Parent Directory | Revision Log | Revision Graph | Patch
revision 1.334 by jmc, Sat Jul 24 02:47:35 2004 UTC | revision 1.1048 by jmc, Tue Dec 30 18:00:09 2008 UTC | |
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# | Line 1 | Line 1 |
1 | $Header$ | $Header$ |
2 | $Name$ | |
3 | ||
4 | Notes on tags used in MITgcmUV | Notes on tags used in MITgcmUV |
5 | ============================== | ============================== |
6 | ||
7 | o pkg/mdsio: read/write vector: | |
8 | - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS | |
9 | - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR | |
10 | & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. | |
11 | - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) | |
12 | (drop to 4 digits matching for grad). But this test does not look very | |
13 | reliable (was already failling on eddy, fc5, at 6.digits). Update output. | |
14 | ||
15 | checkpoint61g | |
16 | o pkg/flt: | |
17 | - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) | |
18 | + make OPTIONS file more standard. | |
19 | - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) | |
20 | - fix _BYTESWAPIO CPP-Flag | |
21 | - standard reading of file-parameter "data.flt" | |
22 | - fix argument list of S/R FLT_RESTART | |
23 | still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F | |
24 | o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell | |
25 | o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to | |
26 | a still unfixed compiler/optimization bug | |
27 | ||
28 | checkpoint61f | |
29 | o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; | |
30 | update results of global_ocean.cs32x15.icedyn test. | |
31 | o move getcon.F from model/src to pkg/fizhi. | |
32 | o pkg/exf: add parameter for extrapolation of temp up to the surface | |
33 | and option to prevent negative evap (in bulk_largeyeager04 only). | |
34 | o Prather Advection scheme: fix tracer conservation for divergent flow | |
35 | (e.g., when using NonLin Free-Surface). | |
36 | o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead | |
37 | o gmredi (Visbeck-variable-K): | |
38 | - add more parameters to Visbeck-variable-K. | |
39 | - use a 5 points average for dSigmaR in Visbeck-K calculation | |
40 | (more "homogenous": same stencil and same weights as in dSigmaH) | |
41 | - update output of ideal_2D_oce experiment. | |
42 | o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 | |
43 | (#undef REAL4_IS_SLOW) | |
44 | - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 | |
45 | coordinate variable | |
46 | - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables | |
47 | (surface forcing fields), removes some of the functionality | |
48 | - model/src/write_grid.F: write _RS variables as RS-netcdf variables | |
49 | - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but | |
50 | probably not all: copy _RS surface flux fields to RL field before | |
51 | calling DIAGNOSTICS_FILL | |
52 | - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into | |
53 | real*4 (CALL EXCH_*_RS) versions. | |
54 | - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 | |
55 | (generate new output). | |
56 | ||
57 | checkpoint61e | |
58 | o gmredi (Visbeck-variable-K): | |
59 | - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h | |
60 | - change computation of Visbeck-K where Slope > Smax : | |
61 | now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) | |
62 | previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. | |
63 | o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic | |
64 | to be the same as with Z-coord. (i.e., m/s & no-units respectively). | |
65 | o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) | |
66 | o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz | |
67 | does not become too large (to avoid precision problems in implicit-diffusion | |
68 | solver); update ideal_2D_oce output. | |
69 | o pkg ggl90: | |
70 | - in ggl90_cal.F: compute only one set of visc/diff, used to | |
71 | step forward TKE/T/S/momentum | |
72 | - default value of GGL90viscMax/GGL90diffMax larger and equal (to | |
73 | have Prandlt =1) | |
74 | o gmredi (fm07): | |
75 | - add lower limit on Transition layer thickness + lower limit on 1/lambda | |
76 | - allow to set few more params from data.gmredi | |
77 | o pkg ggl90: | |
78 | - add missing sqrt(2) factor in computation of mixing length | |
79 | scale in ggl90_calc.F | |
80 | (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) | |
81 | ||
82 | checkpoint61d | |
83 | o adjoint modifs | |
84 | - adapt to new field rhoInSitu | |
85 | - allow to revert from StoreDynVars2D, StoreDynVars3D | |
86 | to individual fields | |
87 | (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) | |
88 | o store 3-D (in-situ) density in commom block (DYNVARS.h) | |
89 | - save 1 rho computation. | |
90 | - no longer modify T & S inland when using down_slope pkg. | |
91 | o gad_som : allow to switch to SOM advection for T & S without corresponding | |
