/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Contents of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph


Revision 1.1550 - (show annotations) (download)
Fri Dec 16 00:12:05 2011 UTC (12 years, 5 months ago) by gforget
Branch: MAIN
Changes since 1.1549: +12 -1 lines
- recent changes

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1549 2011/12/15 22:45:47 jmc Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 o pkg/seaice/seaice_growth.F:
8 fix heat conservation of the coupled ocean-seaice system.
9 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
10 solid vs liquid water treatment is resolved via QNET.
11 o pkg/seaice/seaice_growth.F:
12 add missing term for sublimation in saltFlux, which was breaking conservation.
13 o pkg/seaice/seaice_model.F:
14 Remove this patholigical case treatment in evolution branch,
15 where it is un-necessary and breaks conservation.
16 Update global_ocean.cs32x15/results accordingly for
17 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
18 o model/src:
19 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
20 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
21 o pkg/obcs:
22 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
23 tendency for temperature and salinity that is then applied to update
24 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
25 horizontal advection and diffusion contributions on the boundary (in
26 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
27 removing the mask in S/R timestep_tracer. The advantage of this approach is
28 that the updated tracer values include contributions from the surface
29 forcing and vertical diffusion.
30 This modification changes exp4.stevens because of vertical diffusion.
31 o model/src:
32 change non-curvilinear grid setting to also work with exch2 + blank tiles:
33 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
34 face dimensions.
35 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
36 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
37 and INI_SPHERICAL_POLAR_GRID.
38 change test-experiment global_ocean.90x40x15:
39 - split the domain in many more tiles (9x4 tiles of 10x10 each);
40 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
41 - update results of both test (std & dwnslp).
42 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
43 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
44 o model/src:
45 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
46 and fix initialisation when using sigma-coords.
47 o model/src:
48 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
49 to their current value at the beginning of forward_step.F": add a new run-time
50 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
51 - set doResetHFactors=T in the following test exp:
52 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
53 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
54 and tutorial_global_oce_in_p (nonLinFS in p)
55 o pkg/ecco
56 - added IES cost term
57 o verification/advect_xz
58 - scale down the depth by 1/100 (from 200 km to just 2.km)
59 - add secondary test using divergent flow, r-star and implicit vertical advection.
60 - add note (check_conserve_TS.txt) and matlab script to check global
61 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
62 o pkg/rbcs:
63 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
64 o pkg/obcs (Stevens BCs):
65 - fix various problems in the phase speed computations of the Stevens
66 boundary conditions:
67 - sign error for western and southern boundaries,
68 - time tendencies were underestimated by factor of dTracerLev and some just
69 zero (for multidim advection schemes) -> now estimate time tendencies
70 from difference between previous (n) time level and the one before (n-1);
71 this requires storing a field per tracer per boundary, also in the pickup
72 files.
73 - replace deltaTmom in cflMer/Zon computation with dTracerLev
74 - set default phase velocity to cflMer/Zon
75 - update verification experiment exp4.stevens
76 o pkg/generic_advdiff (implicit_r):
77 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
78 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
79 - fix implicit vertical diffusion or advection with NonLin FreeSurf
80 (was using current recip_hFacC instead of future recip_hFacC): set future
81 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
82 solver S/R ;
83 - fill diagnostics of vertical advective fluxes (computed from tendency)
84 when using implicit vert. advection;
85 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
86 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
87 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
88 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
89 o pkg/diagnostics:
90 - add diags for T & S tendency which goes through Adams-Bashforth.
91
92 checkpoint63f (2011/11/30)
93 o pkg/obcs/obcs_calc_stevens.F:
94 - join some loops to reduce number of if-statements
95 - fix a bug in code for northern and southern boundaries.
96 o pkg/seaice/seaice_init_varia.F
97 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
98 caused zero ice-velocities for the B-grid code
99 o pkg/seaice/seaice_init_fixed.F
100 - fix a bug in the initialisation of the second metric terms
101 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
102 - this affects all seaice configurations with useCurviLinearGrid = .true.
103 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
104 = .true. (default)
105 - the only verification experiment affected is global_ocean.cs32x15:
106 icedyn, seaice, and seaice_dynmix (AD)
107 o pkg/thsice/thsice_diagnostics_state.F
108 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
109 not contain garbage that can lead to surprises in diagstats_calc.F
110 o model/src:
111 - move bi,bj loops inside INTEGR_CONTINUITY ;
112 - call INTEGR_CONTINUITY directly from forward_step.F
113 (previously called from momentum_correction_step.F)
114 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
115 forward_step.F and pkg/ecco/the_main_loop.F
116 o model/src/do_oceanic_phys.F:
117 - reset addMass to zero only if useICEFRONT ;
118 - separated k-loop for rhoInSitu calculation ;
119 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
120 and at constant T,S (= WdRHOdP);
121 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
122 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
123 transport of locally-referenced potential density);
124 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
125 o gluemnc:
126 - replace ncrcat with ncks when adding variables to *.glob.nc
127 - change the way variables without record dimensions are handled so that
128 files that have variables with and without record variables can be glued:
129 add a record dimension with a new unique name to be able to differentiate
130 between variable with and without a-prior record dimensions. Remove
131 this record dimension before adding the variable to the *.glob.nc file.
132 This procedure automatically works also for grid.*.nc files that do not
133 have any record dimension.
134 o verification/cpl_aim+ocn:
135 - generate new reference output on baudelaire (gfortran, mpich2) (previously
136 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
137 o pkg/obcs/obcs_calc_stevens.F:
138 - add code for northern and southern boundaries.
139 - reorder some loops to save some operations and so that drFBar can be scalar
140 o model/src:
141 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
142 truncation) and add diagnostics for Adams-Bashforth tendency increment.
143 - update test-exp. AD output:
144 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
145 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
146 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
147 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
148 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
149 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
150 tutorial_plume_on_slope.
151 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
152 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
153 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
154 does not even come with an F77 compiler anymore, this should not be
155 a limitation
156
157 checkpoint63e (2011/11/06)
158 o pkg/seaice adjoint of LSR:
159 - substantially rework STORE dirs.
160 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
161 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
162 and only perform SOLV_MAX_FIXED adjoint iters.
163 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
164 always goes to same record, meaning that the last forward field will be
165 the one used in the adjoint - an approximation.
166 - now produces non-zero LSR-related gradients, and acceptable gradients for
167 An's zonal (x-z) test case (to be checked in)
168 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
169 (but these are screwed up by the thermodynamics in the first place);
170 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
171 output_adm.txt also reflects changes to seaice_lsr
172 - global_ocean.cs32x15:
173 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
174 (output_adm.seaice.txt was updated)
175 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
176 (output_adm.seaice_dynmix.txt)
177 o test-exp. exp4+stevens:
178 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
179 o pkg/seaice (lsr solver):
180 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
181 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
182 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
183 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
184 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
185 - compute (with new S/R) and print initial (+ free-driff sol. if available)
186 and final residual of linearised system.
187 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
188 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
189 o pkg/obcs: Stevens BCs (still only for east and west)
190 - fix Stevens BCs by using intermediate velocities of previous
191 time step as "baroclinic" contribution rather velocity of one grid cell
192 inside the boundaries; more consistent but makes the entire treatment
193 more complicated, requires new pickup files and two new S/Rs:
194 obcs_copy_uv_n and obcs_save_uv_n
195 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
196 (undefined by default)
197 - silently move computation of some grid factors into separate loops to
198 save some recomputations
199 - add a hack for non-linear free surface
200 - add a verification experiment to exp4 that tests this code
201 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
202
203 checkpoint63d (2011/10/25)
204 o pkg/obcs + seaice-dynamics:
205 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
206 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
207 values (consistent with an implicit method).
208 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
209 return to older implementation (same results as before); note that none of
210 the "experimental" OBCS_SEAICE options are implemented in the new version.
211 - switch test exp. seaice_obcs to use new version (update output).
212 o pkg/seaice:
213 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
214 - add parenthesis in Water-Ice drag calculations (evp & lsr);
215 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
216 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
217 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
218 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
219 o pkg/layers:
220 - Include potential density as new coordinate (Thanks to David Munday)
221 o pkg/dic:
222 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
223 carbonate computation/output to CALC_PCO2_APPROX
224 o pkg/generic_advdiff
225 - make TAF generate code that vectorizes:
226 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
227 o model/src:
228 - improve vectorization also for adjoint code of
229 solve_tridiagonal and solve_pentadiagonal. As this requires up to
230 5 new 3D-fields, this code is only turned on for the combination of
231 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
232 for singular matrix check (only for TARGET_NEC_SX).
233 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
234 ALLOW_AUTODIFF. This flag now needs to be set outside of
235 solve_tri/pentadiagonal.F
236 o pkg/exf:
237 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
238 optional namelist EXF_NML_OBCS).
239 - add many debug-print (to trace down where pkg/cal error msg comes from)
240 o pkg/mom_vecinv/mom_vi_hdissip.F
241 - rearrange loops so that vectorization is improved and in particular
242 the adjoint routine vectorizes. The code is a little longer now, but I
243 think easier to read.
244 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
245 o pkg/seaice:
246 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
247 o pkg/exch2:
248 - alternative code (without tile x tile matrix) for cumulated (global) sum;
249 used as default; keep using matrix version in adjustment.cs-32x32x1.
250 o tools/build_options:
251 - after merging some MPI and/or multi-threads specific optfiles so that
252 the modified default optfile support both built (using genmake2 -mpi
253 for the MPI built, using genmake2 -omp for OpenMP built),
254 move now obsolete optfiles to tools/build_options/unsupported/
255 (add copy of email sent to support list in doc/optfiles_changes.txt)
256
257 checkpoint63c (2011/09/28)
258 o pkg/ebm:
259 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
260 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
261 o pkg/seaice (SItracer pickup)
262 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
263 To be done:
264 - thorough testing of missing fields in S/R seaice_read_pickup
265 - thorough matching between generic tracers and specific fields used
266 (e.g. volume-weighted age, area-weighted age, salinity, ...)
267 o pkg/grdchk:
268 - all procs calculate and print finite-difference gradient (for testreport)
269 - change description output used by testreport;
270 - AD testing: also compare and report Finite-difference gradient;
271 => update all output_adm*.txt
272 o test exp. global_ocean_ebm:
273 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
274 and turn on exactConserve; update (fwd) output.
275 o pkg/seaice (LSR):
276 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
277 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
278 * identical results with non-CS topology (but save up to half of EXCH calls)
279 * no much changes in cs-32 verification tests since no ice at face edges
280 (differences due to convergence criteria, since nb of iterations changed)
281 * expect some differences on lat-lon-cap grid.
282 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
283 o pkg/exch2:
284 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
285 many tiles); until alternative coding is added, just add a stop.
286 o pkg/kpp:
287 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
288 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
289 o optfiles:
290 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
291 into corresponding standard one, which now support different build:
292 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
293 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
294 o pkg/obcs (seaice):
295 - add missing EXCH for uIce,vIce after applying OBCS;
296 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
297 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
298 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
299 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
300 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
301 and eedata.mth for MPI and mutlti-threaded testing.
302 o pkg/flt:
303 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
304 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
305 - fix pickup and trajectories + profiles output with multi-threads;
306 - add parameter to select group of fields to write along trajectory and
307 profile (default unchanged);
308 - only call PORT_RAND* function when flt_noise <> 0;
309 - add multi-threaded test for verification exp. flt_example.
310 o eesupp/src:
311 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
312 - USE_OMP_THREADING: check that number of threads (from eedata) matches
313 actual number (from env.var. setting).
314 o pkg/ebm:
315 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
316 - add multi-threaded test for verification exp. global_ocean_ebm
317
318 checkpoint63b (2011/08/29)
319 o pkg/ebm:
320 - fix sign of runoff;
321 - update directly forcing fields (Qnet,EmPmR) to use standard
322 external_forcing_surf.F (remove ebm_forcing_surf.F);
323 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
324 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
325 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
326 - update global_ocean_ebm parameters file data and update output (fwd+ad).
327 o verification/matrix_example:
328 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
329 MPI and mutlti-threaded testing.
330 o pkg/matrix:
331 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
332 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
333 - fix for multi-threaded (remove DATA statement);
334 - use standard DIFFERENT_MULTIPLE function;
335 - add MATRIX_OPTIONS.h
336 o verification/matrix_example:
337 To allow to split the domain in several tiles, change the domain size
338 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
339 Western side) of land points.
340 o (*_)write_pickup:
341 - fix few bugs in mypackage_read/write_pickup.F
342 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
343 array of length 1 (was caught by compiler syntax-check).
344 o pkg/diagnostics (velocity potential solver):
345 - fix initialisation of main diagonal matrix (for overlap values)
346 o tools/build_options:
347 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
348 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
349 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
350 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
351 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
352 and use "-devel" testreport option for standard testing on baudelaire.
353 o pkg/grdchk:
354 - Assume that all gradient-check position are within the same tile
355 corresponding to global indices (iGloTile,jGloTile) and that
356 positions (i,j indices or nbeg) are local to this tile;
357 - set tile local-indices and proc. number according to tile global-indices;
358 - remove grdchkwhichproc from namelist (retired param);
359 - send adjoint gradient to all procs so that all procs print it to STDOUT;
360 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
361 o adding package bbl (Bottom Boundary Layer)
362 description in MITgcm/pkg/bbl/bbl_description.tex
363 example/test experiment in MITgcm_contrib/bbl
364 o adjoint verifications
365 - changed 5 experiments to multi-tiles
366 * global_ocean.90x40x15
367 * obcs_ctrl
368 * offline_exf_seaice
369 * tutorial_dic_adjoffline
370 * tutorial_tracer_adjsens
371 changed reference output for those that crossed tile boundaries
372 (changed choices of gradient check positions)
373 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
374 - temporary bug fix in grdchk_loc.F for obcs
375 o genmake2 & testreport
376 - add target "obj" (just for OBJFILES files) to Makefile;
377 - add option to specify FEXTRAFLAGS on command line.
378 o pkg/mypackage:
379 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
380
381 checkpoint63a (2011/08/02)
382 o pkg/diagnostics (velocity potential):
383 - fix velocity-potential calculation when using OBCS: balance net inflow
384 at each level (new S/R OBCS_DIAG_BALANCE).
385 - fix some of the problems with OBCS in stream-function calculation.
386 o pkg/exf/exf_readparms.F
387 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
388 EXF_NML_OBCS) more consistent, so that you need not have these lists
389 in data.exf when they are not used.
390 o optim/optim_readdata.F:
391 - add some output about obcs variables that might help debugging
392 - add a check about nvarlength
393 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
394 o pkg/diagnostics (velocity potential):
395 - fix mask for OBCS (still problems in stream-function with OBCS);
396 - add specific parameter (default = main code CG2D params) for solver;
397 - in case of poor convergence, use solution corresponding to lowest residual.
398 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
399 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
400 and should be avoided where possible.
401 o model/src (rStar):
402 - include r* effect on reference-state (PhiRef) in totPhiHyd
403 (so that it's really the potential anomaly at the cell center);
404 affect solution only if z* with full pressure in EOS.
405 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
406 update output (because of z* in totPhiHyd and viscA4 changes);
407 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
408 @ constant r) until interpolation at constant r is implemented.
409 o pkg/diagnostics
410 - fix RCENTER diagnostics in case cell center is not at interface middle
411 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
412 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
413 that THETA and SALT are "conservative temperature" and "absolute
414 salinity"
415 o pkg/ctrl
416 - fix computation of endrec in s/r ctrl_init_rec
417 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
418 o pkg/seaice/seaice_growth.F
419 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
420 remove then obsolete STORE directives
421 - fix STORE directives for tice and tices, so that only the
422 appropriate part of the fields are stored (and not the entire
423 field); update global_ocean.cs32x15.seaice AD output.
424 - cosmetic changes: adjust CPP flags and indentation for better
425 legibilty
426 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
427 Chris Wilson)
428 o pkg/gmredi:
429 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
430 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
431
432 checkpoint63 (2011/07/11)
433 o pkg/exch2:
434 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
435 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
436 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
437 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
438 o pkg/diagnostics:
439 - deal with pairs of post-processed diags which are computed together; in
440 particular, re-order list of diags within 1 file to save 2nd computation.
441 - add S/R to compute velocity stream-function (called after velocity-potential
442 calculation) from divergence free transport -> new diagnostics "PsiVEL".
443 - add parameter to select grid-point location where PsiVEL == 0.
444 o eesupp/src:
445 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
446 (specific S/R needed with exch2 topology - for now, just print an error msg)
447 o pkg/shelfice
448 - Implement friction velocity-dependent transfer coefficients following
449 Holland and Jenkins, JPO, 1999
450 Original code by M. Losch with small modifs.
451 Enable with CPP option SHI_ALLOW_GAMMAFRICT
452 and runtime flag SHELFICEuseGammaFrict
453 o verification lab_sea & global_ocean.cs32x15:
454 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
455 does not miss some dependencies (but is slower) and also works with many files
456 (default makedepend limitation for AD built).
457 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
458 o pkg/diagnostics:
459 - add run-time parameter "useMissingValue" (def=False) to fill land-point
460 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
461 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
462 - Extend the use of "missing_value" setting from data.diagnostics for the case
463 of counter-diagnostics (where fraction-weight is zero). This applies both to
464 MNC and MDS output files.
465 o pkg/seaice/seaice_growth.F:
466 - add 'a priori' cap of latent heat flux based on actual mass considerations
467 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
468 non-legacy seaice_solve4temp.
469 - add diagnostic of the residual sublimation freshwater flux (the freshwater
470 flux taken from the ocean if the total actual latent heat fluxes exceed
471 the maximum)
472 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
473 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
474 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
475 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
476 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
477 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
478 o verification 1D_ocean_ice_column:
479 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
480 update results
481 o pkg/diagnostics:
482 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
483 which are not filled-up but computed from other diags ; In this case, the mate
484 diag points to the primary (filled-up) diag to used for post processing.
485 - Update Velocity-potential computation using post-processed diag framework.
486 ==> Change the ordering of fields and time-periods in MDS output file
487 when using periodic averaging: now writes one time record with the full set
488 of fields for this time period, then the next time reccord (it used to be
489 one field with the full set of time records then the next field).
490 Note: this is now similar to NetCDF (MNC) output file. <==
491
492 checkpoint62z (2011/06/21)
493 o adjoint monitor:
494 - Add adjoint monitor output for packages exf, seaice
495 and update relevant testreport output
496 o pkg/seaice:
497 - re-order diags inits so that they appear in order in available_diagnostics.log
498 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
499 area/heff/hsnow preceeding thermodynamic growth/melt.
500 - modified diag: SIdA; output actual effect, as the description states.
501 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
502 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
503 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
504 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
505 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
506 - added diagnostics for seaice generic tracers (SItr*).
507 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
508 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
509 I. Fenty: 18-Jun-2011:
510 Minor changes to seaice package:
511 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
512 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
513 - Differentiated "regularization variables" from "floor variables"
514 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
515 * hiceMin became SEAICE_hice_reg (old hiceMin)
516 (with _reg meaning regularization variable)
517 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
518 so as to ensure energy conservation when going between phases
519 - A22 was not used anywhere
520 2) Changed regularization procedure for heffActual and hsnowActual to ensure
521 well-boundedness and smooth adjoint in seaice_growth.F
522 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
523 because the old regularization always set heffActual >= 0.05 cm
524 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
525 on AREA when HEFF > 0.
526 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
527 requiring that DISABLE_AREA_FLOOR *not* be defined
528 Affected verifications:
529 - 1D_ocean_ice_column (output.txt output_adm.txt)
530 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
531 o pkg/diagnostics:
532 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
533 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
534 (was _RL, now integer) with option = 0 to retrieve all levels.
535 - add pieces of code to compute velocity potential at each level (new diagnostics
536 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
537 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
538 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
539 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
540 and in diagnostics_fract_fill.F (do not need a valid pointer for the
541 diagnostics counter-mate); check that definition of counter-diagnostic
542 includes a valid counter-mate (in diagnostics_set_levels.F).
543 o model/src (rStar):
544 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
545 affect solution only if z* with full pressure in EOS;
546 update output of test-exp global_ocean.90x40x15.
547 o pkg/seaice:
548 - introduce siEps=1e-5 parameter
549 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
550 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
551 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
552 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
553 as well as ice cover age and ridging index (attached to AREA).
554 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
555 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
556 Up to SItrMaxNum=3 tracers can be used simultaneously.
557 o pkg/salt_plume:
558 -introduce SPsalFRAC run time parameter that sets the fraction of the
559 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
560 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
561 o model debug options:
562 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
563 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
564 - Refine debug-msg printing selection (3 new levels):
565 debugMode : controls printing of debug messages (sequence of S/R calls).
566 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
567 debLevZero = 0 ; /* level of disabled aux. msg printing */
568 debLevA = 1 ; /* level of minimum aux. msg printing */
569 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
570 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
571 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
572 debLevE = 5 ; /* level of extensive debug printing */
573 New debugLevel default: with default debugMode value (=F),
574 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
575 and if debugMode=T, default debugLevel = 4 (debLevD).
576 Relation with previous settings:
577 debLevB (=2) corresponds to former debLevA (=1)
578 debLevD (=4) corresponds to former debLevB (=2)
579 Note:
580 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
581 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
582 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
583 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
584 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
585 o pkg/obcs:
586 - change OBCSfixTopo default from True to False (should not change the results);
587 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
588 o pkg/thsice:
589 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
590 2nd layer seaice sublimation (unlikely to happen)
591 - use Interior mask for OBCS in thsice_advection.F (similar to what is
592 done in gad_advection & seaice_advection).
593 o adjoint:
594 bug fix spotted by Gael Forget:
595 seaice_advection and thsice_advection still had
596 legacy CPP options to avoid CS corner updates for adjoint
597 o pkg/seaice:
598 => Change some of the defaults (2011/05/29):
599 - change SEAICEuseFluxForm default (from False to True)
600 - change DIFF1 default (from 0.004 m/s to 0. m/s)
601 And print warnings if DIFF1 is not set in data.seaice and centered
602 avection scheme is used without any diffusion.
603 also:
604 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
605 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
606 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
607 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
608 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
609 update results of test exp.:
610 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
611 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
612 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
613 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
614 seaice_obcs: output (SEAICEuseFluxForm=T)
615 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
616 for standard fwd & AD lab_sea tests (to keep the same output).
617 o pkg/seaice/seaice_growth.F:
618 - use Ian Fenty's capping formulas for actual ice
619 thickness thoughout EVOLUTION branch.
620 - put treatment pathological case #2) in CPP brackets
621 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
622 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
623 o pkg/seaice:
624 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
625 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
626 also pass fac as a param, which can be 1. (to update the tendency
627 field) or the time step (to update the field itself).
628 - seaice_advdiff.F: for multidim, call seaice_diffusion with
629 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
630 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
631 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
632 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
633 o pkg/seaice:
634 diffusion with centered advection scheme (diffus.F & advect.F):
635 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
636 to just compute the laplacian of input-field.
637 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
638 - fix flux-form version in diffus.F to conserve tracer.
639 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
640 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
641
642 checkpoint62y (2011/05/26)
643 o pkg/seaice:
644 - seaice_growth.F : in EVOLUTION branch, always include
645 a_QSWbyATM_cover in qnet (as it should be).
646 - verification/global_ocean.cs32x15 : update results accordingly
647 (output.seaice.txt output_adm.seaice.txt).
648 o pkg/seaice + obcs:
649 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
650 equivalent of assuming no tracer gradient outside the OB region.
651 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
652 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
653 after changes above);
654 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
655 only at OB location (instead of over a band of OLx width).
656 o pkg/seaice:
657 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
658 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
659 o pkg/obcs:
660 - split header file "OBCS.h" into 4 separated files:
661 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
662 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
663 (contain no conditional statement which depends on OBCS options).
664 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
665 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
666 o ctrl, cost, grdchk & autodiff pkgs:
667 - make options file more standard (like other {PKG}_OPTIONS.h file but
668 with AD_CONFIG.h); clean-up some of the included header files.
669 o pkg/obcs:
670 - do not mask tracer when applying OB (tracer == 0 could generate problems)
671 - apply tracer OB values to tracer field only at OB location (instead of
672 over a band of OLx width)
673 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
674 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
675 obcs_apply_tloc.F & obcs_apply_sloc.F
676 o obcs in model/src:
677 - call OBCS_APPLY_W only if NonHydrostatic.
678 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
679 - reset dEtaHdt and wVel to zero outside OB interior region ;
680 - leave tracer unchanged outside OB interior region: This has no effect
681 on the solution but just to prevent unrealistic tracer value outside OB.
682 - zero out velocity outside OB interior region: This has no effect on
683 the solution but just to prevent unrealistic velocity outside OB.
684 o obcs and non-lin free-surf:
685 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
686 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
687 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
688 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
689 update results of test-exp. exp4(nlfs).
690 o exp4 (nlfs) test-exp:
691 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
692 with NonLin-FreeSurf); update output.nlfs.txt
693 o obcs and 2d/3d solver norm:
694 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
695 and outside OB interior region (will allow to place OB further inside the
696 domain). Depending on the domain, can affects cg2d-Norm (previous
697 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
698 and cg3d-Norm (previous Norm was computed before canceling OB terms),
699 e.g. in tutorial_plume_on_slope.
700 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
701 o pkg rbcs:
702 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
703 - add capability to apply relaxation to horizontal velocity uVel & vVel.
704 o pkg/grdchk: add gradient check for control variable xx_shifwflx
705 o pkg/shelfice/shelfice_init_fixed.F
706 fix CPP-flag combinations
707 o pkg/seaice: Merge iceage code of Pierre Rampal
708 * update/change/correct ice age calculations
709 * add age updates for pathological cases
710 Probably needs more testing...
711
712 checkpoint62x (2011/05/13)
713 o pkg/mom_vecinv:
714 high-order vorticity scheme: use interior masks (maskInW & S)
715 to zero-out (outside OB) gradient of vorticity.
716 o verification exp.:
717 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
718 hs94.128x64x5 and seaice_obcs ; update results.
719 o pkg/obcs:
720 fix bug in OBeta for YZ sections in obcs_exf_load.F
721 o pkg/ctrl, pkg/shelfice, and optim:
722 - add new control variable xx_shifwflx (fresh water flux underneath ice
723 shelves). This is almost as tedious as obcs-ctrl, because the
724 variables needs its own mask.
725 - add a cost function term that penalizes the deviation of xx_shifwflx
726 from the first guess (zero) in analogy to other control variables
727 o pkg/shelfice:
728 - start basic adjoint
729 o pkg/ctrl:
730 - remove extra 2D field "for good measure" when initializing in
731 ctrl_set_globfld_[xy/xz/yz].F
732 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
733 - improve error messages in ctrl_set_unpack_*
734 o OBC implementation in momentum:
735 use interior masks (maskInC,W & S) in momentum S/R:
736 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
737 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
738 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
739 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
740 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
741 (and also with Leith/Smagorinsky harmonic-viscosity).
742 Update output of experiment dome and exp4 (+nlfs).
743 o exp4 test-exp:
744 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
745 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
746 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
747 time-varying OB at Western-side for wVel (NonHyd); update output.
748 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
749 and biharmonic-viscosity ; also use prescribed time varying OB.
750 o pkg/obcs:
751 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
752 o model/src:
753 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
754 - initialise startTime & nIter0 with unlikely values: allows to set one
755 from the other without ambiguity.
756 o seaice_obcs test-exp.:
757 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
758 o pkg/obcs:
759 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
760 no longer needed with maskInC,W,S in pkg/generic_advdiff.
761 o pkg/seaice:
762 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
763 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
764 - fixed bug in the initialization of sea ice salinity variable HSALT
765 in seaice_init_varia.F (removed dependence on ICE2WATR)
766 o fizhi-cs test exp.:
767 switch reference output convention for these 2 non-standard test-exp,
768 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
769 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
770 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
771 o model/inc:
772 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
773 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
774 o pkg/seaice:
775 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
776 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
777 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
778 and initial HSALT
779
780 checkpoint62w (2011/04/26)
781 o pkg/mom_fluxform:
782 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
783 - use parameter "sideDragFactor" in no-slip BC side-drag part.
784 - update output of exp. global_ocean.90x40x15
785 o pkg/mom_vecinv:
786 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
787 o update seaice exp.:
788 use more consistent parameter values (remove "backward compatability only":
789 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
790 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
791 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
792 o update test-exp global_ocean.90x40x15:
793 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
794 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
795 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
796 o turn on zStar & viscA4 in standard set-up (dir input/)
797 and update output files: output.txt & output.dwnslp.txt
798 o new AD-test experiment: obcs_ctrl
799 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
800 o pkg/dic:
801 fix two bugs in handling water vapour pressure in carbonate chemistry
802 and air-sea fluxes. Found by Val Bennington and Galen McKinley
803 (add DIC Option = WATERVAP_BUG to recover old results)
804 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
805 o adding allowInteriorFreezing option to check for water below freezing point
806 at depth and bring the negative heat anomaly to the surface level
807 o pkgs _fields_load:
808 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
809 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
810 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
811 rbcs to get interpolation weights and time reccord number.
812 - fix multi-threading in aim_fields_load.F
813 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
814 o external_fields_load:
815 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
816 interpolation weights) to use in a periodic time-series ; do not divide by
817 time-step to convert to integer:
818 - this fixes case where externForcingPeriod is not multiple of time-step
819 (Thanks to Christopher L. Wolfe)
820 - this fixes case where externForcingPeriod is an odd multiple of time-step
821 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
822 store index of time-record which is currently loaded:
823 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
824 - needed for the adjoint but not yet used because of extensive recomputations;
825 (to be fixed soon)
826
827 checkpoint62v (2011/04/02)
828 o verification/1D_ocean_ice_column added to test Ian Fenty's
829 pkg/seaice_growth.F modifications for improving sea ice code differentiability
830 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
831 (new velocity statistics after changing maskInW & maskInS definition)
832 o pkg/generic_advdiff with OBCS:
833 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
834 equivalent to assumption of no tracer gradient outside the OB region.
835 This will affect the results if using obcs+biharmonic diffusion.
836 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
837 o pkg/obcs:
838 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
839 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
840 in Interior region. No impact on solution but affects Velocity monitor stats.
841 o pkg/ptracers (adjoint)
842 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
843 tape file for each tracer
844 o model/inc/src and pkg/autodiff: add parameters that allow to turn
845 of parts of the adjoint code at run time. For now, there are only
846 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
847 parameters are set in data.pkg.
848 This is the lazy coward's version of doing this, but still useful for
849 debugging. In order to do it right, everything needs to be moved to
850 pkg/autodiff.
851 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
852 the end; this fixes the adjoint balancing code for open boundaries.
853 o pkg/ctrl:
854 - change behavior of xx_${varname}period to be analogous to exf-conventions:
855 xx_${varname}period = 0., means time-independent control part
856 xx_${varname}period = -12., means one-year-periodic monthly control part
857 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
858 clean up ctrl_init a little, remove unused variables
859 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
860 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
861
862 checkpoint62u (2011/03/15)
863 o model/src:
864 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
865 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
866 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
867 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
868 o pkg/ctrl/obcs/ecco:
869 - remove obsolete, unused, and partially broken code:
870 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
871 ALLOW_CTRL_OBCS_BALANCE
872 - put a stop statement into ecco/cost_obcsvol.F, but also add
873 cost_obcsvol to ecco_ad_diff.list
874 o pkg/ecco: fix counting cost function contributions for obcs (code
875 by Matt M.) and diffkr for diagnostics
876 o pkg/ecco, pkg/ctrl, pkg/grdchk:
877 add cost penalty terms for initial uvel, vvel, eta controls
878 and I/O for prior error files
879 o pkg/mdsio:
880 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
881 (new argument) to check for tiled file in mdsioLocalDir : this fix the
882 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
883 o pkg/ctrl:
884 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
885 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
886 unused and superfluous variables
887 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
888 o pkg/ecco
889 - enable adjoint of Stevens OB
890 o pkg/ctrl/ecco/grdchk:
891 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
892 Fortunately, we do not have any tests for the numerous cpp-flagged
893 option of "obcs as control parameters" so we will never know
894 if this is an improvement (but at least now things compile).
