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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/cheapaml: |
8 |
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- from Nico Wienders: New version of this package. |
9 |
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o pkg/flt: |
10 |
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- add CPP options to prevent floats to re-enter the opposite side of |
11 |
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a periodic domain (default: keep periodicity) |
12 |
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o pkg/gmredi: |
13 |
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- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
14 |
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(needed for multi-dim advection). |
15 |
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- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
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o model/src: |
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- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
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o tutorial_tracer_adjsens |
19 |
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- extend to NLFS and replace maskC by hFacC |
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(change reference output accordingly) |
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|
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checkpoint62r (2011/01/24) |
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o testreport: |
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- add option -deloutp (-do) to remove output file after successful run |
25 |
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- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
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extract exact list of procs from this file ; adjust COMMAND by |
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replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
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o pkg/ecco: replace old ineffective way of penalizing deviations from |
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first guess (of obcs) with code by Matt Mazloff |
30 |
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o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
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exf/cal |
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- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
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and handle case of obcs?period == 0 |
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Not affected by these changes: There is still an inconsistency in |
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the computation of start/endrec for the obcs variables for ALLOW_CAL |
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defined (see comment by Menemenlis, 7-Mar-2003) |
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- make S/R ctrl_get_gen_rec return something meaningful even if |
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ALLOW_CAL is not defined |
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- ctrl_getobcs?: simplify code so that it does not need to use |
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S/R exf_swapfields |
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o testreport: |
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allow to test MPI with different number of processors for each experiment: |
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create file "SIZE.h.mpi" in each build dir. |
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Note: update of "-command" argument not yet implemented. |
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o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
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alleviate the need for additional 3D tapes when using |
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the non-inear free surface in the adjoint. This is done |
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by adding an 'update' of hfacc etc. to their current |
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value at the beginning of forward_step.F. |
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o pkg/seaice |
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seaice_lsr: move stress-divergence computations out of outer pseudo- |
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timestepping loop |
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o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
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up, so that the calls of the ctrl_* subroutines are really at the end |
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of the routine. |
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o pkg/gmredi: |
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allow to specify a 2-D horizontal map and a 1-D vertical profil |
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as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
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o pkg/seaice: |
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move lsr iterations from seaice_dynsolver to seaice_lsr. |
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o pkg/seaice: |
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reduce memory footprint of seaice mutldim advection tapes, |
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by using a 2D tape independent of the generic_advdiff ones, |
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and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
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|
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checkpoint62q (2010/12/29) |
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o model/src: |
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- check horizontal grid-spacing for unset or zero/negative values. |
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- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
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o pkg/flt: |
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- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
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- precision of input and output files set according to readBinaryPrec |
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and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
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- initial float position from tiled file was not converted to index space |
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(looks like a bug): fixed to make it similar to initial pos. global file. |
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o global_ocean.cs32x15: |
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change SIZE.h of AD set-up to get same tiling as with MPI. |
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Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
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o model/src: |
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add flag to control printing of domain fields (bathymetry, hFac ...) in |
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ini_mask_etc (call to plot_fieds_xy*). |
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o pkg/thsice: |
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if useEXF, some forcing fields are not valid in overlap: fixed by computing |
84 |
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over the interior only + apply EXCH at the end (like with SEAICE advection). |
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o pkg/mdsio: |
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- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
87 |
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to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
88 |
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- change barrier call for safe multi-threads access to 3-D shared buffer. |
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- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
90 |
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- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
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remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
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o pkg/flt: |
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- add fourth-order Runge-Kutta integration |
94 |
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- add basic exch2 support (only 1 facet supported so far!) |
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o pkg/mdsio+rw: |
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new S/R to read local (or tile independent) vector (read counterpart of |
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mds_writevec_loc, and front-end write_glvec_rl/rs). |
98 |
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o global_ocean.cs32x15: additional input_ad.seaice experiment |
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that uses pkg/seaice rather than pkg/thsice. |
100 |
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(using multidim advection for seaice) |
101 |
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o towards more F95 syntax for array specification in namelist: |
102 |
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- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
103 |
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of all verification experiments. |
104 |
