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Revision 1.1845 - (show annotations) (download)
Sun Mar 31 16:30:33 2013 UTC (11 years, 2 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint64f
Changes since 1.1844: +15 -8 lines
tag checkpoint64f

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1844 2013/03/29 23:21:39 heimbach Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 checkpoint64f (2013/03/31)
8 o verification/OpenAD:
9 - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
10 o verification/isomip, pkg/shelfice and OpenAD:
11 - add OpenAD setup to this exp and make shelfice package work with OpenAD
12 o verification/tutorial_global_oce_biogeo:
13 - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
14 o verification/offline_exf_seaice:
15 - replace adjoint experiment (now similar to fwd input.thermo/ setup).
16 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
17 - add OpenAD setup to this exp and make ptracers package work with OpenAD
18 o pkg/seaice/seaice_evp.F:
19 mask the asymmetric contribution of the ice-ocean stress (when
20 the turningAngle is non-zero) over open water to avoid stripes
21 in the EVP-solutions after many EVP-substeps. This does not change
22 the verification experiment (because turningAngle=0 in that experiment),
23 but will affect other EVP solutions with turningAngle.ne.0
24 o verification, AD & TLM output:
25 - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
26 additions and multiplications which affect results at machine truncation
27 level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
28 lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
29 (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
30 digits of matching.
31 o pkg/seaice:
32 modify lsr-algorithm so that it vectorizes AND converges by using a
33 "zebra" method: split vector loop into two with step size 2; this
34 solves a general convergence problem for the JFNK solver on a vector
35 computer. It has the potential to even improve convergence for
36 non-vector machines, but it does change the results so it is turned
37 off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
38 SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
39
40 checkpoint64e (2013/03/05)
41 o pkg/ecco and several verification experiments:
42 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
43 from ecco package, and revert to unified routine in model/src/
44 Adjust verification experiments accordingly, especially gloal_oce_llc90
45 Should conclude long-standing work by Gael to reconsile the_main_loop with
46 ECCO and will enable OpenAD's revolve loop in ECCO setup.
47 o pkg/generic_advdiff:
48 - implement compressible flow method for multi-dim advection (similar to
49 gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
50 TAF generates many recomputations) to use it; no yet coded with implicit
51 vertical advection.
52 - change experiment advect_cs (new output) and advect_xy (same output)
53 to test compressible flow multi-dim advection.
54 o pkg/generic_advdiff:
55 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
56 cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
57 o pkg/seaice:
58 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
59 bug affects two verification experiments (lab_sea and lab_sea.hb87),
60 recover old (wrong) results by setting noSlipFac = 2. in
61 seaice_calc_strainrates.F;
62 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
63 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
64 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
65 - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
66 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
67 - new subroutines seaice_lsr_tridiagu/v
68 - introduce loop bounds i/jmin/max to be able to use a restricted
69 additive Schwarz method, but not used for now.
70 - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
71 - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
72 o OpenAD support
73 Reorganize S/R call for overall time-stepping loop to facilitate
74 OpenAD revolve loop replacement
75 (new S/R main_do_loop.F)
76 o model/src:
77 - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
78 - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
79 ADAMS_BASHFORTH2.
80 o pkg/cheapaml:
81 - add new parameter (default=F, same as before) to disable full domain
82 (including land) periodicity in X & Y dir.
83 - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
84 prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
85 into single S/R CHEAPAML_TIMESTEP.
86
87 checkpoint64d (2013/02/17)
88 o pkg/monitor (angular momentum):
89 - do not add Eta contribution to the total AM if using rigid-lid;
90 - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
91 - horizontal discretisation: compute Zonal wind contribution separately for
92 each component (instead of from cell centered averaged) and use the 4
93 grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
94 - Check that AM is conserved with linear dynamics (momAdvection=F and linear
95 FreeSurf) if using vectorInvariant momentum.
96 o model/src (horizontal grid):
97 - move initialisation of all horizontal grid arrays to null value
98 from specific horizontal grid S/R to main S/R INI_GRID;
99 - add 2 new arrays to project model C-grid velocity on to zonal direction
100 (similar to AngleCosC & -AngleSinC but at U and V point location) and
101 compute them in S/R CALC_GRID_ANGLES.
102 o pkg/seaice: replace a hard coded parameter by a runtime parameter
103 SEAICE_JFNK_tolIter
104 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
105 preconditioner for JFNK (run LSR into the overlaps as far as possible,
106 i.e OLx/y-2, but overwrite the solution in the overlaps)
107 - extend loop range in seaice_calc_viscosity
108 - add new parameters SEAICE_OLx/y (default = OLx/y-2)
109 - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
110 - slightly modify loops in tridiagonal solver lsr-preconditioner
111 - by default remove the extra exchange in seaice_preconditioner with a
112 replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
113 - modify offline_exf_seaice so that old results without RAS are reproduced
114 for output.dyn_jfnk.txt
115 in seaice_fgmres.F (unrelated to RAS)
116 - add a cpp-flag option for a re-ordered mapping (potentially more
117 efficient), but because this changes the results, turn it off by
118 default
119 - replace the save statement by local common blocks
120 o utils/matlab:
121 - fix tile-offset in rdmnc.m when output was produced using EXCH2.
122 - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
123 instead of local script "load_cs.m".
124 o pkg/seaice:
125 - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
126 to the scalarProductMetric and the unrolling. By chance this does not
127 change the verification experiment, because of the particular domain
128 decomposition
129 o pkg/diagnostics:
130 - change default missing_value from UNSET_RL to -999.
131 o pkg/layers: improve vectorization of layers_fluxcalc.F
132 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
133 time spent in this routine by more than a factor of 3 on an NEC-SX8
134 - step 2: replace search algorithm by a bisection algorithm found in
135 Press et al. Numerical Recipes in Fortran. This algorithm can be
136 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
137 For now, use this algorithm only for TARGET_NEC_SX defined.
138 - moved the search algorithm into a separate subroutine, that is kept
139 within the same file for automatic inlining.
140 - modified catching potential errors
141 o pkg/ecco:
142 - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
143 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
144 - modifications for ALLOW_GENTIM2D_CONTROL
145 -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
146 -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
147 -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
148 -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
149 o model/src:
150 - account for moist thermodynamics in (dry) potential temperature equation;
151 update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
152 and cpl_aim+ocn.
153 - also switch to standard compiler (gfortran, was using ifort previously)
154 for fizhi-cs experiments reference output.
155 o pkg/ctrl:
156 - 1st step toward generic time-varying control variable (2D) via CPP option
157 ALLOW_GENTIM2D_CONTROL
158 - note new namelist ctrl_nml_genarr in data.ctrl
159 o verification/global_ocean.cs32x15:
160 - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
161 thsice calling sequence and update "output.icedyn.txt" output file.
162 o pkg/ptracers:
163 - from Ryan A.: code to allow to restart a tracer at regular time interval
164 specifying a reset frequency and a reset-phase (for each tracers).
165 o pkg/thsice:
166 - implement new sequence of calls for thsice+seaice:
167 previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
168 new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
169 - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
170 in CPP_OPTIONS.h) to recover old sequence;
171 - update diagnostics for Intermediate State thsice diagnostics: now filled
172 just before advection (instead of just after advection in old sequence);
173 - update output of experiment offline_exf_seaice (standard test);
174 - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
175 by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
176 o pkg/aim_v23:
177 - use tiled array for aim_CO2 and surface wind speed for export to coupler;
178 - use standard pkg/mdsio routines to read & write CO2 pickup file;
179 - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
180 - Implement new sequence of calls for seaice advection (with thsice and
181 seaice diffusion): do ice advection after ice-Thermodynamic (previously
182 was done before); change aim_do_physics.F (split the bi,bj loops block);
183 - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
184 o pkg/thsice:
185 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
186 where just seaice diffusion is used without seaice-dynamics.
187
188 checkpoint64c (2013/01/18)
189 o pkg/seaice:
190 - add a parameter JFNKres_tFac that can replace JFNKres_t
191 (= JFNKres_tFac*JFNKresidual before JFNK solver)
192 - add a line search option to the JFNK solver
193 - move update of u/vIce and computation of initial residual into a separate
194 routine (same file); makes the code a little easier to read (?)
195 - the line search requires computation of the residual and for some reason
196 I cannot do the update of u/vIce at the beginning of the Newton loop
197 without changing the results, so we move computation of the new residual
198 also to the end of the Newton loop, even without the line search
199 o pkg/mdsio:
200 - write missing value (corresponding to undefined array value) to meta files;
201 skip this if missing value is one (UNSET_RL would be a better value for the
202 case of undefined missing value but it's current the default missing-value);
203 Also update mdsio_read_meta.F (reading timeInterval & missing-value).
204 o pkg/exf & thsice:
205 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
206 diagnostics) even when SHORTWAVE_HEATING is #undef;
207 o verification/cfc_example:
208 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
209 illustrate how to use it).
210 o verification/offline_exf_seaice:
211 in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
212 files to only one time-record.
213 in input.thermo: narrow the 2 bands of low initial ice-concentration near
214 N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
215 snapshot output; same mcPheePiston value as in thsice with
216 surf-current=0.2m/s.
217 in input.thsice: similar set-up as in input.thermo (channel with same seaice
218 initial conditions).
219 o verification/cfc_example:
220 - update file "data" with more standard choice (default rotationPeriod,
221 exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
222 set deltaTFreeSurf to deltaTtracer) and update the output.
223 o pkg/layers:
224 - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
225 - ensure that "layers_bolus" is switched to False when useGMRedi=False.
226 o verification/offline_exf_seaice:
227 - set all {field}period to zero for constant-in-time forcing (not tested
228 anywhere else).
229 o verification/offline_exf_seaice:
230 - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
231 - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
232 o model/src:
233 - implement Finite-Volume method for (hydrostatic) presure gradient
234 from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
235 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
236 - In order to be compatible with the default EVP code, this requires changing
237 the EVP code around a little; and because any small change immediately
238 breaks the lab_sea.hb87 verification experiment, the reference output is
239 updated two times (each time the remaining aggrement was only 2 digits):
240 - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
241 - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
242 The adjoint test lab_sea.evp also needed to be updated.
243 - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
244 SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
245 a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
246 explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
247 INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
248 kept obscure, because I need to test it a little more.
249 o pkg/cheapaml:
250 - fix few incorrect type (_RL/_RS) in subroutine calls.
251 o pkg/seaice:
252 - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
253 to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
254 o model/src:
255 - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
256 change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
257 experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
258 o pkg/cheapaml:
259 - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
260 update output of experiment cheapAML_box.
261 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
262 and set them only in one place (cheapaml_readparms.F).
263 - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
264 - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
265 and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
266 o model/src/the_main_loop.F:
267 - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
268 o pkg/seaice:
269 - remove legacy branch code.
270 - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
271 o verification/*/code*/SEAICE_OPTIONS.h:
272 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
273 SEAICE_CAP_HEFF).
274 o pkg/cheapaml:
275 - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
276 to load new forcing fields.
277 - add missing "_d 0" where it's needed; + some editing (improve indentation).
278 - remove switch to "-r8" compiler option (no longer needed) in verification
279 cheapAML_box, keep same output (small trucation error differences).
280 o verification/offline_exf_seaice:
281 - add thermodynamics only test.
282 o verification/cheapAML_box:
283 - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
284 keep same output (same 14 digits for cg2d).
285 - switch on "-r8" compiler option (some numerical values are missing
286 the "_d 0") and update output (only 6 digits for cg2d were preserved).
287
288 checkpoint64b (2012/12/24)
289 o pkg/cheapaml:
290 - remove un-used variables (Qnet,EmPmR) from pickup files.
291 - store tendency of advected variables into cheapaml pickup file
292 and fix the AB-2 restart.
293 o verification/offline_exf_seaice and lab_sea adjoint:
294 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
295 - switch to 4 time steps in offline, consistent with lab_sea.
296 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
297 - update results after change of experiment seaice.
298 o pkg/seaice:
299 - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
300 parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
301 still defined since SEAICE_multDim needs to be set to MULTDIM value (from
302 SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
303 o model/src:
304 - add run-time parameter to select CG2D solver minimum-residual solution
305 (in case of a poor convergence).
306 o pkg/seaice/seaice_lsr.F
307 - move calculation of matrix coefficients into new
308 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
309 file; the main purpose of this change is to be able to reuse the code
310 in S/R SEAICE_PRECONDITIONER
311 - modify the computation of the residual so that the mass of sea-ice
312 is not used twice; this simplifies the calculations, but since
313 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
314 not tested in testreport---this does not affect the testreport results.
315 o verification/seaice_obcs:
316 - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
317 verification/lab_sea/input.salt_plume; changes results/output.txt*
318 o model/src:
319 - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
320 o pkg/seaice:
321 - improve description of parameters in seaice_fgmres.F and start
322 cleaning up the code
323 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
324 second argument
325 - add a metric based on grid cell area to SEAICE_SCALPROD; update
326 results of offline_exf_seaice.dyn_jfnk
327 - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
328 o pkg/aim_v23:
329 - fix an other bug in dissipation heating (grid-cell area was missing).
330 o model/src + pkg/seaice:
331 - add global (multi-tile) linear solver for pair of tri-diagonal system
332 along X and Y lines, respectively for U and V component.
333 Note: 1) MPI and cube-exchange not yet coded.
334 2) probably not accurate for poorly conditioned / large size problem.
335 - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
336 default: not compiled and not used.
337 o pkg/seaice:
338 - first attempt at a multi-threaded fgmres solver for the JFNK solver:
339 introduce bi/bj loops and use global_sum_tile_rl instead of
340 mpi_allreduce in seaice_fgmres.F
341 - improve diagnostics output for fgmres solver (seaice_fgmres.F)
342 - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
343 - add a verification experiment for JFNK in offline_exf_seaice
344 o verification:
345 - change (for now, only fwd test) offline_exf_seaice experiment:
346 use a re-entrant channel with idealized coastline (trapezoidal shape)
347 at southern boundary to explore seaice dynamics and thermodynamics
348 with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
349 secondary test (input.thsice) use thermodynamics only with SST relaxation.
350 - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
351 o pkg/exf:
352 - disable "sstExtrapol" when Nr=1
353 o verification:
354 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
355 to test pkg/cheapaml.
356 o pkg/aim_v23 & pkg/shap_filt:
357 - fix dissipation heating (erroneous gravity multiplication factor).
358 o pkg/seaice:
359 - remove unused field pressPre from jfnk solver
360 - rename two subroutines in seaice_preconditioner.F
361 o eesupp/src:
362 - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
363 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
364 - remove wrong parts of the rhs and the lhs (were in there
365 because I did not understand the concept of this preconditioner)
366 - add an exchange between u- and v-sweep. This increases communication
367 by a factor of two but improves the convergence of jfnk. Ideally,
368 one would like the u- and v-sweep to be independent. So far within
369 undocumented ifdefs
370 - reorganize the extra computations for printing the residuals
371 o tools/genmake2:
372 - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
373 since it's not necessary (and was preventing to use MNC in some cases).
374
375 checkpoint64a (2012/11/16)
376 o pkg/autodiff:
377 - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
378 autodiff_readparms.F no longer depends on calling order (within
379 packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
380 rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
381 and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
382 o pkg/obcs:
383 - adding tidal velocity forcing capability to obcs
384 for usage example, see verification/seaice_obcs/input.tides
385 o pkg/seaice:
386 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
387 SEAICE_LSRrelaxU/V
388 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
389 o pkg/aim_v23:
390 - implement heating from friction (bottom friction and stratospheric drag).
391 o pkg/shap_filt:
392 - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
393 dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
394 o model/src:
395 - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
396 time-constant addMass field from file (addMassFile);
397 - support for heating due to friction (and Kinetic Energy dissipation):
398 add option, run-time switch and 3-D field array + support code ; each pkg
399 or S/R can add heating contribution (if there is a sink of KE); the sum is
400 accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
401 o pkg/seaice:
402 - complete merge of ITD code into seaice_growth.F
403 from MITgcm_contrib/torge/itd/code/
404 no verification so far, but Torge Martin tested
405 "1-D test case and Beaufort set up;
406 deliver okay results after 1 model year."
407 - complete merge of SEAICE_SIZE.h into all relevant routines
408 - move computation of eta at Z-points into calc_viscosities
409 + introduce global field etaZ
410 + add different methods for computing etaZ, for now the old
411 method (simple averages of eta to Z-points) is hardwired
412 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
413 seaice_preconditioner
414 - simplify computations for SEAICE_ZETA_SMOOTHREG
415 - seaice_preconditioner:
416 + replace one remaining press by pressLoc (mistake)
417 + adjust printing of residuals
418 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
419 + add (SEAICE.h) and rename some counters (initiliased in
420 seaice_init_fixed.F)
421 + add _BEGIN/END_MASTER (myThid) around print statements
422 + print total number of iterations and failures over SEAICE_monFreq
423 interval to STDOUT
424 - move control over output-messages by fgmres to seaice_jfnk to save
425 some operations
426 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
427 in order to make restarts with sol .ne. zero (fgmres with restarts)
428 (seaice_jfnk.F, seaice_fgmres.F)
429 - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
430 a serious convergence problem when open boundaries are involved
431 o pkg/ggl90: fix computation of control volumes for the case of
432 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
433 up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
434 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
435 o pkg/autodiff
436 - Add inAdMode switch for SEAICEuseDYNAMICS:
437 SEAICEuseDYNAMICSinAdMode
438 (extend logic in ADAUTODIFF_INADMODE_SET)
439 o pkg/seaice
440 - Step 1 of merging ice-thickness distribution (ITD) code from
441 MITgcm_contrib/torge/itd/ (author: Torge Martin)
442 The code implements concept laid out in Thorndike et al. (1975);
443 code is enabled via CPP flag SEAICE_ITD
444 nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
445 code is not complete yet!!
446 - SEAICE_SIZE.h now included in almost all seaice routines
447 o verification (using seaice):
448 - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
449 global_ocean.cs32x15.seaice ; update results.
450 - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
451 - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
452 offline_exf_seaice (previously compiling B-grid).
453 o pkg/exf:
454 - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
455 to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
456 forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
457 o pkg/layers (adjust changes from Sept 19):
458 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
459 this allows to remove "layers_maxNum" dimension from all layers arrays.
460 o pkg/layers (adjust changes from Sept 19):
461 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
462 - snap-shot extended to all type of layers (not just the 1rst type);
463 - remove layers variables when corresponding CPP option is undef.
464 o pkg/layers:
465 - rename pkg/layers variable and add new output (layer exist & un-weighted
466 velocity in layer)
467 o pkg/seaice:
468 - simplify (?) ocean-drag coefficent computations by using
469 the same routine in all three solvers (saves some code lines)
470 - remove global fields DRAGA and DRAGS from C-grid code and
471 declare them locally in lsr.F (the only place where they are
472 still used)
473 - update AD output of lab_sea.evp (very sensitive anyway).
474 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
475 (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
476 and SEAICEuseJFNK=.true. A few things to note:
477 - involves a FGMRES, that is parallel but very inefficient,
478 because of many scalar products (global sums) in the Gram-Schmidt
479 orthogonalization method. Needs to be replaced. Original code
480 from J.-F. Lemieux
481 - preconditioner for FGMRES is a stripped down version of LSOR
482 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
483 preconditioner. For the preconditioner, the default is set to 10.
484 - Jacobian times vector is computed with finite differences
485 - marginally related to JFNK-solver: add a smooth regularization for
486 zeta with tanh that will improve convergence (Lemieux and Tremblay,
487 2009) for any implicit solver (not implemented for EVP because EVP
488 does not need this regularization in the first place). Define
489 SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
490 o eesupp/src:
491 - check in genmake2 that intrinsic S/R flush is available.
492 - add S/R to flush IO unit (if intrinsic S/R flush is available)
493 - flush standard & error msg unit before MPI termination
494 - if debugMode, flush IO unit after printing msg
495 o pkg/ctrl:
496 - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
497 to ctrl_set_unpack_xyz.
498
499 checkpoint64 (2012/10/09)
500 o pkg/shelfice
501 - in mom_fluxform.F, mom_vecinv.F:
502 CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
503 Bug fix KappaRU -> KappaRV
504 does not change verification/isomip but may change other setups
505 (presumably constant KappaRU=KappaRV)
506 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
507 o pkg/obcs:
508 - fixed some indexing bugs in obcs_seaice_sponge.F
509 - added obcs relaxation subroutines for HSALT and HSNOW
510 - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
511 o pkg/seaice:
512 - add "multicategory" parameterization for snow in analogy to ice,
513 default is off for now.
514 o pkg/obcs:
515 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
516 see verification/seaice_obcs/input.seaiceSponge for example application.
517 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
518 index setting by master-thread. This fix multi-threads Pb in previous modifs.
519 o pkg/layers :
520 - add diagnostics to pkg/layers
521 - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
522 (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
523 o pkg/generic_advdiff/gad_implicit_r.F :
524 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
525 o pkg/seaice/seaice_growth.F:
526 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
527 o pkg/obcs:
528 - change default setting of OBCS_UVICE_OLD from defined to undef;
529 - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
530 in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
531 - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
532 - change OB null index value (OB_indexNone) to -99 ; this fix the problem
533 with Southern & Western OB at a tile edge (at least in a simple set-up).
534 o pkg/obcs:
535 - change settings of OB index in case OB coincides with tile edge (shared by
536 2 tiles), so that common OB location is registered by both tiles (instead of
537 only 1). However, for Southern and Western OB, index value = 0 is not
538 recognized as valid OB index (=default null value) and needs to be fixed.
539 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
540 - new parameter "OB_indexNone" for null index value (for now, still zero)
541 to replace hard-coded null index value of zero.
542 o pkg/exch2:
543 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
544 always check buffer-size (but outside the loop); move checking for valid
545 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
546 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
547 o pkg/ctrl (pack & unpack):
548 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
549 (locally defined) for different variables (+ remove the variable-specific
550 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
551 (to be extended to other local file names in ctrl.h).
552 o pkg/flt:
553 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
554 o pkg/mdsio:
555 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
556 o tools/genmake2:
557 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
558 (added by Alistair in version 1.51 for building without make depend);
559 - remove Header files list (H_SRC_FILES) from the dependence of targets
560 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
561 place in version 1.23): this save going through staf when unrelated header
562 file has been modified.
563 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
564 "make depend" step, still need to do "make links" before "make adtaf".
565 o eesupp/src (+ few pkg src files) & genmake2:
566 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
567 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
568 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
569 upper/lower case ; account for space between "#" and undef/define)
570 o pkg/flt (with exch2):
571 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
572 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
573
574 checkpoint63s (2012/09/05)
575 o pkg/ecco:
576 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
577 - add more relevant #ifdef ALLOW_SMOOTH ones.
578 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
579 o pkg/ctrl:
580 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
581 ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
582 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
583 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
584 ctrlSmoothCorrel3D (new).
585 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
586 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
587 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
588 controls when useAtmWind, and vice versa.
589 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
590 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
591 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
592 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
593 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
594 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
595 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
596 o pkg/smooth:
597 - remove un-necessary includes.
598 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
599 Those CPP options were never defined, and not necessary.
600 o model/src:
601 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
602 - standard treatment of useSMOOTH.
603 o pkg/autodiff:
604 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
605 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
606 o pkg/exch2:
607 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
608 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
609 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
610 and tiles to process mapping.
611 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
612 moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
613 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
614 from w2_eeboot.F to w2_readparms.F.
615 o eesupp/src:
616 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
617 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
618 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
619 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
620 is defined (remove condition on usingMPI) to match cases where MPI_INIT
621 has been called.
622 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
623 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
624 (so that on 1 proc, get same myPid independently of usingMPI)
625 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
626 useCubedSphereExchange with EXCH-1 (safer).
627 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
628 o pkg/ggl90:
629 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
630 used in ALLOW_GGL90_SMOOTH code.
631 o pkg/flt:
632 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
633 floats at the Southern end of the domain).
634 o eesupp/inc:
635 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
636 but not used (and not to be used) anywhere, just for documentation.
637 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
638 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
639 a) can damage previously written records in any other multi-record files.
640 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
641 o tools/genmake2:
642 - define variable MAKE within Makefile and use it in place of 'make';
643 - update AD_CONFIG.h (if needed) before building any of the executable
644 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
645 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
646 - always print usual warning comment 'this file is automatically generated'
647 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
648 o pkg/cheapaml:
649 - updated to correspond to the code used in accepted paper (Nico Wienders).
650 o pkg/exf:
651 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
652 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
653 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
654 o pkg/exf, autodiff, ctrl, ecco and seaice:
655 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
656 o pkg/ctrl, ecco:
657 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
658 Depending on useAtmWind, one is inactive, and the other is active (see
659 exf_getffields.F/exf_getsurfacefluxes.F).
660 o tools/genmake2:
661 - improve error msg when failing in 2nd test of check_for_broken_Ff
662 - fix option '-makefile' short-name (-mf according to genmake2 -help)
663 - source local config file "genmake_local" just after processing the genmake2
664 command arguments (previously done before processing arg).
665 o pkg/grdchk:
666 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
667 to this routine from cost_final has been dropped in g_cost_final)
668 - improve printed information (more explicit msg, no longer using "print *,"
669 fix fcpertminus printed value).
670 o model/src:
671 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
672 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
673 this prevents getting cost-funct reset in adinitialise_varia recomputations.
674 o pkg/dic:
675 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
676 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
677 o pkg/grdchk:
678 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
679 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
680 o pkg/autodiff/ctrl/grdchk :
681 - attempt to sort out what works and what does not,
682 with regard to I/O, and to warn/stop accordingly.
683 o pkg/grdchk:
684 - attempt to fix grdchk in the case of useSingleCpuIO.
685 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
686 statements were moved from grdchk_main.F and into
687 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
688 - a global sum is applied to record numbers icvrec/layer
689 out of grdchk_loc so that they be passed to I/O routines.
690 o pkg/smooth:
691 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
692 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
693 o verification/testreport:
694 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
695 - can also use compressed (gzip) reference output file;
696 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
697 to be easier to collect by testreport.
698 - update existing TLM output (half out-of-date by more than 3 yrs).
699 - report NETCDF & LAPACK settings (from genmake2) in output dir.
700 - report run-time in each individual summary (previously only for AD test);
701 for TLM test, add also TAF version.
702 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
703
704 checkpoint63r (2012/08/15)
705 o tools/genmake2:
706 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
707 o pkg/ecco/ecco_cost_final.F :
708 - fix fc print statements (to stdout and costfunction0000) so
709 that the printed value is always after the global sum.
710 o pkg/seaice/seaice_dynsolver.F :
711 - fix ice strength assymptote at SEAICE_area_max<1
712 (no change for the standard case of SEAICE_area_max=1)
713 o some cleaning:
714 - pkg source files: ensure that all *.F files from each pkg included the
715 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
716 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
717 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
718 includes;
719 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
720 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
721 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
722 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
723 - update option-file CPP_OPTIONS.h of all AD experiments:
724 * no longer include PACKAGES_CONFIG.h ;
725 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
726 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
727 including ECCO_CPPOPTIONS.h).
728 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
729 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
730 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
731 not necessary accurate).
732 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
733 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
734 deliberately break compilation (a remainder that it needs to be customized)
735 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
736 - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
737 - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
738 o tools/genamke2:
739 - check for lapack.
740 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
741 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
742 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
743 from both packages.
744 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
745 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
746 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
747 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
748 o pkg/cost : add comments to explain special and/or untested setups.
749 o pkg/exf:
750 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
751 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
752 o verification/*/code_ad:
753 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
754 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
755 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
756 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
757 o pkg/seaice :
758 - added possibility to change ice strength/PRESS0 relationship to
759 HEFF, according to the following run time parameters
760 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
761 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
762 SEAICEpresH0 :: HEFF threshold for ice strength (m)
763 o pkg/ggl90 :
764 - added run time flag mxlSurfFlag to include the code that ensure
765 mixing between first and second level (previously included as a comment)
766 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
767 - add test of newly added dumpAdByRec=T option where
768 we write all records to one file per variable.
769 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
770 - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
771 to check that this code is ok with taf and compiles in adjoint.
772 o pkg/autodiff :
773 - added run time param dumpAdByRec : ad dump format switch.
774 If true then write all records to one file per variable.
775 Else write one file per record (remains the default).
776 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
777 o pkg/seaice:
778 - Added SEAICEuseTILT run time switch : if set to
779 false then omit the tilt term in seaice dynamics.
780 - Fix free drift calculation.
781 o pkg/shelfice:
782 When initializing SHELFICEDragQuadratic, set default to be
783 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
784 but retain option to set it independently
785 (inconsistenty spotted by Veronique Dansereau)
786 o eesupp/inc:
787 - in EEPARAMS.h, add real-type constant for some frequently used simple number
788 (0,1,2,1/2), with name explicitly referring to RS/RL type.
789 o model/src:
790 - move balancing of relaxation terms to new S/R balance_relax.F.
791 o pkg/autodiff:
792 re-write active I/O high-level (control) S/R:
793 - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
794 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
795 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
796 MDS_READ/WRITE_FIELD); change loops to multi-threads.
797 - update and merge active_file_control_slice.flow into active_file_control.flow
798 - update the calls in lower level S/R (active_file.F, active_file_g.F and
799 active_file_ad.F) keeping the argument list and function unchanged.
800 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
801 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
802 - new low-level active I/O routines, one for each type (RL/RS), for active var
803 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
804 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
805 right type.
806 o autodiff and RS=real*4:
807 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
808 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
809 - change argument type of 3-D mask argument to _RS to match type in the call
810 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
811 o pkg/thsice:
812 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
813 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
814 fresh-water flux: uniform correction or proportional to local precip.
815 o pkg/ctrl:
816 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
817 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
818 ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
819 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
820
821 checkpoint63q (2012/07/30)
822 o pkg/autodiff:
823 note about monitor and snap-shot of ad-variables:
824 a) need to apply ADEXCH before monitor or output of ad-vars to include
825 overlap contributions (was done for adjDump but missing for monitor).
826 b) since ADEXCH implies adding overlap values to interior array, machine
827 truncation error is expected when adding an ADEXCH call in the middle of
828 the time-stepping (although mathematically identical).
829 modifs:
830 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
831 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
832 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
833 apply ADEXCH before monitor or snap-shot of ad-variables:
834 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
835 - implement new method (copy+adexch) for snap-shot and monitor of main model
836 ad-vars (initially not used by default -> output unchanged).
837 - change default (set to 2) to use new method and update few output_adm.txt
838 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
839 and both tutorial_tracer_adjsens tests).
840 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
841 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
842 o pkg/ctrl:
843 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
844 generic control variables via
845 #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
846 Only required customization should be S/R ctrl_map_ini_genarr.F
847 (routine in repository contains example)
848 o pkg/exf:
849 - fix and refine checking of surface-relaxation setting when using EXF
850 o verification (adjoint exp):
851 - reduce length of simulation by half for experiment global_ocean.cs32x15
852 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
853 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
854 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
855 of KE that can occur with aggressive optimization
856 + put quadratic bottom drag calculation in separated loops (only done if
857 using bottomDragQuadratic)
858 o model/src: CG2D_NSA
859 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
860 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
861 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
862 change cg2d residual target to be expressed in Wunits (=> do not normalise
863 RHS ; this fix global_max Pb with TAF); update output.
864 o verification/tutorial_tracer_adjsens:
865 improve parameter consistency (and get rid of warnings):
866 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
867 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
868 - use staggerTimeStep (for stability) in som81; use default rotation period.
869 o pkg/exch2:
870 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
871 reset to 0 = 1 long line in X)
872 o pkg/mdsio:
873 - fix reading of dimensions from meta file for large-size domain
874 o model/src:
875 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
876 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
877 Cubed-Sphere Exch with CS-corners inside the domain;
878 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
879 globalArea and to set hasWetCSCorners.
880 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
881 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
882 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
883 useCDscheme and useCubedSphereExchange).
884 o pkg/seaice/seaice_growth.F :
885 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
886 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
887 when the previous code was not correct.
888 - in all cases diagnoze the boundary condition mismatch to SIaaflux
889 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
890 that term to QNET (essentially to set the melt/freeze water to 0degC).
891 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
892 o verification/global_ocean.cs32x15/input.seaice :
893 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
894 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
895 - update results (output.seaice.txt) accordingly.
896 o verification/lab_sea/input/data.seaice :
897 - remove SEAICEheatConsFix, which is now be tested
898 in global_ocean.cs32x15. The presently coded fix
899 is only consistent with real fresh water + nlfs.
900 - update results (output.txt) accordingly.
901 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
902 o AD_CONFIG.h file:
903 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
904 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
905 add it explicitly in each fortran src file where it is needed.
906 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
907 thus introducing potentially wrong dependency; therefore, better to include
908 it only where it's really needed, and after any other included OPTIONS file
909 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
910 or ALLOW_TANGENTLINEAR_RUN).
911
912 checkpoint63p (2012/07/06)
913 o pkg/autodiff:
914 - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
915 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
916 which are now read from new parameter file "data.autodiff" (inAdExact
917 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
918 - add file "data.autodiff" in all verification/*/input_ad/ directories.
919 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
920 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
921 o verification/tutorial_tracer_adjsens/
922 - add extra sub-verification which uses "SOM" advection scheme
923 (2nd Order-Moment Advection Scheme, Prather Limiter) with
924 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
925 and in data:
926 multiDimAdvection=.TRUE.,
927 tempAdvScheme=81,
928 saltAdvScheme=81,
929 o model/src:
930 - introduce ALLOW_BALANCE_RELAX which allow the removal
931 of the global mean of relaxation terms by setting
932 balanceThetaClimRelax and balanceSaltClimRelax
933 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
934 This case is now treated appropriately in seaice_growth.F
935 o pkg/seaice:
936 - do balanceEmPmR and balanceQnet based on the net fluxes
937 (SItflux) that enter the ocean+ice system rather than QNET
938 and EMPMR. Works best in real fresh water.
939 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
940 out of the diagnotics bloc, and stored in global arrays.
941
942 checkpoint63o (2012/06/29)
943 o vertical mixing schemes:
944 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
945 - replace computation of density (in Function STATE1, opps_calc.F) by a call
946 to S/R FIND_RHO_SCALAR
947 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
948 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
949 affects output (vermix.ggl90) at truncation level.
950 o testreport:
951 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
952 (nSx,nSy) for the number of threads (from eedata.mth)
953 o model/src:
954 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
955 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
956 o verification/tutorial_tracer_adjsens/
957 - compile with ALLOW_CG2D_NSA
958 - run with nonlinFreeSurf=3
959 - update reference output_adm.txt
960 o tools/genmake2:
961 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
962 refine usePROFILES switching off (only when NetCDF is not available).
963 o verification (atmospheric set-up):
964 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
965 o pkg/profiles : refine profiles and files handling.
966 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
967 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
968 - changes to use model/src/the_main_loop.F rather than the ecco version
969 in ecco type adjoint runs.
970 o model/src:
971 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
972 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
973 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
974 o model/src:
975 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
976 update output of test experiment bottom_ctrl_5x5.
977 o pkg/generic_advdiff:
978 - implement vertical bi-harmonic diffusion (for now, only for T & S and
979 only explicitly).
980 o verification/bottom_ctrl_5x5/
981 update reference output (results changed quite some time ago,
982 not sure when; but new reference results look ok in terms of grdchk)
983 o verification/1D_ocean_ice_column/
984 For verification purposes, the exact adjoint rather than an approx.
985 should be used (e.g., to comare against F.D. or TLM).
986 removed autodiff_inadmode*_ad.F routines in code_ad/
987 Update results/ accordingly.
988 o pkg/cal:
989 - change cal_getdate.F so that output date is function of input time only
990 (less ambiguous, not mixed up with input iteration number).
991 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
992 o pkg/diagnostics:
993 - implement calendarDumps also for stats-diags
994 - implement calendarDumps also for snap-shot output (negative freq)
995 - for now, ignores calendarDumps if non-zero phase-lag.
996
997 checkpoint63n (2012/06/04)
998 o model/src:
999 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
1000 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
1001 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
1002 similar to calc_r_star.F); update results of experiment internal_wave and
1003 tutorial_global_oce_in_p (affected @ truncation level).
1004 o pkg/shelfice:
1005 - add parameterisation of advective-diffusive flux into the ice shelf
1006 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1007 - simply eps3/3a computation
1008 o eesupp:
1009 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
1010 between tiles, just fill-in edges assuming locally periodic subdomain) and
1011 add corresponding exchange subroutines (EXCH0);
1012 - new CG-solver version (_EX0) for disconnected-tiles special case.
1013 o model/src (CG-solvers):
1014 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
1015 (similar final residual output and max-Iter number as with standard version);
1016 - allows to store and use lowest-residual solution (standard & _SR versions);
1017 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
1018 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
1019 o eesup/src:
1020 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
1021 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
1022 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
1023
1024 checkpoint63m (2012/04/27)
1025 o pkg/shelfice:
1026 - account for partical cells in surface level below ice-shelf for hydrostatic
1027 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
1028 o ad test experiments:
1029 - update and rename to "ad_optfile.local" local AD-optfile specific to a
1030 particular adjoint verification experiment (in verification/*/code_ad/)
1031 o pkg/seaice & pkg/exf:
1032 - Part two of ECCO-CLIVAR code merges.
1033 Completes merge of seaice area relax. code.
1034 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
1035 to be set in EXF_OPTIONS.h since this pkg controls its I/O
1036 (and avoids second CPP option in SEAICE_OPTIONS.h)
1037 - change default value of costIceStart & costIceEnd to a valid date.
1038 - add snowPrecip to HSNOW in seaice_growth
1039 o pkg/ptracers:
1040 - move ptracers summary and setup check into separated S/R ; add a check for
1041 valid PTRACERS_Iter0 value (error+stop or just warning).
1042 o pkg/cal (+ pkg/ecco):
1043 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
1044 as input; and for AD, unless both are not differentiable (e.g., k index)).
1045 o model/src:
1046 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
1047 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
1048 temporary set to usingZCoords value (to be changed to F when using shelfice).
1049 - hydrostatic pressure: implement partial cell near the surface also for
1050 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
1051 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
1052 o pkg/ctrl/ctrl_init.F:
1053 - add a formal parameter to s/r ctrl_init_rec to print
1054 xx_$(ctrl_valiable)_file for easier debugging
1055 - move call of cal_* routines into the if-block where they are really
1056 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1057 to specify a startdate
1058 o pkg/seaice:
1059 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1060 global_ocean.cs32x15/code versions).
1061 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1062 verification experiment global_ocean.cs32x15.seaice and update results.
1063 o pkg/exf:
1064 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1065 (according to useExfYearlyFields).
1066 o pkg/cal:
1067 - move calendar setting & summary (previously in cal_readparams.F) into new
1068 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1069 length of the simulation is set (after SET_PARMS call); This is an attempt
1070 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1071 - For safety: keep a record of pkg/cal parameter settings status
1072 to allow to STOP if one pkg/cal S/R is called too early.
1073 - add a stop in all basic pkg/cal subroutines if called before setting is done.
1074 - modify cal_getdate.F: stop when nothing was returned;
1075 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1076 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1077
1078 checkpoint63l (2012/04/04)
1079 o pkg/bbl:
1080 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1081 update global_with_exf output.yearly.txt file.
