. |
620 |
|
o tools: |
621 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
622 |
|
to local /tmp disk (but would be easy to move them back); |
623 |
|
- xmakedepend: apply the same switch for temp-files. |
624 |
|
o pkg/offline: |
625 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
626 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
627 |
|
output files) and apply r* scaling at each time-step (function of the time |
628 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
629 |
|
o adjoint with OpenAD: |
630 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
631 |
|
package openad. This package has to be compiled for all runs with OpenAD |
632 |
|
instead of specifying code_oad_all as a modification directory. |
633 |
|
- link the fortran templates from tools/OAD_support to the build directory |
634 |
|
for preprocessing to avoid conflicts between different setups compiled |
635 |
|
simultaneously and simplify cleanup. |
636 |
|
o pkg/exf: |
637 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
638 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
639 |
|
o model/src: |
640 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
641 |
|
(similar to do_fields_blocking_exchanges.F). |
642 |
|
o tools/genmake2: |
643 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
644 |
|
built, will stop if things go wrong with staf). |
645 |
|
- fix target "adobj" (left from TAF version-2 transition) |
646 |
|
o pkg/diagnostics: |
647 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
648 |
|
this replace/extend the use of logical param "settingDiags" (to check |
649 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
650 |
|
New S/R to print error message and stop when pkgStatus is not right. |
651 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
652 |
|
|
653 |
|
checkpoint64m (2013/08/13) |
654 |
|
o model/inc: |
655 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
656 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
657 |
|
o pkg/kpp & aim_v23: |
658 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
659 |
|
o pkg/seaice: |
660 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
661 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
662 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
663 |
|
o eesupp/src: |
664 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
665 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
666 |
|
o switch to TAF version-2: |
667 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
668 |
|
are used in I/O routines of adjoint state and associated common blocks |
669 |
|
that are used in adcommon.h (backward compatible with version-1) |
670 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
671 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
672 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
673 |
|
out except for diva). |
674 |
|
- the major change with TAF version-2 is that both the differentiated |
675 |
|
routines and the forward routines (new) are returned as part of the TAF |
676 |
|
output source code. Update genmake2 accordingly. |
677 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
678 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
679 |
|
output show minor changes (machine truncation level); update the few AD & |
680 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
681 |
|
|
682 |
|
checkpoint64l (2013/08/05) |
683 |
|
o model/src: |
684 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
685 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
686 |
|
when using TAF but only if using OpenAD. |
687 |
|
o pkg/mom_common+fluxform+vecinv: |
688 |
|
- always set horiz. viscosity arrays to background value before calling |
689 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
690 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
691 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
692 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
693 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
694 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
695 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
696 |
|
useBiharmonicVisc & useVariableVisc. |
697 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
698 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
699 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
700 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
701 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
702 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
703 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
704 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
705 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
706 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
707 |
|
default viscAh,viscA4 is zero). |
708 |
|
o model/src: |
709 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
710 |
|
o Divided Adjoint (DIVA) with MPI: |
711 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
712 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
713 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
714 |
|
|
715 |
|
checkpoint64k (2013/07/23) |
716 |
|
o tools/OAD_support: |
717 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
718 |
|
and remove it from genmake2. |
719 |
|
o tools/build_options: |
720 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
721 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
722 |
|
o verification/halfpipe_streamice: |
723 |
|
- change to driving stress formulation; update both Fwd & AD output. |
724 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
725 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
726 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
727 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
728 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
729 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
730 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
731 |
|
o testreport: |
732 |
|
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
733 |
|
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
734 |
|
from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
735 |
|
o verification/lab_sea (AD test): |
736 |
|
- change to test Divided Adjoint Run in this set-up (both standard AD test |
737 |
|
and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
738 |
|
o pkg atm_ & ocn_compon_interf: |
739 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
740 |
|
staggerTimeStep implementation) and disable (retired) corresponding |
741 |
|
parameter. |
742 |
|
o pkg/offline: |
743 |
|
- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
744 |
|
- add S/R OFFLINE_CHECK to print offline parameter summary |
745 |
|
and stop if loading a file that is not used; |
746 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
747 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
748 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
749 |
|
for monitoring CFL numbers and checking offline fields. |
750 |
|
o OpenAD: |
751 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
752 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
753 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
754 |
|
o model/src: |
755 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
756 |
|
(where external_forcing_adjust was called) and change list of arguments; |
757 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
758 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
759 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
760 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
761 |
|
arrays in FFIELDS.h. |
762 |
|
- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
763 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
764 |
|
ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
765 |
|
- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
766 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
767 |
|
error in AD code). |
768 |
|
|
769 |
|
checkpoint64j (2013/07/04) |
770 |
|
o pkg/offline: |
771 |
|
- to enable the use of other features with pkg offline (e.g., obcs), |
772 |
|
also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
773 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
774 |
|
o pkg/exf ALLOW_RUNOFTEMP |
775 |
|
- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
776 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
777 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
778 |
|
o pkg/atm_phys: |
779 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
780 |
|
o verification, ad-tests: |
781 |
|
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
782 |
|
global_ocean_ebm and offline_exf_seaice.thsice. |
783 |
|
o verification/halfpipe_streamice: |
784 |
|
- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
785 |
|
flux input boundary conditions to be ignored; a fix for this bug changed |
786 |
|
verification results for forward test. |
787 |
|
- add adjoint test. |
788 |
|
o pkg/ptracers: |
789 |
|
- allow to restart without SOM pickup (resetting SOM to zero). |
790 |
|
o pkg/gmredi: |
791 |
|
- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
792 |
|
- It uses mixing length theory and suppression by steering level effects to |
793 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
794 |
|
to JPO, for more details). |
795 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
796 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
797 |
|
- New files added to pkg/gmredi: |
798 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
799 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
800 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
801 |
|
for use in gmredi_k3d |
802 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
803 |
|
the eddy diffusivity |
804 |
|
|
805 |
|
checkpoint64i (2013/06/18) |
806 |
|
o pkg/cheapaml: |
807 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
808 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
809 |
|
with pkg/cheapaml. |
810 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
811 |
|
simple cs.pcol to plot 2D fields on a map |
812 |
|
o pkg/streamice: |
813 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
814 |
|
sheets and ice streams |
815 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
816 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