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e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
105 |
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was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
106 |
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- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
107 |
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o global_ocean.cs32x15: additional input.seaice experiment |
108 |
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that uses pkg/seaice rather than pkg/thsice. |
109 |
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|
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checkpoint62p (2010/12/17) |
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o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
112 |
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to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
113 |
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o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
114 |
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allow for use of multim. advection in seaice adjoint. |
115 |
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o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
116 |
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- first attempt to close budgets by taking into account the freshwater |
117 |
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flux implied by the sublimation of snow and ice. So far only the |
118 |
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volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
119 |
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SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
120 |
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o eesupp/src: |
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new S/R with new option (NML_EXTENDED_F77) to change array specification |
122 |
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from F95 standard to commonly accepted extended F77 form. |
123 |
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This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
124 |
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and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
125 |
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for less tolerant f77 compiler (e.g., pgf77, g77). |
126 |
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o globalFiles: |
127 |
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commented out in parameter file "data" since it's not safe with MPI |
128 |
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(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
129 |
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in this case); no longer commented out in restart test (tst_2+2). |
130 |
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o add adTapeDir to specify a special directory where adjoint tapes are |
131 |
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written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
132 |
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and cannot be used together with mdsioLocalDir. |
133 |
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o nesting pkgs: |
134 |
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- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
135 |
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- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
136 |
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- add parameter files + utils dir + output from short run on beagle. |
137 |
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o pkg/seaice: |
138 |
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fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
139 |
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o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
140 |
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unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
141 |
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|
142 |
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checkpoint62o (2010/11/25) |
143 |
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o pkg/exf: |
144 |
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- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
145 |
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o pkg/seaice: |
146 |
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- seaice_ocean_stress: split a loop for better vectorization of the |
147 |
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adjoint code |
148 |
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- seaice_growth.F: fix bug in conservation of freshwater connected to |
149 |
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capping of heff, put contribution into d_HEFFbyNEG |
150 |
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- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
151 |
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by something more sensible (parameters that are what their name implies) |
152 |
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- change some defaults, so that by default exf-parameters are used for |
153 |
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things like rhoAir, cpAir,latent/sensible heat parameters, in order |
154 |
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to reproduce the old results, many data.seaice now contain funny values |
155 |
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for cpAir and latent heat of sublimation |
156 |
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o packages_readparms.F: move exf_readparms up in line so that |
157 |
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exf-parameters are visible for other packages (e.g. seaice) |
158 |
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o debugMode & debugLevel=2: |
159 |
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- differentiate between debugMode & debugLevel=2: |
160 |
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debugMode: controls printing of debug messages (sequence of S/R calls). |
161 |
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debugLevel: controls printing of algorithm intermediate results and stats. |
162 |
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- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
163 |
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=> allows to print debug-stats without all sequence of call messages. |
164 |
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- switch control of debug print from debugLevel to debugMode in many S/R. |
165 |
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o pkg/obcs (obcs-sponge): |
166 |
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fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
167 |
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call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
168 |
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o pkg/generic_advdiff: |
169 |
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- record overlap minimum size for each advection scheme; |
170 |
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- refine criteria on overlap minimum size; |
171 |
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- check and stop (in gad_check) if overlap size is too small. |
172 |
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o pkg/obcs: |
173 |
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- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
174 |
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once, in ptracers_implicit.F) |
175 |
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- with seaice: remove test on empty file name in obcs_apply_seaice (always |
176 |
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apply OB values when tile has OB) |
177 |
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o model/src, coriolis setting: |
178 |
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- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
179 |
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useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
180 |
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files (selectCoriMap=3) with any grid. |
181 |
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- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
182 |
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o pkg/seaice/seaice_growth.F: |
183 |
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a few cosmetic changes that reduce the number of lines of code |
184 |
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o pkg/obcs: add boundary conditions following Stevens (1990) |
185 |
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- the code follows old MOM/NAOSIM code |
186 |
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- so far it is only implemented for the eastern and western boundaries |
187 |
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and NOT for pTracers |
188 |
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o pkg/rbcs: |
189 |
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- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
190 |
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beginning of the first rbcs forcing period. |
191 |
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- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
192 |
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offline package, i.e., one file per time, labeled by iteration number; |
193 |
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deltaTrbcs sets the timestep with which the data was generated; |