1082 o pkg/cal:
1083 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1084 - remove 2 unsused and very short (1 line only) functions ;
1085 - remove unsused subroutines from AD-Diff list.
1086 o model/src:
1087 - start to implement clean wait to stop in initialization S/R (config_check.F,
1088 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1089 o folowing PRINT_MESSAGE changes:
1090 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1091 o pkg/bbl:
1092 - modification so it can work with z*
1093 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1094 - global_with_exf/input.yearly verification; changes output.yearly.txt
1095 o eesupp/src:
1096 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1097 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1098 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1099 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1100 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1101 - when using MPI, always set usingMPI=T ; set default accordingly and stop
1102 if not consistent.
1103 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1104 argument is zero (in case called within single-thread section).
1105 o pkg/fizhi:
1106 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1107 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1108 o pkg/exch2:
1109 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1110 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1111 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1112 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1113 with bad ones coming from a not-yet-updated halo.
1114 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1115 o pkg/frazil:
1116 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1117 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1118 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1119 o verification/lab_sea
1120 * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1121 * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1122 * nTimeSteps 3 -> 4
1123 * changed reference output accordingly
1124 o pkg/ctrl:
1125 * fix ctrl_get_gen for xx_sst, xx_sss
1126 o pkg/fizhi:
1127 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1128 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1129 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1130 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1131 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1132 o pkg/gmredi:
1133 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1134 o pkg/fizhi:
1135 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1136 (old)aces open64 tuv test.
1137 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1138 o pkg/mom_vecinv:
1139 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1140 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1141 with non-lin free-surf).
1142 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1143 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1144 some compilers (gfortran 4.6.0 on MacOS)
1145 o momentum:
1146 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1147 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1148 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1149
1150 checkpoint63k (2012/03/17)
1151 o model/src:
1152 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1153 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1154 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1155 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1156 o model/src: solve_*diagonal.F
1157 - replace division with multiplication by inverse (similar to original version)
1158 update output of AD exp. global_ocean.90x40x15.
1159 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1160 to enable the use of the vectorized & differentiable solve_tridiagonal.F
1161 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1162 vertical advection (to get solve_tridiagonal tested in AD mode).
1163 o pkg/seaice: ECCO-CLIVAR merge:
1164 1. seaice AREA relaxation
1165 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1166 * runtime flag: SEAICE_tauAreaObsRelax
1167 2. modified global mean cost imbalance code: CPP option
1168 ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1169 o another iteration on solve_*diagonal.F
1170 Make choices independent of AUTODIFF
1171 Default will be the adjoinable vectorized version.
1172 Alternative choices are:
1173 * non-adjoinable original version with low memory footprint:
1174 #define SOLVE_DIAGONAL_LOWMEMORY
1175 * still adjoinable but does not vectorize (k as inner-most loop):
1176 #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1177 o testreport
1178 - add option to use a home made wrapper around "make"
1179 - remove MITGCM_IEEE env. variable (no longer active)
1180 o pkg/shelfice
1181 - improve computation of friction velocity for velocity dependent
1182 exchange coefficients: include velocities into SHELFICEBoundaryLayer
1183 block to average velocities vertically
1184 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1185 o Modify diagonal solvers, now three versions (upon request):
1186 #ifndef SOLVE_DIAGONAL_AUTODIFF
1187 1. default version (dating back a while ago)
1188 #else /* def SOLVE_DIAGONAL_AUTODIFF */
1189 # ifdef SOLVE_DIAGONAL_KINNER
1190 2. adjoinable version with k-innermost loop (G. Forget)
1191 # else
1192 3. adjoinable vectorized version of 2.
1193 # endif
1194 #endif /* SOLVE_DIAGONAL_AUTODIFF */
1195 All flags are currently set within routines, but could/should be moved to CPP-options.
1196 Array bounds for 1. are as before, for 2.,3. cover the entire domain
1197 (could be changed for 1. too).
1198 o verification/lab_sea (fwd):
1199 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1200 use 7 categories (except hb87), new solve4temp params (except salt_plume),
1201 constant salinity (=4) or variable salinity (salt_plume) done through
1202 SItracer.
1203 o pkg/seaice:
1204 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1205 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1206 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1207 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1208 SEAICE_freeze got retired) but already better than previously with
1209 SEAICE_freeze=123456.7 deg.C;
1210 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1211 (safer multi-threaded setting); always set SEAICEuseEVP;
1212 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1213 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1214 stop if multiple specifications for the same coeff; make sure default
1215 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1216 o pkg/obcs:
1217 - allow to switch to upwind 1rst order advection scheme for the advective
1218 flux computation at the open-boundary; disabled for adjoint built.
1219 o pkg/ptracers:
1220 - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1221 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1222 - add parameter to decide when to start a tracer; use internal flag to
1223 know which tracer to step-forward; switch this internal flag at the top
1224 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1225 for adjoint built.
1226 o pkg/seaice:
1227 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1228 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1229 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1230 o pkg/ecco:
1231 - fix writing of output file DiagnosCost_ClimSalt/Theta
1232 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1233 o pkg/seaice:
1234 - add missing initialisation of COR_ICE array in dynsolver.F
1235 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1236 compiled either way, and is tested in all exps (multidim was only tested
1237 in lab_sea ad before).
1238 - cosmetic change to prepare for future addition of ITD. no change to results.
1239 no defaults change.
1240 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1241 - by lack of adequate verification experiments, I further used custom versions
1242 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1243 should be correct.
1244 - avoid recomputations in ad.
1245 o array initialisation in adjoint mode:
1246 1) pkg/mom_common/mom_calc_ke.F:
1247 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1248 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1249 part this initialisation is gone, resulting in Floating Point Exception
1250 (caught by open64 compiler with debug option).
1251 2) model/src/convective_weights.F
1252 set output convectCount over the full array range (instead of doing
1253 an update): this fix a similar issue when called within recomputation (adjoint)
1254 which could by-pass the initialisation (normally done in the caller S/R).
1255 o pkg/seaice:
1256 - final version of turbulent flux params, as agreed at MIT ice meet:
1257 SEAICE_mcPheePiston (default is ~ 0.000875)
1258 SEAICE_mcPheeTaper (default is 0.)
1259 SEAICE_frazilFrac (defualt is 1.)
1260 SEAICE_mcPheeStepFunc (default is false)
1261 - changes results at trunction error level
1262 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1263 o added pkg/frazil:
1264 - see frazil_description.tex for details
1265 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1266 o pkg/shelfice/shelfice_thermodynamics.F
1267 - fix exponents for velocity dependent exchange coefficients: change
1268 from 2/3(=0) to 0.66666666666666667
1269 - move computation of velocity dependent exchange coefficients into
1270 separate loop, so that it applies to both thermodynamics
1271 - move some divisions by constants out of loops
1272
1273 checkpoint63j (2012/02/16)
1274 o pkg/seaice:
1275 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1276 - SItracer: added run time params, and allow coupling to ocn salinity.
1277 o pkg/seaice: remove (almost) all divisions by constants within loops
1278 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1279 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1280 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1281 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1282 o pkg/seaice :
1283 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1284 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1285 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1286 - add permanent SItflux diag that corresponds to TFLUX but includes
1287 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1288 - allow activation/testing of a fix for suspected missing term in
1289 ocn-ice heat budget (to be confirmed). To test this, you want to
1290 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1291 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1292 - no change in results, fwd or ad.
1293 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1294 - switch to variable freezing point.
1295 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1296 - bug fix : the sublimation term that was missing is now activated.
1297 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1298 - bug fix : flooding sign term for SIsal0.NE.0.
1299 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1300 o pkg/seaice:
1301 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1302 is now the default, and the old default constant freezing point is recovered
1303 with SEAICE_tempFrz0 = -1.96,
1304 SEAICE_dTempFrz_dS = 0.,
1305 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1306 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1307 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1308 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1309 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1310 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1311 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
1312 seaice_growth r149 for legacy branch (no results change).
1313 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1314 from I. Fenty).
1315 - results did not change except for global_ocean.cs32x15, mostly due to the
1316 switch to variable freezing point (see above item for detail).
1317 o pkg/thsice:
1318 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1319 seawater freezing in thsice_calc_thickn (not used).
1320 o pkg/seaice: turbulent flux term specification via run time params.
1321 - replace CPP switches with run time switches to facilitate testing
1322 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1323 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1324 - added runtime parameter : SEAICEturbFluxFormula
1325 - move Mcphee constants to SEAICE_PARAMS.h
1326 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1327 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1328 remove seaice_summary call (moved to seaice_init_fixed)
1329 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1330 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1331 - seaice_summary.F : add missing report of read turbulent flux term set up
1332 and SITRACER.
1333 - seaice_check.F : check range; inform and stop if retired CPPs are used
1334 (incl. SEAICE_AGE).
1335 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1336 CPP switch, same computation as before for the different options.
1337 - change results at the truncation level.
1338 o pkg/seaice:
1339 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1340 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1341 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1342 - update verification/*/input*/data.seaice:
1343 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1344 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1345 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1346 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1347 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1348 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1349 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1350 difference in results only due to machine truncation.
1351 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1352 MaykutPolySatVap; keep MIN_LWDOWN.
1353 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1354 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1355 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1356 o pkg/salt_plume:
1357 - isolate saltPlumeFlux array exch into a specific S/R called from
1358 do_oceanic_phys.F
1359 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1360 o verification:
1361 - move untested set-up to MITgcm_contrib/verification_other.
1362 o pkg/seaice:
1363 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1364 o pkg/seaice:
1365 - seaice_solve4temp.F (keeping results unchanged):
1366 * add 2 future run-time params to select which saturation vapor pressure
1367 formula is used and how post-iteration fluxes are set.
1368 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1369 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1370 the linearized expression to stay consistent with tsurf finding.
1371 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1372 can be < 0.
1373 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1374 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1375 conductive heat flux F_c , and add it explicitly when updating tsurf as
1376 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1377 so that now F_ia has a consistent meaning through the entire routine.
1378 This causes differences at truncation level: update output of fwd exp.
1379 global_ocean.cs32x15.seaice.
1380 o pkg/seaice:
1381 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1382 of arrays, sign/direction of fluxes; no effect on results.
1383 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1384 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1385 note: this should have been done before changing celsius2K default.
1386 - to keep results unchanged, add back old value of celsius2K in verification
1387 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1388 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1389 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1390 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1391 freezing temp is consistent with value in seaice_growth.F ; this causes
1392 differences at machine truncation level: update lab_sea AD output (3/4).
1393 o pkg/seaice:
1394 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1395 and climsst/sss even when using seaice (to prevent calculation that might
1396 use SST on land); does not affect any verification exp.
1397 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1398 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1399 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1400 over land (non-legacy code)
1401 o vectorize salt_plume package:
1402 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1403 - this code computes plumebk everywhere (also over land), thus requires
1404 code to avoid divisions by zero and catch the case of kLev=Nr.
1405 - efficiency of salt_plume_frac is still sub-optimal
1406 o tools (genmake2):
1407 - fix makefile NAME specification (option: -makefile NAME) by adding
1408 "-f $MAKEFILE" in few places where it was missing including makedepend
1409 command (contribution from Paul).
1410
1411 checkpoint63i (2012/01/24)
1412 o model/src:
1413 - add factorized versions of some EOS code to find_rho.F,
1414 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1415 o model/src:
1416 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1417 - change default celsius2K from 273.16 to 273.15
1418 - to keep results unchanged, add back old value of celsius2K in verification
1419 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1420 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1421 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1422 to make TAF generate vectorizable code
1423 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1424 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1425 have flags that do this more efficiently.
1426 o pkg/diagnostics/diagstats_calc.F
1427 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1428 o pkg/obcs (with exch2):
1429 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1430 and remove code (in obcs_readparms.F) which was based on EXCH of indices
1431 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1432 o pkg/exf and seaice exp:
1433 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1434 so that switching off area & heff advection flags does not affect results.
1435 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1436 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1437 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1438 results of verification experiments: 1D_ocean_ice_column(fwd),
1439 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1440 and offline_exf_seaice (all 4).
1441 o pkg/seaice:
1442 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1443 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
1444 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
1445 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
1446 not multi-dim advection;
1447 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
1448 SHORTWAVE_HEATING #undef.
1449 o optim: make Makefile more robust (?)
1450 o pkg/obcs:
1451 * fix treatment of obcs_read_pickup for TAF
1452 o pkg/shelfice:
1453 * add missing initialisation of num_shifwflx
1454 * new adjoint verification exp. for isomip
1455 * change Prandtl and Schmidt numbers from generic formulations
1456 (in terms of model diffus. and visc.) to separate runtime
1457 parameters, with Holland and Jenkins (1999) default values.
1458 o pkg/exf (interpolation):
1459 - extended input field (2 rows) near the N & S poles:
1460 * fill in with the symetric value (when even Nb of data in longitude)
1461 * add average value at the poles only for scalar quantities ; for vector
1462 component interpolation, skip the averaging and keep duplicated values,
1463 unless the 2 components have same location (uvInterp=T) in which case
1464 interpolate the 2 components together using S/R EXF_INTERP_UV.
1465 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1466 together: this allows to account properly for local orientation when
1467 averaging at N & S pole.
1468 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1469 exf-interpolation near N & S poles. Undef by default.
1470 - add debug check/print on 1rst iter if debugLevel >=2.
1471 o pkg/exf:
1472 - change masking flags definition (no longer "parameter"), put them in
1473 common block and set them in S/R EXF_INIT_FIXED.
1474 - change recognized masking flag from s,u,v to c,w,s since the mask
1475 to use (maskC,W,S) depends on position on model grid and has little to
1476 do with scalar/vector difference; fix masking if using P-coordinates.
1477 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1478 and update results of exp. global_with_exf (x2).
1479 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1480 o pkg/obcs
1481 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1482 o pkg/exf (interpolation):
1483 - assume periodicity in X only if input field cover full longitude range.
1484 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1485 and should vectorise).
1486 - fix input lat of the 2 added row (in case we provide N.pole data).
1487
1488 checkpoint63h (2011/12/30)
1489 o pkg/seaice:
1490 - change declaration of UVM from _RL to _RS in order to get B-grid
1491 uIce,vIce monitor when _RS = real*4
1492 o pkg/offline:
1493 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1494 - compute vertical velocity if not read from file (switch on exactConserv
1495 & staggerTimeStep);
1496 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1497 o verification:
1498 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1499 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1500 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1501 - update output of exp. global_ocean.cs32x15.viscA4 after changing
1502 grid-file angles (used here for coriolis-3d);
1503 - remove (or gzip) few files not needed to run fizhi-cs experiments.
1504 o pkg/exf (vector interpolation):
1505 - rotate vector component toward local grid-axis orientation using grid-angles
1506 (stored in GRID.h) instead of locally computed rotation angle; keep old code
1507 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1508 o pkg/seaice:
1509 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1510 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1511 o pkg/PKG_OPTIONS.h files:
1512 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1513 outside of the #ifdef ALLOW_THISPKG / #endif block.
1514 - update verification/*/code/PKG_OPTIONS.h files.
1515 o add a verification experiment (offline_exf_seaice/input.seaice) that test
1516 the B-grid LSOR solver
1517 o pkg/seaice: sort out emissivity and long wave radiation step 2:
1518 - add emissivity for snow and ice as new run-time parameters
1519 (unfortunately) that default to the corresponding exf values; this
1520 changes results in most verification experiments so that for backward
1521 compatibility these parameter have to be set explicitly to inconsistent
1522 values (ugly);
1523 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1524 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1525 until we agree how to handle this bug properly
1526 o pkg/exf (interpolation):
1527 - add a set of run-time param ({inputfield}_interpMethod), one for
1528 each interpolated input field, to select the interpolation method
1529 with a value of zero switching off the interpolation;
1530 - print interpolation parameters to standard output;
1531 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1532 (to use instead runoff_interpMethod=0 in data.exf).
1533 - simplify default setting of interpolation parameters (for all fields,
1534 set position to match model grid cell-center position, leading to trivial
1535 interpolation in case of regular Lat-Lon grid) and fix for the case of
1536 non-uniform delY.
1537 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1538 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1539 this factor is absolutely required, because the lw exitance (= out-going
1540 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1541 where the reflectivity rho = 1-emissivity for conservation reasons. Once
1542 this is established, we can remove the CPP-Flag (if we want to).
1543 o pkg/seaice:
1544 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1545 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1546 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1547 what the name implies (and not emissivity*BoltzmannConstant), this means
1548 the old default value of 5.5e-8 now means
1549 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1550 S/R exf_readparms
1551 - FV-discretization of the B-grid LSOR solver, turn on with
1552 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1553 of the calling routine dynsolver, so that B and C-grid code look a
1554 little more alike.
1555 - fix index bugs in ostres.F (B-grid code)
1556 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1557 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1558 default for SEAICE_emissivity, if useEXF; requires setting a wrong
1559 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1560 backward compatiblity
1561 o model/src: use sigmaR in calc_ivdc
1562
1563 checkpoint63g (2011/12/16)
1564 o pkg/seaice/seaice_growth.F:
1565 fix heat conservation of the coupled ocean-seaice system.
1566 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1567 solid vs liquid water treatment is resolved via QNET.
1568 o pkg/seaice/seaice_growth.F:
1569 add missing term for sublimation in saltFlux, which was breaking conservation.
1570 o pkg/seaice/seaice_model.F:
1571 Remove this patholigical case treatment in evolution branch,
1572 where it is un-necessary and breaks conservation.
1573 Update global_ocean.cs32x15/results accordingly for
1574 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1575 o model/src:
1576 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1577 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1578 o pkg/obcs:
1579 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1580 tendency for temperature and salinity that is then applied to update
1581 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1582 horizontal advection and diffusion contributions on the boundary (in
1583 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1584 removing the mask in S/R timestep_tracer. The advantage of this approach is
1585 that the updated tracer values include contributions from the surface
1586 forcing and vertical diffusion.
1587 This modification changes exp4.stevens because of vertical diffusion.
1588 o model/src:
1589 change non-curvilinear grid setting to also work with exch2 + blank tiles:
1590 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1591 face dimensions.
1592 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1593 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1594 and INI_SPHERICAL_POLAR_GRID.
1595 change test-experiment global_ocean.90x40x15:
1596 - split the domain in many more tiles (9x4 tiles of 10x10 each);
1597 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1598 - update results of both test (std & dwnslp).
1599 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1600 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1601 o model/src:
1602 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1603 and fix initialisation when using sigma-coords.
1604 o model/src:
1605 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1606 to their current value at the beginning of forward_step.F": add a new run-time
1607 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1608 - set doResetHFactors=T in the following test exp:
1609 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1610 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1611 and tutorial_global_oce_in_p (nonLinFS in p)
1612 o pkg/ecco
1613 - added IES cost term
1614 o verification/advect_xz
1615 - scale down the depth by 1/100 (from 200 km to just 2.km)
1616 - add secondary test using divergent flow, r-star and implicit vertical advection.
1617 - add note (check_conserve_TS.txt) and matlab script to check global
1618 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1619 o pkg/rbcs:
1620 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1621 o pkg/obcs (Stevens BCs):
1622 - fix various problems in the phase speed computations of the Stevens
1623 boundary conditions:
1624 - sign error for western and southern boundaries,
1625 - time tendencies were underestimated by factor of dTracerLev and some just
1626 zero (for multidim advection schemes) -> now estimate time tendencies
1627 from difference between previous (n) time level and the one before (n-1);
1628 this requires storing a field per tracer per boundary, also in the pickup
1629 files.
1630 - replace deltaTmom in cflMer/Zon computation with dTracerLev
1631 - set default phase velocity to cflMer/Zon
1632 - update verification experiment exp4.stevens
1633 o pkg/generic_advdiff (implicit_r):
1634 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1635 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1636 - fix implicit vertical diffusion or advection with NonLin FreeSurf
1637 (was using current recip_hFacC instead of future recip_hFacC): set future
1638 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1639 solver S/R ;
1640 - fill diagnostics of vertical advective fluxes (computed from tendency)
1641 when using implicit vert. advection;
1642 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1643 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1644 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1645 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1646 o pkg/diagnostics:
1647 - add diags for T & S tendency which goes through Adams-Bashforth.
1648
1649 checkpoint63f (2011/11/30)
1650 o pkg/obcs/obcs_calc_stevens.F:
1651 - join some loops to reduce number of if-statements
1652 - fix a bug in code for northern and southern boundaries.
1653 o pkg/seaice/seaice_init_varia.F
1654 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1655 caused zero ice-velocities for the B-grid code
1656 o pkg/seaice/seaice_init_fixed.F
1657 - fix a bug in the initialisation of the second metric terms
1658 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
1659 - this affects all seaice configurations with useCurviLinearGrid = .true.
1660 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
1661 = .true. (default)
1662 - the only verification experiment affected is global_ocean.cs32x15:
1663 icedyn, seaice, and seaice_dynmix (AD)
1664 o pkg/thsice/thsice_diagnostics_state.F
1665 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
1666 not contain garbage that can lead to surprises in diagstats_calc.F
1667 o model/src:
1668 - move bi,bj loops inside INTEGR_CONTINUITY ;
1669 - call INTEGR_CONTINUITY directly from forward_step.F
1670 (previously called from momentum_correction_step.F)
1671 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
1672 forward_step.F and pkg/ecco/the_main_loop.F
1673 o model/src/do_oceanic_phys.F:
1674 - reset addMass to zero only if useICEFRONT ;
1675 - separated k-loop for rhoInSitu calculation ;
1676 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
1677 and at constant T,S (= WdRHOdP);
1678 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
1679 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
1680 transport of locally-referenced potential density);
1681 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
1682 o gluemnc:
1683 - replace ncrcat with ncks when adding variables to *.glob.nc
1684 - change the way variables without record dimensions are handled so that
1685 files that have variables with and without record variables can be glued:
1686 add a record dimension with a new unique name to be able to differentiate
1687 between variable with and without a-prior record dimensions. Remove
1688 this record dimension before adding the variable to the *.glob.nc file.
1689 This procedure automatically works also for grid.*.nc files that do not
1690 have any record dimension.
1691 o verification/cpl_aim+ocn:
1692 - generate new reference output on baudelaire (gfortran, mpich2) (previously
1693 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
1694 o pkg/obcs/obcs_calc_stevens.F:
1695 - add code for northern and southern boundaries.
1696 - reorder some loops to save some operations and so that drFBar can be scalar
1697 o model/src:
1698 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
1699 truncation) and add diagnostics for Adams-Bashforth tendency increment.
1700 - update test-exp. AD output:
1701 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
1702 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
1703 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
1704 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
1705 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
1706 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
1707 tutorial_plume_on_slope.
1708 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
1709 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
1710 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
1711 does not even come with an F77 compiler anymore, this should not be
1712 a limitation
1713
1714 checkpoint63e (2011/11/06)
1715 o pkg/seaice adjoint of LSR:
1716 - substantially rework STORE dirs.
1717 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
1718 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
1719 and only perform SOLV_MAX_FIXED adjoint iters.
1720 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
1721 always goes to same record, meaning that the last forward field will be
1722 the one used in the adjoint - an approximation.
1723 - now produces non-zero LSR-related gradients, and acceptable gradients for
1724 An's zonal (x-z) test case (to be checked in)
1725 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
1726 (but these are screwed up by the thermodynamics in the first place);
1727 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
1728 output_adm.txt also reflects changes to seaice_lsr
1729 - global_ocean.cs32x15:
1730 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
1731 (output_adm.seaice.txt was updated)
1732 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
1733 (output_adm.seaice_dynmix.txt)
1734 o test-exp. exp4+stevens:
1735 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1736 o pkg/seaice (lsr solver):
1737 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1738 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1739 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1740 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1741 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1742 - compute (with new S/R) and print initial (+ free-driff sol. if available)
1743 and final residual of linearised system.
1744 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1745 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1746 o pkg/obcs: Stevens BCs (still only for east and west)
1747 - fix Stevens BCs by using intermediate velocities of previous
1748 time step as "baroclinic" contribution rather velocity of one grid cell
1749 inside the boundaries; more consistent but makes the entire treatment
1750 more complicated, requires new pickup files and two new S/Rs:
1751 obcs_copy_uv_n and obcs_save_uv_n
1752 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1753 (undefined by default)
1754 - silently move computation of some grid factors into separate loops to
1755 save some recomputations
1756 - add a hack for non-linear free surface
1757 - add a verification experiment to exp4 that tests this code
1758 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1759
1760 checkpoint63d (2011/10/25)
1761 o pkg/obcs + seaice-dynamics:
1762 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1763 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1764 values (consistent with an implicit method).
1765 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1766 return to older implementation (same results as before); note that none of
1767 the "experimental" OBCS_SEAICE options are implemented in the new version.
1768 - switch test exp. seaice_obcs to use new version (update output).
1769 o pkg/seaice:
1770 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1771 - add parenthesis in Water-Ice drag calculations (evp & lsr);
1772 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1773 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1774 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1775 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1776 o pkg/layers:
1777 - Include potential density as new coordinate (Thanks to David Munday)
1778 o pkg/dic:
1779 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1780 carbonate computation/output to CALC_PCO2_APPROX
1781 o pkg/generic_advdiff
1782 - make TAF generate code that vectorizes:
1783 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1784 o model/src:
1785 - improve vectorization also for adjoint code of
1786 solve_tridiagonal and solve_pentadiagonal. As this requires up to
1787 5 new 3D-fields, this code is only turned on for the combination of
1788 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1789 for singular matrix check (only for TARGET_NEC_SX).
1790 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1791 ALLOW_AUTODIFF. This flag now needs to be set outside of
1792 solve_tri/pentadiagonal.F
1793 o pkg/exf:
1794 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1795 optional namelist EXF_NML_OBCS).
1796 - add many debug-print (to trace down where pkg/cal error msg comes from)
1797 o pkg/mom_vecinv/mom_vi_hdissip.F
1798 - rearrange loops so that vectorization is improved and in particular
1799 the adjoint routine vectorizes. The code is a little longer now, but I
1800 think easier to read.
1801 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1802 o pkg/seaice:
1803 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1804 o pkg/exch2:
1805 - alternative code (without tile x tile matrix) for cumulated (global) sum;
1806 used as default; keep using matrix version in adjustment.cs-32x32x1.
1807 o tools/build_options:
1808 - after merging some MPI and/or multi-threads specific optfiles so that
1809 the modified default optfile support both built (using genmake2 -mpi
1810 for the MPI built, using genmake2 -omp for OpenMP built),
1811 move now obsolete optfiles to tools/build_options/unsupported/
1812 (add copy of email sent to support list in doc/optfiles_changes.txt)
1813
1814 checkpoint63c (2011/09/28)
1815 o pkg/ebm:
1816 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1817 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1818 o pkg/seaice (SItracer pickup)
1819 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1820 To be done:
1821 - thorough testing of missing fields in S/R seaice_read_pickup
1822 - thorough matching between generic tracers and specific fields used
1823 (e.g. volume-weighted age, area-weighted age, salinity, ...)
1824 o pkg/grdchk:
1825 - all procs calculate and print finite-difference gradient (for testreport)
1826 - change description output used by testreport;
1827 - AD testing: also compare and report Finite-difference gradient;
1828 => update all output_adm*.txt
1829 o test exp. global_ocean_ebm:
1830 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1831 and turn on exactConserve; update (fwd) output.
1832 o pkg/seaice (LSR):
1833 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1834 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1835 * identical results with non-CS topology (but save up to half of EXCH calls)
1836 * no much changes in cs-32 verification tests since no ice at face edges
1837 (differences due to convergence criteria, since nb of iterations changed)
1838 * expect some differences on lat-lon-cap grid.
1839 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1840 o pkg/exch2:
1841 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1842 many tiles); until alternative coding is added, just add a stop.
1843 o pkg/kpp:
1844 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1845 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1846 o optfiles:
1847 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1848 into corresponding standard one, which now support different build:
1849 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1850 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1851 o pkg/obcs (seaice):
1852 - add missing EXCH for uIce,vIce after applying OBCS;
1853 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1854 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1855 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1856 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1857 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1858 and eedata.mth for MPI and mutlti-threaded testing.
1859 o pkg/flt:
1860 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1861 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1862 - fix pickup and trajectories + profiles output with multi-threads;
1863 - add parameter to select group of fields to write along trajectory and
1864 profile (default unchanged);
1865 - only call PORT_RAND* function when flt_noise <> 0;
1866 - add multi-threaded test for verification exp. flt_example.
1867 o eesupp/src:
1868 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1869 - USE_OMP_THREADING: check that number of threads (from eedata) matches
1870 actual number (from env.var. setting).
1871 o pkg/ebm:
1872 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1873 - add multi-threaded test for verification exp. global_ocean_ebm
1874
1875 checkpoint63b (2011/08/29)
1876 o pkg/ebm:
1877 - fix sign of runoff;
1878 - update directly forcing fields (Qnet,EmPmR) to use standard
1879 external_forcing_surf.F (remove ebm_forcing_surf.F);
1880 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1881 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1882 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1883 - update global_ocean_ebm parameters file data and update output (fwd+ad).
1884 o verification/matrix_example:
1885 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1886 MPI and mutlti-threaded testing.
1887 o pkg/matrix:
1888 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1889 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1890 - fix for multi-threaded (remove DATA statement);
1891 - use standard DIFFERENT_MULTIPLE function;
1892 - add MATRIX_OPTIONS.h
1893 o verification/matrix_example:
1894 To allow to split the domain in several tiles, change the domain size
1895 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1896 Western side) of land points.
1897 o (*_)write_pickup:
1898 - fix few bugs in mypackage_read/write_pickup.F
1899 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1900 array of length 1 (was caught by compiler syntax-check).
1901 o pkg/diagnostics (velocity potential solver):
1902 - fix initialisation of main diagonal matrix (for overlap values)
1903 o tools/build_options:
1904 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1905 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1906 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1907 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1908 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1909 and use "-devel" testreport option for standard testing on baudelaire.
1910 o pkg/grdchk:
1911 - Assume that all gradient-check position are within the same tile
1912 corresponding to global indices (iGloTile,jGloTile) and that
1913 positions (i,j indices or nbeg) are local to this tile;
1914 - set tile local-indices and proc. number according to tile global-indices;
1915 - remove grdchkwhichproc from namelist (retired param);
1916 - send adjoint gradient to all procs so that all procs print it to STDOUT;
1917 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1918 o adding package bbl (Bottom Boundary Layer)
1919 description in MITgcm/pkg/bbl/bbl_description.tex
1920 example/test experiment in MITgcm_contrib/bbl
1921 o adjoint verifications
1922 - changed 5 experiments to multi-tiles
1923 * global_ocean.90x40x15
1924 * obcs_ctrl
1925 * offline_exf_seaice
1926 * tutorial_dic_adjoffline
1927 * tutorial_tracer_adjsens
1928 changed reference output for those that crossed tile boundaries
1929 (changed choices of gradient check positions)
1930 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1931 - temporary bug fix in grdchk_loc.F for obcs
1932 o genmake2 & testreport
1933 - add target "obj" (just for OBJFILES files) to Makefile;
1934 - add option to specify FEXTRAFLAGS on command line.
1935 o pkg/mypackage:
1936 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1937
1938 checkpoint63a (2011/08/02)
1939 o pkg/diagnostics (velocity potential):
1940 - fix velocity-potential calculation when using OBCS: balance net inflow
1941 at each level (new S/R OBCS_DIAG_BALANCE).
1942 - fix some of the problems with OBCS in stream-function calculation.
1943 o pkg/exf/exf_readparms.F
1944 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1945 EXF_NML_OBCS) more consistent, so that you need not have these lists
1946 in data.exf when they are not used.
1947 o optim/optim_readdata.F:
1948 - add some output about obcs variables that might help debugging
1949 - add a check about nvarlength
1950 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1951 o pkg/diagnostics (velocity potential):
1952 - fix mask for OBCS (still problems in stream-function with OBCS);
1953 - add specific parameter (default = main code CG2D params) for solver;
1954 - in case of poor convergence, use solution corresponding to lowest residual.
1955 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1956 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1957 and should be avoided where possible.
1958 o model/src (rStar):
1959 - include r* effect on reference-state (PhiRef) in totPhiHyd
1960 (so that it's really the potential anomaly at the cell center);
1961 affect solution only if z* with full pressure in EOS.
1962 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1963 update output (because of z* in totPhiHyd and viscA4 changes);
1964 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1965 @ constant r) until interpolation at constant r is implemented.
1966 o pkg/diagnostics
1967 - fix RCENTER diagnostics in case cell center is not at interface middle
1968 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1969 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1970 that THETA and SALT are "conservative temperature" and "absolute
1971 salinity"
1972 o pkg/ctrl
1973 - fix computation of endrec in s/r ctrl_init_rec
1974 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1975 o pkg/seaice/seaice_growth.F
1976 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1977 remove then obsolete STORE directives
1978 - fix STORE directives for tice and tices, so that only the
1979 appropriate part of the fields are stored (and not the entire
1980 field); update global_ocean.cs32x15.seaice AD output.
1981 - cosmetic changes: adjust CPP flags and indentation for better
1982 legibilty
1983 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1984 Chris Wilson)
1985 o pkg/gmredi:
1986 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1987 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1988
1989 checkpoint63 (2011/07/11)
1990 o pkg/exch2:
1991 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1992 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1993 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1994 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1995 o pkg/diagnostics:
1996 - deal with pairs of post-processed diags which are computed together; in
1997 particular, re-order list of diags within 1 file to save 2nd computation.
1998 - add S/R to compute velocity stream-function (called after velocity-potential
1999 calculation) from divergence free transport -> new diagnostics "PsiVEL".
2000 - add parameter to select grid-point location where PsiVEL == 0.
2001 o eesupp/src:
2002 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
2003 (specific S/R needed with exch2 topology - for now, just print an error msg)
2004 o pkg/shelfice
2005 - Implement friction velocity-dependent transfer coefficients following
2006 Holland and Jenkins, JPO, 1999
2007 Original code by M. Losch with small modifs.
2008 Enable with CPP option SHI_ALLOW_GAMMAFRICT
2009 and runtime flag SHELFICEuseGammaFrict
2010 o verification lab_sea & global_ocean.cs32x15:
2011 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
2012 does not miss some dependencies (but is slower) and also works with many files
2013 (default makedepend limitation for AD built).
2014 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
2015 o pkg/diagnostics:
2016 - add run-time parameter "useMissingValue" (def=False) to fill land-point
2017 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
2018 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
2019 - Extend the use of "missing_value" setting from data.diagnostics for the case
2020 of counter-diagnostics (where fraction-weight is zero). This applies both to
2021 MNC and MDS output files.
2022 o pkg/seaice/seaice_growth.F:
2023 - add 'a priori' cap of latent heat flux based on actual mass considerations
2024 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
2025 non-legacy seaice_solve4temp.
2026 - add diagnostic of the residual sublimation freshwater flux (the freshwater
2027 flux taken from the ocean if the total actual latent heat fluxes exceed
2028 the maximum)
2029 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
2030 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
2031 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
2032 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
2033 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
2034 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
2035 o verification 1D_ocean_ice_column:
2036 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
2037 update results
2038 o pkg/diagnostics:
2039 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
2040 which are not filled-up but computed from other diags ; In this case, the mate
2041 diag points to the primary (filled-up) diag to used for post processing.
2042 - Update Velocity-potential computation using post-processed diag framework.
2043 ==> Change the ordering of fields and time-periods in MDS output file
2044 when using periodic averaging: now writes one time record with the full set
2045 of fields for this time period, then the next time reccord (it used to be
2046 one field with the full set of time records then the next field).
2047 Note: this is now similar to NetCDF (MNC) output file. <==
2048
2049 checkpoint62z (2011/06/21)
2050 o adjoint monitor:
2051 - Add adjoint monitor output for packages exf, seaice
2052 and update relevant testreport output
2053 o pkg/seaice:
2054 - re-order diags inits so that they appear in order in available_diagnostics.log
2055 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
2056 area/heff/hsnow preceeding thermodynamic growth/melt.
2057 - modified diag: SIdA; output actual effect, as the description states.
2058 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
2059 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
2060 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
2061 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
2062 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
2063 - added diagnostics for seaice generic tracers (SItr*).
2064 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
2065 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
2066 I. Fenty: 18-Jun-2011:
2067 Minor changes to seaice package:
2068 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
2069 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
2070 - Differentiated "regularization variables" from "floor variables"
2071 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
2072 * hiceMin became SEAICE_hice_reg (old hiceMin)
2073 (with _reg meaning regularization variable)
2074 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
2075 so as to ensure energy conservation when going between phases
2076 - A22 was not used anywhere
2077 2) Changed regularization procedure for heffActual and hsnowActual to ensure
2078 well-boundedness and smooth adjoint in seaice_growth.F
2079 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
2080 because the old regularization always set heffActual >= 0.05 cm
2081 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
2082 on AREA when HEFF > 0.
2083 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
2084 requiring that DISABLE_AREA_FLOOR *not* be defined
2085 Affected verifications:
2086 - 1D_ocean_ice_column (output.txt output_adm.txt)
2087 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
2088 o pkg/diagnostics:
2089 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
2090 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
2091 (was _RL, now integer) with option = 0 to retrieve all levels.
2092 - add pieces of code to compute velocity potential at each level (new diagnostics
2093 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
2094 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
2095 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
2096 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
2097 and in diagnostics_fract_fill.F (do not need a valid pointer for the
2098 diagnostics counter-mate); check that definition of counter-diagnostic
2099 includes a valid counter-mate (in diagnostics_set_levels.F).
2100 o model/src (rStar):
2101 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
2102 affect solution only if z* with full pressure in EOS;
2103 update output of test-exp global_ocean.90x40x15.
2104 o pkg/seaice:
2105 - introduce siEps=1e-5 parameter
2106 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
2107 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
2108 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
2109 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
2110 as well as ice cover age and ridging index (attached to AREA).
2111 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
2112 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
2113 Up to SItrMaxNum=3 tracers can be used simultaneously.
2114 o pkg/salt_plume:
2115 -introduce SPsalFRAC run time parameter that sets the fraction of the
2116 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
2117 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
2118 o model debug options:
2119 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
2120 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
2121 - Refine debug-msg printing selection (3 new levels):
2122 debugMode : controls printing of debug messages (sequence of S/R calls).
2123 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
2124 debLevZero = 0 ; /* level of disabled aux. msg printing */
2125 debLevA = 1 ; /* level of minimum aux. msg printing */
2126 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
2127 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
2128 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
2129 debLevE = 5 ; /* level of extensive debug printing */
2130 New debugLevel default: with default debugMode value (=F),
2131 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
2132 and if debugMode=T, default debugLevel = 4 (debLevD).
2133 Relation with previous settings:
2134 debLevB (=2) corresponds to former debLevA (=1)
2135 debLevD (=4) corresponds to former debLevB (=2)
2136 Note:
2137 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
2138 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
2139 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
2140 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
2141 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
2142 o pkg/obcs:
2143 - change OBCSfixTopo default from True to False (should not change the results);
2144 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
2145 o pkg/thsice:
2146 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
2147 2nd layer seaice sublimation (unlikely to happen)
2148 - use Interior mask for OBCS in thsice_advection.F (similar to what is
2149 done in gad_advection & seaice_advection).