817 |
|
ed that this will change) |
818 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
819 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
820 |
|
rectangular embayment |
821 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
822 |
|
- for questions, email dgoldber@mit.edu |
823 |
|
o pkg/thsice: |
824 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
825 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
826 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
827 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
828 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
829 |
|
o pkg/cfc: |
830 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
831 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
832 |
|
- change some hard-coded constant to run time parameter for reading and |
833 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
834 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
835 |
|
- put arguments in standard order: myTime, myIter, myThid |
836 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
837 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
838 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
839 |
|
- new routine to print summary of CFC params and check for consistency. |
840 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
841 |
|
similar to thsice_advdiff. |
842 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
843 |
|
o pkg/cfc: |
844 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
845 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
846 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
847 |
|
hemisphere value. |
848 |
|
o pkg/seaice: |
849 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
850 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
851 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
852 |
|
- requires an additional time level that is stored in the pickup |
853 |
|
- you can start with AB2 from a pickup without this time level with |
854 |
|
pickupStrictlyMatch = .false. |
855 |
|
|
856 |
|
checkpoint64h (2013/05/26) |
857 |
|
o pkg/cheapaml: |
858 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
859 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
860 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
861 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
862 |
|
(Note: was already the case for Tair,Qair advection); |
863 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
864 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
865 |
|
- fill in array "Qsw" (for short-wave heating); |
866 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
867 |
|
before any update (consistent with MITgcm state var diagnostics); |
868 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
869 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
870 |
|
o pkg/seaice: |
871 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
872 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
873 |
|
- allows to compile pkg/seaice without pkg/exf. |
874 |
|
o tools/OAD_support: |
875 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
876 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
877 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
878 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
879 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
880 |
|
o pkg/offline: |
881 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
882 |
|
(previously called from pkg/dic_surfforcing_init.F) |
883 |
|
o model/src: |
884 |
|
- re-order sequence of calls within packages_init_variables.F, using |
885 |
|
standard order, except for: |
886 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
887 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
888 |
|
o new pkg: atm_phys |
889 |
|
- add entry point and source code (previously in contrib |
890 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
891 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
892 |
|
- re-order sequence of calls within packages_readparms.F, |
893 |
|
packages_init_fixed.F and packages_write_pickup.F |
894 |
|
(but skip packages_init_variables.F because of TAF issues). |
895 |
|
- update contrib/*/atm_gray/ experiment. |
896 |
|
o pkg/seaice (ITD code): |
897 |
|
- simplify and fix the writing of pickup-files for ITD case |
898 |
|
o pkg/seaice (ITD code): |
899 |
|
- introduce floe size dependent lateral melt for ITD case; |
900 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
901 |
|
- update seaice_itd experiment main output. |
902 |
|
o pkg/thsice: |
903 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
904 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
905 |
|
changed accordingly pkg/atm2d. |
906 |
|
|
907 |
|
checkpoint64g (2013/05/01) |
908 |
|
o pkg/exf ALLOW_RUNOFTEMP |
909 |
|
- if defined, river and glacier runoff temperature can be read-in from |
910 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
911 |
|
o pkg/thsice (& pkg/bulk_force): |
912 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
913 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
914 |
|
- change computation domain to always be the interior (without overlap). |
915 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
916 |
|
o verification/tutorial_global_oce_biogeo: |
917 |
|
- add preliminary OpenAD setup (still has problems) |
918 |
|
o pkg/seaice: |
919 |
|
- turn some parameters for choosing the convergence criterion of |
920 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
921 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
922 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
923 |
|
the results of lab_sea/input because a division has been replaced by |
924 |
|
a multiplication with the reciprocal (sumNorm) |
925 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
926 |
|
convergence of solver (changes results, of course), and to test some |
927 |
|
new features |
928 |
|
o model/src: |
929 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
930 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
931 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
932 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
933 |
|
o pkg/shelfice: |
934 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
935 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
936 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
937 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
938 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
939 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
940 |
|
- update isomip experiment forward output (get machine truncation error |
941 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
942 |
|
o verification/offline_exf_seaice: |
943 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
944 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
945 |
|
SEAICE_growMeltByConv = .TRUE., |
946 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
947 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
948 |
|
o verification/global_ocean.cs32x15: |
949 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
950 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
951 |
|
o verification/offline_exf_seaice: |
952 |
|
- adjust list of tested variables (with testreport) and update |
953 |
|
standard test output with better slection of monitored fields. |
954 |
|
o pkg/cd_code: |
955 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
956 |
|
experiment lab_sea.hb87 |
957 |
|
o tools/genmake2: |
958 |
|
- change default makedepend from the system default to tools/xmakedepend: |
959 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
960 |
|
otherwise select the system default (if exist and pass the test) or |
961 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
962 |
|
o pkg/exf & pkg/thsice: |
963 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
964 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
965 |
|
1) Rain has same temp as Air. |
966 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
967 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
968 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
969 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
970 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
971 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
972 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
973 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
974 |
|
o pkg/thsice: |
975 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
976 |
|
implementation): move THSICE_AVE call after the advection (called directly |
977 |
|
from thsice_do_advect.F). |
978 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
979 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
980 |
|
multiDimAdvection=.FALSE., |
981 |
|
There is still an issue with this. |
982 |
|
o pkg/thsice: |
983 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
984 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
985 |
|
and offline_exf_seaice (main test). |
986 |
|
|
987 |
|
checkpoint64f (2013/03/31) |
988 |
|
o verification/OpenAD: |
989 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
990 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
991 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
992 |
|
o verification/tutorial_global_oce_biogeo: |
993 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
994 |
|
o verification/offline_exf_seaice: |
995 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
996 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
997 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
998 |
|
o pkg/seaice/seaice_evp.F: |
999 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
1000 |
|
the turningAngle is non-zero) over open water to avoid stripes |
1001 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
1002 |
|
the verification experiment (because turningAngle=0 in that experiment), |
1003 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
1004 |
|
o verification, AD & TLM output: |
1005 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
1006 |
|
additions and multiplications which affect results at machine truncation |
1007 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
1008 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
1009 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
1010 |