92 | pickup files (using new S/R: MDS_CHECK4FILE). | |
93 | o keep removing _BEGIN/_END_MASTER between MDSIO S/R call | |
94 | (for useSingleCpuIO to work in multi-threaded) | |
95 | o pkg/shelfice: | |
96 | - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute | |
97 | with SHELFICEtopoFile in data.shelfice | |
98 | - move code for reading ice shelf topography and modifying hFacC into separate | |
99 | subroutines of the shelfice package | |
100 | - separate initialisation of "fixed" and "variable" variables | |
101 | - kTopC is not (yet) replaced by kSurfC, although this is possible | |
102 | o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s | |
103 | o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) | |
104 | and rename: | |
105 | ini_phiref.F --> set_ref_state.F (+ set anelastic factors) | |
106 | ini_reference_state.F --> load_ref_files.F (- set anelastic factors) | |
107 | o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) | |
108 | ||
109 | checkpoint61c | |
110 | o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" | |
111 | to add mass source/sink of fluid in the interior (3-D generalisation | |
112 | of oceanic real-fresh water flux). | |
113 | o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) | |
114 | o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) | |
115 | o new pkg: down_slope | |
116 | density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). | |
117 | - presently, modify T & S inland (dwnslp_calc_rho.F). | |
118 | can be avoided if rho was stored in common bloc and used in calc_phi_hyd. | |
119 | - implementation for ocean in P-coords not tested. | |
120 | - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. | |
121 | o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) | |
122 | (to facilitate conversion of oceanic pkg to p-coordinate). | |
123 | o change FIND_RHO to FIND_RHO_2D : | |
124 | pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. | |
125 | o new pkg: cheapaml | |
126 | ||
127 | checkpoint61b | |
128 | o exch2: | |
129 | change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) | |
130 | - no longer depend on the order sequence (N,S,E,W). | |
131 | - 3rd exchange no longer needed (tested with 24 tiles). | |
132 | - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) | |
133 | - exch_UV_A-grid readily available (but not yet tested). | |
134 | comment out 3rd exch call and remove copy of V to U at SE & NE face-corners | |
135 | (both are no longer needed) in exch_uv: no effect in forward run; but | |
136 | get truncation error differences with adjoint exch. | |
137 | o exch2: | |
138 | - change index-bounds storage (moved from target to local tile, | |
139 | more intuitive this way) ; rename/remove some variables. | |
140 | - change utils/exch2/matlab-topology-generator & code_mods accordingly. | |
141 | ||
142 | checkpoint61a | |
143 | o exch2/matlab-topology-generator: | |
144 | fix bug in index bounds for N-S internal exchange (hard to tell if this | |
145 | had any effect on the solution). | |
146 | o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf | |
147 | is exceeded | |
148 | o testreport: modify syntax of awk, so that it works also with | |
149 | awk, and not only with nawk and gawk | |
150 | ||
151 | checkpoint61 | |
152 | o autodiff | |
153 | Change default for TAF usage by removing argument '-nonew_arg' | |
154 | This changes TAF subroutine argument list (ordering of active var.) | |
155 | Omission of this flag leads to incompatibility w.r.t. TAMC | |
156 | To restore TAMC-compatibility, need following modifs: | |
157 | * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility | |
158 | * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY | |
159 | Tested TAF version is 1.9.22 | |
160 | N.B.: exch2 hand-written adjoint code currently not TAMC compatible | |
161 | ||
162 | checkpoint60 | |
163 | --->>> This is the last checkpoint for which generating the adjoint | |
164 | --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" | |
165 | --->>> by default. | |
166 | --->>> Future checkpoints will ommit this flag by default. | |
167 | o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. | |
168 | o pkg/grdchk: Add gradient check to etan0 perturbations. | |
169 | o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). | |
170 | o pkg/autodiff: more flexibility in zeroadj. | |
171 | model/src: modifying do_oceanic_phys.F accordingly. | |
172 | o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. | |
173 | o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option | |
174 | special setup of gmredi for which the adjoint is stable | |
175 | enough for parameter optimization. | |
176 | o bridging the gap between eddy stress and GM. | |
177 | -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) | |
178 | along with a change in CPP option (now ALLOW_EDDYPSI). | |
179 | -> when using GM w/ GM_AdvForm: | |