895 - remove an obsolete initialization from ecco_cost_init_barfiles.F
896 - fix some problems within never used ifdefs to make the code compile
897 o pkg/obcs:
898 - Refine Interior mask definition to work with more complex OB (e.g.
899 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
900 read in Interior mask from file. Check if Interior mask is consistent
901 with OB list of indices.
902 o pkg/seaice
903 - beginning code for a seaice tracer package,
904 but currently only used for seaice age: SEAICE_AGE
905 SEAICE_num = 4
906 iTracer = 1: area-weighted ice age
907 = 2: volume-weighted ice age
908 = 3, 4: template for one-year vs. multi-year ice
909 data.seaice has new namelist SEAICE_PARM03 for arrays related to
910 SEAICE_num
911
912 checkpoint62t (2011/03/05)
913 o pkg/obcs:
914 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
915 then normal component. This ensures that the normal component is set
916 correctly even when it conficts with tangential setting from an other OB.
917 Affects results of test-experiment seaice_obcs: update the output.txt
918 o pkg/obcs:
919 - add code to monitor statistics of dynamical fields at OB.
920 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
921 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
922 - change default: balance the Net inflow through all OB (instead of balancing
923 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
924 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
925 to match Nortern OB inflow (OBCS_balanceFacN=0).
926 o pkg/seaice:
927 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
928 o pkg/seaice (seaice_growth v 1.113):
929 - reverting seaice_growth to v 1.111 in order to have code with exact bit
930 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
931 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
932 runtime flag SEAICEareaFormula is kept but is inactive
933 o model/src:
934 - add new param to scale curvilinear grid distance and area when using
935 a different sphere radius from the grid-files.
936 - test/check multi-threads EXCH applied to local variable (cg2d_x)
937 o adjoint:
938 - enable adjoint of Stevens OB
939 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
940 (a bit delicate because of potentially modified adj. common block structure;
941 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
942
943 checkpoint62s (2011/02/15)
944 o pkg/seaice (seaice_growth v 1.112):
945 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
946 computing the ice cover tendency from effective thickness tendencies. Include
947 Ian Fenty's formula.
948 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
949 SEAICEareaFormula.
950 - simplify notations for the various d_HEFF/d_AREA terms.
951 o pkg/gmredi:
952 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
953 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
954 add a verification test-run (front_relax.bvp) to test GM_useBVP.
955 o pkg/seaice (seaice_growth v 1.111):
956 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
957 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
958 also melt ice.
959 o pkg/seaice:
960 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
961 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
962 o pkg/cheapaml:
963 - from Nico Wienders: New version of this package.
964 o pkg/flt:
965 - add CPP options to prevent floats to re-enter the opposite side of
966 a periodic domain (default: keep periodicity)
967 o pkg/gmredi:
968 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
969 (needed for multi-dim advection).
970 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
971 o model/src:
972 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
973 o tutorial_tracer_adjsens
974 - extend to NLFS and replace maskC by hFacC
975 (change reference output accordingly)
976
977 checkpoint62r (2011/01/24)
978 o testreport:
979 - add option -deloutp (-do) to remove output file after successful run
980 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
981 extract exact list of procs from this file ; adjust COMMAND by
982 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
983 o pkg/ecco: replace old ineffective way of penalizing deviations from
984 first guess (of obcs) with code by Matt Mazloff
985 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
986 exf/cal
987 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
988 and handle case of obcs?period == 0
989 Not affected by these changes: There is still an inconsistency in
990 the computation of start/endrec for the obcs variables for ALLOW_CAL
991 defined (see comment by Menemenlis, 7-Mar-2003)
992 - make S/R ctrl_get_gen_rec return something meaningful even if
993 ALLOW_CAL is not defined
994 - ctrl_getobcs?: simplify code so that it does not need to use
995 S/R exf_swapfields
996 o testreport:
997 allow to test MPI with different number of processors for each experiment:
998 create file "SIZE.h.mpi" in each build dir.
999 Note: update of "-command" argument not yet implemented.
1000 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
1001 alleviate the need for additional 3D tapes when using
1002 the non-inear free surface in the adjoint. This is done
1003 by adding an 'update' of hfacc etc. to their current
1004 value at the beginning of forward_step.F.
1005 o pkg/seaice
1006 seaice_lsr: move stress-divergence computations out of outer pseudo-
1007 timestepping loop
1008 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
1009 up, so that the calls of the ctrl_* subroutines are really at the end
1010 of the routine.
1011 o pkg/gmredi:
1012 allow to specify a 2-D horizontal map and a 1-D vertical profil
1013 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
1014 o pkg/seaice:
1015 move lsr iterations from seaice_dynsolver to seaice_lsr.
1016 o pkg/seaice:
1017 reduce memory footprint of seaice mutldim advection tapes,
1018 by using a 2D tape independent of the generic_advdiff ones,
1019 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
1020
1021 checkpoint62q (2010/12/29)
1022 o model/src:
1023 - check horizontal grid-spacing for unset or zero/negative values.
1024 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
1025 o pkg/flt:
1026 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
1027 - precision of input and output files set according to readBinaryPrec
1028 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
1029 - initial float position from tiled file was not converted to index space
1030 (looks like a bug): fixed to make it similar to initial pos. global file.
1031 o global_ocean.cs32x15:
1032 change SIZE.h of AD set-up to get same tiling as with MPI.
1033 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
1034 o model/src:
1035 add flag to control printing of domain fields (bathymetry, hFac ...) in
1036 ini_mask_etc (call to plot_fieds_xy*).
1037 o pkg/thsice:
1038 if useEXF, some forcing fields are not valid in overlap: fixed by computing
1039 over the interior only + apply EXCH at the end (like with SEAICE advection).
1040 o pkg/mdsio:
1041 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
1042 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
1043 - change barrier call for safe multi-threads access to 3-D shared buffer.
1044 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
1045 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
1046 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
1047 o pkg/flt:
1048 - add fourth-order Runge-Kutta integration
1049 - add basic exch2 support (only 1 facet supported so far!)
1050 o pkg/mdsio+rw:
1051 new S/R to read local (or tile independent) vector (read counterpart of
1052 mds_writevec_loc, and front-end write_glvec_rl/rs).
1053 o global_ocean.cs32x15: additional input_ad.seaice experiment
1054 that uses pkg/seaice rather than pkg/thsice.
1055 (using multidim advection for seaice)
1056 o towards more F95 syntax for array specification in namelist:
1057 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
1058 of all verification experiments.
1059 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
1060 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
1061 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
1062 o global_ocean.cs32x15: additional input.seaice experiment
1063 that uses pkg/seaice rather than pkg/thsice.
1064
1065 checkpoint62p (2010/12/17)
1066 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
1067 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
1068 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
1069 allow for use of multim. advection in seaice adjoint.
1070 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
1071 - first attempt to close budgets by taking into account the freshwater
1072 flux implied by the sublimation of snow and ice. So far only the
1073 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
1074 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
1075 o eesupp/src:
1076 new S/R with new option (NML_EXTENDED_F77) to change array specification
1077 from F95 standard to commonly accepted extended F77 form.
1078 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
1079 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
1080 for less tolerant f77 compiler (e.g., pgf77, g77).
1081 o globalFiles:
1082 commented out in parameter file "data" since it's not safe with MPI
1083 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
1084 in this case); no longer commented out in restart test (tst_2+2).
1085 o add adTapeDir to specify a special directory where adjoint tapes are
1086 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
1087 and cannot be used together with mdsioLocalDir.
1088 o nesting pkgs:
1089 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
1090 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1091 - add parameter files + utils dir + output from short run on beagle.
1092 o pkg/seaice:
1093 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
1094 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
1095 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
1096
1097 checkpoint62o (2010/11/25)
1098 o pkg/exf:
1099 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
1100 o pkg/seaice:
1101 - seaice_ocean_stress: split a loop for better vectorization of the
1102 adjoint code
1103 - seaice_growth.F: fix bug in conservation of freshwater connected to
1104 capping of heff, put contribution into d_HEFFbyNEG
1105 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
1106 by something more sensible (parameters that are what their name implies)
1107 - change some defaults, so that by default exf-parameters are used for
1108 things like rhoAir, cpAir,latent/sensible heat parameters, in order
1109 to reproduce the old results, many data.seaice now contain funny values
1110 for cpAir and latent heat of sublimation
1111 o packages_readparms.F: move exf_readparms up in line so that
1112 exf-parameters are visible for other packages (e.g. seaice)
1113 o debugMode & debugLevel=2:
1114 - differentiate between debugMode & debugLevel=2:
1115 debugMode: controls printing of debug messages (sequence of S/R calls).
1116 debugLevel: controls printing of algorithm intermediate results and stats.
1117 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
1118 => allows to print debug-stats without all sequence of call messages.
1119 - switch control of debug print from debugLevel to debugMode in many S/R.
1120 o pkg/obcs (obcs-sponge):
1121 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
1122 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
1123 o pkg/generic_advdiff:
1124 - record overlap minimum size for each advection scheme;
1125 - refine criteria on overlap minimum size;
1126 - check and stop (in gad_check) if overlap size is too small.
1127 o pkg/obcs:
1128 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
1129 once, in ptracers_implicit.F)
1130 - with seaice: remove test on empty file name in obcs_apply_seaice (always
1131 apply OB values when tile has OB)
1132 o model/src, coriolis setting:
1133 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
1134 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
1135 files (selectCoriMap=3) with any grid.
1136 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
1137 o pkg/seaice/seaice_growth.F:
1138 a few cosmetic changes that reduce the number of lines of code
1139 o pkg/obcs: add boundary conditions following Stevens (1990)
1140 - the code follows old MOM/NAOSIM code
1141 - so far it is only implemented for the eastern and western boundaries
1142 and NOT for pTracers
1143 o pkg/rbcs:
1144 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
1145 beginning of the first rbcs forcing period.
1146 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
1147 offline package, i.e., one file per time, labeled by iteration number;
1148 deltaTrbcs sets the timestep with which the data was generated;
1149 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
1150 - rbcsForcingCycle=0 makes forcing non-cyclic.
1151 - make arithmetic safe for negative times and odd forcing periods.
1152
1153 checkpoint62n (2010/11/09)
1154 o pkg/seaice:
1155 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
1156 o pkg/obcs:
1157 New S/R to copy tracer value from the OB location to narrow band region
1158 (width = same as overlap) beyond the OB: preserve OB value (needed for
1159 high-order scheme) which were overwritten by EXCH call if in overlap
1160 region. Applied to theta, salt, ptracer and advected seaice variables.
1161 With seaice: use maskInC in similar way as in gad_advection.F,
1162 in seaice_advection.F and advect.F.
1163 Update output of experiment seaice_obcs and change exp4 to test OBCS with
1164 4th order Adv.Scheme. for pasive salt and ptracer.
1165 o tools/genmake2:
1166 - when looking for an optfile (not specified), only search for Fortran compiler
1167 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
1168 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
1169 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
1170 - set default for CPP to "cpp -traditional -P" (was the case without specifying
1171 an optfile, but otherwise default was just "cpp".
1172 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
1173 - when "CC" is not set in the optfile, look for possible C compiler
1174 (instead of just setting CC=cc)
1175 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
1176 => add a ".F" to ".o" rule for source files with no "#include" (such as
1177 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
1178 - move gfortran before g77 in list of possible Fortran compiler (consistent
1179 with reference compiler switch from g77 to gfortran)
1180 o pkg/seaice:
1181 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
1182 seaice_check that stops the model, when the CPP flag is used.
1183 o seaice_growth.F: make capping of ice volume conserving by returning the
1184 capped ice as freshwater to EmPmR. This does not change the verification
1185 experiments but will change runs where the capping is acutally active
1186 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
1187 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
1188 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
1189 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
1190 o tools/genmake2:
1191 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
1192 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
1193 - clean previous genmake log files before anything else.
1194 - change Makefile to remove testreport log files (*.tr_log) and genmake log
1195 files only with "CLEAN" target (instead of "Clean");
1196 o pkg/generic_advdiff:
1197 Change OBCS in multiDim advection (gad_advection.F):
1198 Use maskInC to prevent intermediate update of tracer-field in OB regions,
1199 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1200 which were applying future time-step OB values.
1201 This way, all explicit calculations use current-time-step OB values
1202 (simpler and more consistent).
1203 Affects results when set-up uses time-varying OBC and multi-dim advection;
1204 update output of experiment seaice_obcs.
1205 o pkg/seaice:
1206 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1207 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1208 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1209 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1210 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1211 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1212 o pkg aim (2010/10/26):
1213 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1214 formulation with obliquity, eccentricity, ... as run-time parameters,
1215 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1216 upward shortwave radition at the surface (all-sky and clear-sky).
1217 o pkg/obcs:
1218 - writing sections with globalFiles=T does not work: switch to tiled-files
1219 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
1220 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
1221 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
1222
1223 checkpoint62m (2010/10/21)
1224 o pkg/seaice: vectorize seaice_solve4temp.F
1225 - move iterations loops outside of i/j-loops
1226 - requires 2D arrays for TB and effConduct
1227 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
1228 modified in this routine
1229 - a little bit of clean up, adjusting indentation, etc.
1230 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
1231 performance and '**TWO' by '**2' (because TWO is a float),
1232 replaced ONE, ZERO
1233 o eesupp/src:
1234 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
1235 o pkg/seaice/seaice_growth.F
1236 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
1237 merging process. The merged routine has two branches, and one activates the 'evolution'
1238 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
1239 In summary, here is what the '10/10 revision' did consist of
1240 part 1: seaice_growth.F revisions 1.71 to 1.75
1241 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
1242 The emphasis here was on improving readability (e.g. by trying to use meaningful
1243 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
1244 part 1.5:
1245 - revising the lab_sea experiment to make it a more useful (i.e. stable
1246 and representative of an actual model run). This was done by generating a
1247 (winter) pickup to start from, switching back the main experiment dynamic
1248 solver from evp to lsr, having one of the experiments use the free drift solution.
1249 part 2: seaice_growth.F revisions 1.76 to 1.85
1250 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
1251 - Sorting out the various fields units and sign (set early on and reset at the end)
1252 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
1253 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
1254 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
1255 and simplifying logical expressions to further improve readibility.
1256 part 3: seaice_growth.F revisions 1.86 to 1.89
1257 - Re-organize the blocks of code more logically.
1258 - Merging the '_if.F' pieces that add something new.
1259 o pkg/thsice:
1260 - vectorize thsice_solve4temp and thsice_get_exf.
1261 Problem: thsice_solve4temp has an unvectorizable statement that
1262 might also be problematic for TAF
1263 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
1264 does not change the verifcation experiment, but will change all
1265 experiments that have this flag undefined (not tested in verification);
1266 a little reorganization to save a few 2D fields and recomputations
1267 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1268 - 2nd step: fix some store dirs
1269 o seems to work somewhat, i.e. using ifort but not g77
1270 o likely cause are incomplete init. or recomputation
1271 o start verification/global_ocean.cs32x15/input_ad.thsice
1272 o pkg/obcs: add support for exch2
1273 - the position of the boundary and prescribed values are specified using
1274 a global domain with exch2 facets stacked
1275 - in x for N,S boundaries (like W2_mapIO=-1)
1276 - in y for E,W boundaries (so E,W boundaries do not overlap)
1277 o pkg/mdsio: add support for writing global sections with exch2
1278 file layout is as for obcs described above:
1279 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1280 - for y-z sections, facets are stacked in y
1281 o pkg/thsice:
1282 - change a few routines for better vectorization: thsice_albedo.F,
1283 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1284 not affected, but in particular the latter routine has changed
1285 dramatically (not necessarily easier to read now).
1286 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1287 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1288 o verification/lab_sea:
1289 - overhaul of the forward model experiments. The main motivation
1290 for this revision is that lab_sea has proven quite fragile (when
1291 changing the sea-ice code, and switching platforms) to a point
1292 when failures were very hard to attribute to specific code problems.
1293 - the suspected reason for this fragility is noise amplification by evp so,
1294 to start with, we decided to replace evp with lsr in the main experiment.
1295 - the input.lsr experiment thus became obsolete and was removed.
1296 - it was replaced with the input.fd experiment that uses an
1297 analytical "free drift" solution as the ice velocity field.
1298 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
1299 will hopefully allow us to discriminate problems due to dynamic solvers
1300 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
1301 us to test additional options, along with the salt plume package.
1302 - Finally a pickup was generated (at the end of a one year run) to
1303 make the tests more representative of an actual model run. Previously
1304 the tests starting point was a 1m thickness of ice everywhere.
1305 o pkg/seaice:
1306 - introducing S\R seaice_freedrift.F that compute the
1307 analytical solution to an approximate ice momentum
1308 equation (i.e. the simple stress/coriolis balance).
1309 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
1310 of the free drift velocity field, and enable its use.
1311 To actually use the free drift solution as the model ice
1312 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1313 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1314
1315 checkpoint62l (2010/10/04)
1316 o pkg/seaice:
1317 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1318 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1319 version (with USE_ORIGINAL_SBI undef);
1320 o add hooks for new packages OASIS, the package will follow
1321 (hooks exclude the seaice pkg for now)
1322 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1323 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1324 rather than mdsio_readvector.F/mdsio_writevector.F, within
1325 adread_adwrite.F to read/write adjoint-related tapes to disk.
1326 o eesupp and pkg/mdsio: ALLOW_WHIO
1327 Option to write/read 2D fields to files including tiles halos.
1328 The main purpose is for adjoint related "tape I/O".
1329 The secondary purpose is for debugging phases.
1330 A word on those rather specifically intended purposes.
1331 The code was meant to be stripped down to the bare minimum.
1332 Typically, there is a unique and basic mapping to the global
1333 buffer (tile by tile, then proc by proc, then level by level), and
1334 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1335 meant to generate user friendly outputs of various shapes and forms.
1336 Rather it is intended, for the knowledgeabale developers,
1337 to be largely independent of the many mdsio options, to allow
1338 outputs of tiles+halos in debugging phases and in adjoint runs,
1339 and to allow some flexibility in tuning (adoint) I/O depending on each
1340 file system behavior. With regard to tuning, most of the potential knobs
1341 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1342 to specify directories, to specify the typical size of I/O calls, etc.)
1343 are not yet included, and will be added if they prove useful.
1344 o pkg/seaice:
1345 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1346 o pkg/seaice:
1347 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1348 code (seaice_budget_ice_if.F) which enable to recover old standard
1349 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1350 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1351 o model/src (rStar):
1352 use simple average (not area weighted) of rStarFac at U,V point when using
1353 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1354 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1355
1356 checkpoint62k (2010/09/17)
1357 o adjoint
1358 * changed verification/global_ocean.cs32x15 ; adjoint now tests
1359 Adams-Bashforth 3 + NLFS + RSTAR
1360 * some more modifs required for ECCO-GODAE v4
1361 o pkg/seaice
1362 add SEAICE_AGE_VOL option to use volume instead of area for
1363 integrating SEAICE_AGE
1364 o model/src:
1365 first check-in of sigma & hybrid-sigma coordinate code ; also includes
1366 non-linear free-surface parts ; but pressure-gradient not yet coded.
1367 o pkg/ptracers:
1368 option for ptracer to convert Salt Relax into additional EmP.
1369 tested in exp. global_ocean.90x40x15.dwnslp (update output)
1370
1371 checkpoint62j (2010/08/25)
1372 o pkg/ggl90:
1373 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1374 o pkg/dic: car_flux.F, phos_flux.F
1375 - reduce number of exp-calls in order to improve performance
1376 - clean up a little (replace fields by their macros, etc., fix
1377 typo in CPP-flag)
1378 o pkg/ggl90: minor changes
1379 - GGL90diffKrS was removed --> always use GGL90diffKr
1380 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1381 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1382 (commented out for now)
1383 - change in max/min operations to ensure that smoothing is ok
1384 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1385 - always use diffKrNrT as background profile (i.e. never use diffKr field)
1386 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1387 o pkg/dic:
1388 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1389 vectorization
1390 - small bug fix in insol for the unlikely case of a cartesian grid
1391 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1392 + now vectorize, which also removes adjoint recomputations;
1393 + replace integer maksp1 by _RL maskp1
1394 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1395
1396 checkpoint62i (2010/07/21)
1397 o pkg/flt:
1398 - with OBCS: stop floats which enter the OB region
1399 o model/src:
1400 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1401 for implicit vertical advection.
1402 o pkg/seaice:
1403 - account for melting in seaice age evolution.
1404 - remove double counting of seaice ridging effect on seaice age.
1405
1406 checkpoint62h (2010/06/18)
1407 o pkg/exch2:
1408 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1409 o tools/genmake2
1410 - remove "-pdefault" option: redundant with the use of "packages.conf";
1411 - remove file pkg/pkg_default : set the default as a pkg group
1412 ("default_pkg_list") defined in pkg/pkg_groups;
1413 - fix for case pkg/pkg_depend is missing (was hanging before);
1414 - add option "-pgroups" to specify a different pkg_groups than the default.
1415 o verification/adjustment.cs-32x32x1:
1416 add a "minimal" set-up test (code_min & input_min) which only compiles
1417 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1418 o tools/genmake2
1419 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1420 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1421 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1422 files are nearly the same anyway.
1423 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1424 - redefinition of tau(i,i) (by a factor of ustar)
1425 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1426 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1427 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1428 - replace
1429 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1430 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1431 by
1432 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1433 (changes results)
1434 -> exf_bulkformulae v1.22,
1435 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1436 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1437 output.txt 1.63
1438 offline_exf_seaice: output.seaicetd.txt 1.7
1439 seaice_obcs: output.txt 1.10)
1440 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1441 -> exf_bulkformulae v1.23,
1442 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1443 and global_ocean.cs32x15.icedyn (only 11 matching digits)
1444 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1445 o adjoint of exch-1:
1446 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1447 (note: was already like this when using EXCH-2) and remove flow dir
1448 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1449 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1450 - update pkg/exch2 diff list.
1451
1452 checkpoint62g (2010/05/19)
1453 o eesupp/src (exch-1):
1454 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1455 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1456 (renamed to exch1_*rx_cube.F).
1457 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1458 to call new exch1 S/R ; update Makefile and .cvsignore.
1459 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1460 exch2_xy_rx later)
1461 Note: after updating your code, need to run "make clean" in eesupp/src
1462 o test experiment bottom_ctrl_5x5:
1463 new output_adm.txt with fewer grdchk & less monitor output.
1464 o model/src:
1465 remove the call to ini_cori in initialise_varia.F (just keep the usual one
1466 in initialise_fixed.F). More consistent with coriolis & horizontal grid
1467 beeing treated in the same way (ini_grid is not called a 2nd time).
1468 o pkg/exf:
1469 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1470 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1471 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1472 - cosmetic changes to exf_bulkformulae.F to make it look more like
1473 exf_bulk_largeyeager04.F
1474 o eesupp/src (exch-1):
1475 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1476 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1477 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1478 (even without using MPI).
1479 - Message mode: move RecvAck setting (indicator of buffer being ready)
1480 from send_put to recv_get S/R (was useless before, but not sure if
1481 it's much more useful now);
1482 - Switch the order of sync: MPI-proc 1rst and then threads;
1483 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1484 - fix AD code for communication mode ='get' (but not used).
1485 o model/src:
1486 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1487 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1488 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1489 o pkg/ctrl: require a specific set of control variables and exf-flags for
1490 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1491 o model/src:
1492 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1493 1rst forward sweep, to avoid over-writing output files during recomputations
1494 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1495 b) 2nd version:
1496 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1497 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1498 writePickupAtEnd) + seaice & ptracers output;
1499 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1500 o model/src:
1501 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1502 o pkg/exch2:
1503 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1504 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1505 o pkg/autodiff & exch2:
1506 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1507 (for now, only if ALLOW_EXCH2 is defined).
1508 o pkg/autodiff:
1509 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1510 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1511 + clean-up comments (_RS is not always real*4)
1512 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1513 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1514 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1515 o testreport (AD-tests):
1516 no longer link files from dir "../input" (1rst link files from
1517 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1518
1519 checkpoint62f (2010/04/29)
1520 o model/src/the_main_loop.F:
1521 adjust store directives for seaice evp and multicategory according to
1522 pkg/ecco/the_main_loop.F
1523 o adjoint:
1524 global_sum_ad was incomplete (noted many times by many people ;)
1525 nice description by Jean U. as follows:
1526 * allreduce(var) in global_sum.F can be interpreted as
1527 reduce(sum) followed by broadcast of sum.
1528 * The adjoint of that is
1529 sum(adjoint) followed by broadcast(summed adjoint value)
1530 or in other words, allreduce(sum, adjoint vars)
1531 We were missing the sum(adjoint)!
1532 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1533 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1534 The fix should produce 16-digit accuracy between
1535 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1536 multi-CPU single-tile (e.g. nSx=1, nPx-2)
1537 We'll probably change this yet again shortly
1538 o eesupp/src:
1539 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1540 o pkg/icefront
1541 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1542 specification of addmass array based on a 2D field, which is added
1543 at bottommost wet level at each horizontal location.
1544 o model/src:
1545 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1546 layout; (not always compatible with delX,delY setting; commented out for now).
1547 o pkg/exch2:
1548 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1549 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1550
1551 checkpoint62e (2010/04/15)
1552 o pkg/obcs:
1553 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1554 o pkg/dic:
1555 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1556 (note: not presently tested in any forward verification exp.)
1557 update tutorial_global_oce_biogeo AD output file.
1558 o pkg/exf:
1559 - account for the variation of albedo as a function of zenith angle
1560 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1561 o build_options:
1562 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1563 o pkg/dic:
1564 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1565 - use binary pickup file for restart;
1566 - initialise atmos-CO2 box from dic_pCO2 parameter;
1567 - fix multi-threaded.
1568 o pkg/rbcs:
1569 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1570 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1571 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1572 and update output.txt
1573 o pkg/kpp:
1574 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1575 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1576 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1577 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1578 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1579 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1580 o pkg/offline:
1581 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1582 (bug was added in version 1.10 on 2007-08-23).
1583 o pkg/offline:
1584 - no need to specify periodicExternalForcing, etc ... to use offline pack
1585 - offline input files no longer just single prec --> parameter offlineLoadPrec
1586 o verification/lab_sea:
1587 change AD test to multi-tile setup and update all 4 AD output.
1588 NOTE: while cost function values remain very similar,
1589 gradients are very different, although gradient checks are self-consistent
1590 Should try to get to the bottom of this (cost function summation order?)
1591 o pkg/dic:
1592 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1593 a weakness of TAF that drops part of double precision in log10 derivative.
1594 <= changes removed since problem has been fixed in current TAF version 1.9.71
1595 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1596 o pkg/ecco:
1597 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1598 update all 4 lab_sea AD output.
1599
1600 checkpoint62d (2010/03/22)
1601 o build_options:
1602 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1603 o remove unbalanced quote (single or double) in commented line of source code
1604 (may cause some warning with some preprocessor/makedepend versions).
1605 o pkg/seaice:
1606 fix seaice_model.F for adjoint (gael) and update AD results of experiments
1607 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1608 o testreport:
1609 add option '-runonly' (short: '-ro') to just do the run part (without make).
1610 o eesupp: remove JAM communication code (obsolete).
1611 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1612 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1613 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1614 (update also the output).
1615
1616 checkpoint62c (2010/03/02)
1617 o tools/build_options :
1618 move (some) old optfiles from build_options/ to build_options/unsupported/
1619 o model/src and pkg/exf
1620 surface relaxation -- separating data and data.exf options
1621 The point is to ensure that we specify the surface relaxation
1622 either in data or in data.exf (but not half and half) and to
1623 avoid an accidental relaxation to 0 (which happened if a time
1624 scale was specified but the file name was left empty)
1625 o model/src model/inc and pkg/mom_common
1626 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1627 => addition to the viscosity field as computed by others schemes
1628 o tools/build_options:
1629 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1630 but keep the former optfile for few weeks for smooth transition
1631 o pkg/ecco
1632 - allow user defined cost function contributions
1633 CPP: ALLOW_USERCOST_CONTRIBUTION
1634 USAGE: compute contributions in cost_usercost_all.F
1635 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1636 the two options are complementary.
1637 o pkg/smooth
1638 - migration from contrib to the main repository
1639
1640 checkpoint62b (2010/01/26)
1641 o pkg/monitor:
1642 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1643 (in case someone forgot to update customized pieces of code)
1644 o nonHydrostatic:
1645 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1646 - add a simple 2-D experiment (short_surf_wave) to test it.
1647 o pkg/icefront:
1648 adding the shell of, and the hooks to, a new package that
1649 will model melting and freezing of vertical glacier ice fronts
1650 o momentum:
1651 add diagnostics of momentum tendency from Hydrostatic pressure gradient
1652 (without surf.pressure term: would need a 2nd filling since implicit term).
1653 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1654 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1655 cannot deal with the former
1656 o cleaning:
1657 - remove all (except OpenAD) old TLM output from results_ad dirs.
1658 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1659 - comment out maskH definition (replaced by maskInC)
1660 o pkg/monitor:
1661 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1662 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1663
1664 checkpoint62a (2010/01/15)
1665 o model/src:
1666 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1667 o pkg/diagnostics:
1668 - add optional level number diagnostics (i.e., level number to be define
1669 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
1670 - strictly check for valid parser-code(10) ;
1671 - check if adding diag to the list from the right place.
1672 o pkg/longstep:
1673 - change parameters and fix tracer conservation with rstar/nonlinear free surface
1674 o diagnostics:
1675 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
1676 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
1677 o pkg/diagnostics:
1678 - Add option for writing vertical integral (sum of selected levels) of an output
1679 field instead of writing output field levels. Activate this option on a per
1680 output-file basis, by setting the 2nd character of fileflag to 'I'.
1681 - Add field-specific information relative to level integral in 3rd postion
1682 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
1683 vertically (x level-thickness x hFac), "r"=same but without hFac.
1684 o do_the_model_io:
1685 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
1686 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
1687 writing pickups and stopping.
1688 o pkg/diagnostics (for now, only with mdsio):
1689 - write time information to meta file (and modify accordingly rdmds.m) :
1690 time-averaged diagnostics output: write starting and ending time of the
1691 time-averaging interval ; snap-shot diagnostics output remains unchanged;
1692 o pkg/timeave:
1693 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
1694 always Nr), now assumed to be equal to number of levels of averaged field;
1695 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
1696 o pkg/sbo:
1697 - fix ocean bottom pressure global-average & 2-D time-ave output (was
1698 neither initialised nor filled).
1699 - add starting iteration in suffix of global-average output file
1700 (to avoid over-writing the file after a restart)
1701 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
1702 o time-average:
1703 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
1704 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
1705 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
1706 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
1707 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
1708 - fix missing accumulation for pkg/opps.
1709 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
1710 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
1711 - fix initialisation of time-ave vars and do only full time-step increment
1712 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
1713 o pkg/layers:
1714 - use standard RW pkg S/R to write the output
1715 and remove local write_fld version (which had a problem).
1716 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
1717 - fix LAYERS_CALC argument list.
1718 o pkg/timeave:
1719 - store cumulative-time in a simple tiled array (drop the level index)
1720 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
1721 o pkg/ocn,aim_compon_interf
1722 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
1723
1724 checkpoint62 (2009/12/23)
1725 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
1726 (was not previously tested in any other exp.)
1727 o pkg/monitor:
1728 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
1729 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
1730 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
1731 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
1732 - change del2 calculation.
1733 - use interior masks (instead of maskH, <- to be remove).
1734 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
1735 o mask & obcs:
1736 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
1737 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
1738 (called after packages_init_fixed)
1739 o pkg/obcs:
1740 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
1741 Fixes bug in obcs+exf with nSx*nSy.GT.1
1742 - fix multi-tile handling in obcs balance code
1743 o nonHydrostatic:
1744 - Implement AB-3 for non-hydrostatic vertical momentum ;
1745 (change ordering of var. stored in pickup file when using NH)
1746 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
1747 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
1748 (in prep. for new NH free surface form).