194 |
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rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
195 |
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- rbcsForcingCycle=0 makes forcing non-cyclic. |
196 |
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- make arithmetic safe for negative times and odd forcing periods. |
197 |
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|
198 |
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checkpoint62n (2010/11/09) |
199 |
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o pkg/seaice: |
200 |
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fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
201 |
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o pkg/obcs: |
202 |
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New S/R to copy tracer value from the OB location to narrow band region |
203 |
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(width = same as overlap) beyond the OB: preserve OB value (needed for |
204 |
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high-order scheme) which were overwritten by EXCH call if in overlap |
205 |
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region. Applied to theta, salt, ptracer and advected seaice variables. |
206 |
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With seaice: use maskInC in similar way as in gad_advection.F, |
207 |
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in seaice_advection.F and advect.F. |
208 |
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Update output of experiment seaice_obcs and change exp4 to test OBCS with |
209 |
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4th order Adv.Scheme. for pasive salt and ptracer. |
210 |
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o tools/genmake2: |
211 |
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- when looking for an optfile (not specified), only search for Fortran compiler |
212 |
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(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
213 |
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- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
214 |
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(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
215 |
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- set default for CPP to "cpp -traditional -P" (was the case without specifying |
216 |
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an optfile, but otherwise default was just "cpp". |
217 |
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- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
218 |
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- when "CC" is not set in the optfile, look for possible C compiler |
219 |
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(instead of just setting CC=cc) |
220 |
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- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
221 |
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=> add a ".F" to ".o" rule for source files with no "#include" (such as |
222 |
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port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
223 |
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- move gfortran before g77 in list of possible Fortran compiler (consistent |
224 |
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with reference compiler switch from g77 to gfortran) |
225 |
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o pkg/seaice: |
226 |
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o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
227 |
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seaice_check that stops the model, when the CPP flag is used. |
228 |
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o seaice_growth.F: make capping of ice volume conserving by returning the |
229 |
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capped ice as freshwater to EmPmR. This does not change the verification |
230 |
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experiments but will change runs where the capping is acutally active |
231 |
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o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
232 |
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(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
233 |
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global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
234 |
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lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
235 |
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o tools/genmake2: |
236 |
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- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
237 |
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- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
238 |
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- clean previous genmake log files before anything else. |
239 |
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- change Makefile to remove testreport log files (*.tr_log) and genmake log |
240 |
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files only with "CLEAN" target (instead of "Clean"); |
241 |
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o pkg/generic_advdiff: |
242 |
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Change OBCS in multiDim advection (gad_advection.F): |
243 |
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Use maskInC to prevent intermediate update of tracer-field in OB regions, |
244 |
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thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
245 |
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which were applying future time-step OB values. |
246 |
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This way, all explicit calculations use current-time-step OB values |
247 |
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(simpler and more consistent). |
248 |
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Affects results when set-up uses time-varying OBC and multi-dim advection; |
249 |
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update output of experiment seaice_obcs. |
250 |
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o pkg/seaice: |
251 |
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move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
252 |
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this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
253 |
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SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
254 |
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Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
255 |
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but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
256 |
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unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
257 |
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o pkg aim (2010/10/26): |
258 |
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- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
259 |
|
formulation with obliquity, eccentricity, ... as run-time parameters, |
260 |
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- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
261 |
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upward shortwave radition at the surface (all-sky and clear-sky). |
262 |
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o pkg/obcs: |
263 |
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- writing sections with globalFiles=T does not work: switch to tiled-files |
264 |
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when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
265 |
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- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
266 |
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- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
267 |
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|
268 |
|
checkpoint62m (2010/10/21) |
269 |
o pkg/seaice: vectorize seaice_solve4temp.F |
o pkg/seaice: vectorize seaice_solve4temp.F |
270 |
- move iterations loops outside of i/j-loops |
- move iterations loops outside of i/j-loops |
271 |
- requires 2D arrays for TB and effConduct |
- requires 2D arrays for TB and effConduct |
272 |
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
273 |
modified in this routine |
modified in this routine |
274 |
- a little bit of clean up, adjusting indentation, etc. |
- a little bit of clean up, adjusting indentation, etc. |
275 |
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
276 |
performance and '**TWO' by '**2' (because TWO is a float), |
performance and '**TWO' by '**2' (because TWO is a float), |
277 |
replaced ONE, ZERO |
replaced ONE, ZERO |
278 |
o eesupp/src: |
o eesupp/src: |
279 |
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
675 |
but keep the former optfile for few weeks for smooth transition |
but keep the former optfile for few weeks for smooth transition |
676 |
o pkg/ecco |
o pkg/ecco |
677 |
- allow user defined cost function contributions |
- allow user defined cost function contributions |
678 |
CPP: ALLOW_USERCOST_CONTRIBUTION |
CPP: ALLOW_USERCOST_CONTRIBUTION |
679 |
USAGE: compute contributions in cost_usercost_all.F |
USAGE: compute contributions in cost_usercost_all.F |
680 |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
681 |
the two options are complementary. |
the two options are complementary. |
682 |
o pkg/smooth |
o pkg/smooth |