|
digits of matching. |
1011 |
|
o pkg/seaice: |
1012 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
1013 |
|
"zebra" method: split vector loop into two with step size 2; this |
1014 |
|
solves a general convergence problem for the JFNK solver on a vector |
1015 |
|
computer. It has the potential to even improve convergence for |
1016 |
|
non-vector machines, but it does change the results so it is turned |
1017 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
1018 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
1019 |
|
|
1020 |
|
checkpoint64e (2013/03/05) |
1021 |
|
o pkg/ecco and several verification experiments: |
1022 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
1023 |
|
from ecco package, and revert to unified routine in model/src/ |
1024 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
1025 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
1026 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
1027 |
|
o pkg/generic_advdiff: |
1028 |
|
- implement compressible flow method for multi-dim advection (similar to |
1029 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
1030 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
1031 |
|
vertical advection. |
1032 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
1033 |
|
to test compressible flow multi-dim advection. |
1034 |
|
o pkg/generic_advdiff: |
1035 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
1036 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
1037 |
|
o pkg/seaice: |
1038 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
1039 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
1040 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
1041 |
|
seaice_calc_strainrates.F; |
1042 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
1043 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
1044 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
1045 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
1046 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
1047 |
|
- new subroutines seaice_lsr_tridiagu/v |
1048 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
1049 |
|
additive Schwarz method, but not used for now. |
1050 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
1051 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
1052 |
|
o OpenAD support |
1053 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
1054 |
|
OpenAD revolve loop replacement |
1055 |
|
(new S/R main_do_loop.F) |
1056 |
|
o model/src: |
1057 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
1058 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
1059 |
|
ADAMS_BASHFORTH2. |
1060 |
|
o pkg/cheapaml: |
1061 |
|
- add new parameter (default=F, same as before) to disable full domain |
1062 |
|
(including land) periodicity in X & Y dir. |
1063 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
1064 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
1065 |
|
into single S/R CHEAPAML_TIMESTEP. |
1066 |
|
|
1067 |
|
checkpoint64d (2013/02/17) |
1068 |
|
o pkg/monitor (angular momentum): |
1069 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
1070 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
1071 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
1072 |
|
each component (instead of from cell centered averaged) and use the 4 |
1073 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
1074 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
1075 |
|
FreeSurf) if using vectorInvariant momentum. |
1076 |
|
o model/src (horizontal grid): |
1077 |
|
- move initialisation of all horizontal grid arrays to null value |
1078 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
1079 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
1080 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
1081 |
|
compute them in S/R CALC_GRID_ANGLES. |
1082 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
1083 |
|
SEAICE_JFNK_tolIter |
1084 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
1085 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
1086 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
1087 |
|
- extend loop range in seaice_calc_viscosity |
1088 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
1089 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
1090 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
1091 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
1092 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
1093 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
1094 |
|
for output.dyn_jfnk.txt |
1095 |
|
in seaice_fgmres.F (unrelated to RAS) |
1096 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
1097 |
|
efficient), but because this changes the results, turn it off by |
1098 |
|
default |
1099 |
|
- replace the save statement by local common blocks |
1100 |
|
o utils/matlab: |
1101 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
1102 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
1103 |
|
instead of local script "load_cs.m". |
1104 |
|
o pkg/seaice: |
1105 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
1106 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
1107 |
|
change the verification experiment, because of the particular domain |
1108 |
|
decomposition |
1109 |
|
o pkg/diagnostics: |
1110 |
|
- change default missing_value from UNSET_RL to -999. |
1111 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
1112 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
1113 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
1114 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
1115 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
1116 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
1117 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
1118 |
|
- moved the search algorithm into a separate subroutine, that is kept |
1119 |
|
within the same file for automatic inlining. |
1120 |
|
- modified catching potential errors |
1121 |
|
o pkg/ecco: |
1122 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
1123 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
1124 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
1125 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
1126 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
1127 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
1128 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
1129 |
|
o model/src: |
1130 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
1131 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
1132 |
|
and cpl_aim+ocn. |
1133 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
1134 |
|
for fizhi-cs experiments reference output. |
1135 |
|
o pkg/ctrl: |
1136 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
1137 |
|
ALLOW_GENTIM2D_CONTROL |
1138 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
1139 |
|
o verification/global_ocean.cs32x15: |
1140 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
1141 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
1142 |
|
o pkg/ptracers: |
1143 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
1144 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
1145 |
|
o pkg/thsice: |
1146 |
|
- implement new sequence of calls for thsice+seaice: |
1147 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
1148 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
1149 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
1150 |
|
in CPP_OPTIONS.h) to recover old sequence; |
1151 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
1152 |
|
just before advection (instead of just after advection in old sequence); |
1153 |
|
- update output of experiment offline_exf_seaice (standard test); |
1154 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
1155 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
1156 |
|
o pkg/aim_v23: |
1157 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
1158 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
1159 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
1160 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
1161 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
1162 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
1163 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
1164 |
|
o pkg/thsice: |
1165 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
1166 |
|
where just seaice diffusion is used without seaice-dynamics. |
1167 |
|
|
1168 |
|
checkpoint64c (2013/01/18) |
1169 |
|
o pkg/seaice: |
1170 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
1171 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
1172 |
|
- add a line search option to the JFNK solver |
1173 |
|
- move update of u/vIce and computation of initial residual into a separate |
1174 |
|
routine (same file); makes the code a little easier to read (?) |
1175 |
|
- the line search requires computation of the residual and for some reason |
1176 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
1177 |
|
without changing the results, so we move computation of the new residual |
1178 |
|
also to the end of the Newton loop, even without the line search |
1179 |
|
o pkg/mdsio: |
1180 |
|
- write missing value (corresponding to undefined array value) to meta files; |
1181 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
1182 |
|
case of undefined missing value but it's current the default missing-value); |
1183 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
1184 |
|
o pkg/exf & thsice: |
1185 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
1186 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
1187 |
|
o verification/cfc_example: |
1188 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
1189 |
|
illustrate how to use it). |
1190 |
|
o verification/offline_exf_seaice: |
1191 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
1192 |
|
files to only one time-record. |
1193 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
1194 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
1195 |
|
snapshot output; same mcPheePiston value as in thsice with |
1196 |
|
surf-current=0.2m/s. |
1197 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
1198 |
|
initial conditions). |
1199 |
|
o verification/cfc_example: |
1200 |
|
- update file "data" with more standard choice (default rotationPeriod, |