180 | The total eddy streamfunction (Psi = eddyPsi + K x Slope) | |
181 | is applied either in the tracer Eq. or in momentum Eq. | |
182 | depending on data.gmredi (intro. GM_InMomAsStress). | |
183 | -> ALLOW_EDDYPSI_CONTROL for estimation purpose. | |
184 | The key modifications are in model/src/taueddy_external_forcing.F | |
185 | pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F | |
186 | ||
187 | checkpoint59r | |
188 | o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array | |
189 | from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); | |
190 | fix option to read coriolis(@ cell-corner) from files with CS-grid. | |
191 | o pkg/mnc: add some attributes to standard 1D-coordinate variables | |
192 | o pkg/diagnostics: enforce missing_value attribute for scalar variables at | |
193 | mass points, when using mnc for output | |
194 | - add runtime parameter (missing_value, missing_value_int) to override | |
195 | default (which is the value of getcon('UNDEF')) | |
196 | o pkg/mnc: prepare mnc for the actual use of missing values with the | |
197 | diagnostics package: small fix in mnc_cw_readwrite.template and more | |
198 | initialisation of never used fields | |
199 | - replace mnc_common.h and mnc_id_header.h with corresponding upper case | |
200 | versions | |
201 | o pkg/thsice/thsice_ini_vars.F added default initial values so that | |
202 | thermodynamics sea ice solver does not blow up when some initial fields | |
203 | are missing. | |
204 | o move from external_forcing_surf.F to ini_forcing.F | |
205 | the p-coord. hack consisting in using pLoad to set phi0surf ; | |
206 | update output of tutorial_global_oce_in_p (affected @ truncation level). | |
207 | o Freshen up a bit hs94.1x64x5, notably: | |
208 | remove rotationPeriod and tRef=5*0. (adjoint only), and add | |
209 | exactConserv=.TRUE. | |
210 | o pkg/generic_advdiff: | |
211 | change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only | |
212 | applies to files where Temperature & Salinity 2nd Order moments are used. | |
213 | o pkg/ptracers: add second-order moment advection schemes (80 and 81); | |
214 | this uses a dynamically allocated internal state data structure | |
215 | (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) | |
216 | and requires a fortran 90 compiler | |
217 | ||
218 | checkpoint59q | |
219 | o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) | |
220 | (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) | |
221 | o Refresh tutorial_global_oce_biogeo, notably: | |
222 | - change bathymetry (put back seamounts in ACC, use hFacs) | |
223 | - change EOS (POLY3 --> JMD95Z) | |
224 | - use Bryan-Lewis vertical diffusivity | |
225 | - use multidimensional advection | |
226 | - remove old virtual virtual in dic pkg, now done through ptracer pkg | |
227 | - change a couple of parameters in dic pkg | |
228 | o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F | |
229 | o pkg/obcs: change default to OBCSfixTopo = .true., | |
230 | - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result | |
231 | - replace "debugMode" with "debugLevel .GE. debLevB" | |
232 | o implementation of TAF directives for gchem,cfc,dic | |
233 | o remove "exp5" (replaced by tutorial_deep_convection). | |
234 | o pkg/obcs: add code to fix topography gradients normal to open boundaries; | |
235 | this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; | |
236 | the code can be turned on by setting OBCSfixTopo = .true. in data.obcs | |
237 | --> changes results in exp4, seaice_obcs | |
238 | o tutorial_deep_convection : | |
239 | update the set-up and increase resolution and domain size ; start | |
240 | from pseudo initial conditions = output at t=120mn in order to see | |
241 | something happening when running testreport. | |
242 | o pkg/seaice: add os7mp as an advection scheme | |
243 | add check for advection schemes | |
244 | add a flag for restoring T and S underneath sea ice | |
245 | o pkg/my82: add netcdf-support and diagnostics | |
246 | o thsice pkg: | |
247 | - Now hsMax limits snow height by turning it into ice following | |
248 | flooding scheme (and now conserving energy) | |
249 | - Slight rewriting of the formula in thsice_calc_thick.F | |
250 | - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos | |
251 | --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice | |
252 | ||
253 | checkpoint59p | |
254 | o gchem / dic / cfc : | |
255 | - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); | |
256 | - add new parameter files: "data.dic" & "data.cfc" ; | |
257 | - various re-arrangement in initialisation & header file ; | |
258 | - fix tutorial_global_oce_biogeo for multi-threaded test. | |
259 | o pkg/dic: test for "pickup_dic" file when restarting ; | |
260 | if no pickup-file, can restart with a re-initialised pH (same as it did | |
261 | before) providing pickupStrictlyMatch is set to False. | |
262 | o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP | |
263 | + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP | |
264 | o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 | |
265 | and staggerTimeStep is off (needed for stability of Internal-wave dynamics). | |
266 | o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, | |
267 | & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers | |
268 | (note: not clear to me what lambdaTr1ClimRelax is still used for ...) | |
269 | o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which | |
270 | scheme to use for vorticty-term ; | |
271 | - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F | |
272 | (with default selectVortScheme, return to original discretisation) | |
273 | - remove weird combination (e.g.: upwindVorticity & highOrderVorticity) | |
274 | o pkg/seaice: add a line to the summary to indicate grid type (B/C) | |
275 | o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the | |
276 | bottom ; only used with variable horizontal viscosity and non-hydrostatic. | |
277 | also fix diagnostics VISCAHW & VISCA4W. | |
278 | ||
279 | checkpoint59o | |
280 | o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). | |
281 | o change the loop ordering in most gad_*_adv_x.F to improve vectorization: | |
282 | move a few statemens out the main loop into separate loops | |
283 | o pkg/shelfice: | |
284 | - sort out freshwater flux; convert freshwater fluxes to mass fluxes | |
285 | (kg/m^2/s), does not break tests, because in verification/isomip, | |
286 | rhoConstFresh=rhoConst (by accident) | |
287 | - rearrange computation of tLoc, sLoc, pLoc to make code more efficient | |
288 | - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into | |
289 | new file model/src/seawater.F, so that they are available for all pkgs. | |
290 | - convert potential temperature into in-situ temperature. This changes the | |
291 | isomip tests => update tests | |
292 | o add a flag writePickupAtEnd (default=true) to be able to suppress | |
293 | writing a pickup at the last timestep | |
294 | o tools/mpack-1.6 : | |
295 | - disable automake (not working) and autoconf (not needed). | |
296 | - update to version 1.6.4 which fix MD5 code on some 64 bits platforms | |
297 | also cleaner with much less compilation warnings. | |
298 | o pkg/profiles: | |
299 | rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg | |
300 | (for "less than 32 characters name" compiler requirement) | |
301 | o pkg/obcs and pkg/exf: added capability to specify seaice open boundary | |
302 | conditions that have a different sampling frequency than S/T/U/V obcs | |
303 | o pkg/diagnostics (stats-diags): | |
304 | - fix global Min/Max in case 1 processor get only empty tiles | |
305 | o genmake2: replace (4 times) | |
306 | make genmake_tc_1.o >> genmake_warnings 2>&1 | |
307 | with | |
308 | COMM="$CC $CFLAGS -c genmake_tc_1.c" | |
309 | echo $COMM >> genmake_warnings | |
310 | $COMM >> genmake_warnings 2>&1 | |
311 | to make genmake2 always see the value of CC as specified in the optfile. | |
312 | o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. | |
313 | - add diagnostics for 1srt & 2nd Order moments and sub-grid variance. | |
314 | - modify verification advect_cs test to test SOM-advection on CS-grid. | |
315 | o pkg/ctrl: | |
316 | - Rewrite of ctrl_map_ini_ecco.F, | |
317 | introducing a generic routine (ctrl_map_ini_gen.F). | |
318 | - Modification of ctrl_bound/adctrl_bound handling control vector bounds. | |
319 | ||
320 | checkpoint59n | |
321 | o pkg/diagnostics: for large number of diagnostics, store diagnostic mate | |
322 | number in dedicate array "hdiag": | |
323 | - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST | |
324 | with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. | |
325 | - many small changes (integer format) for large number of diagnostics | |
326 | - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with | |
327 | a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. | |
328 | o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For | |
329 | usingSphericalGrid, this allows to define the rotated grid coordinates | |
330 | via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the | |
331 | geographical coordinates according to the inverse of the rotation defined | |
332 | by the Euler angles, so that Coriolis parameter and online-interpolation by | |
333 | exf works with the geographical coordinates on XC/YC/XG/YG. | |
334 | Naturally, this feature does not work with all packages, so some | |
335 | combinations are prohibited in config_summary (flt, flt_zonal, ecco, | |
336 | profiles), because there the coordinates are assumed to be regular | |
337 | spherical grid coordinates. | |
338 | o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: | |
339 | - introduce isopycnal diffusion coefficient control. | |
340 | o tools/adjoint_options: | |
341 | - additional control vector components. | |
342 | o pkg/mnc: have mnc create marginally meaning full coordinate variables | |