1749 o pkg/obcs:
1750 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
1751 o model/src:
1752 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
1753
1754 checkpoint61z (2009/12/01)
1755 o nonHydrostatic:
1756 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
1757 a spurious source of energy in simple baroclinic adjusment test case.
1758 Update all non-hydrostatic exp output.
1759 o model/src (3-d solver):
1760 Change again 3-D solver free-surface RHS term when exactConserv=T:
1761 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
1762 (which was not the case with previous formulation).
1763 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
1764 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
1765 o nonHydrostatic:
1766 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
1767 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
1768 - change 3-D solver to work with r* (for now, only with linear free-surf.)
1769 - add few debug diagnostics (cg3d_x, residual)
1770 o model/src:
1771 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
1772 update output of exp. global_ocean.cs32x15.viscA4
1773 o update output of exp. global_ocean.cs32x15.icedyn after removing
1774 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
1775 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1776 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
1777 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
1778 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
1779 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
1780 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
1781 to test this code
1782 o pkg/cd_code:
1783 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
1784 C-grid momentum. D-grid velocity used to be stepped forward in time with
1785 Adams-Bashforth only on surface pressure term. Tests show that using AB on
1786 D-grid coriolis term improves stability (as expected from CD-scheme paper).
1787 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
1788 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
1789 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
1790 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
1791 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
1792 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
1793 o pkg/obcs:
1794 - fix bug in initialisation (broken since Oct 1rst modification)
1795 for useOBCSprescribe without useEXF.
1796
1797 checkpoint61y (2009/11/15)
1798 o pkg/seaice
1799 - change (once again) the discretization for the evp solver: rather than
1800 squaring the averages of strain rates, average the squares to give
1801 a better approximation to VP behavior (in simple test); this breaks
1802 verification experiments that use EVP (lab_sea and lab_sea.hb87)
1803 --> update outputs
1804 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
1805 to improve vectorization of adjoint code on TARGET_NEC_SX
1806 o verification/vermix:
1807 - change vermix to a more "classical" 1d column with high vertical
1808 resolution, seasonal heat flux forcing and constant wind forcing
1809 --> update outputs
1810 o pkg/seaice
1811 - fix diagnostics of principal stress components for EVP
1812 - add optional diagnostics of non-linear convergence for LSOR solver
1813 - make maximum zeta a runtime parameter
1814 o model/src (3-d solver):
1815 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
1816 which consisted in removing the Surf. Non-Hydrostatic pressure from the
1817 whole column and adding it to Eta (inspired from Casualli, 1999):
1818 Only affects 3-D solver initial guess and only if using ExactConserv,
1819 but tests did show a degradation of solver convergence. For this reason,
1820 decide to disable this piece of code.
1821 to recover previous version, just set zeroPsNH = exactConserv (line 78).
1822 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
1823 o pkg/ggl90:
1824 - fix previous modif (unfortunatly has not been documented here).
1825 o pkg/seaice/autodiff:
1826 - add CPP flag to include clipping of zeta in EVP code;
1827 although clipping of zeta is not necessary for EVP and not recommended
1828 it was done by default, now clipping is disabled by default
1829 - modify computation and store zetaC/Z in seaice_evp for TAF
1830 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
1831 - change seaice_calc_viscosities/strainrates for better
1832 vectorization after AD by TAF
1833 - rearrange common blocks in SEAICE.h once again for easier dumps of
1834 adjoint output, adjust adcommon.h and g_common.h
1835 - change flux form of default advection scheme for better vectorization
1836 of adjoint code
1837 - modify lab_sea/input.lsr to test the flux form of default advection
1838 scheme
1839 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
1840 transition in checkpoint61r)
1841
1842 checkpoint61x (2009/10/19)
1843 o adjoint: adding two new verification experiments
1844 * tutorial_global_biogeo: an online dic sensitivity experiment
1845 (work with G. Forget)
1846 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
1847 (an update of the Dutkiewicz et al., 2006 paper)
1848 Both use the same CO2FLUX cost function, but different controls
1849 Gradient checks look good, but some recomp. could still be traightened out
1850 Should add xx_dic control variable to test at some point
1851 o model/src:
1852 add run-time parameters to check and/or mask initial Temp & Salt
1853 o pkg/ptracers:
1854 apply zonal filter (if used) to all passive tracers
1855
1856 checkpoint61w (2009/10/12)
1857 o adjoint:
1858 * update and finish work on adjoint of dic package (G. Forget)
1859 * start adjoint of offline package
1860 * bug fix for cube-sphere TLM code (active_file_g.F)
1861 o tutorial_global_oce_optim:
1862 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
1863 and add SIZE.h_mpi for MPI testing
1864 o pkg autodiff
1865 - fix bug in autodiff_restore
1866 - make genmake2 remove comments and empty lines from ad_input_code.f in
1867 order to reduce file size (new script file remove_comments_sed)
1868 o allows to specify vertical profile of vertical viscosity (viscArNr)
1869 o pkg autodiff
1870 autodiff_ini_model_io: comment out writing of grid information to netcdf
1871 files, because at this time the grid fields are a bunch of zeros
1872 (this is analogous to ini_mnc_vars.F)
1873 o pkg seaice/autodiff:
1874 left-over from removing the 3-time-level fields:
1875 - small rearrangement of common blocks (SEAICE.h)
1876 - fix field declaration in order to get meaningful output in
1877 adseaice.*.nc (adcommon.h)
1878 o pkg obcs:
1879 - go through NH code only if nonHydrostatic=T
1880 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
1881 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
1882 => Update output of experiment seaice_obcs
1883 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
1884 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
1885 - fix restart for useOBCSprescribe + useEXF
1886 o pkg ctrl
1887 - make obcs as control parameter work also with useSingleCPUio
1888 - replace a few sny and snx by Ny and Nx to be consistent with
1889 ctrl_set_globfld_x/yz.F
1890 o pkg seaice
1891 - re-introduce global field frWtrAtm for the case of
1892 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
1893 - catch the case of an empty filename in seaice_cost_init_fixed.F
1894 o pkg ecco:
1895 - small bug fixes in the_main_loop
1896 . fix order of monitor arguments
1897 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
1898 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
1899 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
1900 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
1901 imbalance diagnostics for wmean_h/sflux = 0
1902 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
1903 - catch the case of empty filenames in ecco_cost_init_fixed.F
1904 and ecco_readparms.F
1905 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
1906 to make this statement meaningfull in ecco_cost_weights.F
1907 o pkg zonal_filt:
1908 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
1909 - when using rStar, filter uVel*hFacW instead of uVel
1910 (tested without topography: fix a Pb of growing instability with NLFS)
1911 o pkg/aim/thsice:
1912 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
1913 (works as SST restoring)
1914 o pkg/thsice:
1915 -add specific parameter for salt restoring in slab mixed-layer
1916 (by default equal to the temperature restoring)
1917
1918 checkpoint61v (2009/09/21)
1919 o pkg/kpp:
1920 -add double diffusive contributions as a hack, turned off by default
1921 for now, and the code can be excluded with a CPP-flag
1922 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
1923 -add a verification experiments to "vermix" to test this code
1924 o pkg/mom_common:
1925 Move computation of length scales to mom_init_fixed.F (avoid recomputation
1926 at each time-steps*levels).
1927 o pkg/layers:
1928 Created a new package for computing volume fluxes in temperature or
1929 [not yet implemented] density layers, e.g. for calculating residual
1930 overturning circulations.
1931 o pkg/diagnostics:
1932 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
1933 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
1934 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
1935 To avoid mixing type (RS/RL) of input/output array argument,
1936 replace single mixed-type array with a pair from each type (RS/RL).
1937 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
1938 is now implemented for all pkgs (previously only done for the main pickup)
1939
1940 checkpoint61u (2009/08/25)
1941 o pkg/obcs:
1942 - change OB?eta from _RS to _RL and put them into a separate commen block
1943 - add code to read OB?eta from a file via obcs_prescribe_read: the code
1944 compiles and does not destroy any other experiments, the data is read
1945 properly, but the code is not tested in actual applications
1946 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
1947 create a meaningful unit attribute for the time coordinate variable
1948 o pkg/ebm: add plenty of missing "_d 0" ;
1949 update results of experiment global_ocean_ebm (fwd + adjoint tests)
1950 Notes: several pieces of code only works for (very) specific set up
1951 (domain size, lat range, etc ...); should be documented & stop if one
1952 of those assumptions is not meet.
1953 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
1954 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
1955 and offline_exf_seaice (seaicetd + adjoint).
1956 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
1957 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
1958 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
1959 o few changes to pass when compiling with strick checking of arguments
1960 across S/R (allow to find few bugs in S/R calls).
1961 o pkg/seaice:
1962 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
1963 2d-fields, for slightly better performance
1964
1965 checkpoint61t (2009/07/22)
1966 o pkg/seaice:
1967 - remove unused variables in seaice_evp
1968 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
1969 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
1970 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
1971 each processor opens a different file (a fix from Matt).
1972 o cg2d:
1973 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
1974 this reduces number of EXCH calls by 2 when using exch2.
1975 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
1976 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
1977 o pkg/thsice:
1978 add code for Near Infra-Red albedo (from Jeff)
1979 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
1980 o ini_model_io:
1981 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
1982 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
1983 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
1984
1985 checkpoint61s (2009/06/30)
1986 o pkg/exch2 (exch2_rxN_cube*):
1987 remove last BARRIER (no need to synchronise after getting data from shared
1988 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
1989 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
1990 and generate new output (for the 2 tests) using default rotationPeriod.
1991 o pkg/exch2:
1992 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
1993 (was already the case with AUTODIFF_EXCH2 defined)
1994 - add bj in exch2 arrays and S/R.
1995 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
1996 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
1997 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
1998 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
1999 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
2000 - verification experiment natl_box.longstep
2001 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
2002 allow different versions of ifort (8 or 9) and different versions
2003 of mpi (mpich or mpich2) to be used with the same optfile.
2004 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
2005 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
2006 o pkg/seaice:
2007 fix previous modif (3-level field removed) for old-pickup reading
2008
2009 checkpoint61r (2009/06/25)
2010 o pkg/seaice:
2011 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
2012 1. introduce fields for time step (N-1)
2013 2. do not use levels 2 and 3 anymore (but keep them)
2014 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
2015 includes changes to pkg/thsice/thsice_get_velocity.F,
2016 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
2017 pkg/obcs/obcs_apply_uvice.F.
2018 - completely remove code for leap-frog time stepping for second order
2019 advection
2020 - adjusted adjoint accordingly;
2021 gradient checks have improved by an order of magnitude!
2022
2023 checkpoint61q (2009/06/22)
2024 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
2025 - the boundary conditions along open boundaries are unclear, because the
2026 associated masks are set to zero and are thus treated as closed when
2027 applying the slip-boundary conditions.
2028 - move initialisation of grid variables from seaice_init_varia to _fixed
2029 o adding doc/diags_changes.txt
2030 o model/src:
2031 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
2032 to avoid "_diags" naming if no relation to pkg/diagnostics.
2033 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
2034 file and only call PLOT_FIELD_XYZ if debugMode=T.
2035 remove few PLOT_FIELD_XY calls outside initialisation.
2036 remove few unnecessary BARRIER.
2037 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
2038 of salt_plume package in Southern Ocean
2039 o pkg/thsice:
2040 - fix hOceMxL in overlap (needed for sea-ice advection);
2041 update output of experiment global_ocean.cs32x15.icedyn.
2042 o pkg/seaice:
2043 - make the (placeholder-)tracer IceAge a little more meaningful
2044 by avoiding ridging of age due to convergent ice flow
2045 - add diagnostics for surface temperature, atmospheric and oceanic
2046 heat flux, and atmospheric and oceanic ice growth
2047
2048 checkpoint61p (2009/06/10)
2049 o eesupp (global_max & global_sum):
2050 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
2051 - remove starting & endding barrier (no longer needed)
2052 o pkg/mdsio, writelocal:
2053 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
2054 (remove the STOP): uses shared buffer IO to store data from all threads
2055 and then let master-thread write nThreads tiles.
2056 o pkg/mdsio (read/write field):
2057 - tiled IO done in 1 piece (all levels at a time);
2058 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
2059 - multi-threaded: allow to read/write local (non-shared) array
2060 (was already working with singleCpuIO ; now works also without);
2061 => no longer needs barrier call after reading a file (added inside
2062 mds_read/write field).
2063 - move barrier calls outside gather/scatter_2d to mds_read/write_field
2064 o pkg/obcs/exf
2065 - exf_getffieldrec.F: add a few ". _d 0" and
2066 add code to catch the case fldperiod = 0.
2067 - obcs_precribe_read.F: change if statements so that they match
2068 the variable type (_RL)
2069 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
2070 exf_iprec) as part of namelist EXF_NML_01
2071 o pkg/mdsio:
2072 - read/write tiled (local) files: read/write 1-level tile chunk at a time
2073 (instead of segment of length sNx); expected to speed up tiled IO.
2074 o pkg/exch2:
2075 - take buffer copy from/to array out of S/R exch2_send/recv into new
2076 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
2077 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
2078 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
2079 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
2080 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
2081 including Topology header file (and common blocks).
2082 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
2083 remove 2nd exch call in exch2_s3d_rx (no longer needed).
2084 - document S/R arg. list (+ update some comments)
2085 o pkg/seaice:
2086 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
2087 temperature and humidity over sea ice based on climatological values.
2088 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
2089 of LSR (this change is expected to change the results slightly because now
2090 it uses slightly difference moduli from the second last LSR solution, but
2091 that is more consistent with the stress computations; this part of the code
2092 is not tested in the verification experiments)
2093 - fix diagnostics for flux of ice in case of B-grid
2094 - turn strain rates eij and press into global fields within global
2095 common block in SEAICE.h for more straighforward diagnostics
2096 - fix diagnostics for principal stress components, press, zeta, eta
2097 to give something meaning full
2098 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
2099 new output (all 4 tests) using default rotationPeriod.
2100 o pkg KPP:
2101 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
2102 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
2103 and normal grid from 1 to Nr)
2104 o Fix computations of L4rdt in mom_calc_visc.F
2105 o eesupp:
2106 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
2107 should be called before a "stop" if we know that all process are going
2108 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
2109
2110 checkpoint61o (2009/05/26)
2111 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
2112 o model/src/ini_curvilinear_grid.F:
2113 compute angleSin/CosC when they are not read from a file
2114 o pkg/seaice:
2115 add pseudo time stepping for LSOR
2116 o pkg/exch2:
2117 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
2118 o pkg/seaice:
2119 Adding separate sea ice albedo, drag coefficients, and HO in Southern
2120 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
2121 o SingleCpuIO:
2122 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
2123 o pkg/seaice:
2124 put exchanged variable in (local) common block for MPI+Multi-Threads
2125 to work (necessary with exch1, and for now with exch2 too).
2126 o verification: to get more experiments tested with mpi, mth and mpi+mth,
2127 change tiling of:
2128 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
2129 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
2130 update output of exp:
2131 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
2132 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
2133 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
2134 (note: output.txt generated on faulks using only 1 tile)
2135 o eesupp & mdsio (SingleCpuIO):
2136 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
2137 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
2138 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
2139 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
2140 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
2141 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
2142 o pkg/exch2:
2143 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
2144 read parameter file "data.exch2" if it exists; otherwise try default regular
2145 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
2146 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
2147 with new code (not to be used, just as a backup solution).
2148 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
2149 in utils/exch2/input.
2150
2151 checkpoint61n (2009/05/12)
2152 o eesupp & mdsio (SingleCpuIO):
2153 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
2154 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
2155 receive real*4 array (instead of real*8) to read/write 32.bit files.
2156 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
2157 and remove new mapping S/R)
2158 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
2159 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
2160 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
2161 when using exch2. Add S/R to map global io-buffer to global model array.
2162 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
2163
2164 checkpoint61m (2009/04/29)
2165 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
2166 and add 3 other S/R for other types (R4,R8,RS).
2167 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
2168 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
2169 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
2170 - reduce number of macro definitions (keep only those which are used);
2171 can always call directly the corrresponding S/R if needed.
2172 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
2173 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
2174 Fixed wrong type of arg in:
2175 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
2176 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
2177 To fix: global_sum of var in common block is wrong (multi-threaded) in:
2178 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
2179 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
2180 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
2181 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
2182 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
2183 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
2184 edges are closed (zero depth); might happen with "blank tiles";
2185 for now, disabled if using OBCS.
2186 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
2187 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
2188 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
2189 to reduce length of 1.D array print in STDOUT.
2190 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
2191 + use 48 tiles (16x8): this will allow to test "blank tiles".
2192 o start to test MPI + multi-threaded (change testreport to skip tests
2193 where number of tiles do not match).
2194 o genmake2: add option "-omp" to turn on Open-MP ;
2195 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
2196 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
2197 and keep the original tile numbering. Note: compatible with old
2198 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
2199
2200 checkpoint61l (2009/04/07)
2201 o Overlaps had been forgotten in calculating ijk keys : fixed
2202 o fix cyrus makedepend for gcc 4.4
2203 o experiment fizhi-cs-aqualev20:
2204 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
2205 and generate new output. Note: new output is much closer to the old
2206 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
2207 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
2208 o pkg/fizhi:
2209 - change to avoid indices going deliberately over array-bounds
2210 - remove unnecessary MPI stuff
2211 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
2212 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
2213 does not go over array-bounds and therefore returns reliable output.
2214 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
2215 this S/R has 4 output arguments, which are used inside "get_alarm";
2216 when it is called with the same variable "ndum" in place of several
2217 output arguments, this produces weird side effect inside "get_alarm"
2218 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
2219 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
2220 address) and produces error.
2221 o tools/gemake2: (March 27-29 2009)
2222 with option "-mpi": link *_mpi files from "MODS" dir (this is what
2223 testreport does).
2224 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
2225 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
2226 update lab_sea.lsr & lab_sea.salt_plume results
2227 o pkg/seaice:
2228 Major overhaul of the LSOR solver: change discretization from original
2229 finite differences to finite volume. The old routine is still in the
2230 file seaice_lsr.F and can be turned on with the CPP-flag
2231 SEAICE_OLD_AND_BAD_DISCRETIZATION
2232 Along with this change, the discretization of the strain rates is changed.
2233 The same flag turns on the old discretization in seaice_calc_strainrates.F
2234 All verification experiments with seaice are affected (except for
2235 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
2236 results by setting the above flag.
2237 Further changes involve changes in defaults:
2238 - ALLOW_FLOODING is defined and turned on by default
2239 - SEAICEadvSnow = .true. is now the default
2240 - SEAICEadvSalt = .true. is now the default
2241 - SEAICEadvAge = .true. is now the default
2242 - SEAICE_clipVelocities = .false. is now the default
2243 (as per J. Zhang's recommendation)
2244 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
2245 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
2246 - seaice_growth: replace computation of UG by a simple copy from wspeed
2247
2248 checkpoint61k (2009/03/18)
2249 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
2250 seaice_lsr: fixed a few metric terms,
2251 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
2252 add more debugging diagnostics
2253 seaice_evp: removed superfluous many metric terms of FV discretization
2254 of stress divergence
2255 affects lab_sea, lab_sea.hb87
2256 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
2257 of stress divergence for non-evp solver
2258 (this part is not tested anywhere)
2259 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
2260 they were effectively only half slip
2261 affects lab_sea.hb87
2262 updated all relevant verification experiments (except lab_sea//output_adm.txt
2263 which was left over, but fails at level 7 & 6)
2264
2265 checkpoint61j (2009/03/17)
2266 o pkg/seaice: turn a few hard wired parameters into run time parameters
2267 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
2268 time in seconds as promised by the usints in seaice_monitor and exf_monitor
2269 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
2270 that are not cubed-sphere grids
2271 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
2272 o pkg/ctrl:
2273 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
2274 o non-hydrostatic (calc_gw.F):
2275 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
2276 update output of exp. global_ocean.cs32x15.viscA4
2277 o remove backward compatibility for thetaMin,phiMin
2278 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
2279 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
2280 interpolated wind field not only for curvilineargrid=.true., but also
2281 for a rotated grid (rotateGrid=.true.)
2282 o pkg/exf: add capability to bypass interpolation for runoff
2283 by setting yet another CPP-flag
2284 o eesupp/src, B-grid exchange:
2285 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
2286 o autodiff
2287 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
2288 allows to switch to single-prec common blocks;
2289 corresponding switch occurs in tamc.h, integer isbyte
2290 TAF store directivs "byte" and "kind" seem equivalent;
2291 Most tamc.h have been updated correspondingly.
2292
2293 checkpoint61i (2009/02/13)
2294 o autodiff:
2295 fix autodiff_sore/_restore indices for obcs
2296 (spotted by I. Hoteit, M. Mazloff)
2297 o pkg/autodiff, pkg/ctrl:
2298 Add flag to reduce all tapelev I/O to single-prec.
2299 In data.ctrl set
2300 doSinglePrecTapelev = .TRUE.
2301 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
2302 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
2303 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
2304 real fresh water flux (not yet)
2305 o pkg/mdsio & rw:
2306 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
2307 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
2308 o pkg/flt:
2309 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
2310 init_fixed & ini_varia.
2311 - clean-up & simplify linear interpolation S/R:
2312 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
2313 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
2314 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
2315 - add vert. coordinate & horiz. indices to output files.
2316 - change vertical position in initial condition, from index to depth [m].
2317 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
2318 (easier to get to a curvilinear grid) ; delX,delY no longer used.
2319 o pkg/ggl90: a few modifications:
2320 - fix bottom boundary condition, and interpolation of KappaE
2321 near top and bottom
2322 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
2323 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
2324 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
2325 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
2326 (maintain temporary backward compatibility, until next checkpoint)
2327
2328 checkpoint61h (2009/01/27)
2329 o pkg/diagnostics with "periodic averaging diagnostics":
2330 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
2331 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
2332 o pkg/obcs: fix loop ranges for balancing code
2333 o pkg/flt:
2334 - improve criteria for finding which tile owns a float.
2335 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
2336 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
2337 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
2338 with ocean biogeo)
2339 o pkg/flt:
2340 - do some cleaning and fix the restart ;
2341 - add output.txt in flt_example/results to get this pkg tested.
2342 o genmake2: add an EXTENDED_SRC option and flag.
2343 for now, cannot be turned on on command line (only through genmake_local)
2344 o pkg/mdsio: read/write vector:
2345 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
2346 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
2347 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
2348 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
2349 (drop to 4 digits matching for grad). But this test does not look very
2350 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
2351
2352 checkpoint61g (2008/12/29)
2353 o pkg/flt:
2354 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
2355 + make OPTIONS file more standard.
2356 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
2357 - fix _BYTESWAPIO CPP-Flag
2358 - standard reading of file-parameter "data.flt"
2359 - fix argument list of S/R FLT_RESTART
2360 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
2361 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
2362 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
2363 a still unfixed compiler/optimization bug
2364
2365 checkpoint61f (2008/11/21)
2366 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
2367 update results of global_ocean.cs32x15.icedyn test.
2368 o move getcon.F from model/src to pkg/fizhi.
2369 o pkg/exf: add parameter for extrapolation of temp up to the surface
2370 and option to prevent negative evap (in bulk_largeyeager04 only).
2371 o Prather Advection scheme: fix tracer conservation for divergent flow
2372 (e.g., when using NonLin Free-Surface).
2373 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
2374 o gmredi (Visbeck-variable-K):
2375 - add more parameters to Visbeck-variable-K.
2376 - use a 5 points average for dSigmaR in Visbeck-K calculation
2377 (more "homogenous": same stencil and same weights as in dSigmaH)
2378 - update output of ideal_2D_oce experiment.
2379 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
2380 (#undef REAL4_IS_SLOW)
2381 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
2382 coordinate variable
2383 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
2384 (surface forcing fields), removes some of the functionality
2385 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
2386 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
2387 probably not all: copy _RS surface flux fields to RL field before
2388 calling DIAGNOSTICS_FILL
2389 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
2390 real*4 (CALL EXCH_*_RS) versions.
2391 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
2392 (generate new output).
2393
2394 checkpoint61e (2008/10/23)
2395 o gmredi (Visbeck-variable-K):
2396 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
2397 - change computation of Visbeck-K where Slope > Smax :
2398 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
2399 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
2400 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
2401 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
2402 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
2403 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
2404 does not become too large (to avoid precision problems in implicit-diffusion
2405 solver); update ideal_2D_oce output.
2406 o pkg ggl90:
2407 - in ggl90_cal.F: compute only one set of visc/diff, used to
2408 step forward TKE/T/S/momentum
2409 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
2410 have Prandlt =1)
2411 o gmredi (fm07):
2412 - add lower limit on Transition layer thickness + lower limit on 1/lambda
2413 - allow to set few more params from data.gmredi
2414 o pkg ggl90:
2415 - add missing sqrt(2) factor in computation of mixing length
2416 scale in ggl90_calc.F
2417 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
2418
2419 checkpoint61d (2008/09/25)
2420 o adjoint modifs
2421 - adapt to new field rhoInSitu
2422 - allow to revert from StoreDynVars2D, StoreDynVars3D
2423 to individual fields
2424 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
2425 o store 3-D (in-situ) density in commom block (DYNVARS.h)
2426 - save 1 rho computation.
2427 - no longer modify T & S inland when using down_slope pkg.
2428 o gad_som : allow to switch to SOM advection for T & S without corresponding
2429 pickup files (using new S/R: MDS_CHECK4FILE).
2430 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
2431 (for useSingleCpuIO to work in multi-threaded)
2432 o pkg/shelfice:
2433 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
2434 with SHELFICEtopoFile in data.shelfice
2435 - move code for reading ice shelf topography and modifying hFacC into separate
2436 subroutines of the shelfice package
2437 - separate initialisation of "fixed" and "variable" variables
2438 - kTopC is not (yet) replaced by kSurfC, although this is possible
2439 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
2440 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
2441 and rename:
2442 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
2443 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
2444 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
2445
2446 checkpoint61c (2008/08/30)
2447 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
2448 to add mass source/sink of fluid in the interior (3-D generalisation
2449 of oceanic real-fresh water flux).
2450 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
2451 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
2452 o new pkg: down_slope
2453 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
2454 - presently, modify T & S inland (dwnslp_calc_rho.F).
2455 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
2456 - implementation for ocean in P-coords not tested.
2457 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
2458 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
2459 (to facilitate conversion of oceanic pkg to p-coordinate).
2460 o change FIND_RHO to FIND_RHO_2D :
2461 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
2462 o new pkg: cheapaml
2463
2464 checkpoint61b (2008/08/05)
2465 o exch2:
2466 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
2467 - no longer depend on the order sequence (N,S,E,W).
2468 - 3rd exchange no longer needed (tested with 24 tiles).
2469 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
2470 - exch_UV_A-grid readily available (but not yet tested).
2471 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
2472 (both are no longer needed) in exch_uv: no effect in forward run; but
2473 get truncation error differences with adjoint exch.
2474 o exch2:
2475 - change index-bounds storage (moved from target to local tile,
2476 more intuitive this way) ; rename/remove some variables.
2477 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
2478
2479 checkpoint61a (2008/07/29)
2480 o exch2/matlab-topology-generator:
2481 fix bug in index bounds for N-S internal exchange (hard to tell if this
2482 had any effect on the solution).
2483 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
2484 is exceeded
2485 o testreport: modify syntax of awk, so that it works also with
2486 awk, and not only with nawk and gawk
2487
2488 checkpoint61 (2008/06/24)
2489 o autodiff
2490 Change default for TAF usage by removing argument '-nonew_arg'
2491 This changes TAF subroutine argument list (ordering of active var.)
2492 Omission of this flag leads to incompatibility w.r.t. TAMC
2493 To restore TAMC-compatibility, need following modifs:
2494 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
2495 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
2496 Tested TAF version is 1.9.22
2497 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
2498
2499 checkpoint60 (2008/06/19)
2500 --->>> This is the last checkpoint for which generating the adjoint
2501 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
2502 --->>> by default.
2503 --->>> Future checkpoints will ommit this flag by default.
2504 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
2505 o pkg/grdchk: Add gradient check to etan0 perturbations.
2506 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
2507 o pkg/autodiff: more flexibility in zeroadj.
2508 model/src: modifying do_oceanic_phys.F accordingly.
2509 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
2510 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
2511 special setup of gmredi for which the adjoint is stable
2512 enough for parameter optimization.
2513 o bridging the gap between eddy stress and GM.
2514 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
2515 along with a change in CPP option (now ALLOW_EDDYPSI).
2516 -> when using GM w/ GM_AdvForm:
2517 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
2518 is applied either in the tracer Eq. or in momentum Eq.
2519 depending on data.gmredi (intro. GM_InMomAsStress).
2520 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
2521 The key modifications are in model/src/taueddy_external_forcing.F
2522 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
2523
2524 checkpoint59r (2008/05/29)
2525 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
2526 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
2527 fix option to read coriolis(@ cell-corner) from files with CS-grid.
2528 o pkg/mnc: add some attributes to standard 1D-coordinate variables
2529 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
2530 mass points, when using mnc for output
2531 - add runtime parameter (missing_value, missing_value_int) to override
2532 default (which is the value of getcon('UNDEF'))
2533 o pkg/mnc: prepare mnc for the actual use of missing values with the
2534 diagnostics package: small fix in mnc_cw_readwrite.template and more
2535 initialisation of never used fields
2536 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
2537 versions
2538 o pkg/thsice/thsice_ini_vars.F added default initial values so that
2539 thermodynamics sea ice solver does not blow up when some initial fields
2540 are missing.
2541 o move from external_forcing_surf.F to ini_forcing.F
2542 the p-coord. hack consisting in using pLoad to set phi0surf ;
2543 update output of tutorial_global_oce_in_p (affected @ truncation level).
2544 o Freshen up a bit hs94.1x64x5, notably:
2545 remove rotationPeriod and tRef=5*0. (adjoint only), and add
2546 exactConserv=.TRUE.
2547 o pkg/generic_advdiff:
2548 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
2549 applies to files where Temperature & Salinity 2nd Order moments are used.
2550 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
2551 this uses a dynamically allocated internal state data structure
2552 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
2553 and requires a fortran 90 compiler
2554
2555 checkpoint59q (2008/05/06)
2556 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
2557 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
2558 o Refresh tutorial_global_oce_biogeo, notably:
2559 - change bathymetry (put back seamounts in ACC, use hFacs)
2560 - change EOS (POLY3 --> JMD95Z)
2561 - use Bryan-Lewis vertical diffusivity
2562 - use multidimensional advection
2563 - remove old virtual virtual in dic pkg, now done through ptracer pkg
2564 - change a couple of parameters in dic pkg
2565 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
2566 o pkg/obcs: change default to OBCSfixTopo = .true.,
2567 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
2568 - replace "debugMode" with "debugLevel .GE. debLevB"
2569 o implementation of TAF directives for gchem,cfc,dic
2570 o remove "exp5" (replaced by tutorial_deep_convection).
2571 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
2572 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
2573 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
2574 --> changes results in exp4, seaice_obcs
2575 o tutorial_deep_convection :
2576 update the set-up and increase resolution and domain size ; start
2577 from pseudo initial conditions = output at t=120mn in order to see
2578 something happening when running testreport.
2579 o pkg/seaice: add os7mp as an advection scheme
2580 add check for advection schemes
2581 add a flag for restoring T and S underneath sea ice
2582 o pkg/my82: add netcdf-support and diagnostics
2583 o thsice pkg:
2584 - Now hsMax limits snow height by turning it into ice following
2585 flooding scheme (and now conserving energy)
2586 - Slight rewriting of the formula in thsice_calc_thick.F
2587 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
2588 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
2589
2590 checkpoint59p (2008/04/10)
2591 o gchem / dic / cfc :
2592 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
2593 - add new parameter files: "data.dic" & "data.cfc" ;
2594 - various re-arrangement in initialisation & header file ;
2595 - fix tutorial_global_oce_biogeo for multi-threaded test.
2596 o pkg/dic: test for "pickup_dic" file when restarting ;
2597 if no pickup-file, can restart with a re-initialised pH (same as it did
2598 before) providing pickupStrictlyMatch is set to False.
