4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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|
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o nesting pkgs: |
8 |
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- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
9 |
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- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
10 |
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- add parameter files + utils dir + output from short run on beagle. |
11 |
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o pkg/seaice: |
12 |
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fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
13 |
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o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
14 |
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unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
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|
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checkpoint62o (2010/11/25) |
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o pkg/exf: |
18 |
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- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
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o pkg/seaice: |
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- seaice_ocean_stress: split a loop for better vectorization of the |
21 |
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adjoint code |
22 |
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- seaice_growth.F: fix bug in conservation of freshwater connected to |
23 |
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capping of heff, put contribution into d_HEFFbyNEG |
24 |
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- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
25 |
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by something more sensible (parameters that are what their name implies) |
26 |
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- change some defaults, so that by default exf-parameters are used for |
27 |
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things like rhoAir, cpAir,latent/sensible heat parameters, in order |
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to reproduce the old results, many data.seaice now contain funny values |
29 |
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for cpAir and latent heat of sublimation |
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o packages_readparms.F: move exf_readparms up in line so that |
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exf-parameters are visible for other packages (e.g. seaice) |
32 |
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o debugMode & debugLevel=2: |
33 |
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- differentiate between debugMode & debugLevel=2: |
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debugMode: controls printing of debug messages (sequence of S/R calls). |
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debugLevel: controls printing of algorithm intermediate results and stats. |
36 |
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- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
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=> allows to print debug-stats without all sequence of call messages. |
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- switch control of debug print from debugLevel to debugMode in many S/R. |
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o pkg/obcs (obcs-sponge): |
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fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
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call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
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o pkg/generic_advdiff: |
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- record overlap minimum size for each advection scheme; |
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- refine criteria on overlap minimum size; |
45 |
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- check and stop (in gad_check) if overlap size is too small. |
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o pkg/obcs: |
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- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
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once, in ptracers_implicit.F) |
49 |
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- with seaice: remove test on empty file name in obcs_apply_seaice (always |
50 |
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apply OB values when tile has OB) |
51 |
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o model/src, coriolis setting: |
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- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
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useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
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files (selectCoriMap=3) with any grid. |
55 |
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- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
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o pkg/seaice/seaice_growth.F: |
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a few cosmetic changes that reduce the number of lines of code |
58 |
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o pkg/obcs: add boundary conditions following Stevens (1990) |
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- the code follows old MOM/NAOSIM code |
60 |
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- so far it is only implemented for the eastern and western boundaries |
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and NOT for pTracers |
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o pkg/rbcs: |
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- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
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beginning of the first rbcs forcing period. |
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- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
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offline package, i.e., one file per time, labeled by iteration number; |
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deltaTrbcs sets the timestep with which the data was generated; |
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rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
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- rbcsForcingCycle=0 makes forcing non-cyclic. |
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- make arithmetic safe for negative times and odd forcing periods. |
71 |
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|
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checkpoint62n (2010/11/09) |
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o pkg/seaice: |
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fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
75 |
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o pkg/obcs: |