2150 o adjoint:
2151 bug fix spotted by Gael Forget:
2152 seaice_advection and thsice_advection still had
2153 legacy CPP options to avoid CS corner updates for adjoint
2154 o pkg/seaice:
2155 => Change some of the defaults (2011/05/29):
2156 - change SEAICEuseFluxForm default (from False to True)
2157 - change DIFF1 default (from 0.004 m/s to 0. m/s)
2158 And print warnings if DIFF1 is not set in data.seaice and centered
2159 avection scheme is used without any diffusion.
2160 also:
2161 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
2162 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
2163 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
2164 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
2165 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
2166 update results of test exp.:
2167 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
2168 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
2169 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
2170 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
2171 seaice_obcs: output (SEAICEuseFluxForm=T)
2172 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
2173 for standard fwd & AD lab_sea tests (to keep the same output).
2174 o pkg/seaice/seaice_growth.F:
2175 - use Ian Fenty's capping formulas for actual ice
2176 thickness thoughout EVOLUTION branch.
2177 - put treatment pathological case #2) in CPP brackets
2178 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
2179 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
2180 o pkg/seaice:
2181 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
2182 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
2183 also pass fac as a param, which can be 1. (to update the tendency
2184 field) or the time step (to update the field itself).
2185 - seaice_advdiff.F: for multidim, call seaice_diffusion with
2186 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
2187 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
2188 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
2189 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
2190 o pkg/seaice:
2191 diffusion with centered advection scheme (diffus.F & advect.F):
2192 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
2193 to just compute the laplacian of input-field.
2194 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
2195 - fix flux-form version in diffus.F to conserve tracer.
2196 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
2197 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
2198
2199 checkpoint62y (2011/05/26)
2200 o pkg/seaice:
2201 - seaice_growth.F : in EVOLUTION branch, always include
2202 a_QSWbyATM_cover in qnet (as it should be).
2203 - verification/global_ocean.cs32x15 : update results accordingly
2204 (output.seaice.txt output_adm.seaice.txt).
2205 o pkg/seaice + obcs:
2206 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
2207 equivalent of assuming no tracer gradient outside the OB region.
2208 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
2209 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
2210 after changes above);
2211 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
2212 only at OB location (instead of over a band of OLx width).
2213 o pkg/seaice:
2214 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
2215 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
2216 o pkg/obcs:
2217 - split header file "OBCS.h" into 4 separated files:
2218 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
2219 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
2220 (contain no conditional statement which depends on OBCS options).
2221 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
2222 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
2223 o ctrl, cost, grdchk & autodiff pkgs:
2224 - make options file more standard (like other {PKG}_OPTIONS.h file but
2225 with AD_CONFIG.h); clean-up some of the included header files.
2226 o pkg/obcs:
2227 - do not mask tracer when applying OB (tracer == 0 could generate problems)
2228 - apply tracer OB values to tracer field only at OB location (instead of
2229 over a band of OLx width)
2230 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
2231 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
2232 obcs_apply_tloc.F & obcs_apply_sloc.F
2233 o obcs in model/src:
2234 - call OBCS_APPLY_W only if NonHydrostatic.
2235 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
2236 - reset dEtaHdt and wVel to zero outside OB interior region ;
2237 - leave tracer unchanged outside OB interior region: This has no effect
2238 on the solution but just to prevent unrealistic tracer value outside OB.
2239 - zero out velocity outside OB interior region: This has no effect on
2240 the solution but just to prevent unrealistic velocity outside OB.
2241 o obcs and non-lin free-surf:
2242 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
2243 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
2244 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
2245 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
2246 update results of test-exp. exp4(nlfs).
2247 o exp4 (nlfs) test-exp:
2248 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
2249 with NonLin-FreeSurf); update output.nlfs.txt
2250 o obcs and 2d/3d solver norm:
2251 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
2252 and outside OB interior region (will allow to place OB further inside the
2253 domain). Depending on the domain, can affects cg2d-Norm (previous
2254 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
2255 and cg3d-Norm (previous Norm was computed before canceling OB terms),
2256 e.g. in tutorial_plume_on_slope.
2257 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
2258 o pkg rbcs:
2259 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
2260 - add capability to apply relaxation to horizontal velocity uVel & vVel.
2261 o pkg/grdchk: add gradient check for control variable xx_shifwflx
2262 o pkg/shelfice/shelfice_init_fixed.F
2263 fix CPP-flag combinations
2264 o pkg/seaice: Merge iceage code of Pierre Rampal
2265 * update/change/correct ice age calculations
2266 * add age updates for pathological cases
2267 Probably needs more testing...
2268
2269 checkpoint62x (2011/05/13)
2270 o pkg/mom_vecinv:
2271 high-order vorticity scheme: use interior masks (maskInW & S)
2272 to zero-out (outside OB) gradient of vorticity.
2273 o verification exp.:
2274 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
2275 hs94.128x64x5 and seaice_obcs ; update results.
2276 o pkg/obcs:
2277 fix bug in OBeta for YZ sections in obcs_exf_load.F
2278 o pkg/ctrl, pkg/shelfice, and optim:
2279 - add new control variable xx_shifwflx (fresh water flux underneath ice
2280 shelves). This is almost as tedious as obcs-ctrl, because the
2281 variables needs its own mask.
2282 - add a cost function term that penalizes the deviation of xx_shifwflx
2283 from the first guess (zero) in analogy to other control variables
2284 o pkg/shelfice:
2285 - start basic adjoint
2286 o pkg/ctrl:
2287 - remove extra 2D field "for good measure" when initializing in
2288 ctrl_set_globfld_[xy/xz/yz].F
2289 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
2290 - improve error messages in ctrl_set_unpack_*
2291 o OBC implementation in momentum:
2292 use interior masks (maskInC,W & S) in momentum S/R:
2293 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
2294 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
2295 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
2296 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
2297 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
2298 (and also with Leith/Smagorinsky harmonic-viscosity).
2299 Update output of experiment dome and exp4 (+nlfs).
2300 o exp4 test-exp:
2301 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
2302 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
2303 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
2304 time-varying OB at Western-side for wVel (NonHyd); update output.
2305 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
2306 and biharmonic-viscosity ; also use prescribed time varying OB.
2307 o pkg/obcs:
2308 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
2309 o model/src:
2310 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
2311 - initialise startTime & nIter0 with unlikely values: allows to set one
2312 from the other without ambiguity.
2313 o seaice_obcs test-exp.:
2314 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
2315 o pkg/obcs:
2316 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
2317 no longer needed with maskInC,W,S in pkg/generic_advdiff.
2318 o pkg/seaice:
2319 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
2320 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
2321 - fixed bug in the initialization of sea ice salinity variable HSALT
2322 in seaice_init_varia.F (removed dependence on ICE2WATR)
2323 o fizhi-cs test exp.:
2324 switch reference output convention for these 2 non-standard test-exp,
2325 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
2326 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
2327 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
2328 o model/inc:
2329 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
2330 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
2331 o pkg/seaice:
2332 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
2333 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
2334 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
2335 and initial HSALT
2336
2337 checkpoint62w (2011/04/26)
2338 o pkg/mom_fluxform:
2339 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
2340 - use parameter "sideDragFactor" in no-slip BC side-drag part.
2341 - update output of exp. global_ocean.90x40x15
2342 o pkg/mom_vecinv:
2343 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
2344 o update seaice exp.:
2345 use more consistent parameter values (remove "backward compatability only":
2346 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
2347 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
2348 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
2349 o update test-exp global_ocean.90x40x15:
2350 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
2351 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
2352 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
2353 o turn on zStar & viscA4 in standard set-up (dir input/)
2354 and update output files: output.txt & output.dwnslp.txt
2355 o new AD-test experiment: obcs_ctrl
2356 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
2357 o pkg/dic:
2358 fix two bugs in handling water vapour pressure in carbonate chemistry
2359 and air-sea fluxes. Found by Val Bennington and Galen McKinley
2360 (add DIC Option = WATERVAP_BUG to recover old results)
2361 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
2362 o adding allowInteriorFreezing option to check for water below freezing point
2363 at depth and bring the negative heat anomaly to the surface level
2364 o pkgs _fields_load:
2365 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
2366 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
2367 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
2368 rbcs to get interpolation weights and time reccord number.
2369 - fix multi-threading in aim_fields_load.F
2370 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
2371 o external_fields_load:
2372 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
2373 interpolation weights) to use in a periodic time-series ; do not divide by
2374 time-step to convert to integer:
2375 - this fixes case where externForcingPeriod is not multiple of time-step
2376 (Thanks to Christopher L. Wolfe)
2377 - this fixes case where externForcingPeriod is an odd multiple of time-step
2378 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
2379 store index of time-record which is currently loaded:
2380 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
2381 - needed for the adjoint but not yet used because of extensive recomputations;
2382 (to be fixed soon)
2383
2384 checkpoint62v (2011/04/02)
2385 o verification/1D_ocean_ice_column added to test Ian Fenty's
2386 pkg/seaice_growth.F modifications for improving sea ice code differentiability
2387 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
2388 (new velocity statistics after changing maskInW & maskInS definition)
2389 o pkg/generic_advdiff with OBCS:
2390 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
2391 equivalent to assumption of no tracer gradient outside the OB region.
2392 This will affect the results if using obcs+biharmonic diffusion.
2393 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
2394 o pkg/obcs:
2395 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
2396 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
2397 in Interior region. No impact on solution but affects Velocity monitor stats.
2398 o pkg/ptracers (adjoint)
2399 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
2400 tape file for each tracer
2401 o model/inc/src and pkg/autodiff: add parameters that allow to turn
2402 of parts of the adjoint code at run time. For now, there are only
2403 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
2404 parameters are set in data.pkg.
2405 This is the lazy coward's version of doing this, but still useful for
2406 debugging. In order to do it right, everything needs to be moved to
2407 pkg/autodiff.
2408 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
2409 the end; this fixes the adjoint balancing code for open boundaries.
2410 o pkg/ctrl:
2411 - change behavior of xx_${varname}period to be analogous to exf-conventions:
2412 xx_${varname}period = 0., means time-independent control part
2413 xx_${varname}period = -12., means one-year-periodic monthly control part
2414 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
2415 clean up ctrl_init a little, remove unused variables
2416 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
2417 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
2418
2419 checkpoint62u (2011/03/15)
2420 o model/src:
2421 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
2422 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
2423 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
2424 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
2425 o pkg/ctrl/obcs/ecco:
2426 - remove obsolete, unused, and partially broken code:
2427 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
2428 ALLOW_CTRL_OBCS_BALANCE
2429 - put a stop statement into ecco/cost_obcsvol.F, but also add
2430 cost_obcsvol to ecco_ad_diff.list
2431 o pkg/ecco: fix counting cost function contributions for obcs (code
2432 by Matt M.) and diffkr for diagnostics
2433 o pkg/ecco, pkg/ctrl, pkg/grdchk:
2434 add cost penalty terms for initial uvel, vvel, eta controls
2435 and I/O for prior error files
2436 o pkg/mdsio:
2437 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
2438 (new argument) to check for tiled file in mdsioLocalDir : this fix the
2439 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
2440 o pkg/ctrl:
2441 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
2442 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
2443 unused and superfluous variables
2444 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
2445 o pkg/ecco
2446 - enable adjoint of Stevens OB
2447 o pkg/ctrl/ecco/grdchk:
2448 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
2449 Fortunately, we do not have any tests for the numerous cpp-flagged
2450 option of "obcs as control parameters" so we will never know
2451 if this is an improvement (but at least now things compile).
2452 - remove an obsolete initialization from ecco_cost_init_barfiles.F
2453 - fix some problems within never used ifdefs to make the code compile
2454 o pkg/obcs:
2455 - Refine Interior mask definition to work with more complex OB (e.g.
2456 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2457 read in Interior mask from file. Check if Interior mask is consistent
2458 with OB list of indices.
2459 o pkg/seaice
2460 - beginning code for a seaice tracer package,
2461 but currently only used for seaice age: SEAICE_AGE
2462 SEAICE_num = 4
2463 iTracer = 1: area-weighted ice age
2464 = 2: volume-weighted ice age
2465 = 3, 4: template for one-year vs. multi-year ice
2466 data.seaice has new namelist SEAICE_PARM03 for arrays related to
2467 SEAICE_num
2468
2469 checkpoint62t (2011/03/05)
2470 o pkg/obcs:
2471 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2472 then normal component. This ensures that the normal component is set
2473 correctly even when it conficts with tangential setting from an other OB.
2474 Affects results of test-experiment seaice_obcs: update the output.txt
2475 o pkg/obcs:
2476 - add code to monitor statistics of dynamical fields at OB.
2477 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2478 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2479 - change default: balance the Net inflow through all OB (instead of balancing
2480 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2481 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2482 to match Nortern OB inflow (OBCS_balanceFacN=0).
2483 o pkg/seaice:
2484 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2485 o pkg/seaice (seaice_growth v 1.113):
2486 - reverting seaice_growth to v 1.111 in order to have code with exact bit
2487 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2488 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2489 runtime flag SEAICEareaFormula is kept but is inactive
2490 o model/src:
2491 - add new param to scale curvilinear grid distance and area when using
2492 a different sphere radius from the grid-files.
2493 - test/check multi-threads EXCH applied to local variable (cg2d_x)
2494 o adjoint:
2495 - enable adjoint of Stevens OB
2496 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2497 (a bit delicate because of potentially modified adj. common block structure;
2498 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2499
2500 checkpoint62s (2011/02/15)
2501 o pkg/seaice (seaice_growth v 1.112):
2502 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2503 computing the ice cover tendency from effective thickness tendencies. Include
2504 Ian Fenty's formula.
2505 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2506 SEAICEareaFormula.
2507 - simplify notations for the various d_HEFF/d_AREA terms.
2508 o pkg/gmredi:
2509 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
2510 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
2511 add a verification test-run (front_relax.bvp) to test GM_useBVP.
2512 o pkg/seaice (seaice_growth v 1.111):
2513 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
2514 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
2515 also melt ice.
2516 o pkg/seaice:
2517 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
2518 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
2519 o pkg/cheapaml:
2520 - from Nico Wienders: New version of this package.
2521 o pkg/flt:
2522 - add CPP options to prevent floats to re-enter the opposite side of
2523 a periodic domain (default: keep periodicity)
2524 o pkg/gmredi:
2525 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
2526 (needed for multi-dim advection).
2527 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2528 o model/src:
2529 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2530 o tutorial_tracer_adjsens
2531 - extend to NLFS and replace maskC by hFacC
2532 (change reference output accordingly)
2533
2534 checkpoint62r (2011/01/24)
2535 o testreport:
2536 - add option -deloutp (-do) to remove output file after successful run
2537 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2538 extract exact list of procs from this file ; adjust COMMAND by
2539 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2540 o pkg/ecco: replace old ineffective way of penalizing deviations from
2541 first guess (of obcs) with code by Matt Mazloff
2542 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2543 exf/cal
2544 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2545 and handle case of obcs?period == 0
2546 Not affected by these changes: There is still an inconsistency in
2547 the computation of start/endrec for the obcs variables for ALLOW_CAL
2548 defined (see comment by Menemenlis, 7-Mar-2003)
2549 - make S/R ctrl_get_gen_rec return something meaningful even if
2550 ALLOW_CAL is not defined
2551 - ctrl_getobcs?: simplify code so that it does not need to use
2552 S/R exf_swapfields
2553 o testreport:
2554 allow to test MPI with different number of processors for each experiment:
2555 create file "SIZE.h.mpi" in each build dir.
2556 Note: update of "-command" argument not yet implemented.
2557 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2558 alleviate the need for additional 3D tapes when using
2559 the non-inear free surface in the adjoint. This is done
2560 by adding an 'update' of hfacc etc. to their current
2561 value at the beginning of forward_step.F.
2562 o pkg/seaice
2563 seaice_lsr: move stress-divergence computations out of outer pseudo-
2564 timestepping loop
2565 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2566 up, so that the calls of the ctrl_* subroutines are really at the end
2567 of the routine.
2568 o pkg/gmredi:
2569 allow to specify a 2-D horizontal map and a 1-D vertical profil
2570 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2571 o pkg/seaice:
2572 move lsr iterations from seaice_dynsolver to seaice_lsr.
2573 o pkg/seaice:
2574 reduce memory footprint of seaice mutldim advection tapes,
2575 by using a 2D tape independent of the generic_advdiff ones,
2576 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2577
2578 checkpoint62q (2010/12/29)
2579 o model/src:
2580 - check horizontal grid-spacing for unset or zero/negative values.
2581 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2582 o pkg/flt:
2583 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
2584 - precision of input and output files set according to readBinaryPrec
2585 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
2586 - initial float position from tiled file was not converted to index space
2587 (looks like a bug): fixed to make it similar to initial pos. global file.
2588 o global_ocean.cs32x15:
2589 change SIZE.h of AD set-up to get same tiling as with MPI.
2590 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
2591 o model/src:
2592 add flag to control printing of domain fields (bathymetry, hFac ...) in
2593 ini_mask_etc (call to plot_fieds_xy*).
2594 o pkg/thsice:
2595 if useEXF, some forcing fields are not valid in overlap: fixed by computing
2596 over the interior only + apply EXCH at the end (like with SEAICE advection).
2597 o pkg/mdsio:
2598 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
2599 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
2600 - change barrier call for safe multi-threads access to 3-D shared buffer.
2601 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
2602 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
2603 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
2604 o pkg/flt:
2605 - add fourth-order Runge-Kutta integration
2606 - add basic exch2 support (only 1 facet supported so far!)
2607 o pkg/mdsio+rw:
2608 new S/R to read local (or tile independent) vector (read counterpart of
2609 mds_writevec_loc, and front-end write_glvec_rl/rs).
2610 o global_ocean.cs32x15: additional input_ad.seaice experiment
2611 that uses pkg/seaice rather than pkg/thsice.
2612 (using multidim advection for seaice)
2613 o towards more F95 syntax for array specification in namelist:
2614 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
2615 of all verification experiments.
2616 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
2617 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
2618 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
2619 o global_ocean.cs32x15: additional input.seaice experiment
2620 that uses pkg/seaice rather than pkg/thsice.
2621
2622 checkpoint62p (2010/12/17)
2623 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
2624 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
2625 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
2626 allow for use of multim. advection in seaice adjoint.
2627 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
2628 - first attempt to close budgets by taking into account the freshwater
2629 flux implied by the sublimation of snow and ice. So far only the
2630 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
2631 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
2632 o eesupp/src:
2633 new S/R with new option (NML_EXTENDED_F77) to change array specification
2634 from F95 standard to commonly accepted extended F77 form.
2635 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
2636 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
2637 for less tolerant f77 compiler (e.g., pgf77, g77).
2638 o globalFiles:
2639 commented out in parameter file "data" since it's not safe with MPI
2640 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
2641 in this case); no longer commented out in restart test (tst_2+2).
2642 o add adTapeDir to specify a special directory where adjoint tapes are
2643 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
2644 and cannot be used together with mdsioLocalDir.
2645 o nesting pkgs:
2646 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
2647 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2648 - add parameter files + utils dir + output from short run on beagle.
2649 o pkg/seaice:
2650 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
2651 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
2652 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
2653
2654 checkpoint62o (2010/11/25)
2655 o pkg/exf:
2656 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
2657 o pkg/seaice:
2658 - seaice_ocean_stress: split a loop for better vectorization of the
2659 adjoint code
2660 - seaice_growth.F: fix bug in conservation of freshwater connected to
2661 capping of heff, put contribution into d_HEFFbyNEG
2662 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
2663 by something more sensible (parameters that are what their name implies)
2664 - change some defaults, so that by default exf-parameters are used for
2665 things like rhoAir, cpAir,latent/sensible heat parameters, in order
2666 to reproduce the old results, many data.seaice now contain funny values
2667 for cpAir and latent heat of sublimation
2668 o packages_readparms.F: move exf_readparms up in line so that
2669 exf-parameters are visible for other packages (e.g. seaice)
2670 o debugMode & debugLevel=2:
2671 - differentiate between debugMode & debugLevel=2:
2672 debugMode: controls printing of debug messages (sequence of S/R calls).
2673 debugLevel: controls printing of algorithm intermediate results and stats.
2674 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
2675 => allows to print debug-stats without all sequence of call messages.
2676 - switch control of debug print from debugLevel to debugMode in many S/R.
2677 o pkg/obcs (obcs-sponge):
2678 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
2679 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
2680 o pkg/generic_advdiff:
2681 - record overlap minimum size for each advection scheme;
2682 - refine criteria on overlap minimum size;
2683 - check and stop (in gad_check) if overlap size is too small.
2684 o pkg/obcs:
2685 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
2686 once, in ptracers_implicit.F)
2687 - with seaice: remove test on empty file name in obcs_apply_seaice (always
2688 apply OB values when tile has OB)
2689 o model/src, coriolis setting:
2690 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
2691 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
2692 files (selectCoriMap=3) with any grid.
2693 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
2694 o pkg/seaice/seaice_growth.F:
2695 a few cosmetic changes that reduce the number of lines of code
2696 o pkg/obcs: add boundary conditions following Stevens (1990)
2697 - the code follows old MOM/NAOSIM code
2698 - so far it is only implemented for the eastern and western boundaries
2699 and NOT for pTracers
2700 o pkg/rbcs:
2701 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
2702 beginning of the first rbcs forcing period.
2703 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
2704 offline package, i.e., one file per time, labeled by iteration number;
2705 deltaTrbcs sets the timestep with which the data was generated;
2706 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
2707 - rbcsForcingCycle=0 makes forcing non-cyclic.
2708 - make arithmetic safe for negative times and odd forcing periods.
2709
2710 checkpoint62n (2010/11/09)
2711 o pkg/seaice:
2712 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
2713 o pkg/obcs:
2714 New S/R to copy tracer value from the OB location to narrow band region
2715 (width = same as overlap) beyond the OB: preserve OB value (needed for
2716 high-order scheme) which were overwritten by EXCH call if in overlap
2717 region. Applied to theta, salt, ptracer and advected seaice variables.
2718 With seaice: use maskInC in similar way as in gad_advection.F,
2719 in seaice_advection.F and advect.F.
2720 Update output of experiment seaice_obcs and change exp4 to test OBCS with
2721 4th order Adv.Scheme. for pasive salt and ptracer.
2722 o tools/genmake2:
2723 - when looking for an optfile (not specified), only search for Fortran compiler
2724 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
2725 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
2726 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
2727 - set default for CPP to "cpp -traditional -P" (was the case without specifying
2728 an optfile, but otherwise default was just "cpp".
2729 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
2730 - when "CC" is not set in the optfile, look for possible C compiler
2731 (instead of just setting CC=cc)
2732 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
2733 => add a ".F" to ".o" rule for source files with no "#include" (such as
2734 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
2735 - move gfortran before g77 in list of possible Fortran compiler (consistent
2736 with reference compiler switch from g77 to gfortran)
2737 o pkg/seaice:
2738 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
2739 seaice_check that stops the model, when the CPP flag is used.
2740 o seaice_growth.F: make capping of ice volume conserving by returning the
2741 capped ice as freshwater to EmPmR. This does not change the verification
2742 experiments but will change runs where the capping is acutally active
2743 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
2744 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
2745 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
2746 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
2747 o tools/genmake2:
2748 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
2749 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
2750 - clean previous genmake log files before anything else.
2751 - change Makefile to remove testreport log files (*.tr_log) and genmake log
2752 files only with "CLEAN" target (instead of "Clean");
2753 o pkg/generic_advdiff:
2754 Change OBCS in multiDim advection (gad_advection.F):
2755 Use maskInC to prevent intermediate update of tracer-field in OB regions,
2756 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
2757 which were applying future time-step OB values.
2758 This way, all explicit calculations use current-time-step OB values
2759 (simpler and more consistent).
2760 Affects results when set-up uses time-varying OBC and multi-dim advection;
2761 update output of experiment seaice_obcs.
2762 o pkg/seaice:
2763 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
2764 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
2765 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
2766 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
2767 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
2768 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
2769 o pkg aim (2010/10/26):
2770 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
2771 formulation with obliquity, eccentricity, ... as run-time parameters,
2772 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
2773 upward shortwave radition at the surface (all-sky and clear-sky).
2774 o pkg/obcs:
2775 - writing sections with globalFiles=T does not work: switch to tiled-files
2776 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
2777 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
2778 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
2779
2780 checkpoint62m (2010/10/21)
2781 o pkg/seaice: vectorize seaice_solve4temp.F
2782 - move iterations loops outside of i/j-loops
2783 - requires 2D arrays for TB and effConduct
2784 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
2785 modified in this routine
2786 - a little bit of clean up, adjusting indentation, etc.
2787 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
2788 performance and '**TWO' by '**2' (because TWO is a float),
2789 replaced ONE, ZERO
2790 o eesupp/src:
2791 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
2792 o pkg/seaice/seaice_growth.F
2793 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
2794 merging process. The merged routine has two branches, and one activates the 'evolution'
2795 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
2796 In summary, here is what the '10/10 revision' did consist of
2797 part 1: seaice_growth.F revisions 1.71 to 1.75
2798 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2799 The emphasis here was on improving readability (e.g. by trying to use meaningful
2800 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2801 part 1.5:
2802 - revising the lab_sea experiment to make it a more useful (i.e. stable
2803 and representative of an actual model run). This was done by generating a
2804 (winter) pickup to start from, switching back the main experiment dynamic
2805 solver from evp to lsr, having one of the experiments use the free drift solution.
2806 part 2: seaice_growth.F revisions 1.76 to 1.85
2807 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2808 - Sorting out the various fields units and sign (set early on and reset at the end)
2809 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
2810 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
2811 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
2812 and simplifying logical expressions to further improve readibility.
2813 part 3: seaice_growth.F revisions 1.86 to 1.89
2814 - Re-organize the blocks of code more logically.
2815 - Merging the '_if.F' pieces that add something new.
2816 o pkg/thsice:
2817 - vectorize thsice_solve4temp and thsice_get_exf.
2818 Problem: thsice_solve4temp has an unvectorizable statement that
2819 might also be problematic for TAF
2820 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
2821 does not change the verifcation experiment, but will change all
2822 experiments that have this flag undefined (not tested in verification);
2823 a little reorganization to save a few 2D fields and recomputations
2824 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
2825 - 2nd step: fix some store dirs
2826 o seems to work somewhat, i.e. using ifort but not g77
2827 o likely cause are incomplete init. or recomputation
2828 o start verification/global_ocean.cs32x15/input_ad.thsice
2829 o pkg/obcs: add support for exch2
2830 - the position of the boundary and prescribed values are specified using
2831 a global domain with exch2 facets stacked
2832 - in x for N,S boundaries (like W2_mapIO=-1)
2833 - in y for E,W boundaries (so E,W boundaries do not overlap)
2834 o pkg/mdsio: add support for writing global sections with exch2
2835 file layout is as for obcs described above:
2836 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
2837 - for y-z sections, facets are stacked in y
2838 o pkg/thsice:
2839 - change a few routines for better vectorization: thsice_albedo.F,
2840 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
2841 not affected, but in particular the latter routine has changed
2842 dramatically (not necessarily easier to read now).
2843 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
2844 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
2845 o verification/lab_sea:
2846 - overhaul of the forward model experiments. The main motivation
2847 for this revision is that lab_sea has proven quite fragile (when
2848 changing the sea-ice code, and switching platforms) to a point
2849 when failures were very hard to attribute to specific code problems.
2850 - the suspected reason for this fragility is noise amplification by evp so,
2851 to start with, we decided to replace evp with lsr in the main experiment.
2852 - the input.lsr experiment thus became obsolete and was removed.
2853 - it was replaced with the input.fd experiment that uses an
2854 analytical "free drift" solution as the ice velocity field.
2855 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
2856 will hopefully allow us to discriminate problems due to dynamic solvers
2857 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
2858 us to test additional options, along with the salt plume package.
2859 - Finally a pickup was generated (at the end of a one year run) to
2860 make the tests more representative of an actual model run. Previously
2861 the tests starting point was a 1m thickness of ice everywhere.
2862 o pkg/seaice:
2863 - introducing S\R seaice_freedrift.F that compute the
2864 analytical solution to an approximate ice momentum
2865 equation (i.e. the simple stress/coriolis balance).
2866 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2867 of the free drift velocity field, and enable its use.
2868 To actually use the free drift solution as the model ice
2869 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
2870 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
2871
2872 checkpoint62l (2010/10/04)
2873 o pkg/seaice:
2874 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
2875 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
2876 version (with USE_ORIGINAL_SBI undef);
2877 o add hooks for new packages OASIS, the package will follow
2878 (hooks exclude the seaice pkg for now)
2879 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
2880 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
2881 rather than mdsio_readvector.F/mdsio_writevector.F, within
2882 adread_adwrite.F to read/write adjoint-related tapes to disk.
2883 o eesupp and pkg/mdsio: ALLOW_WHIO
2884 Option to write/read 2D fields to files including tiles halos.
2885 The main purpose is for adjoint related "tape I/O".
2886 The secondary purpose is for debugging phases.
2887 A word on those rather specifically intended purposes.
2888 The code was meant to be stripped down to the bare minimum.
2889 Typically, there is a unique and basic mapping to the global
2890 buffer (tile by tile, then proc by proc, then level by level), and
2891 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
2892 meant to generate user friendly outputs of various shapes and forms.
2893 Rather it is intended, for the knowledgeabale developers,
2894 to be largely independent of the many mdsio options, to allow
2895 outputs of tiles+halos in debugging phases and in adjoint runs,
2896 and to allow some flexibility in tuning (adoint) I/O depending on each
2897 file system behavior. With regard to tuning, most of the potential knobs
2898 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
2899 to specify directories, to specify the typical size of I/O calls, etc.)
2900 are not yet included, and will be added if they prove useful.
2901 o pkg/seaice:
2902 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
2903 o pkg/seaice:
2904 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
2905 code (seaice_budget_ice_if.F) which enable to recover old standard
2906 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
2907 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
2908 o model/src (rStar):
2909 use simple average (not area weighted) of rStarFac at U,V point when using
2910 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
2911 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
2912
2913 checkpoint62k (2010/09/17)
2914 o adjoint
2915 * changed verification/global_ocean.cs32x15 ; adjoint now tests
2916 Adams-Bashforth 3 + NLFS + RSTAR
2917 * some more modifs required for ECCO-GODAE v4
2918 o pkg/seaice
2919 add SEAICE_AGE_VOL option to use volume instead of area for
2920 integrating SEAICE_AGE
2921 o model/src:
2922 first check-in of sigma & hybrid-sigma coordinate code ; also includes
2923 non-linear free-surface parts ; but pressure-gradient not yet coded.
2924 o pkg/ptracers:
2925 option for ptracer to convert Salt Relax into additional EmP.
2926 tested in exp. global_ocean.90x40x15.dwnslp (update output)
2927
2928 checkpoint62j (2010/08/25)
2929 o pkg/ggl90:
2930 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
2931 o pkg/dic: car_flux.F, phos_flux.F
2932 - reduce number of exp-calls in order to improve performance
2933 - clean up a little (replace fields by their macros, etc., fix
2934 typo in CPP-flag)
2935 o pkg/ggl90: minor changes
2936 - GGL90diffKrS was removed --> always use GGL90diffKr
2937 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
2938 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
2939 (commented out for now)
2940 - change in max/min operations to ensure that smoothing is ok
2941 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
2942 - always use diffKrNrT as background profile (i.e. never use diffKr field)
2943 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
2944 o pkg/dic:
2945 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
2946 vectorization
2947 - small bug fix in insol for the unlikely case of a cartesian grid
2948 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
2949 + now vectorize, which also removes adjoint recomputations;
2950 + replace integer maksp1 by _RL maskp1
2951 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
2952
2953 checkpoint62i (2010/07/21)
2954 o pkg/flt:
2955 - with OBCS: stop floats which enter the OB region
2956 o model/src:
2957 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
2958 for implicit vertical advection.
2959 o pkg/seaice:
2960 - account for melting in seaice age evolution.
2961 - remove double counting of seaice ridging effect on seaice age.
2962
2963 checkpoint62h (2010/06/18)
2964 o pkg/exch2:
2965 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
2966 o tools/genmake2
2967 - remove "-pdefault" option: redundant with the use of "packages.conf";
2968 - remove file pkg/pkg_default : set the default as a pkg group
2969 ("default_pkg_list") defined in pkg/pkg_groups;
2970 - fix for case pkg/pkg_depend is missing (was hanging before);
2971 - add option "-pgroups" to specify a different pkg_groups than the default.
2972 o verification/adjustment.cs-32x32x1:
2973 add a "minimal" set-up test (code_min & input_min) which only compiles
2974 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
2975 o tools/genmake2
2976 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
2977 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
2978 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
2979 files are nearly the same anyway.
2980 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
2981 - redefinition of tau(i,i) (by a factor of ustar)
2982 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
2983 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
2984 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
2985 - replace
2986 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
2987 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
2988 by
2989 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
2990 (changes results)
2991 -> exf_bulkformulae v1.22,
2992 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
2993 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
2994 output.txt 1.63
2995 offline_exf_seaice: output.seaicetd.txt 1.7
2996 seaice_obcs: output.txt 1.10)
2997 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
2998 -> exf_bulkformulae v1.23,
2999 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
3000 and global_ocean.cs32x15.icedyn (only 11 matching digits)
3001 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
3002 o adjoint of exch-1:
3003 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
3004 (note: was already like this when using EXCH-2) and remove flow dir
3005 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
3006 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
3007 - update pkg/exch2 diff list.
3008
3009 checkpoint62g (2010/05/19)
3010 o eesupp/src (exch-1):
3011 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
3012 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
3013 (renamed to exch1_*rx_cube.F).
3014 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
3015 to call new exch1 S/R ; update Makefile and .cvsignore.
3016 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
3017 exch2_xy_rx later)
3018 Note: after updating your code, need to run "make clean" in eesupp/src
3019 o test experiment bottom_ctrl_5x5:
3020 new output_adm.txt with fewer grdchk & less monitor output.
3021 o model/src:
3022 remove the call to ini_cori in initialise_varia.F (just keep the usual one
3023 in initialise_fixed.F). More consistent with coriolis & horizontal grid
3024 beeing treated in the same way (ini_grid is not called a 2nd time).
3025 o pkg/exf:
3026 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
3027 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
3028 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
3029 - cosmetic changes to exf_bulkformulae.F to make it look more like
3030 exf_bulk_largeyeager04.F
3031 o eesupp/src (exch-1):
3032 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
3033 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
3034 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
3035 (even without using MPI).
3036 - Message mode: move RecvAck setting (indicator of buffer being ready)
3037 from send_put to recv_get S/R (was useless before, but not sure if
3038 it's much more useful now);
3039 - Switch the order of sync: MPI-proc 1rst and then threads;
3040 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
3041 - fix AD code for communication mode ='get' (but not used).
3042 o model/src:
3043 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
3044 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
3045 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
3046 o pkg/ctrl: require a specific set of control variables and exf-flags for
3047 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
3048 o model/src:
3049 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
3050 1rst forward sweep, to avoid over-writing output files during recomputations
3051 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
3052 b) 2nd version:
3053 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
3054 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
3055 writePickupAtEnd) + seaice & ptracers output;
3056 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
3057 o model/src:
3058 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
3059 o pkg/exch2:
3060 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
3061 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
3062 o pkg/autodiff & exch2:
3063 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
3064 (for now, only if ALLOW_EXCH2 is defined).
3065 o pkg/autodiff:
3066 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
3067 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
3068 + clean-up comments (_RS is not always real*4)
3069 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
3070 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
3071 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
3072 o testreport (AD-tests):
3073 no longer link files from dir "../input" (1rst link files from
3074 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
3075
3076 checkpoint62f (2010/04/29)
3077 o model/src/the_main_loop.F:
3078 adjust store directives for seaice evp and multicategory according to
3079 pkg/ecco/the_main_loop.F
3080 o adjoint:
3081 global_sum_ad was incomplete (noted many times by many people ;)
3082 nice description by Jean U. as follows:
3083 * allreduce(var) in global_sum.F can be interpreted as
3084 reduce(sum) followed by broadcast of sum.
3085 * The adjoint of that is
3086 sum(adjoint) followed by broadcast(summed adjoint value)
3087 or in other words, allreduce(sum, adjoint vars)
3088 We were missing the sum(adjoint)!
3089 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
3090 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
3091 The fix should produce 16-digit accuracy between
3092 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
3093 multi-CPU single-tile (e.g. nSx=1, nPx-2)
3094 We'll probably change this yet again shortly
3095 o eesupp/src:
3096 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
3097 o pkg/icefront
3098 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
3099 specification of addmass array based on a 2D field, which is added
3100 at bottommost wet level at each horizontal location.
3101 o model/src:
3102 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
3103 layout; (not always compatible with delX,delY setting; commented out for now).
3104 o pkg/exch2:
3105 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
3106 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
3107
3108 checkpoint62e (2010/04/15)
3109 o pkg/obcs:
3110 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
3111 o pkg/dic:
3112 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
3113 (note: not presently tested in any forward verification exp.)
3114 update tutorial_global_oce_biogeo AD output file.
3115 o pkg/exf:
3116 - account for the variation of albedo as a function of zenith angle
3117 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
3118 o build_options:
3119 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
3120 o pkg/dic:
3121 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
3122 - use binary pickup file for restart;
3123 - initialise atmos-CO2 box from dic_pCO2 parameter;
3124 - fix multi-threaded.
3125 o pkg/rbcs:
3126 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
3127 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
3128 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
3129 and update output.txt
3130 o pkg/kpp:
3131 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
3132 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
3133 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
3134 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
3135 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
3136 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
3137 o pkg/offline:
3138 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
3139 (bug was added in version 1.10 on 2007-08-23).
3140 o pkg/offline:
3141 - no need to specify periodicExternalForcing, etc ... to use offline pack
3142 - offline input files no longer just single prec --> parameter offlineLoadPrec
3143 o verification/lab_sea:
3144 change AD test to multi-tile setup and update all 4 AD output.
3145 NOTE: while cost function values remain very similar,
3146 gradients are very different, although gradient checks are self-consistent
3147 Should try to get to the bottom of this (cost function summation order?)
3148 o pkg/dic:
3149 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
3150 a weakness of TAF that drops part of double precision in log10 derivative.
3151 <= changes removed since problem has been fixed in current TAF version 1.9.71
3152 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
3153 o pkg/ecco:
3154 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
3155 update all 4 lab_sea AD output.
3156
3157 checkpoint62d (2010/03/22)
3158 o build_options:
3159 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
3160 o remove unbalanced quote (single or double) in commented line of source code
3161 (may cause some warning with some preprocessor/makedepend versions).
3162 o pkg/seaice:
3163 fix seaice_model.F for adjoint (gael) and update AD results of experiments
3164 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3165 o testreport:
3166 add option '-runonly' (short: '-ro') to just do the run part (without make).
3167 o eesupp: remove JAM communication code (obsolete).
3168 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
3169 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
3170 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
3171 (update also the output).