2599 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
2600 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
2601 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
2602 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
2603 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
2604 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
2605 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2606 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
2607 scheme to use for vorticty-term ;
2608 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2609 (with default selectVortScheme, return to original discretisation)
2610 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
2611 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
2612 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
2613 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
2614 also fix diagnostics VISCAHW & VISCA4W.
2615
2616 checkpoint59o (2008/03/07)
2617 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
2618 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
2619 move a few statemens out the main loop into separate loops
2620 o pkg/shelfice:
2621 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
2622 (kg/m^2/s), does not break tests, because in verification/isomip,
2623 rhoConstFresh=rhoConst (by accident)
2624 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
2625 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
2626 new file model/src/seawater.F, so that they are available for all pkgs.
2627 - convert potential temperature into in-situ temperature. This changes the
2628 isomip tests => update tests
2629 o add a flag writePickupAtEnd (default=true) to be able to suppress
2630 writing a pickup at the last timestep
2631 o tools/mpack-1.6 :
2632 - disable automake (not working) and autoconf (not needed).
2633 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
2634 also cleaner with much less compilation warnings.
2635 o pkg/profiles:
2636 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
2637 (for "less than 32 characters name" compiler requirement)
2638 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
2639 conditions that have a different sampling frequency than S/T/U/V obcs
2640 o pkg/diagnostics (stats-diags):
2641 - fix global Min/Max in case 1 processor get only empty tiles
2642 o genmake2: replace (4 times)
2643 make genmake_tc_1.o >> genmake_warnings 2>&1
2644 with
2645 COMM="$CC $CFLAGS -c genmake_tc_1.c"
2646 echo $COMM >> genmake_warnings
2647 $COMM >> genmake_warnings 2>&1
2648 to make genmake2 always see the value of CC as specified in the optfile.
2649 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
2650 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
2651 - modify verification advect_cs test to test SOM-advection on CS-grid.
2652 o pkg/ctrl:
2653 - Rewrite of ctrl_map_ini_ecco.F,
2654 introducing a generic routine (ctrl_map_ini_gen.F).
2655 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2656
2657 checkpoint59n (2008/02/09)
2658 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
2659 number in dedicate array "hdiag":
2660 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
2661 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
2662 - many small changes (integer format) for large number of diagnostics
2663 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
2664 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
2665 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
2666 usingSphericalGrid, this allows to define the rotated grid coordinates
2667 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
2668 geographical coordinates according to the inverse of the rotation defined
2669 by the Euler angles, so that Coriolis parameter and online-interpolation by
2670 exf works with the geographical coordinates on XC/YC/XG/YG.
2671 Naturally, this feature does not work with all packages, so some
2672 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
2673 profiles), because there the coordinates are assumed to be regular
2674 spherical grid coordinates.
2675 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
2676 - introduce isopycnal diffusion coefficient control.
2677 o tools/adjoint_options:
2678 - additional control vector components.
2679 o pkg/mnc: have mnc create marginally meaning full coordinate variables
2680 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
2681 o pkg/mypackage:
2682 - add example of read/write pickup for state-var ;
2683 - add entry points to the main code for state-vars diags & write-pickup.
2684 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
2685 transitions for useExfYearlyFields
2686 - add new subroutine that determines the file to read from for
2687 use*YearlyFields = .TRUE. and .FALSE.
2688 - add a verification experiment to global_with_exf that tests
2689 useExfYearlyFields with USE_EXF_INTERPOLATION defined
2690 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
2691 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
2692 subroutines (which could be generated from a template, because they are
2693 almost identical), for now they are included in obcs_prescribe_read.F for
2694 simplicity
2695 o pkg/exf:
2696 - add a little more diagnostic to exf_interp_read (in analogy to
2697 mds_read_field, can be turned off with debugLevel < debugLevA=1)
2698 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
2699 ugly but fast by unrolling short inner loops, inserting a unroll=8
2700 directive in routine lagran, and splitting a loop and making do while the
2701 outermost loop (the latter requires the intoduction of index arrays)
2702 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
2703 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
2704 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
2705 o verification/seaice_obcs: updated for restart test and latest options
2706 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
2707 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
2708 for now this is only available for the C-grid code and also within
2709 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
2710
2711 checkpoint59m (2008/01/14)
2712 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
2713 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
2714 o gad_som : fix flux output (& diagnostics) to have same units as other
2715 advection scheme fluxes (was previously multiplied by deltaT).
2716 o added verification/seaice_obcs both to test seaice open boundaries
2717 and to provide an example matlab scrpt for generating them
2718 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
2719 o pkg/salt_plume: clean up salt_plume_frac.F to
2720 remove redundancy in PlumeMethod 1 and 4
2721 o pkg/kpp: added saltplume diagnostics
2722 o pkg/obcs and pkg/seaice:
2723 - do not set uice and vice to zero when OB*icefile are unspecified
2724 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
2725 - moved seaice tracer obcs after call to seaice_growth
2726 o pkg/salt_plume: added various options for salt plume depth
2727 criterion and for vertical distribution of the salt
2728
2729 checkpoint59l (2007/12/18)
2730 o pkg/ptracers: new version of ptracers pickup:
2731 read meta file and write only fields which are needed to restart.
2732 ( same logic as main pickup file ; also using pickupStrictlyMatch )
2733 o pkg/seaice:
2734 - add timescale for melting due to warm mixed layer as a means of
2735 setting SEAICE_availHeatFrac more conveniently
2736 - add a CPP-flag/runtime parameter check for flooding algorithm
2737 - reformulated availHeat in seaice_growth.F to be independent of AREA
2738 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
2739 unit changes
2740 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
2741 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
2742 SX vector computer.
2743 o pkg/seaice:
2744 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
2745 seaice forcing fields can now be read only through pkg/exf
2746 - removed some unused halos
2747 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
2748 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
2749 or U/VICE from U/VWIND before computing U/VSTRESS
2750
2751 checkpoint59k (2007/11/30)
2752 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
2753 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
2754 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
2755 all experiments pass when compile with un-initialised var. checking option.
2756 o added pkg/salt_plume
2757 o script to test restart (for now, in MITgcm_contrib/jmc_script)
2758 o pkg/seaice: new read/write pickup version.
2759 read meta file and write only fields which are needed to restart.
2760 ( same logic as main pickup file ; also using pickupStrictlyMatch )
2761 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
2762 o lab_sea.hb87: modify the domain & update output.hb87.txt :
2763 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
2764 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
2765 process. Fixed here by closing the domain at the Northern boundary.
2766 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
2767 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
2768 a set of consecutive levels in/from a 3-D array.
2769 o pkg/ptracers:
2770 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
2771 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
2772
2773 checkpoint59j (2007/11/09)
2774 o in pkgs: dic, obcs, offline, rbcs:
2775 standard way to compute coeff. for time interpolation between 2 time reccords
2776 which retains full precision (& make results less dependent on compiler).
2777 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
2778 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
2779 packages instead of reading ice cover and wind speed separately
2780 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
2781 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
2782 to allow to compile customized code before the update)
2783 o cleaning-up:
2784 - fix CPP instruction syntax in pkg/obcs
2785 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
2786 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
2787 - fix some threads issue in IO parts.
2788 o pkg/dic:
2789 - add tons of "_d 0" (--> much better testreports !)
2790 and then update outputs of tutorial_global_oce_biogeo
2791 o pkg/mom_fluxform:
2792 add a special version of momentum advection intended to conserve momentum
2793 next to a bathymetry step or a coastline edge. (default = off = #undef)
2794 o new read/write pickup version:
2795 - for now, only implemented for main (mdsio) pickup file.
2796 - write out only what is needed to restart; merge pickup_nh , pickup_ph
2797 and main pickup together.
2798 - read meta file; read only what is needed to restart; stop if a field
2799 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
2800 if it make sense (even if the restart is not perfect).
2801 - if no meta file, assume that pickup to read corresponds exactly to
2802 a pickup that would currently be written.
2803 - read pickup written in the old format (until checkpoint59i) if it
2804 recognizes an old meta file (no field-list).
2805 - add a meta file in exp. which starts from a pickup: 2 cases:
2806 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
2807 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
2808 b) a meta file describing the content of the associated pickup file
2809 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
2810 o pkg/mdsio & pkg/rw:
2811 - new routine to read a meta file ; new set of routine to read
2812 Multiple-fields file (with meta file).
2813 o added open boundary conditions capability for seaice
2814 HSNOW, HSALT, UICE, and VICE
2815
2816 checkpoint59i (2007/10/21)
2817 o adjoint:
2818 * fix multiDimAdvection adjoint
2819 (partial recomputation problem by TAF for fVerT(:,:,kDown)
2820 and comlev1 size definition (maxpass vs. max. number of tracers)
2821 * verification/global_ocean.90x45x15 adjoint now tests
2822 NLFS and multiDimAdvection using DST3 (=30)
2823 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
2824 o pkg/kpp: add "_d 0" to real constant (if missing);
2825 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
2826 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
2827 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
2828 for internal parameters related to restart process (formerly from PARAMS.h)
2829 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
2830 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
2831 as argument. (only atm2d & obcs write_pickup have not yet been updated)
2832 o pkg/monitor:
2833 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
2834 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
2835 - account for deep Atmosphere factor and density factor (anelastic)
2836 o added open boundary conditions capability for seaice HEFF and AREA
2837 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
2838 thermodynamics
2839 - requires a little reorganization, which affects the testreport results
2840 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
2841 so that now the conservative form is tested
2842 - add a few comments
2843 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
2844 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
2845 o add new diagnostics to seaice: advective, diffusive fluxes (only for
2846 multidim-advection, for scheme 2 they are not filled) and transports,
2847 thermodynamic growth rates
2848 o change units of EmPmR (inside the code, + within coupling interface)
2849 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
2850 Affects results @ truncation level (cg2d match) and update output of
2851 experiments: lab_sea(6), global_ocean.90x40x15(10),
2852 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
2853 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
2854 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
2855 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
2856
2857 checkpoint59h (2007/09/29)
2858 o pkg/exf:
2859 - improve vectorization by moving if-statement out of loops in
2860 exf_mapfields, exf_radiation
2861 - exf_bulkformulae.F: introduce 2D fields and vectorize code
2862 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
2863 o testreport:
2864 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
2865 monitor & update offline_exf_seaice exp. output.
2866 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
2867 o pkg/seaice:
2868 - bug fix in the evp solver: boundary conditions were affected be
2869 masking of zMax/zMin (changes results)
2870 - minor bug fix in boundary conditions in seaice_calc_strainrates
2871 (changes results for no_slip)
2872 - seaice_lsr.F: make interpolation of eta dependent on boundaries
2873 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
2874 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
2875 stress formulation and no-slip boundary conditions
2876 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
2877 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
2878 o pkg/seaice: a first HSALT time stepping equation has been checked in
2879 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
2880 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
2881 without requiring DO-IF statements
2882 o pkg/thsice:
2883 use continuous power-law function for partition of energy between lateral
2884 melting/freezing and thinning/thickening ; old code using step function
2885 still available with #undef THSICE_FRACEN_POWERLAW
2886 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
2887 o testreport: change AD testing : check against results/output_adm.txt
2888 using same scripts as for forward test.
2889
2890 checkpoint59g (2007/09/17)
2891 o adjoint testing: in preparation for changing testreport:
2892 - output format: cost and grad written on separated lines
2893 - ad output results in directory "results" (instead of "results_ad")
2894 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
2895 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
2896 o pkg/ecco: allow user defined cost function contributions
2897 o testreport:
2898 Allow to choose (per experiment) the list of tested output variables
2899 and the main variable (used to issue a pass/FAIL ) ;
2900 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
2901 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
2902 Also modify printing of summary:
2903 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
2904 b) echo the list of tested variables in the individual summary.txt of
2905 each experiment.
2906 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
2907 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
2908 (but still depend on the tile decompostion of the domain).
2909 o pkg/seaice: change a discretization detail to make the B-grid code
2910 "more symmetric". This change is likely to remove all "ridges/leads" that
2911 where quasi-aligned with the grid in B-grid solutions. It may also be
2912 the solution to the stress coupling issues with the B-grid.
2913 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
2914 remove .cvsignore from input dir. (since testreport no longer run here).
2915 o pkg/thsice:
2916 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
2917 - fix reshaping of sea-ice just after advection:
2918 melt all the ice only if ice-volume is too small.
2919 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
2920 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
2921 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
2922 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
2923 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
2924 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
2925 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
2926 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
2927 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
2928 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
2929 -> update output.txt
2930 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
2931 this affects truncation error: -> update output.txt of exp:
2932 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
2933 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
2934
2935 checkpoint59f (2007/08/21)
2936 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
2937 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
2938 a bounded range (in forward mode)
2939 o pkg/ecco, ctrl, autodiff and mom_common:
2940 internal parameter controls, completements of implementations
2941 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
2942 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
2943 (not seem any difference in testing results).
2944 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
2945 at face corners.
2946 o pkg/generic_advdiff:
2947 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
2948 loop range indices for computing vertical advection tendency
2949 and do the calculation in the interior only (no overlap) ;
2950 for now, only implemented for SOM advection (to save CPU time).
2951 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
2952 o exch2 adjoint
2953 First set of changes:
2954 - add exch2 hand-written adjoint templates
2955 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
2956 This will require cleanup in pkg/autodiff/*.F
2957 (changed routines currently kept separate in verif. code/)
2958 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
2959 that used to hide exch2 or cubed-sphere specific code
2960 (commented via 'cph-exch2')
2961 o pkg/seaice
2962 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
2963 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
2964 output of global_ocean.cs32x15.thsice .
2965
2966 checkpoint59e (2007/07/26)
2967 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
2968 for B-grid vector (not yet tested) and C-grid vector (<- only used
2969 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
2970 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
2971 (#ifdef ALLOW_SALT_PLUME)
2972 o gather_2d/scatter_2d: removed halo regions
2973 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
2974 scheme and the corresponding test case (under front_relax dir). For now,
2975 only available with Skew-flux form and not yet tested in realistic set-up.
2976 adjoint: store directives updated, but gradient checks deteriorated,
2977 so maybe GM/Redi adjoint is now broken.
2978 o seaice adjoint
2979 * add AREA, HEFF, HSNOW as control variable
2980 (should not change lab_sea results)
2981 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
2982 o pkg/seaice:
2983 * added computation of saltFlux in seaice_growth;
2984 For time being, sea ice salinity is assumed constant
2985 contribution of snow flooding to freshening of sea ice is neglected.
2986 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
2987 defaults to 0.0 in order to maintain backward compatibility.
2988 Typical values for SEAICE_salinity are 4 to 10 g/kg.
2989 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
2990 * added SEAICE_availHeatFrac, which specifies fraction of surface level
2991 heat content used to melt or grow ice
2992 * commented out cap of HICE: it helps keep ice thinner
2993 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
2994 * applied OBCS T/S mask to HEFFM sea ice mask
2995
2996 checkpoint59d (2007/06/21)
2997 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
2998 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
2999 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
3000 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
3001 and change default value of parameter "GM_Small_Number";
3002 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
3003 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
3004 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
3005 o pkg/ecco: cost function when applying pkg/smooth to controls
3006 o pkg/ctrl: add forcingPrecond run time parameter
3007 o pkg/seaice:
3008 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
3009 - fix bug in metric terms of u-equation in LSR solver (implicit part),
3010 changes verification/lab_sea
3011 - rearrange implicit part of u-equation in LSR solver to make it easier to
3012 read, understand, and debug. This causes changes at the truncation level.
3013 - fix (serious) bug in the boundary conditions (sign error in the implicit
3014 part) of the LSR solver. Changes all LSR results.
3015 - fixed problem with HSNOW initialization to avoid thick snow when AREA
3016 is initilized with small values - does not change lab_sea results.
3017 - added HsnowFile initialization capability
3018 o pkg/smooth: addition to model/src and pkg/ctrl so allow
3019 initialization of pkg/smooth and application to control vector
3020 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
3021 o dependencies: pkg/profiles requires pkg/cal
3022 o pkg/profiles:
3023 - added option ALLOW_PROFILES_GENERICGRID
3024 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
3025 that interpolation information (grid points and coefficients) is provided
3026 within the netcdf input files.
3027 -> sample matlab scripts can be found in MITgcm_contrib/gael
3028 that allow you to prepare netcdf input files.
3029 - also modified: cleaner include statements, cleaner error print statements,
3030 cleaner stops when error, and more tests of the netcdf input files consistency.
3031 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
3032 o pkg/seaice:
3033 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
3034 requires a new routine: seaice_diagnostics_fill.F
3035 - make sure that seaice does not move if not forced (pressure replacement
3036 method, Hibler and Ip, 1995), changes results
3037 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
3038 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
3039 It is turned off by default (=-1.), because it changes the results.
3040 - make it possible to read AREA from a file, too.
3041
3042 checkpoint59c (2007/06/04)
3043 o add S/R and diagnostics for oceanic mixed-layer depth
3044 o move GMRedi call after all vertical mixing schemes (including KPP)
3045 o pkg/thsice:
3046 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
3047 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
3048 o pkg/obcs:
3049 - bug fix for balance code
3050 o pkg/seaice:
3051 - allow values of SEAICE_elasticParm > 1
3052 - add new parameter SEAICE_evpTauRelax as an alternative
3053 to SEAICE_elasticParm
3054 - make lsr boundary conditions free slip (by default), changes result
3055 - add code for no slip boundary conditions for lsr
3056 - set minimum of zeta to zero (and not 4e8) (changes results)
3057 - add a cap on AREA after advecting AREA if seaice_growth is not called
3058 o change calculation of Visbeck K:
3059 - no longer depend on tapering scheme; instead, compute slope (limited
3060 by GM_maxSlope). this is equivalent to what was comuted before with
3061 clipping or linear tappering.
3062 - fix vertical averaging (wrong by 1/2 level)
3063 - leave the old version (but will not be maintained) within
3064 #ifdef OLD_VISBECK_CALC / #endif
3065 - update output of exp. ideal_2D_oce
3066 o change error catch in calc_r_star to improve vectorization
3067 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
3068 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
3069 o adjoint:
3070 Re-organized adjoint checkpointing according to Matt Mazloff
3071 (but with modifs/completions/cleanups)
3072 Storing is now bundled into large arrays to optimized I/O
3073 (and second step in cleanup of the_main_loop)
3074
3075 checkpoint59b (2007/05/16)
3076 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
3077 - export/import (between ocean & coupler) fields needed for ocean DIC.
3078 o pkg/seaice:
3079 - get rid of three more exchanges seaice_calc_viscosities (required
3080 different loop boundaries in seaice_lsr and seaice_ocean_stress)
3081 - bug fix in seaice_ocean_stress (update of lab_sea required)
3082 - reduce loop boundaries to necessary minimum also in seaice_evp
3083 - go back to the old way of computing deltaC/Z as the adjoint likes that
3084 better
3085 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
3086 passive tracer to an Age Tracer) + update output.txt
3087 o pkg/exf:
3088 - implement A-grid / C-grid selection for wind-stress input files.
3089 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
3090 for now, in exf_bulk_largeyeager04.F only :
3091 - change implementation for case where windspeed + 2. components wind-stress
3092 are read-in. AND use rhoConstFresh to convert evap.
3093 o pkg/seaice:
3094 - use correct EXCH_UV for wind-forcing (on A-grid).
3095 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
3096 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
3097 o pkg/exf:
3098 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
3099 EXF_INTERPOLATION:
3100 - merge global_with_exf/code version of exf_interp_read.F
3101 to the main code ;
3102 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
3103 reading the file ; Important: This options needs to be defined to recover
3104 previous code.
3105 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
3106 - no longer loose real*8 precision along the way when using exf_iprec=64.
3107 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
3108 - change discretisation of evp-solver in order to avoid another exchange
3109 (changes lab_sea) and clean up a little
3110 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
3111 help the adjoint (this also changes the results slightly)
3112 - add a few "_d 0" where they had been missing in seaice_evp.F
3113 - cleaning up: remove unused seaice_calc_rhs.F
3114 o pkg/exf: some cleaning-up:
3115 - change various "constants" into runtime parameters
3116 - cleaned-up Large&Yeager04 routine which should eventually
3117 replace exf_bulkformulae.F (changed names of S/R and CPP)
3118 and merged various ALLOW_ATM_WIND options
3119 only used with thsice pkg (in thsice_get_exf.F):
3120 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
3121 which are used when useStabilityFct_overIce=TRUE (= the default)
3122 - change default values of ice & snow emissivity and scale downward LW
3123 by ice & snow emissivity.
3124 o pkg/thsice:
3125 fix few little problems, in thsice_calc_thickn.F:
3126 - growth vertically (and not laterally) if iceFrac == iceMaskMax
3127 - melt only laterally if hIce < hThinIce (as the comments say)
3128 and in thsice_extend.F:
3129 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
3130 - start to form ice as soon as the minimum ice-volume is reachable.
3131 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
3132 and cpl_aim+ocn
3133 o pkg/kpp
3134 - move computation of surface related input fields to KPP into a new
3135 subroutine kpp_forcing_surf.F
3136 - remove wrong (within bi,bj loops) EXCH calls.
3137 - little cleaning (add argument myThid in last position, cvs header ...)
3138 - for now, fix conservation problem by exchanging KPPviscAz (may not
3139 be the best fix)
3140 o pkg/seaice
3141 - check for inconsistent evp parameter/cpp-flag combination
3142 - remove leftover errIO flat for obsolete name list error handling
3143 o OpenAD
3144 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
3145
3146 checkpoint59a (2007/05/01)
3147 o pkg/seaice: some parameter clarifications and a little bit of clean up
3148 o pkg/thsice: rename run-time parameters:
3149 himin -> hIceMin
3150 himin0 -> hThinIce
3151 hihig -> hThickIce
3152 i0 -> i0swFrac
3153 transCoef -> bMeltCoef
3154 frac_energy -> fracMelting
3155 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
3156 with default values (for now) that do not change the results.
3157 remove old version of thsice vars advection in pkg/seaice.
3158 o in FFIELDS.h:
3159 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
3160 - make pLoad & sIceLoad always available (but still only used if
3161 ATMOSPHERIC_LOADING is #define).
3162 o pkg/kpp: replaced _KPP_RL with _RL
3163 o bug fixes for vertical diffusivity computations when both KPP and
3164 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
3165 are no longer updating the vertical diffusivity array
3166 (passed as argument) but are (re-) setting those arrays.
3167 o pkg/seaice: fix bug in evp solver, while doing that
3168 - change (improve?) discretization of stress computations for both
3169 cgrid-lsr and evp solver
3170 - add a new routine to compute strain rates
3171 - the above changes lab_sea results
3172 - add no slip conditions for evp solver (off by default), lsr-version
3173 may follow
3174 - fix exchange for shear at Z-points (does not change lab_sea)
3175 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
3176 (to force the user to pick a time step since there is not "safe" way
3177 of choosing it)
3178 - add principal stress diagnostics
3179 - rearrange fields for evp a little to avoid having to call a: too many
3180 exchanges and b: exchanges for stress trensor components which we do
3181 not have.
3182 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
3183 of evp, complete rewrite for lsr case (latter is does not yet work
3184 in all cases)
3185 o pkg/kpp: add code to have mixing in shelf ice caverns
3186 - add myThid to all kpp routines (long overdue)
3187
3188 checkpoint59 (2007/04/19)
3189 o pkg/exf:
3190 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
3191 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
3192 - move exf header files from lower_case.h to UPPER_CASE.h ;
3193 add missing cvs Header & Name
3194 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
3195 - add namelist param. selectStressGridPosition, exf_monFreq
3196 - retire many _CLIM routines, and remove data.exf_clim
3197 + params moved to data.exf
3198 + climsst, climsss now handled by exf_set_gen, i.e.
3199 climss?period=0 refers to constant field,
3200 climss?period=-12 to monthly forcing
3201 - split up namelists in data.exf
3202 o pkg/seaice:
3203 - remove seaice_exch and seaice_exch_uv
3204 - remove superfluous exchange of theta
3205 - add myThid to seaice_budget_ocean/ice
3206 - add new interface for atmospheric wind forcing (C-grid only)
3207 + new routine
3208 + two new field (taux, tauy for stress over ice)
3209 + removed one global field (DAIRN) for C-grid case only
3210 o pkg/thsise
3211 - 2nd set of modifs for thsice adjoint in conjunction with exf
3212 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
3213
3214 checkpoint58y_post (2007/04/15)
3215 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
3216 vertical diffusivity, similar to that in MOM4; turned on using
3217 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
3218 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
3219 o Added capability for 3D specification of background vertical diffusion
3220 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
3221 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
3222 "data" file that contains the 3D vertical diffusivity coefficients.
3223 o ice dynamics (pkg/seaice) with thsice thermodynamics:
3224 - add code within pkg thsice to advect & diffuse sea-ice fields
3225 similar to (and will replace) what has been added in seaice_advdiff.F,
3226 but: - conserving Mass, Heat & Salt.
3227 - better when using non-linear advection scheme (not yet fully tested)
3228 - can also be used in atmospheric set-up (for now, only the diffusion).
3229
3230 checkpoint58x_post (2007/04/04)
3231 o IO option for global-file compact format:
3232 - add options when generating topology (utils/exch2/matlab-topology-generator)
3233 - add I/O capability (pkg/mdsio).
3234 - adapt utils/matlab/rdmds.m to read this format.
3235 for now long-line format not yet supported by pkg/mdsio (& exch2).
3236 o shelfice: add a few diagnostics
3237
3238 checkpoint58w_post (2007/03/13)
3239 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
3240 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
3241 (and replace horiVertRatio in NH code).
3242 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
3243 and tutorial_plume_on_slope (sensitive to truncation)
3244 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
3245 directly to drive seaice model (C-grid only)
3246 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
3247 - reintroduce computation of wind from stress,
3248 - compute tau (in exf_bulkformulae.F) from windstress averaged to
3249 mass points to avoid tau = 0
3250 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
3251 o rdmnc.m: make it work with "global" files created with gluemnc
3252 o rdmnc.m : some improvements in dealing with singleton dimension
3253 (tested on all testreport mnc output files).
3254 o genmake2: disable pkg/profiles if netcdf test fails.
3255 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
3256 o move call to cal_readparms up to make calendar parameters/variable available
3257 to all packages
3258
3259 checkpoint58v_post (2007/02/08)
3260 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
3261 useDynP_inEos_Zc tested.
3262 o pkg/exf: changes to properly interpolate/mask/scale initial fields
3263 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
3264 and portions thereof. See read_cs.txt for description and examples.
3265 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
3266 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
3267 following the great-circle arc between those 2 points.
3268 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
3269 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
3270 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
3271 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
3272 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
3273 - still needs work (not working with some options ; efficiency to improve)
3274 and serious testing.
3275 - use this scheme for temperature & salinity in 2 advection test exp.:
3276 advect_xy & advect_xz, respectively.
3277
3278 checkpoint58u_post (2007/01/12)
3279 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
3280 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
3281 o testreport: add option "-skipdir" to skip some test.
3282 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
3283 momentum calculation.
3284 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
3285 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
3286 remove checkpoint.F and the_correction_step.F (no longer used);
3287 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
3288 o add option (linFSConserveTr) to correct for tracer source/sink due to
3289 Linear Free surface
3290 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
3291 o pkg/thsice: fix reading mnc-pickups
3292
3293 checkpoint58t_post (2006/12/30)
3294 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
3295 o pkg/mdsio:
3296 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
3297 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
3298 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
3299 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
3300 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
3301 either MDS_READ_FIELD or MDS_WRITE_FIELD )
3302 - new S/R (to replace MDSWRITEMETA), which allows to write more
3303 informations (variable names, time ...) to meta files.
3304 - modify rdmds.m to give back the meta file content.
3305 o pkg/diagnostics: change vertical interpolation to be safer, and more
3306 flexible (define p-levels to interpolate to in data.diagnostics);
3307 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
3308 diagnostic pointer.
3309 o pkg/seaice: more cleaning up of seaice_growth, added many comments
3310 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
3311 o fix multi-category seaice:
3312 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
3313 SEAICE_MULTICATEGORY
3314 - fix short wave heat flux
3315 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
3316 and allow to use EVP solver. Change forward lab_sea: test both EVP
3317 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
3318 o Initial check-in of lab_sea adjoint
3319 (very similar to natl_box_adjoint/code_seaice)
3320 * used C-grid and EVP solver
3321 * used KPP, GM/Redi
3322 * uses inAdExact=.TRUE.
3323 * gradient checks fail for both ADM and TLM
3324 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
3325 f.d. gradients actually seem more problematic than ADM, TLM gradients;
3326 issue is related to forward mismatch between g77 an ifort
3327 o pkg/seaice: overhaul of thermodynamics
3328 - growth.F and groatb.F are replaced by new routine seaice_growth.F
3329 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
3330 - move a few global fields out of SEAICE.h into seaice_growth.F and
3331 make them 2D (FICE/QNETO/ ...)
3332 - remove FO (it is the same as QNETO)
3333 - introduce a few local fields to avoid modifying external fields such
3334 as atemp, etc.
3335
3336 checkpoint58s_post (2006/12/11)
3337 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
3338 changed exf_set_gen.F so that
3339 genperiod=0 means input file is one time-constant field and
3340 genperiod=-12 means input file contains 12 monthly means
3341 o CG2D: use pre-computed solver main-diagonal (stored in common block);
3342 this affects truncation error ; generate new output file for exp. which
3343 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
3344 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
3345 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
3346 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
3347 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
3348 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
3349 o start implementation of deep-atmosphere and anelastic formulation
3350 o verification: remove 2nd copy of input files and use script "prepare_run"
3351 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
3352 o mom_common/vecinv/fluxform: fix a few initialisation isssues
3353 o profiles: fix for multithreaded case
3354
3355 o diagnostics: rename few diags:
3356 s/'PRESSURE'/'RCENTER '/g
3357 s/'TICE '/'oceFreez'/g
3358 s/'TAUX '/'oceTAUX '/g
3359 s/'TAUY '/'oceTAUY '/g
3360 s/'SWFLUX '/'oceQsw '/g
3361 s/DIFx/DFxE/g
3362 s/DIFy/DFyE/g
3363 and add few ocean-forcing diagnostics:
3364 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
3365 o modifications to pkg/seaice/growth.F and budget.F, which change results of
3366 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
3367 as actual snow thickness. It now refers everywhere to effective snow
3368 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
3369
3370 checkpoint58r_post (2006/11/17)
3371 o modifications to pkg/seaice/growth.F, which change results of
3372 lab_sea experiment: fixes pertain to melting snow over open water, to
3373 masking EVAP under sea ice, and to using the correct AREA variable for
3374 computations of EVAP, PRECIP, HSNOW, and GHEFF
3375 o add ability to read bathy, salt, and theta using MNC (off by def)
3376 o add flooding algorithm and advection of HSNOW for pkg/seaice;
3377 both are turned off by default and do no change any results
3378 o seaice advection with pkg/thsice: a step toward the use of non-linear
3379 advection scheme, but #ifdef or commented out for now (requires more EXCH).
3380 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
3381 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
3382 in natl_box (affects results @ truncation level: update output.txt)
3383 o multi-threading and IO:
3384 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
3385 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
3386 (needed to work with SingleCpuIO): tested in all verif. exp.
3387 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
3388 affects the results (but none of the verification test uses this scheme).
3389 o Adding some pkg/diagnostics capability to pkg/seaice
3390 (will certainly be subject to changes)
3391 o ctrl: adding new control variables:
3392 lwflux, lwdown, evap, snowprecip, apressure, runoff
3393
3394 checkpoint58q_post (2006/10/20)
3395 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
3396 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
3397 high_res_cube configuration by 4% on Columbia.
3398 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
3399 add (in global_with_exf/code) a version of EXF_INTERP_READ without
3400 dynamical allocation (seems to work in multi-threaded).
3401 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
3402 single CPU io) so that TAF does not have to see EESUPPORT.h
3403 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
3404
3405 checkpoint58p_post (2006/09/08)
3406 o obcs: stop if obcs is used with useCDscheme = .true.