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New S/R to copy tracer value from the OB location to narrow band region |
77 |
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(width = same as overlap) beyond the OB: preserve OB value (needed for |
78 |
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high-order scheme) which were overwritten by EXCH call if in overlap |
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region. Applied to theta, salt, ptracer and advected seaice variables. |
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With seaice: use maskInC in similar way as in gad_advection.F, |
81 |
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in seaice_advection.F and advect.F. |
82 |
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Update output of experiment seaice_obcs and change exp4 to test OBCS with |
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4th order Adv.Scheme. for pasive salt and ptracer. |
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o tools/genmake2: |
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- when looking for an optfile (not specified), only search for Fortran compiler |
86 |
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(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
87 |
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- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
88 |
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(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
89 |
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- set default for CPP to "cpp -traditional -P" (was the case without specifying |
90 |
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an optfile, but otherwise default was just "cpp". |
91 |
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- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
92 |
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- when "CC" is not set in the optfile, look for possible C compiler |
93 |
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(instead of just setting CC=cc) |
94 |
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- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
95 |
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=> add a ".F" to ".o" rule for source files with no "#include" (such as |
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port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
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- move gfortran before g77 in list of possible Fortran compiler (consistent |
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with reference compiler switch from g77 to gfortran) |
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o pkg/seaice: |
100 |
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o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
101 |
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seaice_check that stops the model, when the CPP flag is used. |
102 |
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o seaice_growth.F: make capping of ice volume conserving by returning the |
103 |
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capped ice as freshwater to EmPmR. This does not change the verification |
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experiments but will change runs where the capping is acutally active |
105 |
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o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
106 |
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(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
107 |
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global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
108 |
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lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
109 |
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o tools/genmake2: |
110 |
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- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
111 |
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- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
112 |
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- clean previous genmake log files before anything else. |
113 |
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- change Makefile to remove testreport log files (*.tr_log) and genmake log |
114 |
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files only with "CLEAN" target (instead of "Clean"); |
115 |
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o pkg/generic_advdiff: |
116 |
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Change OBCS in multiDim advection (gad_advection.F): |
117 |
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Use maskInC to prevent intermediate update of tracer-field in OB regions, |
118 |
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thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
119 |
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which were applying future time-step OB values. |
120 |
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This way, all explicit calculations use current-time-step OB values |
121 |
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(simpler and more consistent). |
122 |
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Affects results when set-up uses time-varying OBC and multi-dim advection; |
123 |
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update output of experiment seaice_obcs. |
124 |
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o pkg/seaice: |
125 |
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move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
126 |
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this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
127 |
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SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
128 |
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Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
129 |
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but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
130 |
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unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
131 |
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o pkg aim (2010/10/26): |
132 |
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- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
133 |
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formulation with obliquity, eccentricity, ... as run-time parameters, |
134 |
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- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
135 |
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upward shortwave radition at the surface (all-sky and clear-sky). |
136 |
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o pkg/obcs: |
137 |
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- writing sections with globalFiles=T does not work: switch to tiled-files |
138 |
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when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
139 |