3172
3173 checkpoint62c (2010/03/02)
3174 o tools/build_options :
3175 move (some) old optfiles from build_options/ to build_options/unsupported/
3176 o model/src and pkg/exf
3177 surface relaxation -- separating data and data.exf options
3178 The point is to ensure that we specify the surface relaxation
3179 either in data or in data.exf (but not half and half) and to
3180 avoid an accidental relaxation to 0 (which happened if a time
3181 scale was specified but the file name was left empty)
3182 o model/src model/inc and pkg/mom_common
3183 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
3184 => addition to the viscosity field as computed by others schemes
3185 o tools/build_options:
3186 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
3187 but keep the former optfile for few weeks for smooth transition
3188 o pkg/ecco
3189 - allow user defined cost function contributions
3190 CPP: ALLOW_USERCOST_CONTRIBUTION
3191 USAGE: compute contributions in cost_usercost_all.F
3192 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
3193 the two options are complementary.
3194 o pkg/smooth
3195 - migration from contrib to the main repository
3196
3197 checkpoint62b (2010/01/26)
3198 o pkg/monitor:
3199 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
3200 (in case someone forgot to update customized pieces of code)
3201 o nonHydrostatic:
3202 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
3203 - add a simple 2-D experiment (short_surf_wave) to test it.
3204 o pkg/icefront:
3205 adding the shell of, and the hooks to, a new package that
3206 will model melting and freezing of vertical glacier ice fronts
3207 o momentum:
3208 add diagnostics of momentum tendency from Hydrostatic pressure gradient
3209 (without surf.pressure term: would need a 2nd filling since implicit term).
3210 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
3211 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
3212 cannot deal with the former
3213 o cleaning:
3214 - remove all (except OpenAD) old TLM output from results_ad dirs.
3215 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
3216 - comment out maskH definition (replaced by maskInC)
3217 o pkg/monitor:
3218 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
3219 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
3220
3221 checkpoint62a (2010/01/15)
3222 o model/src:
3223 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
3224 o pkg/diagnostics:
3225 - add optional level number diagnostics (i.e., level number to be define
3226 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
3227 - strictly check for valid parser-code(10) ;
3228 - check if adding diag to the list from the right place.
3229 o pkg/longstep:
3230 - change parameters and fix tracer conservation with rstar/nonlinear free surface
3231 o diagnostics:
3232 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
3233 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
3234 o pkg/diagnostics:
3235 - Add option for writing vertical integral (sum of selected levels) of an output
3236 field instead of writing output field levels. Activate this option on a per
3237 output-file basis, by setting the 2nd character of fileflag to 'I'.
3238 - Add field-specific information relative to level integral in 3rd postion
3239 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
3240 vertically (x level-thickness x hFac), "r"=same but without hFac.
3241 o do_the_model_io:
3242 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
3243 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
3244 writing pickups and stopping.
3245 o pkg/diagnostics (for now, only with mdsio):
3246 - write time information to meta file (and modify accordingly rdmds.m) :
3247 time-averaged diagnostics output: write starting and ending time of the
3248 time-averaging interval ; snap-shot diagnostics output remains unchanged;
3249 o pkg/timeave:
3250 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
3251 always Nr), now assumed to be equal to number of levels of averaged field;
3252 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
3253 o pkg/sbo:
3254 - fix ocean bottom pressure global-average & 2-D time-ave output (was
3255 neither initialised nor filled).
3256 - add starting iteration in suffix of global-average output file
3257 (to avoid over-writing the file after a restart)
3258 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
3259 o time-average:
3260 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
3261 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
3262 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
3263 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
3264 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
3265 - fix missing accumulation for pkg/opps.
3266 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
3267 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
3268 - fix initialisation of time-ave vars and do only full time-step increment
3269 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
3270 o pkg/layers:
3271 - use standard RW pkg S/R to write the output
3272 and remove local write_fld version (which had a problem).
3273 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
3274 - fix LAYERS_CALC argument list.
3275 o pkg/timeave:
3276 - store cumulative-time in a simple tiled array (drop the level index)
3277 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
3278 o pkg/ocn,aim_compon_interf
3279 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
3280
3281 checkpoint62 (2009/12/23)
3282 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
3283 (was not previously tested in any other exp.)
3284 o pkg/monitor:
3285 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
3286 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
3287 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
3288 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
3289 - change del2 calculation.
3290 - use interior masks (instead of maskH, <- to be remove).
3291 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
3292 o mask & obcs:
3293 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
3294 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
3295 (called after packages_init_fixed)
3296 o pkg/obcs:
3297 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
3298 Fixes bug in obcs+exf with nSx*nSy.GT.1
3299 - fix multi-tile handling in obcs balance code
3300 o nonHydrostatic:
3301 - Implement AB-3 for non-hydrostatic vertical momentum ;
3302 (change ordering of var. stored in pickup file when using NH)
3303 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
3304 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
3305 (in prep. for new NH free surface form).
3306 o pkg/obcs:
3307 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
3308 o model/src:
3309 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
3310
3311 checkpoint61z (2009/12/01)
3312 o nonHydrostatic:
3313 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
3314 a spurious source of energy in simple baroclinic adjusment test case.
3315 Update all non-hydrostatic exp output.
3316 o model/src (3-d solver):
3317 Change again 3-D solver free-surface RHS term when exactConserv=T:
3318 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
3319 (which was not the case with previous formulation).
3320 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
3321 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
3322 o nonHydrostatic:
3323 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
3324 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
3325 - change 3-D solver to work with r* (for now, only with linear free-surf.)
3326 - add few debug diagnostics (cg3d_x, residual)
3327 o model/src:
3328 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
3329 update output of exp. global_ocean.cs32x15.viscA4
3330 o update output of exp. global_ocean.cs32x15.icedyn after removing
3331 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
3332 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3333 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
3334 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
3335 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
3336 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
3337 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
3338 to test this code
3339 o pkg/cd_code:
3340 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
3341 C-grid momentum. D-grid velocity used to be stepped forward in time with
3342 Adams-Bashforth only on surface pressure term. Tests show that using AB on
3343 D-grid coriolis term improves stability (as expected from CD-scheme paper).
3344 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
3345 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
3346 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
3347 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
3348 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
3349 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
3350 o pkg/obcs:
3351 - fix bug in initialisation (broken since Oct 1rst modification)
3352 for useOBCSprescribe without useEXF.
3353
3354 checkpoint61y (2009/11/15)
3355 o pkg/seaice
3356 - change (once again) the discretization for the evp solver: rather than
3357 squaring the averages of strain rates, average the squares to give
3358 a better approximation to VP behavior (in simple test); this breaks
3359 verification experiments that use EVP (lab_sea and lab_sea.hb87)
3360 --> update outputs
3361 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
3362 to improve vectorization of adjoint code on TARGET_NEC_SX
3363 o verification/vermix:
3364 - change vermix to a more "classical" 1d column with high vertical
3365 resolution, seasonal heat flux forcing and constant wind forcing
3366 --> update outputs
3367 o pkg/seaice
3368 - fix diagnostics of principal stress components for EVP
3369 - add optional diagnostics of non-linear convergence for LSOR solver
3370 - make maximum zeta a runtime parameter
3371 o model/src (3-d solver):
3372 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
3373 which consisted in removing the Surf. Non-Hydrostatic pressure from the
3374 whole column and adding it to Eta (inspired from Casualli, 1999):
3375 Only affects 3-D solver initial guess and only if using ExactConserv,
3376 but tests did show a degradation of solver convergence. For this reason,
3377 decide to disable this piece of code.
3378 to recover previous version, just set zeroPsNH = exactConserv (line 78).
3379 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
3380 o pkg/ggl90:
3381 - fix previous modif (unfortunatly has not been documented here).
3382 o pkg/seaice/autodiff:
3383 - add CPP flag to include clipping of zeta in EVP code;
3384 although clipping of zeta is not necessary for EVP and not recommended
3385 it was done by default, now clipping is disabled by default
3386 - modify computation and store zetaC/Z in seaice_evp for TAF
3387 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
3388 - change seaice_calc_viscosities/strainrates for better
3389 vectorization after AD by TAF
3390 - rearrange common blocks in SEAICE.h once again for easier dumps of
3391 adjoint output, adjust adcommon.h and g_common.h
3392 - change flux form of default advection scheme for better vectorization
3393 of adjoint code
3394 - modify lab_sea/input.lsr to test the flux form of default advection
3395 scheme
3396 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
3397 transition in checkpoint61r)
3398
3399 checkpoint61x (2009/10/19)
3400 o adjoint: adding two new verification experiments
3401 * tutorial_global_biogeo: an online dic sensitivity experiment
3402 (work with G. Forget)
3403 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
3404 (an update of the Dutkiewicz et al., 2006 paper)
3405 Both use the same CO2FLUX cost function, but different controls
3406 Gradient checks look good, but some recomp. could still be traightened out
3407 Should add xx_dic control variable to test at some point
3408 o model/src:
3409 add run-time parameters to check and/or mask initial Temp & Salt
3410 o pkg/ptracers:
3411 apply zonal filter (if used) to all passive tracers
3412
3413 checkpoint61w (2009/10/12)
3414 o adjoint:
3415 * update and finish work on adjoint of dic package (G. Forget)
3416 * start adjoint of offline package
3417 * bug fix for cube-sphere TLM code (active_file_g.F)
3418 o tutorial_global_oce_optim:
3419 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
3420 and add SIZE.h_mpi for MPI testing
3421 o pkg autodiff
3422 - fix bug in autodiff_restore
3423 - make genmake2 remove comments and empty lines from ad_input_code.f in
3424 order to reduce file size (new script file remove_comments_sed)
3425 o allows to specify vertical profile of vertical viscosity (viscArNr)
3426 o pkg autodiff
3427 autodiff_ini_model_io: comment out writing of grid information to netcdf
3428 files, because at this time the grid fields are a bunch of zeros
3429 (this is analogous to ini_mnc_vars.F)
3430 o pkg seaice/autodiff:
3431 left-over from removing the 3-time-level fields:
3432 - small rearrangement of common blocks (SEAICE.h)
3433 - fix field declaration in order to get meaningful output in
3434 adseaice.*.nc (adcommon.h)
3435 o pkg obcs:
3436 - go through NH code only if nonHydrostatic=T
3437 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
3438 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
3439 => Update output of experiment seaice_obcs
3440 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
3441 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
3442 - fix restart for useOBCSprescribe + useEXF
3443 o pkg ctrl
3444 - make obcs as control parameter work also with useSingleCPUio
3445 - replace a few sny and snx by Ny and Nx to be consistent with
3446 ctrl_set_globfld_x/yz.F
3447 o pkg seaice
3448 - re-introduce global field frWtrAtm for the case of
3449 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
3450 - catch the case of an empty filename in seaice_cost_init_fixed.F
3451 o pkg ecco:
3452 - small bug fixes in the_main_loop
3453 . fix order of monitor arguments
3454 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
3455 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
3456 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
3457 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
3458 imbalance diagnostics for wmean_h/sflux = 0
3459 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
3460 - catch the case of empty filenames in ecco_cost_init_fixed.F
3461 and ecco_readparms.F
3462 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
3463 to make this statement meaningfull in ecco_cost_weights.F
3464 o pkg zonal_filt:
3465 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
3466 - when using rStar, filter uVel*hFacW instead of uVel
3467 (tested without topography: fix a Pb of growing instability with NLFS)
3468 o pkg/aim/thsice:
3469 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
3470 (works as SST restoring)
3471 o pkg/thsice:
3472 -add specific parameter for salt restoring in slab mixed-layer
3473 (by default equal to the temperature restoring)
3474
3475 checkpoint61v (2009/09/21)
3476 o pkg/kpp:
3477 -add double diffusive contributions as a hack, turned off by default
3478 for now, and the code can be excluded with a CPP-flag
3479 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
3480 -add a verification experiments to "vermix" to test this code
3481 o pkg/mom_common:
3482 Move computation of length scales to mom_init_fixed.F (avoid recomputation
3483 at each time-steps*levels).
3484 o pkg/layers:
3485 Created a new package for computing volume fluxes in temperature or
3486 [not yet implemented] density layers, e.g. for calculating residual
3487 overturning circulations.
3488 o pkg/diagnostics:
3489 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
3490 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
3491 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
3492 To avoid mixing type (RS/RL) of input/output array argument,
3493 replace single mixed-type array with a pair from each type (RS/RL).
3494 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
3495 is now implemented for all pkgs (previously only done for the main pickup)
3496
3497 checkpoint61u (2009/08/25)
3498 o pkg/obcs:
3499 - change OB?eta from _RS to _RL and put them into a separate commen block
3500 - add code to read OB?eta from a file via obcs_prescribe_read: the code
3501 compiles and does not destroy any other experiments, the data is read
3502 properly, but the code is not tested in actual applications
3503 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
3504 create a meaningful unit attribute for the time coordinate variable
3505 o pkg/ebm: add plenty of missing "_d 0" ;
3506 update results of experiment global_ocean_ebm (fwd + adjoint tests)
3507 Notes: several pieces of code only works for (very) specific set up
3508 (domain size, lat range, etc ...); should be documented & stop if one
3509 of those assumptions is not meet.
3510 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
3511 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
3512 and offline_exf_seaice (seaicetd + adjoint).
3513 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
3514 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
3515 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
3516 o few changes to pass when compiling with strick checking of arguments
3517 across S/R (allow to find few bugs in S/R calls).
3518 o pkg/seaice:
3519 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
3520 2d-fields, for slightly better performance
3521
3522 checkpoint61t (2009/07/22)
3523 o pkg/seaice:
3524 - remove unused variables in seaice_evp
3525 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
3526 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
3527 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
3528 each processor opens a different file (a fix from Matt).
3529 o cg2d:
3530 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
3531 this reduces number of EXCH calls by 2 when using exch2.
3532 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
3533 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
3534 o pkg/thsice:
3535 add code for Near Infra-Red albedo (from Jeff)
3536 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
3537 o ini_model_io:
3538 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
3539 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
3540 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
3541
3542 checkpoint61s (2009/06/30)
3543 o pkg/exch2 (exch2_rxN_cube*):
3544 remove last BARRIER (no need to synchronise after getting data from shared
3545 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
3546 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
3547 and generate new output (for the 2 tests) using default rotationPeriod.
3548 o pkg/exch2:
3549 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
3550 (was already the case with AUTODIFF_EXCH2 defined)
3551 - add bj in exch2 arrays and S/R.
3552 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
3553 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
3554 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
3555 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
3556 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
3557 - verification experiment natl_box.longstep
3558 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
3559 allow different versions of ifort (8 or 9) and different versions
3560 of mpi (mpich or mpich2) to be used with the same optfile.
3561 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
3562 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
3563 o pkg/seaice:
3564 fix previous modif (3-level field removed) for old-pickup reading
3565
3566 checkpoint61r (2009/06/25)
3567 o pkg/seaice:
3568 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
3569 1. introduce fields for time step (N-1)
3570 2. do not use levels 2 and 3 anymore (but keep them)
3571 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
3572 includes changes to pkg/thsice/thsice_get_velocity.F,
3573 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
3574 pkg/obcs/obcs_apply_uvice.F.
3575 - completely remove code for leap-frog time stepping for second order
3576 advection
3577 - adjusted adjoint accordingly;
3578 gradient checks have improved by an order of magnitude!
3579
3580 checkpoint61q (2009/06/22)
3581 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
3582 - the boundary conditions along open boundaries are unclear, because the
3583 associated masks are set to zero and are thus treated as closed when
3584 applying the slip-boundary conditions.
3585 - move initialisation of grid variables from seaice_init_varia to _fixed
3586 o adding doc/diags_changes.txt
3587 o model/src:
3588 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
3589 to avoid "_diags" naming if no relation to pkg/diagnostics.
3590 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
3591 file and only call PLOT_FIELD_XYZ if debugMode=T.
3592 remove few PLOT_FIELD_XY calls outside initialisation.
3593 remove few unnecessary BARRIER.
3594 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
3595 of salt_plume package in Southern Ocean
3596 o pkg/thsice:
3597 - fix hOceMxL in overlap (needed for sea-ice advection);
3598 update output of experiment global_ocean.cs32x15.icedyn.
3599 o pkg/seaice:
3600 - make the (placeholder-)tracer IceAge a little more meaningful
3601 by avoiding ridging of age due to convergent ice flow
3602 - add diagnostics for surface temperature, atmospheric and oceanic
3603 heat flux, and atmospheric and oceanic ice growth
3604
3605 checkpoint61p (2009/06/10)
3606 o eesupp (global_max & global_sum):
3607 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
3608 - remove starting & endding barrier (no longer needed)
3609 o pkg/mdsio, writelocal:
3610 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
3611 (remove the STOP): uses shared buffer IO to store data from all threads
3612 and then let master-thread write nThreads tiles.
3613 o pkg/mdsio (read/write field):
3614 - tiled IO done in 1 piece (all levels at a time);
3615 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
3616 - multi-threaded: allow to read/write local (non-shared) array
3617 (was already working with singleCpuIO ; now works also without);
3618 => no longer needs barrier call after reading a file (added inside
3619 mds_read/write field).
3620 - move barrier calls outside gather/scatter_2d to mds_read/write_field
3621 o pkg/obcs/exf
3622 - exf_getffieldrec.F: add a few ". _d 0" and
3623 add code to catch the case fldperiod = 0.
3624 - obcs_precribe_read.F: change if statements so that they match
3625 the variable type (_RL)
3626 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
3627 exf_iprec) as part of namelist EXF_NML_01
3628 o pkg/mdsio:
3629 - read/write tiled (local) files: read/write 1-level tile chunk at a time
3630 (instead of segment of length sNx); expected to speed up tiled IO.
3631 o pkg/exch2:
3632 - take buffer copy from/to array out of S/R exch2_send/recv into new
3633 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
3634 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
3635 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
3636 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
3637 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
3638 including Topology header file (and common blocks).
3639 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
3640 remove 2nd exch call in exch2_s3d_rx (no longer needed).
3641 - document S/R arg. list (+ update some comments)
3642 o pkg/seaice:
3643 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
3644 temperature and humidity over sea ice based on climatological values.
3645 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
3646 of LSR (this change is expected to change the results slightly because now
3647 it uses slightly difference moduli from the second last LSR solution, but
3648 that is more consistent with the stress computations; this part of the code
3649 is not tested in the verification experiments)
3650 - fix diagnostics for flux of ice in case of B-grid
3651 - turn strain rates eij and press into global fields within global
3652 common block in SEAICE.h for more straighforward diagnostics
3653 - fix diagnostics for principal stress components, press, zeta, eta
3654 to give something meaning full
3655 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
3656 new output (all 4 tests) using default rotationPeriod.
3657 o pkg KPP:
3658 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
3659 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
3660 and normal grid from 1 to Nr)
3661 o Fix computations of L4rdt in mom_calc_visc.F
3662 o eesupp:
3663 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
3664 should be called before a "stop" if we know that all process are going
3665 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
3666
3667 checkpoint61o (2009/05/26)
3668 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
3669 o model/src/ini_curvilinear_grid.F:
3670 compute angleSin/CosC when they are not read from a file
3671 o pkg/seaice:
3672 add pseudo time stepping for LSOR
3673 o pkg/exch2:
3674 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
3675 o pkg/seaice:
3676 Adding separate sea ice albedo, drag coefficients, and HO in Southern
3677 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
3678 o SingleCpuIO:
3679 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
3680 o pkg/seaice:
3681 put exchanged variable in (local) common block for MPI+Multi-Threads
3682 to work (necessary with exch1, and for now with exch2 too).
3683 o verification: to get more experiments tested with mpi, mth and mpi+mth,
3684 change tiling of:
3685 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
3686 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
3687 update output of exp:
3688 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
3689 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
3690 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
3691 (note: output.txt generated on faulks using only 1 tile)
3692 o eesupp & mdsio (SingleCpuIO):
3693 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
3694 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
3695 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
3696 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
3697 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
3698 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
3699 o pkg/exch2:
3700 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
3701 read parameter file "data.exch2" if it exists; otherwise try default regular
3702 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
3703 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
3704 with new code (not to be used, just as a backup solution).
3705 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
3706 in utils/exch2/input.
3707
3708 checkpoint61n (2009/05/12)
3709 o eesupp & mdsio (SingleCpuIO):
3710 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
3711 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
3712 receive real*4 array (instead of real*8) to read/write 32.bit files.
3713 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
3714 and remove new mapping S/R)
3715 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
3716 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
3717 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
3718 when using exch2. Add S/R to map global io-buffer to global model array.
3719 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
3720
3721 checkpoint61m (2009/04/29)
3722 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
3723 and add 3 other S/R for other types (R4,R8,RS).
3724 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
3725 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
3726 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
3727 - reduce number of macro definitions (keep only those which are used);
3728 can always call directly the corrresponding S/R if needed.
3729 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
3730 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
3731 Fixed wrong type of arg in:
3732 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
3733 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
3734 To fix: global_sum of var in common block is wrong (multi-threaded) in:
3735 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
3736 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
3737 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
3738 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
3739 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
3740 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
3741 edges are closed (zero depth); might happen with "blank tiles";
3742 for now, disabled if using OBCS.
3743 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
3744 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
3745 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
3746 to reduce length of 1.D array print in STDOUT.
3747 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
3748 + use 48 tiles (16x8): this will allow to test "blank tiles".
3749 o start to test MPI + multi-threaded (change testreport to skip tests
3750 where number of tiles do not match).
3751 o genmake2: add option "-omp" to turn on Open-MP ;
3752 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
3753 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
3754 and keep the original tile numbering. Note: compatible with old
3755 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
3756
3757 checkpoint61l (2009/04/07)
3758 o Overlaps had been forgotten in calculating ijk keys : fixed
3759 o fix cyrus makedepend for gcc 4.4
3760 o experiment fizhi-cs-aqualev20:
3761 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
3762 and generate new output. Note: new output is much closer to the old
3763 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
3764 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
3765 o pkg/fizhi:
3766 - change to avoid indices going deliberately over array-bounds
3767 - remove unnecessary MPI stuff
3768 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
3769 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
3770 does not go over array-bounds and therefore returns reliable output.
3771 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
3772 this S/R has 4 output arguments, which are used inside "get_alarm";
3773 when it is called with the same variable "ndum" in place of several
3774 output arguments, this produces weird side effect inside "get_alarm"
3775 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
3776 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
3777 address) and produces error.
3778 o tools/gemake2: (March 27-29 2009)
3779 with option "-mpi": link *_mpi files from "MODS" dir (this is what
3780 testreport does).
3781 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
3782 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
3783 update lab_sea.lsr & lab_sea.salt_plume results
3784 o pkg/seaice:
3785 Major overhaul of the LSOR solver: change discretization from original
3786 finite differences to finite volume. The old routine is still in the
3787 file seaice_lsr.F and can be turned on with the CPP-flag
3788 SEAICE_OLD_AND_BAD_DISCRETIZATION
3789 Along with this change, the discretization of the strain rates is changed.
3790 The same flag turns on the old discretization in seaice_calc_strainrates.F
3791 All verification experiments with seaice are affected (except for
3792 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
3793 results by setting the above flag.
3794 Further changes involve changes in defaults:
3795 - ALLOW_FLOODING is defined and turned on by default
3796 - SEAICEadvSnow = .true. is now the default
3797 - SEAICEadvSalt = .true. is now the default
3798 - SEAICEadvAge = .true. is now the default
3799 - SEAICE_clipVelocities = .false. is now the default
3800 (as per J. Zhang's recommendation)
3801 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
3802 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
3803 - seaice_growth: replace computation of UG by a simple copy from wspeed
3804
3805 checkpoint61k (2009/03/18)
3806 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
3807 seaice_lsr: fixed a few metric terms,
3808 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
3809 add more debugging diagnostics
3810 seaice_evp: removed superfluous many metric terms of FV discretization
3811 of stress divergence
3812 affects lab_sea, lab_sea.hb87
3813 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
3814 of stress divergence for non-evp solver
3815 (this part is not tested anywhere)
3816 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
3817 they were effectively only half slip
3818 affects lab_sea.hb87
3819 updated all relevant verification experiments (except lab_sea//output_adm.txt
3820 which was left over, but fails at level 7 & 6)
3821
3822 checkpoint61j (2009/03/17)
3823 o pkg/seaice: turn a few hard wired parameters into run time parameters
3824 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
3825 time in seconds as promised by the usints in seaice_monitor and exf_monitor
3826 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
3827 that are not cubed-sphere grids
3828 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
3829 o pkg/ctrl:
3830 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
3831 o non-hydrostatic (calc_gw.F):
3832 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
3833 update output of exp. global_ocean.cs32x15.viscA4
3834 o remove backward compatibility for thetaMin,phiMin
3835 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
3836 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
3837 interpolated wind field not only for curvilineargrid=.true., but also
3838 for a rotated grid (rotateGrid=.true.)
3839 o pkg/exf: add capability to bypass interpolation for runoff
3840 by setting yet another CPP-flag
3841 o eesupp/src, B-grid exchange:
3842 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
3843 o autodiff
3844 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
3845 allows to switch to single-prec common blocks;
3846 corresponding switch occurs in tamc.h, integer isbyte
3847 TAF store directivs "byte" and "kind" seem equivalent;
3848 Most tamc.h have been updated correspondingly.
3849
3850 checkpoint61i (2009/02/13)
3851 o autodiff:
3852 fix autodiff_sore/_restore indices for obcs
3853 (spotted by I. Hoteit, M. Mazloff)
3854 o pkg/autodiff, pkg/ctrl:
3855 Add flag to reduce all tapelev I/O to single-prec.
3856 In data.ctrl set
3857 doSinglePrecTapelev = .TRUE.
3858 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
3859 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
3860 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
3861 real fresh water flux (not yet)
3862 o pkg/mdsio & rw:
3863 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
3864 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
3865 o pkg/flt:
3866 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
3867 init_fixed & ini_varia.
3868 - clean-up & simplify linear interpolation S/R:
3869 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
3870 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
3871 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
3872 - add vert. coordinate & horiz. indices to output files.
3873 - change vertical position in initial condition, from index to depth [m].
3874 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
3875 (easier to get to a curvilinear grid) ; delX,delY no longer used.
3876 o pkg/ggl90: a few modifications:
3877 - fix bottom boundary condition, and interpolation of KappaE
3878 near top and bottom
3879 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
3880 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
3881 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
3882 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
3883 (maintain temporary backward compatibility, until next checkpoint)
3884
3885 checkpoint61h (2009/01/27)
3886 o pkg/diagnostics with "periodic averaging diagnostics":
3887 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
3888 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
3889 o pkg/obcs: fix loop ranges for balancing code
3890 o pkg/flt:
3891 - improve criteria for finding which tile owns a float.
3892 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
3893 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
3894 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
3895 with ocean biogeo)
3896 o pkg/flt:
3897 - do some cleaning and fix the restart ;
3898 - add output.txt in flt_example/results to get this pkg tested.
3899 o genmake2: add an EXTENDED_SRC option and flag.
3900 for now, cannot be turned on on command line (only through genmake_local)
3901 o pkg/mdsio: read/write vector:
3902 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
3903 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
3904 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
3905 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
3906 (drop to 4 digits matching for grad). But this test does not look very
3907 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
3908
3909 checkpoint61g (2008/12/29)
3910 o pkg/flt:
3911 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
3912 + make OPTIONS file more standard.
3913 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
3914 - fix _BYTESWAPIO CPP-Flag
3915 - standard reading of file-parameter "data.flt"
3916 - fix argument list of S/R FLT_RESTART
3917 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
3918 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
3919 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
3920 a still unfixed compiler/optimization bug
3921
3922 checkpoint61f (2008/11/21)
3923 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
3924 update results of global_ocean.cs32x15.icedyn test.
3925 o move getcon.F from model/src to pkg/fizhi.
3926 o pkg/exf: add parameter for extrapolation of temp up to the surface
3927 and option to prevent negative evap (in bulk_largeyeager04 only).
3928 o Prather Advection scheme: fix tracer conservation for divergent flow
3929 (e.g., when using NonLin Free-Surface).
3930 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
3931 o gmredi (Visbeck-variable-K):
3932 - add more parameters to Visbeck-variable-K.
3933 - use a 5 points average for dSigmaR in Visbeck-K calculation
3934 (more "homogenous": same stencil and same weights as in dSigmaH)
3935 - update output of ideal_2D_oce experiment.
3936 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
3937 (#undef REAL4_IS_SLOW)
3938 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
3939 coordinate variable
3940 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
3941 (surface forcing fields), removes some of the functionality
3942 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
3943 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
3944 probably not all: copy _RS surface flux fields to RL field before
3945 calling DIAGNOSTICS_FILL
3946 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
3947 real*4 (CALL EXCH_*_RS) versions.
3948 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
3949 (generate new output).
3950
3951 checkpoint61e (2008/10/23)
3952 o gmredi (Visbeck-variable-K):
3953 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
3954 - change computation of Visbeck-K where Slope > Smax :
3955 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
3956 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
3957 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
3958 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
3959 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
3960 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
3961 does not become too large (to avoid precision problems in implicit-diffusion
3962 solver); update ideal_2D_oce output.
3963 o pkg ggl90:
3964 - in ggl90_cal.F: compute only one set of visc/diff, used to
3965 step forward TKE/T/S/momentum
3966 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
3967 have Prandlt =1)
3968 o gmredi (fm07):
3969 - add lower limit on Transition layer thickness + lower limit on 1/lambda
3970 - allow to set few more params from data.gmredi
3971 o pkg ggl90:
3972 - add missing sqrt(2) factor in computation of mixing length
3973 scale in ggl90_calc.F
3974 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
3975
3976 checkpoint61d (2008/09/25)
3977 o adjoint modifs
3978 - adapt to new field rhoInSitu
3979 - allow to revert from StoreDynVars2D, StoreDynVars3D
3980 to individual fields
3981 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
3982 o store 3-D (in-situ) density in commom block (DYNVARS.h)
3983 - save 1 rho computation.
3984 - no longer modify T & S inland when using down_slope pkg.
3985 o gad_som : allow to switch to SOM advection for T & S without corresponding
3986 pickup files (using new S/R: MDS_CHECK4FILE).
3987 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
3988 (for useSingleCpuIO to work in multi-threaded)
3989 o pkg/shelfice:
3990 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
3991 with SHELFICEtopoFile in data.shelfice
3992 - move code for reading ice shelf topography and modifying hFacC into separate
3993 subroutines of the shelfice package
3994 - separate initialisation of "fixed" and "variable" variables
3995 - kTopC is not (yet) replaced by kSurfC, although this is possible
3996 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
3997 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
3998 and rename:
3999 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
4000 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
4001 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
4002
4003 checkpoint61c (2008/08/30)
4004 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
4005 to add mass source/sink of fluid in the interior (3-D generalisation
4006 of oceanic real-fresh water flux).
4007 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
4008 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
4009 o new pkg: down_slope
4010 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
4011 - presently, modify T & S inland (dwnslp_calc_rho.F).
4012 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
4013 - implementation for ocean in P-coords not tested.
4014 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
4015 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
4016 (to facilitate conversion of oceanic pkg to p-coordinate).
4017 o change FIND_RHO to FIND_RHO_2D :
4018 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
4019 o new pkg: cheapaml
4020
4021 checkpoint61b (2008/08/05)
4022 o exch2:
4023 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
4024 - no longer depend on the order sequence (N,S,E,W).
4025 - 3rd exchange no longer needed (tested with 24 tiles).
4026 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
4027 - exch_UV_A-grid readily available (but not yet tested).
4028 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
4029 (both are no longer needed) in exch_uv: no effect in forward run; but
4030 get truncation error differences with adjoint exch.
4031 o exch2:
4032 - change index-bounds storage (moved from target to local tile,
4033 more intuitive this way) ; rename/remove some variables.
4034 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
4035
4036 checkpoint61a (2008/07/29)
4037 o exch2/matlab-topology-generator:
4038 fix bug in index bounds for N-S internal exchange (hard to tell if this
4039 had any effect on the solution).
4040 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
4041 is exceeded
4042 o testreport: modify syntax of awk, so that it works also with
4043 awk, and not only with nawk and gawk
4044
4045 checkpoint61 (2008/06/24)
4046 o autodiff
4047 Change default for TAF usage by removing argument '-nonew_arg'
4048 This changes TAF subroutine argument list (ordering of active var.)
4049 Omission of this flag leads to incompatibility w.r.t. TAMC
4050 To restore TAMC-compatibility, need following modifs:
4051 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
4052 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
4053 Tested TAF version is 1.9.22
4054 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
4055
4056 checkpoint60 (2008/06/19)
4057 --->>> This is the last checkpoint for which generating the adjoint
4058 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
4059 --->>> by default.
4060 --->>> Future checkpoints will ommit this flag by default.
4061 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
4062 o pkg/grdchk: Add gradient check to etan0 perturbations.
4063 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
4064 o pkg/autodiff: more flexibility in zeroadj.
4065 model/src: modifying do_oceanic_phys.F accordingly.
4066 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
4067 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
4068 special setup of gmredi for which the adjoint is stable
4069 enough for parameter optimization.
4070 o bridging the gap between eddy stress and GM.
4071 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
4072 along with a change in CPP option (now ALLOW_EDDYPSI).
4073 -> when using GM w/ GM_AdvForm:
4074 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
4075 is applied either in the tracer Eq. or in momentum Eq.
4076 depending on data.gmredi (intro. GM_InMomAsStress).
4077 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
4078 The key modifications are in model/src/taueddy_external_forcing.F
4079 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
4080
4081 checkpoint59r (2008/05/29)
4082 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
4083 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
4084 fix option to read coriolis(@ cell-corner) from files with CS-grid.
4085 o pkg/mnc: add some attributes to standard 1D-coordinate variables
4086 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
4087 mass points, when using mnc for output
4088 - add runtime parameter (missing_value, missing_value_int) to override
4089 default (which is the value of getcon('UNDEF'))
4090 o pkg/mnc: prepare mnc for the actual use of missing values with the
4091 diagnostics package: small fix in mnc_cw_readwrite.template and more
4092 initialisation of never used fields
4093 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
4094 versions
4095 o pkg/thsice/thsice_ini_vars.F added default initial values so that
4096 thermodynamics sea ice solver does not blow up when some initial fields
4097 are missing.
4098 o move from external_forcing_surf.F to ini_forcing.F
4099 the p-coord. hack consisting in using pLoad to set phi0surf ;
4100 update output of tutorial_global_oce_in_p (affected @ truncation level).
4101 o Freshen up a bit hs94.1x64x5, notably:
4102 remove rotationPeriod and tRef=5*0. (adjoint only), and add
4103 exactConserv=.TRUE.
4104 o pkg/generic_advdiff:
4105 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
4106 applies to files where Temperature & Salinity 2nd Order moments are used.
4107 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
4108 this uses a dynamically allocated internal state data structure
4109 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
4110 and requires a fortran 90 compiler
4111
4112 checkpoint59q (2008/05/06)
4113 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
4114 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
4115 o Refresh tutorial_global_oce_biogeo, notably:
4116 - change bathymetry (put back seamounts in ACC, use hFacs)
4117 - change EOS (POLY3 --> JMD95Z)
4118 - use Bryan-Lewis vertical diffusivity
4119 - use multidimensional advection
4120 - remove old virtual virtual in dic pkg, now done through ptracer pkg
4121 - change a couple of parameters in dic pkg
4122 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
4123 o pkg/obcs: change default to OBCSfixTopo = .true.,
4124 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
4125 - replace "debugMode" with "debugLevel .GE. debLevB"
4126 o implementation of TAF directives for gchem,cfc,dic
4127 o remove "exp5" (replaced by tutorial_deep_convection).
4128 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
4129 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
4130 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
4131 --> changes results in exp4, seaice_obcs
4132 o tutorial_deep_convection :
4133 update the set-up and increase resolution and domain size ; start
4134 from pseudo initial conditions = output at t=120mn in order to see
4135 something happening when running testreport.
4136 o pkg/seaice: add os7mp as an advection scheme
4137 add check for advection schemes
4138 add a flag for restoring T and S underneath sea ice
4139 o pkg/my82: add netcdf-support and diagnostics
4140 o thsice pkg:
4141 - Now hsMax limits snow height by turning it into ice following
4142 flooding scheme (and now conserving energy)
4143 - Slight rewriting of the formula in thsice_calc_thick.F
4144 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
4145 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
4146
4147 checkpoint59p (2008/04/10)
4148 o gchem / dic / cfc :
4149 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
4150 - add new parameter files: "data.dic" & "data.cfc" ;
4151 - various re-arrangement in initialisation & header file ;
4152 - fix tutorial_global_oce_biogeo for multi-threaded test.
4153 o pkg/dic: test for "pickup_dic" file when restarting ;
4154 if no pickup-file, can restart with a re-initialised pH (same as it did
4155 before) providing pickupStrictlyMatch is set to False.
4156 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
4157 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
4158 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
4159 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
4160 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
4161 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
4162 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
4163 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
4164 scheme to use for vorticty-term ;
4165 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
4166 (with default selectVortScheme, return to original discretisation)
4167 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
4168 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
4169 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
4170 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
4171 also fix diagnostics VISCAHW & VISCA4W.
4172
4173 checkpoint59o (2008/03/07)
4174 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
4175 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
4176 move a few statemens out the main loop into separate loops
4177 o pkg/shelfice:
4178 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
4179 (kg/m^2/s), does not break tests, because in verification/isomip,
4180 rhoConstFresh=rhoConst (by accident)
4181 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
4182 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
4183 new file model/src/seawater.F, so that they are available for all pkgs.
4184 - convert potential temperature into in-situ temperature. This changes the
4185 isomip tests => update tests
4186 o add a flag writePickupAtEnd (default=true) to be able to suppress
4187 writing a pickup at the last timestep
4188 o tools/mpack-1.6 :
4189 - disable automake (not working) and autoconf (not needed).
4190 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
4191 also cleaner with much less compilation warnings.
4192 o pkg/profiles:
4193 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
4194 (for "less than 32 characters name" compiler requirement)
4195 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
4196 conditions that have a different sampling frequency than S/T/U/V obcs
4197 o pkg/diagnostics (stats-diags):
4198 - fix global Min/Max in case 1 processor get only empty tiles
4199 o genmake2: replace (4 times)
4200 make genmake_tc_1.o >> genmake_warnings 2>&1
4201 with
4202 COMM="$CC $CFLAGS -c genmake_tc_1.c"
4203 echo $COMM >> genmake_warnings
4204 $COMM >> genmake_warnings 2>&1
4205 to make genmake2 always see the value of CC as specified in the optfile.
4206 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
4207 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
4208 - modify verification advect_cs test to test SOM-advection on CS-grid.
4209 o pkg/ctrl:
4210 - Rewrite of ctrl_map_ini_ecco.F,
4211 introducing a generic routine (ctrl_map_ini_gen.F).
4212 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
4213
4214 checkpoint59n (2008/02/09)
4215 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
4216 number in dedicate array "hdiag":
4217 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
4218 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
4219 - many small changes (integer format) for large number of diagnostics
4220 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
4221 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
4222 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
4223 usingSphericalGrid, this allows to define the rotated grid coordinates
4224 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
4225 geographical coordinates according to the inverse of the rotation defined
4226 by the Euler angles, so that Coriolis parameter and online-interpolation by
4227 exf works with the geographical coordinates on XC/YC/XG/YG.
4228 Naturally, this feature does not work with all packages, so some
4229 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
4230 profiles), because there the coordinates are assumed to be regular
4231 spherical grid coordinates.
4232 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
4233 - introduce isopycnal diffusion coefficient control.
4234 o tools/adjoint_options:
4235 - additional control vector components.