3407 o shelfice:
3408 - fix a sign error so that no slip at shelfice interface works
3409 - remove stop for combination non-hydrostatic code and shelfice. That does
3410 not mean, that the results are correct, but at least they are numerically
3411 stable
3412 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
3413 o added adjoint exch routined for all exch*3d* routines
3414 and updated flow directives
3415
3416 checkpoint58o_post (2006/08/28)
3417 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
3418 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
3419 o change controling S/R for writing pickup file (new S/R do_write_pickup)
3420 and clean-up reading/writing of pickup files.
3421 o fix local version of read/write pickup (NH part) in rotating_tank/code
3422 o simplify EXCH interface:
3423 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
3424 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
3425 o added the regrid package
3426 o shelfice:
3427 - add a simple boundary layer scheme to reduce noise
3428 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
3429
3430 checkpoint58n_post (2006/08/14)
3431 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
3432 local variable (not in common block).
3433 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
3434 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
3435 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
3436 to work with SingleCpuIO.
3437 o add "_d 0" to real constant of pkg/cfc subroutines ;
3438 update exp. cfc_exemple & tutorial_cfc_offline output files.
3439 o multi-threading and IO:
3440 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
3441 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
3442 - barrier before and after reading.
3443 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
3444 - avoid using MDS_WRITELOCAL for LAND pkg output.
3445 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
3446 common-block variables ; Allows multi-threading with master-thread IO.
3447 o change default MAX_NO_THREADS from 32 to 4 ;
3448 and stop cleanly when MAX_NO_THREADS is too small.
3449 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
3450
3451 checkpoint58m_post (2006/07/17)
3452 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
3453 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
3454 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
3455 keep global_ocean.90x40x15 (for AD testing) with former secondary test
3456 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
3457 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
3458 add MITgcm_tutorials (= code + all the tutorials)
3459 o ecco, option to compute cost for total ssh (mean+anom)
3460 o consistent with addition of ptracer and ssh in pkg/profiles
3461 o profiles: adding ptracer and ssh
3462 o testreport: change multi-test output-file name
3463 (from output.txt.{name} to output.{name}.txt)
3464 o profiles: now ok for mutli-tiles case
3465 o seaice: add 4 parameters for different advection schemes for area,
3466 (effective) seaice thickness, enthalphy, and snow height. Their default
3467 is the standard parameter SEAICEadvScheme
3468 o calc_gw:
3469 - add cosFacU in zonal viscous flux (harmonic.visc.).
3470 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
3471 of tutorial_plume_on_slope.
3472 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
3473 o calc_gw: true flux-form, account for horizontal grid spacing.
3474 update rotating_tank results, but not plume_on_slope (affected at
3475 truncation level, 11 digits).
3476
3477 checkpoint58l_post (2006/07/12)
3478 o calc_gw:
3479 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
3480 - remove side-drag for now (need to fix it); update plume_on_slope results.
3481 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
3482 o commit code to make SST/SSS weights spatially variable
3483 (based on either variable in-situ or variable initial T/S weights)
3484 o pkg/ecco:
3485 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
3486 now based on horizontally varying weights wthetaLev, wsaltLev
3487 * cost_averagesflags now returns year indices in addition to day, month
3488 * sflux balance is performed on annual basis
3489 (sflxumm, sfluxmm2, bal_sfluxmm)
3490 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
3491 including separate counting and multipliers
3492 o pkg/rbcs
3493 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
3494
3495 checkpoint58k_post (2006/07/06)
3496 o testreport:
3497 - always build in dir. "build" (if not there, mkdir build instead of building
3498 & running in input)
3499 - run in dir run (if it exists), in build otherwise.
3500 - call prepare_run (if input/prepare_run exists)
3501 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
3502 o pkg/exf modifications to interpolation and rotation routines for more
3503 reasonable treatment of North Pole singularity: for tracers North Pole
3504 value is set to northernmost zonal-mean value, for zonal velocity it is
3505 set to zero, and for meridional velocity it is set to northernmost value.
3506 o pkg/exf/exf_check_range.F
3507 - add tile index to diagnostics and move stop statement to the very
3508 end of the routine.
3509 o pkg/diagnostics: (diagnostics_main_init.F)
3510 define title of isomorphic variables according to the current config.
3511 o pkg/thsice with pkg/seaice dynamics:
3512 - fix domain of computation (interior only, required for exf) and do exchanges
3513 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
3514 o towards a standard way of dealing with multi-threading in MONITOR
3515 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
3516 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
3517 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
3518 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
3519 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
3520 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
3521 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
3522 o tracer advection:
3523 - clean-up and simplify calc_common_factors.F
3524 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
3525 advection subroutine (but still not used within DST advection S/R)
3526 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
3527
3528 checkpoint58j_post (2006/06/15)
3529 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
3530 from file (collects calls previously in FORWARD_STEP)
3531 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
3532 o adjoint store dir. adjusted accordingly
3533 o genmake2
3534 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
3535
3536 checkpoint58i_post (2006/06/14)
3537 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
3538 on wind stress (SEAICEstressFactor defaults to 1.)
3539 o Total number of Timers is finite (<=40): comment out 2 non-essential one
3540 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
3541 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
3542 on CS-grid: no longer loosing mass.
3543 o exf & curvilinear-grid: no longer modify longitude xC & xG.
3544 o pkg/ggl90: fix sloppy output and fix a bug
3545 o pkg/seaice: added SEAICEuseEVPpickup parameter
3546 - Set to false in order to start EVP solver with
3547 non-EVP pickup files when using SEAICEuseEVP
3548 - fix sign error in diffusion in seaice_calc_rhs
3549
3550 checkpoint58h_post (2006/06/07)
3551 * Modifications for bottom topography control
3552 o replace hFacC by _hFacC at various places
3553 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
3554 o add non-self-adjoint cg2d_nsa
3555 o update autodiff support routines
3556 o re-initialise hfac after ctrl_depth_ini
3557 o works for 5x5 box, doesnt work for global_ocean.90x40x15
3558 * Adding verification for 5x5 box (4-layer) bottom topography control
3559
3560 checkpoint58g_post (2006/06/07)
3561 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
3562 used for mean seasonal cycle, mean diurnal cycle); add an example
3563 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
3564 o pkg/ggl90:
3565 - add parameter (minimum surface kinetic energy)
3566 - fix bug (avoiding division by zero)
3567 o couple pkg/thsice to pkg/seaice:
3568 - modify advection in seaice to accomodate new scalar fields to be advected
3569 - only muliDimAdection scheme work with seaice/thsice
3570 - mapping of thsice-variables to seaice-variables, back and forth
3571 - does not break the verification experiments, but does not give the
3572 desired results either
3573 o pkg/seaice
3574 - make (default) second order advection a bit less confusing?
3575
3576 checkpoint58f_post (2006/06/05)
3577 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
3578 to pkg/seaice):
3579 - new routines thsice_map_exf and thsice_get_exf provide the interface
3580 - add an additional formal parameter to thsice_solve4temp
3581 o pkg/exf:
3582 - add new fields wspeed, snowprecip (to be able to couple to thsice)
3583 - correct Stefan-Boltzmann constant
3584 - new parameter for longwave surface emittance
3585 - separate some stuff from exf_bulkformulae into new routines
3586 exf_radiation, exf_wind
3587 - add new parameters and constants: longwave emissivity for ocean, ice
3588 and snow, evaporation parameters over ice
3589 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
3590 either wind from stress or stress from wind
3591 o pkg/thSIce:
3592 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
3593 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
3594 and THSICE_CALC_THICKN
3595 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
3596 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
3597 to make debugging easier.
3598 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
3599 o pkg/bulk_force:
3600 - clean-up comments and parameters ;
3601 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
3602 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
3603 generate new output for test-experiment: aim.5l_cs.thSI
3604 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
3605 testreport accordingly
3606
3607 checkpoint58e_post (2006/05/17)
3608 o SEAICE_CGRID adjoint done
3609 o R_STAR adjoint implemented.
3610 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
3611 * need to sort out init. of h0facc, etc.
3612 o Make pkg/profile fully independent of ecco,cost, etc. stuff
3613 to be able to use it in pure forward.
3614
3615 checkpoint58d_post (2006/04/21)
3616 o upgrade simple test-experiment to tutorial example:
3617 step.1: duplicate the experiment and (step.2) will remove the old copy.
3618 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
3619 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
3620 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
3621 tutorial_global_oce_biogeo <- copy of dic_example
3622 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
3623 tutorial_plume_on_slope <- copy of plume_on_slope
3624 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
3625 tutorial_global_oce_optim <- empty for now (David ?)
3626 tutorial_global_oce_in_p <- copy of global_ocean_pressure
3627 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
3628 o correct a sign problem in cost_scat.F
3629 o obcs and ptracers: fix boundary conditions for advections schemes
3630 with larger stencil
3631 o thsice adjoint: start
3632 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
3633 completeness
3634 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
3635 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
3636 o ptracers adjoint:
3637 * avoid extensive recomputatations
3638 * fix missing re-init. of gptr (missed by TAF)
3639 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
3640 me to turn off the excessive output to STDOUT that this package produces
3641 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
3642 and add those terms in Vector-Invariant formulation.
3643 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
3644 if the control period (xx_hfluxperiod etc) is 0
3645 o in profiles pkg, clean routines and fix details
3646 o in ecco pkg, reading ssh data:
3647 fix problem in case the model does not start at iter0=0
3648 o fix mnc-pickup/restart for ptracers
3649 o new package prifiles:
3650 code to compute profile-based cost by Gael Forget
3651 (modifs in ecco, ctrl, autodiff)
3652 o Benign bug fix in initialization (spotted by M. Mazloff) of
3653 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
3654
3655 checkpoint58c_post (2006/03/23)
3656 o adjoint: finish NLFS adjoint and provide reference output in
3657 verification/global_ocean.90x40x15/results_ad_nlfs
3658 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
3659 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
3660 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
3661 with SEAICE_CGRID defined.
3662 o move calendarDumps from "data" to "data.cal" and clean-up the code
3663 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
3664 o add useEXF & useCAL flags (for now, set in hard-coded way)
3665 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
3666 (were missing in NH mode, and wrong in quasihydrostatic mode).
3667 waiting for Chris updated version of calc_gw to add those CALLs.
3668 o fix bug in quasihydrostatic S/R ;
3669 add a test for this option: global_ocean.90x40x15.qshyd
3670 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
3671 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
3672 o add on/off flag useOffLine for package OFFLINE
3673 o seaice:
3674 - modify advection so that it works also on the C-grid
3675 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
3676 problem in multi-tile runs with C-grid
3677 - add flags for clipping ice velocities and/or masking solver forcing
3678 - fix drag (ocean on ice) formulation and a bug that caused noise in the
3679 C-grid solver
3680 - added a few comments to seaice_diffusion.F
3681 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
3682 are now exclusive)
3683 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
3684 required re-ordering the code a little:
3685 + make DAIRN global variable (defined in SEAICE)
3686 + move computation of the viscosities eta and zeta into a new separate
3687 routine (because I need to recompute them in seaice_ocean_stress.F)
3688
3689 checkpoint58b_post (2006/03/13)
3690 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
3691 update output.txt of exp. aim.5l_cs.thSI
3692 o various mnc cleanups and improvements:
3693 + shrink lookup tables by factor of ~4
3694 + better error reporting when running out of lookup space
3695 + able to handle longer path/file names (up to 500 chars)
3696 o adjoint:
3697 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
3698 - TBD: "hidden" mom_vecinv recomp. in dynamics
3699 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
3700 (allow to differentiate between forcing components using new integer flags:
3701 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
3702 and add new flag to put Dissipation tendency out of Adams-Bashforth.
3703 o ecco
3704 - enable trend removal from SSH anomaly obs.
3705 o adjoint
3706 - a fix for PmEpR when #undef EXACT_CONSERV
3707 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
3708 - try to fix "hidden" recomp. in forward_step for NLFS
3709 (NLFS seems broken sometimes after I checked it in)
3710 o seaice:
3711 - add c-grid version of the dynamic solver:
3712 + three new routines that are the c-grid substitute lsr, dynsolver
3713 and ostres
3714 + put a few fields that were local to dynsolver into global common
3715 blocks, so that I can move the computation of stresses etc into
3716 seaice_lsr (saves coding but may break the adjoint).
3717 - replace more hardwired parameters by runtime parameters
3718 - add ice masks that mask the rhs of the implicit solvers where there
3719 is no ice (commented out in seaice_dynsolver, because i am not sure
3720 if this works properly), eventually this should replace the clipping
3721 of ice velocities in seaice_dynsolver to +/-40cm/s.
3722 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
3723 include it only where its needed
3724 o move balancing of fluxes before the call of external_forcing_surf
3725 o seaice:
3726 - correct units of turning angles (now they are really in degrees)
3727 - move computation of GWATX/Y out of main routine into dynsolver
3728 - initialize GWATX/Y in seaice_init
3729 o Apply mask on Fresh-Water flux (needed for SSH forcing).
3730 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
3731 o seaice: add runtime flags for turning angles (default to zero)
3732 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
3733 and trend from exf forcing and ctrl control adjustments
3734 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
3735 (since checkpoint57x_post)
3736 o change the default rotation period to 86164.s = the Earth rotation
3737 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
3738 and based on a reference stratification. Tested within hs94.cs-32x32x5.
3739 o seaice advection: add code for choosing between the default (2nd order
3740 central differences) and multiDim advection schemes provided by
3741 pkg/generic_advdiff
3742 o seaice:
3743 - removed all references to SEAICE_GRID.h fields from
3744 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
3745 (cubed-sphere configuration will change a little)
3746 - grid computations in seaice_init are obsolete now.
3747 - cleaned up code a little so that is easier to read (hopefully).
3748 - added new (better?) discretizations of default advection and diffusion
3749 (turn on with SEAICEuseFluxForm)
3750 - replace 1 in 3d global fields by kSurface in growth.F
3751
3752 checkpoint58a_post (2006/02/13)
3753 o seaice:
3754 - bug fix in advect.F
3755 o shelfice:
3756 - separate shelfice load anomaly from pload (breaks with time
3757 dependent forcing), => introduce constant field shelficeLoadAnomaly.
3758 Its default is 0., but it may be computed more cleverly from (unknown)
3759 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
3760 done offline. A good approximation of the pressure load anomaly is
3761 necessary to avoid large initial adjustment processes underneath
3762 deep-reaching shelfice.
3763 - small fix in ISOMIP shelfice_thermodynamics
3764 - add more sophisticated thermodynamics of Hellmer (1989), this is
3765 now the default
3766 - give a few constants more intuitive names
3767 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
3768 if bulk formulae are used in long integration (especially EmPmR). Turn
3769 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
3770 if balancePrintMean, the imbalance that is substracted is printed to
3771 STDOUT.
3772 o fix bug (typo) in obcs_apply_eta.F
3773 o add a new package shelfice which enables us to model the circulation
3774 underneath shelf-ice with draughts of hundreds of meters.
3775 - works
3776 - to do: + include improved thermodynamics
3777 + check whether kSurfC (from model/inc/SURFACE.h) can be used
3778 instead of new field kTopC
3779 + can we use topoFile, Ro_surf and existing code in ini_depth.F
3780 instead of new field R_shelfIce and new code in ini_depth.F
3781 and ini_mask_etc.F?
3782 + adjust vertical mixing schemes?
3783 o seaice pkg:
3784 - add a cpp-flag to include a simple formula for a salinity dependent
3785 freezing point of sea water at the surface
3786 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
3787 meridional stresses are now different (and hopefully correct)
3788 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
3789 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
3790 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
3791 o pkg/diagnostics: add options and parameters for regional-statistics
3792 diagnostics ; define regions by reading a region-mask from a file
3793 (might add other options later)
3794 o pkg/bulk_force:
3795 - add option and parameters to use AIM surface-flux formulae.
3796 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
3797 others forcing fields (defined in PARM05, parameter file "data") are loaded
3798 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
3799 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
3800 - use the right EXCH call for uwind,vwind (to work on CS-grid).
3801 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
3802 and parameters (note: calcWindStress replaces .NOT.readwindstress).
3803 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
3804
3805 checkpoint58 (2006/01/12)
3806 o add "--embed-source" option to genmake2 which, when the supporting
3807 tools can be compiled (as determined by genmake2) will turn on the
3808 embed_files package which then embeds the entire MITgcm source code
3809 (*.[fFhc] + Makefile) used for the build within the executable
3810 - requested by CNH but off by default
3811 - adds a paltry <9MB to the mitgcmuv executable in most cases
3812 - only writes the output when useEMBEDSRC in eedata is true
3813 o clean up 3-dim. relaxation codes:
3814 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
3815 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
3816 * Thanks to Tom Haine for testing!
3817
3818 checkpoint57z_post (2005/12/31)
3819 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
3820 affects output (@ truncation level) of exp. plume_on_slope ; updated.
3821 o fix the pickup behavior for obcs in combination with ptracers
3822 o fix a bug in ptracers_external_fields_load
3823 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
3824 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
3825 o transfered surface NH pressure to eta field (if exactConserv).
3826 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
3827 and update lab_sea output.txt file.
3828 o completing 3-dim. relaxation code: additional term
3829 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
3830 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
3831 * At compile time, in "EXF_OPTIONS.h" set
3832 #define ALLOW_CLIMTEMP_RELAXATION
3833 #define ALLOW_CLIMSALT_RELAXATION
3834 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
3835 tauThetaClimRelax3Dim = 15552000.0,
3836 tauSaltClimRelax3Dim = 15552000.0,
3837 * 3 cases:
3838 1) Use a constant-in-time 3-dim. field
3839 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
3840 3) Real-time relax. to time-evolving prescribed field
3841 o Adding Laplacian-type smoothness constraint on
3842 initial and boundary (forcing) controls (ic, bc)
3843 * enable at compile-time via
3844 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
3845 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
3846 * Absolute scale somewhat unclear so far
3847 * no area weighting was included since no other cost term does so far
3848
3849 checkpoint57y_post (2005/12/08)
3850 First step for a NLFS adjoint
3851 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
3852 o new init. routines for calc_r_star, calc_surf_dr
3853 o still need to deal with ini_masks_etc
3854 o testreport seemed happy
3855 checkpoint57y_pre (2005/12/08)
3856
3857 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
3858 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
3859 o add new offset feature to offline pkg (plus minor cleanup)
3860 o cfc fixes for final year of integration
3861 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
3862 be in GCHEM_OPTIONS).
3863
3864 checkpoint57x_post (2005/12/04)
3865 o fix testreport Pb in multiple test experiment.
3866 o cleanup our namelist syntax in verification:
3867 - make it more F95 standards compliant (some work still needed)
3868 - allows the vast majority of our tests to work with gfortran
3869 o Non-Hydrostatic:
3870 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
3871 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
3872 o Allow to apply AB on T,S rather than on AB(gT,gS):
3873 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
3874 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
3875 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
3876 - need a "clever" read_pickup to restart from the other AB formulation
3877 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
3878 o remove some unused variables (reduces number of compiler warnings)
3879 o adjoint
3880 * Disable useVariableViscosity for adjoint for time being
3881 (there are a number of extensive recomputations)
3882 * Initialize certain variables needed for adjoint
3883
3884 checkpoint57w_post (2005/11/03)
3885 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
3886 fix the singleCpuIO RS version of MDSWRITEFIELD
3887 and add a WARNING if using globalFiles=T with multi-processors.
3888 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
3889 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
3890 o tracer advection scheme:
3891 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
3892 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
3893 was not very convenient).
3894 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
3895 (further tests needed for the implicit DST & Flux-Limiter schemes).
3896 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
3897 and sRef for convenience, handy, when you want to initialize
3898 ptracers in a large domain with a constant non-zero value. Also,
3899 untangle ptracers_init.F a little.
3900
3901 checkpoint57v_post (2005/10/13)
3902 o change dome exp. to use variable viscosity in side-drag terms.
3903 o remove all the files from the cfc_offline test since they are now
3904 incorporated into tutorial_cfc_offline which has been producing
3905 identical results for a few days of testing
3906 o add new parameter: sideDragFactor to enable half-slip-side BC
3907 and change side-drag S/R to use viscosity from mom_calc_visc
3908 (can switch back by setting sideDragFactor=0.); affects results at
3909 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
3910 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
3911 o vorticity & strain are now computed without masking, to account for
3912 no-slip-side BC in variable viscosity calculation ; mask is applied
3913 anyway later on, before computing advection/coriolis terms.
3914 o modify exp4 to test new obcs support for reading from external files
3915 and for passive tracers
3916 o fix behavior of ptracers_monitor when monitor output is written to a
3917 netcdf-file; still not independent of monitor.F (writes in the same
3918 file).
3919 o change default value of tRef (put a uniform, meaningful value for ocean
3920 & atmos) and initialize sRef (was missing, as Martin mentioned).
3921 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
3922 to be proportional to enstrophy dissipation length. Thus,
3923 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
3924 This is now consistent with Smagorinsky and with the manual.
3925
3926 checkpoint57u_post
3927 o OBCS and PTRACERS: add open boundary support for passive tracers
3928 - either use homogenous (pseudo) v.Neumann conditions or prescribe
3929 OB-values from file; this is not different from the way theta and salinity
3930 are treated
3931 - however, Orlanski-radiation conditions are not supported, and the model
3932 will stop if you use pTracers and Orlanski at the same time.
3933 - beefed up the rountine obcs_external_fields_load: now only those open
3934 boundary values are overwritten with values from files for which there
3935 are really files, otherwise the OB-fields remain untouched. This makes
3936 it possible to use different OBs at different ends of the domain (as
3937 with EXF)
3938 o reduce number of exch calls in shap_filt (s2).
3939 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
3940 truncation level) 4/5 MLAdjust test results (11&12 digits match).
3941
3942 checkpoint57t_post (2005/10/03)
3943 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
3944 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
3945 same truncation, independent of the face number: affects affects several
3946 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
3947 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
3948 note that biharmonic viscosity + no-slip was not tested in any experiment.
3949 o fix bug in non-linear free-surf side-drag ; generate new output for
3950 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
3951 o make mnc honor the writeBinaryPrec flag for most kinds of output
3952 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
3953 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
3954 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
3955 o add brackets in multi-terms sum to get same truncation, independent of
3956 the face number (manage to get exactly same value of gU,gV at the cs-edge)
3957 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
3958 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
3959 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
3960 a maximum grid-scale Reynolds number. Also, changes all length calculations
3961 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
3962 Suggested values of viscosity parameters found in mom_calc_visc.
3963 Many new viscosity diagnostics available.
3964
3965 checkpoint57s_post (2005/09/20)
3966 o Add clearing-house for viscosity calculations, mom_calc_visc and
3967 correct numerous bugs in LeithD and Smagorinsky discretizations.
3968 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
3969 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
3970 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
3971 and with Strain-Tension viscous term calculation (mom_hdissip.F).
3972 The Strain-Tension form is now called with useStrainTensonVisc=.true.
3973 ViscAhStrain and viscAhTension are now retired.
3974 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
3975 o In response to JMC's bug report, genmake2 now ignores any soft-links
3976 that it finds in the *current* directory when searching for files.
3977 Soft-links found in any other source directories will still work as
3978 they did before.
3979 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
3980 a C routine to unlimit the stack size
3981 o mnc-ify pkg/aim snapshot vars
3982 o mnc-ify pkg/land as requested by Daniel
3983 o various changes to mnc including:
3984 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
3985 - output can now be grouped so that all files within a group
3986 change the ITER portion of their names in lock-step together
3987 - can now read ("global") PER-FACE (in addition to PER-TILE) files
3988 and works with both EXCH1 and EXCH2 (but needs more testing)
3989 - writing works for all verification test cases w/ g77 on Linux
3990
3991 checkpoint57r_post (2005/09/07)
3992 o make MNC variable initialization happen earlier
3993 o add diagnostics for (almost) each term of the momentum Eq.
3994 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
3995 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
3996 o remove MINIMAL_TAVE_OUTPUT option ;
3997 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
3998 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
3999 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
4000 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
4001 o add time-dependent SST, SSS control
4002 o cost terms in ecco/ modularized (new cost_generic.F)
4003 o cost_averages routines are modularized (new cost_averagesgeneric.F)
4004 o new infrastructure for seaice model vs. obs misfits in seaice/
4005 * driver from the_main_loop.F is seaice_cost_driver.F
4006 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
4007 * gradient check in Exp. 6a of natl_box_adjoint/
4008 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
4009 (see README file)
4010
4011 checkpoint57q_post (2005/08/19)
4012 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
4013 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
4014 - bug was reported by Jean-Michel and Ian Fenty
4015 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
4016 update exp. cpl_aim+ocn output.
4017 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
4018 Needed for high-res. runs with large global files
4019 to be able to limit tapelev size
4020 o Changed some tests for adjoint:
4021 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
4022 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
4023 * global_ocean.90x40x15/ back to default 3-level checkpointing
4024 o Modifications to enable scripted COMMON to MODULE conversion
4025 * verification/OpenAD/code/ has necessary scripts and description;
4026 * converts, compiles and runs successfully;
4027
4028 checkpoint57p_post (2005/08/01)
4029 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
4030 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
4031 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
4032 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
4033 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
4034 (was already the case for dissipation with mom_vecinv,
4035 and also the case for grad.PhiHyd when staggered-timeStep)
4036 This will allow to put dissipation out-off the AB time-stepping.
4037 Unfortunately, affects truncation error. Update output of exp. that "fails"
4038 (cg2d matching number) and leave the others for later: front_relax(10),
4039 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
4040 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
4041
4042 checkpoint57o_post (2005/07/30)
4043 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
4044 (2) its ready to be documented during the 20050801 DocFest
4045 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
4046 for ideal_2D_oce and lab_sea on linux_ia32_g77
4047 o set to #undef CTRL_SET_OLD_MAXCVARS_30
4048 in global1x1_tot/code_seaice_adj to access indices 32, 33
4049 (worth another tag)
4050
4051 checkpoint57n_post (2005/07/29)
4052 o adding precip control xx_precip 32
4053 o adding swflux control xx_swflux 33
4054 o Replacing 10 forcing penalty cost routines by 1 generic.
4055 o Implementing partitioning in time-mean and variable adjustment
4056 for atmos. state.
4057 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
4058 o in natl_box_adjoint:
4059 * updated exp 1 to 10
4060 (but does not have time-mean vs. variable split results yet)
4061 o updated global1x1/*_seaice_adj/
4062 to incorporate latest changes
4063 o enable useSingleCpuIO for mdsio vector routines
4064 (applies in particular to tapelev I/O)
4065 o removed inefficient K-loop in all active_file*control*.F
4066
4067 checkpoint57m_post (2005/07/28)
4068 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
4069 and advect_cs (use EXCH-2 and standard cs-32 grid files).
4070 o pkg/exch2: filling of face-corner halo regions is optional
4071 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
4072
4073 checkpoint57l_post (2005/07/14)
4074 tag before updating tutorials (pre-release-2)
4075 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
4076 for output and interpolation of input fields onto model grid)
4077 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
4078 Affects results of exp. rotating_tank ; update output.txt.
4079 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
4080 and taking the square quantity and/or using a fraction-weight field.
4081 o fix aim_diagnostics_init.F mate numbers.
4082 o add mnc output capability to diagnostics/diagstat and update
4083 our cvsignore files for the ACSII output generated
4084
4085 checkpoint57k_post (2005/07/02)
4086 o lab_sea now uses diagnostics package and provides a suite of
4087 new EXF diagnostics output.
4088
4089 checkpoint57j_post (2005/06/30)
4090 o exf
4091 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
4092 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
4093 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
4094 * extended diagnostics output
4095 - now includes all EXF variables
4096 - hs, hl moved to common block
4097 - separate S/R for diagnostics, called after ctrl vector is added
4098 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
4099 - EXFqnet contains true Qnet (i.e. includes qsw)
4100 * updated verif. lab_sea, global_with_exf
4101 * Rearranging hflux (exf_mapfields -> exf_getforcing)
4102 to ensure that diagnostics sees a true EXFqnet
4103 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
4104 o diagnostics pkg: change pointers so that 1 diagnostic can be used
4105 several times with different frequencies.
4106 o mnc-ify the thsice package as requested by Daniel Enderton
4107 - the monitor--MNC output needs work
4108 - many attributes need to be added (most are currently blank)
4109 o mnc-ify theaim_v23 package as requested by Daniel Enderton
4110 - many attributes need to be added (most are currently blank)
4111 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
4112 o add Sadourny like discretization to the 4th.O vorticity advection scheme
4113 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
4114 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
4115 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
4116 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
4117 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
4118
4119 checkpoint57i_post (2005/06/19)
4120 o Diagnostics package was changed: diagnostic allocation is now deactivated
4121 by setting an empty file name in the namelist (used to be by setting 0 frequency)
4122 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
4123 add 1rst Order upwind vertical Shear.
4124 o add a quick fix for A/B checkpointing in OFFLINE mode
4125 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
4126 end-run around the C/Fortran linking horror in eesup/src/timers.F
4127 o added pkg/runclock: allows user to terminate run based on wall clock
4128 o added non-hydrostatic scaling parameter: nh_am2
4129 o pkg/my82: futile attempt to make results compiler-independent by adding
4130 some "_d 0", etc. no effect.
4131 o for mnc output, fill the 'T' coordinate var with myTime and create a
4132 separate 'iter' variable for iteration count
4133 o pkg/diagnostics:
4134 add new capability: output of Global/Regional & per-level statistics ;
4135 tested against monitor output (including land & thSIce) on various exp.
4136 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
4137
4138 checkpoint57h_done (2005/05/19)
4139 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
4140 data.diagnostics, data.gchem, data.ptracers) is done.
4141
4142 o pkg/diagnostics: prepare for Global/Regional statistics.
4143 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
4144 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
4145 and rename it: DIFFERENT_MULTIPLE
4146
4147 checkpoint57h_post (2005/05/14)
4148 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
4149 o pkg/diagnostics: change output frequency, now in seconds (instead
4150 of Nb of iterations). This requires to change data.diagnostics.
4151 checkpoint57h_pre (2005/05/12)
4152
4153 o in mnc, let the user create the output dir if both mnc_outdir_date
4154 and mnc_outdir_num are false
4155 o add fflags() to pkg/diagnostics which allows one to specify, on a
4156 per-file basis, the file precision [default behavior is unchanged]
4157 o added diagnostics to pkg/kpp, including computation of mixed layer
4158 depth based on a temperature/density criterion
4159 o updated verification/natl_box to test the new pkg/kpp diagnostics
4160 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
4161 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
4162 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
4163 not mnc -- this mistake was found by JMC and is now corrected
4164
4165 checkpoint57g_post (2005/04/15)
4166 o add Adams-Bashforth 3rd Order time stepping:
4167 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
4168 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
4169 checkpoint57g_pre (2005/04/15)
4170
4171 o make lambda[Theta,Salt]ClimRelax spatially varying
4172 (default remains spatially uniform constant based on tau)
4173 o added new control variables
4174 * init. uVel, vVel, etanN
4175 * lambda[Theta,Salt]ClimRelax
4176 o separate masks used for ctrl_pack/unpack 'from write_grid' output
4177 (suggested by G. Forget)
4178
4179 checkpoint57f_post (2005/04/06)
4180 o add parameter "baseTime" = model base time = time at iteration zero
4181 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
4182 account for baseTime shift
4183 o move Coriolis arrays from PARAMS.h to GRID.h
4184 checkpoint57f_pre (2005/04/06)
4185
4186 o mnc-ifying the seaice package
4187 o introduced an alternative length scale calculation for use in the limiting
4188 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
4189 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
4190 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
4191 as well as grad(vort3). Made it compatible with both approximate form
4192 for the cubed sphere and full form of these gradients. Added flag
4193 useFullLeith to select between approximate and full form.
4194 o add "d0" in getcon.F to reduce differences between compilers/platforms
4195 update output.txt of exp. fizhi-gridalt-hs
4196 o change port_rand funtion to allow to set the seed.