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- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
140 |
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- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
141 |
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|
142 |
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checkpoint62m (2010/10/21) |
143 |
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o pkg/seaice: vectorize seaice_solve4temp.F |
144 |
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- move iterations loops outside of i/j-loops |
145 |
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- requires 2D arrays for TB and effConduct |
146 |
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- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
147 |
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modified in this routine |
148 |
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- a little bit of clean up, adjusting indentation, etc. |
149 |
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- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
150 |
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performance and '**TWO' by '**2' (because TWO is a float), |
151 |
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replaced ONE, ZERO |
152 |
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o eesupp/src: |
153 |
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fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
154 |
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o pkg/seaice/seaice_growth.F |
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Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and |
156 |
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merging process. The merged routine has two branches, and one activates the 'evolution' |
157 |
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branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). |
158 |
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In summary, here is what the '10/10 revision' did consist of |
159 |
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part 1: seaice_growth.F revisions 1.71 to 1.75 |
160 |
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- Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. |
161 |
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The emphasis here was on improving readability (e.g. by trying to use meaningful |
162 |
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variable names) and modularity (e.g. by adding arrays to store heff etc. updates). |
163 |
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part 1.5: |
164 |
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- revising the lab_sea experiment to make it a more useful (i.e. stable |
165 |
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and representative of an actual model run). This was done by generating a |
166 |
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(winter) pickup to start from, switching back the main experiment dynamic |
167 |
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solver from evp to lsr, having one of the experiments use the free drift solution. |
168 |
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part 2: seaice_growth.F revisions 1.76 to 1.85 |
169 |
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- Sorting out hard-coded constants that prevented heat and fresh water conservation. |
170 |
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- Sorting out the various fields units and sign (set early on and reset at the end) |
171 |
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to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and |
172 |
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fresh water stock is 'effective ice meters', and >0 implies more ice/snow. |
173 |
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- Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, |
174 |
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and simplifying logical expressions to further improve readibility. |
175 |
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part 3: seaice_growth.F revisions 1.86 to 1.89 |
176 |
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- Re-organize the blocks of code more logically. |
177 |
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- Merging the '_if.F' pieces that add something new. |
178 |
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o pkg/thsice: |
179 |
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- vectorize thsice_solve4temp and thsice_get_exf. |
180 |
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Problem: thsice_solve4temp has an unvectorizable statement that |
181 |
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might also be problematic for TAF |
182 |
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- thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This |
183 |
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does not change the verifcation experiment, but will change all |
184 |
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experiments that have this flag undefined (not tested in verification); |
185 |
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a little reorganization to save a few 2D fields and recomputations |
186 |
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- 1st step of revisiting thsice adjoint (major recomp. sorted out) |
187 |
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- 2nd step: fix some store dirs |
188 |
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o seems to work somewhat, i.e. using ifort but not g77 |
189 |
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o likely cause are incomplete init. or recomputation |
190 |
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o start verification/global_ocean.cs32x15/input_ad.thsice |
191 |
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o pkg/obcs: add support for exch2 |
192 |
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- the position of the boundary and prescribed values are specified using |
193 |
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a global domain with exch2 facets stacked |
194 |
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- in x for N,S boundaries (like W2_mapIO=-1) |
195 |
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- in y for E,W boundaries (so E,W boundaries do not overlap) |
196 |
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o pkg/mdsio: add support for writing global sections with exch2 |
197 |
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file layout is as for obcs described above: |
198 |
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- for x-z sections, facets are stacked in x (like W2_mapIO=-1) |
199 |
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- for y-z sections, facets are stacked in y |
200 |
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o pkg/thsice: |
201 |
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- change a few routines for better vectorization: thsice_albedo.F, |
202 |
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thsice_step_temp.F, and in thsice_calc_thickn.F. Results are |