4236 o pkg/mnc: have mnc create marginally meaning full coordinate variables
4237 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
4238 o pkg/mypackage:
4239 - add example of read/write pickup for state-var ;
4240 - add entry points to the main code for state-vars diags & write-pickup.
4241 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
4242 transitions for useExfYearlyFields
4243 - add new subroutine that determines the file to read from for
4244 use*YearlyFields = .TRUE. and .FALSE.
4245 - add a verification experiment to global_with_exf that tests
4246 useExfYearlyFields with USE_EXF_INTERPOLATION defined
4247 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
4248 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
4249 subroutines (which could be generated from a template, because they are
4250 almost identical), for now they are included in obcs_prescribe_read.F for
4251 simplicity
4252 o pkg/exf:
4253 - add a little more diagnostic to exf_interp_read (in analogy to
4254 mds_read_field, can be turned off with debugLevel < debugLevA=1)
4255 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
4256 ugly but fast by unrolling short inner loops, inserting a unroll=8
4257 directive in routine lagran, and splitting a loop and making do while the
4258 outermost loop (the latter requires the intoduction of index arrays)
4259 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
4260 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
4261 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
4262 o verification/seaice_obcs: updated for restart test and latest options
4263 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
4264 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
4265 for now this is only available for the C-grid code and also within
4266 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
4267
4268 checkpoint59m (2008/01/14)
4269 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
4270 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
4271 o gad_som : fix flux output (& diagnostics) to have same units as other
4272 advection scheme fluxes (was previously multiplied by deltaT).
4273 o added verification/seaice_obcs both to test seaice open boundaries
4274 and to provide an example matlab scrpt for generating them
4275 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
4276 o pkg/salt_plume: clean up salt_plume_frac.F to
4277 remove redundancy in PlumeMethod 1 and 4
4278 o pkg/kpp: added saltplume diagnostics
4279 o pkg/obcs and pkg/seaice:
4280 - do not set uice and vice to zero when OB*icefile are unspecified
4281 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
4282 - moved seaice tracer obcs after call to seaice_growth
4283 o pkg/salt_plume: added various options for salt plume depth
4284 criterion and for vertical distribution of the salt
4285
4286 checkpoint59l (2007/12/18)
4287 o pkg/ptracers: new version of ptracers pickup:
4288 read meta file and write only fields which are needed to restart.
4289 ( same logic as main pickup file ; also using pickupStrictlyMatch )
4290 o pkg/seaice:
4291 - add timescale for melting due to warm mixed layer as a means of
4292 setting SEAICE_availHeatFrac more conveniently
4293 - add a CPP-flag/runtime parameter check for flooding algorithm
4294 - reformulated availHeat in seaice_growth.F to be independent of AREA
4295 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
4296 unit changes
4297 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
4298 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
4299 SX vector computer.
4300 o pkg/seaice:
4301 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
4302 seaice forcing fields can now be read only through pkg/exf
4303 - removed some unused halos
4304 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
4305 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
4306 or U/VICE from U/VWIND before computing U/VSTRESS
4307
4308 checkpoint59k (2007/11/30)
4309 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
4310 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
4311 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
4312 all experiments pass when compile with un-initialised var. checking option.
4313 o added pkg/salt_plume
4314 o script to test restart (for now, in MITgcm_contrib/jmc_script)
4315 o pkg/seaice: new read/write pickup version.
4316 read meta file and write only fields which are needed to restart.
4317 ( same logic as main pickup file ; also using pickupStrictlyMatch )
4318 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
4319 o lab_sea.hb87: modify the domain & update output.hb87.txt :
4320 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
4321 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
4322 process. Fixed here by closing the domain at the Northern boundary.
4323 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
4324 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
4325 a set of consecutive levels in/from a 3-D array.
4326 o pkg/ptracers:
4327 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
4328 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
4329
4330 checkpoint59j (2007/11/09)
4331 o in pkgs: dic, obcs, offline, rbcs:
4332 standard way to compute coeff. for time interpolation between 2 time reccords
4333 which retains full precision (& make results less dependent on compiler).
4334 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
4335 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
4336 packages instead of reading ice cover and wind speed separately
4337 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
4338 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
4339 to allow to compile customized code before the update)
4340 o cleaning-up:
4341 - fix CPP instruction syntax in pkg/obcs
4342 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
4343 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
4344 - fix some threads issue in IO parts.
4345 o pkg/dic:
4346 - add tons of "_d 0" (--> much better testreports !)
4347 and then update outputs of tutorial_global_oce_biogeo
4348 o pkg/mom_fluxform:
4349 add a special version of momentum advection intended to conserve momentum
4350 next to a bathymetry step or a coastline edge. (default = off = #undef)
4351 o new read/write pickup version:
4352 - for now, only implemented for main (mdsio) pickup file.
4353 - write out only what is needed to restart; merge pickup_nh , pickup_ph
4354 and main pickup together.
4355 - read meta file; read only what is needed to restart; stop if a field
4356 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
4357 if it make sense (even if the restart is not perfect).
4358 - if no meta file, assume that pickup to read corresponds exactly to
4359 a pickup that would currently be written.
4360 - read pickup written in the old format (until checkpoint59i) if it
4361 recognizes an old meta file (no field-list).
4362 - add a meta file in exp. which starts from a pickup: 2 cases:
4363 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
4364 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
4365 b) a meta file describing the content of the associated pickup file
4366 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
4367 o pkg/mdsio & pkg/rw:
4368 - new routine to read a meta file ; new set of routine to read
4369 Multiple-fields file (with meta file).
4370 o added open boundary conditions capability for seaice
4371 HSNOW, HSALT, UICE, and VICE
4372
4373 checkpoint59i (2007/10/21)
4374 o adjoint:
4375 * fix multiDimAdvection adjoint
4376 (partial recomputation problem by TAF for fVerT(:,:,kDown)
4377 and comlev1 size definition (maxpass vs. max. number of tracers)
4378 * verification/global_ocean.90x45x15 adjoint now tests
4379 NLFS and multiDimAdvection using DST3 (=30)
4380 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
4381 o pkg/kpp: add "_d 0" to real constant (if missing);
4382 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
4383 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
4384 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
4385 for internal parameters related to restart process (formerly from PARAMS.h)
4386 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
4387 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
4388 as argument. (only atm2d & obcs write_pickup have not yet been updated)
4389 o pkg/monitor:
4390 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
4391 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
4392 - account for deep Atmosphere factor and density factor (anelastic)
4393 o added open boundary conditions capability for seaice HEFF and AREA
4394 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
4395 thermodynamics
4396 - requires a little reorganization, which affects the testreport results
4397 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
4398 so that now the conservative form is tested
4399 - add a few comments
4400 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
4401 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
4402 o add new diagnostics to seaice: advective, diffusive fluxes (only for
4403 multidim-advection, for scheme 2 they are not filled) and transports,
4404 thermodynamic growth rates
4405 o change units of EmPmR (inside the code, + within coupling interface)
4406 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
4407 Affects results @ truncation level (cg2d match) and update output of
4408 experiments: lab_sea(6), global_ocean.90x40x15(10),
4409 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
4410 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
4411 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
4412 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
4413
4414 checkpoint59h (2007/09/29)
4415 o pkg/exf:
4416 - improve vectorization by moving if-statement out of loops in
4417 exf_mapfields, exf_radiation
4418 - exf_bulkformulae.F: introduce 2D fields and vectorize code
4419 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
4420 o testreport:
4421 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
4422 monitor & update offline_exf_seaice exp. output.
4423 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
4424 o pkg/seaice:
4425 - bug fix in the evp solver: boundary conditions were affected be
4426 masking of zMax/zMin (changes results)
4427 - minor bug fix in boundary conditions in seaice_calc_strainrates
4428 (changes results for no_slip)
4429 - seaice_lsr.F: make interpolation of eta dependent on boundaries
4430 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
4431 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
4432 stress formulation and no-slip boundary conditions
4433 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
4434 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
4435 o pkg/seaice: a first HSALT time stepping equation has been checked in
4436 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
4437 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
4438 without requiring DO-IF statements
4439 o pkg/thsice:
4440 use continuous power-law function for partition of energy between lateral
4441 melting/freezing and thinning/thickening ; old code using step function
4442 still available with #undef THSICE_FRACEN_POWERLAW
4443 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
4444 o testreport: change AD testing : check against results/output_adm.txt
4445 using same scripts as for forward test.
4446
4447 checkpoint59g (2007/09/17)
4448 o adjoint testing: in preparation for changing testreport:
4449 - output format: cost and grad written on separated lines
4450 - ad output results in directory "results" (instead of "results_ad")
4451 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
4452 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
4453 o pkg/ecco: allow user defined cost function contributions
4454 o testreport:
4455 Allow to choose (per experiment) the list of tested output variables
4456 and the main variable (used to issue a pass/FAIL ) ;
4457 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
4458 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
4459 Also modify printing of summary:
4460 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
4461 b) echo the list of tested variables in the individual summary.txt of
4462 each experiment.
4463 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
4464 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
4465 (but still depend on the tile decompostion of the domain).
4466 o pkg/seaice: change a discretization detail to make the B-grid code
4467 "more symmetric". This change is likely to remove all "ridges/leads" that
4468 where quasi-aligned with the grid in B-grid solutions. It may also be
4469 the solution to the stress coupling issues with the B-grid.
4470 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
4471 remove .cvsignore from input dir. (since testreport no longer run here).
4472 o pkg/thsice:
4473 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
4474 - fix reshaping of sea-ice just after advection:
4475 melt all the ice only if ice-volume is too small.
4476 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
4477 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
4478 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
4479 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
4480 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
4481 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
4482 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
4483 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
4484 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
4485 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
4486 -> update output.txt
4487 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
4488 this affects truncation error: -> update output.txt of exp:
4489 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
4490 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
4491
4492 checkpoint59f (2007/08/21)
4493 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
4494 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
4495 a bounded range (in forward mode)
4496 o pkg/ecco, ctrl, autodiff and mom_common:
4497 internal parameter controls, completements of implementations
4498 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
4499 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
4500 (not seem any difference in testing results).
4501 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
4502 at face corners.
4503 o pkg/generic_advdiff:
4504 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
4505 loop range indices for computing vertical advection tendency
4506 and do the calculation in the interior only (no overlap) ;
4507 for now, only implemented for SOM advection (to save CPU time).
4508 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
4509 o exch2 adjoint
4510 First set of changes:
4511 - add exch2 hand-written adjoint templates
4512 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
4513 This will require cleanup in pkg/autodiff/*.F
4514 (changed routines currently kept separate in verif. code/)
4515 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
4516 that used to hide exch2 or cubed-sphere specific code
4517 (commented via 'cph-exch2')
4518 o pkg/seaice
4519 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
4520 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
4521 output of global_ocean.cs32x15.thsice .
4522
4523 checkpoint59e (2007/07/26)
4524 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
4525 for B-grid vector (not yet tested) and C-grid vector (<- only used
4526 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
4527 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
4528 (#ifdef ALLOW_SALT_PLUME)
4529 o gather_2d/scatter_2d: removed halo regions
4530 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
4531 scheme and the corresponding test case (under front_relax dir). For now,
4532 only available with Skew-flux form and not yet tested in realistic set-up.
4533 adjoint: store directives updated, but gradient checks deteriorated,
4534 so maybe GM/Redi adjoint is now broken.
4535 o seaice adjoint
4536 * add AREA, HEFF, HSNOW as control variable
4537 (should not change lab_sea results)
4538 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
4539 o pkg/seaice:
4540 * added computation of saltFlux in seaice_growth;
4541 For time being, sea ice salinity is assumed constant
4542 contribution of snow flooding to freshening of sea ice is neglected.
4543 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
4544 defaults to 0.0 in order to maintain backward compatibility.
4545 Typical values for SEAICE_salinity are 4 to 10 g/kg.
4546 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
4547 * added SEAICE_availHeatFrac, which specifies fraction of surface level
4548 heat content used to melt or grow ice
4549 * commented out cap of HICE: it helps keep ice thinner
4550 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
4551 * applied OBCS T/S mask to HEFFM sea ice mask
4552
4553 checkpoint59d (2007/06/21)
4554 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
4555 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
4556 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
4557 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
4558 and change default value of parameter "GM_Small_Number";
4559 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
4560 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
4561 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
4562 o pkg/ecco: cost function when applying pkg/smooth to controls
4563 o pkg/ctrl: add forcingPrecond run time parameter
4564 o pkg/seaice:
4565 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
4566 - fix bug in metric terms of u-equation in LSR solver (implicit part),
4567 changes verification/lab_sea
4568 - rearrange implicit part of u-equation in LSR solver to make it easier to
4569 read, understand, and debug. This causes changes at the truncation level.
4570 - fix (serious) bug in the boundary conditions (sign error in the implicit
4571 part) of the LSR solver. Changes all LSR results.
4572 - fixed problem with HSNOW initialization to avoid thick snow when AREA
4573 is initilized with small values - does not change lab_sea results.
4574 - added HsnowFile initialization capability
4575 o pkg/smooth: addition to model/src and pkg/ctrl so allow
4576 initialization of pkg/smooth and application to control vector
4577 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
4578 o dependencies: pkg/profiles requires pkg/cal
4579 o pkg/profiles:
4580 - added option ALLOW_PROFILES_GENERICGRID
4581 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
4582 that interpolation information (grid points and coefficients) is provided
4583 within the netcdf input files.
4584 -> sample matlab scripts can be found in MITgcm_contrib/gael
4585 that allow you to prepare netcdf input files.
4586 - also modified: cleaner include statements, cleaner error print statements,
4587 cleaner stops when error, and more tests of the netcdf input files consistency.
4588 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
4589 o pkg/seaice:
4590 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
4591 requires a new routine: seaice_diagnostics_fill.F
4592 - make sure that seaice does not move if not forced (pressure replacement
4593 method, Hibler and Ip, 1995), changes results
4594 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
4595 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
4596 It is turned off by default (=-1.), because it changes the results.
4597 - make it possible to read AREA from a file, too.
4598
4599 checkpoint59c (2007/06/04)
4600 o add S/R and diagnostics for oceanic mixed-layer depth
4601 o move GMRedi call after all vertical mixing schemes (including KPP)
4602 o pkg/thsice:
4603 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
4604 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
4605 o pkg/obcs:
4606 - bug fix for balance code
4607 o pkg/seaice:
4608 - allow values of SEAICE_elasticParm > 1
4609 - add new parameter SEAICE_evpTauRelax as an alternative
4610 to SEAICE_elasticParm
4611 - make lsr boundary conditions free slip (by default), changes result
4612 - add code for no slip boundary conditions for lsr
4613 - set minimum of zeta to zero (and not 4e8) (changes results)
4614 - add a cap on AREA after advecting AREA if seaice_growth is not called
4615 o change calculation of Visbeck K:
4616 - no longer depend on tapering scheme; instead, compute slope (limited
4617 by GM_maxSlope). this is equivalent to what was comuted before with
4618 clipping or linear tappering.
4619 - fix vertical averaging (wrong by 1/2 level)
4620 - leave the old version (but will not be maintained) within
4621 #ifdef OLD_VISBECK_CALC / #endif
4622 - update output of exp. ideal_2D_oce
4623 o change error catch in calc_r_star to improve vectorization
4624 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
4625 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
4626 o adjoint:
4627 Re-organized adjoint checkpointing according to Matt Mazloff
4628 (but with modifs/completions/cleanups)
4629 Storing is now bundled into large arrays to optimized I/O
4630 (and second step in cleanup of the_main_loop)
4631
4632 checkpoint59b (2007/05/16)
4633 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
4634 - export/import (between ocean & coupler) fields needed for ocean DIC.
4635 o pkg/seaice:
4636 - get rid of three more exchanges seaice_calc_viscosities (required
4637 different loop boundaries in seaice_lsr and seaice_ocean_stress)
4638 - bug fix in seaice_ocean_stress (update of lab_sea required)
4639 - reduce loop boundaries to necessary minimum also in seaice_evp
4640 - go back to the old way of computing deltaC/Z as the adjoint likes that
4641 better
4642 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
4643 passive tracer to an Age Tracer) + update output.txt
4644 o pkg/exf:
4645 - implement A-grid / C-grid selection for wind-stress input files.
4646 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
4647 for now, in exf_bulk_largeyeager04.F only :
4648 - change implementation for case where windspeed + 2. components wind-stress
4649 are read-in. AND use rhoConstFresh to convert evap.
4650 o pkg/seaice:
4651 - use correct EXCH_UV for wind-forcing (on A-grid).
4652 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
4653 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
4654 o pkg/exf:
4655 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
4656 EXF_INTERPOLATION:
4657 - merge global_with_exf/code version of exf_interp_read.F
4658 to the main code ;
4659 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
4660 reading the file ; Important: This options needs to be defined to recover
4661 previous code.
4662 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
4663 - no longer loose real*8 precision along the way when using exf_iprec=64.
4664 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
4665 - change discretisation of evp-solver in order to avoid another exchange
4666 (changes lab_sea) and clean up a little
4667 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
4668 help the adjoint (this also changes the results slightly)
4669 - add a few "_d 0" where they had been missing in seaice_evp.F
4670 - cleaning up: remove unused seaice_calc_rhs.F
4671 o pkg/exf: some cleaning-up:
4672 - change various "constants" into runtime parameters
4673 - cleaned-up Large&Yeager04 routine which should eventually
4674 replace exf_bulkformulae.F (changed names of S/R and CPP)
4675 and merged various ALLOW_ATM_WIND options
4676 only used with thsice pkg (in thsice_get_exf.F):
4677 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
4678 which are used when useStabilityFct_overIce=TRUE (= the default)
4679 - change default values of ice & snow emissivity and scale downward LW
4680 by ice & snow emissivity.
4681 o pkg/thsice:
4682 fix few little problems, in thsice_calc_thickn.F:
4683 - growth vertically (and not laterally) if iceFrac == iceMaskMax
4684 - melt only laterally if hIce < hThinIce (as the comments say)
4685 and in thsice_extend.F:
4686 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
4687 - start to form ice as soon as the minimum ice-volume is reachable.
4688 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
4689 and cpl_aim+ocn
4690 o pkg/kpp
4691 - move computation of surface related input fields to KPP into a new
4692 subroutine kpp_forcing_surf.F
4693 - remove wrong (within bi,bj loops) EXCH calls.
4694 - little cleaning (add argument myThid in last position, cvs header ...)
4695 - for now, fix conservation problem by exchanging KPPviscAz (may not
4696 be the best fix)
4697 o pkg/seaice
4698 - check for inconsistent evp parameter/cpp-flag combination
4699 - remove leftover errIO flat for obsolete name list error handling
4700 o OpenAD
4701 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
4702
4703 checkpoint59a (2007/05/01)
4704 o pkg/seaice: some parameter clarifications and a little bit of clean up
4705 o pkg/thsice: rename run-time parameters:
4706 himin -> hIceMin
4707 himin0 -> hThinIce
4708 hihig -> hThickIce
4709 i0 -> i0swFrac
4710 transCoef -> bMeltCoef
4711 frac_energy -> fracMelting
4712 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
4713 with default values (for now) that do not change the results.
4714 remove old version of thsice vars advection in pkg/seaice.
4715 o in FFIELDS.h:
4716 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
4717 - make pLoad & sIceLoad always available (but still only used if
4718 ATMOSPHERIC_LOADING is #define).
4719 o pkg/kpp: replaced _KPP_RL with _RL
4720 o bug fixes for vertical diffusivity computations when both KPP and
4721 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
4722 are no longer updating the vertical diffusivity array
4723 (passed as argument) but are (re-) setting those arrays.
4724 o pkg/seaice: fix bug in evp solver, while doing that
4725 - change (improve?) discretization of stress computations for both
4726 cgrid-lsr and evp solver
4727 - add a new routine to compute strain rates
4728 - the above changes lab_sea results
4729 - add no slip conditions for evp solver (off by default), lsr-version
4730 may follow
4731 - fix exchange for shear at Z-points (does not change lab_sea)
4732 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
4733 (to force the user to pick a time step since there is not "safe" way
4734 of choosing it)
4735 - add principal stress diagnostics
4736 - rearrange fields for evp a little to avoid having to call a: too many
4737 exchanges and b: exchanges for stress trensor components which we do
4738 not have.
4739 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
4740 of evp, complete rewrite for lsr case (latter is does not yet work
4741 in all cases)
4742 o pkg/kpp: add code to have mixing in shelf ice caverns
4743 - add myThid to all kpp routines (long overdue)
4744
4745 checkpoint59 (2007/04/19)
4746 o pkg/exf:
4747 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
4748 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
4749 - move exf header files from lower_case.h to UPPER_CASE.h ;
4750 add missing cvs Header & Name
4751 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
4752 - add namelist param. selectStressGridPosition, exf_monFreq
4753 - retire many _CLIM routines, and remove data.exf_clim
4754 + params moved to data.exf
4755 + climsst, climsss now handled by exf_set_gen, i.e.
4756 climss?period=0 refers to constant field,
4757 climss?period=-12 to monthly forcing
4758 - split up namelists in data.exf
4759 o pkg/seaice:
4760 - remove seaice_exch and seaice_exch_uv
4761 - remove superfluous exchange of theta
4762 - add myThid to seaice_budget_ocean/ice
4763 - add new interface for atmospheric wind forcing (C-grid only)
4764 + new routine
4765 + two new field (taux, tauy for stress over ice)
4766 + removed one global field (DAIRN) for C-grid case only
4767 o pkg/thsise
4768 - 2nd set of modifs for thsice adjoint in conjunction with exf
4769 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
4770
4771 checkpoint58y_post (2007/04/15)
4772 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
4773 vertical diffusivity, similar to that in MOM4; turned on using
4774 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
4775 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
4776 o Added capability for 3D specification of background vertical diffusion
4777 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
4778 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
4779 "data" file that contains the 3D vertical diffusivity coefficients.
4780 o ice dynamics (pkg/seaice) with thsice thermodynamics:
4781 - add code within pkg thsice to advect & diffuse sea-ice fields
4782 similar to (and will replace) what has been added in seaice_advdiff.F,
4783 but: - conserving Mass, Heat & Salt.
4784 - better when using non-linear advection scheme (not yet fully tested)
4785 - can also be used in atmospheric set-up (for now, only the diffusion).
4786
4787 checkpoint58x_post (2007/04/04)
4788 o IO option for global-file compact format:
4789 - add options when generating topology (utils/exch2/matlab-topology-generator)
4790 - add I/O capability (pkg/mdsio).
4791 - adapt utils/matlab/rdmds.m to read this format.
4792 for now long-line format not yet supported by pkg/mdsio (& exch2).
4793 o shelfice: add a few diagnostics
4794
4795 checkpoint58w_post (2007/03/13)
4796 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
4797 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
4798 (and replace horiVertRatio in NH code).
4799 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
4800 and tutorial_plume_on_slope (sensitive to truncation)
4801 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
4802 directly to drive seaice model (C-grid only)
4803 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
4804 - reintroduce computation of wind from stress,
4805 - compute tau (in exf_bulkformulae.F) from windstress averaged to
4806 mass points to avoid tau = 0
4807 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
4808 o rdmnc.m: make it work with "global" files created with gluemnc
4809 o rdmnc.m : some improvements in dealing with singleton dimension
4810 (tested on all testreport mnc output files).
4811 o genmake2: disable pkg/profiles if netcdf test fails.
4812 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
4813 o move call to cal_readparms up to make calendar parameters/variable available
4814 to all packages
4815
4816 checkpoint58v_post (2007/02/08)
4817 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
4818 useDynP_inEos_Zc tested.
4819 o pkg/exf: changes to properly interpolate/mask/scale initial fields
4820 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
4821 and portions thereof. See read_cs.txt for description and examples.
4822 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
4823 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
4824 following the great-circle arc between those 2 points.
4825 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
4826 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
4827 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
4828 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
4829 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
4830 - still needs work (not working with some options ; efficiency to improve)
4831 and serious testing.
4832 - use this scheme for temperature & salinity in 2 advection test exp.:
4833 advect_xy & advect_xz, respectively.
4834
4835 checkpoint58u_post (2007/01/12)
4836 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
4837 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
4838 o testreport: add option "-skipdir" to skip some test.
4839 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
4840 momentum calculation.
4841 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
4842 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
4843 remove checkpoint.F and the_correction_step.F (no longer used);
4844 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
4845 o add option (linFSConserveTr) to correct for tracer source/sink due to
4846 Linear Free surface
4847 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
4848 o pkg/thsice: fix reading mnc-pickups
4849
4850 checkpoint58t_post (2006/12/30)
4851 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
4852 o pkg/mdsio:
4853 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
4854 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
4855 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
4856 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
4857 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
4858 either MDS_READ_FIELD or MDS_WRITE_FIELD )
4859 - new S/R (to replace MDSWRITEMETA), which allows to write more
4860 informations (variable names, time ...) to meta files.
4861 - modify rdmds.m to give back the meta file content.
4862 o pkg/diagnostics: change vertical interpolation to be safer, and more
4863 flexible (define p-levels to interpolate to in data.diagnostics);
4864 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
4865 diagnostic pointer.
4866 o pkg/seaice: more cleaning up of seaice_growth, added many comments
4867 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
4868 o fix multi-category seaice:
4869 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
4870 SEAICE_MULTICATEGORY
4871 - fix short wave heat flux
4872 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
4873 and allow to use EVP solver. Change forward lab_sea: test both EVP
4874 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
4875 o Initial check-in of lab_sea adjoint
4876 (very similar to natl_box_adjoint/code_seaice)
4877 * used C-grid and EVP solver
4878 * used KPP, GM/Redi
4879 * uses inAdExact=.TRUE.
4880 * gradient checks fail for both ADM and TLM
4881 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
4882 f.d. gradients actually seem more problematic than ADM, TLM gradients;
4883 issue is related to forward mismatch between g77 an ifort
4884 o pkg/seaice: overhaul of thermodynamics
4885 - growth.F and groatb.F are replaced by new routine seaice_growth.F
4886 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
4887 - move a few global fields out of SEAICE.h into seaice_growth.F and
4888 make them 2D (FICE/QNETO/ ...)
4889 - remove FO (it is the same as QNETO)
4890 - introduce a few local fields to avoid modifying external fields such
4891 as atemp, etc.
4892
4893 checkpoint58s_post (2006/12/11)
4894 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
4895 changed exf_set_gen.F so that
4896 genperiod=0 means input file is one time-constant field and
4897 genperiod=-12 means input file contains 12 monthly means
4898 o CG2D: use pre-computed solver main-diagonal (stored in common block);
4899 this affects truncation error ; generate new output file for exp. which
4900 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
4901 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
4902 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
4903 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
4904 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
4905 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
4906 o start implementation of deep-atmosphere and anelastic formulation
4907 o verification: remove 2nd copy of input files and use script "prepare_run"
4908 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
4909 o mom_common/vecinv/fluxform: fix a few initialisation isssues
4910 o profiles: fix for multithreaded case
4911
4912 o diagnostics: rename few diags:
4913 s/'PRESSURE'/'RCENTER '/g
4914 s/'TICE '/'oceFreez'/g
4915 s/'TAUX '/'oceTAUX '/g
4916 s/'TAUY '/'oceTAUY '/g
4917 s/'SWFLUX '/'oceQsw '/g
4918 s/DIFx/DFxE/g
4919 s/DIFy/DFyE/g
4920 and add few ocean-forcing diagnostics:
4921 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
4922 o modifications to pkg/seaice/growth.F and budget.F, which change results of
4923 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
4924 as actual snow thickness. It now refers everywhere to effective snow
4925 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
4926
4927 checkpoint58r_post (2006/11/17)
4928 o modifications to pkg/seaice/growth.F, which change results of
4929 lab_sea experiment: fixes pertain to melting snow over open water, to
4930 masking EVAP under sea ice, and to using the correct AREA variable for
4931 computations of EVAP, PRECIP, HSNOW, and GHEFF
4932 o add ability to read bathy, salt, and theta using MNC (off by def)
4933 o add flooding algorithm and advection of HSNOW for pkg/seaice;
4934 both are turned off by default and do no change any results
4935 o seaice advection with pkg/thsice: a step toward the use of non-linear
4936 advection scheme, but #ifdef or commented out for now (requires more EXCH).
4937 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
4938 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
4939 in natl_box (affects results @ truncation level: update output.txt)
4940 o multi-threading and IO:
4941 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
4942 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
4943 (needed to work with SingleCpuIO): tested in all verif. exp.
4944 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
4945 affects the results (but none of the verification test uses this scheme).
4946 o Adding some pkg/diagnostics capability to pkg/seaice
4947 (will certainly be subject to changes)
4948 o ctrl: adding new control variables:
4949 lwflux, lwdown, evap, snowprecip, apressure, runoff
4950
4951 checkpoint58q_post (2006/10/20)
4952 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
4953 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
4954 high_res_cube configuration by 4% on Columbia.
4955 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
4956 add (in global_with_exf/code) a version of EXF_INTERP_READ without
4957 dynamical allocation (seems to work in multi-threaded).
4958 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
4959 single CPU io) so that TAF does not have to see EESUPPORT.h
4960 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
4961
4962 checkpoint58p_post (2006/09/08)
4963 o obcs: stop if obcs is used with useCDscheme = .true.
4964 o shelfice:
4965 - fix a sign error so that no slip at shelfice interface works
4966 - remove stop for combination non-hydrostatic code and shelfice. That does
4967 not mean, that the results are correct, but at least they are numerically
4968 stable
4969 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
4970 o added adjoint exch routined for all exch*3d* routines
4971 and updated flow directives
4972
4973 checkpoint58o_post (2006/08/28)
4974 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
4975 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
4976 o change controling S/R for writing pickup file (new S/R do_write_pickup)
4977 and clean-up reading/writing of pickup files.
4978 o fix local version of read/write pickup (NH part) in rotating_tank/code
4979 o simplify EXCH interface:
4980 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
4981 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
4982 o added the regrid package
4983 o shelfice:
4984 - add a simple boundary layer scheme to reduce noise
4985 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
4986
4987 checkpoint58n_post (2006/08/14)
4988 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
4989 local variable (not in common block).
4990 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
4991 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
4992 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
4993 to work with SingleCpuIO.
4994 o add "_d 0" to real constant of pkg/cfc subroutines ;
4995 update exp. cfc_exemple & tutorial_cfc_offline output files.
4996 o multi-threading and IO:
4997 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
4998 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
4999 - barrier before and after reading.
5000 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
5001 - avoid using MDS_WRITELOCAL for LAND pkg output.
5002 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
5003 common-block variables ; Allows multi-threading with master-thread IO.
5004 o change default MAX_NO_THREADS from 32 to 4 ;
5005 and stop cleanly when MAX_NO_THREADS is too small.
5006 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
5007
5008 checkpoint58m_post (2006/07/17)
5009 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
5010 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
5011 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
5012 keep global_ocean.90x40x15 (for AD testing) with former secondary test
5013 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
5014 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
5015 add MITgcm_tutorials (= code + all the tutorials)
5016 o ecco, option to compute cost for total ssh (mean+anom)
5017 o consistent with addition of ptracer and ssh in pkg/profiles
5018 o profiles: adding ptracer and ssh
5019 o testreport: change multi-test output-file name
5020 (from output.txt.{name} to output.{name}.txt)
5021 o profiles: now ok for mutli-tiles case
5022 o seaice: add 4 parameters for different advection schemes for area,
5023 (effective) seaice thickness, enthalphy, and snow height. Their default
5024 is the standard parameter SEAICEadvScheme
5025 o calc_gw:
5026 - add cosFacU in zonal viscous flux (harmonic.visc.).
5027 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
5028 of tutorial_plume_on_slope.
5029 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
5030 o calc_gw: true flux-form, account for horizontal grid spacing.
5031 update rotating_tank results, but not plume_on_slope (affected at
5032 truncation level, 11 digits).
5033
5034 checkpoint58l_post (2006/07/12)
5035 o calc_gw:
5036 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
5037 - remove side-drag for now (need to fix it); update plume_on_slope results.
5038 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
5039 o commit code to make SST/SSS weights spatially variable
5040 (based on either variable in-situ or variable initial T/S weights)
5041 o pkg/ecco:
5042 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
5043 now based on horizontally varying weights wthetaLev, wsaltLev
5044 * cost_averagesflags now returns year indices in addition to day, month
5045 * sflux balance is performed on annual basis
5046 (sflxumm, sfluxmm2, bal_sfluxmm)
5047 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
5048 including separate counting and multipliers
5049 o pkg/rbcs
5050 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
5051
5052 checkpoint58k_post (2006/07/06)
5053 o testreport:
5054 - always build in dir. "build" (if not there, mkdir build instead of building
5055 & running in input)
5056 - run in dir run (if it exists), in build otherwise.
5057 - call prepare_run (if input/prepare_run exists)
5058 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
5059 o pkg/exf modifications to interpolation and rotation routines for more
5060 reasonable treatment of North Pole singularity: for tracers North Pole
5061 value is set to northernmost zonal-mean value, for zonal velocity it is
5062 set to zero, and for meridional velocity it is set to northernmost value.
5063 o pkg/exf/exf_check_range.F
5064 - add tile index to diagnostics and move stop statement to the very
5065 end of the routine.
5066 o pkg/diagnostics: (diagnostics_main_init.F)
5067 define title of isomorphic variables according to the current config.
5068 o pkg/thsice with pkg/seaice dynamics:
5069 - fix domain of computation (interior only, required for exf) and do exchanges
5070 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
5071 o towards a standard way of dealing with multi-threading in MONITOR
5072 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
5073 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
5074 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
5075 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
5076 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
5077 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
5078 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
5079 o tracer advection:
5080 - clean-up and simplify calc_common_factors.F
5081 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
5082 advection subroutine (but still not used within DST advection S/R)
5083 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
5084
5085 checkpoint58j_post (2006/06/15)
5086 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
5087 from file (collects calls previously in FORWARD_STEP)
5088 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
5089 o adjoint store dir. adjusted accordingly
5090 o genmake2
5091 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
5092
5093 checkpoint58i_post (2006/06/14)
5094 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
5095 on wind stress (SEAICEstressFactor defaults to 1.)
5096 o Total number of Timers is finite (<=40): comment out 2 non-essential one
5097 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
5098 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
5099 on CS-grid: no longer loosing mass.
5100 o exf & curvilinear-grid: no longer modify longitude xC & xG.
5101 o pkg/ggl90: fix sloppy output and fix a bug
5102 o pkg/seaice: added SEAICEuseEVPpickup parameter
5103 - Set to false in order to start EVP solver with
5104 non-EVP pickup files when using SEAICEuseEVP
5105 - fix sign error in diffusion in seaice_calc_rhs
5106
5107 checkpoint58h_post (2006/06/07)
5108 * Modifications for bottom topography control
5109 o replace hFacC by _hFacC at various places
5110 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
5111 o add non-self-adjoint cg2d_nsa
5112 o update autodiff support routines
5113 o re-initialise hfac after ctrl_depth_ini
5114 o works for 5x5 box, doesnt work for global_ocean.90x40x15
5115 * Adding verification for 5x5 box (4-layer) bottom topography control
5116
5117 checkpoint58g_post (2006/06/07)
5118 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
5119 used for mean seasonal cycle, mean diurnal cycle); add an example
5120 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
5121 o pkg/ggl90:
5122 - add parameter (minimum surface kinetic energy)
5123 - fix bug (avoiding division by zero)
5124 o couple pkg/thsice to pkg/seaice:
5125 - modify advection in seaice to accomodate new scalar fields to be advected
5126 - only muliDimAdection scheme work with seaice/thsice
5127 - mapping of thsice-variables to seaice-variables, back and forth
5128 - does not break the verification experiments, but does not give the
5129 desired results either
5130 o pkg/seaice
5131 - make (default) second order advection a bit less confusing?
5132
5133 checkpoint58f_post (2006/06/05)
5134 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
5135 to pkg/seaice):
5136 - new routines thsice_map_exf and thsice_get_exf provide the interface
5137 - add an additional formal parameter to thsice_solve4temp
5138 o pkg/exf:
5139 - add new fields wspeed, snowprecip (to be able to couple to thsice)
5140 - correct Stefan-Boltzmann constant
5141 - new parameter for longwave surface emittance
5142 - separate some stuff from exf_bulkformulae into new routines
5143 exf_radiation, exf_wind
5144 - add new parameters and constants: longwave emissivity for ocean, ice
5145 and snow, evaporation parameters over ice
5146 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
5147 either wind from stress or stress from wind
5148 o pkg/thSIce:
5149 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
5150 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
5151 and THSICE_CALC_THICKN
5152 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
5153 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
5154 to make debugging easier.
5155 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
5156 o pkg/bulk_force:
5157 - clean-up comments and parameters ;
5158 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
5159 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
5160 generate new output for test-experiment: aim.5l_cs.thSI
5161 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
5162 testreport accordingly
5163
5164 checkpoint58e_post (2006/05/17)
5165 o SEAICE_CGRID adjoint done
5166 o R_STAR adjoint implemented.
5167 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
5168 * need to sort out init. of h0facc, etc.
5169 o Make pkg/profile fully independent of ecco,cost, etc. stuff
5170 to be able to use it in pure forward.
5171
5172 checkpoint58d_post (2006/04/21)
5173 o upgrade simple test-experiment to tutorial example:
5174 step.1: duplicate the experiment and (step.2) will remove the old copy.
5175 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
5176 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
5177 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
5178 tutorial_global_oce_biogeo <- copy of dic_example
5179 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
5180 tutorial_plume_on_slope <- copy of plume_on_slope
5181 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
5182 tutorial_global_oce_optim <- empty for now (David ?)
5183 tutorial_global_oce_in_p <- copy of global_ocean_pressure
5184 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
5185 o correct a sign problem in cost_scat.F
5186 o obcs and ptracers: fix boundary conditions for advections schemes
5187 with larger stencil
5188 o thsice adjoint: start
5189 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
5190 completeness
5191 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
5192 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
5193 o ptracers adjoint:
5194 * avoid extensive recomputatations
5195 * fix missing re-init. of gptr (missed by TAF)
5196 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
5197 me to turn off the excessive output to STDOUT that this package produces
5198 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
5199 and add those terms in Vector-Invariant formulation.
5200 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
5201 if the control period (xx_hfluxperiod etc) is 0
5202 o in profiles pkg, clean routines and fix details
5203 o in ecco pkg, reading ssh data:
5204 fix problem in case the model does not start at iter0=0
5205 o fix mnc-pickup/restart for ptracers
5206 o new package prifiles:
5207 code to compute profile-based cost by Gael Forget
5208 (modifs in ecco, ctrl, autodiff)
5209 o Benign bug fix in initialization (spotted by M. Mazloff) of
5210 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
5211
5212 checkpoint58c_post (2006/03/23)
5213 o adjoint: finish NLFS adjoint and provide reference output in
5214 verification/global_ocean.90x40x15/results_ad_nlfs
5215 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
5216 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
5217 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
5218 with SEAICE_CGRID defined.
5219 o move calendarDumps from "data" to "data.cal" and clean-up the code
5220 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
5221 o add useEXF & useCAL flags (for now, set in hard-coded way)
5222 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
5223 (were missing in NH mode, and wrong in quasihydrostatic mode).
5224 waiting for Chris updated version of calc_gw to add those CALLs.