343 | (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 | |
344 | o pkg/mypackage: | |
345 | - add example of read/write pickup for state-var ; | |
346 | - add entry points to the main code for state-vars diags & write-pickup. | |
347 | o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year | |
348 | transitions for useExfYearlyFields | |
349 | - add new subroutine that determines the file to read from for | |
350 | use*YearlyFields = .TRUE. and .FALSE. | |
351 | - add a verification experiment to global_with_exf that tests | |
352 | useExfYearlyFields with USE_EXF_INTERPOLATION defined | |
353 | o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in | |
354 | analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new | |
355 | subroutines (which could be generated from a template, because they are | |
356 | almost identical), for now they are included in obcs_prescribe_read.F for | |
357 | simplicity | |
358 | o pkg/exf: | |
359 | - add a little more diagnostic to exf_interp_read (in analogy to | |
360 | mds_read_field, can be turned off with debugLevel < debugLevA=1) | |
361 | - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code | |
362 | ugly but fast by unrolling short inner loops, inserting a unroll=8 | |
363 | directive in routine lagran, and splitting a loop and making do while the | |
364 | outermost loop (the latter requires the intoduction of index arrays) | |
365 | o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice | |
366 | o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver | |
367 | http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html | |
368 | o verification/seaice_obcs: updated for restart test and latest options | |
369 | o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different | |
370 | ice rheology (so-called truncated ellipse, that gets rid of tensile stress); | |
371 | for now this is only available for the C-grid code and also within | |
372 | #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code | |
373 | ||
374 | checkpoint59m | |
375 | o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) | |
376 | and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature | |
377 | o gad_som : fix flux output (& diagnostics) to have same units as other | |
378 | advection scheme fluxes (was previously multiplied by deltaT). | |
379 | o added verification/seaice_obcs both to test seaice open boundaries | |
380 | and to provide an example matlab scrpt for generating them | |
381 | o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume | |
382 | o pkg/salt_plume: clean up salt_plume_frac.F to | |
383 | remove redundancy in PlumeMethod 1 and 4 | |
384 | o pkg/kpp: added saltplume diagnostics | |
385 | o pkg/obcs and pkg/seaice: | |
386 | - do not set uice and vice to zero when OB*icefile are unspecified | |
387 | - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default | |
388 | - moved seaice tracer obcs after call to seaice_growth | |
389 | o pkg/salt_plume: added various options for salt plume depth | |
390 | criterion and for vertical distribution of the salt | |
391 | ||
392 | checkpoint59l | |
393 | o pkg/ptracers: new version of ptracers pickup: | |
394 | read meta file and write only fields which are needed to restart. | |
395 | ( same logic as main pickup file ; also using pickupStrictlyMatch ) | |
396 | o pkg/seaice: | |
397 | - add timescale for melting due to warm mixed layer as a means of | |
398 | setting SEAICE_availHeatFrac more conveniently | |
399 | - add a CPP-flag/runtime parameter check for flooding algorithm | |
400 | - reformulated availHeat in seaice_growth.F to be independent of AREA | |
401 | o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent | |
402 | unit changes | |
403 | o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint | |
404 | o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC | |
405 | SX vector computer. | |
406 | o pkg/seaice: | |
407 | - removed SEAICE_FFIELDS.h and seaice_get_forcing.F | |
408 | seaice forcing fields can now be read only through pkg/exf | |
409 | - removed some unused halos | |
410 | o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP | |
411 | o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL | |
412 | or U/VICE from U/VWIND before computing U/VSTRESS | |
413 | ||
414 | checkpoint59k | |
415 | o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between | |
416 | dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. | |
417 | o fix un-initialised variable problem (in mom_vecinv & shap_filt): | |
418 | all experiments pass when compile with un-initialised var. checking option. | |
419 | o added pkg/salt_plume | |
420 | o script to test restart (for now, in MITgcm_contrib/jmc_script) | |
421 | o pkg/seaice: new read/write pickup version. | |
422 | read meta file and write only fields which are needed to restart. | |
423 | ( same logic as main pickup file ; also using pickupStrictlyMatch ) | |