203 |
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not affected, but in particular the latter routine has changed |
204 |
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dramatically (not necessarily easier to read now). |
205 |
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- re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops |
206 |
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iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. |
207 |
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o verification/lab_sea: |
208 |
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- overhaul of the forward model experiments. The main motivation |
209 |
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for this revision is that lab_sea has proven quite fragile (when |
210 |
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changing the sea-ice code, and switching platforms) to a point |
211 |
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when failures were very hard to attribute to specific code problems. |
212 |
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- the suspected reason for this fragility is noise amplification by evp so, |
213 |
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to start with, we decided to replace evp with lsr in the main experiment. |
214 |
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- the input.lsr experiment thus became obsolete and was removed. |
215 |
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- it was replaced with the input.fd experiment that uses an |
216 |
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analytical "free drift" solution as the ice velocity field. |
217 |
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- Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) |
218 |
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will hopefully allow us to discriminate problems due to dynamic solvers |
219 |
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from problems due to the thermodynamic code. input.salt_plume (lsr) allows |
220 |
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us to test additional options, along with the salt plume package. |
221 |
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- Finally a pickup was generated (at the end of a one year run) to |
222 |
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make the tests more representative of an actual model run. Previously |
223 |
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the tests starting point was a 1m thickness of ice everywhere. |
224 |
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o pkg/seaice: |
225 |
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- introducing S\R seaice_freedrift.F that compute the |
226 |
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analytical solution to an approximate ice momentum |
227 |
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equation (i.e. the simple stress/coriolis balance). |
228 |
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- define SEAICE_ALLOW_FREEDRIFT to trigger the computation |
229 |
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of the free drift velocity field, and enable its use. |
230 |
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To actually use the free drift solution as the model ice |
231 |
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velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. |
232 |
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o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" |
233 |
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|
234 |
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checkpoint62l (2010/10/04) |
235 |
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o pkg/seaice: |
236 |
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-fix the USE_ORIGINAL_SBI version (for variable freezing point); |
237 |
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-use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new |
238 |
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version (with USE_ORIGINAL_SBI undef); |
239 |
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o add hooks for new packages OASIS, the package will follow |
240 |
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(hooks exclude the seaice pkg for now) |
241 |
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o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
242 |
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Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
243 |
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rather than mdsio_readvector.F/mdsio_writevector.F, within |
244 |
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adread_adwrite.F to read/write adjoint-related tapes to disk. |
245 |
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o eesupp and pkg/mdsio: ALLOW_WHIO |
246 |
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Option to write/read 2D fields to files including tiles halos. |
247 |
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The main purpose is for adjoint related "tape I/O". |
248 |
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The secondary purpose is for debugging phases. |
249 |
|
A word on those rather specifically intended purposes. |
250 |
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The code was meant to be stripped down to the bare minimum. |
251 |
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Typically, there is a unique and basic mapping to the global |
252 |
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buffer (tile by tile, then proc by proc, then level by level), and |
253 |
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byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
254 |
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meant to generate user friendly outputs of various shapes and forms. |
255 |
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Rather it is intended, for the knowledgeabale developers, |
256 |
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to be largely independent of the many mdsio options, to allow |
257 |
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outputs of tiles+halos in debugging phases and in adjoint runs, |
258 |
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and to allow some flexibility in tuning (adoint) I/O depending on each |
259 |
|
file system behavior. With regard to tuning, most of the potential knobs |
260 |
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(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
261 |
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to specify directories, to specify the typical size of I/O calls, etc.) |
262 |
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are not yet included, and will be added if they prove useful. |
263 |
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o pkg/seaice: |
264 |
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fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
265 |
|
o pkg/seaice: |
266 |
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new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