1201 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
1202 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
1203 |
|
o pkg/layers: |
1204 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
1205 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
1206 |
|
o verification/offline_exf_seaice: |
1207 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
1208 |
|
anywhere else). |
1209 |
|
o verification/offline_exf_seaice: |
1210 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
1211 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
1212 |
|
o model/src: |
1213 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
1214 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
1215 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
1216 |
|
- In order to be compatible with the default EVP code, this requires changing |
1217 |
|
the EVP code around a little; and because any small change immediately |
1218 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
1219 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
1220 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
1221 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
1222 |
|
The adjoint test lab_sea.evp also needed to be updated. |
1223 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
1224 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
1225 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
1226 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
1227 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
1228 |
|
kept obscure, because I need to test it a little more. |
1229 |
|
o pkg/cheapaml: |
1230 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
1231 |
|
o pkg/seaice: |
1232 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
1233 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
1234 |
|
o model/src: |
1235 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
1236 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
1237 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
1238 |
|
o pkg/cheapaml: |
1239 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
1240 |
|
update output of experiment cheapAML_box. |
1241 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
1242 |
|
and set them only in one place (cheapaml_readparms.F). |
1243 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
1244 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
1245 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
1246 |
|
o model/src/the_main_loop.F: |
1247 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
1248 |
|
o pkg/seaice: |
1249 |
|
- remove legacy branch code. |
1250 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
1251 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
1252 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
1253 |
|
SEAICE_CAP_HEFF). |
1254 |
|
o pkg/cheapaml: |
1255 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
1256 |
|
to load new forcing fields. |
1257 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
1258 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
1259 |
|
cheapAML_box, keep same output (small trucation error differences). |
1260 |
|
o verification/offline_exf_seaice: |
1261 |
|
- add thermodynamics only test. |
1262 |
|
o verification/cheapAML_box: |
1263 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
1264 |
|
keep same output (same 14 digits for cg2d). |
1265 |
|
- switch on "-r8" compiler option (some numerical values are missing |
1266 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
1267 |
|
|
1268 |
|
checkpoint64b (2012/12/24) |
1269 |
|
o pkg/cheapaml: |
1270 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
1271 |
|
- store tendency of advected variables into cheapaml pickup file |
1272 |
|
and fix the AB-2 restart. |
1273 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
1274 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
1275 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
1276 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
1277 |
|
- update results after change of experiment seaice. |
1278 |
|
o pkg/seaice: |
1279 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
1280 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
1281 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
1282 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
1283 |
|
o model/src: |
1284 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
1285 |
|
(in case of a poor convergence). |
1286 |
|
o pkg/seaice/seaice_lsr.F |
1287 |
|
- move calculation of matrix coefficients into new |
1288 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
1289 |
|
file; the main purpose of this change is to be able to reuse the code |
1290 |
|
in S/R SEAICE_PRECONDITIONER |
1291 |
|
- modify the computation of the residual so that the mass of sea-ice |
1292 |
|
is not used twice; this simplifies the calculations, but since |
1293 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
1294 |
|
not tested in testreport---this does not affect the testreport results. |
1295 |
|
o verification/seaice_obcs: |
1296 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
1297 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
1298 |
|
o model/src: |
1299 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
1300 |
|
o pkg/seaice: |
1301 |
|
- improve description of parameters in seaice_fgmres.F and start |
1302 |
|
cleaning up the code |
1303 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
1304 |
|
second argument |
1305 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
1306 |
|
results of offline_exf_seaice.dyn_jfnk |
1307 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
1308 |
|
o pkg/aim_v23: |
1309 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
1310 |
|
o model/src + pkg/seaice: |
1311 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
1312 |
|
along X and Y lines, respectively for U and V component. |
1313 |
|
Note: 1) MPI and cube-exchange not yet coded. |
1314 |
|
2) probably not accurate for poorly conditioned / large size problem. |
1315 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
1316 |
|
default: not compiled and not used. |
1317 |
|
o pkg/seaice: |
1318 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
1319 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
1320 |
|
mpi_allreduce in seaice_fgmres.F |
1321 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
1322 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
1323 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
1324 |
|
o verification: |
1325 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
1326 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
1327 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
1328 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
1329 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
1330 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
1331 |
|
o pkg/exf: |
1332 |
|
- disable "sstExtrapol" when Nr=1 |
1333 |
|
o verification: |
1334 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
1335 |
|
to test pkg/cheapaml. |
1336 |
|
o pkg/aim_v23 & pkg/shap_filt: |
1337 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
1338 |
|
o pkg/seaice: |
1339 |
|
- remove unused field pressPre from jfnk solver |
1340 |
|
- rename two subroutines in seaice_preconditioner.F |
1341 |
|
o eesupp/src: |
1342 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
1343 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
1344 |
|
- remove wrong parts of the rhs and the lhs (were in there |
1345 |
|
because I did not understand the concept of this preconditioner) |
1346 |
|
- add an exchange between u- and v-sweep. This increases communication |
1347 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
1348 |
|
one would like the u- and v-sweep to be independent. So far within |
1349 |
|
undocumented ifdefs |
1350 |
|
- reorganize the extra computations for printing the residuals |
1351 |
|
o tools/genmake2: |
1352 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
1353 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
1354 |
|
|
1355 |
|
checkpoint64a (2012/11/16) |
1356 |
|
o pkg/autodiff: |
1357 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
1358 |
|
autodiff_readparms.F no longer depends on calling order (within |
1359 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
1360 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
1361 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
1362 |
|
o pkg/obcs: |
1363 |
|
- adding tidal velocity forcing capability to obcs |
1364 |
|
for usage example, see verification/seaice_obcs/input.tides |
1365 |
|
o pkg/seaice: |
1366 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
1367 |
|
SEAICE_LSRrelaxU/V |
1368 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
1369 |
|
o pkg/aim_v23: |
1370 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
1371 |
|
o pkg/shap_filt: |
1372 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
1373 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
1374 |
|
o model/src: |
1375 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
1376 |
|
time-constant addMass field from file (addMassFile); |
1377 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
1378 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
1379 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
1380 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
1381 |
|
o pkg/seaice: |
1382 |
|
- complete merge of ITD code into seaice_growth.F |
1383 |
|
from MITgcm_contrib/torge/itd/code/ |
1384 |
|
no verification so far, but Torge Martin tested |
1385 |
|
"1-D test case and Beaufort set up; |
1386 |
|
deliver okay results after 1 model year." |
1387 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
1388 |
|
- move computation of eta at Z-points into calc_viscosities |
1389 |
|
+ introduce global field etaZ |
1390 |
|
+ add different methods for computing etaZ, for now the old |
1391 |
|
method (simple averages of eta to Z-points) is hardwired |
1392 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
1393 |
|
seaice_preconditioner |
1394 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
1395 |
|
- seaice_preconditioner: |
1396 |
|
+ replace one remaining press by pressLoc (mistake) |
1397 |
|
+ adjust printing of residuals |
1398 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