5225 o fix bug in quasihydrostatic S/R ;
5226 add a test for this option: global_ocean.90x40x15.qshyd
5227 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
5228 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
5229 o add on/off flag useOffLine for package OFFLINE
5230 o seaice:
5231 - modify advection so that it works also on the C-grid
5232 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
5233 problem in multi-tile runs with C-grid
5234 - add flags for clipping ice velocities and/or masking solver forcing
5235 - fix drag (ocean on ice) formulation and a bug that caused noise in the
5236 C-grid solver
5237 - added a few comments to seaice_diffusion.F
5238 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
5239 are now exclusive)
5240 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
5241 required re-ordering the code a little:
5242 + make DAIRN global variable (defined in SEAICE)
5243 + move computation of the viscosities eta and zeta into a new separate
5244 routine (because I need to recompute them in seaice_ocean_stress.F)
5245
5246 checkpoint58b_post (2006/03/13)
5247 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
5248 update output.txt of exp. aim.5l_cs.thSI
5249 o various mnc cleanups and improvements:
5250 + shrink lookup tables by factor of ~4
5251 + better error reporting when running out of lookup space
5252 + able to handle longer path/file names (up to 500 chars)
5253 o adjoint:
5254 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
5255 - TBD: "hidden" mom_vecinv recomp. in dynamics
5256 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
5257 (allow to differentiate between forcing components using new integer flags:
5258 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
5259 and add new flag to put Dissipation tendency out of Adams-Bashforth.
5260 o ecco
5261 - enable trend removal from SSH anomaly obs.
5262 o adjoint
5263 - a fix for PmEpR when #undef EXACT_CONSERV
5264 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
5265 - try to fix "hidden" recomp. in forward_step for NLFS
5266 (NLFS seems broken sometimes after I checked it in)
5267 o seaice:
5268 - add c-grid version of the dynamic solver:
5269 + three new routines that are the c-grid substitute lsr, dynsolver
5270 and ostres
5271 + put a few fields that were local to dynsolver into global common
5272 blocks, so that I can move the computation of stresses etc into
5273 seaice_lsr (saves coding but may break the adjoint).
5274 - replace more hardwired parameters by runtime parameters
5275 - add ice masks that mask the rhs of the implicit solvers where there
5276 is no ice (commented out in seaice_dynsolver, because i am not sure
5277 if this works properly), eventually this should replace the clipping
5278 of ice velocities in seaice_dynsolver to +/-40cm/s.
5279 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
5280 include it only where its needed
5281 o move balancing of fluxes before the call of external_forcing_surf
5282 o seaice:
5283 - correct units of turning angles (now they are really in degrees)
5284 - move computation of GWATX/Y out of main routine into dynsolver
5285 - initialize GWATX/Y in seaice_init
5286 o Apply mask on Fresh-Water flux (needed for SSH forcing).
5287 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
5288 o seaice: add runtime flags for turning angles (default to zero)
5289 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
5290 and trend from exf forcing and ctrl control adjustments
5291 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
5292 (since checkpoint57x_post)
5293 o change the default rotation period to 86164.s = the Earth rotation
5294 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
5295 and based on a reference stratification. Tested within hs94.cs-32x32x5.
5296 o seaice advection: add code for choosing between the default (2nd order
5297 central differences) and multiDim advection schemes provided by
5298 pkg/generic_advdiff
5299 o seaice:
5300 - removed all references to SEAICE_GRID.h fields from
5301 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
5302 (cubed-sphere configuration will change a little)
5303 - grid computations in seaice_init are obsolete now.
5304 - cleaned up code a little so that is easier to read (hopefully).
5305 - added new (better?) discretizations of default advection and diffusion
5306 (turn on with SEAICEuseFluxForm)
5307 - replace 1 in 3d global fields by kSurface in growth.F
5308
5309 checkpoint58a_post (2006/02/13)
5310 o seaice:
5311 - bug fix in advect.F
5312 o shelfice:
5313 - separate shelfice load anomaly from pload (breaks with time
5314 dependent forcing), => introduce constant field shelficeLoadAnomaly.
5315 Its default is 0., but it may be computed more cleverly from (unknown)
5316 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
5317 done offline. A good approximation of the pressure load anomaly is
5318 necessary to avoid large initial adjustment processes underneath
5319 deep-reaching shelfice.
5320 - small fix in ISOMIP shelfice_thermodynamics
5321 - add more sophisticated thermodynamics of Hellmer (1989), this is
5322 now the default
5323 - give a few constants more intuitive names
5324 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
5325 if bulk formulae are used in long integration (especially EmPmR). Turn
5326 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
5327 if balancePrintMean, the imbalance that is substracted is printed to
5328 STDOUT.
5329 o fix bug (typo) in obcs_apply_eta.F
5330 o add a new package shelfice which enables us to model the circulation
5331 underneath shelf-ice with draughts of hundreds of meters.
5332 - works
5333 - to do: + include improved thermodynamics
5334 + check whether kSurfC (from model/inc/SURFACE.h) can be used
5335 instead of new field kTopC
5336 + can we use topoFile, Ro_surf and existing code in ini_depth.F
5337 instead of new field R_shelfIce and new code in ini_depth.F
5338 and ini_mask_etc.F?
5339 + adjust vertical mixing schemes?
5340 o seaice pkg:
5341 - add a cpp-flag to include a simple formula for a salinity dependent
5342 freezing point of sea water at the surface
5343 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
5344 meridional stresses are now different (and hopefully correct)
5345 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
5346 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
5347 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
5348 o pkg/diagnostics: add options and parameters for regional-statistics
5349 diagnostics ; define regions by reading a region-mask from a file
5350 (might add other options later)
5351 o pkg/bulk_force:
5352 - add option and parameters to use AIM surface-flux formulae.
5353 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
5354 others forcing fields (defined in PARM05, parameter file "data") are loaded
5355 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
5356 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
5357 - use the right EXCH call for uwind,vwind (to work on CS-grid).
5358 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
5359 and parameters (note: calcWindStress replaces .NOT.readwindstress).
5360 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
5361
5362 checkpoint58 (2006/01/12)
5363 o add "--embed-source" option to genmake2 which, when the supporting
5364 tools can be compiled (as determined by genmake2) will turn on the
5365 embed_files package which then embeds the entire MITgcm source code
5366 (*.[fFhc] + Makefile) used for the build within the executable
5367 - requested by CNH but off by default
5368 - adds a paltry <9MB to the mitgcmuv executable in most cases
5369 - only writes the output when useEMBEDSRC in eedata is true
5370 o clean up 3-dim. relaxation codes:
5371 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
5372 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
5373 * Thanks to Tom Haine for testing!
5374
5375 checkpoint57z_post (2005/12/31)
5376 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
5377 affects output (@ truncation level) of exp. plume_on_slope ; updated.
5378 o fix the pickup behavior for obcs in combination with ptracers
5379 o fix a bug in ptracers_external_fields_load
5380 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
5381 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
5382 o transfered surface NH pressure to eta field (if exactConserv).
5383 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
5384 and update lab_sea output.txt file.
5385 o completing 3-dim. relaxation code: additional term
5386 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
5387 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
5388 * At compile time, in "EXF_OPTIONS.h" set
5389 #define ALLOW_CLIMTEMP_RELAXATION
5390 #define ALLOW_CLIMSALT_RELAXATION
5391 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
5392 tauThetaClimRelax3Dim = 15552000.0,
5393 tauSaltClimRelax3Dim = 15552000.0,
5394 * 3 cases:
5395 1) Use a constant-in-time 3-dim. field
5396 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
5397 3) Real-time relax. to time-evolving prescribed field
5398 o Adding Laplacian-type smoothness constraint on
5399 initial and boundary (forcing) controls (ic, bc)
5400 * enable at compile-time via
5401 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
5402 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
5403 * Absolute scale somewhat unclear so far
5404 * no area weighting was included since no other cost term does so far
5405
5406 checkpoint57y_post (2005/12/08)
5407 First step for a NLFS adjoint
5408 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
5409 o new init. routines for calc_r_star, calc_surf_dr
5410 o still need to deal with ini_masks_etc
5411 o testreport seemed happy
5412 checkpoint57y_pre (2005/12/08)
5413
5414 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
5415 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
5416 o add new offset feature to offline pkg (plus minor cleanup)
5417 o cfc fixes for final year of integration
5418 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
5419 be in GCHEM_OPTIONS).
5420
5421 checkpoint57x_post (2005/12/04)
5422 o fix testreport Pb in multiple test experiment.
5423 o cleanup our namelist syntax in verification:
5424 - make it more F95 standards compliant (some work still needed)
5425 - allows the vast majority of our tests to work with gfortran
5426 o Non-Hydrostatic:
5427 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
5428 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
5429 o Allow to apply AB on T,S rather than on AB(gT,gS):
5430 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
5431 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
5432 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
5433 - need a "clever" read_pickup to restart from the other AB formulation
5434 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
5435 o remove some unused variables (reduces number of compiler warnings)
5436 o adjoint
5437 * Disable useVariableViscosity for adjoint for time being
5438 (there are a number of extensive recomputations)
5439 * Initialize certain variables needed for adjoint
5440
5441 checkpoint57w_post (2005/11/03)
5442 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
5443 fix the singleCpuIO RS version of MDSWRITEFIELD
5444 and add a WARNING if using globalFiles=T with multi-processors.
5445 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
5446 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
5447 o tracer advection scheme:
5448 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
5449 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
5450 was not very convenient).
5451 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
5452 (further tests needed for the implicit DST & Flux-Limiter schemes).
5453 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
5454 and sRef for convenience, handy, when you want to initialize
5455 ptracers in a large domain with a constant non-zero value. Also,
5456 untangle ptracers_init.F a little.
5457
5458 checkpoint57v_post (2005/10/13)
5459 o change dome exp. to use variable viscosity in side-drag terms.
5460 o remove all the files from the cfc_offline test since they are now
5461 incorporated into tutorial_cfc_offline which has been producing
5462 identical results for a few days of testing
5463 o add new parameter: sideDragFactor to enable half-slip-side BC
5464 and change side-drag S/R to use viscosity from mom_calc_visc
5465 (can switch back by setting sideDragFactor=0.); affects results at
5466 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
5467 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
5468 o vorticity & strain are now computed without masking, to account for
5469 no-slip-side BC in variable viscosity calculation ; mask is applied
5470 anyway later on, before computing advection/coriolis terms.
5471 o modify exp4 to test new obcs support for reading from external files
5472 and for passive tracers
5473 o fix behavior of ptracers_monitor when monitor output is written to a
5474 netcdf-file; still not independent of monitor.F (writes in the same
5475 file).
5476 o change default value of tRef (put a uniform, meaningful value for ocean
5477 & atmos) and initialize sRef (was missing, as Martin mentioned).
5478 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
5479 to be proportional to enstrophy dissipation length. Thus,
5480 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
5481 This is now consistent with Smagorinsky and with the manual.
5482
5483 checkpoint57u_post
5484 o OBCS and PTRACERS: add open boundary support for passive tracers
5485 - either use homogenous (pseudo) v.Neumann conditions or prescribe
5486 OB-values from file; this is not different from the way theta and salinity
5487 are treated
5488 - however, Orlanski-radiation conditions are not supported, and the model
5489 will stop if you use pTracers and Orlanski at the same time.
5490 - beefed up the rountine obcs_external_fields_load: now only those open
5491 boundary values are overwritten with values from files for which there
5492 are really files, otherwise the OB-fields remain untouched. This makes
5493 it possible to use different OBs at different ends of the domain (as
5494 with EXF)
5495 o reduce number of exch calls in shap_filt (s2).
5496 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
5497 truncation level) 4/5 MLAdjust test results (11&12 digits match).
5498
5499 checkpoint57t_post (2005/10/03)
5500 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
5501 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
5502 same truncation, independent of the face number: affects affects several
5503 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
5504 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
5505 note that biharmonic viscosity + no-slip was not tested in any experiment.
5506 o fix bug in non-linear free-surf side-drag ; generate new output for
5507 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
5508 o make mnc honor the writeBinaryPrec flag for most kinds of output
5509 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
5510 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
5511 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
5512 o add brackets in multi-terms sum to get same truncation, independent of
5513 the face number (manage to get exactly same value of gU,gV at the cs-edge)
5514 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
5515 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
5516 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
5517 a maximum grid-scale Reynolds number. Also, changes all length calculations
5518 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
5519 Suggested values of viscosity parameters found in mom_calc_visc.
5520 Many new viscosity diagnostics available.
5521
5522 checkpoint57s_post (2005/09/20)
5523 o Add clearing-house for viscosity calculations, mom_calc_visc and
5524 correct numerous bugs in LeithD and Smagorinsky discretizations.
5525 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
5526 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
5527 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
5528 and with Strain-Tension viscous term calculation (mom_hdissip.F).
5529 The Strain-Tension form is now called with useStrainTensonVisc=.true.
5530 ViscAhStrain and viscAhTension are now retired.
5531 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
5532 o In response to JMC's bug report, genmake2 now ignores any soft-links
5533 that it finds in the *current* directory when searching for files.
5534 Soft-links found in any other source directories will still work as
5535 they did before.
5536 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
5537 a C routine to unlimit the stack size
5538 o mnc-ify pkg/aim snapshot vars
5539 o mnc-ify pkg/land as requested by Daniel
5540 o various changes to mnc including:
5541 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
5542 - output can now be grouped so that all files within a group
5543 change the ITER portion of their names in lock-step together
5544 - can now read ("global") PER-FACE (in addition to PER-TILE) files
5545 and works with both EXCH1 and EXCH2 (but needs more testing)
5546 - writing works for all verification test cases w/ g77 on Linux
5547
5548 checkpoint57r_post (2005/09/07)
5549 o make MNC variable initialization happen earlier
5550 o add diagnostics for (almost) each term of the momentum Eq.
5551 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
5552 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
5553 o remove MINIMAL_TAVE_OUTPUT option ;
5554 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
5555 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
5556 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5557 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
5558 o add time-dependent SST, SSS control
5559 o cost terms in ecco/ modularized (new cost_generic.F)
5560 o cost_averages routines are modularized (new cost_averagesgeneric.F)
5561 o new infrastructure for seaice model vs. obs misfits in seaice/
5562 * driver from the_main_loop.F is seaice_cost_driver.F
5563 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
5564 * gradient check in Exp. 6a of natl_box_adjoint/
5565 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
5566 (see README file)
5567
5568 checkpoint57q_post (2005/08/19)
5569 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
5570 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
5571 - bug was reported by Jean-Michel and Ian Fenty
5572 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
5573 update exp. cpl_aim+ocn output.
5574 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
5575 Needed for high-res. runs with large global files
5576 to be able to limit tapelev size
5577 o Changed some tests for adjoint:
5578 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
5579 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
5580 * global_ocean.90x40x15/ back to default 3-level checkpointing
5581 o Modifications to enable scripted COMMON to MODULE conversion
5582 * verification/OpenAD/code/ has necessary scripts and description;
5583 * converts, compiles and runs successfully;
5584
5585 checkpoint57p_post (2005/08/01)
5586 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
5587 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
5588 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
5589 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
5590 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
5591 (was already the case for dissipation with mom_vecinv,
5592 and also the case for grad.PhiHyd when staggered-timeStep)
5593 This will allow to put dissipation out-off the AB time-stepping.
5594 Unfortunately, affects truncation error. Update output of exp. that "fails"
5595 (cg2d matching number) and leave the others for later: front_relax(10),
5596 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
5597 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
5598
5599 checkpoint57o_post (2005/07/30)
5600 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
5601 (2) its ready to be documented during the 20050801 DocFest
5602 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
5603 for ideal_2D_oce and lab_sea on linux_ia32_g77
5604 o set to #undef CTRL_SET_OLD_MAXCVARS_30
5605 in global1x1_tot/code_seaice_adj to access indices 32, 33
5606 (worth another tag)
5607
5608 checkpoint57n_post (2005/07/29)
5609 o adding precip control xx_precip 32
5610 o adding swflux control xx_swflux 33
5611 o Replacing 10 forcing penalty cost routines by 1 generic.
5612 o Implementing partitioning in time-mean and variable adjustment
5613 for atmos. state.
5614 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
5615 o in natl_box_adjoint:
5616 * updated exp 1 to 10
5617 (but does not have time-mean vs. variable split results yet)
5618 o updated global1x1/*_seaice_adj/
5619 to incorporate latest changes
5620 o enable useSingleCpuIO for mdsio vector routines
5621 (applies in particular to tapelev I/O)
5622 o removed inefficient K-loop in all active_file*control*.F
5623
5624 checkpoint57m_post (2005/07/28)
5625 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
5626 and advect_cs (use EXCH-2 and standard cs-32 grid files).
5627 o pkg/exch2: filling of face-corner halo regions is optional
5628 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
5629
5630 checkpoint57l_post (2005/07/14)
5631 tag before updating tutorials (pre-release-2)
5632 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
5633 for output and interpolation of input fields onto model grid)
5634 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
5635 Affects results of exp. rotating_tank ; update output.txt.
5636 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
5637 and taking the square quantity and/or using a fraction-weight field.
5638 o fix aim_diagnostics_init.F mate numbers.
5639 o add mnc output capability to diagnostics/diagstat and update
5640 our cvsignore files for the ACSII output generated
5641
5642 checkpoint57k_post (2005/07/02)
5643 o lab_sea now uses diagnostics package and provides a suite of
5644 new EXF diagnostics output.
5645
5646 checkpoint57j_post (2005/06/30)
5647 o exf
5648 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
5649 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
5650 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
5651 * extended diagnostics output
5652 - now includes all EXF variables
5653 - hs, hl moved to common block
5654 - separate S/R for diagnostics, called after ctrl vector is added
5655 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
5656 - EXFqnet contains true Qnet (i.e. includes qsw)
5657 * updated verif. lab_sea, global_with_exf
5658 * Rearranging hflux (exf_mapfields -> exf_getforcing)
5659 to ensure that diagnostics sees a true EXFqnet
5660 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
5661 o diagnostics pkg: change pointers so that 1 diagnostic can be used
5662 several times with different frequencies.
5663 o mnc-ify the thsice package as requested by Daniel Enderton
5664 - the monitor--MNC output needs work
5665 - many attributes need to be added (most are currently blank)
5666 o mnc-ify theaim_v23 package as requested by Daniel Enderton
5667 - many attributes need to be added (most are currently blank)
5668 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
5669 o add Sadourny like discretization to the 4th.O vorticity advection scheme
5670 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
5671 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
5672 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
5673 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
5674 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
5675
5676 checkpoint57i_post (2005/06/19)
5677 o Diagnostics package was changed: diagnostic allocation is now deactivated
5678 by setting an empty file name in the namelist (used to be by setting 0 frequency)
5679 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
5680 add 1rst Order upwind vertical Shear.
5681 o add a quick fix for A/B checkpointing in OFFLINE mode
5682 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
5683 end-run around the C/Fortran linking horror in eesup/src/timers.F
5684 o added pkg/runclock: allows user to terminate run based on wall clock
5685 o added non-hydrostatic scaling parameter: nh_am2
5686 o pkg/my82: futile attempt to make results compiler-independent by adding
5687 some "_d 0", etc. no effect.
5688 o for mnc output, fill the 'T' coordinate var with myTime and create a
5689 separate 'iter' variable for iteration count
5690 o pkg/diagnostics:
5691 add new capability: output of Global/Regional & per-level statistics ;
5692 tested against monitor output (including land & thSIce) on various exp.
5693 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
5694
5695 checkpoint57h_done (2005/05/19)
5696 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
5697 data.diagnostics, data.gchem, data.ptracers) is done.
5698
5699 o pkg/diagnostics: prepare for Global/Regional statistics.
5700 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
5701 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
5702 and rename it: DIFFERENT_MULTIPLE
5703
5704 checkpoint57h_post (2005/05/14)
5705 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
5706 o pkg/diagnostics: change output frequency, now in seconds (instead
5707 of Nb of iterations). This requires to change data.diagnostics.
5708 checkpoint57h_pre (2005/05/12)
5709
5710 o in mnc, let the user create the output dir if both mnc_outdir_date
5711 and mnc_outdir_num are false
5712 o add fflags() to pkg/diagnostics which allows one to specify, on a
5713 per-file basis, the file precision [default behavior is unchanged]
5714 o added diagnostics to pkg/kpp, including computation of mixed layer
5715 depth based on a temperature/density criterion
5716 o updated verification/natl_box to test the new pkg/kpp diagnostics
5717 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
5718 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
5719 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
5720 not mnc -- this mistake was found by JMC and is now corrected
5721
5722 checkpoint57g_post (2005/04/15)
5723 o add Adams-Bashforth 3rd Order time stepping:
5724 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
5725 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
5726 checkpoint57g_pre (2005/04/15)
5727
5728 o make lambda[Theta,Salt]ClimRelax spatially varying
5729 (default remains spatially uniform constant based on tau)
5730 o added new control variables
5731 * init. uVel, vVel, etanN
5732 * lambda[Theta,Salt]ClimRelax
5733 o separate masks used for ctrl_pack/unpack 'from write_grid' output
5734 (suggested by G. Forget)
5735
5736 checkpoint57f_post (2005/04/06)
5737 o add parameter "baseTime" = model base time = time at iteration zero
5738 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
5739 account for baseTime shift
5740 o move Coriolis arrays from PARAMS.h to GRID.h
5741 checkpoint57f_pre (2005/04/06)
5742
5743 o mnc-ifying the seaice package
5744 o introduced an alternative length scale calculation for use in the limiting
5745 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
5746 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
5747 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
5748 as well as grad(vort3). Made it compatible with both approximate form
5749 for the cubed sphere and full form of these gradients. Added flag
5750 useFullLeith to select between approximate and full form.
5751 o add "d0" in getcon.F to reduce differences between compilers/platforms
5752 update output.txt of exp. fizhi-gridalt-hs
5753 o change port_rand funtion to allow to set the seed.
5754 o fix obscure MNC bug involving conversion between reals and integers
5755 - it caused no problems with certain (eg. gcc, ifc) compilers but the
5756 new version is now more standards-compliant
5757 o adjoint-related modifications
5758 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
5759 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
5760 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
5761
5762 checkpoint57e_post (2005/02/28)
5763 o Adding eddy stress controls a la Ferreira et al.
5764 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
5765
5766 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
5767 update output.txt of exp. fizhi-gridalt-hs
5768 o add more "Z" dimensions and associated coordinate vars to MNC
5769 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
5770 o parameter calendarDumps: when set, approximate months (30-31 days) and years
5771 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
5772 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
5773 months and years. Requires pkg/cal.
5774 o diagnostics: add pickup functionality
5775 - off by default for backwards compatibility
5776 - current version only uses MDSIO -- MNC will be added
5777 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
5778 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
5779
5780 checkpoint57d_post (2005/02/11)
5781 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
5782 o modify verification/ideal_2D_oce so that it tests the creation of mnc
5783 output from the diagnostics package
5784 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
5785 o make genmake2 more portable by using ".$FS" instead of ".f" for more
5786 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
5787 o add coordinate variables to the MNC output from the diagnostics package
5788 o change MNC-flags default value: true when useMNC=TRUE
5789 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
5790 the ability (off by default) to read the grid information using MNC
5791 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
5792 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
5793 o do snap-shot diagnostics at the middle of the time-interval (instead of
5794 at the end).
5795 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
5796 new test for AIM with thSIce + slab-ocean
5797 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
5798 o move state variable diagnostics to the beginning of the time step ;
5799 (note: still needs some work specially for snap-shot diagnostics)
5800 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
5801
5802 checkpoint57c_post (2005/01/27)
5803 o Change testing option (-ieee) to get closer agreement between g77 & ifort
5804 o generate new output.txt files on faulks with g77 & the new -ieee option
5805 checkpoint57c_pre (2005/01/27)
5806
5807 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
5808 update output.txt of exp. global_ocean.90x40x15
5809 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
5810 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
5811 o add saltFlux(+File) forcing capability with periodicExternalForcing
5812 o allow to use pkg diagnostics for GM-Redi & ThSIce output
5813 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
5814 o improvements for the MNC output from DIAGNOSTICS:
5815 - correct handling of the unlimitied dimension
5816 - all dims now have associated coordinate variables
5817 - variables located at U, V, and Corner ("Z") points are now written
5818 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
5819 *all* data points are output
5820 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
5821 o added pkg/seaice/seaice_monitor.F
5822 o mdsio_readfield.F can now read files visible only to master MPI process.
5823 o pkg/seaice: some test code for ice-modified ocean stress
5824 o exf_getffields interpolation defaults to bilinear for all scalar forcing
5825 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
5826 spurious negative numbers for precipitation and humidity. Will cause
5827 some small numerical differences for integrations using pkg/exf/exf_interp.F.
5828 o pkg/ctrl/
5829 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
5830 May be enabled via doPackDiag
5831 * introduce z-scaling of
5832 + gradient (doZscalePack) and
5833 + control (doZscaleUnpack)
5834 o pkg/mdsio/
5835 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
5836 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
5837
5838 checkpoint57b_post (2004/12/20)
5839 o simplify options in diagnostics_fill arguments (remove weird combinations)
5840 o fix MNC coordinate variables so that they now contain per-face index
5841 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
5842 general, EXCH2 grids are only aligned to a "local" coordinate system
5843 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
5844 o Implement instantaneous output within pkg diagnostics:
5845 setting a negative frequency in data.diagnostics produces
5846 "snap-shot" output (as opposed to time-average if freq > 0)
5847 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
5848 NOTE: change ptracer diagnostics name: use 2 characters to work with
5849 more than 9 tracers. Add also diagnostics of advect & diffus flux.
5850 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
5851 becomes the coordinate variable for the 'T' dimension
5852 o add CF-style coordinate variables to MNC
5853 - just a first cut: numbers are meaningless on the cubesphere and
5854 missing along the T axis but otherwise it works!
5855 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
5856 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
5857 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
5858 this is based directly on what the model compute, so that the content of
5859 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
5860 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
5861 o clean up build options files for SunOS, in particular
5862 - remove -traditional from xmakedepend
5863 - change -xarch=v9 to -xarch=native for f77
5864 - restore use of make (not gmake)
5865 - add CC=gcc if using g77
5866 o changes per discussion of AM, JMC, & EH3 today:
5867 - move redundant "grid" variables out of "state" -- in preparation of
5868 creating proper CF-style coordinate variables and in recognition
5869 that any/all grid variables can be easily copied (eg. w/NCO) from
5870 the grid files into any of the other NetCDF files
5871 - *always* output grid variables with MDSIO (this will eventually be
5872 changed)
5873 - output MNC grid file if useMNC is true
5874 o every instance of _END_MASTER() has been found and replaced with
5875 _END_MASTER( myThid ) in order to satisfy certain picky Sun
5876 preprocessors
5877 o re-arrange diagnostics pkg initialisation:
5878 - allow each package to extend the available diagnostics list
5879 - add some checking and fix small problems (multi-threaded, ...)
5880 - new S/R diagnostics_fill (replace fill_diagnostics):
5881 look through the short list of active diag. (instead of the long list)
5882 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
5883
5884 checkpoint57a_post (2004/12/10)
5885 o this set of changes restores TAMC compatibility
5886 tested for global_ocean.90x40x15 adjoint on trough
5887 (what a pain)
5888
5889 checkpoint57a_pre (2004/12/10)
5890 o some modifs in tools/build_options for sunos
5891 o call ctrl_pack for ctrl at end for optimcycle=0
5892
5893 checkpoint57 (2004/12/09)
5894 o add horizontal bi-harmonic viscosity for vertical velocity
5895 - new parameter viscA4W (defaults to viscA4)
5896 - affects only non-hydrostatic code
5897 - to be done: no-slip lateral boundary conditions
5898 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
5899 o implement Implicit Vertical advection for pTracers
5900 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
5901 (implemented also for implicit vertical diffusion & advection)
5902 o OBCS: extend application of tracer open boundary conditions
5903 to a strip beyond the boundary of width Olx/Oly
5904 o add call monitor to TAF set of required calls (flow directives)
5905 and include in natl_box_adjoint
5906 o untangle a few ifdefs related to cost, ctrl, autodiff
5907 untangel a few ALLOW_ECCO_OPTIMIZATION
5908 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
5909 (theta2, salt2 in ecco_cost_weights)
5910
5911 checkpoint56c_post (2004/12/03)
5912 o OBCS as control variables
5913 - update ctrl_ad_diff.list, obcs_ad_diff.list
5914 - remove balance of obcs controls from default
5915 - fix index bug nobcs in ctrl_init
5916 - fix dummy fields filen in ctrl_pack
5917 - add dummy weights for obcs
5918 o lsopt: comment out fort.94 output
5919 o optim:
5920 - remove unnecessary header files
5921 - adjusted namelists
5922 - add xerbla.F to Makefile
5923 o exf:
5924 - multiple modifications of exf_check_range
5925 - unit change in exf_init_runoff from [m/year] to [m/s]
5926 o mdsio:
5927 - i/o-vector change debugLevel from debLevA to debLevB
5928
5929 checkpoint56b_post (2004/12/01)
5930 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
5931 is called from DO_THE_MODEL_IO
5932 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
5933 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
5934 - clean up PTRACERS_WRITE_TIMEAVE a little
5935 o add another verification experiment that tests both the cfc-pkg and
5936 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
5937 reactive tendencies treated inline with regular timestepping
5938 o testreport previously did a lousy job of comparing small numbers, so
5939 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
5940 implemented in the little c-progam tmp_cmpnum.c which is embedded in
5941 testreport.
5942 o ptracers_monitor: bug fix for MPI
5943
5944 checkpoint56a_post (2004/11/28)
5945 o GCHEM: finish reorganizating the package
5946 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
5947 (introduces another 3D-array for each passive tracer, but only if
5948 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
5949 gchemTendency is not needed because the timestep is done separately)
5950 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
5951 - GCHEM is now---more or less cleanly---separate from PTRACERS
5952 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
5953 so clear to me how that should be done in a general way.
5954 o CFC: improve formatting of output in CFC_ATMOS
5955 o PTRACERS:
5956 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
5957 that ALL experiments with ptracers enable can be checked. This makes
5958 GCHEM_MONITOR obsolete.
5959 - include a runtime parameter PTRACERS_monitorFreq that defaults to
5960 monitorFreq
5961 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
5962 o add PTRACERS (PTR0[1-5]) to testreport output
5963 o exf_check_range:
5964 * default changed to .TRUE.
5965 * will check values for niter0 if debLevA, every timestep if debLevB
5966 * STOP in exf_check_range if 'out of range'
5967 * range chosen generous to allow for potential extema
5968 TBD: a version with stricter range
5969 permitted range would be runtime parameters
5970 o GMredi:
5971 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
5972 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
5973 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
5974 o GCHEM:
5975 - move call to GCHEM_FORCING_SEP, so that it is now called before
5976 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
5977 - introduced a useGCHEM runtime flag and applied it everywhere.
5978 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
5979 this flag is now only visible within GCHEM-pkg routines.
5980 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
5981 be replaced by a 3D array that is computed before thermodynamics; for
5982 this, the tracer ID iTracer had to be included into the parameter list
5983 of ptracers_forcing
5984 - set up forward_step to call gchem_forcing, that will replace
5985 gchem_forcing_int in ptracers_forcing
5986 - cleaning up
5987 o small cleaning of exch2: remove files that are also in eesupp/src
5988
5989 checkpoint56 (2004/11/17)
5990 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
5991 o mnc: cleanup "full" files--fixes out-of-memory problem
5992 o ECCO-GODAE
5993 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
5994 * fully merged and updated from SIO code
5995 windstress sign change affects
5996 - exf_inscal_[u/v]stress
5997 - sign of xx_tau[u/v] adjustments
5998 - signs in cost_scat
5999 * ctrl_get_gen: avoid update of tau[u/v] for first few days
6000 * natl_box_adjoint updated and compressed
6001 * 2-level checkpoint switch added
6002 (tested in EXP. 1 of natl_box_adjoint)
6003 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
6004 o SVD
6005 * first complete, non-hacked version for SVD calculations
6006 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
6007 performed via direct access files admtlm_vector.it????
6008 (via ctrl_[un]pack)
6009 * optimcycle is used for ARPACK iteration counter
6010 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
6011 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
6012 and add linear transforms where necessary
6013 * controls are initial/final SST, SSS (can be extended; need to check
6014 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
6015 o mdsio: filename info to both stderr, stdout
6016 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
6017 from sign change
6018
6019 checkpoint55j_post (2004/11/10)
6020 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
6021 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6022 o add consistent build directories and .cvsignore files to verification
6023 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
6024 o make all subroutines 30 or less characters in length for certain older
6025 compilers to work (a thorough search only turns up two routines in
6026 pkg/ptracers)
6027 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
6028 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6029
6030 checkpoint55i_post (2004/10/28)
6031 o change arrays for total vertical diffusivity (2.D if explicit,
6032 3.D if implicit) ; each ptracer uses its own background value.
6033 o added mnc/NetCDF output capability to ocn_compon_interf
6034 - added bits to verification/cpl_aim+ocn so that it can run on
6035 ITRDA and other clusters without the mpirun "-wd" option
6036 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
6037 configuration
6038 o give MNC the ability to create additional files rather than
6039 exceeding a specified file size limit "MNC_MAX_FILESIZE"
6040 - the default is just less than 2GB which is a practical limit
6041 on many systems
6042 o Compute the non-local term using either KPP vertical diffusivity (=default)
6043 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
6044
6045 checkpoint55h_post (2004/10/20)
6046 o add verification test "vermix"
6047 o remove all the *_ioinc flags and replace with the single global
6048 outputTypesInclusive flag
6049 o allow to set a vertical profile of vertical diffusivity for T & S
6050 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
6051 o useMNC moved from data.mnc to data.pkg
6052
6053 checkpoint55g_post (2004/10/14)
6054 o Renaming carbon AD experiments to comply with testreport conventions
6055 o Updating adjoint of Held-Suarez hs94.1x64x5
6056 o Fixing directives for non-ECCO forward_step, after ECCO directives
6057 have been fixed to avoid recomp. of do_oceanic_phys
6058 Works well for global_ocean.90x40x15,
6059 but recomp. issue remains for carbon
6060 o Updating adjoint output for natl_box_adjoint after
6061 pkg/ecco has been modified (see taga c55d_post)
6062
6063 checkpoint55f_post (2004/10/13)
6064 o rename to timeave_init_fixed
6065
6066 checkpoint55e_post (2004/10/13)
6067 o some delicate re-shuffle of store directives to avoid one
6068 extra call of do_oceanic_physics
6069 affects ecco_the_main_loop.F, do_oceanic_physics.F
6070 checkpoint_lev1_directives.h
6071 o NB: this may break global_ocean adjoint temporarily,
6072 but it is clear how to fix it. Will do later, need this now.
6073
6074 checkpoint55d_post (2004/10/11)
6075 o ECCO specific cost function terms (up-to-date with 1x1 runs)
6076 o ecco_cost_weights is modified to 1x1 runs
6077 o modifs to allow observations to be read in as
6078 single file or yearly files
6079 o enable to read exf forcing fields as either
6080 single file or yearly files (flag useExfYearlyFields)
6081 checkpoint55d_pre (2004/10/08)
6082
6083 o switch between 2-level and 3-level checkpointing
6084 o add ability of MNC to write local and "partial" (eg. 2D slices where
6085 the full 3D field is never actually stored) arrays to NetCDF files
6086 with the correct (that is, the complete multi-dimensional) set of
6087 array indicies
6088 - used in mom_vecinv() to write the diagFreq output
6089 - tested (demonstrated) in verification/aim.5l_cs
6090 o further mnc-ification
6091 - add verification/lab_sea to the list with mnc setups
6092 - fix undefined mnc v-names in cd_code
6093 - add kpp to mnc output (both snapshot and timeave)
6094 o non-hydrostatic code
6095 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
6096 in calc_gw.F
6097 - defaults to viscAh
6098 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
6099 friction or Leith) in non-hydrostatic mode, as long as there is
6100 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
6101 o pkg/cost
6102 extend simple cost functions to treat time mean quantities
6103 (T,U,V) via cost_accumulate_state from cost_tile
6104 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
6105 be 2 times larger than the minimum size the advection scheme requires.
6106 now get a perfect conservation of salt in advect_cs test-exp (updated)
6107 o GGL90 (Gaspar's TKE mixed layer)
6108 - add horizontal diffusion of TKE, requires exchanges in
6109 do_fields_blocking_exchanges, horizontal diffusivity is zero by
6110 default. In OPA there is no horizontal diffusion of TKE but the
6111 mixing coefficients are computed from a horizontal average of TKE of
6112 6 points or so. I think that diffusion has a little more physical
6113 justification.
6114 - clean up ggl90_calc in the hope of reducing memory usage (this hope
6115 was in vain)
6116 - mask tke-variable in ggl90_init
6117 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
6118 o fix biharmonic diffusion on CS-grid.
6119 o more obcs stuff
6120 - added obcs_external_fields_load as an alternative to the EXF-pkg option
6121 for reading boundary values. This routine is called from
6122 obcs_prescribe_read
6123 - updated obcs_check
6124 - changed sponge layer relaxation parameter units for days to seconds
6125 - turned off sponge layer by default
6126 - changed argument list of OBCS_CALC to myTime+deltaTclock
6127 - fixed about 35 bugs in obcs_external_fields_load
6128
6129 checkpoint55c_post (2004/09/23)
6130 o obcs stuff
6131 - new runtime flags useOBCSprescribe, useOBCSbalance
6132 - re-arranged obcs_calc
6133 - moved exf_getobcs to obcs_prescibe_read
6134 obcs_prescibe_read is called after ORLANSKI stuff
6135 and independent of it (executable can contain all).
6136 - updated obcs_check
6137 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
6138 These may be necessary only if tangential velocities are
6139 prescribed at OB, not sure, needs testing.
6140 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
6141 which simplifies the calls and passes the ifc check-bounds test
6142
6143 checkpoint55b_post (2004/09/22)
6144 o add a 2D scalar, Z location, exchange_2 routine.
6145 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
6146 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
6147 affects advect_cs results (for the wrong reason): update output.txt
6148 o use a more standard discretization for biharmonic viscosity ;
6149 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
6150 affects results of dome set-up: update output.txt
6151 o fix gad_advection.F (CubedSphere part), back to version 1.23
6152 o fix bug in mom_vi_del2uv.F (CubedSphere part).