267 |
|
code (seaice_budget_ice_if.F) which enable to recover old standard |
268 |
|
code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
269 |
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temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
270 |
|
o model/src (rStar): |
271 |
|
use simple average (not area weighted) of rStarFac at U,V point when using |
272 |
|
vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
273 |
|
update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
274 |
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|
275 |
|
checkpoint62k (2010/09/17) |
276 |
|
o adjoint |
277 |
|
* changed verification/global_ocean.cs32x15 ; adjoint now tests |
278 |
|
Adams-Bashforth 3 + NLFS + RSTAR |
279 |
|
* some more modifs required for ECCO-GODAE v4 |
280 |
|
o pkg/seaice |
281 |
|
add SEAICE_AGE_VOL option to use volume instead of area for |
282 |
|
integrating SEAICE_AGE |
283 |
|
o model/src: |
284 |
|
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
285 |
|
non-linear free-surface parts ; but pressure-gradient not yet coded. |
286 |
|
o pkg/ptracers: |
287 |
|
option for ptracer to convert Salt Relax into additional EmP. |
288 |
|
tested in exp. global_ocean.90x40x15.dwnslp (update output) |
289 |
|
|
290 |
|
checkpoint62j (2010/08/25) |
291 |
|
o pkg/ggl90: |
292 |
|
other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
293 |
|
o pkg/dic: car_flux.F, phos_flux.F |
294 |
|
- reduce number of exp-calls in order to improve performance |
295 |
|
- clean up a little (replace fields by their macros, etc., fix |
296 |
|
typo in CPP-flag) |
297 |
|
o pkg/ggl90: minor changes |
298 |
|
- GGL90diffKrS was removed --> always use GGL90diffKr |
299 |
|
- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
300 |
|
- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
301 |
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(commented out for now) |
302 |
|
- change in max/min operations to ensure that smoothing is ok |
303 |
|
- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
304 |
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- always use diffKrNrT as background profile (i.e. never use diffKr field) |
305 |
|
o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
306 |
|
o pkg/dic: |
307 |
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- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
308 |
|
vectorization |
309 |
|
- small bug fix in insol for the unlikely case of a cartesian grid |
310 |
|
- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
311 |
|
+ now vectorize, which also removes adjoint recomputations; |
312 |
|
+ replace integer maksp1 by _RL maskp1 |
313 |
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+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
314 |
|
|
315 |
|
checkpoint62i (2010/07/21) |
316 |
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o pkg/flt: |
317 |
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- with OBCS: stop floats which enter the OB region |
318 |
|
o model/src: |
319 |
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- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
320 |
|
for implicit vertical advection. |
321 |
|
o pkg/seaice: |
322 |
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- account for melting in seaice age evolution. |
323 |
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- remove double counting of seaice ridging effect on seaice age. |
324 |
|
|
325 |
|
checkpoint62h (2010/06/18) |
326 |
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o pkg/exch2: |
327 |
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- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
328 |
|
o tools/genmake2 |
329 |
|
- remove "-pdefault" option: redundant with the use of "packages.conf"; |
330 |
|
- remove file pkg/pkg_default : set the default as a pkg group |
331 |
|
("default_pkg_list") defined in pkg/pkg_groups; |
332 |
|
- fix for case pkg/pkg_depend is missing (was hanging before); |
333 |
|
- add option "-pgroups" to specify a different pkg_groups than the default. |
334 |
|
o verification/adjustment.cs-32x32x1: |
335 |
|
add a "minimal" set-up test (code_min & input_min) which only compiles |
336 |
|
eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
337 |
|
o tools/genmake2 |
338 |
|
- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
339 |
|
- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
340 |
|
o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
341 |
|
files are nearly the same anyway. |
342 |
|
Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
343 |
|
- redefinition of tau(i,i) (by a factor of ustar) |
344 |
|
- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
345 |
|
- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
346 |
|
- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
347 |
|
- replace |
348 |
|
rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
349 |
|
shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
350 |
|
by |
351 |
|
shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
352 |
|
(changes results) |
353 |
|
-> exf_bulkformulae v1.22, |
354 |
|
update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
355 |
|
(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
356 |
|
output.txt 1.63 |
357 |
|
offline_exf_seaice: output.seaicetd.txt 1.7 |
358 |
|
seaice_obcs: output.txt 1.10) |
359 |
|
Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
360 |
|
-> exf_bulkformulae v1.23, |
361 |
|
unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
362 |
|
and global_ocean.cs32x15.icedyn (only 11 matching digits) |
363 |
|
Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
364 |
|
o adjoint of exch-1: |
365 |
|
- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
366 |
|
(note: was already like this when using EXCH-2) and remove flow dir |
367 |
|
and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
368 |
|
- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
369 |
|
- update pkg/exch2 diff list. |
370 |
|
|
371 |
|
checkpoint62g (2010/05/19) |
372 |
|
o eesupp/src (exch-1): |
373 |
|
- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
374 |
|
and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
375 |
|
(renamed to exch1_*rx_cube.F). |
376 |
|
- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
377 |
|
to call new exch1 S/R ; update Makefile and .cvsignore. |
378 |
|
- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
379 |
|
exch2_xy_rx later) |
380 |
|
Note: after updating your code, need to run "make clean" in eesupp/src |
381 |
|
o test experiment bottom_ctrl_5x5: |
382 |
|
new output_adm.txt with fewer grdchk & less monitor output. |
383 |
|
o model/src: |
384 |
|
remove the call to ini_cori in initialise_varia.F (just keep the usual one |
385 |
|
in initialise_fixed.F). More consistent with coriolis & horizontal grid |
386 |
|
beeing treated in the same way (ini_grid is not called a 2nd time). |
387 |
|
o pkg/exf: |
388 |
|
- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
389 |
|
global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
390 |
|
- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
391 |
|
- cosmetic changes to exf_bulkformulae.F to make it look more like |