4197 o fix obscure MNC bug involving conversion between reals and integers
4198 - it caused no problems with certain (eg. gcc, ifc) compilers but the
4199 new version is now more standards-compliant
4200 o adjoint-related modifications
4201 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
4202 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
4203 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
4204
4205 checkpoint57e_post (2005/02/28)
4206 o Adding eddy stress controls a la Ferreira et al.
4207 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
4208
4209 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
4210 update output.txt of exp. fizhi-gridalt-hs
4211 o add more "Z" dimensions and associated coordinate vars to MNC
4212 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
4213 o parameter calendarDumps: when set, approximate months (30-31 days) and years
4214 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
4215 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
4216 months and years. Requires pkg/cal.
4217 o diagnostics: add pickup functionality
4218 - off by default for backwards compatibility
4219 - current version only uses MDSIO -- MNC will be added
4220 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
4221 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
4222
4223 checkpoint57d_post (2005/02/11)
4224 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
4225 o modify verification/ideal_2D_oce so that it tests the creation of mnc
4226 output from the diagnostics package
4227 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
4228 o make genmake2 more portable by using ".$FS" instead of ".f" for more
4229 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
4230 o add coordinate variables to the MNC output from the diagnostics package
4231 o change MNC-flags default value: true when useMNC=TRUE
4232 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
4233 the ability (off by default) to read the grid information using MNC
4234 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
4235 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
4236 o do snap-shot diagnostics at the middle of the time-interval (instead of
4237 at the end).
4238 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
4239 new test for AIM with thSIce + slab-ocean
4240 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
4241 o move state variable diagnostics to the beginning of the time step ;
4242 (note: still needs some work specially for snap-shot diagnostics)
4243 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
4244
4245 checkpoint57c_post (2005/01/27)
4246 o Change testing option (-ieee) to get closer agreement between g77 & ifort
4247 o generate new output.txt files on faulks with g77 & the new -ieee option
4248 checkpoint57c_pre (2005/01/27)
4249
4250 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
4251 update output.txt of exp. global_ocean.90x40x15
4252 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
4253 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
4254 o add saltFlux(+File) forcing capability with periodicExternalForcing
4255 o allow to use pkg diagnostics for GM-Redi & ThSIce output
4256 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
4257 o improvements for the MNC output from DIAGNOSTICS:
4258 - correct handling of the unlimitied dimension
4259 - all dims now have associated coordinate variables
4260 - variables located at U, V, and Corner ("Z") points are now written
4261 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
4262 *all* data points are output
4263 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
4264 o added pkg/seaice/seaice_monitor.F
4265 o mdsio_readfield.F can now read files visible only to master MPI process.
4266 o pkg/seaice: some test code for ice-modified ocean stress
4267 o exf_getffields interpolation defaults to bilinear for all scalar forcing
4268 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
4269 spurious negative numbers for precipitation and humidity. Will cause
4270 some small numerical differences for integrations using pkg/exf/exf_interp.F.
4271 o pkg/ctrl/
4272 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
4273 May be enabled via doPackDiag
4274 * introduce z-scaling of
4275 + gradient (doZscalePack) and
4276 + control (doZscaleUnpack)
4277 o pkg/mdsio/
4278 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
4279 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
4280
4281 checkpoint57b_post (2004/12/20)
4282 o simplify options in diagnostics_fill arguments (remove weird combinations)
4283 o fix MNC coordinate variables so that they now contain per-face index
4284 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
4285 general, EXCH2 grids are only aligned to a "local" coordinate system
4286 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
4287 o Implement instantaneous output within pkg diagnostics:
4288 setting a negative frequency in data.diagnostics produces
4289 "snap-shot" output (as opposed to time-average if freq > 0)
4290 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
4291 NOTE: change ptracer diagnostics name: use 2 characters to work with
4292 more than 9 tracers. Add also diagnostics of advect & diffus flux.
4293 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
4294 becomes the coordinate variable for the 'T' dimension
4295 o add CF-style coordinate variables to MNC
4296 - just a first cut: numbers are meaningless on the cubesphere and
4297 missing along the T axis but otherwise it works!
4298 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
4299 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
4300 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
4301 this is based directly on what the model compute, so that the content of
4302 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
4303 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
4304 o clean up build options files for SunOS, in particular
4305 - remove -traditional from xmakedepend
4306 - change -xarch=v9 to -xarch=native for f77
4307 - restore use of make (not gmake)
4308 - add CC=gcc if using g77
4309 o changes per discussion of AM, JMC, & EH3 today:
4310 - move redundant "grid" variables out of "state" -- in preparation of
4311 creating proper CF-style coordinate variables and in recognition
4312 that any/all grid variables can be easily copied (eg. w/NCO) from
4313 the grid files into any of the other NetCDF files
4314 - *always* output grid variables with MDSIO (this will eventually be
4315 changed)
4316 - output MNC grid file if useMNC is true
4317 o every instance of _END_MASTER() has been found and replaced with
4318 _END_MASTER( myThid ) in order to satisfy certain picky Sun
4319 preprocessors
4320 o re-arrange diagnostics pkg initialisation:
4321 - allow each package to extend the available diagnostics list
4322 - add some checking and fix small problems (multi-threaded, ...)
4323 - new S/R diagnostics_fill (replace fill_diagnostics):
4324 look through the short list of active diag. (instead of the long list)
4325 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
4326
4327 checkpoint57a_post (2004/12/10)
4328 o this set of changes restores TAMC compatibility
4329 tested for global_ocean.90x40x15 adjoint on trough
4330 (what a pain)
4331
4332 checkpoint57a_pre (2004/12/10)
4333 o some modifs in tools/build_options for sunos
4334 o call ctrl_pack for ctrl at end for optimcycle=0
4335
4336 checkpoint57 (2004/12/09)
4337 o add horizontal bi-harmonic viscosity for vertical velocity
4338 - new parameter viscA4W (defaults to viscA4)
4339 - affects only non-hydrostatic code
4340 - to be done: no-slip lateral boundary conditions
4341 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
4342 o implement Implicit Vertical advection for pTracers
4343 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
4344 (implemented also for implicit vertical diffusion & advection)
4345 o OBCS: extend application of tracer open boundary conditions
4346 to a strip beyond the boundary of width Olx/Oly
4347 o add call monitor to TAF set of required calls (flow directives)
4348 and include in natl_box_adjoint
4349 o untangle a few ifdefs related to cost, ctrl, autodiff
4350 untangel a few ALLOW_ECCO_OPTIMIZATION
4351 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
4352 (theta2, salt2 in ecco_cost_weights)
4353
4354 checkpoint56c_post (2004/12/03)
4355 o OBCS as control variables
4356 - update ctrl_ad_diff.list, obcs_ad_diff.list
4357 - remove balance of obcs controls from default
4358 - fix index bug nobcs in ctrl_init
4359 - fix dummy fields filen in ctrl_pack
4360 - add dummy weights for obcs
4361 o lsopt: comment out fort.94 output
4362 o optim:
4363 - remove unnecessary header files
4364 - adjusted namelists
4365 - add xerbla.F to Makefile
4366 o exf:
4367 - multiple modifications of exf_check_range
4368 - unit change in exf_init_runoff from [m/year] to [m/s]
4369 o mdsio:
4370 - i/o-vector change debugLevel from debLevA to debLevB
4371
4372 checkpoint56b_post (2004/12/01)
4373 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
4374 is called from DO_THE_MODEL_IO
4375 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
4376 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
4377 - clean up PTRACERS_WRITE_TIMEAVE a little
4378 o add another verification experiment that tests both the cfc-pkg and
4379 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
4380 reactive tendencies treated inline with regular timestepping
4381 o testreport previously did a lousy job of comparing small numbers, so
4382 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
4383 implemented in the little c-progam tmp_cmpnum.c which is embedded in
4384 testreport.
4385 o ptracers_monitor: bug fix for MPI
4386
4387 checkpoint56a_post (2004/11/28)
4388 o GCHEM: finish reorganizating the package
4389 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
4390 (introduces another 3D-array for each passive tracer, but only if
4391 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
4392 gchemTendency is not needed because the timestep is done separately)
4393 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
4394 - GCHEM is now---more or less cleanly---separate from PTRACERS
4395 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
4396 so clear to me how that should be done in a general way.
4397 o CFC: improve formatting of output in CFC_ATMOS
4398 o PTRACERS:
4399 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
4400 that ALL experiments with ptracers enable can be checked. This makes
4401 GCHEM_MONITOR obsolete.
4402 - include a runtime parameter PTRACERS_monitorFreq that defaults to
4403 monitorFreq
4404 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
4405 o add PTRACERS (PTR0[1-5]) to testreport output
4406 o exf_check_range:
4407 * default changed to .TRUE.
4408 * will check values for niter0 if debLevA, every timestep if debLevB
4409 * STOP in exf_check_range if 'out of range'
4410 * range chosen generous to allow for potential extema
4411 TBD: a version with stricter range
4412 permitted range would be runtime parameters
4413 o GMredi:
4414 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
4415 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
4416 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
4417 o GCHEM:
4418 - move call to GCHEM_FORCING_SEP, so that it is now called before
4419 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
4420 - introduced a useGCHEM runtime flag and applied it everywhere.
4421 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
4422 this flag is now only visible within GCHEM-pkg routines.
4423 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
4424 be replaced by a 3D array that is computed before thermodynamics; for
4425 this, the tracer ID iTracer had to be included into the parameter list
4426 of ptracers_forcing
4427 - set up forward_step to call gchem_forcing, that will replace
4428 gchem_forcing_int in ptracers_forcing
4429 - cleaning up
4430 o small cleaning of exch2: remove files that are also in eesupp/src
4431
4432 checkpoint56 (2004/11/17)
4433 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
4434 o mnc: cleanup "full" files--fixes out-of-memory problem
4435 o ECCO-GODAE
4436 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
4437 * fully merged and updated from SIO code
4438 windstress sign change affects
4439 - exf_inscal_[u/v]stress
4440 - sign of xx_tau[u/v] adjustments
4441 - signs in cost_scat
4442 * ctrl_get_gen: avoid update of tau[u/v] for first few days
4443 * natl_box_adjoint updated and compressed
4444 * 2-level checkpoint switch added
4445 (tested in EXP. 1 of natl_box_adjoint)
4446 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
4447 o SVD
4448 * first complete, non-hacked version for SVD calculations
4449 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
4450 performed via direct access files admtlm_vector.it????
4451 (via ctrl_[un]pack)
4452 * optimcycle is used for ARPACK iteration counter
4453 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
4454 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
4455 and add linear transforms where necessary
4456 * controls are initial/final SST, SSS (can be extended; need to check
4457 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
4458 o mdsio: filename info to both stderr, stdout
4459 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
4460 from sign change
4461
4462 checkpoint55j_post (2004/11/10)
4463 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
4464 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4465 o add consistent build directories and .cvsignore files to verification
4466 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
4467 o make all subroutines 30 or less characters in length for certain older
4468 compilers to work (a thorough search only turns up two routines in
4469 pkg/ptracers)
4470 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
4471 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4472
4473 checkpoint55i_post (2004/10/28)
4474 o change arrays for total vertical diffusivity (2.D if explicit,
4475 3.D if implicit) ; each ptracer uses its own background value.
4476 o added mnc/NetCDF output capability to ocn_compon_interf
4477 - added bits to verification/cpl_aim+ocn so that it can run on
4478 ITRDA and other clusters without the mpirun "-wd" option
4479 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
4480 configuration
4481 o give MNC the ability to create additional files rather than
4482 exceeding a specified file size limit "MNC_MAX_FILESIZE"
4483 - the default is just less than 2GB which is a practical limit
4484 on many systems
4485 o Compute the non-local term using either KPP vertical diffusivity (=default)
4486 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
4487
4488 checkpoint55h_post (2004/10/20)
4489 o add verification test "vermix"
4490 o remove all the *_ioinc flags and replace with the single global
4491 outputTypesInclusive flag
4492 o allow to set a vertical profile of vertical diffusivity for T & S
4493 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
4494 o useMNC moved from data.mnc to data.pkg
4495
4496 checkpoint55g_post (2004/10/14)
4497 o Renaming carbon AD experiments to comply with testreport conventions
4498 o Updating adjoint of Held-Suarez hs94.1x64x5
4499 o Fixing directives for non-ECCO forward_step, after ECCO directives
4500 have been fixed to avoid recomp. of do_oceanic_phys
4501 Works well for global_ocean.90x40x15,
4502 but recomp. issue remains for carbon
4503 o Updating adjoint output for natl_box_adjoint after
4504 pkg/ecco has been modified (see taga c55d_post)
4505
4506 checkpoint55f_post (2004/10/13)
4507 o rename to timeave_init_fixed
4508
4509 checkpoint55e_post (2004/10/13)
4510 o some delicate re-shuffle of store directives to avoid one
4511 extra call of do_oceanic_physics
4512 affects ecco_the_main_loop.F, do_oceanic_physics.F
4513 checkpoint_lev1_directives.h
4514 o NB: this may break global_ocean adjoint temporarily,
4515 but it is clear how to fix it. Will do later, need this now.
4516
4517 checkpoint55d_post (2004/10/11)
4518 o ECCO specific cost function terms (up-to-date with 1x1 runs)
4519 o ecco_cost_weights is modified to 1x1 runs
4520 o modifs to allow observations to be read in as
4521 single file or yearly files
4522 o enable to read exf forcing fields as either
4523 single file or yearly files (flag useExfYearlyFields)
4524 checkpoint55d_pre (2004/10/08)
4525
4526 o switch between 2-level and 3-level checkpointing
4527 o add ability of MNC to write local and "partial" (eg. 2D slices where
4528 the full 3D field is never actually stored) arrays to NetCDF files
4529 with the correct (that is, the complete multi-dimensional) set of
4530 array indicies
4531 - used in mom_vecinv() to write the diagFreq output
4532 - tested (demonstrated) in verification/aim.5l_cs
4533 o further mnc-ification
4534 - add verification/lab_sea to the list with mnc setups
4535 - fix undefined mnc v-names in cd_code
4536 - add kpp to mnc output (both snapshot and timeave)
4537 o non-hydrostatic code
4538 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
4539 in calc_gw.F
4540 - defaults to viscAh
4541 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
4542 friction or Leith) in non-hydrostatic mode, as long as there is
4543 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
4544 o pkg/cost
4545 extend simple cost functions to treat time mean quantities
4546 (T,U,V) via cost_accumulate_state from cost_tile
4547 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
4548 be 2 times larger than the minimum size the advection scheme requires.
4549 now get a perfect conservation of salt in advect_cs test-exp (updated)
4550 o GGL90 (Gaspar's TKE mixed layer)
4551 - add horizontal diffusion of TKE, requires exchanges in
4552 do_fields_blocking_exchanges, horizontal diffusivity is zero by
4553 default. In OPA there is no horizontal diffusion of TKE but the
4554 mixing coefficients are computed from a horizontal average of TKE of
4555 6 points or so. I think that diffusion has a little more physical
4556 justification.
4557 - clean up ggl90_calc in the hope of reducing memory usage (this hope
4558 was in vain)
4559 - mask tke-variable in ggl90_init
4560 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
4561 o fix biharmonic diffusion on CS-grid.
4562 o more obcs stuff
4563 - added obcs_external_fields_load as an alternative to the EXF-pkg option
4564 for reading boundary values. This routine is called from
4565 obcs_prescribe_read
4566 - updated obcs_check
4567 - changed sponge layer relaxation parameter units for days to seconds
4568 - turned off sponge layer by default
4569 - changed argument list of OBCS_CALC to myTime+deltaTclock
4570 - fixed about 35 bugs in obcs_external_fields_load
4571
4572 checkpoint55c_post (2004/09/23)
4573 o obcs stuff
4574 - new runtime flags useOBCSprescribe, useOBCSbalance
4575 - re-arranged obcs_calc
4576 - moved exf_getobcs to obcs_prescibe_read
4577 obcs_prescibe_read is called after ORLANSKI stuff
4578 and independent of it (executable can contain all).
4579 - updated obcs_check
4580 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
4581 These may be necessary only if tangential velocities are
4582 prescribed at OB, not sure, needs testing.
4583 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
4584 which simplifies the calls and passes the ifc check-bounds test
4585
4586 checkpoint55b_post (2004/09/22)
4587 o add a 2D scalar, Z location, exchange_2 routine.
4588 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
4589 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
4590 affects advect_cs results (for the wrong reason): update output.txt
4591 o use a more standard discretization for biharmonic viscosity ;
4592 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
4593 affects results of dome set-up: update output.txt
4594 o fix gad_advection.F (CubedSphere part), back to version 1.23
4595 o fix bug in mom_vi_del2uv.F (CubedSphere part).
4596
4597 checkpoint55a_post (2004/09/20)
4598 o merged code to
4599 * prescribe/read time-dependent open boundaries
4600 (works in conjunction with exf, cal)
4601 * sponge layer code for open boundaries
4602 * each boundary N/S/E/W now has its own CPP option
4603 (healthy for the adjoint)
4604
4605 checkpoint55 (2004/09/17)
4606 o up-to-date adjoint of previous breaks
4607 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
4608 - global_ocean_ebm: adjoint still needs fix (TLM ok)
4609 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
4610 - carbon: * remove tr1-related adjoint verification
4611 * add ptracer as control variable
4612 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
4613 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
4614
4615 checkpoint54f_post (2004/09/16)
4616 o in verification/carbin/ remove experiment related to
4617 ALLOW_PASSIVE_TRACER (array tr1 etc)
4618 code_ad/ input_ad/ results_ad
4619
4620 o add two new packages
4621 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
4622 + subject to optimization (memory)
4623 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
4624 + subject to reordering (many GOTOs in the original code)
4625 + so far opps is called for every (i,j) point, and then operates in
4626 the vertical; one may want to reorder the scheme in order operate in
4627 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
4628 fields)
4629 o overhaul of IO so that we now have flags for MDSIO and/or MNC
4630 - all verification tests compile and run with linux_ia32_g77
4631 - defaults are compatible with current input files--nothing
4632 should change if you were not previously using MNC
4633 - MNC output has been added in numerous places (eg. timeave)
4634 but there are still a few writes not yet do-able with MNC
4635 (this is in progress)
4636 - flags now allow for either/or/both use of MDSIO and MNC and
4637 documentation will soon follow
4638 - numerous small formatting cleanups for ProTeX
4639 o add version info (via BUILD_INFO.h) to MNC and stdout
4640
4641 checkpoint54e_post (2004/09/02)
4642 o add two new packages
4643 - pp81 (Packanowski and Philander, 1981), Richardson number and
4644 stratification dependent mixing
4645 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
4646 - these scheme operate in a similar manner as KPP (without ghat, of
4647 course), however there is only one diffusivity that is used for both
4648 temperature and salinity (and passive tracers)
4649 o add offline package
4650 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
4651 provided by Stephanie Dutkiewicz
4652 o genmake2: add ability to search for C compilers and cleanup test output
4653 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
4654
4655 checkpoint54d_post (2004/07/27)
4656 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
4657 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
4658 leading to additional shift by 5 days each year of integration
4659 (i.e. leading to considerable offset over the years)
4660 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
4661 o start with no AB and no initial filtering (staggerTimeStep):
4662 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
4663 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
4664 (external loading & cpl import/export stay in forward_step.F)
4665 o update coupling interface to work with new staggerTimeStep
4666 o change MDSIO ptracers_pickup.
4667 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
4668 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
4669 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
4670
4671 checkpoint54c_post (2004/07/18)
4672 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
4673 this affects (truncation error) output.txt of test-exp:
4674 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
4675 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
4676 o change Qnet to always be the net heat flux, (+upward).
4677 affects (truncation error) output of natl_box exp.: updated
4678 o define the max number of passive tracers in PTRACERS_SIZE.h
4679 o start to test mnc routinely in exp0
4680 o add sea-ice loading (sIceLoad) as a new forcing field.
4681
4682 checkpoint54b_post (2004/07/08)
4683 o add testreport "-j JOBS" option for parallel builds (tested and pretty
4684 impressive on Altix and Opteron systems)
4685 o diagnostics can now write NetCDF files through the mnc package
4686 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
4687 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
4688 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
4689 affects (truncation error) output of lab_sea & natl_box exp.: updated
4690 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
4691
4692 checkpoint54a_post (2004/07/06)
4693 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
4694 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
4695 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
4696 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
4697 + internal_wave (shift in writing cg2d_ini_res)
4698 checkpoint54a_pre (2004/07/05)
4699
4700 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
4701 - modified verification/lab_sea and natl_box_adjoint accordingly
4702
4703 checkpoint54 (2004/07/02)
4704 checkpoint53g_post (2004/07/02)
4705 o prepare splitting of thermodynamics: store convect.counter in common block
4706 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
4707 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
4708 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
4709 o new parameter "nShapS": allow to treat differently S from T (nShapT)
4710 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
4711 o restore adjointability
4712
4713 checkpoint53f_post (2004/06/25)
4714 o modifications that affect AIM experiment results (update output.txt):
4715 - no advection of S at top interface Nr (pkg/generic_advdiff)
4716 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
4717 o AIM pkg:
4718 - include stability function into surf.Flux derivative relative to Tsurf
4719 - calculate clear-sky radiation & surface temp. change (for diagnostics)
4720
4721 checkpoint53e_post
4722 o merged cylindrical coord configuration
4723 o added rotating_tank experiment
4724 checkpoint53e_pre
4725
4726 checkpoint53d_post (2004/06/14)
4727 o faulks upgraded: re-generate output.txt that have changed:
4728 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
4729 o Added Bryan and Lewis, 1979, vertical diffusivity profile
4730 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
4731 o added Sadourny discretization of Coriolis
4732 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
4733 - re-enabled use of omega3 (useAbsVorticity)
4734 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
4735 vector-invariant equations
4736 - note: does *NOT* yet use same variable visc. for no-slip BC's.
4737 o recoded the lateral boundary conditions for non-hydrostatic w, this time
4738 hopefully without new bugs
4739 - still to do: biharmonic friction for non-hydrostatic w
4740 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
4741 o regenerated output for global_ocean_ebm (using -ieee)
4742 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
4743 of mom_common/
4744 - simple re-arrangement of instructions within computing loop
4745 checkpoint53d_pre (2004/05/21)
4746
4747 checkpoint53c_post (2004/05/21)
4748 o new version of coupler for AIM+thSIce and Ocean models
4749 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
4750 - land: change Evaporation of snow
4751 - aim with thSIce: fix bug in snow-precip.
4752 o changes to calc_gw.F
4753 - bug fix for w^2 term near the bottom boundary
4754 - (hopefully) improve the lateral slip boundary condtions for use with
4755 partial/looped cells
4756 - because the bug fix changes two verification experiments anyway (exp5
4757 and plume on slope), change the lateral boundary condition from half slip
4758 to the value of no_slip_sides
4759 o ebm package wasnt quite up to the parallel task. Fixed that.
4760 o Adjoint of EBM package + verification
4761 * TLM OK
4762 * ADM not sufficient accuracy yet (needs further testing)
4763
4764 checkpoint53b_post (2004/05/14)
4765 o Commiting new energy balance model to repository
4766 * package is pkg/ebm
4767 * verif. is verification/global_ocean_ebm
4768 * references are in ebm_driver.F
4769 C * X. Wang, P. Stone and J. Marotzke, 1999:
4770 C Global thermohaline circulation. Part I:
4771 C Sensitivity to atmospheric moisture transport.
4772 C J. Climate 12(1), 71-82
4773 C * X. Wang, P. Stone and J. Marotzke, 1999:
4774 C Global thermohaline circulation. Part II:
4775 C Sensitivity with interactive transport.
4776 C J. Climate 12(1), 83-91
4777 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
4778 C Destabilization of the thermohaline circulation
4779 C by atmospheric eddy transports.
4780 C J. Climate 7(12), 1870-1882
4781 o Will need long integration testing.
4782 checkpoint53b_pre (2004/05/14)
4783
4784 o created pkg/mom_common in preparation for variable viscosity code
4785 o renamed and split ini_mnc_io
4786 o pkg/land: only liquid water can diffuse or run-off
4787 o AIM using land: soil wetness availability account for snow
4788 o added printMapIncludesZeros to EEPARMS namelist
4789
4790 checkpoint53a_post (2004/05/11)
4791 o restore TAMC compatiility for exf_constants.h
4792 (no usage of _d in .h)
4793 o Additional storing in KPP in an attempt to fix
4794 TAMC problem with adjoint of KPP code.
4795 (no success...)
4796 Identical code works fine with TAF.
4797 o Fixed verification/natl_box_adjoint experiments.
4798 Initial conditions for Experiments 4 and 5 are now
4799 set to "SEAICE_initialHEFF=0", which is more reasonable,
4800 and hence gives results closer to that of Experiment 2.
4801 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
4802
4803 checkpoint53 (2004/05/06)
4804 o stable checkpoint with up to date adjoint
4805 TLM tests only run for 1st grdchk at the moment. Its unclear if
4806 this is a code problem or a problem with resetting code for g_
4807 variables that is being autogenerated wrong.
4808 Otherwise:
4809 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
4810 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
4811 are both still in chaos following their security messes.
4812
4813 checkpoint52n_post (2004/05/06)
4814 o various build (mostly genmake2) changes including:
4815 - ability to build/run more easily within Cygwin and MacOS X
4816 - more complicated Makefiles with a stronger dependence on Gnu Make
4817 o pkg/seaice modifications
4818 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
4819 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
4820 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
4821 - changed proxy for geostrophic velocity and updated
4822 verification/lab_sea/results/* accordingly
4823 - removed ADI dynamic solver from pkg/seaice
4824 - replaced all occurrences of 1/CSTICE or 1/CSUICE
4825 they caused a segmentation fault under certain circumstances
4826 - removed unused field WATR
4827 o bug fix in exf-package:
4828 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
4829 now reflect that.
4830 o small fixes in the cal-package:
4831 - set reference date to first of January for the 'model'-calendar
4832 - failing of cal_CheckDate in cal_FullDate now actually results in a
4833 warning
4834 o small modifications in exf-package to increase flexibility:
4835 - change climtempfreeze from a constant to a runtime parameter that
4836 is specified in data.exf_clim (default = -1.9)
4837 - introduce runtime parameter windstressmax (default = 2.0) that is
4838 specified in data.exf
4839 o fix in pkg/thsice:
4840 - update Evap (Tsf changes) to be consistent with Latent heat flux
4841 - maintain snow precipitation unchanged (even if Tsf >=0).
4842 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
4843
4844 checkpoint52m_post (2004/04/18)
4845 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
4846 this does not change any of the results, because myIter=0 in swfrac always
4847 lead to jwtype=2 (the default anyway), but the call makes little sense
4848 as a default
4849 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
4850 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
4851 atmospheric model (AIM) to use it ; add a "slab ocean" component.
4852 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
4853 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
4854 o extending useSingleCpuIO option to work with new exch2 I/O format
4855 - old-style, missing-tile I/O is still accessible by defining CPP
4856 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
4857 o monitor package can write to NetCDF files and/or STDOUT
4858 o fix re-definition bug in MNC_GRID_INIT_ALL()
4859 o doc/api_reference added
4860 - a framework for building an API Reference Manual using all
4861 the "protex" comments embedded in the code
4862 - see pkg/generic_advdiff, pkg/mnc for examples
4863 o MNC:
4864 - make myThid the last argument for all subroutines
4865 - new default for the grid files: NO halos
4866 - add useMNC and other run-time flags
4867 - separate per-file-group handling of the unlimited dimension
4868 - early initialization of MNC w/ flags read at the eeboot stage
4869 and lookup tables set in initialize_fixed
4870 - write all MNC output to a freshly-created directory
4871 o thermodynamics sea-ice (thsice) is now tested with testreport.
4872 o test exp. advect_cs: use the standard cs32 grid ; update output.
4873 o Added functionality to grdchk:
4874 pick global i,j,k position (or nearest wet) where to perform check.
4875
4876 checkpoint52l_post (2004/03/11)
4877 o new land formulation:
4878 a) use ground enthalpy as prognostic variable to ensure exact
4879 energy conservation.
4880 b) account for water temperature and for latent heat of freezing
4881 in all processes (rain, run-off, ground storage)
4882 c) compute surface and ground temperature implicitly.
4883 o aim_v23 modification for new land model:
4884 a) Treat separately land / ocean / sea-ice surface fluxes
4885 to allow implicit computation of land & sea-ice surface temp.
4886 b) add snow precipitation.
4887 checkpoint52l_pre (2004/03/11)
4888
4889 o fix problem (when 1 tile is empty) in min/max monitor.
4890 o fix bug in timeAve (u,vZetatave in common block)
4891 o no restoring terms under ice for pkg/seaice
4892 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
4893 o bug fix for pkg/seaice pickups
4894 o change MNC call locations and add coordinate attributes
4895 o mask vorticity at the corner ; affects global_ocean.cs output
4896 o fix ini_curvilinear_grid ; test CS experiments with mpi
4897 o aim.5l_cs: modify sea-ice fraction input file ; update output
4898 o exf: Adding simple range check routine for exf fields after read
4899
4900 checkpoint52k_post (2004/02/23)
4901 o removed top-level directory "diags"
4902 - we migrated these functions to pkg/timeave a long time ago
4903 o fixed bug introduced in pkg/monitor
4904 o accuracy ctrlprec = 32 insuffient for gradient checks using
4905 averaged fields (I/O via cost_averages)
4906 -> use ctrl.h in active_file*.F to control I/O precision.
4907 o paramter list of CALL ADTHE_MAIN_LOOP
4908 o added initial do_the_model_io to ecco
4909 o set all ...Freq to zero after cost_final
4910 taveFreq, dumpFreq, pChkptFreq
4911 o MAIN and ECCO differentiability restored
4912
4913 checkpoint52j_post (2004/02/18)
4914 o fix nchklev in tamc.h for global_ocean...
4915 o Bringing flow and store directives up-to-date
4916 o Really weird thing!
4917 call do_the_model_io from the_main_loop with parameters
4918 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
4919 TAF places a faulty re-call of initialise_varia
4920 after cost_final call which should not be there!
4921 checkpoint52j_pre (2004/02/03)
4922
4923 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
4924 error messages
4925 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
4926 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
4927 debug output
4928 o modfied mdsio_writefield.F to handle non-global files under exch2
4929 o update AIM Cubed-Sphere exp (aim.5l_cs):
4930 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
4931 o update AIM Equatorial Channel exp:
4932 use standard aim_v23 pkg and change the SST fields to be more realistic.
4933 o globalFile now works with exch2
4934 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
4935 mon_vort3.F to make exch2 friendly with >1 tile per cube face
4936 o limit timeave output for hi-res integrations
4937
4938 checkpoint52i_post (2004/01/21)
4939 o removed CPP_EEOPTIONS.h from verification/*/code
4940 o updated the tiling for global_ocean_pressure
4941 checkpoint52i_pre (2004/01/20)
4942
4943 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
4944 the old pkg/aim).
4945
4946 checkpoint52h_pre (2004/01/20)
4947 o shortened offending lines in exch2_send_rx?.template
4948 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
4949 o genmake2: add build & execute test for NetCDF code
4950 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
4951 old grid files, moved CPP_EEMACROS.h to pkg/exch2
4952 o added useSingleCPUIO flag to monitor.F and mon_out.F
4953 o added temporary hack for sea-ice dynamics on the cube:
4954 metric terms are ignored and it is assumed that
4955 there is no sea-ice on cube faces 1, 2, 4, and 5.
4956
4957 checkpoint52f_post (2004/01/09)
4958 o added exch2 cube routines to pkg/exch2
4959 o modified hs94.cs-32x32x5 to use it
4960 o added new grid files to hs94.cs-32x32x5
4961 checkpoint52f_pre (2004/01/07)
4962
4963 checkpoint52e_post (2004/01/07)
4964 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
4965 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
4966 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
4967 to work with implicit vertical advection and AB ;
4968 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
4969 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
4970 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
4971 checkpoint52e_pre (2004/01/02)
4972
4973 o fix bug in impldiff when Nr=1 or Nr=2.