6153
6154 checkpoint55a_post (2004/09/20)
6155 o merged code to
6156 * prescribe/read time-dependent open boundaries
6157 (works in conjunction with exf, cal)
6158 * sponge layer code for open boundaries
6159 * each boundary N/S/E/W now has its own CPP option
6160 (healthy for the adjoint)
6161
6162 checkpoint55 (2004/09/17)
6163 o up-to-date adjoint of previous breaks
6164 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
6165 - global_ocean_ebm: adjoint still needs fix (TLM ok)
6166 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
6167 - carbon: * remove tr1-related adjoint verification
6168 * add ptracer as control variable
6169 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
6170 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
6171
6172 checkpoint54f_post (2004/09/16)
6173 o in verification/carbin/ remove experiment related to
6174 ALLOW_PASSIVE_TRACER (array tr1 etc)
6175 code_ad/ input_ad/ results_ad
6176
6177 o add two new packages
6178 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
6179 + subject to optimization (memory)
6180 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
6181 + subject to reordering (many GOTOs in the original code)
6182 + so far opps is called for every (i,j) point, and then operates in
6183 the vertical; one may want to reorder the scheme in order operate in
6184 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
6185 fields)
6186 o overhaul of IO so that we now have flags for MDSIO and/or MNC
6187 - all verification tests compile and run with linux_ia32_g77
6188 - defaults are compatible with current input files--nothing
6189 should change if you were not previously using MNC
6190 - MNC output has been added in numerous places (eg. timeave)
6191 but there are still a few writes not yet do-able with MNC
6192 (this is in progress)
6193 - flags now allow for either/or/both use of MDSIO and MNC and
6194 documentation will soon follow
6195 - numerous small formatting cleanups for ProTeX
6196 o add version info (via BUILD_INFO.h) to MNC and stdout
6197
6198 checkpoint54e_post (2004/09/02)
6199 o add two new packages
6200 - pp81 (Packanowski and Philander, 1981), Richardson number and
6201 stratification dependent mixing
6202 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
6203 - these scheme operate in a similar manner as KPP (without ghat, of
6204 course), however there is only one diffusivity that is used for both
6205 temperature and salinity (and passive tracers)
6206 o add offline package
6207 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
6208 provided by Stephanie Dutkiewicz
6209 o genmake2: add ability to search for C compilers and cleanup test output
6210 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
6211
6212 checkpoint54d_post (2004/07/27)
6213 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
6214 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
6215 leading to additional shift by 5 days each year of integration
6216 (i.e. leading to considerable offset over the years)
6217 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
6218 o start with no AB and no initial filtering (staggerTimeStep):
6219 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
6220 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
6221 (external loading & cpl import/export stay in forward_step.F)
6222 o update coupling interface to work with new staggerTimeStep
6223 o change MDSIO ptracers_pickup.
6224 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
6225 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
6226 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
6227
6228 checkpoint54c_post (2004/07/18)
6229 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
6230 this affects (truncation error) output.txt of test-exp:
6231 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
6232 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
6233 o change Qnet to always be the net heat flux, (+upward).
6234 affects (truncation error) output of natl_box exp.: updated
6235 o define the max number of passive tracers in PTRACERS_SIZE.h
6236 o start to test mnc routinely in exp0
6237 o add sea-ice loading (sIceLoad) as a new forcing field.
6238
6239 checkpoint54b_post (2004/07/08)
6240 o add testreport "-j JOBS" option for parallel builds (tested and pretty
6241 impressive on Altix and Opteron systems)
6242 o diagnostics can now write NetCDF files through the mnc package
6243 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
6244 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
6245 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
6246 affects (truncation error) output of lab_sea & natl_box exp.: updated
6247 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
6248
6249 checkpoint54a_post (2004/07/06)
6250 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
6251 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
6252 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
6253 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
6254 + internal_wave (shift in writing cg2d_ini_res)
6255 checkpoint54a_pre (2004/07/05)
6256
6257 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
6258 - modified verification/lab_sea and natl_box_adjoint accordingly
6259
6260 checkpoint54 (2004/07/02)
6261 checkpoint53g_post (2004/07/02)
6262 o prepare splitting of thermodynamics: store convect.counter in common block
6263 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
6264 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
6265 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
6266 o new parameter "nShapS": allow to treat differently S from T (nShapT)
6267 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
6268 o restore adjointability
6269
6270 checkpoint53f_post (2004/06/25)
6271 o modifications that affect AIM experiment results (update output.txt):
6272 - no advection of S at top interface Nr (pkg/generic_advdiff)
6273 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
6274 o AIM pkg:
6275 - include stability function into surf.Flux derivative relative to Tsurf
6276 - calculate clear-sky radiation & surface temp. change (for diagnostics)
6277
6278 checkpoint53e_post
6279 o merged cylindrical coord configuration
6280 o added rotating_tank experiment
6281 checkpoint53e_pre
6282
6283 checkpoint53d_post (2004/06/14)
6284 o faulks upgraded: re-generate output.txt that have changed:
6285 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
6286 o Added Bryan and Lewis, 1979, vertical diffusivity profile
6287 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
6288 o added Sadourny discretization of Coriolis
6289 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
6290 - re-enabled use of omega3 (useAbsVorticity)
6291 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
6292 vector-invariant equations
6293 - note: does *NOT* yet use same variable visc. for no-slip BC's.
6294 o recoded the lateral boundary conditions for non-hydrostatic w, this time
6295 hopefully without new bugs
6296 - still to do: biharmonic friction for non-hydrostatic w
6297 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
6298 o regenerated output for global_ocean_ebm (using -ieee)
6299 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
6300 of mom_common/
6301 - simple re-arrangement of instructions within computing loop
6302 checkpoint53d_pre (2004/05/21)
6303
6304 checkpoint53c_post (2004/05/21)
6305 o new version of coupler for AIM+thSIce and Ocean models
6306 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
6307 - land: change Evaporation of snow
6308 - aim with thSIce: fix bug in snow-precip.
6309 o changes to calc_gw.F
6310 - bug fix for w^2 term near the bottom boundary
6311 - (hopefully) improve the lateral slip boundary condtions for use with
6312 partial/looped cells
6313 - because the bug fix changes two verification experiments anyway (exp5
6314 and plume on slope), change the lateral boundary condition from half slip
6315 to the value of no_slip_sides
6316 o ebm package wasnt quite up to the parallel task. Fixed that.
6317 o Adjoint of EBM package + verification
6318 * TLM OK
6319 * ADM not sufficient accuracy yet (needs further testing)
6320
6321 checkpoint53b_post (2004/05/14)
6322 o Commiting new energy balance model to repository
6323 * package is pkg/ebm
6324 * verif. is verification/global_ocean_ebm
6325 * references are in ebm_driver.F
6326 C * X. Wang, P. Stone and J. Marotzke, 1999:
6327 C Global thermohaline circulation. Part I:
6328 C Sensitivity to atmospheric moisture transport.
6329 C J. Climate 12(1), 71-82
6330 C * X. Wang, P. Stone and J. Marotzke, 1999:
6331 C Global thermohaline circulation. Part II:
6332 C Sensitivity with interactive transport.
6333 C J. Climate 12(1), 83-91
6334 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
6335 C Destabilization of the thermohaline circulation
6336 C by atmospheric eddy transports.
6337 C J. Climate 7(12), 1870-1882
6338 o Will need long integration testing.
6339 checkpoint53b_pre (2004/05/14)
6340
6341 o created pkg/mom_common in preparation for variable viscosity code
6342 o renamed and split ini_mnc_io
6343 o pkg/land: only liquid water can diffuse or run-off
6344 o AIM using land: soil wetness availability account for snow
6345 o added printMapIncludesZeros to EEPARMS namelist
6346
6347 checkpoint53a_post (2004/05/11)
6348 o restore TAMC compatiility for exf_constants.h
6349 (no usage of _d in .h)
6350 o Additional storing in KPP in an attempt to fix
6351 TAMC problem with adjoint of KPP code.
6352 (no success...)
6353 Identical code works fine with TAF.
6354 o Fixed verification/natl_box_adjoint experiments.
6355 Initial conditions for Experiments 4 and 5 are now
6356 set to "SEAICE_initialHEFF=0", which is more reasonable,
6357 and hence gives results closer to that of Experiment 2.
6358 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
6359
6360 checkpoint53 (2004/05/06)
6361 o stable checkpoint with up to date adjoint
6362 TLM tests only run for 1st grdchk at the moment. Its unclear if
6363 this is a code problem or a problem with resetting code for g_
6364 variables that is being autogenerated wrong.
6365 Otherwise:
6366 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
6367 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
6368 are both still in chaos following their security messes.
6369
6370 checkpoint52n_post (2004/05/06)
6371 o various build (mostly genmake2) changes including:
6372 - ability to build/run more easily within Cygwin and MacOS X
6373 - more complicated Makefiles with a stronger dependence on Gnu Make
6374 o pkg/seaice modifications
6375 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
6376 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
6377 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
6378 - changed proxy for geostrophic velocity and updated
6379 verification/lab_sea/results/* accordingly
6380 - removed ADI dynamic solver from pkg/seaice
6381 - replaced all occurrences of 1/CSTICE or 1/CSUICE
6382 they caused a segmentation fault under certain circumstances
6383 - removed unused field WATR
6384 o bug fix in exf-package:
6385 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
6386 now reflect that.
6387 o small fixes in the cal-package:
6388 - set reference date to first of January for the 'model'-calendar
6389 - failing of cal_CheckDate in cal_FullDate now actually results in a
6390 warning
6391 o small modifications in exf-package to increase flexibility:
6392 - change climtempfreeze from a constant to a runtime parameter that
6393 is specified in data.exf_clim (default = -1.9)
6394 - introduce runtime parameter windstressmax (default = 2.0) that is
6395 specified in data.exf
6396 o fix in pkg/thsice:
6397 - update Evap (Tsf changes) to be consistent with Latent heat flux
6398 - maintain snow precipitation unchanged (even if Tsf >=0).
6399 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
6400
6401 checkpoint52m_post (2004/04/18)
6402 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
6403 this does not change any of the results, because myIter=0 in swfrac always
6404 lead to jwtype=2 (the default anyway), but the call makes little sense
6405 as a default
6406 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
6407 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
6408 atmospheric model (AIM) to use it ; add a "slab ocean" component.
6409 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
6410 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
6411 o extending useSingleCpuIO option to work with new exch2 I/O format
6412 - old-style, missing-tile I/O is still accessible by defining CPP
6413 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
6414 o monitor package can write to NetCDF files and/or STDOUT
6415 o fix re-definition bug in MNC_GRID_INIT_ALL()
6416 o doc/api_reference added
6417 - a framework for building an API Reference Manual using all
6418 the "protex" comments embedded in the code
6419 - see pkg/generic_advdiff, pkg/mnc for examples
6420 o MNC:
6421 - make myThid the last argument for all subroutines
6422 - new default for the grid files: NO halos
6423 - add useMNC and other run-time flags
6424 - separate per-file-group handling of the unlimited dimension
6425 - early initialization of MNC w/ flags read at the eeboot stage
6426 and lookup tables set in initialize_fixed
6427 - write all MNC output to a freshly-created directory
6428 o thermodynamics sea-ice (thsice) is now tested with testreport.
6429 o test exp. advect_cs: use the standard cs32 grid ; update output.
6430 o Added functionality to grdchk:
6431 pick global i,j,k position (or nearest wet) where to perform check.
6432
6433 checkpoint52l_post (2004/03/11)
6434 o new land formulation:
6435 a) use ground enthalpy as prognostic variable to ensure exact
6436 energy conservation.
6437 b) account for water temperature and for latent heat of freezing
6438 in all processes (rain, run-off, ground storage)
6439 c) compute surface and ground temperature implicitly.
6440 o aim_v23 modification for new land model:
6441 a) Treat separately land / ocean / sea-ice surface fluxes
6442 to allow implicit computation of land & sea-ice surface temp.
6443 b) add snow precipitation.
6444 checkpoint52l_pre (2004/03/11)
6445
6446 o fix problem (when 1 tile is empty) in min/max monitor.
6447 o fix bug in timeAve (u,vZetatave in common block)
6448 o no restoring terms under ice for pkg/seaice
6449 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
6450 o bug fix for pkg/seaice pickups
6451 o change MNC call locations and add coordinate attributes
6452 o mask vorticity at the corner ; affects global_ocean.cs output
6453 o fix ini_curvilinear_grid ; test CS experiments with mpi
6454 o aim.5l_cs: modify sea-ice fraction input file ; update output
6455 o exf: Adding simple range check routine for exf fields after read
6456
6457 checkpoint52k_post (2004/02/23)
6458 o removed top-level directory "diags"
6459 - we migrated these functions to pkg/timeave a long time ago
6460 o fixed bug introduced in pkg/monitor
6461 o accuracy ctrlprec = 32 insuffient for gradient checks using
6462 averaged fields (I/O via cost_averages)
6463 -> use ctrl.h in active_file*.F to control I/O precision.
6464 o paramter list of CALL ADTHE_MAIN_LOOP
6465 o added initial do_the_model_io to ecco
6466 o set all ...Freq to zero after cost_final
6467 taveFreq, dumpFreq, pChkptFreq
6468 o MAIN and ECCO differentiability restored
6469
6470 checkpoint52j_post (2004/02/18)
6471 o fix nchklev in tamc.h for global_ocean...
6472 o Bringing flow and store directives up-to-date
6473 o Really weird thing!
6474 call do_the_model_io from the_main_loop with parameters
6475 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
6476 TAF places a faulty re-call of initialise_varia
6477 after cost_final call which should not be there!
6478 checkpoint52j_pre (2004/02/03)
6479
6480 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
6481 error messages
6482 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
6483 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
6484 debug output
6485 o modfied mdsio_writefield.F to handle non-global files under exch2
6486 o update AIM Cubed-Sphere exp (aim.5l_cs):
6487 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
6488 o update AIM Equatorial Channel exp:
6489 use standard aim_v23 pkg and change the SST fields to be more realistic.
6490 o globalFile now works with exch2
6491 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
6492 mon_vort3.F to make exch2 friendly with >1 tile per cube face
6493 o limit timeave output for hi-res integrations
6494
6495 checkpoint52i_post (2004/01/21)
6496 o removed CPP_EEOPTIONS.h from verification/*/code
6497 o updated the tiling for global_ocean_pressure
6498 checkpoint52i_pre (2004/01/20)
6499
6500 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
6501 the old pkg/aim).
6502
6503 checkpoint52h_pre (2004/01/20)
6504 o shortened offending lines in exch2_send_rx?.template
6505 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
6506 o genmake2: add build & execute test for NetCDF code
6507 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
6508 old grid files, moved CPP_EEMACROS.h to pkg/exch2
6509 o added useSingleCPUIO flag to monitor.F and mon_out.F
6510 o added temporary hack for sea-ice dynamics on the cube:
6511 metric terms are ignored and it is assumed that
6512 there is no sea-ice on cube faces 1, 2, 4, and 5.
6513
6514 checkpoint52f_post (2004/01/09)
6515 o added exch2 cube routines to pkg/exch2
6516 o modified hs94.cs-32x32x5 to use it
6517 o added new grid files to hs94.cs-32x32x5
6518 checkpoint52f_pre (2004/01/07)
6519
6520 checkpoint52e_post (2004/01/07)
6521 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
6522 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
6523 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
6524 to work with implicit vertical advection and AB ;
6525 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
6526 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
6527 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
6528 checkpoint52e_pre (2004/01/02)
6529
6530 o fix bug in impldiff when Nr=1 or Nr=2.
6531 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
6532 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
6533 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
6534 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
6535 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
6536 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
6537 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
6538
6539 checkpoint52d_post (2003/12/16)
6540 o re-tiled many expts to allow comparison in multi-processor mode
6541 - updated output accordingly
6542 - changed hs94.128x64x5 to use intial T from file rather than use the
6543 random number generator
6544 o add infrastructure in model routines for fizhi and gridalt packages
6545 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
6546 o changes to permit hi-res, cubed-sphere, configuration
6547 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
6548 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
6549 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
6550 of surface winds for the cube
6551 (A verification experiment, based on global_ocean.cs32x15, but with
6552 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
6553 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
6554 complete with example surface forcing files and matlab scripts to look
6555 at the output and compare it with that of global_ocean.cs32x15.)
6556 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
6557 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
6558 to conform to the common rule.
6559 o check-in the first version of the coupler + interfaces for multi-components
6560 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
6561 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
6562 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
6563 - ocean and atmos. share the same horizontal grid (no interpolation).
6564 - exchanges between component and coupler is done in forward_step
6565 o new verification experiment, cpl_aim+ocn:
6566 coupled ocean - AIM atmosphere on cs32 grid.
6567
6568 checkpoint52d_pre (2003/12/06)
6569 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
6570 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
6571
6572 checkpoint52c_post (2003/11/25)
6573 o Fixing OPTIONS files for use of exf:
6574 - ALLOW_ECCO not needed
6575 - ECCO_CPPOPTIONS.h should not be included from
6576 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
6577 as has been the case in the past
6578 - All cal/exf related options are currently set in
6579 single header file. Should remain so until we
6580 agree on a consistent new policy.
6581 o Removed all CPP options for cal package.
6582 cal has no more CPP options.
6583 o modified STOREs in GAD_ADVECTION
6584 o corrected key comp. for passkey
6585
6586 checkpoint52b_post (2003/11/23)
6587 o new version: "thsice" of thermodynamic sea-ice pkg:
6588 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
6589 - modify fluxes but do not change theta directly;
6590 - light cleaning of bulk_force pkg (still needed with thsice).
6591 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
6592 + output_thsice.txt to test thsice & bulk_force pkgs.
6593 o put back grid & coriolis monitor output.
6594 checkpoint52b_pre (2003/11/23)
6595
6596 o call "do_the_model_io" at the beginning (=> dump initial state)
6597 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
6598 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
6599 (need info on NUMBER_OF_PTRACERS)
6600 o missing PTRACERS headers in some routines
6601 o default tamc.h in pkg/autodiff supposed to crash
6602 to ensure proper customization
6603
6604 checkpoint52a_post (2003/11/17)
6605 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
6606 - moved surfaceTendencyTice from pkg/seaice to main code
6607 - subroutine FREEZE_SURFACE now limits only surface temperature
6608 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
6609 => new output.txt for global_ocean.cs32x15 & global_with_exf
6610 - keep the old version of FREEZE for backward compatibility;
6611 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
6612 - corresponding modifs for TAF directives
6613 o added surface flux output variables to TIMEAVE_STATVARS
6614 o time-averaged output for pkg/ptracers
6615 o fix problem with ECCO-related divided adjoint
6616 snapshot file was missing some ad-variables,
6617 but no warning issued by TAF
6618
6619 checkpoint52a_pre (2003/11/12)
6620 o some bug fixes for #undef REAL4_IS_SLOW
6621
6622 checkpoint52 = ecco_c52_e35
6623 o after testing adjoints of checkpoint51u_post
6624
6625 checkpoint51u_post (2003/11/06)
6626 o this is the post-merge tag of the ecco-branch
6627 (needs another clean checkout and re-testing)
6628 o various natl_box_adjoint configs and results
6629 but no input fields
6630 o obcs adjoint not yet merged!
6631 o adding ECCO global 1x1 and 2x2 degree configs
6632 o updated/extended some store directives for seaice
6633 o pkg/ecco now containes ecco-specific part of cost function
6634 o top level routines the_main_loop, forward_step
6635 supersede those in model/src/
6636 previous input data.cost now in data.ecco
6637 (new namelist ecco_cost_nml)
6638 o in ctrl/ cleaned some cross-dependencies and updated CPP options
6639
6640 checkpoint51t_post (2003/11/04)
6641 o this is the pre-merge tag of the ecco-branch
6642
6643 checkpoint51s_post (2003/11/04)
6644 o cleanup: removed various obsolete #define-s
6645 o pkg/grdchk
6646 - renamed 'ph-grd 3' to 'grad-res'
6647 - merged from ecco-branch
6648 (remaining bug fixes for obcs gradient checks)
6649 - additional high-precision output for testreport
6650 (grep for 'precision_grdchk_result')
6651
6652 checkpoint51r_post (2003/11/03)
6653 o cleaned up or removed CPP_OPTIONS.h files
6654 o updated results for some of the tests to reflect the new
6655 optfiles (-ieee: -O0 instead of -O3)
6656
6657 checkpoint51q_post (2003/10/30)
6658 o cd_code:
6659 - moved cd_scheme.F -> cd_code_scheme.F
6660 - separate read_checkpoint from cd_code_ini_vars.F
6661 - separated cd_code part from write_checkpoint
6662 - updated AD_SOURCE, generated .flow
6663 - added CD_CODE_VARS.h to the_main_loop
6664 - Moving cd_code specific store dir.s to pkg/cd_code
6665 o ctrl package totally restructured
6666 - pack/unpack now optional and decoupled from
6667 xx_/adxx_ I/O
6668 - ctrl_pack/unpack cleaned
6669 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
6670 - confined inclusion of AD_CONFIG.h to where necessary.
6671 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
6672
6673 checkpoint51p_post (2003/10/30)
6674 o create initial cd_code package
6675 - WARNING: the initialization of fields within packages
6676 is broken because INI_FIELDS (where READ_CHECKPOINT is
6677 called) is called *before* PACKAGES_INIT_VARIABLES.
6678 This seems to be backwards since
6679 1) its important to initially zero the entire field including
6680 the "halo" region
6681 2) zeroing needs to be done *before* reading pickup info
6682 and the pickup call might or might not happen in any
6683 particular run
6684 - this needs an overhaul for R2
6685 o cleanup verification/*/code/GMREDI_OPTIONS.h
6686 o cleanup testreport
6687
6688 checkpoint51o_post (2003/10/27)
6689 o bringing AD-related verif's up to date with genmake2
6690 - carbon/
6691 - global_ocean.90x40x15/
6692 - hs.94.1x64x5/
6693 - (front_relax/ )
6694 o (more) consistent directory structure for AD-related verif.'s
6695 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
6696 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
6697 o bug fix in find_alpha.F for MDJWF:
6698 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
6699 change rho -> rho-rhoConst
6700 - replace call find_rho to find_rhonum
6701 o initialisation of rFlx extended to full array (required by TAF)
6702 and shifted to thermodynamics
6703 o removed PTRACERS.h in ptracers routine
6704 o added surfacetendencyPtr to S/R parameter list pracers_forcing
6705 o Correcting initialisations for fVerU, fVerV.
6706 o helping TAF to recognize dependency on kUp for
6707 fVerU, fVerV
6708 o Replacing delZ by delR in pkg/ctrl/
6709 checkpoint51o_pre (2003/10/24)
6710
6711 o undid all of cp51 pending some cleanups and discussion
6712 o added the [#include "AD_CONFIG.h"] statement to all files that need
6713 it for adjoint/tl #defines
6714 o re-worked the build logic in genmake2 to support AD_CONFIG.h
6715 o removed tools/genmake since it no longer works
6716
6717 checkpoint51n_post (2003/10/23)
6718 o modifications to make FREEZE flux visible to pkg/kpp
6719 - moved surfaceTendencyTice from pkg/seaice to main code
6720 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
6721 - subroutine FREEZE now limits only surface temperature
6722 (this means new output.txt for global_ocean.90x40x15,
6723 global_ocean.cs32x15, and global_with_exf)
6724 o added surface flux output variables to TIMEAVE_STATVARS
6725
6726 checkpoint51n_pre (2003/10/23)
6727 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
6728 o added [#include "AD_CONFIG.h"] to all files that use the following
6729 defines:
6730 - ALLOW_ADJOINT_RUN
6731 - ALLOW_TANGENTLINEAR_RUN
6732 - ALLOW_ECCO_OPTIMIZATION
6733
6734 checkpoint51m_post (2003/10/21)
6735 o incorporating changes to get TAMC/TAF working in genmake2
6736 - added new TAMC/TAF targets to the Makefile
6737 - various cleanups related to package handling
6738 - these changes should have no impact on the forward model
6739
6740 checkpoint51l_post (2003/10/20)
6741 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
6742 - faster algorithm for cal_addtime.F
6743 - higher precision arithmetic, where needed
6744 - pkg/exf *startdate variables changed from calendar date to
6745 model integration time
6746
6747 checkpoint51l_pre (2003/10/17)
6748 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
6749 o enable to apply restoring on S & T only in a latitude band.
6750 o update output (external_forcing_surf modif. change truncation errors)
6751 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
6752
6753 checkpoint51k_post (2003/10/16)
6754 o change default to: useNHMTerms=.FALSE.
6755 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
6756 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
6757 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
6758 exp1, ideal_2D_oce
6759 - change data file of oceanic exp (leave the results unchanged for now)
6760 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
6761 o set gravitySign automatically according to the vertical coordinate used
6762 (and change sign: back to "logical" value: +1 when R increases downward)
6763 o added an include barrier to the default CPP_OPTIONS.h and
6764 removed the #include "PACKAGES_CONFIG.h" from it
6765 o fix a bug in mom_fluxform (from chk51j_post)
6766
6767 checkpoint51j_post (2003/10/10)
6768 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
6769 o adjusted some flow directives (dynamics, thermodynamics)
6770 o added cubed-sphere case to test cost function
6771 o heckpoint_lev?_directives.h now include
6772 pkg-specific directives, whenever those are enabled.
6773 o Moving pkg-specific flow directives to corresponding pkg
6774 Moving pkg-specific differentiation list to corresponding pkg
6775 Moving pkg-specific checkpoint-lev storing to corresponding pkg
6776 ---> conventions are
6777 - pkg_ad.flow
6778 - pkg_ad_diff.list
6779 - pkg_ad_check_lev?_dir.h
6780
6781 checkpoint51i_post (2003/10/09)
6782 o merge of the branch-genmake2
6783 - knowingly breaks the older genmake
6784 - automatic generation of all ALLOW_${PKG_NAME} defines
6785 - new testreport supersedes older testscript
6786 o large number of package inclusion and header cleanups
6787 checkpoint51i_pre (2003/10/08)
6788
6789 o new output for adjoin of global ocean vector invariant
6790 o fix for checkpoint of thermodynamic seaice and bulk_force
6791 o Steph gchem various cleanups
6792
6793 checkpoint 51h_pre
6794 o fixed some single quotes
6795 o modify gchem pkg to be more versatile
6796 o modifications to clean up dic pkg
6797 o add pkg/cfc
6798
6799 checkpoint51g_post (2003/10/02)
6800 o provide links for ARPACK and ADM*TLM
6801 o start removing verification/vero/
6802 o update AD-related stuff
6803 (in particular some IF-statements in model/src/ routines)
6804 o adding to verification/global_ocean.90x40x15/ adjoint of
6805 vector invariant setup
6806
6807 checkpoint51f_post (2003/10/02)
6808 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
6809 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
6810 of tracer Green's fucntions for ocean inversion project.
6811
6812 checkpoint51f_pre (2003/08/07)
6813 o Added on-the-fly spatial interpolation capability
6814 "USE_EXF_INTERPOLATION" to pkg/exf.
6815 - This is a temporary Cartesian-grid hack until
6816 the super-duper ESMF coupler becomes available.
6817 - See verification/global_with_exf/README for usage example.
6818 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
6819 flags and modified pkg/seaice accordingly.
6820 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
6821 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
6822 non-local transport term.
6823
6824 checkpoint51e_post (2003/08/03)
6825 o pkg/mom_vecinv:
6826 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
6827 - add time-ave diagnostic of vorticity advection.
6828 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
6829 o atmospheric geopotential: - include water vapor effect;
6830 - use p^kappa in p* scaling.
6831 o land pkg: read initial state from files.
6832 o AIM : add stratospheric drag in the upper level
6833
6834 checkpoint51d_post (2003/07/18)
6835 o change function ILNBLNK (=> last non-blank char.) to return zero
6836 (instead of the string length) when the string. char is empty
6837 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
6838 o modif's to restore TAMC compatibility
6839 - avoid "_d" constructs in PARAMETER declarations
6840 - avoid interrupting lines by comment lines
6841 o Use cluster local disks for purely local I/O
6842 vs. globally visible disks needed for ctrl stuff
6843 (merged from ecco-branch)
6844 - new active_file_loc... and mdsio_..._loc routines
6845 - affected packages: autodiff, ctrl, grdchk, mdsio
6846
6847 checkpoint51c_post (2003/07/08)
6848 o introducing integer flag debugLevel
6849 - debLevZero: suppress all output
6850 - debLevA: standard
6851 - debLevB: equivalent to current debugMode=.TRUE.
6852 o introducing pathname variable mdsioLocalDir for mdsio
6853 that can be specified at runtime
6854 (relevant for cluster I/O to local disk)
6855 `
6856 >>>checkpoint51b_post
6857 adjoint of ptracers
6858 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
6859 o extended state in checkpoint_lev?, etc.
6860 o alternative ctrl/cost with tr1 or ptracer
6861 o new comlev1_bibj_ptracers
6862 o new ptracers.flow
6863 o made ptracers_forcing same as external_forcing_s
6864 o added verification for adjoint with ptracers
6865 - adm. grdchk fail so far
6866 - tlm. grdchk OK
6867 - checked tapelev/comlev recomputations: OK
6868 <<<checkpoint51b_pre
6869
6870 checkpoint51a_post (2003/06/25)
6871 o added code for biogeochemistry package
6872 - new pkgs: dic, gchem
6873 - new subroutine in ptracers
6874 o modify code for biogeo packages
6875 - in model/src and pkg/ptracers
6876
6877 checkpoint51 (2003/06/24)
6878 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
6879 - autodiff, ctrl, exf, grdchk, seaice
6880 kept separate packages
6881 - cost, ecco, obcs
6882 o updating verification/internal_wave, verification/lab_sea
6883 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
6884
6885 checkpoint50i_post (2003/06/23)
6886 o Preparing next differentiable checkpoint and sync
6887 of MAIN vs. ecco-branch
6888 - 1st step: this one is differentiable
6889 - 2nd step: next(! not this) checkpoint will have updated packages
6890 from ecco-branch)
6891
6892 checkpoint50h_post (2003/06/20)
6893 o new package "land": provide surface BC for AIM.
6894 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
6895 o AIM: use true log-P extrapolation for near surface temp (= as in
6896 F.Molteni paper) ; update aim.5l_cs output.
6897 o New variable in PARM03 for more flexible pickups
6898 o somewhat cleaned package initialisation sequence for
6899 ctrl/ cost/ ecco/ in packages_... routines
6900
6901 checkpoint50g_post (2003/05/23)
6902 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
6903 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
6904 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
6905 made the default because of faster convergence than ADI
6906
6907 checkpoint50f_post (2003/05/23)
6908 o exf totally restructured
6909 - replaced all exf_set_ routines by one generic exf_set_gen.F
6910 and made sure it's still differentiable
6911 - split exf_getffields.F into new exf_bulkformulae.F
6912 - exf_inscal_/exf_outscal_ suffixes consistent with field names
6913 - updated adjoint/makefile and relevant verif. accordingly
6914
6915 checkpoint50f_pre (2003/05/23)
6916 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
6917 + change Evap over land. (update aim.5l_cs output)
6918 o added missing .cvsignores and made uniform across expts
6919 o changed configuration of tidal_basin_2d expt
6920 o added pkg/debug functions for tracing code in fatal crashes
6921 o tidied pkg/monitor to use MONITOR_OPTIONS.h
6922 o new fn in pkg/monitor to stop model if solution grows too big
6923 o removed lots of single quotes from comments
6924
6925 checkpoint50e_post (2003/05/14)
6926 o make KPP work with PTRACERS
6927 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
6928 nearly a copy of kpp_transport_s
6929 - there is no analogue to SurfaceTendencyS, so I have to use
6930 gPtr(of the surface layer) instead
6931 o add a new platform SunFire+mpi (SunFire 15000) to genmake
6932 checkpoint50e_pre (2003/05/13)
6933
6934 checkpoint50d_post (2003/05/13)
6935 o change kpp output from multiple-record state files to single-record state
6936 files analogous to write_state.F
6937 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
6938 analogous to the cg2d-related output.
6939 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
6940 so that writing to internal file fn (with length 512) fails.
6941 checkpoint50d_pre (2003/05/12)
6942
6943 checkpoint50c_post (2003/05/12)
6944 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
6945 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
6946 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
6947 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
6948 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
6949
6950 checkpoint50c_pre (2003/04/30)
6951 Merging from release1_p13:
6952 o bug fix for pkg/seaice dynamic solver
6953 o Added SEAICE_initialHEFF to pkg/seaice
6954
6955 checkpoint50b_post (2003/04/17)
6956 o store u*,v* in gU,V instead of in guNm1,gvNm1
6957 o in order to put the momForcing out of the Adams-Bashforth:
6958 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
6959 to timestep.F
6960 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
6961 o re-generate output for highly sensitive test-exp:
6962 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
6963
6964 checkpoint50b_pre (2003/04/17)
6965 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
6966 o corrected CPP option mismatch in exf_Bulk... functions for case
6967 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
6968
6969 checkpoint50a_post (2003/03/21)
6970 o Bug fix for merging between c50 and KPP.
6971 ikey was passed from thermodynamics to kpp_calc via
6972 common block rather than being recomputed in kpp_calc,
6973 in contradiction with new key itdkey.
6974 New key ikppkey created, and tamc.h headers updated.
6975
6976 checkpoint50 (2003/03/08)
6977 - 2nd step of merge with ecco-branch:
6978 merge changes in ecco-branch back into main trunk
6979 - bug fix in find_alpha
6980 - more storing in gmredi_calc_tensor.F, kpp_routines.F
6981 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
6982 - merged some sliced AD support routines
6983
6984 checkpoint49 (2003/03/06)
6985 merged from ecco-branch:
6986 o exf:
6987 - Enable initialisation of forcing fields to constant
6988 (runtime) values.
6989 - in exf_getffields.F
6990 Reduce i-/j-loop to interior domain, discarding overlaps.
6991 That also fixes wrong TAF-key computations for key_1, key_2
6992 with bulf formulae.
6993 - exf_init.F modify #ifdef for exf_init_evap
6994 - exf_getffieldrec.F, ctrl_getrec.F
6995 The following INT-usages are not safe:
6996 fldsecs = int(fldsecs/fldperiod)*fldperiod
6997 fldcount = int(fldsecs/fldperiod) + 1
6998 and were modified.
6999 o autodiff: checkpoint_lev...
7000 - updated storing for bulk formulae (some arrays were missing)
7001 - added state for seaice package
7002 - synchronized with main branch
7003 o DIVA:
7004 Modif.s in
7005 - the_main_loop.F
7006 - the_model_main.F
7007 and added cost_final_restore.F cost_final_store.F
7008 o With these changes, it is possible to fully separate
7009 the first forward run to compute the cost function (mdthe_main_loop)
7010 and adjoint runs over individual DIVA intervals (adthe_main_loop)
7011 into separate model executions.
7012 This enables better tuning of DIVA to given queue sizes.
7013 o Loss of cost function value in consecutive DIVA runs is
7014 fixed by storing to 'costfinal' file.
7015 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
7016 beginning/end of adjoint integration is accounted for.
7017 The current changes apply to TAF-1.4.26.
7018 TAF has one remaining bug, requiring one manual change
7019 (see MITgcm manual).
7020 o cal: synchronized between MAIN and ecco-branch
7021
7022 checkpoint48i_post (2003/03/05)
7023 o Changes to restore differentiability of code w.r.t. previous tag
7024 (mostly adding new routines to make list and replacing
7025 pressure by totPhiHyd).
7026 o Updated and merged grdchk package
7027 - has both ADM and TLM checks
7028 - works for single- and multi-proc.
7029 - output cleaned
7030 - worked successfully for parallel DIVA
7031 o genmake:
7032 - Adding -platform=SP4
7033 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
7034 o Modif. for DIVA:
7035 ctrl_unpack should not be called in intermediate DIVA interval.
7036 (similar thing would apply for active files such as
7037 tbar, sbar, psbar, which should not be reinitialised;
7038 only relevant for ecco-branch)
7039
7040 checkpoint48h_post (2003/02/28)
7041 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
7042 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
7043 o Added SEAICE_initialHEFF to pkg/seaice
7044 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
7045
7046 checkpoint48g_post (2003/02/18)
7047 --- EOS:
7048 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
7049 store total Potential in totPhyHyd for diagnostics & EOS.
7050 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
7051 --- Pressure/geopotential gradient:
7052 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
7053 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
7054 ( changes results of global_ocean_pressure )
7055 o NLFS + z-coord.: add eta*Rho' contribution.
7056 o accurate phiHyd when using interface-W at the middle between 2 centers
7057 ( changes results of ideal_2D_oce )
7058 o includes r* 2nd term in potential gradient.
7059
7060 checkpoint48f_post (2003/02/18)
7061 Merging from release1_p12:
7062 o Modifications for using pkg/exf with pkg/seaice
7063 - improved description of the various forcing configurations
7064 - added basic radiation bulk formulae to pkg/exf
7065 - units/sign fix for evap computation in exf_getffields.F
7066 - updated verification/global_with_exf/results/output.txt
7067 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
7068 (SBO) core products, including oceanic mass, center-of-mass,
7069 angular, and bottom pressure (see pkg/sbo/README.sbo).
7070 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
7071 to avoid negative values in shallow regions.
7072 - updated verification/natl_box/results/output.txt
7073 - updated verification/lab_sea/results/output.txt
7074 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
7075 o Added useSingleCpuIO option (see PARAMS.h).
7076 o Updated useSingleCpuIO option in mdsio_writefield.F to
7077 work with multi-field files, e.g., for single-file pickup.
7078 o pkg/seaice:
7079 - bug fix in growth.F: QNET for no shortwave case
7080 - added HeffFile for specifying initial sea-ice thickness
7081 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
7082 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
7083 kpp_transport_t.F, forward_step.F, and the_main_loop.F
7084 o pkg/seaice:
7085 - adjoint-friendly modifications
7086 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
7087
7088 checkpoint48e_post (2003/02/12)
7089 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
7090 o dynamics: change definition of computational domain & adapt mom_fluxform
7091 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
7092 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
7093 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
7094 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
7095 global_ocean.90x40x15 global_with_exf global_ocean_pressure
7096 inverted_barometer solid-body.cs-32x32x1
7097 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
7098
7099 checkpoint48d_post (2003/02/09)
7100 o in preparation for r*:
7101 a) use pre-computed gradient of hydrostatic potential:
7102 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
7103 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
7104 => affects results of glob_oce_pressure (different truncation error)
7105 update output.txt of ideal_2D_oce & global_ocean_pressure
7106
7107 checkpoint48d_pre (2003/02/08)
7108 o in preparation for r*:
7109 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
7110 pass the 2 comp. of the grad. as arguments to momentum S/R.
7111 but for the moment, only used if it does not change the results.
7112 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
7113
7114 checkpoint48c_post (2003/02/06)
7115 Modifications in treatment of initial flux forcing controls
7116 to avoid extra storing of flux fields.
7117
7118 checkpoint48c_pre (2003/01/21)
7119 o Added tidal_basin_2d experiment (currently 1D!)
7120 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
7121
7122 checkpoint48b_post (2003/01/27)
7123 o r* coordinate added in #ifdef NONLIN_FRSURF block.
7124 (modification to pressure gradient not yet implemented)
7125 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
7126 (for U & V) that are used for vertical advection of momentum.
7127
7128 checkpoint48a_post (2003/01/24)
7129 o In preparation for r*, use temp. array to compute vertical transport
7130 in flux-form momentum pkg. => change results of few test-exp.
7131 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
7132 lab_sea, natl_box & plume_on_slope
7133
7134 checkpoint48 (2003/01/23)
7135 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
7136
7137 checkpoint47j_post (2003/01/21)
7138 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
7139 o moved adexch from forward_step to addummy_in_stepping
7140 o added exch in ctrl_map_...