392 |
|
exf_bulk_largeyeager04.F |
393 |
|
o eesupp/src (exch-1): |
394 |
|
- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
395 |
|
- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
396 |
|
array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
397 |
|
(even without using MPI). |
398 |
|
- Message mode: move RecvAck setting (indicator of buffer being ready) |
399 |
|
from send_put to recv_get S/R (was useless before, but not sure if |
400 |
|
it's much more useful now); |
401 |
|
- Switch the order of sync: MPI-proc 1rst and then threads; |
402 |
|
- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
403 |
|
- fix AD code for communication mode ='get' (but not used). |
404 |
|
o model/src: |
405 |
|
initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
406 |
|
not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
407 |
|
o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
408 |
|
o pkg/ctrl: require a specific set of control variables and exf-flags for |
409 |
|
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
410 |
|
o model/src: |
411 |
|
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
412 |
|
1rst forward sweep, to avoid over-writing output files during recomputations |
413 |
|
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
414 |
|
b) 2nd version: |
415 |
|
- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
416 |
|
- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
417 |
|
writePickupAtEnd) + seaice & ptracers output; |
418 |
|
- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
419 |
|
o model/src: |
420 |
|
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
421 |
|
o pkg/exch2: |
422 |
|
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
423 |
|
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
424 |
|
o pkg/autodiff & exch2: |
425 |
|
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
426 |
|
(for now, only if ALLOW_EXCH2 is defined). |
427 |
|
o pkg/autodiff: |
428 |
|
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
429 |
|
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
430 |
|
+ clean-up comments (_RS is not always real*4) |
431 |
|
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
432 |
|
- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
433 |
|
was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
434 |
|
o testreport (AD-tests): |
435 |
|
no longer link files from dir "../input" (1rst link files from |
436 |
|
"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
437 |
|
|
438 |
|
checkpoint62f (2010/04/29) |
439 |
|
o model/src/the_main_loop.F: |
440 |
|
adjust store directives for seaice evp and multicategory according to |
441 |
|
pkg/ecco/the_main_loop.F |
442 |
|
o adjoint: |
443 |
|
global_sum_ad was incomplete (noted many times by many people ;) |
444 |
|
nice description by Jean U. as follows: |
445 |
|
* allreduce(var) in global_sum.F can be interpreted as |
446 |
|
reduce(sum) followed by broadcast of sum. |
447 |
|
* The adjoint of that is |
448 |
|
sum(adjoint) followed by broadcast(summed adjoint value) |
449 |
|
or in other words, allreduce(sum, adjoint vars) |
450 |
|
We were missing the sum(adjoint)! |
451 |
|
Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
452 |
|
(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
453 |
|
The fix should produce 16-digit accuracy between |
454 |
|
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
455 |
|
multi-CPU single-tile (e.g. nSx=1, nPx-2) |
456 |
|
We'll probably change this yet again shortly |
457 |
|
o eesupp/src: |
458 |
|
- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
459 |
|
o pkg/icefront |
460 |
|
- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
461 |
|
specification of addmass array based on a 2D field, which is added |
462 |
|
at bottommost wet level at each horizontal location. |
463 |
|
o model/src: |
464 |
|
horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
465 |
|
layout; (not always compatible with delX,delY setting; commented out for now). |
466 |
|
o pkg/exch2: |
467 |
|
change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
468 |
|
(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
469 |
|
|
470 |
|
checkpoint62e (2010/04/15) |
471 |
|
o pkg/obcs: |
472 |
|
- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
473 |
|
o pkg/dic: |
474 |
|
-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
475 |
|
(note: not presently tested in any forward verification exp.) |
476 |
|
update tutorial_global_oce_biogeo AD output file. |
477 |
|
o pkg/exf: |
478 |
|
- account for the variation of albedo as a function of zenith angle |
479 |
|
by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
480 |
|
o build_options: |
481 |
|
- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
482 |
|
o pkg/dic: |
483 |
|
change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
484 |
|
- use binary pickup file for restart; |
485 |
|
- initialise atmos-CO2 box from dic_pCO2 parameter; |
486 |
|
- fix multi-threaded. |
487 |
|
o pkg/rbcs: |
488 |
|
- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
489 |
|
change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
490 |
|
- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
491 |
|
and update output.txt |
492 |
|
o pkg/kpp: |
493 |
|
- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
494 |
|
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
495 |
|
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
496 |
|
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
497 |
|
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
498 |
|
KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
499 |
|
o pkg/offline: |
500 |
|
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
501 |
|
(bug was added in version 1.10 on 2007-08-23). |
502 |
|
o pkg/offline: |
503 |
|
- no need to specify periodicExternalForcing, etc ... to use offline pack |
504 |
|
- offline input files no longer just single prec --> parameter offlineLoadPrec |
505 |
o verification/lab_sea: |
o verification/lab_sea: |
506 |
change to multi-tile setup. |
change AD test to multi-tile setup and update all 4 AD output. |
507 |
NOTE: while cost function values remain very similar, |
NOTE: while cost function values remain very similar, |
508 |
gradients are very different, although gradient checks are self-consistent |
gradients are very different, although gradient checks are self-consistent |
509 |
Should try to get to the bottom of this (cost function summation order?) |
Should try to get to the bottom of this (cost function summation order?) |
549 |
but keep the former optfile for few weeks for smooth transition |
but keep the former optfile for few weeks for smooth transition |
550 |
o pkg/ecco |
o pkg/ecco |
551 |
- allow user defined cost function contributions |
- allow user defined cost function contributions |
552 |
CPP: ALLOW_USERCOST_CONTRIBUTION |
CPP: ALLOW_USERCOST_CONTRIBUTION |
553 |
USAGE: compute contributions in cost_usercost_all.F |
USAGE: compute contributions in cost_usercost_all.F |
554 |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
555 |
the two options are complementary. |
the two options are complementary. |
556 |
o pkg/smooth |
o pkg/smooth |