424 | o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) | |
425 | o lab_sea.hb87: modify the domain & update output.hb87.txt : | |
426 | lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 | |
427 | at j=1 & j=Ny+1 : this case is not treated correctly in the restart | |
428 | process. Fixed here by closing the domain at the Northern boundary. | |
429 | o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. | |
430 | o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing | |
431 | a set of consecutive levels in/from a 3-D array. | |
432 | o pkg/ptracers: | |
433 | use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). | |
434 | to-do: fix pkg/diagnostics when large number of diagnostics are defined. | |
435 | ||
436 | checkpoint59j | |
437 | o in pkgs: dic, obcs, offline, rbcs: | |
438 | standard way to compute coeff. for time interpolation between 2 time reccords | |
439 | which retains full precision (& make results less dependent on compiler). | |
440 | update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. | |
441 | o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those | |
442 | packages instead of reading ice cover and wind speed separately | |
443 | o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h | |
444 | (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad | |
445 | to allow to compile customized code before the update) | |
446 | o cleaning-up: | |
447 | - fix CPP instruction syntax in pkg/obcs | |
448 | - replace (some) call to MDSIO S/R with call to RW interface S/R ; and | |
449 | add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) | |
450 | - fix some threads issue in IO parts. | |
451 | o pkg/dic: | |
452 | - add tons of "_d 0" (--> much better testreports !) | |
453 | and then update outputs of tutorial_global_oce_biogeo | |
454 | o pkg/mom_fluxform: | |
455 | add a special version of momentum advection intended to conserve momentum | |
456 | next to a bathymetry step or a coastline edge. (default = off = #undef) | |
457 | o new read/write pickup version: | |
458 | - for now, only implemented for main (mdsio) pickup file. | |
459 | - write out only what is needed to restart; merge pickup_nh , pickup_ph | |
460 | and main pickup together. | |
461 | - read meta file; read only what is needed to restart; stop if a field | |
462 | is missing (if pickupStrictlyMatch=T, = the default) or try to restart | |
463 | if it make sense (even if the restart is not perfect). | |
464 | - if no meta file, assume that pickup to read corresponds exactly to | |
465 | a pickup that would currently be written. | |
466 | - read pickup written in the old format (until checkpoint59i) if it | |
467 | recognizes an old meta file (no field-list). | |
468 | - add a meta file in exp. which starts from a pickup: 2 cases: | |
469 | a) minimal meta file (with just file precision) + pickupStrictlyMatch=F | |
470 | e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta | |
471 | b) a meta file describing the content of the associated pickup file | |
472 | e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta | |
473 | o pkg/mdsio & pkg/rw: | |
474 | - new routine to read a meta file ; new set of routine to read | |
475 | Multiple-fields file (with meta file). | |
476 | o added open boundary conditions capability for seaice | |
477 | HSNOW, HSALT, UICE, and VICE | |
478 | ||
479 | checkpoint59i | |
480 | o adjoint: | |
481 | * fix multiDimAdvection adjoint | |
482 | (partial recomputation problem by TAF for fVerT(:,:,kDown) | |
483 | and comlev1 size definition (maxpass vs. max. number of tracers) | |
484 | * verification/global_ocean.90x45x15 adjoint now tests | |
485 | NLFS and multiDimAdvection using DST3 (=30) | |
486 | * verification/lab_sea now tests multiDimAdvection using DST3 (=30) | |
487 | o pkg/kpp: add "_d 0" to real constant (if missing); | |
488 | update output of exp: natl_box (10.digits); vermix (std, 7.digits) | |
489 | and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). | |
490 | o prepare for "clever pickup" implementation: add new header file "RESTART.h" | |
491 | for internal parameters related to restart process (formerly from PARAMS.h) | |
492 | and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. | |
493 | o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed | |
494 | as argument. (only atm2d & obcs write_pickup have not yet been updated) | |
495 | o pkg/monitor: | |
496 | - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM | |
497 | - fix mon_stats_rs (statistics over the full domain, even where field is zero) | |
498 | - account for deep Atmosphere factor and density factor (anelastic) | |
499 | o added open boundary conditions capability for seaice HEFF and AREA | |
500 | o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) | |
501 | thermodynamics | |
502 | - requires a little reorganization, which affects the testreport results | |
503 | of isomip.htd (only 7 digits of cg2d agree) => update/m |