7141 o aveFreq.=0. at end of cost_final to avoid overwrite in
7142 reverse checkpointing loop
7143 o Yet more changes in gmredi:
7144 * adgmredi_calc_tensor
7145 avoiding all recomputation of gmredi_slope_limit
7146 * adgmredi_x/y/rtransport
7147 added flag for excessive storing to avoid recomp. of
7148 u/v/rtans, dTdx/y/z
7149 -> this is not really necessary and very memory-consuming
7150 * adgmredi_slope_psi:
7151 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
7152 * gmredi_slope_limit
7153 re-activated full calculation of taperfct for case 'ac02'
7154 o updating verification/ adjoints of carbon, global_ocean.90x40x15
7155
7156 checkpoint47i_post (2003/01/13)
7157 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
7158 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
7159 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
7160 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
7161 o gmredi: fix few bugs.
7162
7163 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
7164 This will be a good checkpoint to plug into the ecco-branch.
7165 o few modif.'s to get latest version adjointed
7166 (mainly kick out code in ini_linear_phisurf)
7167 o modif's to run adjoint with exactConserv
7168 o case GM_BOLUS_ADVEC should be cleaned
7169 S/R gmredi_slope_psi should be cleaned
7170 o verification/carbon now has exactConserv=.TRUE.
7171
7172 checkpoint47g_post (2003/01/10)
7173 o time-average AIM output: becomes independent from statvars time-average
7174 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
7175 o After TAF bug fix:
7176 Tested adjoint of gmredi package.
7177 Tests were done with checkpoint47 rather than with latest
7178 checkpoint47f_post since the latter is broken for the adjoint
7179 verification/carbon/ contains both ADM and TLM gradient checks.
7180 Here they are, before they get changed/lost/stolen.
7181 Mostly modif.'s to fix numerical sensitivities.
7182 Gradient checks OK for
7183 - GM_taper_scheme:
7184 * clipping
7185 * ac02
7186 * linear
7187 * glw91
7188 * dm95
7189 * ldd97
7190 - GMREDI_OPTIONS:
7191 * GM_VISBECK_VARIABLE_K
7192 * GM_NON_UNITY_DIAGONAL
7193 * GM_EXTRA_DIAGONAL
7194 * GM_BOLUS_ADVEC
7195 in conjunction with data.gmredi parameters to be checked in
7196 in a few minutes under verification/carbon/code/
7197
7198 checkpoint47f_post (2002/12/28)
7199 Merging from release1_p10:
7200 o modifications for using pkg/exf with pkg/seaice
7201 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
7202 and SEAICE_EXTERNAL_FLUXES
7203 - pkg/exf CPP options EXF_READ_EVAP and
7204 EXF_NO_BULK_COMPUTATIONS
7205 - usage examples are Experiments 8 and 9 in
7206 verification/lab_sea/README
7207 - verification/lab_sea default experiment now uses
7208 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
7209
7210 checkpoint47e_post (2002/12/27)
7211 o created a tag prior to creating a branch
7212
7213 checkpoint47d_post (2002/12/16)
7214 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
7215 at the bottom boundary had an erroneous half slip boundary condition
7216 o added bottom drag and no slip boundary condition capabilities to
7217 oceanic pressure coordinates code
7218 o added new verification experiment global_ocean_pressure, this experiment is
7219 also described in the tutorial section of the manual
7220 checkpoint47d_pre (2002/12/16)
7221
7222 checkpoint47c_post (2002/12/16)
7223 o Added a verification experiment for a global cubed-sphere ocean run
7224 - verification/global_ocean.cubed32x32x30
7225 - uses pkg/therm_seaice and pkg/bulk_forcing
7226
7227 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
7228 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
7229 when using P-coordinate; only implemented for atmospheric config.
7230 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
7231 NOTES: requires option NONLIN_FRSURF to be "#define".
7232 o update advect_xz/results/output.txt (left from checkpoint44g_post)
7233
7234 checkpoint47b_post (2002/12/05)
7235 Merging from release1_p9:
7236 o pkg/seaice
7237 - removed GOTO's and added taf directives
7238 - double precision constants to reduce the g77 (Linux)
7239 to F77 (SGI) differences reported in release1_p8
7240 o tools/genmake
7241 - added SGI options
7242 o verification/testscript
7243 - updated to that of checkpoint47a_post
7244 o verification/global_ocean.90x40x15/input/eedata
7245 - modified for SGI f77 compatibility
7246 o verification/lab_sea
7247 - added description of sea-ice model
7248 - added missing matlab routines
7249 - added test of thermodynamics parallelization
7250
7251 checkpoint47a_post (2002/11/23)
7252 o new pkg: aim_v23
7253 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
7254 for now, keep the same surface forcing as before.
7255 - Part-Cell implemented into AIM; check that Heat & Water are conserved
7256 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
7257 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
7258 o add diagnostic of surface correction term in monitor output
7259
7260 o bulk_force and therm_seaice
7261 - Two packages: bulk_force (Bulk forcing)
7262 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
7263 - Earlier integration from Stephaine Dutkiewicz
7264 and Patrick Heimbach.
7265 - Two ifdef statements for compile time,
7266 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
7267
7268 checkpoint47 (2002/11/15)
7269 differentiable version of checkpoint46n_post
7270 o bug fix in quasihydrostaticterms
7271 o * "clean" adjoint code (in terms of extensive recomputations)
7272 can now be obtained for all GMREDI options (i.e. for
7273 - GM_VISBECK_VARIABLE_K
7274 - GM_NON_UNITY_DIAGONAL
7275 - GM_EXTRA_DIAGONAL
7276 - GM_BOLUS_ADVEC )
7277 * However, wrong gradient check problem remains unsolved.
7278 * New CPP options have been introduced for different
7279 tapering schemes
7280 o external_fields_load now part of differentiation list
7281 o pressure needs multiple storing;
7282 would be nice to have store_pressure at beginning or
7283 end of forward_step, e.g. by having phiHyd global (5-dim.)
7284 (NB: pressure is needed for certain cases in find_rho,
7285 which is also invoked through convective_adjustment).
7286 o recomputations in find_rho for cases
7287 'JMD95'/'UNESCO' or 'MDJWF' are OK.
7288 o #define ATMOSPHERIC_LOADING should be differentiable
7289 o ini_forcing shifted to begining of initialise_varia
7290 o Incorporating QNVS line search routines into MITgcm
7291 (this is separate code, and therefore not under pkg)
7292 lsopt/, optim/
7293 o Updated verification/carbon/
7294 - #define GM_VISBECK_VARIABLE_K
7295 - GM_taper_scheme = 'ldd97'
7296
7297 checkpoint46n_post (2002/11/12)
7298 Merging from release1_p8:
7299 o verification/natl_box:
7300 updating new external_fields_load routine
7301 o New package: pkg/seaice
7302 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
7303 The sea-ice code is based on Hibler (1979-1980).
7304 Two sea-ice dynamic solvers, ADI and LSR, are included.
7305 In addition to computing prognostic sea-ice variables and diagnosing
7306 the forcing/external data fields that drive the ocean model,
7307 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
7308 The implied surface heat flux is then stored in variable
7309 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
7310 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
7311 non-local transport term. Because this call precedes model
7312 thermodynamics, temperature under sea-ice may not be "exactly" at
7313 the freezing point by the time theta is dumped or time-averaged.
7314 N.B.: fairly large differences in accuracy occur across
7315 different platforms/compilers; comparison between
7316 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
7317 generated output gives:
7318 T S U V
7319 C D M c m s m s m s m s
7320 n p a R g m m e . m m e . m m e . m m e .
7321 f n k u 2 i a a d i a a d i a a d i a a d
7322 g d e n d n x n . n x n . n x n . n x n .
7323
7324 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
7325 o GAD:
7326 - generated new common blocks to account for call of
7327 same gad routines with differing traceridentities
7328 (needed to modify tracerIdentity indices in GAD.h)
7329 - generated separate common blocks for case useCubedSphereExchange
7330 (Department of Futurology)
7331 - parameter lists to gmredi_?transport: added tracerIdentity
7332 - added new key indices to tamc.h
7333 o external_fields_load:
7334 - added this routine to TAF list
7335 - needed to make some common blocks global and additional storing
7336 along the same lines as exf package (checkpoint_lev?_directives.h)
7337 o exf:
7338 updated external forcing package
7339 - bug fixes carried over from ecco-branch
7340 (missing OBCS_OPTIONS.h in two routines)
7341 - enable easy to use "no forcing".
7342 - added exf I/O for atmospheric loading
7343 - added exf I/O for runoff data
7344 - transfered scaling between exf <-> MITgcm to exf namelist
7345 o Adding new verification experiment global_with_exf.
7346 This verification experiment is almost identical to the
7347 global_ocean.90x40x15 experiment, except that it uses
7348 the exf (and cal) package instead of the
7349 external_fields_load routine (cf README file).
7350
7351 checkpoint46m_post (2002/11/07)
7352 o modified testscript to return -- when there are no lines of "%MON" output
7353 o added new flag "quasiHydrostatic" for QH mode
7354 and new routine quasihydrostaticterms()
7355 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
7356 New routine: mom_u_coriolis_nh()
7357 o fixed sign of non-hydrostatic metric terms in u and v equations.
7358 Depend on correct sign of gravitySign.
7359 o added work.pc* to .cvsignore in aim directories using ifc
7360 o introduced flag for controllin non-hydrostatic metric terms
7361 o removed gravitySign from PARM04
7362 o switched to g77/ifc from pgf77 in aim experiments
7363
7364 checkpoint46l_post (2002/11/01)
7365 o made convective adjustment work with pressure coordinates:
7366 - changed the direction of k-loop in convective_adjustment.F for the
7367 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
7368 - adjusted the reference pressure k-index in convective_adjustment.F
7369 - adjusted the convection condition in convect.F (in analogy to
7370 calc_ivdc.F)
7371 - convective_adjustment no longer computes anything on the halos
7372 - removed the warnings about negative salinity from find_rho.F and
7373 find_alpha.F; instead the new routine look_for_neg_salinity, called
7374 at the beginning of find_rho, find_alpha, and find_beta, does a
7375 check of the entire slice, if CPP-option
7376 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
7377 checkpoint46l_pre (2002/10/23)
7378
7379 checkpoint46k_post (2002/10/23)
7380 o fixed the verification/global_ocean.90x40x15 experiment:
7381 - new bathymetry (the world according to A., JMC, and M.)
7382 - new initial fields and forcing fields (*.bin files)
7383 - new POLY3.COEFFS (for the next release one should switch to a full
7384 equation of state: JMD95P or MDJWF)
7385 - fixed several errors and redundancies in the data file
7386 - experiment uses looped cells
7387 - added matlab directory with diagnostic scripts for plotting of output
7388
7389 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
7390 - read AIM physics parameters from a file (data.aimphys)
7391 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
7392
7393 checkpoint46j_post (2002/10/07)
7394 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
7395 o move wVel computation at the end of the time step, in S/R integr_continuity
7396 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
7397 o update timeave pkg for wVel diagnostic.
7398 checkpoint46j_pre (2002/09/27)
7399
7400 checkpoint46i_post (2002/09/25)
7401 o Clean up AIM package (and keep the results unchanged):
7402 include CPP_OPTION and use IMPLICT NONE in all routines ;
7403 declare all the variables _RL ; use _d 0 for all numerical constants.
7404 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
7405
7406 checkpoint46h_post (2002/09/25)
7407 o cleaned up the use of rhoNil and rhoConst.
7408 - rhoNil should only appear in the LINEAR equation of state, everywhere
7409 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
7410 and the dynamical equations are all divided by rhoConst
7411 o introduced new parameter rhoConstFresh, a reference density of fresh
7412 water, to remove the fresh water flux's dependence on rhoNil. The default
7413 value is 999.8 kg/m^3
7414 o cleanup up external_forcing.F and external_forcing_surf.F
7415 - can now be used by both OCEANIC and OCEANICP
7416 checkpoint46h_pre (2002/09/18)
7417
7418 Added code to convert surface volume flux (fresh water) into
7419 a mass flux when using P coordinates in the ocean (OCEANICP).
7420 Note: It assumes you have set rho0=rhoConst=density of fresh water.
7421
7422 checkpoint46g_post (2002/09/18)
7423 o Include a new diagnostic variable phiHydLow for the ocean model
7424 - in z-coordinates, it is the bottom pressure anomaly
7425 - in p-coordinates, it is the sea surface elevation
7426 - in both cases, these variable have global drift, reflecting the mass
7427 drift in z-coordinates and the volume drift in p-coordinates
7428 - included time averaging for phiHydLow, be aware of the drift!
7429 o depth-dependent computation of Bo_surf for pressure coordinates
7430 in the ocean (buoyancyRelation='OCEANICP')
7431 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
7432 Theta, Salinity, and Pressure in the parameter list. This routine is
7433 presently contained in find_rho.F. This routine does not give the
7434 correct density for 'POLY3', which would be a z-dependent reference
7435 density.
7436 o cleaned up find_rho
7437 - removed obsolete 'eqn' from the parameter list.
7438 o added two new verification experiments: gop and goz
7439 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
7440 checkpoint46g_pre (2002/09/16)
7441
7442 checkpoint46f_post (2002/09/16)
7443 o Enable tangent linear (forward mode) gradient checks:
7444 - extended active file handling to g_... files
7445 - added TANGENT_SIMULATION to theSimulationMode
7446 - extended grdchk package accordingly
7447 o added tangent linear setup in verification/carbon/code_ftl
7448 o added adjoint setup in verification/front_relax/code_ad
7449
7450 checkpoint46e_post (2002/09/05)
7451 o Added new equation of state -> MDJWF
7452 - EOS of McDougall et al., 2002, JAOT, submitted
7453 - caveat: the equation of state is only valid for a smaller (more
7454 realistic?) range of values than JMD95P/Z and UNESCO
7455 - added masks to the calculation of pressure in store_pressure
7456 - added more check values for density in check_eos (ini_eos.F), some of
7457 the old check values are out of the range of the MDJWF-eos, so don't
7458 expect perfect matches for those
7459 checkpoint46e_pre (2002/08/19)
7460
7461 checkpoint46d_post (2002/08/19)
7462 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
7463 'OCEANICP', also initialised field pressure correctly in ini_eos in the
7464 case of pressure coordinates. eosType='JMD95Z' in
7465 combination with buoyancyRelation='OCEANICP' now causes an error.
7466 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7467 in find_alpha/beta.
7468 checkpoint46d_pre (2002/08/15)
7469
7470 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7471 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
7472
7473 checkpoint46c_post (2002/08/15)
7474 o Changes necessary for ocean in p-coordinates
7475 - Added new buoyancy relation = 'OCEANICP'
7476 - Added new parameters = gravitySign (this used to be contained inside
7477 the factor dRdZ which I added when we first switched to R coordinates).
7478 X GM/Redi is not compatible (yet)
7479 X bottom drag and no-slip need to be debugged.
7480 checkpoint46c_pre (2002/08/07)
7481
7482 checkpoint46b_post (2002/08/07)
7483 o Added new equation of state -> JMD95Z and JMD95P
7484 - EOS of Jackett and McDougall, 1995, JAOT
7485 - moved all EOS parameters into EOS.h
7486 - new routines ini_eos.F, store_pressure.F
7487 o Added UNESCO EOS, but not recommended because it requires
7488 in-situ temperature (see JMD95)
7489 o Modified formatting for knudsen2.f in utils/knudsen2 and added
7490 unesco.f to be used with POLY3
7491 checkpoint46b_pre (2002/07/31)
7492
7493 checkpoint46a_post (2002/07/31)
7494 o Added (atmospheric) pressure loading
7495 - new field in FFIELDS.h, etc...
7496 - new cpp flag ATMOSPHERIC_LOADING
7497 o Changed hFacC to _hFacC in calc_phi_hyd.F
7498 o Added SHORTWAVE_HEATING to some files for consistency
7499 checkpoint46a_pre (2002/07/13)
7500
7501 checkpoint46 (2002/07/13)
7502 further merges from release1_p5
7503 o new ctrl package
7504 - adopted from ECCO environment to enable optimization
7505 - added Eliassen Palm fluxes to controls
7506 o added Eliassen Palm flux controls to gradient check package
7507 o cost package
7508 - Compatible with new ctrl package
7509 - added Eliassen Palm cost hooks
7510 - modif's of existing cost functions
7511 o Adjoint-related bug fixes in kpp:
7512 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
7513 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
7514 o autodiff package
7515 - flow directives:
7516 + new for S/R do_the_model_io
7517 + enhanced for S/R checkpoint
7518 + new gmredi.flow
7519 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
7520 disable adcommon.h/g_common.h by default.
7521 - fixed problem for adjoint of global_max
7522 o modified verification/carbon/
7523 o New setup for adjoint of global_ocean
7524 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
7525 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
7526 o incorporated hooks for sponge layer code (external_forcing.F)
7527
7528 checkpoint45d_post (2002/07/12)
7529 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7530 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
7531 (affects plume_on_slope "cg2d" output)
7532 o add new parameter deltaTfreesurf for free-surface time stepping
7533 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
7534 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
7535 o change phiMin in exp1 (to agree with documentation)
7536 o add new flags:
7537 - T,S forcing inside/outside Adams-Bashforth
7538 - turn off temp,salt advection and/or forcing
7539 - for each tracer, define internal flag for multiDimAdvection & A-B
7540 o monitor: change definition of KE to check conservation of Energy
7541
7542 checkpoint45c_post (2002/05/30)
7543 o Removed f90 comments ("!")
7544 o Modified initialisations to enable exf package for MITgcm
7545 (without invoking ECCO_PACKAGE).
7546 o modifications to gradient check package (Martin Losch)
7547 - enable centered differences
7548 - modified format of standard output
7549
7550 checkpoint45b_post (2002/05/30)
7551 o cleaned exchange calls in cg2d
7552 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
7553 o included CPP option SINGLE_LAYER_MODE in thermodynamics
7554 to configure barotropic setup (Martin Losch)
7555 o moved some initialisations within bi,bj loop in dynamics
7556 (TAF flow dependency)
7557 o in initialise_varia, moved call packages_init_variables
7558 before convective_adjustment_init
7559 (corresponding adjustment of TAF tape initialisation).
7560 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
7561
7562 checkpoint45a_post (2002/05/01)
7563 o compute Rho over the whole domain (extend iMin,jMin indices)
7564 o specific exchange for X-slice domain (case Ny=1)
7565 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
7566 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
7567
7568 checkpoint44h_post = checkpoint45
7569 o Fix to restore differentiability:
7570 place at which packages_init_variables is called in
7571 initialise_varia is crucial for reverse control flow.
7572 o modifications in GMRedi to enable stable adjoint
7573 (corresponding modif's in thermodynamics, dynamics)
7574 o added missing hook for sponge layer code in external_forcing
7575 o modified test cost functions
7576 o storing in gad_advection (plus removal of write(0,*)!
7577 o missing headers TR1.h added in convective_adjustment routines
7578 o errorMessageUnit set non-equal zero in eeboot
7579 (conflict on some platforms, e.g. IBM SP3)
7580 o modified carbon verif.
7581
7582 checkpoint44h_pre (2002/03/14)
7583 o vertical grid option: allow to put the Interface at the middle between
7584 2 cell-centers ; replace delZ in pkg/kpp by drF.
7585 o GM Advective form: Tracers are advected using the residual transport (=
7586 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
7587
7588 checkpoint44g_post (2002/03/05)
7589 o fix surface correction term in multiDimAdvection (affects plume_on_slope
7590 results) ; ifdef missing in thermodynamics.F
7591
7592 checkpoint44f_pre,checkpoint44f_post
7593 o added PTRACERS package
7594 This allows an arbitrary number of passive tracers to be integrated
7595 forward simultaneously with the dynamicaly model.
7596 + Implemented so far:
7597 - basic forward algorithm (time-stepping, advection, diffusion, convection)
7598 - I/O and checkpointing
7599 - GM/Redi *but* using the GM/Redi coefficient of Salt
7600 + Not implemented so far:
7601 - KPP
7602 - OBCS
7603 + No specific example supplied (yet) but global_ocean.90x40x15 has the
7604 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
7605 line in data.pkg.
7606 + This package is disabled by default since it increases storage.
7607
7608
7609 o testscript: added -cleanup option
7610 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
7611 b) enable to filter 2D fields.
7612
7613 checkpoint44e_pre,post
7614 o re-wrote convective adjustment to use pre-calculated weights
7615 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
7616 Adds: model/src/convective_weights.F, convectively_mixtracer.F
7617 Original calls to convect() still in place.
7618
7619 chkpt44d_pre,post
7620 o added missing EXCLUDE_MONITOR flags
7621 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
7622 (incompatible typ in MIN/MAX expressions caused problems
7623 on IBM SP3)
7624 o in genmake added variable MAKEDEPEND
7625 plus resetting for case SunOS
7626 o added timer_stats.c routine for IBM SP3
7627 o removed variables in dynamics
7628 !!! I forgot to create tag chkpt44d_pre !!!
7629 !!! But chkpt44d_pre = chkpt44c_post !!!
7630
7631 o real fresh water flux implemented with non-linear free-surface.
7632
7633 chkpt44c_pre,post
7634 o few fix (mask in shap_s2, EmPmR in external_field_load,
7635 USE_NATURAL_BCS in solve_for_P);
7636 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
7637
7638 checkpoint44b_pre/_post
7639 o merge of relevant stuff from the ecco-branch:
7640 - genmake: removed $S64 overwrite for case SunOS
7641 - pkg/exf: update and corrections for field swapping and obcs
7642 - pkg/ecco: parameter lists for the_model_main, the_main_loop
7643 harmonized between ECCO and MITgcm
7644 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
7645 updated checkpointing_lev... lists for obcs
7646 - model/src: minor changes in forward_step, plot_field
7647 added directive for divided adjoint in the_main_loop
7648 - pkg/mdsio: added mdsio_gl_slice
7649
7650 o check parameters & config (chkpt44a_pre,post)
7651 o OBC and NonLin_FrSurf.
7652
7653 checkpoint44 (2002/01/18)
7654 o fix bug in mom_vi_del2uv
7655 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
7656 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
7657 o update AIM experiments (NCEP input files)
7658 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
7659 o added some stuff for AD
7660
7661 checkpoint43 (2001/09/28)
7662 o added two new advection tests
7663 o added global 4x4 degree ocean test
7664 o added test of H&S94 with free surface on cube
7665 o some final mods for gradient check, adjoint,...
7666
7667 checkpoint42 (2001/09/27)
7668 Fixed AD-related problems:
7669 o Store directives up-to-date with re-arranged Adams-Bashforth
7670 (mainly thermodynamics.F)
7671 o New store directives for multi-dim. advection schemes
7672 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
7673 * new common block and key passkey
7674 (mainly gad_advection.F)
7675 o Modified store directives for split of dynamics/thermodynamics
7676 for the case ALLOW_KPP
7677 o Cleaned argument list for timestep_tracer.F
7678
7679 checkpoint41 (2001/09/27)
7680 o re-formatted/added comments in prologues of key subroutines
7681 to work with protex
7682
7683 checkpoint40 (2001/09/27)
7684 o moved calc_gs, calc_gt and calc_tr1 back to model/src
7685 o added FLT (floats) package from Arne along with demo. experiment
7686 o re-arranged Adams-Bashforth scheme for tracers to allow easier
7687 implementation of forward-in-time forcing terms
7688 o more mods for non-linear free-surface including new variable
7689 o modified multi-dim method to work on cube
7690 o bug fix in KPP (from DM)
7691
7692 checkpoint40pre9 (2001/09/27)
7693 o added DST advection schemes
7694 o fix MPI bug on SGI's
7695 o modifications for non-linear free-surface
7696 o fixed conditionals for fixed flow/passive tracer only mode
7697 o added tension/strain form of stress tensor
7698 o changes to commenting of arguments for TAF/TAMC
7699 o added/updated many matlab scripts
7700 o added multi-dimensional advection method for tracers
7701
7702 checkpoint40pre8 (2001/09/05)
7703 o new package rw/
7704 Added method for dumping intermediate local arrays:
7705 mdsio_writetile - same as mdsio_writefield except works from inside
7706 bi,bj loop
7707 mdsio_writelocal - same as mdsio_writetile except works for local
7708 arrays
7709 write_local_r? - higher-level wrapper for mdsio_writelocal
7710 Controlled by diagFreq. Defaults to zero (ie. no dumps)
7711 Example given at end of mom_vecinv.F that dumps some local arrays.
7712 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
7713 control flux-form versus vector invariant code.
7714 Switch is runtime flag vectorInvariantMomentum (defaults to false)
7715 or genmake -DISABLE ...
7716 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
7717 (additional storing is now needed for case vecinv;
7718 currently nothing implemented to switch this storing off
7719 in case fluxform is used since no CPP flag available).
7720
7721 checkpoint40pre7 (2001/08/14)
7722 o bug fix in dynamics.F
7723 calc_viscosity called before k=1,Nr loop.
7724 o added some #ifdef's ALLOW_PASSIVE_TRACER
7725 o cleaned initialisations in ctrl_map_ini
7726 related to TAF
7727
7728 checkpoint40pre6 (2001/08/13)
7729 o split dynamics into thermodynamics & dynamics
7730 o corresponding split of calc_diffusivity into
7731 calc_diffusivity, calc_viscosity
7732 (kpp_calc_diff, kpp_calc_visc).
7733 o Added diffkr, kapgm to control variables
7734 o bug fix in gmredi_slope_limit for ldd97
7735
7736 checkpoint40pre5 (2001/07/31)
7737 o proper initialization of Adams-Bashforth time stepping
7738 + uses forward step for very first step of model (iter=0)
7739 o re-generated *all* output since almost all output is modified by this
7740 change (sorry but we've been putting this one off for about 2 years)
7741 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
7742 *not* regenerated since they are already out of date and I don't
7743 want to create the impression that they are suddenly working.
7744 o removed KAP stuff for DEC's
7745 o modified/added many .cvsignore files in */code and */input
7746 o added new expt "solid-body.cs-32x32x1"
7747 + this uses an alternative form of ini_curvilinear_grid.F which
7748 is not necessarily any better than the current one...
7749
7750 checkpoint40pre4 (2001/07/30)
7751 o added re-initialisations of utrans,vtrans,rtrans in
7752 calc_common_factors which are crucial for TAF.
7753 o extended iMin,jMin range for calc_common_factors,
7754 calc_diffusivity
7755 o added option ALLOW_PASSIVE_TRACER
7756 o a few minor updates and fixes
7757
7758 checkpoint40pre3 (2001/07/13)
7759 o created calc_gtr1.F for gad package
7760 o split the_main_loop and re-introduced forward_step
7761 o some recomputations of nIter0 for TAMC
7762
7763 checkpoint40pre2 (2001/07/13)
7764 o Updated to latest branch of AJA, JMC
7765 o Added gradient check package
7766 o Added routines for passive tracer handling
7767 o Added carbon sequestration sensitivity experiment
7768
7769 checkpoint39 (2001/05/14)
7770 o Modifications and fixes to support TAMC
7771 (mainly missing or wrong directives)
7772 o Corrected common blocks when fooling TAMC to produce adjoint I/O
7773 in addummy_in_stepping
7774 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
7775 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
7776 o Included following packages:
7777 cal: calendar
7778 exf: external forcing
7779 ecco: essential routines to control use of cal, exf
7780 (NB: this is not the full ECCO environment)
7781 o disabled some packages by default in genmake
7782
7783 checkpoint38 (2001/04/10)
7784 o see notes_c37_adj.txt
7785 o corrected wrong layer index in external_forcing_t
7786 o replaced the_main_loop/forward_step by the_main_loop
7787 o removed forceoutput from write_state
7788 (replaced criteria for initial/final state)
7789 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
7790
7791 checkpoint37 (2001/03/13)
7792 o mdsio.F routine split and packaged in pkg/mdsio
7793 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
7794 used unless genmake -disable=mdsio)
7795 o allow a more precise surface-geopotential gradient for the atmosphere
7796 taking into account the change in space of Alpha (=1/rho) at the surface.
7797 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
7798 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
7799 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
7800 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
7801 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
7802 o Time-Average diagnostics defined as a pseudo package "timeave".
7803 o pickup files : old pickup (before c35) did not work with new code (c35
7804 and after) unless activating 2 commented lines in initialise-varia.
7805 o Non-Hydrostatic pickup file Pb fixed.
7806 o bug with Rigid-lid version (since c35) fixed.
7807
7808 checkpoint36 (2001/02/20)
7809 o implement Crank-Nickelson barotropic time-stepping
7810 o recover Time-Average diagnostics
7811 o fix Pb in checkpoint (PR#19)
7812 o AIM become a standard package ; clean unused CPP_kees
7813
7814 checkpoint35 (2001/02/08)
7815 o subtantial rewrite of dynamics.f
7816 o allows staggered time-stepping
7817 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
7818 o added bottom drag (linear + quadratic)
7819
7820 checkpoint34 (2001/01/30)
7821 o Modified exchange routines for correct reverse simulation.
7822 o Added verification output to comply with bug fix in impldiff.F
7823 as of c33 (exp2, natl_box).
7824 o Corrected store directives in dynamics.F
7825 o Corrected array boundaries in impldiff.F
7826 o Corrected array dimensions in gmredi.
7827 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
7828 o Added routine GLOBAL_SUM_INT to global_sum.F
7829 o Added mdsio_gl.F for ECCO purposes.
7830
7831 checkpoint33 (2000/11/30)
7832 o Fixed bug in lower BC in impldiff.F
7833 o Fixed confusion about units of forcing arrays in FFIELDS.h
7834 namely Fu,Fv,Qnet,Qsw,EmPmR:
7835 - Removed verification/natl_box/code/external_fields_scale.F
7836 (did not differ from that in model/src)
7837 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
7838 (see FFIELDS.h for description)
7839 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
7840 kpp_calc.F and kpp_transport_t.F
7841 - Removed model/src/external_fields_scale.F and calls to it
7842 - verification/natl_box uses flux data with "atmospheric" sign so
7843 a special version of external_fields_load.F is used to
7844 change the data as it's read in. This way, the arrays
7845 have the right units and signs at all times tha a user could
7846 possibly use them.
7847 o Corrected genmake to delete a temporary file during configuration
7848
7849 checkpoint32 (2000/11/13)
7850 o Scaling of forcing fields moved from external_forcing.F to
7851 external_fields_scale.F, called directly after loading fields.
7852 o Surface relaxation terms added to surface tendency fields in
7853 extra subroutine.
7854 o impldiff.F changed to avoid storing by TAMC of huge intermediate
7855 fields.
7856 o Changes in GMRedi to comply with packaging structure.
7857 o Modifications and bug fixes in KPP package.
7858 o Verification experiment for KPP added (verification/nat_box/)
7859
7860 checkpoint31 (2000/09/11)
7861 o Packages interface brought in line with defined standard
7862 -> new routines packages_...F
7863 -> changes in initialise_fixed.F, initialise_varia.F
7864 -> enables initialisation interface for ECCO package
7865 o Rescaling of external forcing fields immediately after read
7866 (removed from external_forcing.F)
7867 -> new: surface_fields_scale.F
7868 -> affects ini_foorcing.F, external_fields_load.F
7869 o Computation of surface tendencies before tendency updates.
7870 -> new: external_forcing_surf.F
7871 o Change of variable names useGMRedi, useKPP, useECCO
7872 o Further changes in dynamics.F, impldiff.F for TAMC
7873 o Tested for experiments 0, 2, 4.
7874 - not yet tested for GMRedi.
7875 - not yet tested for KPP.
7876
7877 checkpoint30 (2000/07/13)
7878 o Updates for OBCs
7879 o New experiment for test OBCs (internal_wave)
7880 o New output.txt in verification/exp4/results/
7881 o Updates for KPP: calculation of viscosity corrected, new variables
7882 kpp_dumpFreq and kpp_taveFreq
7883 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
7884 and entry for T90 in genmake
7885
7886 checkpoint29 (2000/06/21)
7887 o packaged KPP and GM/Redi
7888
7889 checkpoint28 (2000/06/09)
7890 o Corrected initialization of hFacMin for difference vertical coordinates
7891 o Modified calculation of partial cell thickness to more robust algorithm
7892 o config_summary.F: replaced write_1D_... by write_0D_...
7893 read_write.F: added subroutines write_0D_...
7894 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
7895 included some initialisations required for TAMC.
7896 o routine calc_isoslopes: modified sqrt computation to make it
7897 differentiable for zero argument.
7898 o routines dynamics, impldiff:
7899 included store directives and tape key computations required for TAMC.
7900 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
7901
7902 checkpoint27 (2000/04/10)
7903 o fixed calc_isoslopes() to so that cancellation of terms in tensor
7904 formulation works properly with variable resolution.
7905 o restructured the calling tree between the_model_main() and dynamics()
7906 o split initialise() into initialise_fixed() and initialise_varia()
7907 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
7908 in new routine ini_psurf()
7909
7910 checkpoint26 (2000/04/05)
7911 o moved some #ifdef in optional routines to encompass everything
7912 except the argument declarations. This was using up some memory.
7913 o fixed macros like _ADT to work with both versions of Linux cpp
7914 o cleaned up some unused and uninitialized variables
7915 (helps when debugging with strict compile options)
7916 o split up CPP_EEOPTIONS.h into options and macros
7917 (macros are now in eesupp/inc/CPP_EEMACROS.h)
7918 o patch for 2 processor JAM mode
7919
7920 checkpoint25 (2000/03/15)
7921 o updates for OBCs and NH
7922 o dramatically reduced memory usage
7923 o added "JAM" routines for use on Artic network
7924 o parameterization of convection by implicit vertical diffusion
7925 o added a diagnostic of convective index
7926 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
7927 (this is was partly for OBCs and NH but also in anticipation of
7928 an explicit free-surface option)
7929 o initial state input files for U and V
7930
7931 checkpoint24 (1999/08/02)
7932 o Removed some spurious "REAL"s
7933 o Updated KPP to latest version from JPL
7934 o Added a COS(latitude) in horizontal viscosity
7935
7936 checkpoint23 (1999/05/26)
7937 o Added del^4 diffusion for salt and temperature
7938 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
7939
7940 checkpoint22 (1999/05/18)
7941 o Made many small changes: implicit none, format(i5), etc...
7942 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
7943
7944 checkpoint21 (1999/05/18)
7945 o Introduced new I/O package that supports direct-access records (mdsio.F)
7946 o Split-up mid-level I/O routines
7947 o Updated input data for experiments 0,1,2,4 and 5
7948 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
7949
7950 checkpoint20 (1999/03/22)
7951 o Tidied up open-boundaries some more
7952 o Added non-hydrostatic code
7953 o Fixed some input data
7954 o Modified MPI start-up to work in "coupled" context.
7955
7956 checkpoint19 (1998/12/15)
7957 o Tidied up directory structure for verification experiments.
7958 o Added new code for open boundaries.
7959 o Corrected advective terms near boundaries.
7960 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
7961 o Implemented free-slip/no-slip BCs and del^4 dissipation.
7962 o Split default parameters out of ini_parms.F into set_defaults.F.
7963
7964 checkpoint18 (1998/11/30)
7965 o Further changes for optional code generation with
7966 CPP - ugh!
7967
7968 checkpoint17 (1998/11/03)
7969 o Beginning to incorporating modularity
7970 for supporting atmos. and ocean configs.
7971 o Small changes for TAMC complinace
7972 o New ultra simple test case. Barotropic box
7973 configuration "exp0".
7974
7975 checkpoint16 (1998/10/28)
7976 o Minor changes to exchange routines to support
7977 accumulation in reverse mode. Adjoint of an
7978 assignment is an addition.
7979 o Changes to support compilation by TAMC (LR(1)
7980 syntax) and by g77 under Linux ( 72 character
7981 limit ).
7982
7983 checkpoint15 (1998/09/29)
7984 Rewrote exchange routines to allow
7985 o General tile <-> tile connectivity.
7986 o TAMC reverse mode flag ( is this really needed? )
7987 o Variable width overlap and exchange region widths.
7988 o Hooks for sharing data via DMA, Arctic, Memory Channel,
7989 shmput/shmget, VIA, SYSV shmem and every other cool
7990 communication method.
7991
7992 checkpoint14 (1998/09/09)
7993 Consistent isomorphism chages made. These allow dynamical core
7994 to support both pressure and meters as a vertical coordinate.
7995
7996 checkpoint13 (1998/07/17)
7997 Release which corrects global_max problem and a couple
7998 of KGM time-averaging diagnostic errors. Also contains
7999 a double-gyre experiment setup as well as the baseline
8000 4 degree global template. The double gyre template is
8001 organised to allow it to be applied automatically to
8002 the baseline configuration.
8003
8004 branch-point-rdot
8005 A few tidy-ups have been made bt the real point of this
8006 check-point (excuse the pun) is to allow a branch to be
8007 made for the purposes of adding the rDot alterations.
8008 I don't want to commit the rDot to the main-trunk until
8009 we've actually tested it...
8010
8011 checkpoint12 (1998/07/08)
8012 Tidy up and added generic genmake script (formerly
8013 configure script).
8014 Released to testers.
8015
8016 checkpoint11 (1998/07/02)
8017 Re-arranged initialise() and introduced ini_vertical_grid()
8018 and ini_masks_etc().
8019
8020 checkpoint10 (1998/07/01)
8021 Introduced the configure script.
8022 Separated out the diags package.
8023 Added template for writing time-averages of tile/intermediate quantities.
8024 Updated SIZE.h in exp2 and made the data big-endian.
8025
8026 checkpoint9 (1998/06/22)
8027 MPI fix. Filename changes (meta/data). salbin*y stuff.
8028 General tidy-up.
8029 SST.bin SSS.bin added to verification/exp2
8030
8031 checkpoint8 (1998/06/22)
8032 Inludes time-dependant forcing and time-averaging.
8033 Works at 4x4 and 2.8125x2.8125 global
8034
8035 checkpoint7-4degree-ref
8036 Branch from checkpoint7. Released for application to
8037 global modeling and general modeling - process studies, regional
8038 model etc..
8039 Configured for verification/exp2 - 4 degree global, two process.
8040
8041 checkpoint7 (1998/06/15)
8042 Created by cnh
8043 Simple 4 degree global simulation
8044 configuration.
8045 Includes climatological wind,
8046 hydrography, bathymetry etc
8047 Does not include Heat Flux and E-P
8048
8049 checkpoint6 (1998/06/08)
8050 Created by cnh
8051 merged checkpoint5 with CD and
8052 spherical polar code.
8053 Still some problems with GM Redi
8054 abd full topography.
8055
8056 checkpoint5 (1998/06/08)
8057 Created by AJA
8058 contains updates to GM Redi
8059 and reordered timestepping loop
8060 for Implicit Diffusion.
8061
8062 checkpoint4 (1998/05/30)
8063 Created by cnh
8064 Contains memory saving macros ( _rdxc etc..) for when
8065 grid variations are limited.
8066 Contains polynomial coeffs for EOS and knudsen program
8067 for generation.
8068
8069 checkpoint3 (1998/05/26)
8070 Created by cnh
8071 Added extra flags for runtime options
8072 Added this file
8073 Added implicit free-surface
8074 Added pre-conditioner
8075 Put compare01 into repository ( compare01/... )
8076 Put data and eedata into repository ( verification/exp1 )
8077
8078 checkpoint2
8079 Created by AJA
8080 Added GM/Redi
8081
8082 checkpoint1
8083 Created by AJA
8084 Restructured kloop in dynamics.F
8085 Added non-linear EOS
8086
8087 baseline
8088 Original checked in code

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