1399 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
1400 |
|
seaice_init_fixed.F) |
1401 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
1402 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
1403 |
|
interval to STDOUT |
1404 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
1405 |
|
some operations |
1406 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
1407 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
1408 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
1409 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
1410 |
|
a serious convergence problem when open boundaries are involved |
1411 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
1412 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
1413 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
1414 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
1415 |
|
o pkg/autodiff |
1416 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
1417 |
|
SEAICEuseDYNAMICSinAdMode |
1418 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
1419 |
|
o pkg/seaice |
1420 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
1421 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
1422 |
|
The code implements concept laid out in Thorndike et al. (1975); |
1423 |
|
code is enabled via CPP flag SEAICE_ITD |
1424 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
1425 |
|
code is not complete yet!! |
1426 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
1427 |
|
o verification (using seaice): |
1428 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
1429 |
|
global_ocean.cs32x15.seaice ; update results. |
1430 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
1431 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
1432 |
|
offline_exf_seaice (previously compiling B-grid). |
1433 |
|
o pkg/exf: |
1434 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
1435 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
1436 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
1437 |
|
o pkg/layers (adjust changes from Sept 19): |
1438 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
1439 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
1440 |
|
o pkg/layers (adjust changes from Sept 19): |
1441 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
1442 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
1443 |
|
- remove layers variables when corresponding CPP option is undef. |
1444 |
|
o pkg/layers: |
1445 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
1446 |
|
velocity in layer) |
1447 |
|
o pkg/seaice: |
1448 |
|
- simplify (?) ocean-drag coefficent computations by using |
1449 |
|
the same routine in all three solvers (saves some code lines) |
1450 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
1451 |
|
declare them locally in lsr.F (the only place where they are |
1452 |
|
still used) |
1453 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
1454 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
1455 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
1456 |
|
and SEAICEuseJFNK=.true. A few things to note: |
1457 |
|
- involves a FGMRES, that is parallel but very inefficient, |
1458 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
1459 |
|
orthogonalization method. Needs to be replaced. Original code |
1460 |
|
from J.-F. Lemieux |
1461 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
1462 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
1463 |
|
preconditioner. For the preconditioner, the default is set to 10. |
1464 |
|
- Jacobian times vector is computed with finite differences |
1465 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
1466 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
1467 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
1468 |
|
does not need this regularization in the first place). Define |
1469 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
1470 |
|
o eesupp/src: |
1471 |
|
- check in genmake2 that intrinsic S/R flush is available. |
1472 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
1473 |
|
- flush standard & error msg unit before MPI termination |
1474 |
|
- if debugMode, flush IO unit after printing msg |
1475 |
|
o pkg/ctrl: |
1476 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
1477 |
|
to ctrl_set_unpack_xyz. |
1478 |
|
|
1479 |
|
checkpoint64 (2012/10/09) |
1480 |
|
o pkg/shelfice |
1481 |
|
- in mom_fluxform.F, mom_vecinv.F: |
1482 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
1483 |
|
Bug fix KappaRU -> KappaRV |
1484 |
|
does not change verification/isomip but may change other setups |
1485 |
|
(presumably constant KappaRU=KappaRV) |
1486 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
1487 |
|
o pkg/obcs: |
1488 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
1489 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
1490 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
1491 |
|
o pkg/seaice: |
1492 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
1493 |
|
default is off for now. |
1494 |
|
o pkg/obcs: |
1495 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
1496 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
1497 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
1498 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
1499 |
|
o pkg/layers : |
1500 |
|
- add diagnostics to pkg/layers |
1501 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
1502 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
1503 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
1504 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
1505 |
|
o pkg/seaice/seaice_growth.F: |
1506 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
1507 |
|
o pkg/obcs: |
1508 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
1509 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
1510 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
1511 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
1512 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
1513 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
1514 |
|
o pkg/obcs: |
1515 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
1516 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
1517 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
1518 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
1519 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
1520 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
1521 |
|
to replace hard-coded null index value of zero. |
1522 |
|
o pkg/exch2: |
1523 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
1524 |
|
always check buffer-size (but outside the loop); move checking for valid |
1525 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
1526 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
1527 |
|
o pkg/ctrl (pack & unpack): |
1528 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
1529 |
|
(locally defined) for different variables (+ remove the variable-specific |
1530 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
1531 |
|
(to be extended to other local file names in ctrl.h). |
1532 |
|
o pkg/flt: |
1533 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
1534 |
|
o pkg/mdsio: |
1535 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
1536 |
|
o tools/genmake2: |
1537 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
1538 |
|
(added by Alistair in version 1.51 for building without make depend); |
1539 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
1540 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
1541 |
|
place in version 1.23): this save going through staf when unrelated header |
1542 |
|
file has been modified. |
1543 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
1544 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
1545 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
1546 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
1547 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
1548 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
1549 |
|
upper/lower case ; account for space between "#" and undef/define) |
1550 |
|
o pkg/flt (with exch2): |
1551 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
1552 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
1553 |
|
|
1554 |
|
checkpoint63s (2012/09/05) |
1555 |
|
o pkg/ecco: |
1556 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
1557 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
1558 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
1559 |
|
o pkg/ctrl: |
1560 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
1561 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
1562 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
1563 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
1564 |
|
ctrlSmoothCorrel3D (new). |
1565 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
1566 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
1567 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
1568 |
|
controls when useAtmWind, and vice versa. |
1569 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
1570 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
1571 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
1572 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
1573 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
1574 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
1575 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
1576 |
|
o pkg/smooth: |
1577 |
|
- remove un-necessary includes. |
1578 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
1579 |
|
Those CPP options were never defined, and not necessary. |
1580 |
|
o model/src: |
1581 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
1582 |
|
- standard treatment of useSMOOTH. |
1583 |
|
o pkg/autodiff: |
1584 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
1585 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
1586 |
|
o pkg/exch2: |
1587 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
1588 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
1589 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
1590 |
|
and tiles to process mapping. |
1591 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
1592 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
1593 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