4974 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
4975 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
4976 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
4977 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
4978 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
4979 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
4980 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
4981
4982 checkpoint52d_post (2003/12/16)
4983 o re-tiled many expts to allow comparison in multi-processor mode
4984 - updated output accordingly
4985 - changed hs94.128x64x5 to use intial T from file rather than use the
4986 random number generator
4987 o add infrastructure in model routines for fizhi and gridalt packages
4988 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
4989 o changes to permit hi-res, cubed-sphere, configuration
4990 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
4991 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
4992 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
4993 of surface winds for the cube
4994 (A verification experiment, based on global_ocean.cs32x15, but with
4995 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
4996 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
4997 complete with example surface forcing files and matlab scripts to look
4998 at the output and compare it with that of global_ocean.cs32x15.)
4999 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
5000 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
5001 to conform to the common rule.
5002 o check-in the first version of the coupler + interfaces for multi-components
5003 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
5004 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
5005 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
5006 - ocean and atmos. share the same horizontal grid (no interpolation).
5007 - exchanges between component and coupler is done in forward_step
5008 o new verification experiment, cpl_aim+ocn:
5009 coupled ocean - AIM atmosphere on cs32 grid.
5010
5011 checkpoint52d_pre (2003/12/06)
5012 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
5013 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
5014
5015 checkpoint52c_post (2003/11/25)
5016 o Fixing OPTIONS files for use of exf:
5017 - ALLOW_ECCO not needed
5018 - ECCO_CPPOPTIONS.h should not be included from
5019 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
5020 as has been the case in the past
5021 - All cal/exf related options are currently set in
5022 single header file. Should remain so until we
5023 agree on a consistent new policy.
5024 o Removed all CPP options for cal package.
5025 cal has no more CPP options.
5026 o modified STOREs in GAD_ADVECTION
5027 o corrected key comp. for passkey
5028
5029 checkpoint52b_post (2003/11/23)
5030 o new version: "thsice" of thermodynamic sea-ice pkg:
5031 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
5032 - modify fluxes but do not change theta directly;
5033 - light cleaning of bulk_force pkg (still needed with thsice).
5034 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
5035 + output_thsice.txt to test thsice & bulk_force pkgs.
5036 o put back grid & coriolis monitor output.
5037 checkpoint52b_pre (2003/11/23)
5038
5039 o call "do_the_model_io" at the beginning (=> dump initial state)
5040 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
5041 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
5042 (need info on NUMBER_OF_PTRACERS)
5043 o missing PTRACERS headers in some routines
5044 o default tamc.h in pkg/autodiff supposed to crash
5045 to ensure proper customization
5046
5047 checkpoint52a_post (2003/11/17)
5048 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
5049 - moved surfaceTendencyTice from pkg/seaice to main code
5050 - subroutine FREEZE_SURFACE now limits only surface temperature
5051 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
5052 => new output.txt for global_ocean.cs32x15 & global_with_exf
5053 - keep the old version of FREEZE for backward compatibility;
5054 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
5055 - corresponding modifs for TAF directives
5056 o added surface flux output variables to TIMEAVE_STATVARS
5057 o time-averaged output for pkg/ptracers
5058 o fix problem with ECCO-related divided adjoint
5059 snapshot file was missing some ad-variables,
5060 but no warning issued by TAF
5061
5062 checkpoint52a_pre (2003/11/12)
5063 o some bug fixes for #undef REAL4_IS_SLOW
5064
5065 checkpoint52 = ecco_c52_e35
5066 o after testing adjoints of checkpoint51u_post
5067
5068 checkpoint51u_post (2003/11/06)
5069 o this is the post-merge tag of the ecco-branch
5070 (needs another clean checkout and re-testing)
5071 o various natl_box_adjoint configs and results
5072 but no input fields
5073 o obcs adjoint not yet merged!
5074 o adding ECCO global 1x1 and 2x2 degree configs
5075 o updated/extended some store directives for seaice
5076 o pkg/ecco now containes ecco-specific part of cost function
5077 o top level routines the_main_loop, forward_step
5078 supersede those in model/src/
5079 previous input data.cost now in data.ecco
5080 (new namelist ecco_cost_nml)
5081 o in ctrl/ cleaned some cross-dependencies and updated CPP options
5082
5083 checkpoint51t_post (2003/11/04)
5084 o this is the pre-merge tag of the ecco-branch
5085
5086 checkpoint51s_post (2003/11/04)
5087 o cleanup: removed various obsolete #define-s
5088 o pkg/grdchk
5089 - renamed 'ph-grd 3' to 'grad-res'
5090 - merged from ecco-branch
5091 (remaining bug fixes for obcs gradient checks)
5092 - additional high-precision output for testreport
5093 (grep for 'precision_grdchk_result')
5094
5095 checkpoint51r_post (2003/11/03)
5096 o cleaned up or removed CPP_OPTIONS.h files
5097 o updated results for some of the tests to reflect the new
5098 optfiles (-ieee: -O0 instead of -O3)
5099
5100 checkpoint51q_post (2003/10/30)
5101 o cd_code:
5102 - moved cd_scheme.F -> cd_code_scheme.F
5103 - separate read_checkpoint from cd_code_ini_vars.F
5104 - separated cd_code part from write_checkpoint
5105 - updated AD_SOURCE, generated .flow
5106 - added CD_CODE_VARS.h to the_main_loop
5107 - Moving cd_code specific store dir.s to pkg/cd_code
5108 o ctrl package totally restructured
5109 - pack/unpack now optional and decoupled from
5110 xx_/adxx_ I/O
5111 - ctrl_pack/unpack cleaned
5112 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
5113 - confined inclusion of AD_CONFIG.h to where necessary.
5114 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
5115
5116 checkpoint51p_post (2003/10/30)
5117 o create initial cd_code package
5118 - WARNING: the initialization of fields within packages
5119 is broken because INI_FIELDS (where READ_CHECKPOINT is
5120 called) is called *before* PACKAGES_INIT_VARIABLES.
5121 This seems to be backwards since
5122 1) its important to initially zero the entire field including
5123 the "halo" region
5124 2) zeroing needs to be done *before* reading pickup info
5125 and the pickup call might or might not happen in any
5126 particular run
5127 - this needs an overhaul for R2
5128 o cleanup verification/*/code/GMREDI_OPTIONS.h
5129 o cleanup testreport
5130
5131 checkpoint51o_post (2003/10/27)
5132 o bringing AD-related verif's up to date with genmake2
5133 - carbon/
5134 - global_ocean.90x40x15/
5135 - hs.94.1x64x5/
5136 - (front_relax/ )
5137 o (more) consistent directory structure for AD-related verif.'s
5138 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
5139 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
5140 o bug fix in find_alpha.F for MDJWF:
5141 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
5142 change rho -> rho-rhoConst
5143 - replace call find_rho to find_rhonum
5144 o initialisation of rFlx extended to full array (required by TAF)
5145 and shifted to thermodynamics
5146 o removed PTRACERS.h in ptracers routine
5147 o added surfacetendencyPtr to S/R parameter list pracers_forcing
5148 o Correcting initialisations for fVerU, fVerV.
5149 o helping TAF to recognize dependency on kUp for
5150 fVerU, fVerV
5151 o Replacing delZ by delR in pkg/ctrl/
5152 checkpoint51o_pre (2003/10/24)
5153
5154 o undid all of cp51 pending some cleanups and discussion
5155 o added the [#include "AD_CONFIG.h"] statement to all files that need
5156 it for adjoint/tl #defines
5157 o re-worked the build logic in genmake2 to support AD_CONFIG.h
5158 o removed tools/genmake since it no longer works
5159
5160 checkpoint51n_post (2003/10/23)
5161 o modifications to make FREEZE flux visible to pkg/kpp
5162 - moved surfaceTendencyTice from pkg/seaice to main code
5163 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
5164 - subroutine FREEZE now limits only surface temperature
5165 (this means new output.txt for global_ocean.90x40x15,
5166 global_ocean.cs32x15, and global_with_exf)
5167 o added surface flux output variables to TIMEAVE_STATVARS
5168
5169 checkpoint51n_pre (2003/10/23)
5170 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
5171 o added [#include "AD_CONFIG.h"] to all files that use the following
5172 defines:
5173 - ALLOW_ADJOINT_RUN
5174 - ALLOW_TANGENTLINEAR_RUN
5175 - ALLOW_ECCO_OPTIMIZATION
5176
5177 checkpoint51m_post (2003/10/21)
5178 o incorporating changes to get TAMC/TAF working in genmake2
5179 - added new TAMC/TAF targets to the Makefile
5180 - various cleanups related to package handling
5181 - these changes should have no impact on the forward model
5182
5183 checkpoint51l_post (2003/10/20)
5184 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
5185 - faster algorithm for cal_addtime.F
5186 - higher precision arithmetic, where needed
5187 - pkg/exf *startdate variables changed from calendar date to
5188 model integration time
5189
5190 checkpoint51l_pre (2003/10/17)
5191 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
5192 o enable to apply restoring on S & T only in a latitude band.
5193 o update output (external_forcing_surf modif. change truncation errors)
5194 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
5195
5196 checkpoint51k_post (2003/10/16)
5197 o change default to: useNHMTerms=.FALSE.
5198 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
5199 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
5200 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
5201 exp1, ideal_2D_oce
5202 - change data file of oceanic exp (leave the results unchanged for now)
5203 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
5204 o set gravitySign automatically according to the vertical coordinate used
5205 (and change sign: back to "logical" value: +1 when R increases downward)
5206 o added an include barrier to the default CPP_OPTIONS.h and
5207 removed the #include "PACKAGES_CONFIG.h" from it
5208 o fix a bug in mom_fluxform (from chk51j_post)
5209
5210 checkpoint51j_post (2003/10/10)
5211 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
5212 o adjusted some flow directives (dynamics, thermodynamics)
5213 o added cubed-sphere case to test cost function
5214 o heckpoint_lev?_directives.h now include
5215 pkg-specific directives, whenever those are enabled.
5216 o Moving pkg-specific flow directives to corresponding pkg
5217 Moving pkg-specific differentiation list to corresponding pkg
5218 Moving pkg-specific checkpoint-lev storing to corresponding pkg
5219 ---> conventions are
5220 - pkg_ad.flow
5221 - pkg_ad_diff.list
5222 - pkg_ad_check_lev?_dir.h
5223
5224 checkpoint51i_post (2003/10/09)
5225 o merge of the branch-genmake2
5226 - knowingly breaks the older genmake
5227 - automatic generation of all ALLOW_${PKG_NAME} defines
5228 - new testreport supersedes older testscript
5229 o large number of package inclusion and header cleanups
5230 checkpoint51i_pre (2003/10/08)
5231
5232 o new output for adjoin of global ocean vector invariant
5233 o fix for checkpoint of thermodynamic seaice and bulk_force
5234 o Steph gchem various cleanups
5235
5236 checkpoint 51h_pre
5237 o fixed some single quotes
5238 o modify gchem pkg to be more versatile
5239 o modifications to clean up dic pkg
5240 o add pkg/cfc
5241
5242 checkpoint51g_post (2003/10/02)
5243 o provide links for ARPACK and ADM*TLM
5244 o start removing verification/vero/
5245 o update AD-related stuff
5246 (in particular some IF-statements in model/src/ routines)
5247 o adding to verification/global_ocean.90x40x15/ adjoint of
5248 vector invariant setup
5249
5250 checkpoint51f_post (2003/10/02)
5251 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
5252 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
5253 of tracer Green's fucntions for ocean inversion project.
5254
5255 checkpoint51f_pre (2003/08/07)
5256 o Added on-the-fly spatial interpolation capability
5257 "USE_EXF_INTERPOLATION" to pkg/exf.
5258 - This is a temporary Cartesian-grid hack until
5259 the super-duper ESMF coupler becomes available.
5260 - See verification/global_with_exf/README for usage example.
5261 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
5262 flags and modified pkg/seaice accordingly.
5263 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
5264 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
5265 non-local transport term.
5266
5267 checkpoint51e_post (2003/08/03)
5268 o pkg/mom_vecinv:
5269 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
5270 - add time-ave diagnostic of vorticity advection.
5271 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
5272 o atmospheric geopotential: - include water vapor effect;
5273 - use p^kappa in p* scaling.
5274 o land pkg: read initial state from files.
5275 o AIM : add stratospheric drag in the upper level
5276
5277 checkpoint51d_post (2003/07/18)
5278 o change function ILNBLNK (=> last non-blank char.) to return zero
5279 (instead of the string length) when the string. char is empty
5280 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
5281 o modif's to restore TAMC compatibility
5282 - avoid "_d" constructs in PARAMETER declarations
5283 - avoid interrupting lines by comment lines
5284 o Use cluster local disks for purely local I/O
5285 vs. globally visible disks needed for ctrl stuff
5286 (merged from ecco-branch)
5287 - new active_file_loc... and mdsio_..._loc routines
5288 - affected packages: autodiff, ctrl, grdchk, mdsio
5289
5290 checkpoint51c_post (2003/07/08)
5291 o introducing integer flag debugLevel
5292 - debLevZero: suppress all output
5293 - debLevA: standard
5294 - debLevB: equivalent to current debugMode=.TRUE.
5295 o introducing pathname variable mdsioLocalDir for mdsio
5296 that can be specified at runtime
5297 (relevant for cluster I/O to local disk)
5298 `
5299 >>>checkpoint51b_post
5300 adjoint of ptracers
5301 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
5302 o extended state in checkpoint_lev?, etc.
5303 o alternative ctrl/cost with tr1 or ptracer
5304 o new comlev1_bibj_ptracers
5305 o new ptracers.flow
5306 o made ptracers_forcing same as external_forcing_s
5307 o added verification for adjoint with ptracers
5308 - adm. grdchk fail so far
5309 - tlm. grdchk OK
5310 - checked tapelev/comlev recomputations: OK
5311 <<<checkpoint51b_pre
5312
5313 checkpoint51a_post (2003/06/25)
5314 o added code for biogeochemistry package
5315 - new pkgs: dic, gchem
5316 - new subroutine in ptracers
5317 o modify code for biogeo packages
5318 - in model/src and pkg/ptracers
5319
5320 checkpoint51 (2003/06/24)
5321 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
5322 - autodiff, ctrl, exf, grdchk, seaice
5323 kept separate packages
5324 - cost, ecco, obcs
5325 o updating verification/internal_wave, verification/lab_sea
5326 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
5327
5328 checkpoint50i_post (2003/06/23)
5329 o Preparing next differentiable checkpoint and sync
5330 of MAIN vs. ecco-branch
5331 - 1st step: this one is differentiable
5332 - 2nd step: next(! not this) checkpoint will have updated packages
5333 from ecco-branch)
5334
5335 checkpoint50h_post (2003/06/20)
5336 o new package "land": provide surface BC for AIM.
5337 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
5338 o AIM: use true log-P extrapolation for near surface temp (= as in
5339 F.Molteni paper) ; update aim.5l_cs output.
5340 o New variable in PARM03 for more flexible pickups
5341 o somewhat cleaned package initialisation sequence for
5342 ctrl/ cost/ ecco/ in packages_... routines
5343
5344 checkpoint50g_post (2003/05/23)
5345 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
5346 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
5347 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
5348 made the default because of faster convergence than ADI
5349
5350 checkpoint50f_post (2003/05/23)
5351 o exf totally restructured
5352 - replaced all exf_set_ routines by one generic exf_set_gen.F
5353 and made sure it's still differentiable
5354 - split exf_getffields.F into new exf_bulkformulae.F
5355 - exf_inscal_/exf_outscal_ suffixes consistent with field names
5356 - updated adjoint/makefile and relevant verif. accordingly
5357
5358 checkpoint50f_pre (2003/05/23)
5359 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
5360 + change Evap over land. (update aim.5l_cs output)
5361 o added missing .cvsignores and made uniform across expts
5362 o changed configuration of tidal_basin_2d expt
5363 o added pkg/debug functions for tracing code in fatal crashes
5364 o tidied pkg/monitor to use MONITOR_OPTIONS.h
5365 o new fn in pkg/monitor to stop model if solution grows too big
5366 o removed lots of single quotes from comments
5367
5368 checkpoint50e_post (2003/05/14)
5369 o make KPP work with PTRACERS
5370 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
5371 nearly a copy of kpp_transport_s
5372 - there is no analogue to SurfaceTendencyS, so I have to use
5373 gPtr(of the surface layer) instead
5374 o add a new platform SunFire+mpi (SunFire 15000) to genmake
5375 checkpoint50e_pre (2003/05/13)
5376
5377 checkpoint50d_post (2003/05/13)
5378 o change kpp output from multiple-record state files to single-record state
5379 files analogous to write_state.F
5380 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
5381 analogous to the cg2d-related output.
5382 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
5383 so that writing to internal file fn (with length 512) fails.
5384 checkpoint50d_pre (2003/05/12)
5385
5386 checkpoint50c_post (2003/05/12)
5387 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
5388 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
5389 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
5390 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
5391 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
5392
5393 checkpoint50c_pre (2003/04/30)
5394 Merging from release1_p13:
5395 o bug fix for pkg/seaice dynamic solver
5396 o Added SEAICE_initialHEFF to pkg/seaice
5397
5398 checkpoint50b_post (2003/04/17)
5399 o store u*,v* in gU,V instead of in guNm1,gvNm1
5400 o in order to put the momForcing out of the Adams-Bashforth:
5401 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
5402 to timestep.F
5403 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
5404 o re-generate output for highly sensitive test-exp:
5405 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
5406
5407 checkpoint50b_pre (2003/04/17)
5408 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
5409 o corrected CPP option mismatch in exf_Bulk... functions for case
5410 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
5411
5412 checkpoint50a_post (2003/03/21)
5413 o Bug fix for merging between c50 and KPP.
5414 ikey was passed from thermodynamics to kpp_calc via
5415 common block rather than being recomputed in kpp_calc,
5416 in contradiction with new key itdkey.
5417 New key ikppkey created, and tamc.h headers updated.
5418
5419 checkpoint50 (2003/03/08)
5420 - 2nd step of merge with ecco-branch:
5421 merge changes in ecco-branch back into main trunk
5422 - bug fix in find_alpha
5423 - more storing in gmredi_calc_tensor.F, kpp_routines.F
5424 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
5425 - merged some sliced AD support routines
5426
5427 checkpoint49 (2003/03/06)
5428 merged from ecco-branch:
5429 o exf:
5430 - Enable initialisation of forcing fields to constant
5431 (runtime) values.
5432 - in exf_getffields.F
5433 Reduce i-/j-loop to interior domain, discarding overlaps.
5434 That also fixes wrong TAF-key computations for key_1, key_2
5435 with bulf formulae.
5436 - exf_init.F modify #ifdef for exf_init_evap
5437 - exf_getffieldrec.F, ctrl_getrec.F
5438 The following INT-usages are not safe:
5439 fldsecs = int(fldsecs/fldperiod)*fldperiod
5440 fldcount = int(fldsecs/fldperiod) + 1
5441 and were modified.
5442 o autodiff: checkpoint_lev...
5443 - updated storing for bulk formulae (some arrays were missing)
5444 - added state for seaice package
5445 - synchronized with main branch
5446 o DIVA:
5447 Modif.s in
5448 - the_main_loop.F
5449 - the_model_main.F
5450 and added cost_final_restore.F cost_final_store.F
5451 o With these changes, it is possible to fully separate
5452 the first forward run to compute the cost function (mdthe_main_loop)
5453 and adjoint runs over individual DIVA intervals (adthe_main_loop)
5454 into separate model executions.
5455 This enables better tuning of DIVA to given queue sizes.
5456 o Loss of cost function value in consecutive DIVA runs is
5457 fixed by storing to 'costfinal' file.
5458 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
5459 beginning/end of adjoint integration is accounted for.
5460 The current changes apply to TAF-1.4.26.
5461 TAF has one remaining bug, requiring one manual change
5462 (see MITgcm manual).
5463 o cal: synchronized between MAIN and ecco-branch
5464
5465 checkpoint48i_post (2003/03/05)
5466 o Changes to restore differentiability of code w.r.t. previous tag
5467 (mostly adding new routines to make list and replacing
5468 pressure by totPhiHyd).
5469 o Updated and merged grdchk package
5470 - has both ADM and TLM checks
5471 - works for single- and multi-proc.
5472 - output cleaned
5473 - worked successfully for parallel DIVA
5474 o genmake:
5475 - Adding -platform=SP4
5476 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
5477 o Modif. for DIVA:
5478 ctrl_unpack should not be called in intermediate DIVA interval.
5479 (similar thing would apply for active files such as
5480 tbar, sbar, psbar, which should not be reinitialised;
5481 only relevant for ecco-branch)
5482
5483 checkpoint48h_post (2003/02/28)
5484 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
5485 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
5486 o Added SEAICE_initialHEFF to pkg/seaice
5487 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
5488
5489 checkpoint48g_post (2003/02/18)
5490 --- EOS:
5491 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
5492 store total Potential in totPhyHyd for diagnostics & EOS.
5493 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
5494 --- Pressure/geopotential gradient:
5495 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
5496 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
5497 ( changes results of global_ocean_pressure )
5498 o NLFS + z-coord.: add eta*Rho' contribution.
5499 o accurate phiHyd when using interface-W at the middle between 2 centers
5500 ( changes results of ideal_2D_oce )
5501 o includes r* 2nd term in potential gradient.
5502
5503 checkpoint48f_post (2003/02/18)
5504 Merging from release1_p12:
5505 o Modifications for using pkg/exf with pkg/seaice
5506 - improved description of the various forcing configurations
5507 - added basic radiation bulk formulae to pkg/exf
5508 - units/sign fix for evap computation in exf_getffields.F
5509 - updated verification/global_with_exf/results/output.txt
5510 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
5511 (SBO) core products, including oceanic mass, center-of-mass,
5512 angular, and bottom pressure (see pkg/sbo/README.sbo).
5513 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
5514 to avoid negative values in shallow regions.
5515 - updated verification/natl_box/results/output.txt
5516 - updated verification/lab_sea/results/output.txt
5517 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
5518 o Added useSingleCpuIO option (see PARAMS.h).
5519 o Updated useSingleCpuIO option in mdsio_writefield.F to
5520 work with multi-field files, e.g., for single-file pickup.
5521 o pkg/seaice:
5522 - bug fix in growth.F: QNET for no shortwave case
5523 - added HeffFile for specifying initial sea-ice thickness
5524 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
5525 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
5526 kpp_transport_t.F, forward_step.F, and the_main_loop.F
5527 o pkg/seaice:
5528 - adjoint-friendly modifications
5529 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
5530
5531 checkpoint48e_post (2003/02/12)
5532 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5533 o dynamics: change definition of computational domain & adapt mom_fluxform
5534 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
5535 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
5536 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
5537 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
5538 global_ocean.90x40x15 global_with_exf global_ocean_pressure
5539 inverted_barometer solid-body.cs-32x32x1
5540 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
5541
5542 checkpoint48d_post (2003/02/09)
5543 o in preparation for r*:
5544 a) use pre-computed gradient of hydrostatic potential:
5545 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
5546 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
5547 => affects results of glob_oce_pressure (different truncation error)
5548 update output.txt of ideal_2D_oce & global_ocean_pressure
5549
5550 checkpoint48d_pre (2003/02/08)
5551 o in preparation for r*:
5552 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
5553 pass the 2 comp. of the grad. as arguments to momentum S/R.
5554 but for the moment, only used if it does not change the results.
5555 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
5556
5557 checkpoint48c_post (2003/02/06)
5558 Modifications in treatment of initial flux forcing controls
5559 to avoid extra storing of flux fields.
5560
5561 checkpoint48c_pre (2003/01/21)
5562 o Added tidal_basin_2d experiment (currently 1D!)
5563 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
5564
5565 checkpoint48b_post (2003/01/27)
5566 o r* coordinate added in #ifdef NONLIN_FRSURF block.
5567 (modification to pressure gradient not yet implemented)
5568 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
5569 (for U & V) that are used for vertical advection of momentum.
5570
5571 checkpoint48a_post (2003/01/24)
5572 o In preparation for r*, use temp. array to compute vertical transport
5573 in flux-form momentum pkg. => change results of few test-exp.
5574 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5575 lab_sea, natl_box & plume_on_slope
5576
5577 checkpoint48 (2003/01/23)
5578 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
5579
5580 checkpoint47j_post (2003/01/21)
5581 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
5582 o moved adexch from forward_step to addummy_in_stepping
5583 o added exch in ctrl_map_...
5584 o aveFreq.=0. at end of cost_final to avoid overwrite in
5585 reverse checkpointing loop
5586 o Yet more changes in gmredi:
5587 * adgmredi_calc_tensor
5588 avoiding all recomputation of gmredi_slope_limit
5589 * adgmredi_x/y/rtransport
5590 added flag for excessive storing to avoid recomp. of
5591 u/v/rtans, dTdx/y/z
5592 -> this is not really necessary and very memory-consuming
5593 * adgmredi_slope_psi:
5594 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
5595 * gmredi_slope_limit
5596 re-activated full calculation of taperfct for case 'ac02'
5597 o updating verification/ adjoints of carbon, global_ocean.90x40x15
5598
5599 checkpoint47i_post (2003/01/13)
5600 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
5601 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
5602 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
5603 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
5604 o gmredi: fix few bugs.
5605
5606 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
5607 This will be a good checkpoint to plug into the ecco-branch.
5608 o few modif.'s to get latest version adjointed
5609 (mainly kick out code in ini_linear_phisurf)
5610 o modif's to run adjoint with exactConserv
5611 o case GM_BOLUS_ADVEC should be cleaned
5612 S/R gmredi_slope_psi should be cleaned
5613 o verification/carbon now has exactConserv=.TRUE.
5614
5615 checkpoint47g_post (2003/01/10)
5616 o time-average AIM output: becomes independent from statvars time-average
5617 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
5618 o After TAF bug fix:
5619 Tested adjoint of gmredi package.
5620 Tests were done with checkpoint47 rather than with latest
5621 checkpoint47f_post since the latter is broken for the adjoint
5622 verification/carbon/ contains both ADM and TLM gradient checks.
5623 Here they are, before they get changed/lost/stolen.
5624 Mostly modif.'s to fix numerical sensitivities.
5625 Gradient checks OK for
5626 - GM_taper_scheme:
5627 * clipping
5628 * ac02
5629 * linear
5630 * glw91
5631 * dm95
5632 * ldd97
5633 - GMREDI_OPTIONS:
5634 * GM_VISBECK_VARIABLE_K
5635 * GM_NON_UNITY_DIAGONAL
5636 * GM_EXTRA_DIAGONAL
5637 * GM_BOLUS_ADVEC
5638 in conjunction with data.gmredi parameters to be checked in
5639 in a few minutes under verification/carbon/code/
5640
5641 checkpoint47f_post (2002/12/28)
5642 Merging from release1_p10:
5643 o modifications for using pkg/exf with pkg/seaice
5644 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
5645 and SEAICE_EXTERNAL_FLUXES
5646 - pkg/exf CPP options EXF_READ_EVAP and
5647 EXF_NO_BULK_COMPUTATIONS
5648 - usage examples are Experiments 8 and 9 in
5649 verification/lab_sea/README
5650 - verification/lab_sea default experiment now uses
5651 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
5652
5653 checkpoint47e_post (2002/12/27)
5654 o created a tag prior to creating a branch
5655
5656 checkpoint47d_post (2002/12/16)
5657 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
5658 at the bottom boundary had an erroneous half slip boundary condition
5659 o added bottom drag and no slip boundary condition capabilities to
5660 oceanic pressure coordinates code
5661 o added new verification experiment global_ocean_pressure, this experiment is
5662 also described in the tutorial section of the manual
5663 checkpoint47d_pre (2002/12/16)
5664
5665 checkpoint47c_post (2002/12/16)
5666 o Added a verification experiment for a global cubed-sphere ocean run
5667 - verification/global_ocean.cubed32x32x30
5668 - uses pkg/therm_seaice and pkg/bulk_forcing
5669
5670 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
5671 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
5672 when using P-coordinate; only implemented for atmospheric config.
5673 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
5674 NOTES: requires option NONLIN_FRSURF to be "#define".
5675 o update advect_xz/results/output.txt (left from checkpoint44g_post)
5676
5677 checkpoint47b_post (2002/12/05)
5678 Merging from release1_p9:
5679 o pkg/seaice
5680 - removed GOTO's and added taf directives
5681 - double precision constants to reduce the g77 (Linux)
5682 to F77 (SGI) differences reported in release1_p8
5683 o tools/genmake
5684 - added SGI options
5685 o verification/testscript
5686 - updated to that of checkpoint47a_post
5687 o verification/global_ocean.90x40x15/input/eedata
5688 - modified for SGI f77 compatibility
5689 o verification/lab_sea
5690 - added description of sea-ice model
5691 - added missing matlab routines
5692 - added test of thermodynamics parallelization
5693
5694 checkpoint47a_post (2002/11/23)
5695 o new pkg: aim_v23
5696 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
5697 for now, keep the same surface forcing as before.
5698 - Part-Cell implemented into AIM; check that Heat & Water are conserved
5699 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
5700 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
5701 o add diagnostic of surface correction term in monitor output
5702
5703 o bulk_force and therm_seaice
5704 - Two packages: bulk_force (Bulk forcing)
5705 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
5706 - Earlier integration from Stephaine Dutkiewicz
5707 and Patrick Heimbach.
5708 - Two ifdef statements for compile time,
5709 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
5710
5711 checkpoint47 (2002/11/15)
5712 differentiable version of checkpoint46n_post
5713 o bug fix in quasihydrostaticterms
5714 o * "clean" adjoint code (in terms of extensive recomputations)
5715 can now be obtained for all GMREDI options (i.e. for
5716 - GM_VISBECK_VARIABLE_K
5717 - GM_NON_UNITY_DIAGONAL
5718 - GM_EXTRA_DIAGONAL
5719 - GM_BOLUS_ADVEC )
5720 * However, wrong gradient check problem remains unsolved.
5721 * New CPP options have been introduced for different
5722 tapering schemes
5723 o external_fields_load now part of differentiation list
5724 o pressure needs multiple storing;
5725 would be nice to have store_pressure at beginning or
5726 end of forward_step, e.g. by having phiHyd global (5-dim.)
5727 (NB: pressure is needed for certain cases in find_rho,
5728 which is also invoked through convective_adjustment).
5729 o recomputations in find_rho for cases
5730 'JMD95'/'UNESCO' or 'MDJWF' are OK.
5731 o #define ATMOSPHERIC_LOADING should be differentiable
5732 o ini_forcing shifted to begining of initialise_varia
5733 o Incorporating QNVS line search routines into MITgcm
5734 (this is separate code, and therefore not under pkg)
5735 lsopt/, optim/
5736 o Updated verification/carbon/
5737 - #define GM_VISBECK_VARIABLE_K
5738 - GM_taper_scheme = 'ldd97'
5739
5740 checkpoint46n_post (2002/11/12)
5741 Merging from release1_p8:
5742 o verification/natl_box:
5743 updating new external_fields_load routine
5744 o New package: pkg/seaice
5745 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
5746 The sea-ice code is based on Hibler (1979-1980).
5747 Two sea-ice dynamic solvers, ADI and LSR, are included.
5748 In addition to computing prognostic sea-ice variables and diagnosing
5749 the forcing/external data fields that drive the ocean model,
5750 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
5751 The implied surface heat flux is then stored in variable
5752 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
5753 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
5754 non-local transport term. Because this call precedes model
5755 thermodynamics, temperature under sea-ice may not be "exactly" at
5756 the freezing point by the time theta is dumped or time-averaged.
5757 N.B.: fairly large differences in accuracy occur across
5758 different platforms/compilers; comparison between
5759 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
5760 generated output gives:
5761 T S U V
5762 C D M c m s m s m s m s
5763 n p a R g m m e . m m e . m m e . m m e .
5764 f n k u 2 i a a d i a a d i a a d i a a d
5765 g d e n d n x n . n x n . n x n . n x n .