1594 |
|
from w2_eeboot.F to w2_readparms.F. |
1595 |
|
o eesupp/src: |
1596 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
1597 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
1598 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
1599 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
1600 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
1601 |
|
has been called. |
1602 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
1603 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
1604 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
1605 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
1606 |
|
useCubedSphereExchange with EXCH-1 (safer). |
1607 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
1608 |
|
o pkg/ggl90: |
1609 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
1610 |
|
used in ALLOW_GGL90_SMOOTH code. |
1611 |
|
o pkg/flt: |
1612 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
1613 |
|
floats at the Southern end of the domain). |
1614 |
|
o eesupp/inc: |
1615 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
1616 |
|
but not used (and not to be used) anywhere, just for documentation. |
1617 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
1618 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
1619 |
|
a) can damage previously written records in any other multi-record files. |
1620 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
1621 |
|
o tools/genmake2: |
1622 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
1623 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
1624 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
1625 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
1626 |
|
- always print usual warning comment 'this file is automatically generated' |
1627 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
1628 |
|
o pkg/cheapaml: |
1629 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
1630 |
|
o pkg/exf: |
1631 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
1632 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
1633 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
1634 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
1635 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
1636 |
|
o pkg/ctrl, ecco: |
1637 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
1638 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
1639 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
1640 |
|
o tools/genmake2: |
1641 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
1642 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
1643 |
|
- source local config file "genmake_local" just after processing the genmake2 |
1644 |
|
command arguments (previously done before processing arg). |
1645 |
|
o pkg/grdchk: |
1646 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
1647 |
|
to this routine from cost_final has been dropped in g_cost_final) |
1648 |
|
- improve printed information (more explicit msg, no longer using "print *," |
1649 |
|
fix fcpertminus printed value). |
1650 |
|
o model/src: |
1651 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
1652 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
1653 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
1654 |
|
o pkg/dic: |
1655 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
1656 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
1657 |
|
o pkg/grdchk: |
1658 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
1659 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
1660 |
|
o pkg/autodiff/ctrl/grdchk : |
1661 |
|
- attempt to sort out what works and what does not, |
1662 |
|
with regard to I/O, and to warn/stop accordingly. |
1663 |
|
o pkg/grdchk: |
1664 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
1665 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
1666 |
|
statements were moved from grdchk_main.F and into |
1667 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
1668 |
|
- a global sum is applied to record numbers icvrec/layer |
1669 |
|
out of grdchk_loc so that they be passed to I/O routines. |
1670 |
|
o pkg/smooth: |
1671 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
1672 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
1673 |
|
o verification/testreport: |
1674 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
1675 |
|
- can also use compressed (gzip) reference output file; |
1676 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
1677 |
|
to be easier to collect by testreport. |
1678 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
1679 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
1680 |
|
- report run-time in each individual summary (previously only for AD test); |
1681 |
|
for TLM test, add also TAF version. |
1682 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
1683 |
|
|
1684 |
|
checkpoint63r (2012/08/15) |
1685 |
|
o tools/genmake2: |
1686 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
1687 |
|
o pkg/ecco/ecco_cost_final.F : |
1688 |
|
- fix fc print statements (to stdout and costfunction0000) so |
1689 |
|
that the printed value is always after the global sum. |
1690 |
|
o pkg/seaice/seaice_dynsolver.F : |
1691 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
1692 |
|
(no change for the standard case of SEAICE_area_max=1) |
1693 |
|
o some cleaning: |
1694 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
1695 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
1696 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
1697 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
1698 |
|
includes; |
1699 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
1700 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
1701 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
1702 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
1703 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
1704 |
|
* no longer include PACKAGES_CONFIG.h ; |
1705 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
1706 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
1707 |
|
including ECCO_CPPOPTIONS.h). |
1708 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
1709 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
1710 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
1711 |
|
not necessary accurate). |
1712 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
1713 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
1714 |
|
deliberately break compilation (a remainder that it needs to be customized) |
1715 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
1716 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
1717 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
1718 |
|
o tools/genamke2: |
1719 |
|
- check for lapack. |
1720 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
1721 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
1722 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
1723 |
|
from both packages. |
1724 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
1725 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
1726 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
1727 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
1728 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
1729 |
|
o pkg/exf: |
1730 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
1731 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
1732 |
|
o verification/*/code_ad: |
1733 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
1734 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
1735 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
1736 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
1737 |
|
o pkg/seaice : |
1738 |
|
- added possibility to change ice strength/PRESS0 relationship to |
1739 |
|
HEFF, according to the following run time parameters |
1740 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
1741 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
1742 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
1743 |
|
o pkg/ggl90 : |
1744 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
1745 |
|
mixing between first and second level (previously included as a comment) |
1746 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
1747 |
|
- add test of newly added dumpAdByRec=T option where |
1748 |
|
we write all records to one file per variable. |
1749 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
1750 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
1751 |
|
to check that this code is ok with taf and compiles in adjoint. |
1752 |
|
o pkg/autodiff : |
1753 |
|
- added run time param dumpAdByRec : ad dump format switch. |
1754 |
|
If true then write all records to one file per variable. |
1755 |
|
Else write one file per record (remains the default). |
1756 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
1757 |
|
o pkg/seaice: |
1758 |
|
- Added SEAICEuseTILT run time switch : if set to |
1759 |
|
false then omit the tilt term in seaice dynamics. |
1760 |
|
- Fix free drift calculation. |
1761 |
|
o pkg/shelfice: |
1762 |
|
When initializing SHELFICEDragQuadratic, set default to be |
1763 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
1764 |
|
but retain option to set it independently |
1765 |
|
(inconsistenty spotted by Veronique Dansereau) |
1766 |
|
o eesupp/inc: |
1767 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
1768 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
1769 |
|
o model/src: |
1770 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
1771 |
|
o pkg/autodiff: |
1772 |
|
re-write active I/O high-level (control) S/R: |
1773 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
1774 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
1775 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
1776 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
1777 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
1778 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
1779 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
1780 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
1781 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
1782 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
1783 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
1784 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
1785 |
|
right type. |
1786 |
|
o autodiff and RS=real*4: |
1787 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
1788 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
1789 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
1790 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
1791 |
|
o pkg/thsice: |
1792 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
1793 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
1794 |
|
fresh-water flux: uniform correction or proportional to local precip. |
1795 |
|
o pkg/ctrl: |
1796 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
1797 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
1798 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
1799 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
1800 |
|
|
1801 |
|
checkpoint63q (2012/07/30) |
1802 |
|
o pkg/autodiff: |
1803 |
|
note about monitor and snap-shot of ad-variables: |
1804 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
1805 |
|
overlap contributions (was done for adjDump but missing for monitor). |
1806 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
1807 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
1808 |
|
the time-stepping (although mathematically identical). |
1809 |
|
modifs: |
1810 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
1811 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
1812 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
1813 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
1814 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
1815 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
1816 |
|
ad-vars (initially not used by default -> output unchanged). |
1817 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
1818 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
1819 |
|
and both tutorial_tracer_adjsens tests). |
1820 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
1821 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
1822 |
|
o pkg/ctrl: |
1823 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
1824 |
|
generic control variables via |
1825 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
1826 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
1827 |
|
(routine in repository contains example) |
1828 |
|
o pkg/exf: |
1829 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
1830 |
|
o verification (adjoint exp): |
1831 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
1832 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
1833 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
1834 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
1835 |
|
of KE that can occur with aggressive optimization |
1836 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
1837 |
|
using bottomDragQuadratic) |
1838 |
|
o model/src: CG2D_NSA |
1839 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
1840 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
1841 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
1842 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
1843 |
|
RHS ; this fix global_max Pb with TAF); update output. |
1844 |
|
o verification/tutorial_tracer_adjsens: |
1845 |
|
improve parameter consistency (and get rid of warnings): |
1846 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
1847 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
1848 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
1849 |
|
o pkg/exch2: |
1850 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
1851 |
|
reset to 0 = 1 long line in X) |
1852 |
|
o pkg/mdsio: |
1853 |
|
- fix reading of dimensions from meta file for large-size domain |
1854 |
|
o model/src: |
1855 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
1856 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
1857 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
1858 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
1859 |
|
globalArea and to set hasWetCSCorners. |
1860 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
1861 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
1862 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
1863 |
|
useCDscheme and useCubedSphereExchange). |
1864 |
|
o pkg/seaice/seaice_growth.F : |
1865 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
1866 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
1867 |
|
when the previous code was not correct. |
1868 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
1869 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
1870 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
1871 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
1872 |
|
o verification/global_ocean.cs32x15/input.seaice : |
1873 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
1874 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
1875 |
|
- update results (output.seaice.txt) accordingly. |
1876 |
|
o verification/lab_sea/input/data.seaice : |
1877 |
|
- remove SEAICEheatConsFix, which is now be tested |
1878 |
|
in global_ocean.cs32x15. The presently coded fix |
1879 |
|
is only consistent with real fresh water + nlfs. |
1880 |
|
- update results (output.txt) accordingly. |
1881 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
1882 |
|
o AD_CONFIG.h file: |
1883 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
1884 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
1885 |
|
add it explicitly in each fortran src file where it is needed. |
1886 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
1887 |
|
thus introducing potentially wrong dependency; therefore, better to include |
1888 |
|
it only where it's really needed, and after any other included OPTIONS file |
1889 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
1890 |
|
or ALLOW_TANGENTLINEAR_RUN). |
1891 |
|
|
1892 |
|
checkpoint63p (2012/07/06) |
1893 |
|
o pkg/autodiff: |
1894 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
1895 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
1896 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
1897 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
1898 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
1899 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
1900 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
1901 |
|
o verification/tutorial_tracer_adjsens/ |
1902 |
|
- add extra sub-verification which uses "SOM" advection scheme |
1903 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
1904 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
1905 |
|
and in data: |
1906 |
|
multiDimAdvection=.TRUE., |
1907 |
|
tempAdvScheme=81, |
1908 |
|
saltAdvScheme=81, |
1909 |
|
o model/src: |
1910 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
1911 |
|
of the global mean of relaxation terms by setting |
1912 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
1913 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
1914 |
|
This case is now treated appropriately in seaice_growth.F |
1915 |
|
o pkg/seaice: |
1916 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
1917 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
1918 |
|
and EMPMR. Works best in real fresh water. |
1919 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
1920 |
|
out of the diagnotics bloc, and stored in global arrays. |
1921 |
|
|
1922 |
|
checkpoint63o (2012/06/29) |
1923 |
|
o vertical mixing schemes: |
1924 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
1925 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
1926 |
|
to S/R FIND_RHO_SCALAR |
1927 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
1928 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
1929 |
|
affects output (vermix.ggl90) at truncation level. |
1930 |
|
o testreport: |
1931 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
1932 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
1933 |
|
o model/src: |
1934 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
1935 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
1936 |
|
o verification/tutorial_tracer_adjsens/ |
1937 |
|
- compile with ALLOW_CG2D_NSA |
1938 |
|
- run with nonlinFreeSurf=3 |
1939 |
|
- update reference output_adm.txt |
1940 |
|
o tools/genmake2: |
1941 |
|
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
1942 |
|
refine usePROFILES switching off (only when NetCDF is not available). |
1943 |
|
o verification (atmospheric set-up): |
1944 |
|
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
1945 |
|
o pkg/profiles : refine profiles and files handling. |
1946 |
|
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
1947 |
|
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
1948 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
1949 |
|
in ecco type adjoint runs. |
1950 |
|
o model/src: |
1951 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
1952 |
|
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
1953 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
1954 |
|
o model/src: |
1955 |
|
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
1956 |
|
update output of test experiment bottom_ctrl_5x5. |
1957 |
|
o pkg/generic_advdiff: |
1958 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
1959 |
|
only explicitly). |
1960 |
|
o verification/bottom_ctrl_5x5/ |
1961 |
|
update reference output (results changed quite some time ago, |
1962 |
|
not sure when; but new reference results look ok in terms of grdchk) |
1963 |
|
o verification/1D_ocean_ice_column/ |
1964 |
|
For verification purposes, the exact adjoint rather than an approx. |
1965 |
|
should be used (e.g., to comare against F.D. or TLM). |
1966 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
1967 |
|
Update results/ accordingly. |
1968 |
|
o pkg/cal: |
1969 |
|
- change cal_getdate.F so that output date is function of input time only |
1970 |
|
(less ambiguous, not mixed up with input iteration number). |
1971 |
|
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
1972 |
|
o pkg/diagnostics: |
1973 |
|
- implement calendarDumps also for stats-diags |
1974 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
1975 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
1976 |
|
|
1977 |
|
checkpoint63n (2012/06/04) |
1978 |
|
o model/src: |
1979 |
|
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
1980 |
|
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
1981 |
|