5766
5767 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
5768 o GAD:
5769 - generated new common blocks to account for call of
5770 same gad routines with differing traceridentities
5771 (needed to modify tracerIdentity indices in GAD.h)
5772 - generated separate common blocks for case useCubedSphereExchange
5773 (Department of Futurology)
5774 - parameter lists to gmredi_?transport: added tracerIdentity
5775 - added new key indices to tamc.h
5776 o external_fields_load:
5777 - added this routine to TAF list
5778 - needed to make some common blocks global and additional storing
5779 along the same lines as exf package (checkpoint_lev?_directives.h)
5780 o exf:
5781 updated external forcing package
5782 - bug fixes carried over from ecco-branch
5783 (missing OBCS_OPTIONS.h in two routines)
5784 - enable easy to use "no forcing".
5785 - added exf I/O for atmospheric loading
5786 - added exf I/O for runoff data
5787 - transfered scaling between exf <-> MITgcm to exf namelist
5788 o Adding new verification experiment global_with_exf.
5789 This verification experiment is almost identical to the
5790 global_ocean.90x40x15 experiment, except that it uses
5791 the exf (and cal) package instead of the
5792 external_fields_load routine (cf README file).
5793
5794 checkpoint46m_post (2002/11/07)
5795 o modified testscript to return -- when there are no lines of "%MON" output
5796 o added new flag "quasiHydrostatic" for QH mode
5797 and new routine quasihydrostaticterms()
5798 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
5799 New routine: mom_u_coriolis_nh()
5800 o fixed sign of non-hydrostatic metric terms in u and v equations.
5801 Depend on correct sign of gravitySign.
5802 o added work.pc* to .cvsignore in aim directories using ifc
5803 o introduced flag for controllin non-hydrostatic metric terms
5804 o removed gravitySign from PARM04
5805 o switched to g77/ifc from pgf77 in aim experiments
5806
5807 checkpoint46l_post (2002/11/01)
5808 o made convective adjustment work with pressure coordinates:
5809 - changed the direction of k-loop in convective_adjustment.F for the
5810 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
5811 - adjusted the reference pressure k-index in convective_adjustment.F
5812 - adjusted the convection condition in convect.F (in analogy to
5813 calc_ivdc.F)
5814 - convective_adjustment no longer computes anything on the halos
5815 - removed the warnings about negative salinity from find_rho.F and
5816 find_alpha.F; instead the new routine look_for_neg_salinity, called
5817 at the beginning of find_rho, find_alpha, and find_beta, does a
5818 check of the entire slice, if CPP-option
5819 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
5820 checkpoint46l_pre (2002/10/23)
5821
5822 checkpoint46k_post (2002/10/23)
5823 o fixed the verification/global_ocean.90x40x15 experiment:
5824 - new bathymetry (the world according to A., JMC, and M.)
5825 - new initial fields and forcing fields (*.bin files)
5826 - new POLY3.COEFFS (for the next release one should switch to a full
5827 equation of state: JMD95P or MDJWF)
5828 - fixed several errors and redundancies in the data file
5829 - experiment uses looped cells
5830 - added matlab directory with diagnostic scripts for plotting of output
5831
5832 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
5833 - read AIM physics parameters from a file (data.aimphys)
5834 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
5835
5836 checkpoint46j_post (2002/10/07)
5837 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
5838 o move wVel computation at the end of the time step, in S/R integr_continuity
5839 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
5840 o update timeave pkg for wVel diagnostic.
5841 checkpoint46j_pre (2002/09/27)
5842
5843 checkpoint46i_post (2002/09/25)
5844 o Clean up AIM package (and keep the results unchanged):
5845 include CPP_OPTION and use IMPLICT NONE in all routines ;
5846 declare all the variables _RL ; use _d 0 for all numerical constants.
5847 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
5848
5849 checkpoint46h_post (2002/09/25)
5850 o cleaned up the use of rhoNil and rhoConst.
5851 - rhoNil should only appear in the LINEAR equation of state, everywhere
5852 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
5853 and the dynamical equations are all divided by rhoConst
5854 o introduced new parameter rhoConstFresh, a reference density of fresh
5855 water, to remove the fresh water flux's dependence on rhoNil. The default
5856 value is 999.8 kg/m^3
5857 o cleanup up external_forcing.F and external_forcing_surf.F
5858 - can now be used by both OCEANIC and OCEANICP
5859 checkpoint46h_pre (2002/09/18)
5860
5861 Added code to convert surface volume flux (fresh water) into
5862 a mass flux when using P coordinates in the ocean (OCEANICP).
5863 Note: It assumes you have set rho0=rhoConst=density of fresh water.
5864
5865 checkpoint46g_post (2002/09/18)
5866 o Include a new diagnostic variable phiHydLow for the ocean model
5867 - in z-coordinates, it is the bottom pressure anomaly
5868 - in p-coordinates, it is the sea surface elevation
5869 - in both cases, these variable have global drift, reflecting the mass
5870 drift in z-coordinates and the volume drift in p-coordinates
5871 - included time averaging for phiHydLow, be aware of the drift!
5872 o depth-dependent computation of Bo_surf for pressure coordinates
5873 in the ocean (buoyancyRelation='OCEANICP')
5874 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
5875 Theta, Salinity, and Pressure in the parameter list. This routine is
5876 presently contained in find_rho.F. This routine does not give the
5877 correct density for 'POLY3', which would be a z-dependent reference
5878 density.
5879 o cleaned up find_rho
5880 - removed obsolete 'eqn' from the parameter list.
5881 o added two new verification experiments: gop and goz
5882 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
5883 checkpoint46g_pre (2002/09/16)
5884
5885 checkpoint46f_post (2002/09/16)
5886 o Enable tangent linear (forward mode) gradient checks:
5887 - extended active file handling to g_... files
5888 - added TANGENT_SIMULATION to theSimulationMode
5889 - extended grdchk package accordingly
5890 o added tangent linear setup in verification/carbon/code_ftl
5891 o added adjoint setup in verification/front_relax/code_ad
5892
5893 checkpoint46e_post (2002/09/05)
5894 o Added new equation of state -> MDJWF
5895 - EOS of McDougall et al., 2002, JAOT, submitted
5896 - caveat: the equation of state is only valid for a smaller (more
5897 realistic?) range of values than JMD95P/Z and UNESCO
5898 - added masks to the calculation of pressure in store_pressure
5899 - added more check values for density in check_eos (ini_eos.F), some of
5900 the old check values are out of the range of the MDJWF-eos, so don't
5901 expect perfect matches for those
5902 checkpoint46e_pre (2002/08/19)
5903
5904 checkpoint46d_post (2002/08/19)
5905 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
5906 'OCEANICP', also initialised field pressure correctly in ini_eos in the
5907 case of pressure coordinates. eosType='JMD95Z' in
5908 combination with buoyancyRelation='OCEANICP' now causes an error.
5909 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
5910 in find_alpha/beta.
5911 checkpoint46d_pre (2002/08/15)
5912
5913 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
5914 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
5915
5916 checkpoint46c_post (2002/08/15)
5917 o Changes necessary for ocean in p-coordinates
5918 - Added new buoyancy relation = 'OCEANICP'
5919 - Added new parameters = gravitySign (this used to be contained inside
5920 the factor dRdZ which I added when we first switched to R coordinates).
5921 X GM/Redi is not compatible (yet)
5922 X bottom drag and no-slip need to be debugged.
5923 checkpoint46c_pre (2002/08/07)
5924
5925 checkpoint46b_post (2002/08/07)
5926 o Added new equation of state -> JMD95Z and JMD95P
5927 - EOS of Jackett and McDougall, 1995, JAOT
5928 - moved all EOS parameters into EOS.h
5929 - new routines ini_eos.F, store_pressure.F
5930 o Added UNESCO EOS, but not recommended because it requires
5931 in-situ temperature (see JMD95)
5932 o Modified formatting for knudsen2.f in utils/knudsen2 and added
5933 unesco.f to be used with POLY3
5934 checkpoint46b_pre (2002/07/31)
5935
5936 checkpoint46a_post (2002/07/31)
5937 o Added (atmospheric) pressure loading
5938 - new field in FFIELDS.h, etc...
5939 - new cpp flag ATMOSPHERIC_LOADING
5940 o Changed hFacC to _hFacC in calc_phi_hyd.F
5941 o Added SHORTWAVE_HEATING to some files for consistency
5942 checkpoint46a_pre (2002/07/13)
5943
5944 checkpoint46 (2002/07/13)
5945 further merges from release1_p5
5946 o new ctrl package
5947 - adopted from ECCO environment to enable optimization
5948 - added Eliassen Palm fluxes to controls
5949 o added Eliassen Palm flux controls to gradient check package
5950 o cost package
5951 - Compatible with new ctrl package
5952 - added Eliassen Palm cost hooks
5953 - modif's of existing cost functions
5954 o Adjoint-related bug fixes in kpp:
5955 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
5956 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
5957 o autodiff package
5958 - flow directives:
5959 + new for S/R do_the_model_io
5960 + enhanced for S/R checkpoint
5961 + new gmredi.flow
5962 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
5963 disable adcommon.h/g_common.h by default.
5964 - fixed problem for adjoint of global_max
5965 o modified verification/carbon/
5966 o New setup for adjoint of global_ocean
5967 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
5968 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
5969 o incorporated hooks for sponge layer code (external_forcing.F)
5970
5971 checkpoint45d_post (2002/07/12)
5972 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
5973 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
5974 (affects plume_on_slope "cg2d" output)
5975 o add new parameter deltaTfreesurf for free-surface time stepping
5976 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
5977 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
5978 o change phiMin in exp1 (to agree with documentation)
5979 o add new flags:
5980 - T,S forcing inside/outside Adams-Bashforth
5981 - turn off temp,salt advection and/or forcing
5982 - for each tracer, define internal flag for multiDimAdvection & A-B
5983 o monitor: change definition of KE to check conservation of Energy
5984
5985 checkpoint45c_post (2002/05/30)
5986 o Removed f90 comments ("!")
5987 o Modified initialisations to enable exf package for MITgcm
5988 (without invoking ECCO_PACKAGE).
5989 o modifications to gradient check package (Martin Losch)
5990 - enable centered differences
5991 - modified format of standard output
5992
5993 checkpoint45b_post (2002/05/30)
5994 o cleaned exchange calls in cg2d
5995 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
5996 o included CPP option SINGLE_LAYER_MODE in thermodynamics
5997 to configure barotropic setup (Martin Losch)
5998 o moved some initialisations within bi,bj loop in dynamics
5999 (TAF flow dependency)
6000 o in initialise_varia, moved call packages_init_variables
6001 before convective_adjustment_init
6002 (corresponding adjustment of TAF tape initialisation).
6003 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
6004
6005 checkpoint45a_post (2002/05/01)
6006 o compute Rho over the whole domain (extend iMin,jMin indices)
6007 o specific exchange for X-slice domain (case Ny=1)
6008 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
6009 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
6010
6011 checkpoint44h_post = checkpoint45
6012 o Fix to restore differentiability:
6013 place at which packages_init_variables is called in
6014 initialise_varia is crucial for reverse control flow.
6015 o modifications in GMRedi to enable stable adjoint
6016 (corresponding modif's in thermodynamics, dynamics)
6017 o added missing hook for sponge layer code in external_forcing
6018 o modified test cost functions
6019 o storing in gad_advection (plus removal of write(0,*)!
6020 o missing headers TR1.h added in convective_adjustment routines
6021 o errorMessageUnit set non-equal zero in eeboot
6022 (conflict on some platforms, e.g. IBM SP3)
6023 o modified carbon verif.
6024
6025 checkpoint44h_pre (2002/03/14)
6026 o vertical grid option: allow to put the Interface at the middle between
6027 2 cell-centers ; replace delZ in pkg/kpp by drF.
6028 o GM Advective form: Tracers are advected using the residual transport (=
6029 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
6030
6031 checkpoint44g_post (2002/03/05)
6032 o fix surface correction term in multiDimAdvection (affects plume_on_slope
6033 results) ; ifdef missing in thermodynamics.F
6034
6035 checkpoint44f_pre,checkpoint44f_post
6036 o added PTRACERS package
6037 This allows an arbitrary number of passive tracers to be integrated
6038 forward simultaneously with the dynamicaly model.
6039 + Implemented so far:
6040 - basic forward algorithm (time-stepping, advection, diffusion, convection)
6041 - I/O and checkpointing
6042 - GM/Redi *but* using the GM/Redi coefficient of Salt
6043 + Not implemented so far:
6044 - KPP
6045 - OBCS
6046 + No specific example supplied (yet) but global_ocean.90x40x15 has the
6047 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
6048 line in data.pkg.
6049 + This package is disabled by default since it increases storage.
6050
6051
6052 o testscript: added -cleanup option
6053 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
6054 b) enable to filter 2D fields.
6055
6056 checkpoint44e_pre,post
6057 o re-wrote convective adjustment to use pre-calculated weights
6058 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
6059 Adds: model/src/convective_weights.F, convectively_mixtracer.F
6060 Original calls to convect() still in place.
6061
6062 chkpt44d_pre,post
6063 o added missing EXCLUDE_MONITOR flags
6064 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
6065 (incompatible typ in MIN/MAX expressions caused problems
6066 on IBM SP3)
6067 o in genmake added variable MAKEDEPEND
6068 plus resetting for case SunOS
6069 o added timer_stats.c routine for IBM SP3
6070 o removed variables in dynamics
6071 !!! I forgot to create tag chkpt44d_pre !!!
6072 !!! But chkpt44d_pre = chkpt44c_post !!!
6073
6074 o real fresh water flux implemented with non-linear free-surface.
6075
6076 chkpt44c_pre,post
6077 o few fix (mask in shap_s2, EmPmR in external_field_load,
6078 USE_NATURAL_BCS in solve_for_P);
6079 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
6080
6081 checkpoint44b_pre/_post
6082 o merge of relevant stuff from the ecco-branch:
6083 - genmake: removed $S64 overwrite for case SunOS
6084 - pkg/exf: update and corrections for field swapping and obcs
6085 - pkg/ecco: parameter lists for the_model_main, the_main_loop
6086 harmonized between ECCO and MITgcm
6087 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
6088 updated checkpointing_lev... lists for obcs
6089 - model/src: minor changes in forward_step, plot_field
6090 added directive for divided adjoint in the_main_loop
6091 - pkg/mdsio: added mdsio_gl_slice
6092
6093 o check parameters & config (chkpt44a_pre,post)
6094 o OBC and NonLin_FrSurf.
6095
6096 checkpoint44 (2002/01/18)
6097 o fix bug in mom_vi_del2uv
6098 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
6099 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
6100 o update AIM experiments (NCEP input files)
6101 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
6102 o added some stuff for AD
6103
6104 checkpoint43 (2001/09/28)
6105 o added two new advection tests
6106 o added global 4x4 degree ocean test
6107 o added test of H&S94 with free surface on cube
6108 o some final mods for gradient check, adjoint,...
6109
6110 checkpoint42 (2001/09/27)
6111 Fixed AD-related problems:
6112 o Store directives up-to-date with re-arranged Adams-Bashforth
6113 (mainly thermodynamics.F)
6114 o New store directives for multi-dim. advection schemes
6115 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
6116 * new common block and key passkey
6117 (mainly gad_advection.F)
6118 o Modified store directives for split of dynamics/thermodynamics
6119 for the case ALLOW_KPP
6120 o Cleaned argument list for timestep_tracer.F
6121
6122 checkpoint41 (2001/09/27)
6123 o re-formatted/added comments in prologues of key subroutines
6124 to work with protex
6125
6126 checkpoint40 (2001/09/27)
6127 o moved calc_gs, calc_gt and calc_tr1 back to model/src
6128 o added FLT (floats) package from Arne along with demo. experiment
6129 o re-arranged Adams-Bashforth scheme for tracers to allow easier
6130 implementation of forward-in-time forcing terms
6131 o more mods for non-linear free-surface including new variable
6132 o modified multi-dim method to work on cube
6133 o bug fix in KPP (from DM)
6134
6135 checkpoint40pre9 (2001/09/27)
6136 o added DST advection schemes
6137 o fix MPI bug on SGI's
6138 o modifications for non-linear free-surface
6139 o fixed conditionals for fixed flow/passive tracer only mode
6140 o added tension/strain form of stress tensor
6141 o changes to commenting of arguments for TAF/TAMC
6142 o added/updated many matlab scripts
6143 o added multi-dimensional advection method for tracers
6144
6145 checkpoint40pre8 (2001/09/05)
6146 o new package rw/
6147 Added method for dumping intermediate local arrays:
6148 mdsio_writetile - same as mdsio_writefield except works from inside
6149 bi,bj loop
6150 mdsio_writelocal - same as mdsio_writetile except works for local
6151 arrays
6152 write_local_r? - higher-level wrapper for mdsio_writelocal
6153 Controlled by diagFreq. Defaults to zero (ie. no dumps)
6154 Example given at end of mom_vecinv.F that dumps some local arrays.
6155 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
6156 control flux-form versus vector invariant code.
6157 Switch is runtime flag vectorInvariantMomentum (defaults to false)
6158 or genmake -DISABLE ...
6159 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
6160 (additional storing is now needed for case vecinv;
6161 currently nothing implemented to switch this storing off
6162 in case fluxform is used since no CPP flag available).
6163
6164 checkpoint40pre7 (2001/08/14)
6165 o bug fix in dynamics.F
6166 calc_viscosity called before k=1,Nr loop.
6167 o added some #ifdef's ALLOW_PASSIVE_TRACER
6168 o cleaned initialisations in ctrl_map_ini
6169 related to TAF
6170
6171 checkpoint40pre6 (2001/08/13)
6172 o split dynamics into thermodynamics & dynamics
6173 o corresponding split of calc_diffusivity into
6174 calc_diffusivity, calc_viscosity
6175 (kpp_calc_diff, kpp_calc_visc).
6176 o Added diffkr, kapgm to control variables
6177 o bug fix in gmredi_slope_limit for ldd97
6178
6179 checkpoint40pre5 (2001/07/31)
6180 o proper initialization of Adams-Bashforth time stepping
6181 + uses forward step for very first step of model (iter=0)
6182 o re-generated *all* output since almost all output is modified by this
6183 change (sorry but we've been putting this one off for about 2 years)
6184 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
6185 *not* regenerated since they are already out of date and I don't
6186 want to create the impression that they are suddenly working.
6187 o removed KAP stuff for DEC's
6188 o modified/added many .cvsignore files in */code and */input
6189 o added new expt "solid-body.cs-32x32x1"
6190 + this uses an alternative form of ini_curvilinear_grid.F which
6191 is not necessarily any better than the current one...
6192
6193 checkpoint40pre4 (2001/07/30)
6194 o added re-initialisations of utrans,vtrans,rtrans in
6195 calc_common_factors which are crucial for TAF.
6196 o extended iMin,jMin range for calc_common_factors,
6197 calc_diffusivity
6198 o added option ALLOW_PASSIVE_TRACER
6199 o a few minor updates and fixes
6200
6201 checkpoint40pre3 (2001/07/13)
6202 o created calc_gtr1.F for gad package
6203 o split the_main_loop and re-introduced forward_step
6204 o some recomputations of nIter0 for TAMC
6205
6206 checkpoint40pre2 (2001/07/13)
6207 o Updated to latest branch of AJA, JMC
6208 o Added gradient check package
6209 o Added routines for passive tracer handling
6210 o Added carbon sequestration sensitivity experiment
6211
6212 checkpoint39 (2001/05/14)
6213 o Modifications and fixes to support TAMC
6214 (mainly missing or wrong directives)
6215 o Corrected common blocks when fooling TAMC to produce adjoint I/O
6216 in addummy_in_stepping
6217 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
6218 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
6219 o Included following packages:
6220 cal: calendar
6221 exf: external forcing
6222 ecco: essential routines to control use of cal, exf
6223 (NB: this is not the full ECCO environment)
6224 o disabled some packages by default in genmake
6225
6226 checkpoint38 (2001/04/10)
6227 o see notes_c37_adj.txt
6228 o corrected wrong layer index in external_forcing_t
6229 o replaced the_main_loop/forward_step by the_main_loop
6230 o removed forceoutput from write_state
6231 (replaced criteria for initial/final state)
6232 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
6233
6234 checkpoint37 (2001/03/13)
6235 o mdsio.F routine split and packaged in pkg/mdsio
6236 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
6237 used unless genmake -disable=mdsio)
6238 o allow a more precise surface-geopotential gradient for the atmosphere
6239 taking into account the change in space of Alpha (=1/rho) at the surface.
6240 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
6241 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
6242 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
6243 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
6244 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
6245 o Time-Average diagnostics defined as a pseudo package "timeave".
6246 o pickup files : old pickup (before c35) did not work with new code (c35
6247 and after) unless activating 2 commented lines in initialise-varia.
6248 o Non-Hydrostatic pickup file Pb fixed.
6249 o bug with Rigid-lid version (since c35) fixed.
6250
6251 checkpoint36 (2001/02/20)
6252 o implement Crank-Nickelson barotropic time-stepping
6253 o recover Time-Average diagnostics
6254 o fix Pb in checkpoint (PR#19)
6255 o AIM become a standard package ; clean unused CPP_kees
6256
6257 checkpoint35 (2001/02/08)
6258 o subtantial rewrite of dynamics.f
6259 o allows staggered time-stepping
6260 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
6261 o added bottom drag (linear + quadratic)
6262
6263 checkpoint34 (2001/01/30)
6264 o Modified exchange routines for correct reverse simulation.
6265 o Added verification output to comply with bug fix in impldiff.F
6266 as of c33 (exp2, natl_box).
6267 o Corrected store directives in dynamics.F
6268 o Corrected array boundaries in impldiff.F
6269 o Corrected array dimensions in gmredi.
6270 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
6271 o Added routine GLOBAL_SUM_INT to global_sum.F
6272 o Added mdsio_gl.F for ECCO purposes.
6273
6274 checkpoint33 (2000/11/30)
6275 o Fixed bug in lower BC in impldiff.F
6276 o Fixed confusion about units of forcing arrays in FFIELDS.h
6277 namely Fu,Fv,Qnet,Qsw,EmPmR:
6278 - Removed verification/natl_box/code/external_fields_scale.F
6279 (did not differ from that in model/src)
6280 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
6281 (see FFIELDS.h for description)
6282 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
6283 kpp_calc.F and kpp_transport_t.F
6284 - Removed model/src/external_fields_scale.F and calls to it
6285 - verification/natl_box uses flux data with "atmospheric" sign so
6286 a special version of external_fields_load.F is used to
6287 change the data as it's read in. This way, the arrays
6288 have the right units and signs at all times tha a user could
6289 possibly use them.
6290 o Corrected genmake to delete a temporary file during configuration
6291
6292 checkpoint32 (2000/11/13)
6293 o Scaling of forcing fields moved from external_forcing.F to
6294 external_fields_scale.F, called directly after loading fields.
6295 o Surface relaxation terms added to surface tendency fields in
6296 extra subroutine.
6297 o impldiff.F changed to avoid storing by TAMC of huge intermediate
6298 fields.
6299 o Changes in GMRedi to comply with packaging structure.
6300 o Modifications and bug fixes in KPP package.
6301 o Verification experiment for KPP added (verification/nat_box/)
6302
6303 checkpoint31 (2000/09/11)
6304 o Packages interface brought in line with defined standard
6305 -> new routines packages_...F
6306 -> changes in initialise_fixed.F, initialise_varia.F
6307 -> enables initialisation interface for ECCO package
6308 o Rescaling of external forcing fields immediately after read
6309 (removed from external_forcing.F)
6310 -> new: surface_fields_scale.F
6311 -> affects ini_foorcing.F, external_fields_load.F
6312 o Computation of surface tendencies before tendency updates.
6313 -> new: external_forcing_surf.F
6314 o Change of variable names useGMRedi, useKPP, useECCO
6315 o Further changes in dynamics.F, impldiff.F for TAMC
6316 o Tested for experiments 0, 2, 4.
6317 - not yet tested for GMRedi.
6318 - not yet tested for KPP.
6319
6320 checkpoint30 (2000/07/13)
6321 o Updates for OBCs
6322 o New experiment for test OBCs (internal_wave)
6323 o New output.txt in verification/exp4/results/
6324 o Updates for KPP: calculation of viscosity corrected, new variables
6325 kpp_dumpFreq and kpp_taveFreq
6326 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
6327 and entry for T90 in genmake
6328
6329 checkpoint29 (2000/06/21)
6330 o packaged KPP and GM/Redi
6331
6332 checkpoint28 (2000/06/09)
6333 o Corrected initialization of hFacMin for difference vertical coordinates
6334 o Modified calculation of partial cell thickness to more robust algorithm
6335 o config_summary.F: replaced write_1D_... by write_0D_...
6336 read_write.F: added subroutines write_0D_...
6337 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
6338 included some initialisations required for TAMC.
6339 o routine calc_isoslopes: modified sqrt computation to make it
6340 differentiable for zero argument.
6341 o routines dynamics, impldiff:
6342 included store directives and tape key computations required for TAMC.
6343 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
6344
6345 checkpoint27 (2000/04/10)
6346 o fixed calc_isoslopes() to so that cancellation of terms in tensor
6347 formulation works properly with variable resolution.
6348 o restructured the calling tree between the_model_main() and dynamics()
6349 o split initialise() into initialise_fixed() and initialise_varia()
6350 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
6351 in new routine ini_psurf()
6352
6353 checkpoint26 (2000/04/05)
6354 o moved some #ifdef in optional routines to encompass everything
6355 except the argument declarations. This was using up some memory.
6356 o fixed macros like _ADT to work with both versions of Linux cpp
6357 o cleaned up some unused and uninitialized variables
6358 (helps when debugging with strict compile options)
6359 o split up CPP_EEOPTIONS.h into options and macros
6360 (macros are now in eesupp/inc/CPP_EEMACROS.h)
6361 o patch for 2 processor JAM mode
6362
6363 checkpoint25 (2000/03/15)
6364 o updates for OBCs and NH
6365 o dramatically reduced memory usage
6366 o added "JAM" routines for use on Artic network
6367 o parameterization of convection by implicit vertical diffusion
6368 o added a diagnostic of convective index
6369 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
6370 (this is was partly for OBCs and NH but also in anticipation of
6371 an explicit free-surface option)
6372 o initial state input files for U and V
6373
6374 checkpoint24 (1999/08/02)
6375 o Removed some spurious "REAL"s
6376 o Updated KPP to latest version from JPL
6377 o Added a COS(latitude) in horizontal viscosity
6378
6379 checkpoint23 (1999/05/26)
6380 o Added del^4 diffusion for salt and temperature
6381 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
6382
6383 checkpoint22 (1999/05/18)
6384 o Made many small changes: implicit none, format(i5), etc...
6385 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
6386
6387 checkpoint21 (1999/05/18)
6388 o Introduced new I/O package that supports direct-access records (mdsio.F)
6389 o Split-up mid-level I/O routines
6390 o Updated input data for experiments 0,1,2,4 and 5
6391 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
6392
6393 checkpoint20 (1999/03/22)
6394 o Tidied up open-boundaries some more
6395 o Added non-hydrostatic code
6396 o Fixed some input data
6397 o Modified MPI start-up to work in "coupled" context.
6398
6399 checkpoint19 (1998/12/15)
6400 o Tidied up directory structure for verification experiments.
6401 o Added new code for open boundaries.
6402 o Corrected advective terms near boundaries.
6403 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
6404 o Implemented free-slip/no-slip BCs and del^4 dissipation.
6405 o Split default parameters out of ini_parms.F into set_defaults.F.
6406
6407 checkpoint18 (1998/11/30)
6408 o Further changes for optional code generation with
6409 CPP - ugh!
6410
6411 checkpoint17 (1998/11/03)
6412 o Beginning to incorporating modularity
6413 for supporting atmos. and ocean configs.
6414 o Small changes for TAMC complinace
6415 o New ultra simple test case. Barotropic box
6416 configuration "exp0".
6417
6418 checkpoint16 (1998/10/28)
6419 o Minor changes to exchange routines to support
6420 accumulation in reverse mode. Adjoint of an
6421 assignment is an addition.
6422 o Changes to support compilation by TAMC (LR(1)
6423 syntax) and by g77 under Linux ( 72 character
6424 limit ).
6425
6426 checkpoint15 (1998/09/29)
6427 Rewrote exchange routines to allow
6428 o General tile <-> tile connectivity.
6429 o TAMC reverse mode flag ( is this really needed? )
6430 o Variable width overlap and exchange region widths.
6431 o Hooks for sharing data via DMA, Arctic, Memory Channel,
6432 shmput/shmget, VIA, SYSV shmem and every other cool
6433 communication method.
6434
6435 checkpoint14 (1998/09/09)
6436 Consistent isomorphism chages made. These allow dynamical core
6437 to support both pressure and meters as a vertical coordinate.
6438
6439 checkpoint13 (1998/07/17)
6440 Release which corrects global_max problem and a couple
6441 of KGM time-averaging diagnostic errors. Also contains
6442 a double-gyre experiment setup as well as the baseline
6443 4 degree global template. The double gyre template is
6444 organised to allow it to be applied automatically to
6445 the baseline configuration.
6446
6447 branch-point-rdot
6448 A few tidy-ups have been made bt the real point of this
6449 check-point (excuse the pun) is to allow a branch to be
6450 made for the purposes of adding the rDot alterations.
6451 I don't want to commit the rDot to the main-trunk until
6452 we've actually tested it...
6453
6454 checkpoint12 (1998/07/08)
6455 Tidy up and added generic genmake script (formerly
6456 configure script).
6457 Released to testers.
6458
6459 checkpoint11 (1998/07/02)
6460 Re-arranged initialise() and introduced ini_vertical_grid()
6461 and ini_masks_etc().
6462
6463 checkpoint10 (1998/07/01)
6464 Introduced the configure script.
6465 Separated out the diags package.
6466 Added template for writing time-averages of tile/intermediate quantities.
6467 Updated SIZE.h in exp2 and made the data big-endian.
6468
6469 checkpoint9 (1998/06/22)
6470 MPI fix. Filename changes (meta/data). salbin*y stuff.
6471 General tidy-up.
6472 SST.bin SSS.bin added to verification/exp2
6473
6474 checkpoint8 (1998/06/22)
6475 Inludes time-dependant forcing and time-averaging.
6476 Works at 4x4 and 2.8125x2.8125 global
6477
6478 checkpoint7-4degree-ref
6479 Branch from checkpoint7. Released for application to
6480 global modeling and general modeling - process studies, regional
6481 model etc..
6482 Configured for verification/exp2 - 4 degree global, two process.
6483
6484 checkpoint7 (1998/06/15)
6485 Created by cnh
6486 Simple 4 degree global simulation
6487 configuration.
6488 Includes climatological wind,
6489 hydrography, bathymetry etc
6490 Does not include Heat Flux and E-P
6491
6492 checkpoint6 (1998/06/08)
6493 Created by cnh
6494 merged checkpoint5 with CD and
6495 spherical polar code.
6496 Still some problems with GM Redi
6497 abd full topography.
6498
6499 checkpoint5 (1998/06/08)
6500 Created by AJA
6501 contains updates to GM Redi
6502 and reordered timestepping loop
6503 for Implicit Diffusion.
6504
6505 checkpoint4 (1998/05/30)
6506 Created by cnh
6507 Contains memory saving macros ( _rdxc etc..) for when
6508 grid variations are limited.
6509 Contains polynomial coeffs for EOS and knudsen program
6510 for generation.
6511
6512 checkpoint3 (1998/05/26)
6513 Created by cnh
6514 Added extra flags for runtime options
6515 Added this file
6516 Added implicit free-surface
6517 Added pre-conditioner
6518 Put compare01 into repository ( compare01/... )
6519 Put data and eedata into repository ( verification/exp1 )
6520
6521 checkpoint2
6522 Created by AJA
6523 Added GM/Redi
6524
6525 checkpoint1
6526 Created by AJA
6527 Restructured kloop in dynamics.F
6528 Added non-linear EOS
6529
6530 baseline
6531 Original checked in code

  ViewVC Help
Powered by ViewVC 1.1.22