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
1982 |
|
similar to calc_r_star.F); update results of experiment internal_wave and |
1983 |
|
tutorial_global_oce_in_p (affected @ truncation level). |
1984 |
|
o pkg/shelfice: |
1985 |
|
- add parameterisation of advective-diffusive flux into the ice shelf |
1986 |
|
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
1987 |
|
- simply eps3/3a computation |
1988 |
|
o eesupp: |
1989 |
|
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
1990 |
|
between tiles, just fill-in edges assuming locally periodic subdomain) and |
1991 |
|
add corresponding exchange subroutines (EXCH0); |
1992 |
|
- new CG-solver version (_EX0) for disconnected-tiles special case. |
1993 |
|
o model/src (CG-solvers): |
1994 |
|
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
1995 |
|
(similar final residual output and max-Iter number as with standard version); |
1996 |
|
- allows to store and use lowest-residual solution (standard & _SR versions); |
1997 |
|
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
1998 |
|
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
1999 |
|
o eesup/src: |
2000 |
|
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
2001 |
|
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
2002 |
|
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
2003 |
|
|
2004 |
|
checkpoint63m (2012/04/27) |
2005 |
|
o pkg/shelfice: |
2006 |
|
- account for partical cells in surface level below ice-shelf for hydrostatic |
2007 |
|
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
2008 |
|
o ad test experiments: |
2009 |
|
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
2010 |
|
particular adjoint verification experiment (in verification/*/code_ad/) |
2011 |
|
o pkg/seaice & pkg/exf: |
2012 |
|
- Part two of ECCO-CLIVAR code merges. |
2013 |
|
Completes merge of seaice area relax. code. |
2014 |
|
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
2015 |
|
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
2016 |
|
(and avoids second CPP option in SEAICE_OPTIONS.h) |
2017 |
|
- change default value of costIceStart & costIceEnd to a valid date. |
2018 |
|
- add snowPrecip to HSNOW in seaice_growth |
2019 |
|
o pkg/ptracers: |
2020 |
|
- move ptracers summary and setup check into separated S/R ; add a check for |
2021 |
|
valid PTRACERS_Iter0 value (error+stop or just warning). |
2022 |
|
o pkg/cal (+ pkg/ecco): |
2023 |
|
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
2024 |
|
as input; and for AD, unless both are not differentiable (e.g., k index)). |
2025 |
|
o model/src: |
2026 |
|
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
2027 |
|
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
2028 |
|
temporary set to usingZCoords value (to be changed to F when using shelfice). |
2029 |
|
- hydrostatic pressure: implement partial cell near the surface also for |
2030 |
|
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
2031 |
|
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
2032 |
|
o pkg/ctrl/ctrl_init.F: |
2033 |
|
- add a formal parameter to s/r ctrl_init_rec to print |
2034 |
|
xx_$(ctrl_valiable)_file for easier debugging |
2035 |
|
- move call of cal_* routines into the if-block where they are really |
2036 |
|
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
2037 |
|
to specify a startdate |
2038 |
|
o pkg/seaice: |
2039 |
|
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
2040 |
|
global_ocean.cs32x15/code versions). |
2041 |
|
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
2042 |
|
verification experiment global_ocean.cs32x15.seaice and update results. |
2043 |
|
o pkg/exf: |
2044 |
|
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
2045 |
|
(according to useExfYearlyFields). |
2046 |
|
o pkg/cal: |
2047 |
|
- move calendar setting & summary (previously in cal_readparams.F) into new |
2048 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
2049 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
2050 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
2051 |
|
- For safety: keep a record of pkg/cal parameter settings status |
2052 |
|
to allow to STOP if one pkg/cal S/R is called too early. |
2053 |
|
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
2054 |
|
- modify cal_getdate.F: stop when nothing was returned; |
2055 |
|
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
2056 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
2057 |
|
|
2058 |
|
checkpoint63l (2012/04/04) |
2059 |
|
o pkg/bbl: |
2060 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
2061 |
|
update global_with_exf output.yearly.txt file. |
2062 |
|
o pkg/cal: |
2063 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
2064 |
|
- remove 2 unsused and very short (1 line only) functions ; |
2065 |
|
- remove unsused subroutines from AD-Diff list. |
2066 |
|
o model/src: |
2067 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
2068 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
2069 |
|
o folowing PRINT_MESSAGE changes: |
2070 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
2071 |
|
o pkg/bbl: |
2072 |
|
- modification so it can work with z* |
2073 |
|
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
2074 |
|
- global_with_exf/input.yearly verification; changes output.yearly.txt |
2075 |
|
o eesupp/src: |
2076 |
|
- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
2077 |
|
writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
2078 |
|
- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
2079 |
|
# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
2080 |
|
- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
2081 |
|
- when using MPI, always set usingMPI=T ; set default accordingly and stop |
2082 |
|
if not consistent. |
2083 |
|
- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
2084 |
|
argument is zero (in case called within single-thread section). |
2085 |
|
o pkg/fizhi: |
2086 |
|
clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
2087 |
|
in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
2088 |
|
o pkg/exch2: |
2089 |
|
- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
2090 |
|
activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
2091 |
|
- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
2092 |
|
but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
2093 |
|
with bad ones coming from a not-yet-updated halo. |
2094 |
|
This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
2095 |
|
o pkg/frazil: |
2096 |
|
move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
2097 |
|
http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
2098 |
|
o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
2099 |
|
o verification/lab_sea |
2100 |
|
* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
2101 |
|
* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
2102 |
|
* nTimeSteps 3 -> 4 |
2103 |
|
* changed reference output accordingly |
2104 |
|
o pkg/ctrl: |
2105 |
|
* fix ctrl_get_gen for xx_sst, xx_sss |
2106 |
|
o pkg/fizhi: |
2107 |
|
- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
2108 |
|
update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
2109 |
|
- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
2110 |
|
fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
2111 |
|
clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
2112 |
|
o pkg/gmredi: |
2113 |
|
- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
2114 |
|
o pkg/fizhi: |
2115 |
|
- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
2116 |
|
(old)aces open64 tuv test. |
2117 |
|
o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
2118 |
|
o pkg/mom_vecinv: |
2119 |
|
- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
2120 |
|
set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
2121 |
|
with non-lin free-surf). |
2122 |
|
o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
2123 |
|
in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
2124 |
|
some compilers (gfortran 4.6.0 on MacOS) |
2125 |
|
o momentum: |
2126 |
|
- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
2127 |
|
& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
2128 |
|
fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
2129 |
|
|
2130 |
|
checkpoint63k (2012/03/17) |
2131 |
|
o model/src: |
2132 |
|
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
2133 |
|
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
2134 |
|
- SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version |
2135 |
|
(#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. |
2136 |
|
o model/src: solve_*diagonal.F |
2137 |
|
- replace division with multiplication by inverse (similar to original version) |
2138 |
|
update output of AD exp. global_ocean.90x40x15. |
2139 |
|
- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
2140 |
|
to enable the use of the vectorized & differentiable solve_tridiagonal.F |
2141 |
|
- test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for |
2142 |
|
vertical advection (to get solve_tridiagonal tested in AD mode). |
2143 |
|
o pkg/seaice: ECCO-CLIVAR merge: |
2144 |
|
1. seaice AREA relaxation |
2145 |
|
* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
2146 |
|
* runtime flag: SEAICE_tauAreaObsRelax |
2147 |
|
2. modified global mean cost imbalance code: CPP option |
2148 |
|
ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
2149 |
|
o another iteration on solve_*diagonal.F |
2150 |
|
Make choices independent of AUTODIFF |
2151 |
|
Default will be the adjoinable vectorized version. |
2152 |
|
Alternative choices are: |
2153 |
|
* non-adjoinable original version with low memory footprint: |
2154 |
|
#define SOLVE_DIAGONAL_LOWMEMORY |
2155 |
|
* still adjoinable but does not vectorize (k as inner-most loop): |
2156 |
|
#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
2157 |
|
o testreport |
2158 |
|
- add option to use a home made wrapper around "make" |
2159 |
|
- remove MITGCM_IEEE env. variable (no longer active) |
2160 |
o pkg/shelfice |
o pkg/shelfice |
2161 |
- improve computation of friction velocity for velocity dependent |
- improve computation of friction velocity for velocity dependent |
2162 |
exchange coefficients: include velocities into SHELFICEBoundaryLayer |
exchange coefficients: include velocities into SHELFICEBoundaryLayer |